MB352 GENERAL

MICROBIOLOGY
LABORATORY 2021

Alice Lee
North Carolina State University
 North Carolina State University
MB352 General Microbiology Laboratory
2021 (Lee)
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TABLE OF CONTENTS
Licensing

1: Laboratory Safety
1.1: Safety Procedures for the Microbiology Laboratory
1.2: Biosafety levels and PPE
1.3: Review Questions
Review Questions II
Review questions III

2: Cultivation of Microbes
2.1: Introduction Growth Media
2.2: Introduction to Bacterial Growth and Aseptic Techniques
2.3: Examples of Bacterial Growth Characteristics in Broths, Slants and Plates
2.4: Lab Procedures- Prepare solid media, Aseptic Technique, T-streaking
2.5: Results
2.6: Review Questions

3: Microscopy
3.1: Introduction to the Microscope
3.2: Comparison of Sizes and Shapes of Microorganisms
3.3: Lab Procedures- Operating a Microscope
3.4: Results
3.5: Review Questions

4: Staining Techniques
4.1: Introduction to Staining
4.2: Specialized Bacterial Staining Techniques
4.3: Lab Procedures- Bacterial Smear, Simple and Gram Staining
4.4: Results
4.5: Review Questions

5: Enumeration of Bacteria
5.1: Introduction to Enumeration of Bacteria
5.2: Lab Procedures- How to operate a Pipettor
5.3: Lab Procedures- Viable Plate count
5.4: Results
5.5: Review Questions

6: Microbial Physiology
6.1: Introduction to Oxygen Requirements
6.1.1: Determining Oxygen Requirements and Anaerobes
6.2: Temperature, pH, and Osmotic Requirements
6.3: Bacterial Growth Dynamics
6.4: Bacteriophages
6.5: Lab Procedures- Testing Oxygen requirements

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 6.6: Lab Procedures- Plaque Assay
6.7: Results
6.8: Review Questions

7: Microbial Metabolism
7.1: Introduction to Biochemical Tests Part I
7.2: Introduction to Biochemical Tests Part II
7.3: Lab Procedures- Biochemical Tests
7.4: Results
7.5: Review Questions

8: Bacterial Identification
8.1: Introduction to Bacterial Identification using Culture Media
8.2: Introduction to Bacterial Identification using Enterotube test
8.3: Introduction to Bacterial Identification using Genotypic methods
8.4: Lab Procedures- Enterotube inoculation
8.5: Lab Procedures- PCR and Gel Electrophoresis
8.6: Results
8.7: Review Questions

Index
Glossary
Detailed Licensing

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Licensing
A detailed breakdown of this resource's licensing can be found in Back Matter/Detailed Licensing.

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 CHAPTER OVERVIEW

1: Laboratory Safety
1.1: Safety Procedures for the Microbiology Laboratory
1.2: Biosafety levels and PPE
1.3: Review Questions
Review Questions II
Review questions III

1: Laboratory Safety is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

1
1.1: Safety Procedures for the Microbiology Laboratory
Learning Outcomes
Explain & practice safe microbiological procedures, protective measures, and emergency procedures.
Identify safe laboratory practices when working in a microbiology lab

What is Laboratory Safety?

Safety in a microbiology laboratory is important in the prevention of infection that might be caused by the microorganisms being
studied. In addition, many of the reagents, equipment, and procedures used are potentially hazardous. Attention to proper
procedures and prudent laboratory practices are required for your safety and protection.
This laboratory does not require the use of any highly virulent human pathogens. However, some of the organisms used
are potentially pathogenic. This means that, although they may not cause disease in a normal healthy human, they might if the
body's antimicrobial defense mechanisms are impaired. Impairment can arise in a number of different ways: wounds and cuts on
the skin surface or lowered overall resistance to infection due to: another disease, surgery, stress, or immune system disability
(including autoimmune diseases or the use of immuno-suppressive drugs). In addition, infection can occur, albeit very rarely, by
relatively nonpathogenic organisms in healthy individuals.
In addition to organisms, there are some chemicals used in this laboratory that are potentially harmful. Finally, many procedures
involve equipment, glassware, open flames, heat sterilizers, and sharp objects, which can cause injury if used improperly.
Although none of the organisms, procedures, or materials used in this laboratory is very dangerous, proper safety techniques and
precautions should be understood and become part of your reflexive laboratory technique. The following laboratory rules and
regulations should be adhered to at all times, NO EXCEPTIONS.
In addition, specific laboratory rules must be followed for containment of microbial cultures in the laboratory, for the safety of all.
For this laboratory, these practices are listed below.

General Laboratory Safety Practices and Procedures

1. If you are taking immune-suppressants, are pregnant, or have a known medical condition that would prevent full
participation in the laboratory, please contact the course instructor before the first day of lab.
2. Read and understand each laboratory exercise before you come to class.
3. Do not eat, drink, smoke, or chew pens in the laboratory.
4. You must wear close-toed shoes while in the laboratory and long pants.
5. No hats of any kind will be allowed in lab, unless allowed by University policy and cleared with the instructor.
6. Long hair should be pulled back to keep it away from bacterial cultures, bacticinerator or open flames.
7. Follow precautionary statements given in each exercise.
8. Personal electronic devices will be turned off and stored while in this laboratory. *The unauthorized use of any electronic
device (phone, tablet, computer) in lab will result in a loss of course points.
9. Know where specific safety equipment is located in the laboratory, such as the fire extinguisher, safety shower, and the eyewash
station.
10. Recognize the international symbol for biohazards, and know where and how to dispose of all waste materials, particularly
biohazard waste. Note that all biohazard waste must be sterilized by autoclave before it can be included in the waste stream.
11. Keep everything other than the cultures and tools you need OFF the lab bench. Only necessary work
material should be at or on the laboratory bench. Coats, backpacks, and other personal belongings will
not be allowed on the laboratory bench top. Store them in a place designated by your instructor. This
is to prevent cluttering of the workspace and to avoid exposing them to permanent stains, caustic
chemicals, and microorganisms used in the exercises.
12. Leave all laboratory facilities and equipment in good order at the end of each class. Before leaving the
laboratory, check to make sure the bacticinerator heat sterilizer is turned off.
13. Never, under any circumstances, remove equipment, media, or microbial cultures from the laboratory.
14. No pets are allowed in the laboratory.

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 Figure 1: Biohazard Symbol

Microbiology Specific Laboratory Safety Practices

During the course of the semester in the laboratory you will be taught the methods used in the proper handling of microorganisms.
Although you will not be working with any that are human pathogens, exercise caution in handling all material coming in contact
with live microbial cultures. All cultures should be handled with respect and proper aseptic technique as if they were potential
pathogens. This is called "universal precaution". Specific instructions that should be followed:
1. Remember that all bacteria are potential pathogens that may cause harm under unexpected or unusual circumstances. If you as a
student have a compromised immune system or a recent extended illness, you should share those personal circumstances with
your lab instructor.
2. Wear gloves when working with cultures, and when your work is completed, dispose of the gloves in the biohazard garbage.
Lab coats, safety glasses or goggles are also required. These will be stored in the laboratory each week in a ziplock bag.
3. Disinfect your work area both BEFORE and AFTER working with bacterial cultures.
4. Cultures of live microorganisms and any material coming in contact with live cultures must be properly sterilized after use in
the laboratory. Your instructor will inform you of specific procedures. Follow the general rules outlined below.
a. Glassware such as test tubes, bottles, and flasks may be reused and washed after
sterilization. These are normally placed on a cart at the front of the laboratory
after you have finished an experiment or exercise. BE SURE TO REMOVE
LABELS before placing any glassware on the cart. Your instructor will sterilize
and then wash these items.
b. Some materials, such as plastic petri dishes, plastic pipettes, microscope slides,
and swabs, are considered disposable. These are used once and if they become
contaminated by contact with live microorganisms are sterilized and discarded.
All of these disposable contaminated materials should be placed in the designated
waste container containing a BIOHAZARD autoclave bag.
5. Never place contaminated pipette tips (or pipettes), inoculating loop, or any other contaminated material on the bench top.
Sterilize loops before and after each use. Place contaminated pipette tips in the orange biohazard buckets on your bench. Place
all other contaminated materials in their designated waste containers. Do not place or put anything containing live
microorganisms in the sink.
6. Aerosols should be avoided by the use of proper technique for sterilizing the inoculating loops and by performing any mixing
of cultures and reagents in such a way as to avoid splashing.
7. Cultures or reagents should always be transferred with an automatic pipettor that will be provided. In no case should one
employ mouth pipetting.
8. Always keep cultures capped and in proper storage racks when not being used during an exercise.
9. In the event of an accidental spill involving a bacterial culture, completely saturate the spill area with disinfectant, then cover
with paper towels and allow the spill to sit for 10 minutes. Then carefully remove the saturated paper towels, dispose of them in
the biohazard waste, and clean the area again with disinfectant. Notify your instructor about the spill. If the chemical is marked
"danger" or "caustic" you should notify the instructor who will handle this type of spill.
10. Immediately report all accidents such as spills, cuts, burns, or other injuries to the instructor
11. Make sure that lab benches are completely cleared (everything either thrown away or returned to storage area) before you leave
the lab.
12. Clothing worn in the microbiology laboratory should be washed before being subsequently worn in a facility such as a hospital,
clinic or nursing home, or in an area of public food preparation.
13. In the event of a fire alarm, follow the directions of your instructor, and meet at the place designated by your instructor.

Watch these Videos on basic laboratory procedures:

*We will review specific safety procedures for our lab during our first in-person lab session

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 Good Microbiological Practices and Pro…
Pro…

Watch Video 1: start video at 9:55 - end video at 10:26, covers different types of bench surfaces and cleaning methods

The Globus Guide to Putting-on and Re…

Re…

Watch Video 2: How to put on and take off gloves

NOTE: The following recommended practices and procedures for working safely on microbiology projects in a teaching laboratory
environment are based on “Guidelines for Biosafety in Teaching Laboratories,” from the American Society for Microbiology
(ASM). The full documents may be viewed at this URL: https://asm.org/getattachment/3c1eb3...Guidelines.pdf

CC licensed content, Shared previously

Microbiology: a Laboratory Experience. Authored by: Holly Ahern. Provided by: SUNY Adirondack . Located at:
https://textbooks.opensuny.org/microbiology-a-laboratory-experience/. Project: Open SUNY Textbooks. License: CC BY-NC-
SA: Attribution-NonCommercial-ShareAlike

1.1: Safety Procedures for the Microbiology Laboratory is shared under a not declared license and was authored, remixed, and/or curated by
LibreTexts.
2.1: Biosafety Practices and Procedures for the Microbiology Laboratory has no license indicated.

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1.2: Biosafety levels and PPE
Learning Outcomes
Recognize distinctions between Biosafety Levels (BSL) identify PPE used for working in the lab under BSL
classifications
Demonstrate and assess the proper use of Personal Protective Equipment (PPE) and be prepared to safely conduct research

BioSafety Levels

Figure 1: Biosafety levels and risk. Image from CDC. https://www.cdc.gov/training/quicklearns/biosafety/

Handling microbes requires specialized laboratory facilities and techniques. Biosafety is the application of safety precautions that
reduce a scientists’ risk of exposure to a potentially infectious microbe and limit contamination of the work environment. Bacteria
pose varying degrees of risk both in a controlled laboratory environment and in their natural settings. Therefore, the level of
containment necessary for working safely with bacterial cultures also varies according to a system that classifies microbes into one
of four biosafety levels (BSL), which provides minimum standards for safe handling of microbes at each level. BSLs are defined
and containment practices are detailed by the Centers for Disease Control and Prevention (CDC) for laboratories in the United
States. The full document, “BiosafetyinMicrobiologicalandBiomedicalLaboratories,” can be viewed in its entirety
at http://www.cdc.gov/biosafety/publications/bmbl5/index.htm.
We designate most of our labs under 4 special hazard categories called biosafety levels (BSLs). Each level has specific controls for
containment of microbes and biological agents. Each biosafety level builds on the controls of the level before it. All of these
levels follow “standard microbiological practices” : which are those practices common to all labs, which include not eating,
drinking, or applying cosmetics, washing hands after working in the lab, routinely decontaminating work area.
BSL1: If you work in a lab that is designated a BSL-1, the microbes there are not known to consistently cause disease in healthy
adults and present minimal potential hazard to laboratorians and the environment. An example of a microbe that is typically worked
with at a BSL-1 is a nonpathogenic strain of E. coli. Work can be done on an open lab bench, requires a sink. Requires personal
protective equipment (PPE) such as lab coats, gloves, eye protection.
BSL 2: BSL-2 builds upon BSL-1. If you work in a lab that is designated a BSL-2, the microbes there pose moderate hazards to
laboratorians and the environment. The microbes are typically indigenous and associated with diseases of varying severity. An
example of a microbe that is typically worked with at a BSL-2 laboratory is Staphylococcus aureus. It includes various bacteria and
viruses that cause only mild disease to humans, or are difficult to contract via aerosols in a lab setting, such as Clostridium difficile,
most Chlamydiae, hepatitis A, B, and C, influenza A viruses, Salmonella. BSL-2 differs from BSL-1 in that: laboratory personnel
have specific training in handling pathogenic agents and are directed by scientists with advanced training; access to the laboratory
is limited when work is being conducted; extreme precautions are taken with contaminated sharp items; and certain procedures in
which infectious aerosols or splashes may be created are conducted in biological safety cabinets or other physical containment
equipment. The Microbiology Teaching labs at NC State are designated as BSL-2 laboratory space.
BSL-3: is required for work involving indigenous or exotic agents, and they can cause serious or potentially lethal disease that are
transmitted through the air (via aerosols). Respiratory transmission is the inhalation route of exposure. Laboratory personnel must

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receive specific training in handling pathogenic and potentially lethal agents, and must be supervised by scientists competent in
handling infectious agents and associated procedures. Lab personnel are under medical surveillance and might receive
immunizations for microbes they work with. All procedures involving the manipulation of infectious materials must be conducted
within Biosafety Cabinets (BSCs) (shown at the top image), or other physical containment devices, or by personnel wearing
appropriate personal protective equipment (eg respirators). A BSL-3 laboratory has special engineering and design features that
prevent the release of microorganisms to the environment. Facilities have hands free sink, exhaust air cannot be recirculated,
entrance is through two sets of self closing and clocking doors. Microbes that are worked on in BSL3 facilities are Mycobacterium
tuberculosis which cause tuberculosis, etc.

BSL-4 labs builds on the containment requirements of BSL-3 and is the highest level of biological safety. BSL-4 labs is required
for work with dangerous and exotic agents that pose a high individual risk of life-threatening disease, aerosol transmission or
unknown risk of transmission. The microbes in BSL4 labs cause infections that are frequently fatal and generally there are no
vaccines or treatments for these infections. There are only a small number of such labs in the U.S (<10) and the world. Laboratory
staff must have specific and thorough training in handling extremely hazardous infectious agents. Access to the laboratory is
controlled by the laboratory supervisor. All handling of agents must be performed in a gas tight Class III Biosafety Cabinet or by
personnel wearing a positive pressure protective suit. BSL-4 Laboratories have special engineering and design features to prevent
microorganisms from being released into the environment. The lab is in a separate building or isolated restricted zone of the
building, and has a dedicated supply and exhaust air, as well as vacuum lines and decontamination systems. Personnel mush
change clothing before entering and shower upon exiting. Most of the pathogens worked on are viruses: Crimean-Congo
hemorrhagic fever caused by Ebola, Junin, Lassa, Machupo, Marburg viruses , and tick-borne encephalitis virus complex
(including Absettarov, Hanzalova, Hypr, Kumlinge, Kyasanur Forest disease, Omsk hemorrhagic fever, and Russian Spring-
Summer encephalitis).

Personal Protective Equipment (PPE)

Personal Protective Equipment, or PPE, is the clothing and equipment that forms the last line of defense between you and harmful
materials in the laboratory environment. It’s essential that you know what you should be wearing, when you should be wearing it,
and how it should be stored, cleaned, maintained and disposed of. (1)
Basic PPE provided in the Microbiology laboratory includes: Disposable gloves, lab coat, safety glasses. We will have disposable
face masks.
Disposable gloves serve as a barrier between your hands and any chemical, biological, or physical hazards that can enter your body
through your skin. These gloves cannot protect you from all barriers, and most disposable gloves we use in a microbiology lab are
made of some synthetic material, such as nitrile or latex. Any prolonged exposure to a chemical agent can permeate these types of
gloves, so it is critical that you safely remove your gloves if you are exposed to a chemical spill and it comes in contact with your
gloves. Gloves should be changed when they are contaminated by biological or chemical hazards. There are many other types of
gloves, such as ones for handling very hot items out of the autoclave, or for very cold items out of a -80degC freezer or for
handling liquid nitrogen. The type of glove you use depends on the work you are doing in the lab.
Lab coats protect the user's skin and personal clothing from accidental contact with biological or chemical hazards. They
also prevent the spread of contamination outside of the lab (provided they are not worn outside the lab). Lab coats serve as
a removable barrier in the event of an a spill or splash of hazardous substances. They should fit the user well (not too large or it will
get caught on things and not too small as it may hinder movement), be long-sleeved, a secure cuff, knee-length or longer, fire
resistant material, high buttons to provide exposure of the chest or neck area. They come in a variety of materials and provide
varying degrees of protection. There are splash resistant coats, static free coats, chemical resistant coats and flame resistant coats.
Most lab coats we use in a microbiology teaching lab are made of a synthetic material that is fire resistant. Always select a coat
that provides the type of protection that is appropriate for your needs.
Safety glasses/goggles provide a barrier to your eyes and prevent exposure to chemical (eg chemical reagents) physical (eg dust,
flying objects), and biological (eg bacterial culture splashes) hazards. Most microbiology labs have standard safety glasses or
goggles that wrap around the eyes and avoid splashes, they may have features such as UV light barriers, impact features, and some
are designed to be worn over your regular glasses, these are called "Over the glasses" (OTG) safety glasses. There are also labs
that have high intensity light sources such as UV light, lasers and the appropriate safety glasses must be used.

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Face shields should be worn whenever the entire face needs protection. Such as when there is a potential that an aerosol of
chemical or biological hazardous material may be created or whenever chemical or biohazards could splatter, or whenever there is
the potential for flying particles or sparks. A face shield should always be worn whenever handling tissue samples or animals
where there is the potential for infectious transmission. Safety glasses or goggles should always be worn underneath a face shield
for maximal protection.
Masks that are disposable may need to be worn, especially during the COVID-19 pandemic and will limit the transmission of
infectious agents. Disposable masks come in a variety of materials and levels of protection. Typical facemasks are loose-fitting,
disposable masks that cover the nose and mouth, such as surgical masks and nuisance dust masks. Facemasks are not approved by
the National Institute for Occupational Safety and Health (NIOSH) for protection against any regulated hazardous material.
Facemasks help stop droplets from being spread by the person wearing them. They also keep splashes or sprays from reaching the
mouth and nose of the person wearing the facemask and are therefore useful when cleaning up spills of infectious materials. They
are not designed to protect you against breathing in gases, vapors, or very small particles. Facemasks should be used once and then
disposed of. There are different types of masks used for different purposes, specialty disposable face masks such as the N95 or
KN95 masks are respirators which are approved by NIOSH for use against certain selected airborne particulates when used as part
of a respiratory protection program.

Watch video 1
Video 1: proper usage of PPE. Your instructor will explain how to locate, use, and store your PPE in the lab.

Good Microbiological Practices and Pro…

Pro…

Watch Video 1: WHO: Good Microbiological Practices & Procedures. Personal Protective Equipment (PPE) (19:41)
URL: https://youtu.be/Cuw8fqhwDZA

References:
1. WHO. World Health Organization Biosafety Series. https://www.who.int/ihr/publications...deo-series/en/

1.2: Biosafety levels and PPE is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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1.3: Review Questions
1. Discuss 2 safety precautions in a BSL-2 lab.
2. Why do we have to tie long hair back in a microbiology lab? give me 2 reasons
3. True or False? Food and drinks are allowed in the lab, as long as they are kept out of sight.
4. Why must microbiology tools and implements be sterilized?
5. Describe 2 pieces of PPE and why they are important in a microbiology lab.

1.3: Review Questions is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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Review Questions II
"I would literally fall asleep if I was having a conversation or doing anything that involved my brain," she says.

"I would literally fall asleep if I was having a conversation or doing anything that involved my brain," she says.

"I would literally fall asleep if I was having a conversation or doing anything that involved my brain," she says.

lab safety is important

UrL: https://ehs.stonybrook.edu/programs/...b-safety-guide

watch this video

Stroll Through the Playlist (a Biology Re…

Re…

General Lab Safety

watch video 1: General lab safety by the Amoeba sisters. URL: https://youtu.be/MEIXRLcC6RA

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Lab safety Part III

lab safety is important

Lab safety Part I

Exercise 1

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Answer
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Learning Objectives
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Learning Objectives
Explain the following laws within the Ideal Gas Law

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Example 1

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Review Questions II is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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Review questions III
Review questions III is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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 CHAPTER OVERVIEW

2: Cultivation of Microbes
2.1: Introduction Growth Media
2.2: Introduction to Bacterial Growth and Aseptic Techniques
2.3: Examples of Bacterial Growth Characteristics in Broths, Slants and Plates
2.4: Lab Procedures- Prepare solid media, Aseptic Technique, T-streaking
2.5: Results
2.6: Review Questions

2: Cultivation of Microbes is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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2.1: Introduction Growth Media
Learning Outcomes
Recognize various types of growth media: solid, broth.
Understand the uses of selective and differential growth media
Determine the properties of some common bacterial types when grown on selective and differential growth media

Growth Media
To study bacteria and other microorganisms, it is necessary to grow them in controlled conditions in the laboratory. Growth media
contain a variety of nutrients necessary to sustain the growth of microorganisms. There are two commonly used physical forms of
growth media: liquid media and solid growth media. A liquid medium is called a broth (image 2).
Solid growth media usually contains agar (image 1), which is a mixture of polysaccharides derived from red algae. It is used as a
solidification agent because it (1) is not broken down by bacteria, (2) contains no nutrients that can be used by bacteria and (3)
melts at high temperatures, and yet is solid at temperatures used for most bacterial growth. Solid growth media is used in the
following forms: agar plates, agar slants, and agar deeps. To make agar deeps or agar slants, melted agar is poured into a test tube
and then allowed to solidify vertically (agar deep), or at a slant (agar slant). Agar plates are made by pouring melted agar into a
petri dish.

Image 1: Solid Agar slant Image 2: Broth media in test tube. Images by Anne Hanson, University of Maine, Orono.

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Image 3: MacConkey solid agar plate with pure culture of Salmonealla species bacteria. Image by Rebecca Buxton, University of
Utah, Salt Lake City, UT.

Figure 1:
Solid growth media forms

Broths can be used to determine growth patterns in a liquid medium, and for certain types of inoculations and metabolic tests. They
are also the method of choice for growing large quantities of bacteria. Agar slants are commonly used to generate stocks of
bacteria. Agar plates can be used to separate mixtures of bacteria and to observe colony characteristics of different species of
bacteria . Deeps are used for several different types of differential metabolic tests (e.g., the caseinase hydrolysis test)

Types of Growth Media

Growth media can be categorized based on their chemical constituents, or the purpose for which they are used.
Complex (also called Rich) growth media contain ingredients whose exact chemical composition is unknown (e.g. blood,
yeast extract, etc.) Eg TSA, LB agar.
Synthetic (also called chemically defined) growth media are formulated to an exactly defined chemical composition.

Example: A general purpose growth medium: e.g. tryptic soy agar (TSA) or Luria broth (LB) is used to grow a wide variety
of non-fastidious bacteria. This type of medium is often a complex growth medium.

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Image 4: General purpose, Complex/Rich media: LB agar plate streaked with Bacillus cereus and incubated at room
temperature for 24 hours. Image by Kevin Hedetniemi and Min-Ken Liao, Furman University, Greenville, SC.

Specialized media types

A selective growth medium contains chemicals that allow some types of bacteria to grow, while inhibiting the growth of other
types. An example of a purely selective growth medium is PEA, phenylethyl alcohol agar, which allows Gram positive bacteria
to grow while inhibiting the growth of Gram negative bacteria.

Image 5: Staphylococcus aureus, a Gram positive organism, grows on this PEA plate while Serratia marcescens, a Gram negative
organism, does not. Image by WelcometoMicrobugz. URL: https://www.austincc.edu/microbugz/p...cohol_agar.php
A differential growth medium is formulated such that different types of bacteria will grow with different characteristics (e.g.
colony color). An example of a differential growth medium is blood agar, which differentiates among bacteria based on their
ability to break down red blood cells and hemoglobin. Blood agar is also a complex growth medium because it contains blood.

Image 6: Blood agar plate. Image by Rebecca Buxton, University of Utah, Salt Lake City, UT.

A growth medium can be both selective and differential. For example, EMB (eosin methylene blue agar) inhibits the growth
of Gram-positive bacteria. Gram negative bacteria that grow on this medium are differentiated based on their ability to ferment
the sugars lactose and sucrose. Strong fermenters of lactose or sucrose will produce large amounts of acid and will appear dark
purple to black. Escherichia coli, a strong fermenter will frequently appear as colonies with dark black with a green metallic
sheen (Image 7). Weaker fermenters will produce pink colonies. Clear or colorless colonies indicate that bacterium does not
ferment either sugar and is not a fecal coliform. (Note: the Gram staining procedure divides bacteria into 2 main groups: Gram-
positive bacteria and Gram-negative bacteria, based on their cell wall structure.).

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Image 7: Eosin-methylene blue ( EMB) agar plate inoculated with Escherichia coli (a Gram-negative coliform bacterium)
showing good growth of dark blue-black colonies with metallic green sheen indicating vigorous fermentation of lactose and acid
production which precipitates the green metallic pigment. (Naowarat Cheeptham, Thompson Rivers University, Kamloops, BC,
Canada)

Making Media
I. Making culture media requires patience and attention to detail. Watch Video 1: Making Microbiological Media

Making Microbiological Media

Watch Video 1: Making Microbiological Media by Bio-Rad. URL:https://youtu.be/BH4ESgWU_Eo

II. Pouring Agar plates. Watch Video 2: Solid Media Preparation, video was filmed at NC State Microbiology labs.

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 Lab 1: Solid Media Preparation

Watch Video 1: Solid media preparation, video was filmed at NC State Microbiology labs. URL:https://youtu.be/P7M_MCXbZjc

Recap: Media Types

Tryptic soy agar (TSA): General purpose rich/complex growth medium.
Mannitol-salt agar (MSA): Differential and selective growth medium. This medium contains 7.5% NaCl, the carbohydrate
mannitol and the pH indicator phenol red (yellow at pH 8.4). It is selective for staphylococci due to the high concentration of NaCl,
and differentiates based on the ability to ferment mannitol. Staphylococci that ferment mannitol produce acidic byproducts that
cause the phenol red to turn yellow. This produces a yellow halo in the medium around the bacterial growth.
Table 1: MSA Agar
Selectivity Interpretation Identification

Growth Growth Organism not inhibited by NaCl E.g., Staphylococcus, Micrococcus

No Growth Organism inhibited by NaCl Not Staphylococcus

Differentiation

Yellow Halo Organism ferments mannitol Probable S. aureus

Staphylococcus species (other than S. aureus);

No Yellow Halo Organism does not ferment mannitol
Micrococcus (yellow colonies)

Eosin-methylene blue agar (EMB): Differential and selective growth medium. This medium contains peptone, lactose, sucrose
and the dyes eosin Y and methylene blue. Gram positive organisms are inhibited by the dyes, so this medium is selective for Gram
negative bacteria. The medium differentiates based on the ability to ferment lactose (and/or sucrose.) Organisms that cannot
ferment either of the sugars produce colorless colonies. Organisms that ferment the sugars with some acid production produce pink
or purple colonies; organisms that ferment the sugars and produce large amounts of acid form colonies with a green metallic sheen.
This medium is commonly used to detect the presence of fecal coliforms (like E. coli)—bacteria that grow in the intestines of
warm-blooded animals. Fecal coliforms produce large amounts of acid when fermenting lactose and/or sucrose; non-fecal
coliforms will produce less acid and appear as pink or purple colonies.
Table 2: EMB Agar
Result Identification Interpretation

No or poor growth Organism inhibited by dyes Organism is Gram-positive

Good growth Organism not inhibited by dyes Organism is Gram-negative

Colorless growth Organism does not ferment sucrose or lactose Non-coliform

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 Result Identification Interpretation

Organism ferments lactose and/or sucrose with

Growth is pink and mucoid Coliform bacteria
some acid production

Growth is dark (purple to black with or Organism ferments lactose and/or sucrose,
Possible fecal coliform (E. coli)
without green metallic sheen) with large amounts of acid production

References
1) Dr. Gary Kaiser (COMMUNITY COLLEGE OF BALTIMORE COUNTY, CATONSVILLE CAMPUS)

This page titled 2.1: Introduction Growth Media is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by Joan
Petersen & Susan McLaughlin.
2.1: Introduction by Joan Petersen & Susan McLaughlin is licensed CC BY-NC-SA 4.0.

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2.2: Introduction to Bacterial Growth and Aseptic Techniques
Learning Outcomes
Describe general characteristics of bacterial growth on agar plates
Explain how to inoculate growth media using proper aseptic procedures
Describe the process for inoculating sterile media
Describe the procedure (T-streak) for isolation of single bacterial colonies

Characteristics of Bacterial Growth

Even on general purpose growth media, bacteria can exhibit characteristic growth patterns. On agar plates, bacteria grow in
collections of cells called colonies. Each colony arises from a single bacterium or a few bacteria. Although individual cells are too
small to be viewed, masses of cells can be observed. Colonies can have different forms, margins, elevations, and colors. Observing
colony characteristics is one piece of information that microbiologists can use to identify unknown bacteria. Shown below are
isolated colonies of S. aureus on a blood agar plate. Colonies that are visible to the human naked eye contains tens of
thousands or even millions of individual bacteria!!

Image 1: Notice individually isolated colonies: Large, creamy white, circular, beta-hemolytic colonies typical of Staphylococcus
aureus cultured on Blood agar. Image by Rebecca Buxton, University of Utah, Salt Lake City, UT.

Colony morphology can be an aid in the identification of microorganisms.

Although colony morphology cannot be employed as the sole identifying criterion, it is a useful trait in the classification of many
common types of microorganisms. Six parameters are normally used to describe microbial colonies growing on an agar surface:
a. Size: pinpoint, small, medium, or large; range: < l mm - 3cm
b. Color: absolutely white, various degrees of pigmentation
c. Texture: the texture of the colony as determined by touching the colony
with a needle; smooth (buttery), dry (granular), or mucoid (slimy) and the
appearance as judged by the manner in which the colony refracts light;
clear, glistening, dense, opaque, or translucent.
d. Form: the shape of the colony; circular, irregular, filamentous, or rhizoid
e. Elevation: the degree to which colony growth is raised; flat, raised,
convex or umbonate
f. Margin: the shape of the edge or margin of the colony

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Figure 1: Different colony morphologies/characteristics

Image 2: Example of circular formed colonies--Serratia marcescens colonies cultivated on trypticase soy agar. Image by Bryan
MacDonald, Christopher Adams, and Kyle Smith, Brigham Young University, Provo, UT.

Image 3: Undulate form colonies-- Streak plate isolation of Mycobacterium smegmatis on trypticase soy agar (TSA) incubated for
96 hours at 37oC. Note the rough texture of colonies characteristic of this organism. Image by Tasha L. Sturm, Cabrillo College,
Aptos, CA.

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Image 4: Irregular form colonies-- Mycobacterium marinum cultivated on Mycobacterium 7H11 agar with oleic acid-albumin-
dextrose-catalase enrichment. Image by Richard A. Robison, Gable Moffitt, Neal Thomson, and Marissa Cohen, Brigham Young
University, Provo, UT.

Aseptic Technique and Inoculation

In nature, microorganisms usually exist as mixed populations of different species of bacteria, fungi, and even viruses. If we are to
study, characterize, and identify microorganisms, we must have the organisms in the form of a pure culture, that is of only one
species of microorganism. A pure culture is one in which all organisms are descendants of the same organism. In working with
microorganisms we must also have a sterile nutrient-containing-medium in which to grow the organisms. Anything in or on which
we grow a microorganism is termed a medium. A sterile medium is one which is free of all life forms. It is usually sterilized by
heating it to a temperature at which all contaminating microorganisms are destroyed. Finally, in working with microorganisms, we
must have a method of transferring growing organisms (called the inoculum) from a pure culture to a sterile medium without
introducing any unwanted outside contaminants. This method of preventing unwanted microorganisms from gaining access is
termed aseptic technique. (1)
Inoculation is the purposeful introduction of bacteria into a sterile growth medium. A material is sterile when it has no living
organisms present; contamination is the presence of unwanted microorganisms. Aseptic techniques are practices that prevent the
contamination of growth media.
When working in a microbiology laboratory, you must always remember that bacteria are present on all surfaces in the lab, as well
as on your own hands and clothing. Aseptic techniques are designed to prevent the transfer of bacteria from the surrounding
environment into a culture medium. These techniques require care and concentration. Pay attention to what you are doing at all
times!
Aseptic techniques include the following practices:
1. Minimize the time that cultures and growth media are open to the environment.
2. Disinfect the work area before and after use.
3. Do not touch or breathe into the sterile culture media or the stock cultures.
4. Loops, needles, pipets, etc. should be sterilized before they are used.
5. When working with tubes, the tube caps should not be placed on the table top; they should be held in your hand while
inoculating.
6. When removing the caps from test tubes, heat/flame the lip of the test tube after the cap is removed. This heats the air inside the
tube, so the air moves out of the tube, preventing contaminants from entering the tube.
7. Information about the use of the bacticinerator can be found in the Procedures page and view videos 2 and 3 below.

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Watch this video 1: Aseptic Technique Tips

Aseptic Technique Tips

Watch Video 1: Aseptic Techniques tips. Video by Dr. Gary Kaiser (CCBC). (5:56) URL: https://youtu.be/_tMM0F0Pr60

General Procedure for inoculating media

1. Sterilize an inoculating loop or needle in the flame of a Bunsen burner. The portion of the loop or needle that will contact the
stock culture or the growth medium must turn bright orange for effective sterilization. For the most rapid sterilization, place the
loop at the top of the inner blue cone of flame—this is where the temperature of the Bunsen burner is the hottest. Or if it is a
bacticinerator, make sure the loop is in the body of the bacticinerator and heat for 10 sec. Remove the loop from the flame after it is
properly heated- keeping the loops in the flame for too long will eventually cause them to crack.
2. If you are picking a colony from a plate, cool the inoculating loop on agar that does not contain any bacterial colonies.
3. Pick a small amount of bacteria (you do not need much). If you are inoculating a tube of broth or an agar slant, remove the cap of
the tube (do not set the cap down on the table) and flame the lip of the tube. Throughout the procedure, hold the tube at an angle to
reduce the probability of particles entering the opening. Insert the loop into the tube and transfer bacteria to the growth medium. Be
careful that only the sterilized part of the loop touches the tube or enters the growth medium.
4. Flame the lip of the test tube before replacing the cap.
5. Sterilize the inoculating loop again.

Watch this video 2: Aseptic Transfer

Aseptic Transfer

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 Watch Video 2: Aseptic transfers: a variety of transfers from solid to liquid. This video was filmed in the Microbiology teaching
labs at NC State. (7:39) URL: https://youtu.be/sFbJmJeTIFc

Streaking for single colonies: T-streak

In the real world outside the laboratory, bacteria grow in communities made of many bacterial species. If you need to identify the
types of bacteria present in environmental or medical samples, you must have a way to separate out the different types and produce
pure cultures. A pure culture contains a single bacterial species, whereas a mixed culture may contain many different types of
bacteria. The T-streak method describes the method that you will use to separate different types of bacteria in a mixture.
To maintain a pure culture or to obtain a pure culture of a microorganism, a quadrant/T/isolation/streak plate is performed. The T-
streak is a form of dilutions on a solid surface (Franklund, 2018). In this technique, the plate is divided into sections. Bacteria are
deposited in the first section at full strength from the original source. Then the inoculating loop is sterilized. From this point on, no
additional cells are added to the agar surface. The sterile loop is used to spread out cells that have already been placedon the plate.
After spreading cells from the first area to the second, the loop is sterilized again. This eliminates extra cells from the loop. The
sterile loop is used to spread some cells from the second area into the third area diluting them further. (In a quadrant streak, cells
are spread into a forth area as described.) After all the regions have been inoculated, the hope is that in the last section cells are far
enough apart so that they grow up into isolated colonies. This technique allows one to observe isolated colonies and characterize
them and determine if your observations are consistent with our expectations for the organism you are working with. If you are
working with a pure culture, you would expect that all the colonies would look the same, similar size, color, shape etc. One or more
different looking colonies indicates your culture was contaminated or you created contamination by poor aseptic technique.
Recall that each individual colony that you see on an agar plate represents billions of bacteria that originated from a single cell, and
therefore should be clones of each other. If you want a pure culture then, there should only be 1 species or strain of that bacterium
on that plate. We typically do a T-streak in the lab where you draw a large “T” on the back of the agar plate to divide it into 3
sectors. Watch video 3 below for a demonstration.

Image 5: Agar plate with T-streak of E. coli . This is a pure culture and notice the isolated colonies in the last sector of the plate,
they appear as single, individual, round colonies. Image by Rebecca Buxton, University of Utah, Salt Lake City, UT.

Watch video 3: Isolating bacterial colonies using a T-streak method

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 ID Laboratory Videos: Isolating bacterial…
bacterial…

Watch video 3: Isolating bacterial colonies using a T-streak. Excellent summary video of many things we talked about in this
section: the difference between a cell vs a colony, how to separate bacterial species using a T-streak isolation method, common
mistakes when doing a T-streak, and the results of a T-streak. They use disposable loops here and sterilize the loop with 70%
ethanol between each section when doing the T-streak. You can also discard the loop (in biohazard) when streaking between
sections, or use a metal loop (usually made of nickel-chrome wire) that you sterilize using a bunsen burner or a bacticinerator.
Video by ID laboratory videos (9:17) URL: https://youtu.be/c1onYow0O58

Watch Video 4: Doing a T-streak at NC State

T-Streak

Watch video 4: How to perform a T-streak for isolated colonies. This video was filmed in the Microbiology laboratories at NC
State. It will familiarize you with the use of a bacticinerator for sterilizing a metal inoculating loop. (7:39)
URL:https://youtu.be/NsQv7QOmdXo

Notes about Labeling and Incubating Plates

1. Always label your plates/tubes BEFORE you do your inoculations. You can use Sharpies on the plates, but wax markers ONLY
on tubes. When labeling tubes, label the tube itself—don’t label the cap!
2. Make sure you label the bottom of the plates (the part of the plate that holds the agar).
3. Place plates inverted (upside down) for incubation. This prevents condensation from falling on the surface of the agar and
disrupting the streaking pattern.

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Contributions and Attributions
1) Dr. Gary Kaiser (COMMUNITY COLLEGE OF BALTIMORE COUNTY, CATONSVILLE CAMPUS)
2) 2.1: Introduction by Joan Petersen & Susan McLaughlin, is licensed CC BY-NC-SA

2.2: Introduction to Bacterial Growth and Aseptic Techniques is shared under a not declared license and was authored, remixed, and/or curated by
LibreTexts.

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2.3: Examples of Bacterial Growth Characteristics in Broths, Slants and Plates
Even on general purpose growth media, bacteria can exhibit characteristic patterns of growth. Some examples are shown below.
While these growth patterns are an important piece of information when identifying a bacterial species, they are not sufficient for a
positive identification. Staining procedures and metabolic tests must be used for a definitive identification.

Growth Characteristics in Broths

Figure 2.6.1: Bacterial growth in broths

Growth Characteristics on Slants

Figure 2.6.2: Bacterial growth on slants

Growth Characteristics on Plates

Figure 2.6.3: Bacterial growth on plates

This page titled 2.3: Examples of Bacterial Growth Characteristics in Broths, Slants and Plates is shared under a CC BY-NC-SA license and was
authored, remixed, and/or curated by Joan Petersen & Susan McLaughlin.
2.5: Examples of Bacterial Growth Characteristics in Broths, Slants and Plates by Joan Petersen & Susan McLaughlin is licensed CC
BY-NC-SA 4.0.

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2.4: Lab Procedures- Prepare solid media, Aseptic Technique, T-streaking
Learning outcome
To acquaint you with the two types of culture media, Nutrient broth and Nutrient agar.
To familiarize you with aseptic technique.
To learn how to isolate a pure culture.
To observe the ubiquity and diversity of microorganisms

Aseptic Technique
The average human is made up of approximately 1013 eukaryotic animal cells and 1014associated eukaryotic and prokaryotic
microbial cells. This means that 90% of "your" cells are not human.
The purpose of this exercise is to familiarize you with aseptic techniques. Aseptic technique can be thought of as the manipulation
of sterile instruments or culture media in such a way as to maintain sterility.
In nature, microorganisms almost always exist as mixed populations of many widely differing types. However, before most
properties and characteristics of a particular organism can be determined, the organism must first be isolated in pure culture. A
pure culture is one that contains a single strain of microorganism. For example, a pure culture of the bacterium Escherichia coli
contains only Escherichia coli cells of a particular strain - no other living microorganisms are present. The term strain refers to a
population of cells all descended from a single cell. The isolation and maintenance of pure cultures is one of the most important
procedures in microbiology, and one with which all students must be familiar.
Like all other organisms, microorganisms require nutrients and a favorable environment to grow and multiply. Microbes are
generally grown in a culture medium that contains essential nutrients and provides a suitable environment (e.g. proper pH).
Microbes are essentially grown in a liquid medium, broth, or on a solid medium, agar.
Since most laboratory studies are made with pure cultures, it is necessary to sterilize culture media, that is, completely eliminate all
living organisms. This medium must be maintained in a sterile condition, free from living organisms, until inoculated with a pure
culture.
To grow a microbial culture in a sterilized medium, a number of the cells, the inoculum, are transferred, inoculated, into or onto the
medium with special precautions to maintain the purity of the culture. The procedures used in the microbiology laboratory to
prevent contamination of pure cultures are commonly referred to as aseptic technique.
The general rules in following aseptic technique are: 1) put nothing into sterile material that is not itself sterile, except the specific
organism you are studying and, 2) do not expose sterile materials to sources of contamination, for example, laboratory air.
Following inoculation, a microbial culture is grown (incubated) in a specific environment favorable for growth. Growth of
microbes is usually defined in terms of population growth, an increase in numbers of cells in the population, as opposed to
cellular growth, an increase in the size of an individual cell. The resultant growth is visible as cloudiness, turbidity, in a liquid
medium or as an isolated mass, colony, on a solid medium.

Materials:
Cultures
Escherichia coli (broth culture)
Serratia marcescens
mixed broth culture of Escherichia coli and Serratia marcescens
Media
one bottle sterile Nutrient agar
three tubes sterile Nutrient broth
three Nutrient agar plates, pre-dried for 2 days at room temperature

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Supplies
four sterile plastic petri dishes
sterile cotton swabs

The purpose of this exercise is to familiarize you with aseptic techniques. All the procedures have been designed to minimize
contamination. Observe the demonstration by your laboratory instructor and follow the procedures outlined in the manual exactly.
Place the bacticinerator in front of you and put all tubes and other equipment in a suitable location that will allow you to reach them
without any difficulty and without burning yourself.
At first these procedures for manipulating the loop, tubes, and caps will be difficult, but with practice these manipulations
will become more rapid and less cumbersome.
Operation of the Bacticinerator:
The bacticinerator is a gasless, flameless, heat sterilizer for use with inoculating loops, needles, glass tube/pipette mouths and
various metal & borosilicate glass instruments. Sterilization is accomplished through infrared heat. OPERATION: Turn on the
toggle switch to the “High” position; the red indicator light will come on when the switch is in the correct position. Sterilizer
must be heated for 15mins prior to use. Holding the inoculating loop by the handle, gently insert inoculating loop to be
sterilized into cylindrical sterilization area (see image below). Always ensure that the item is held with an insulated material. Do
not directly touch the sterilized item. Do not “park” the loop in there unintended, it will MELT. Avoid scraping sides of element
to ensure the longevity of the loop and heater element. Hold loop for 5 seconds. It is not necessary for loop to be glowing. The
outer, metal shield of the heater element can reach temperatures as high as 400°F. Do not touch outer metal shield or introduce
any flammable or volatile materials in the area surrounding the sterilizer.
Turn off bacticinerator after you have finished using it for the lab exercises for the day.

Lab Procedures:

A. Preparation of Solid Media

Solid medium is usually made by adding a solidifying agent to a broth medium. The most common solidifying agent is agar, a
substance obtained from marine algae and available in dried purified form. Although different agars vary considerably in their
physical properties, the usual melting point is 97-100°C. Thus, solid agar can be added to liquid culture media and melted during
heat sterilization. After sterilization, this liquid media can be poured into test tubes, bottles, or petri dishes. On cooling, this
medium containing agar solidifies at about 42°C. Once solidified, agar media may be incubated over the entire range of
temperatures a bacteriologist is likely to use (up to 70°C, perhaps) without melting.

An agar slant results when the hot molten agar media is allowed to harden in a test tube held in a tilted position. Pouring a molten
agar medium into plastic or glass Petri dishes makes agar plates.
1. Place the four sterile petri plates right side up in front of you.
The bottom of a petri plate is smaller and deeper than the top, often called the lid. Therefore, right side up is when the bottom is in
contact with the bench and the larger lid covers the bottom.

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2. Turn on your bacticinerator.
3. You must work quickly now to prevent the agar from solidifying before you are finished pouring the plates. Remove a bottle of
melted Nutrient agar medium from the 55°C water bath. Carefully wipe the adhering water from the bottle so that, when you tip the
bottle, this contaminated water will not run into the plate.
4. Loosen the cap of the bottle but do not remove it. When the cap is loosened all the way, remove it by encircling the cap with
your right or left little finger and the outside edge of your palm. See Figure 1-1 a. Do not set the cap down on the bench-top.

5. While still holding the cap, grasp the bottle securely with the thumb and forefinger of your right hand. See Figure 1. Lightly pass
the lip of the bottle in front of the bacticinerator to burn off any adhering dust and to also to set up a negative air current. The lip of
the bottle would be sterile from the autoclaving procedure.
6. Lift the lid of a petri plate with your left or right hand just enough to allow you to pour some of the agar medium into the bottom
of the petri plate. See Figure 1-1b.
7. Pour enough medium into the petri plate bottom to just cover the bottom surface. (You should be able to easily pour four plates
and possibly five with 100 mL of medium.)
8. Replace the lid to cover the bottom of the petri plate.
9. Carefully and slowly slide the poured plates to an undisturbed (back) portion of your bench-top to cool and solidify. Do not
disturb these plates for at least 20 minutes.
10. These plates will be used in part D of this exercise.

B. Aseptic Transfers
To the microbiologist, transfer of cultures from tube to tube and from agar plates to tubes is a common and simple procedure but
requires careful attention to certain details. Transfer of microorganisms is often done using a wire loop. Proper use of this
inoculating loop will help insure maintenance of a pure culture.
1. Label the 3 tubes of sterile Nutrient broth. Label one "sterile control", one "broth transfer", and one "colony transfer".
2. The broth cultures of Escherichia coli and plate culture of Serratia marcescens are at the end of your
bench.

3. Holding your loop like a pencil insert the loop into the cylindrical area of the bacticinerator. Heat only the wire in the
sterilizer, NOT the wire holder. If done properly it should only take 5 seconds for the entire length of the wire to be sterile. Once
this has occurred, remove the loop. The wire will now be sterile and very hot. Allow the loop to cool for several seconds in the
air before using it. This avoids killing the cells to be transferred and splattering that can lead to the production of contaminating
aerosols.

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3a. Now pick up the tube containing the pure culture of Escherichia coli with your other hand, while still holding the sterile loop.
With the hand holding the loop, remove the cap from the culture tube by encircling it with your little finger and the outer edge of
your palm. See Figure l. DO NOT put the cap down on your bench. Lightly pass the lip of the tube in front of the bacticinerator.

4. Now insert the loop into the E. coli broth culture and then remove it, carrying out a loopful of culture from the tube. See Figure
2. Replace the tube cap and return the tube to the storage rack.
5. Pick up and remove the cap from the tube of sterile Nutrient broth labeled "broth transfer" in the same manner as outlined in step
3a above.
6. Tilt the tube at about a 45°angle and insert the loop containing the culture into the open tube. Immerse the loop in the broth, swirl
the loop gently, then remove it. Pass the tube in front of the bacticinerator and replace the cap and return the tube to the storage
rack.
7. Sterilize the loop before putting it down by repeating step 3. This is necessary to avoid contaminating of the bench with the
culture.
8. Now, with your other hand, lift the lid of the petri plate containing a pure culture of the Serratia marcescens. Obtain an
inoculum by JUST TOUCHING ONE of the isolated single colonies on the agar surface. Do not dig into the agar. Do not
scrape the loop across the surface of the plate. Replace the lid of the plate immediately.
9. Pick up and remove the cap from the tube of sterile Nutrient broth labeled "colony transfer" in the same manner as outlined in
step 3a above.
10. Repeat steps 6 and 7.
11. To test your ability to properly sterilize your loop, pick a loopful of the culture from the E. coli broth culture tube following the
procedures outlined in steps 3, 3a, 4. Properly sterilize the loop containing the bacterial culture, as in step 7.
12. Pick up and remove the cap from the tube of sterile Nutrient broth labeled "sterile control" in the same manner as outlined in
step 3a above and insert the loop into the broth as described in step 6.
13. Repeat steps 11 and 12 a few times with the same "sterile control" tube.

C. Streak Plates
The streak plate technique is a rapid and simple method of isolating bacteria by mechanically spreading them over the agar surface
of a petri plate. The purpose is to obtain well-isolated colonies, each arising from a single bacterium, so that a pure culture of
each desired species in a mixture can be established. Proper streaking of plates is a relatively simple yet indispensable skill required
of any microbiologist.
The basic method for the preparation of a streak plate involves the spreading of a single loopful of inoculum over the surface of the
agar medium. There are many different techniques used for streaking plates. Choosing a technique is a matter of individual
preference and judgment. Any method can be used as long as the objective, production of well-isolated colonies, is attained and

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there is no evidence of contamination. The procedure described below is commonly called a "T streak", after the marking made on
the bottom of the plate.
1. Draw one line, approximately one third of the way down, across the entire BOTTOM of the plate. Then draw a second
line from the middle of the first through the center to the other side of the plate. This should make a large "T" on your plate,
dividing it into three sectors. See Figure 1-4.

2. Label the bottom of each of the 3 prepared Nutrient agar plate with your name or initials, your lab section, and the bacterial
species to be used. In addition, label one "from broth", one "from agar", and one "mixed
culture".
3. Use the aseptic techniques you learned in part B. Sterilize the loop and allow it to cool.
Obtain an inoculum of bacterial cells from:
• the broth tube containing a pure culture of Escherichia coli
• the agar plate of Serratia marcescens

• the broth tube containing a mixed culture supplied by your instructor.

When obtaining samples from colonies growing on agar plates, it is ONLY necessary and is advised that the loop JUST
TOUCHES THE SURFACE of ONE colony.
When obtaining samples from broth cultures, be sure to MIX the contents to ensure even distribution of microorganisms.
4. Inoculate the surface of the agar plates using the pattern shown in figure 1-5 and the technique described below.
a) deposit the inoculum by touching the loop to the surface of the plate near
the edge, in the top sector of the plate. Draw the loop lightly across the
surface of the agar for 2 cm, from the edge towards the center.
The handling of the plate can be accomplished in number of ways, all of which attempt to minimize possible contamination. Your
lab instructor will demonstrate one or several possible techniques. For all of the following do not keep the agar surface of the plate
unnecessarily uncovered, only expose the surface during the streaking process.
• The plate remains right side up on the bench, and the lid is lifted but kept over the plate while streaking. See figure l-
6a.
• The plate is inverted and while the lid remains on the bench, the bottom is lifted and the agar surface is streaked from
underneath. See figure l-6b.
Then sterilize the loop and allow it to cool in the air for a few seconds. Touch the loop to an unused edge (sterile area) of the agar
surface to cool it completely before continuing.

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b) Beginning at the edge of the plate near the initial inoculum deposit, make
several (10-20) parallel streaks passing through the original inoculum
deposit. Cover one-third of the plate, starting at the edge and moving
towards the center of the plate. Do this by swinging the loop holder back
and forth on the surface of the agar with very gentle and even pressure,
using only a wrist motion. The loop should almost retrace its path with
each swing as it moves down the agar surface from the edge towards the
center of the plate. Try to keep the loop, wire, and loop holder in a plane
parallel to the surface of the agar throughout the streak. Try not to lift the
loop off of the agar. Try to keep the loop in contact with the surface from
the beginning of the streak to the end. Do not dig the loop into the agar
medium,
* Sterilize the loop and allow it to cool as described above.
c) Rotate the plate 90°.
Pull the loop through one edge of the previous streaks 2 or 3 times to re-inoculate the loop. Now streak the second third of the plate
with several (10-20) more parallel streaks again starting at an edge and moving towards the center of the plate. After the initial re-
inoculation, avoid touching the already streaked first third of the plate.
*Sterilize the loop and allow it to cool as described above.
d) Rotate the plate 90°.
Pull the loop through one edge of the streaks in the second third of the plate to re-inoculate the loop. Now streak the last third of the
plate as above, being careful to avoid the already streaked first and second thirds of the plate.
*Sterilize the loop after the last streaking.

D. Ubiquity of Microorganisms
Microorganisms are everywhere. The laboratory is populated with many different types of microbes, in the air, on the benches, on
the floor, and on your clothing and body. This omnipresence of microorganisms is one reason why you have learned good aseptic
techniques in parts A, B, and C of this exercise. This part of the exercise is designed to give you some idea of the kind and numbers
of microbes that are present in the laboratory. There is also some freedom to allow you to satisfy your curiosity about the
microorganisms all around you. Finally, you will be required to isolate one of the bacterial species you obtain from this exercise for
use in the next two exercises.
1. Check to be sure the agar has solidified in your plates from part A by carefully tilting the plates and looking for movement. If
the agar is solid, you may work with the plates. Label one plate on the bottom as "sterile control". Do not open this plate at any
time. This is used to check if you have good aseptic technique when you poured your plates.
2. Use one plate to test for the natural contamination of articles in your environment. Label this your “test plate” and with the
source “finger, cell phone, etc.” Suggested experiments include: lightly rubbing your fingers (no gloves on) over the agar surface
of the plate, call this the “test plate, finger”, or opening a plate to the air for 15-20 minutes, or coughing into a plate, or gently
wiping the agar surface with an object from your pocket or backpack. It is also possible to sample a surface, such as the bench-top,
floor, sink, clothing, or skin. If you wish to do so, wipe the surface with sterile cotton swab then streak the entire agar surface of the
plate with the swab. Use a light touch. The swabs are packaged individually and are sterile until you contaminate them with
something of your choosing. Make sure the cotton tip of the swab does not come in contact with anything other than the surface
you are testing. A moist swab works best for collecting samples from a dry surface. You can moisten a swab on the surface of the
nutrient agar plate (at a corner), then sample the area of interest.

3. Leave the remaining two plates unlabeled and unopened on the bench, these are extra plates for the TA to collect and use for the
next class.

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4. Remember to label the bottom of your sample plate. Include your name or initials, your lab section, date, media type (NA for
nutrient agar) and what was sampled (source).

E. Incubation
In order for microorganisms to grow they need a suitable environment. One of the most critical environmental parameters affecting
growth of microorganisms is temperature. This will be discussed in lecture and is part of a later exercise. For most organisms used
in this laboratory,
30°C is an acceptable temperature for growth. Constant growth temperatures are maintained by incubating microbial cultures in
thermostatically controlled rooms or small ovens called incubators.
1. Incubate all tubes from part B in the 30°C incubator. Make sure labeling of your tubes is clear and complete. Place tubes in
racks provided by your instructor.
2. Incubate all plates from parts C and D in the 30°C incubator. Make sure labeling of your plates is clear
and complete.
Because of the high concentration of water in the agar medium, some water condensation forms in petri plates during incubation. If
plates were incubated right side up, moisture would likely drip from the cover to the surface of the agar and spread out. This would
disrupt individual colony formation and result in a confluent mass of growth. To avoid this, petri plates are routinely inverted
(bottom-side on top) during incubation.

F. Observation
Detailed observations are the key to performing, understanding, and designing scientific experiments. A keen eye and an attention
to subtle differences will help you successfully complete the laboratory report sheets. After incubation, plates and tubes should be
observed for evidence of microbial growth. Record your observations on the outlined report sheets provided. These are only a
guide, feel free to modify or add to them, as you deem necessary. Remember these report sheets constitute your lab notebook and
are the basis for lab grades and evaluations. They should be kept up to date and brought to lab at all times.
DO NOT DISCARD YOUR SAMPLES UNTIL YOU ARE SURE OF THE RESULTS AND ARE CERTAIN THE
SAMPLES ARE NOT NEEDED FOR THE NEXT EXERCISE.

Watch Video 1: Aseptic techniques Inoculating broth, slant, and stab tubes

Aseptic Technique: Inoculating broth tu…

tu…

Watch Video 1: Aseptic techniques Inoculating broth, slant, and stab tubes. URL: https://youtu.be/nMoM8Ku5-8A

Watch Video 2: How to perform a T-streak for isolated colonies.

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 T-Streak

Watch Video 2:How to perform a T-streak for isolated colonies. This video was filmed in the Microbiology laboratories at NC
State. URL:https://youtu.be/NsQv7QOmdXo

This page titled 2.4: Lab Procedures- Prepare solid media, Aseptic Technique, T-streaking is shared under a CC BY-NC-SA license and was
authored, remixed, and/or curated by Joan Petersen & Susan McLaughlin.

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2.5: Results
Record the results of your experiments in the tables below.

A. Pouring plates:
Observe that your plates were poured properly--the bottom of the petri dish should be about half full and the media should be
sterile, even, and contain few or no bubbles.

B. Aseptic transfers
Look for turbidity in the broth indicating growth of microorganisms. Record the turbidity of the Nutrient broth in the three tubes as
+ or -. Recall what your sterile Nutrient broth looked like before it was inoculated.

Nutrient broth tube Turbidity + or -

"sterile control"

"broth transfer"

"colony transfer"

Also note any other distinguishing characteristics (amount and location of turbidity, color, etc.) of the bacterial growth in the broth
and note and record any differences between species of bacteria. An effective method for recording your results is to draw a picture
of the tube and the appearance of the broth due to any growth.

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C. Streak Plates
1. Check to see whether you obtained well-isolated single colonies on the agar streak plates. Describe and compare your results for
each inoculum.

From Broth: Describe growth characteristics and make a sketch in the circle below.

From Agar: Describe growth characteristics and make a sketch in the circle below.

Based on your results, answer the following questions:

2. Were you able to separate and identify the two different bacterial species in your "mixed culture"?
3. Colony morphology can be an aid in the identification of microorganisms.
Although colony morphology cannot be employed as the sole identifying criterion, it is a useful trait in the classification of many
common types of microorganisms. Five parameters are normally used to describe microbial colonies growing on an agar surface.
a. Size: pinpoint, small, medium, or large; range: < l mm - 3cm
b. Color: absolutely white, various degrees of pigmentation
c. Texture: the texture of the colony as determined by touching the colony
with a needle; smooth (buttery), dry (granular), or mucoid (slimy) and the
appearance as judged by the manner in which the colony refracts light;
clear, glistening, dense, opaque, or translucent.
d. Form: the shape of the colony; circular, irregular, filamentous, or rhizoid
(see Figure 1 -7)

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e. Elevation: the degree to which colony growth is raised; flat, raised,
convex or umbonate (see Figure l-7)
f. Margin: the shape of the edge or margin of the colony (see Figure below)

Image 1: Different colony morphologies/characteristics

Compare your bacterial colonies to those of your bench mates. Note and record any differences in the way various bacterial species
grow on agar surfaces.
Escherichia coli:

Serratia marcescens:

D. Ubiquity of Microorganisms
Do not throw these test plates away until you have read Exercise 2, part D ("test plate isolate”).
Check to see if your "sterile control" plates remained sterile and were not contaminated. Observe, record, and DESCRIBE the
numbers and varieties of different microbial colonies that appear on your test plate. Indicate the sample source (finger plate or
other) or exposure method for the test plate.

"sterile control":

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"test plate" and source:

This page titled 2.5: Results is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by Joan Petersen & Susan
McLaughlin.
2.3: Results by Joan Petersen & Susan McLaughlin is licensed CC BY-NC-SA 4.0.

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2.6: Review Questions
PRACTICE QUESTIONS FOR REVIEW
1. What general type of growth medium would you use to:
(a) grow one type of bacteria but inhibit the growth of another type?
(b) discriminate between different types of bacteria?

2. Why is it necessary to sterilize the loop between streaks when streaking for single colonies?

3. Define and/or explain the use of the following:

(a) synthetic medium
(b) agar
(c) broth

4. A bacterial species is inoculated on EMB agar.

(a) The bacteria do not grow. Why?
(b) If the bacteria ferment lactose, what would you expect to see?
(c) The bacteria produce clear colonies. Why?

5. What medium would you use (TSA, EMB, MSA) if you wanted to determine if a Staphylococcus isolate could ferment
mannitol? Describe what you would see on this medium.

6. If you were testing water for the presence of fecal coliforms, what sort of medium would you use: TSA, EMB agar or MSA
agar? If fecal coliforms were present, what would their growth characteristics be on this medium?

This page titled 2.6: Review Questions is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by Joan Petersen &
Susan McLaughlin.
2.4: Review Questions by Joan Petersen & Susan McLaughlin is licensed CC BY-NC-SA 4.0.

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 CHAPTER OVERVIEW

3: Microscopy
3.1: Introduction to the Microscope
3.2: Comparison of Sizes and Shapes of Microorganisms
3.3: Lab Procedures- Operating a Microscope
3.4: Results
3.5: Review Questions

3: Microscopy is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

1
3.1: Introduction to the Microscope
Learning Outcomes
Review the principles of light microscopy and identify the major parts of the microscope.
Learn how to use the microscope to view slides of several different cell types, including the use of the oil immersion lens to
view bacterial cells.

Early Microscopy
The first microscope was developed in 1590 by Dutch lens grinders Hans and Zacharias Jansen. In 1667, Robert Hooke described
the microscopic appearance of cork and used the term cell to describe the compartments he observed. Anton van Leeuwenhoek was
the first person to observe living cells under the microscope in 1675—he described many types of cells, including bacteria. Since
then more sophisticated and powerful scopes have been developed that allow for higher magnification and clearer images.
Microscopy is used by scientists and health care professionals for many purposes, including diagnosis of infectious diseases,
identification of microorganisms (microscopic organisms) in environmental samples (including food and water), and
determination of the effect of pathogenic (disease-causing) microbes on human cells. This exercise will familiarize you with the
microscopes we will be using to look at various types of microorganisms throughout the semester.

The Light Microscope

What does it mean to be microscopic? Objects are said to be microscopic when they are too small to be seen with the unaided eye
—they need to be magnified (enlarged) for the human eye to be able to see them. This includes human cells and many other types
of cells that you will be studying in this class. The microscope you will be using uses visible light and two sets of lenses to produce
a magnified image. The total magnification will depend on which objective lens you are using—the highest magnification possible
on these microscopes is typically 1000X—meaning that objects appear 1000X larger than they actually are.
Resolution vs. Magnification
Magnification refers to the process of making an object appear larger than it is; whereas resolution is the ability to see objects
clearly enough to tell two distinct objects apart. Although it is possible to magnify above 1000X, a higher magnification would
result in a blurry image. (Think about magnifying a digital photograph beyond the point where you can see the image clearly). This
is due to the limitations of visible light (details that are smaller than the wavelength of light used cannot be resolved).
The limit of resolution of the human eye is about 0.1 mm, or 100 microns (see Table 1 for metric review). Objects that are smaller
than this cannot be seen clearly without magnification. Since most cells are much smaller than 100 microns, we need to use
microscopes to see them.
The limit of resolution of a standard brightfield light microscope, also called the resolving power, is ~0.2 µm, or 200 nm.
Biologists typically use microscopes to view all types of cells, including plant cells, animal cells, protozoa, algae, fungi, and
bacteria. The nucleus and chloroplasts of eukaryotic cells can also be seen—however smaller organelles and viruses are beyond the
limit of resolution of the light microscope (see Figure 1).
Resolution is the ability of the lenses to distinguish between two adjacent objects as distinct and separate.
A compound light microscope has a maximum resolution of 0.2 µm, this means it can distinguish between two points ≥ 0.2 µm,
any objects closer than 0.2um will be seen as 1 object. Shorter wavelengths of light provide greater resolution. This is why we
often have a blue filter over our light source in the microscope, it helps to increase resolution since its wavelength is the shortest in
the visible light spectrum. Without resolution, no matter how much the image is magnified, the amount of observable detail is
fixed, and regardless of how much you increase the size of the image, no more detail can be seen. At this point, you will have
reached the limit of resolution or the resolving power of the lens. This property of the lens is fixed by the design and construction
of the lens. To change the resolution, a different lens is often the only answer.

Table 1: Metric units commonly used in Microbiology

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 The basic unit of measurement of length in the metric system is the meter.

There are 1000 millimeters (mm) in one meter. 1 mm = 10-3 meter.

There are 1000 micrometers (microns, or µm) in one millimeter. 1 µm = 10-6 meter.

There are 1000 nanometers in one micrometer. 1 nm = 10-9 meter.

Figure 1: Resolving Power of Microscopes

The microscope is one of the microbiologist's greatest tools. It allows for the visualization of small particles, including microbes,
which individually are too small to be seen with the human eye. With the help of proper illumination, a microscope can magnify a
specimen and optically resolve fine detail. This introduction to microscopy will include an explanation of features and adjustments
of a compound brightfield light microscope, which magnifies images using a two lens system.
Before reading the following discussion of the theory of the microscope, please familiarize yourself with the names of the
microscope parts shown in Figure 2 and their function.
1. Eyepiece/Ocular lens: Lens in which the final magnification occurs. Often is at 10X magnification, but can be different.
2. Revolving nose piece: Holds multiple objective lenses in place. The base of the nose piece can rotate, allowing each of the lens
to be rotated into alignment with the ocular lens.
3. Objective lenses: Initial magnification of your specimen occurs here. Most brightfield light microscopes have 3 objective lenses
seated into the resolving nose piece base.
4. Coarse focusing knob: larger of the two knobs, the coarse adjustment knob moves the stage up or down to bring the specimen
into focus. It is very sensitive, even small partial rotation of this knob can bring about a big change in the vertical movement of the
stage. ONLY use coarse focusing at the beginning with the 4X, 10X low powered objectives in place. If you use it with the higher
powered objectives, it can damage the objective if you crash the lens through your glass specimen slide.

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5. Fine focusing knob: smaller of the two knobs, the fine adjustment knob brings the specimen into sharp focus under low power
and is used for all focusing when using high power lenses such as the 100x oil immersion lens.
6/9. Stage & Mechanical stage: The horizontal surface where you place the slide specimen is called the stage. The slide is held in
place by spring loaded clips and moved around the stage by turning the geared knobs on the mechanical stage. The mechanical
stage has two perpendicular scales that can be used to record the position of an object on a slide, useful to quickly relocate an
object.
7. Illuminator: contains the light source, a lamp made either of an incandescent tungsten-halogen bulb or an LED. There is
normally a switch to turn on/off or a rheostat located on the side that you can use to adjust the brightness of the light.
8. Diaphragm and Condenser: the diaphragm controls the amount of light passing from the illuminator through the bottom of the
slide, there is a small lever used to achieve the optimal lighting. The condenser is a lens system that focuses the light coming up
from the illuminator onto objects on the slide.

Figure 2: Brightfield light microscope used in a Microbiology lab (Lumen)

The Optical System. The optical system of a compound microscope consists of two lens systems: one found in the objective(s)
lens(es) (Fig. 2, part 3); the other in the ocular (eyepiece) (Fig. 2 part 1). The objective lens system is found attached to a rotating
nosepiece (Fig. 2, part 2). A microscope usually has three or four objectives that differ in their magnification and resolving power.
Magnification is the apparent increase in size of an object. Resolving power is the term used to indicate the ability to distinguish
two objects as separate. The most familiar example of resolving power is that of car headlights at night: at a long distance away, the
headlights appear as one light; as the car approaches, the light becomes oblong, then barbell-shaped, and finally it becomes
resolved into two separate lights. Both resolution and magnification are necessary in microscopy in order to give an apparently
larger, finely detailed object to view.
Look at the engravings on the objective lenses and note both the magnification (for example: 10X, 40X, 100X) and the resolution
given as N.A. = numerical aperture, from which the limit of resolution can be calculated:

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limit of resolution = wavelength
2 X numerical aperture
At a wavelength of 550 nm (0.55µm), the 100X objective lens with a N.A. of 1.25 has a resolving power of 0.22 µm. Visible light
has of wavelength from about 400-750 nanometers (nm). Since the limit of resolution decreases at the shorter wavelengths,
microscopes are usually fitted with a blue filter. The resolving power of the lens separates the details of the specimen, and the
magnification increases the apparent size of these details so that they are visible to the human eye. Without both resolution and
magnification, you would either see nothing (good resolution, no magnification) or a big blur (poor resolution, good
magnification).
The objective lens system produces an image of the specimen, which is then further magnified by the ocular lens (eyepiece). The
magnification of this lens is engraved on the ocular. The total magnification of the microscope is determined by the combination of
the magnification of the objective lens and ocular lens that is in use, that is:
Total magnification = objective lens X ocular lens (eyepiece)

For example, with a 10X objective lens and a 10X ocular, the total magnification of the microscope is 100X. If the objective lens is
changed to a 20X objective, then the total magnification is now 200X, whereas if a 10X objective is used with a 12.5X ocular lens,
the total magnification is now 125X. The use of objective and ocular lenses with different magnifications allows greater flexibility
when using the compound microscope. Due to the size of most bacteria (ranges widely from ~1um to over 100um), generally we
require the use of the 100x oil immersion lens with a 10x ocular lense to view bacteria in a standard brightfield light microscope.
The Illumination System. The objective and ocular lens systems can only perform well under optimal illumination conditions. To
achieve these conditions, the light from the light source (bulb) must be centered on the specimen. (In most inexpensive
microscopes, the manufacturer adjusts this centering. In more versatile microscopes, the centering becomes more critical and is a
function performed by the operator.) The parallel light rays from the light source are focused on the specimen by the condenser lens
system (see Fig. 2) The condenser can move up and down to affect this focus. Finally, the amount of light entering the condenser
lens system is adjusted using the condenser diaphragm. It is critical that the amount of light be appropriate for the size of the
objective lens receiving the light. This is important to give sufficient light, while minimizing glare from stray light, which could
otherwise reduce image detail. The higher the magnification and resolving power of the lens, the more light is needed to view the
specimen.
Objective lenses used for observing very small objects such as bacteria are almost always oil immersion lenses. With an oil
immersion lens, a drop of oil is placed between the specimen and the objective lens so that the image light passes through the oil.
Without the oil, light passing through the glass microscope slide and specimen would be refracted (bent) when it entered the air
between the slide and the objective lens. This refracted light might still be able to contribute to the image of the specimen if the
objective lens is large. However, at the higher magnification, the objective lens is small, so is unable to capture this light. The loss
of this light leads to loss of image detail. Therefore, at higher magnifications, the area between the slide and the lens is modified to
have the same (or nearly the same) refracting qualities (refractive index) as the glass and specimen by the addition of immersion
oil. Watch this NC BioNetwork video (https://youtu.be/-0EvnroWpVc) on oil immersion. For more information, read this article
(https://www.microscopeworld.com/t-us...rsion_oil.aspx).
To use an oil immersion lens, place a drop of oil on top of the dried specimen on the slide and carefully focus the microscope so
that the objective lens is immersed in the oil. Any lens, which requires oil, is marked "oil" or "oil immersion." Conversely, any lens
not marked "oil" should NOT be used with oil and is generally not sealed against oil seeping into and ruining the objective.

Watch this Video on how to use a Microscope, filmed at NC State Microbiology labs:

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 Introduction to the microscope

Video 1: Introduction to the Microscope (6:26)

Key Terms

microorganism, magnification, resolution, working distance, parfocal, parcentric, prokaryotic, eukaryotic, bacillus, coccus,
spirillum, spirochete, morphology, bacterial arrangements, depth of field, field of view, taxonomic classification

References:
Contributed by Joan Petersen & Susan McLaughli: Associate Professors (Biological Sciences and Geology) at Queensborough
Community College
Lumen Learning: Figure 3: Brightfield light microscope https://courses.lumenlearning.com/mi...of-microscopy/

3.1: Introduction to the Microscope is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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3.2: Comparison of Sizes and Shapes of Microorganisms
Learning Outcomes
Recognize the shapes and arrangements of some common types of bacteria.

A. BACTERIAL SHAPES, ARRANGEMENTS, AND FORMS

Bacteria are unicellular prokaryotic microorganisms that divide by binary fission, a process by which one bacterium
splits into two.
Scanning electron micrograph of Salmonella typhimurium undergoing binary fission.

YouTube movie of binary fission in bacteria.

YouTube movie of fluorescing imaging of binary fission in

bacteria.

Review of Prokaryotic and Eukaryotic Cells from Unit 1.

There are three common shapes of bacteria:

coccus (singular) or cocci (plural)
bacillus or rod (singular) or bacilli, rods (plural)
spiral (example of a spirochete, a type of spiral is shown in image 1)

Image 1: These are the different shapes of bacteria and their sizes compared with the width of a human hair.
The unit “μm” is a measurement of length, the “micrometer,” or commonly known as the micron. It equals 1×10−6 meters that is,
one millionth of a meter. Image courtesy of Kestin Schulz, Mariya W. Smit, Lydie Herfort and Holly M. Simon
URL: https://commons.wikimedia.org/wiki/F...omparisons.jpg

The cocci come in 5 different arrangements; the bacilli in 3 different arrangements; and the spirals in 3 different forms.
1. Coccus
A coccus-shaped bacterium is usually spherical, although some appear oval, elongated, or flattened on one side.
Most cocci are approximately 0.5 - 1.0 micrometer (µm) in diameter and may be seen, based on their planes of

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division and tendency to remain attached after replication, in one of the following arrangements (see Fig. 1A):
a. Division in one plane produces either a diplococcus (see Fig. 1A and Fig. 1B) or streptococcus (see
Fig. 1A and Fig. 1C) arrangement.
1. diplococcus: a pair of cocci
- Photomicrograph of a diplococcus
- Scanning electron micrograph of a Streptococcus pneumoniae, a diplococcus
- Scanning electron micrograph of a Neisseria, a diplococcus; courtesy of Dennis Kunkel's Microscopy
2. streptococcus: a chain of cocci
- Photomicrograph of a streptococcus
- Scanning electron micrograph of Streptococcus pyogenes; courtesy of Dennis Kunkel's Microscopy
- Transmission electron micrograph of Streptococcus
-Scanning Electron Micrograph of Enterococcus
b. Division in two planes produces a tetrad arrangement (see Fig. 1A and Fig. 1D).
tetrad: a square of 4 cocci
- Photomicrograph of a tetrad
- Scanning electron micrograph of Micrococcus luteus
c. Division in three planes produces a sarcina arrangement (see Fig. 1A).
sarcina: a cube of 8 cocci
- Photomicrograph of a sarcina
It is difficult with a conventional light microscope to tell a tetrad arrangement (square of four cocci) from a
sarcina arrangement (cube of eight) so in our lab, anytime you see ba square of four cocci, say it is either a
tetrad or a sarcina arrangement.
d. Division in random planes produces a staphylococcus arrangement (see Fig. 1A and Fig. 1E).
staphylococcus: cocci in irregular, often grape-like clusters
- Photomicrograph of a staphylococcus, negative image
- Scanning electron micrograph of Staphylococcus aureus; courtesy of Dennis Kunkel's Microscopy
- Scanning electron micrograph of methicillin-resistant Staphylococcus aureus (MRSA); courtesy of CDC
As you observe these different cocci, keep in mind that the procedures used in slide preparation may cause
some arrangements to break apart or clump together (see Figs. 1D and 1E). The correct form, however,
should predominate. Also remember that each coccus in an arrangement represents a complete, individual,
one-celled organism.
2. Bacillus (rod)
A bacillus or rod is a hotdog-shaped bacterium having one of the following arrangements (see Fig 2A):
a. bacillus: a single bacillus (see Fig 2A and Fig 2B)
- Photomicrograph of a bacillus
- Scanning electron micrograph of a bacillus
- Scanning electron micrograph of Escherichia coli O157H7, a bacillus; courtesy of CDC
b. streptobacillus: bacilli in chains (see Fig 2A and Fig 2C)
- Photomicrograph of a streptobacillus

c. coccobacillus: oval and similar to a coccus (see Fig 2A, 2D, and 2E)
A single bacillus is typically 0.5-1.0 µm wide and from 1- 4 µm long. Small bacilli or bacilli that are dividing or
have just divided by binary fission may at first glance be confused for diplococci or cocci (see Fig. 2A) so

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 they must be observed carefully. You will, however, be able to see bacilli that have not divided and are definitely
rod-shaped as well as bacilli in the process of dividing.
3. Spiral
Spiral-shaped bacteria occur in one of three forms (see Fig. 3A):
a. vibrio: an incomplete spiral or comma-shaped (see Fig. 3A and Fig. 3B)
- Photomicrograph of a vibrio
- Scanning electron micrograph of Vibrio cholerae; courtesy of Dennis Kunkel's Microscopy
b. spirillum: a thick, rigid spiral (see Fig. 3A and Fig. 3C)
- Photomicrograph of a spirillum
c. spirochete: a thin, flexible spiral (see Fig. 3A and Fig. 3D)
- Photomicrograph of a spirochete
- Scanning electron micrograph of the spirochete Leptospira; courtesy of CDC
- scanning electron micrograph of the spirochete Treponema pallidum; courtesy of CDC
The spirals you will observe range from 5-40 µm long but some are over 100 µm in length. The spirochetes are the
thinnest of the bacteria, often having a width of only 0.25-0.5 µm.
To view a nice interactive illustration comparing size of cells and microbes, see the Cell Size and Scale Resource at
the University of Utah.

B. YEASTS
Yeasts, such as the common baker's yeast Saccharomyces cerevisiae (see Fig. 4), are unicellular fungi. They usually
appear spherical and have a diameter of 3 - 5 µm. Yeasts commonly reproduce asexually by a process called budding.
Unlike bacteria, which are prokaryotic, yeasts are eukaryotic.
- Scanning electron micrograph of Saccharomyces; courtesy of Dennis Kunkel's Microscopy

Review of Prokaryotic and Eukaryotic Cells from Unit 1.

To view a nice interactive illustration comparing size of cells and microbes, see the Cell Size and Scale Resource at
the University of Utah.

C. MEASUREMENT OF MICROORGANISMS
The approximate size of a microorganism can be determined using an ocular micrometer (see Fig. 5) , an eyepiece that
contains a scale that will appear superimposed upon the focused specimen.
To view a nice interactive illustration comparing size of cells and microbes, see the Cell size & scale resource at the
University of Utah's Learn.genetics site, URL: https://learn.genetics.utah.edu/content/cells/scale/

Contributors
Dr. Gary Kaiser (COMMUNITY COLLEGE OF BALTIMORE COUNTY, CATONSVILLE CAMPUS)

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3.2: Comparison of Sizes and Shapes of Microorganisms is shared under a not declared license and was authored, remixed, and/or curated by
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3.3: Lab Procedures- Operating a Microscope
Brightfield Light Microscope General Operating Procedure:
The following step-by-step operating procedure should be carefully observed when first using the Nikon Alphaphot-2. Go through
these steps now and again when carrying out the procedures for parts B, C, and D. This instrument is designed for fast-simplified
use and correct operating technique should soon become automatic.
1. Plug in and turn on the in-base illuminator.
2. Raise the nosepiece using the coarse adjustment knob. This provides greater access to the stage when the slide is in position.
3. Rotate the nosepiece so that the 10X objective is in operating position. You should feel a definite position stop for the objective.
Turn the nosepiece clockwise and counter-clockwise until you are familiar with this position stop.
4. Open the iris diaphragm approximately half way.
5. Place the slide in the stage slide holder securely. Be sure the slide has the specimen side up. Roughly center the specimen over
the light coming from the condenser.
6. Move the microscope condenser by means of the condenser rack and pinion knob until the top of the condenser is approximately
the thickness of a piece of paper beneath the slide.
7. Lower the objective using the coarse control knob until it reaches a stop. Do not force the knob. The stop should be obvious if
you are moving the controls gently. Again, become familiar with the feel of the position stop.
8. View through the eyepieces and without disturbing the coarse adjustment setting, slowly rotate the fine adjustment knob in the
appropriate direction until the specimen detail is in sharpest possible focus.
9. Adjust the interpupillary distance between the two eyepieces by sliding the eyepiece plates in or out.
10. If your eyes are very different the left eyepiece tube is adjustable to compensate for refraction differences of the eyes. The
correct procedure is to bring the specimen into sharpest possible focus with a fine adjustment knob using the right eyepiece only,
while closing your left eye. To focus for the left eye, view the specimen with the left eye only and turn the knurled collar until the
specimen is in sharp focus. Do not adjust the fine adjustment knob during this procedure.
11. Once the specimen detail is in sharp focus using the 10X objective, it is then possible to rotate the nosepiece to other objectives
without changing the position of the coarse adjustment knob. Very little refocusing with the fine adjustment is required since the
Nikon Alphaphot-2 microscope objectives are parfocal. The term parfocal means that if an object is in focus with one objective
lens, it will be in focus with all of the lenses.
Make certain that the portion of the specimen you wish to view is exactly centered in the field of the low-power objective. This is
necessary because the microscopic field of view is smaller under high magnification than under low magnification.
Remember that the iris diaphragm setting must be changed whenever a different objective is used. As magnification increases the
condenser iris diaphragm is opened as required. With these microscopes you are effectively increasing the light reaching the higher
power objective. Adjustment of the condenser iris diaphragm results in proper contrast for viewing specimens under varying
magnifications.
12. Try the highest magnification, the l00X-oil immersion objective. To focus with the oil immersion lens proceed in the following
manner:
a) Revolve the nosepiece so that there is no objective directly over the specimen. This allows enough space so that a drop of
immersion oil may be placed on the specimen.
b) Place one drop of immersion oil in the center of the circle of light formed on the specimen slide.
c) Turn the nosepiece until the 100X objective snaps into place. The objective should be in the oil but must not touch the slide.
d) Rotate the fine adjustment knob to obtain a sharp focus of the specimen. Remember to make the adjustments noted in step 10.

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Problems:
Certain mechanical difficulties, real or apparent, may be encountered while operating your microscope.
A common problem is the failure of the fine adjustment to turn in the direction required for sharp focusing. This indicates that it
has been screwed to the limits of its threads, either upward or downward, as the case may be. Screw it back to about one-half the
thread distance, use the coarse adjustment to raise or lower the objective sufficiently to bring the specimen into view, and then
refocus with the fine adjustment.
If the coarse adjustment fails to lower the objective sufficiently to bring the specimen into view, the fine adjustment has been
screwed up too far and should be screwed down to about half its thread distance.
Any other problems? Burned-out light bulb? Focus knobs difficult to turn, grinding as they move, or moving by themselves?
Specimen going in and out of focus as the stage is moved? Did you write the word "up" on your microscope slide? Is it still facing
up? Do not attempt to fix these yourself. Get your instructor.

Proper Care of the Microscope:

The compound microscope used in microbiology is a precision instrument. Its mechanical parts, such as the calibrated mechanical
stage and the adjustment knobs, are easily damaged and all lenses, particularly the oil immersion objective, are delicate and
expensive. Thus, the instrument must be handled with care. The following rules, cautions, and maintenance should be observed:
1. Use both hands when carrying the microscope; one firmly grasping the arm of the microscope, the other beneath the base. Avoid
sudden jars.
2. To keep the microscope and lens systems clean:
• Never touch the lenses. If the lenses become dirty, wipe them gently with lens paper.
• Never leave a slide on the microscope when it is not in use.
• Always use lens paper to remove oil from the oil-immersion objective after its use. Do not wipe the lower power objectives with
the same piece of lens paper used to clean the oil-immersion objective. If by accident oil should get on either of the lower power
objectives, wipe it off immediately with clean lens paper.
• Keep the stage of the microscope clean and dry.
3. To avoid breaking the microscope:
• Never force the adjustments. All adjustments should work freely and easily.
• Never allow an objective lens to jam into or even to touch the slide or cover slip.
• Never focus downward with the coarse adjustment while you are looking through the microscope. Always incline your head to
the side with eyes parallel to the slide, so that downward movement can be arrested before the objective touches the slide.
• Never exchange the objectives or eyepieces of different microscopes and never under any circumstance remove the front lenses
from the objectives.
• Never attempt to carry two microscopes at one time.
4. Storage of the microscope:
Make sure the immersion oil has been removed from the lens.
Put the low power (10X) objective into position and turn the stage all the way down.
Be sure the slide holder does not extend beyond the left edge of the microscope.
Wrap the electrical cord around the cord hanger.
Your TA will place the microscope in the cabinet.

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3.4: Results
Results
C. Methylene Blue-A Simple Stain
Sketch cellular shape (rods or cocci) and arrangement (single cells, pairs, clusters, chains) of the organisms observed with the oil-
immersion lens (total magnification 1000X). Compare size and shape of the three microorganisms. You will need to be familiar
with these for the next exercise and for identifying your unknowns.
The only way to become proficient with a microscope is to use it often and be observant while using it.
Saccharomyces cerevisiae- Eukaryotic Yeast

Bacillus megaterium

Micrococcus luteus

D. Test plate isolate

Sketch cellular shape and arrangement of the isolates from your "test plate" (total magnification, 1000X). In the next laboratory we
will do a differential stain of this bacterial culture and show you how to use Bergey's Manual of Determinative Bacteriology.

"test plate isolate"

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E. Demonstration slide

Sketch the cellular shape of Spirillum volutans.

Questions:
1.What are the structures seen on the end of these cells?
2. What is their function?

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3.5: Review Questions
1. Be able to describe the different parts of a microscope and their function
2. Explain this statement: "The limit of resolution for a brightfield light microscope is 0.2um."
3. What is the purpose of using oil in the oil immersion lens?
4. The objective lens is 40X and the ocular lens is 20X, what is the total magnification?

3.5: Review Questions is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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 CHAPTER OVERVIEW

4: Staining Techniques
4.1: Introduction to Staining
4.2: Specialized Bacterial Staining Techniques
4.3: Lab Procedures- Bacterial Smear, Simple and Gram Staining
4.4: Results
4.5: Review Questions

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1
4.1: Introduction to Staining
Learning Objectives
Describe the differences between simple staining and differential staining techniques.
Discuss how to prepare a bacterial smear from cultured organisms.
Distinguish between Gram-positive and Gram-negative bacteria.
Describe the process of the Gram stain procedure.
Use microscopy to examine Gram stained cells.
Describe select special staining procedures and view examples of these under oil immersion.

Why do we have to stain bacteria?

Most types of cells do not have much natural pigment and are therefore difficult to see under the light microscope unless they are
stained. Several types of stains are used to make bacterial cells more visible. In addition, specific staining techniques can be used to
determine the cells’ biochemical or structural properties, such as cell wall type and presence or absence of endospores. This type of
information can help scientists identify and classify microorganisms, and can be used by health care providers to diagnose the
cause of a bacterial infection.

The Simple Stain

One type of staining procedure that can be used is the simple stain, in which only one stain is used, and all types of bacteria appear
as the color of that stain when viewed under the microscope. Some stains commonly used for simple staining include crystal violet,
safranin, and methylene blue. Simple stains can be used to determine a bacterial species’ morphology and arrangement, but they do
not give any additional information. Living bacteria are almost colorless, and do not present sufficient contrast with the water in
which they are suspended to be clearly visible. The purpose of staining is to increase the contrast between the organisms and the
background so that they are more readily seen in the light microscope. In a simple stain, a bacterial smear is stained with a solution
of a single dye that stains all cells the same color without differentiation of cell types or structures. The single dye used here in our
lab is methylene blue, a basic stain. Basic stains, having a positive charge, bind strongly to negatively charged cell components
such as bacterial nucleic acids and cell walls.

Image 1: Microscopic view of Bacillus (rod) shaped bacteria simple stained with crystal violet. Isolated and imaged by Muntasir
Alam, University of Dhaka, Department of Microbiology in 2007. https://commons.wikimedia.org/wiki/F...micrograph.jpg

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Watch Video 1: how to apply a simple stain

Applying a Simple Stain to a Bacterial C…

C…

Watch Video 1: How to apply a simple stain to a bacterial culture by NC BioNetwork (4:05)
URL: https://youtu.be/8ODeT9DLHKI

The Gram Stain

Scientists will often choose to perform a differential stain, as this allows them to gather additional information about the bacteria
they are working with. Differential stains use more than one stain, and cells will have a different appearance based on their
chemical or structural properties. Some examples of differential stains are the Gram stain, acid-fast stain, and endospore stain. You
will learn how to prepare bacterial cells for staining, and learn about the gram staining technique.
This very commonly used staining procedure was first developed by the Danish bacteriologist Hans Christian Gram in 1882
(published in 1884) while working with tissue samples from the lungs of patients who had died from pneumonia. Since then, the
Gram stain procedure has been widely used by microbiologists everywhere to obtain important information about the bacterial
species they are working with. Knowing the Gram reaction of a clinical isolate can help the health care professional make a
diagnosis and choose the appropriate antibiotic for treatment.
Gram stain results reflect differences in cell wall composition. Gram positive cells have thick layers of a peptidoglycan (a
carbohydrate) in their cell walls; Gram negative bacteria have very little. Gram positive bacteria also have teichoic acids, whereas
Gram negatives do not. Gram negative cells have an outer membrane that resembles the phospholipid bilayer of the cell membrane.
The outer membrane contains lipopolysaccharides (LPS), which are released as endotoxins when Gram negative cells die. This can
be of concern to a person with an infection caused by a gram negative organism.

Image 2: Microscopic image of a Gram stain of mixed Gram-positive cocci (Staphylococcus aureus ATCC 25923, purple) and
Gram-negative bacilli (Escherichia coli ATCC 11775, red). Magnification:1,000. Image by Y

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Tambe. https://commons.wikimedia.org/wiki/F...m_stain_01.jpg

Figure 1 below shows the major differences between the Gram positive and Gram negative cell walls. The differences in the cell
wall composition are reflected in the way the cells react with the stains used in the Gram stain procedure.
Gram stains are best performed on fresh cultures—older cells may have damaged cell walls and not give the proper Gram reaction.
Certain species are known as Gram-variable, and so both Gram positive and Gram negative reactions may be visible on your
slide.
Poor staining technique could lead to inaccurate results. One of the most important steps in Gram staining is the decolorizing
step (use of alcohol/acetone). If the decolorizer is not left on long enough, then it will not be able to differentiate between Gram
positive and Gram negative bacteria. This step uses decolorizer, made of an alcohol/acetone mixture. Its function in Gram
negative bacteria is to remove the outer cell membrane and thin layer of peptidoglycan. The cell membrane is mostly made of
lipids and are sensitive to alcohols. By dissolving these layers, the crystal violet-iodine complex is also removed, and thus Gram
negatives are now able to take up the secondary stain, safranin, which is used in the last step of the Gram stain, staining them
pinkish-red and differentiating between them and the Gram positives, who with their thick peptidoglycan layer has retained the
primary stain, crystal violet, and appears purple/blue. On the flip side, if you use too much decolorizer, it can decolorize your
sample on the slide, leading to loss of crystal violet (the primary stain)-iodine complex. The decolorizing step is sensitive because
of the cell wall structure. Even Gram positive bacteria with their thick cell walls could become excessively decolorized, resulting
in the loss of the peptidoglycan layer and the crystal violet-iodine complex. When the use of the secondary stain, safranin, is
applied in the last step, the Gram positive bacteria will pick up this stain and look reddish-pink instead of purple/blue. Watch video
2 for an example of this.
Another common mistake is in the preparation of the bacterial smear, which is in the first step of any staining procedure. This
involves applying a thin film of bacteria on your microscope slide and then heat fixing it with either your bunsen burner,
bacticinerator, or slide warmer. The main purpose of this step is to adhere the bacterial cells to the microscope slide (it also
denatures the proteins and kills them too). If you forget to do this step, then the cells will be 'washed' off in all the subsequent steps
of your staining process. You will literally have no cells on your slide to stain!
Although the vast majority of bacteria are either Gram positive or Gram negative, it is important to remember that not all bacteria
can be stained with this procedure (for example, Mycoplasmas, which have no cell wall, stain poorly with the Gram stain).

Figure 1: Gram positive and Gram negative cell walls

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Watch Video 2: Gram Stain Animation and discussion on what is happening at each step.

Gram Staining Procedure Animation Mi…

Mi…

Watch Video 2: Gram stain animation with description of each step and interpretation of what is happening in each step by
Dr.G Bhanu Prakash Animated Medical Videos. (3:37) URL https://youtu.be/AZS2wb7pMo4

Watch Video 3: Gram staining procedure

Gram Stain

Watch Video 2: Gram Staining procedure, filmed at NC State Microbiology Labs. (5:58). URL: https://youtu.be/H-fxk1be1hQ

Special Stains
There are a variety of staining procedures used to identify specific external or internal structures that are not found in all bacterial
species, such as a capsule stain and a flagella stain. For images and more examples of specialized stains, see below and in the next
section, 4.2 specialized bacterial staining techniques.

Capsule Stain
Some bacteria secrete a polysaccharide-rich structure external to the cell wall called a glycocalyx. If the glycocalyx is thin and
loosely attached, it is called a slime layer; if it is thick and tightly bound to the cell, it is called a capsule. The glycocalyx can
protect the cell from desiccation and can allow the cell to stick to surfaces like tissues in the body. They may also provide cells with
protection against detection and phagocytosis by immune cells and contribute to the formation of a biofilm: in this way a
glycocalyx can act as a virulence factor; (contributes to the ability of an organism to cause disease).
Capsules can be detected using a negative staining procedure in which the background (the slide) and the bacteria are stained, but
the capsule is not stained. The capsule appears as a clear unstained zone around the bacterial cell. Since capsules are destroyed by

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heat, the capsule staining procedure is done without heat-fixing the bacteria.

Silver Stain
Flagella (long whip-like structures used for bacterial motility) and some bacteria (e.g. spirochetes) are too thin to be observed with
regular staining procedures. In these cases, a silver stain is used. Silver nitrate is applied to the bacteria along with a special
mordant; the silver nitrate precipitates around the flagella or the thin bacteria, thus thickening them so they can be observed under
the light microscope.

This page titled 4.1: Introduction to Staining is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by Joan Petersen
& Susan McLaughlin.
3.1: Introduction by Joan Petersen & Susan McLaughlin is licensed CC BY-NC-SA 4.0.

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4.2: Specialized Bacterial Staining Techniques
Learning outcomes
Describe the purpose of each of the stains listed: simple, Gram, Acid-Fast, Endospore, Capsule, Flagella, Spirochete.
Recognize the cellular characteristics revealed by each of the stains listed

Simple Stains:
Commonly used dyes for simple stains: Crystal Violet, Methylene Blue, Safranin
Uses one dye
Used to provide color to otherwise transparent bacterial cells
Can be used to determine cell size, morphology and arrangement
All bacteria are the same color when stained with the single dye that is used

Image 1: Simple stain with crystal violet showing rod shaped bacteria. Note that all bacteria are the same color of the dye, crystal
violet (purple), regardless of its cell wall composition. Image by Muntasir du, 2007
(https://commons.wikimedia.org/wiki/F...micrograph.jpg)

Gram Stain
Primary stain – crystal violet
Mordant – iodine; decolorizer- 95% Ethanol
Counterstain – Safranin
Common differential stain
Gram reaction (positive or negative) reflects cell wall properties
Also used to determine cell size, morphology and arrangement

Image 2. Gram positive, rod, Bacillus subtilis. (Ann C. Smith, University of Maryland, College Park, MD)

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Image 3: Gram stain showing Gram negative rods (pink) and Gram positive cocci
(purple): https://commons.wikimedia.org/wiki/F...m_stain_01.jpg

Acid-Fast Stain
The acid-fast stain is a differential stain used to identify acid-fast organisms such as members of the genus Mycobacterium .
Acid-fast organisms are characterized by wax-like, nearly impermeable cell walls; they contain mycolic acid and large amounts of
fatty acids, waxes, and complex lipids. Acid-fast organisms are highly resistant to disinfectants and dry conditions. (1)
Because the cell wall is so resistant to most compounds, acid-fast organisms require a special staining technique. The primary stain
used in acid-fast staining, carbolfuchsin, is lipid-soluble and contains phenol, which helps the stain penetrate the cell wall. This is
further assisted by the addition of heat. The smear is then rinsed with a very strong decolorizer, which strips the stain from all non-
acid-fast cells but does not permeate the cell wall of acid-fast organisms. The decolorized non-acid-fast cells then take up the
counterstain. (1)
Primary stain – Carbol fuchsin
Decolorizer – acid alcohol
Counterstain – Methylene blue
A differential stain used to detect bacteria with mycolic acid cell walls (genera Mycobacterium and Nocardia)
Developed to detect the bacterial species that causes tuberculosis
Acid-fast organisms resist decolorization with acid-alcohol

Image 4. A mixed culture of Mycobacterium smegmatus (acid-fast, red/pink) and Staphylococcus epidermidis (non-acid-fast, light
blue/purple). (Alan Schenkel, Peter Justice, and Erica Suchman, Colorado State University, Fort Collins, CO )

Endospore Stain
This stain is used to visualize bacterial endospores produced by members of the genera Bacillus and Clostridium. The nature of the
spore makes it impervious to most ordinary stains and staining methods, but, once stained it strongly resists decolorization and
counterstaining. In the Schaeffer-Fulton method, a primary stain with malachite green is forced into the endospore by steaming
the bacterial emulsion. Malachite green is water soluble and has a low affinity for cellular material, so vegetative (actively
dividing) cells may be decolorized with water. Vegetative cells are then counterstained with safranin. Microscopic examination of
stained endospores will reveal their relative size and position in the cell, which are distinctive characteristics of each of the spore-
forming species.

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Primary stain - Malachite green
Counterstain - safranin
Endospores resist staining with basic stains
Endospores stain with malachite green; vegetative cells stain with safranin (red)

Image 5. Endospore stain of a Bacillus cereus culture using the Shaeffer-Fulton method and viewed at 1,000x total magnification
under an oil immersion lens. Vegetative cells of B. cereus are in red; endospores are in green. Due to the age of the culture,
endospores have been released from the cells. (Derek Weber and S. Finazzo, Broward Community College–Central campus,
Davie, FL)

Capsule Stain (Negative staining)

Polysaccharide capsules and slime layers are generally difficult to stain selectively. Instead they are demonstrated by simply
outlining them, staining the background and/or the cells without staining the capsule. This negative stain can be done several ways.
The lab demonstration slide was prepared by staining the background and cells with basic fuchsin. Hence, the capsule appears as a
clear zone or halo surrounding the red cell against a red background.
Uses an acidic stain: (Congo red or Nigrosin) and a basic stain: (crystal violet or safranin)
Negative stains are neither heat-fixed nor rinsed
The background of the slide is stained by acidic stains (capsule remains unstained)
The cells within the capsule are stained with Basic stains
Examples of encapsulated cells: Bacillus anthracis, Streptococcus pneumoniae, and Klebsiella pneumonia

Image 6: Encapsulated Enterobacter aerogenes stained with Anthony's capsule stain. (Gary E. Kaiser, The Community College of
Baltimore County, Catonsville Campus, Baltimore, MD)

Flagella Stain
This stain coats the thin bacterial flagella with heavy metals or other compounds to make them visible in the light microscope.
Once visible, the location and number of the flagella can be used diagnostically. The presence of flagella varies with cultural
conditions, so a negative result is not proof of a cell's inability to produce flagella. The demonstration slide was prepared with a
silver compound to coat the flagella and a red dye, basic fuchsin, to stain the cells.
Silver nitrate
Used to see bacterial flagella that are too slender to be seen with other staining techniques
Silver nitrate makes flagella appear larger than they are
Can be used to determine arrangement of flagella for identification.
Ex: Proteus vulgaris has peritrichous flagella

Image 7: Pseudomonas fluorescens stained with Presque Isle Cultures Flagella Stain. Arrows in the labeled view point to the
flagella. (Jay Mellies and Introductory Biology students, Reed College, Portland, OR)

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Image 8: (A) Schematic of E. coli flagellum. Basal body: Located at the base of the flagellum. The basal body, embedded in the
cell wall and cell membrane, is the output device. It acts as an engine to provide energy for locomotion. The nearby switch
determines the direction of rotation. Hook: This structure points directly away from the cell and has a sharp bend (about 90°) from
which filaments protrude. Filament: This filiform structure protrudes from the bacterial cell. It is a hollow tube made of the protein
flagellin. Its acts like a ship’s or plane’s propeller to move the bacterial cell. (B) Examples of bacterial flagellar arrangement. (C)
Periplasmic flagella (flagella staining). The bacterial cell is stained red and the flagella are stained light red around the bacterial
cell. From the Atlas of Oral Microbiology, edited by: Xuedong Zhou and Yuqing Li, 2015.

Spirochete stain
Silver nitrate
Used to visualize slender spirochetes like Treponema pallidum

Image 9:Photomicrograph of skin biopsy showing secondary syphilis. Spirochete organisms are stained bright red by the
Treponema pallidum immunohistochemical stain. 400x magnification by Jerad M. Gardner,
MD. https://commons.wikimedia.org/wiki/F...high_power.jpg

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References
1. Welcome to microbugz. Acid Fast Stain https://www.austincc.edu/microbugz/a...mplex%20lipids.

This page titled 4.2: Specialized Bacterial Staining Techniques is shared under a CC BY-NC-SA license and was authored, remixed, and/or
curated by Joan Petersen & Susan McLaughlin.
3.4: Summary of Common Bacterial Staining Techniques by Joan Petersen & Susan McLaughlin is licensed CC BY-NC-SA 4.0.

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4.3: Lab Procedures- Bacterial Smear, Simple and Gram Staining
Learning Outcomes
Prepare microorganisms for microscopic observation.
Observe the difference in size between bacteria and other unicellular microorganisms.
Perform a simple stain and a Gram stain.
Observe stained microorganisms and identify their size, shape, and staining properties.

Part I: Preparation of a Bacterial Smear

This semester you will be performing two staining procedures: A Simple Stain and a Gram stain. Both of these staining procedures
begin with the preparation of a bacterial smear.
Materials
Clean microscope slides
Staining trays and newspaper
Water bottle (for rinsing)
Bacterial cultures: Escherichia coli, Staphylococcus aureus, Micrococcus luteus, Pseudomonas aeruginosa,

How to make a Bacterial Smear

1. Label a clean glass slide using a red wax marker. Note that it is important to recognize the side of the glass slide that you put
your bacterial sample on.
2. Add a small drop of saline to the slide (you will usually put two bacteria on one microscope slide- Follow your instructor’s
specific instructions). This can be done by placing a drop of saline onto your inoculation loop and then transferring it to the slide. If
you use the saline dropper directly on the slide, do not release a full drop.
3. With an inoculation loop or needle, pick up a small amount of bacteria. Mix it well with the saline and spread the mixture over a
wider area of the slide.
Be careful not to have the two smears run into each other.
4. Air dry the bacterial specimen on the slide (slide warmers may also be used).
5. When slides are completely air-dry, heat fix the bacterial specimen by passing the slide slowly over the flame twice (your
instructor will demonstrate this).
Heat fixing kills cells, and adheres them to the slide.
Cells will be rinsed off the slides if they are not heat fixed properly.
Be careful not to overheat the slides in this procedure
After heat-fixing is complete, you are ready to simple or gram stain your slide.

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Image 1: Heat Fixing over a bunsen burner

Watch Video 1: on heat fixing using a bacticinerator

How to Heat Fix a Microscope Slide

Watch Video 1: on heat fixing using a bacticinerator from Dr. G. Kaiser at URL: https://youtu.be/Rh0GrcTzjnU

Part II: Simple Stain

Cultures
Bacillus megaterium
Micrococcus luteus
Saccharomyces cerevisiae - a yeast

Materials
Dropper bottle containing staining solution of methylene blue
Brightfield Light Microscope
Oil immersion
lens paper
bibulous paper

Lab Procedures
A. Review Lab procedures for operating a Brightfield Light microscope
B. Preparation of a Bacterial Smear for Staining
Preparations of bacteria for staining can be made from growth on an agar plate or from a broth culture.
1. To prepare a slide from cells grown on an agar medium, first place a SMALL drop, a loopful works well, of water on a clean
grease-free slide. Next, with a sterile loop transfer a SMALL AMOUNT of the growth to the drop of water and rub the loop around
until the material is as evenly distributed as possible to form a just visibly turbid suspension. Spread the drop over a small portion
of the slide to make a thin film with lightly visible turbidity.
2. Prepare three separate smears, one each of Bacillus megaterium. Micrococcus luteus, and Saccharomyces cerevisiae.

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3. Next, heat fix the slide by placing it on the slide warmer for 5 minutes. Put the sample side facing up and label with your initials
on one end of the slide. This process is called heat fixing the specimen to the slide. Its purpose is to bind the specimen to the slide
so that it does not wash off during staining. Killing the cells with heat fixation also increases their permeability to the dyes used in
staining.
Do not under-fix (the smear will wash off) nor over-heat (the cells will be ruptured or distorted) your specimen. The slide should be
warm to the touch, not hot. If you think you have heated the slide too much, do not touch the slide to your hand to find out.
Chances are, your suspicions are correct, and you will burn your hand with the hot glass. Instead, heat-fix the slide for a shorter
period of time next time, then test.
4. After cooling the specimen is ready for the simple stain.

C. Methylene Blue – A Simple Stain

Living bacteria are almost colorless, and do not present sufficient contrast with the water in which they are suspended to be clearly
visible. The purpose of staining is to increase the contrast between the organisms and the background so that they are more readily
seen in the light microscope. In a simple stain, a bacterial smear is stained with a solution of a single dye that stains all cells the
same color without differentiation of cell types or structures. The single dye used here is methylene blue, a basic stain. Basic stains,
having a positive charge, bind strongly to negatively charged cell components such as bacterial nucleic acids and cell walls.
1. Stain by covering the smear completely with methylene blue. This should be
done over a sink with a slide holder.
*Avoid getting stain on your clothes, books, and fingers. It is very difficult to remove.
2. Allow the stain to act 1-2 minutes.
3. Tilt the slide to allow the stain to drain off. Now, rinse the remaining dye off with a gentle stream of water from a faucet or wash
bottle.
4. Blot the slide dry with bibulous paper. Remove excess water from the slide by touching one corner of the slide to the blotting
paper, then place the slide between clean sheets of paper in the blotting pad and blot dry. Be sure you do not rub off the smear.
5. Examine under the microscope using first the 10X and then the 100X oil-immersion objective.
6. Record your observations on the report sheets.

D. Test plate isolate

1. Check your "test plates" from Lab1: Exercise I, part D (ubiquity of microorganisms) for isolated single colonies to be
candidates for your test plate isolate.
2. Attempt a simple stain of your candidate test plate isolate as described in part B of Exercise II. Record your observations.
3. Show an instructor your isolated single test plate isolate and the slide of the simple stain of the specimen you have chosen. This
is to ensure you will be working with a bacterial culture instead of a fungal isolate.
4. If you did not obtain any single colony bacterial isolates on your "test plates" use one from another student in the lab, but make
sure you choose a different isolate than that student has chosen, or use one from the instructor's plates.
5. After picking a candidate for your test plate isolate it is necessary to make sure it is a pure culture. Use a new Nutrient agar plate
to re-streak for single colonies using the technique from Exercise I, part C (the "T" streak). Make certain you try and touch only
one colony, the one you are interested in using as your unknown. Save your original plate. Incubate until the next laboratory period.

E. Demonstration Slide
You have just prepared slides of Bacillus (a rod shape) and Micrococcus (a coccus). We have set up a slide to demonstrate a third
major cellular shape seen in bacteria. Spirillum volutans is a spiral shaped microorganism found in fresh water. View the
demonstration slide and record your observations in the Results page.

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Part III: Gram Staining

Gram Staining Procedure

For all steps in the gram staining procedure, add enough of the solution to cover the areas of the slide that have bacteria on
them. You do not need to flood the entire slide.
All staining should be done over a staining tray. Be sure to put newspaper under the tray in case of spillage.
Gloves should be worn while staining and removed before working with the microscope.

STEPS EXPLANATION

1. Add a few drops of crystal violet (primary stain) to the smear and
let it sit for 60 seconds.

All cells are purple after this step. Stopping here would be a simple
2. Rinse the slide with water.
stain.

3. Add a few drops of Gram's iodine (mordant) to the smear and let it
Gram’s iodine forms a complex with crystal violet
sit for 60 seconds.

4. Rinse the slide with water. All cells are purple after this step.

5. Decolorize with 95% ethanol: let the alcohol run over surface of
Gram positive cells retain crystal violet and remain purple. Gram
slide until no more crystal violet color comes out of the smear (time
negative cells lose crystal violet and are now colorless
varies—no more than 5-10 seconds).

6. Rinse with water. Water rinse stops the decolorization process

7. Add a few drops of safranin (counterstain) and let it sit for 60

Safranin is a pink/red dye
seconds.

8. Rinse with water. Blot dry on bibulous paper. Be careful not to wipe Gram positive cells remain purple; gram negative cells are now
off the bacteria. pink/red

For each organism, determine morphology, arrangement and Gram

9. Observe your slide under the microscope.
reaction

Watch Video 2: on Gram Staining

Gram Stain

Watch Video 2: on Gram Staining. Video filmed at NC State. URL https://youtu.be/H-fxk1be1hQ

This page titled 4.3: Lab Procedures- Bacterial Smear, Simple and Gram Staining is shared under a CC BY-NC-SA license and was authored,
remixed, and/or curated by Joan Petersen & Susan McLaughlin.
3.2: Procedures by Joan Petersen & Susan McLaughlin is licensed CC BY-NC-SA 4.0.

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4.4: Results
Simple Stain Results

Gram Stain Results

Draw sketches for each type of bacteria that you observe. Identify its morphology, arrangement, and Gram reaction.

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Special Stain Results
Observe the special stains set up at the demo microscopes at the back of the lab. Make sketches below.

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4.5: Review Questions
1. Explain the major differences between the gram positive and gram negative cell wall.
2. Salmonella typhi is a gram negative organism.
a. What color will it appear when simple stained with crystal violet?
b. What color would it be if it was gram stained correctly?
3. Explain how bacterial cells would look in the gram staining procedure if the following mistakes were made:
a. Decolorizer left on too long
b. Decolorizer not left on long enough
c. Slide not heat-fixed before staining
4. What is the difference between a simple stain and a differential stain?
5. Explain why it is important to use only a small amount of bacteria when preparing a smear.
6. What are the two things that are stained in a capsule stain? What is NOT stained in a capsule stain?
7. Why would a health care provider be interested in knowing the gram reaction of a pathogenic bacterium?

This page titled 4.5: Review Questions is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by Joan Petersen &
Susan McLaughlin.
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 CHAPTER OVERVIEW

5: Enumeration of Bacteria
5.1: Introduction to Enumeration of Bacteria
5.2: Lab Procedures- How to operate a Pipettor
5.3: Lab Procedures- Viable Plate count
5.4: Results
5.5: Review Questions

5: Enumeration of Bacteria is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

1
5.1: Introduction to Enumeration of Bacteria
Learning Outcomes
Introduction to dilution theory
Estimate the number of microbes in a sample using serial dilution techniques and standard/viable plate counts

Enumeration of Bacteria
Often one needs to determine the number of organisms in a sample of material, for example, in water, foods, or a bacterial culture.
For example, bacterial pathogens can be introduced into foods at any stage: during growth/production at the farm, during
processing, during handling and packaging, and when the food is prepared in the kitchen (1). In general, small numbers of
pathogenic bacteria are not dangerous, but improper storage and/or cooking conditions can allow these bacteria to multiply to
dangerous levels (1).
Fecal contamination of water is another one of the ways in which pathogens can be introduced (1). Coliform bacteria are Gram-
negative non-spore forming bacteria that are capable of fermenting lactose to produce acid and gas. A subset of these bacteria are
the fecal coliforms, which are found at high levels in human and animal intestines. Fecal coliform bacteria such as E. coli, are
often used as indicator species, as they are not commonly found growing in nature in the absence of fecal contamination (1). The
presence of E. coli suggests feces are present, indicating that serious pathogens, such as Salmonella species and Campylobacter
species, could also be present (1).

Methods of Enumeration
Many approaches are commonly employed for enumerating bacteria, including measurements of the direct microscopic count,
culture turbidity, dry weight of cells, etc. In a microbiology lab, we frequently determine the total viable count in a bacterial
culture.
The most common method of measuring viable bacterial cell numbers is the standard or viable plate count or colony count. This
is a viable count, NOT a total cell count. It reveals information related only to viable or live bacteria. Using this method, a small
volume (0.1 - 1.0 mL) of liquid containing an unknown number of bacteria is spread over the surface of an agar plate, creating a
"spread plate." The spread plates are incubated for 24-36 hours. During that time, each individual viable bacterial cell multiplies
to form a readily visible colony. The number of colonies is then counted and this number should equal the number of viable
bacterial cells in the original volume of sample, which was applied to the plate.
For accurate information, it is critical that each colony comes from only one cell, so chains and clumps of cells must be broken
apart. However, many bacterial species grow in pairs, chains, or clusters, or they may have sticky capsules or slime layers, which
cause them to clump together. It is sometimes difficult to separate these into single cells, which in turn makes it difficult to obtain
an accurate count of the original cell numbers. Therefore, the total number of viable cells obtained from this procedure is usually
reported as the number of colony-forming units (CFUs).
A bacterial culture and many other samples usually contain too many cells to be counted directly. Thus, in order to obtain plates,
which are not hopelessly overgrown with colonies, it is often necessary to dilute the sample and spread measured amounts of the
diluted sample on plates. Dilutions are performed by careful aseptic pipetting of a known volume of sample into a known volume
of a sterile buffer or sterile water. This is mixed well and can be used for plating and/or further dilution. If the number of cells in
the original sample is unknown, then a wide range of dilutions are usually prepared and plated. The preparation of dilutions and the
calculation and use of dilution factors to obtain the number of microorganisms present in a sample are important basic techniques
in microbiology.

Method:
Aliquots from a stepwise or serial dilution of the original sample are spread on plates. Only a few of the plates following
incubation will contain a suitable number of colonies to count; those plated from low dilutions may contain too many colonies to
count easily while those plated from high dilutions may contain too few colonies or none at all. Ideally plates containing 30-300
colonies per plate should be counted. At this colony number, the number counted is high enough to have statistical accuracy, yet
low enough to avoid mistakes due to overlapping colonies.

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 Figure 1: Serial dilution series and plating. A wide series of dilutions (e.g. 10-2 to 10-8 ) is normally performed on the
sample culture and spread plates created from the dilutions. A number of spread plates is needed because the exact number of live
bacteria in the sample is usually unknown. Greater accuracy can be achieved by plating duplicates or triplicates of each dilution.

Image 1: Picture of spread plates showing bacterial growth (Escherichia coli, 40 hours, 25°C) on five plates prepared from a ten-
fold dilution series. Care was taken to avoid spreading to the edges of the plates as it is more difficult to count colonies along the
edge of the agar. Note how many colonies are in the plate from the 10-1 & 10-2 dilution plates. These plates have densely
packed colonies, are too numerous to count, and most likely more than 300 CFUs. On the other hand, plates 10-3 , 10-4 and 10-
5
have a countable number (between 30-300) of CFUs. Image by Kathryn Wise and Darel Paulson, Minnesota State University,
Moorhead, MN.

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Calculations
In order to make the calculation of the number of cells/mL in the original sample less formidable, dilutions are designed to be easy
to handle mathematically. The most common dilutions are ten-fold and multiples of ten-fold. A 1/10 or 10-1 dilution can be
achieved by mixing 1 mL of sample with 9 mL of sterile dilution buffer. A subsequent 1/10 dilution of this first ten-fold dilution,
made by mixing 1 mL of this first dilution with 9 mL of fresh sterile dilution buffer, would give a total dilution of the original
sample of 100-fold (1/10 X 1/10 = 1/100 or 10-1 X 10-1 = 10-2). Alternatively, a 100-fold dilution can be made directly from the
original sample by mixing 1 mL of sample and 99 mL of buffer. These dilutions can be made in successive steps or a series to give
a wide range for any given sample.
Once the dilution is made, an aliquot can be spread on an agar plate to create a spread plate. After incubation, the colonies which
arise can be counted and the number of cells (more precisely the number of colony-forming units or CFUs) in the original sample
can be calculated. For example in the image below, you did a serial dilution of a culture of the red pigmented bacterium, Serratia
marcescens and made a series of spread plates. In plate 1, this was the 10-1 dilution, in plate 2 is the 10-2 dilution, and in plate 3 is
the 10-3 dilution. After incubation, you count 241 colonies were present on the plate 10-2 dilution.

Image 2: Three spread plates from serial dilutions. Image by Jackie Reynolds, Richland College, Dallas, TX.
Therefore, there were 241 X 102 CFU/mL in the original sample or expressed 2.41 x 104. To arrive at this final number you only
need to multiply the final number of colonies on the plate, 241, times the total dilution factor. The dilution factor is defined as the
inverse of the dilution. So in this case, the dilution factor is the inverse of 1/100 or 100. In other words, the dilution factor is how
many times the sample was diluted.
It usually works better to spread only 0.1 mL of a sample on a standard-size petri plate. If the above example were changed such
that 0.1 mL of a 100-fold dilution of the same sample was plated, there would ideally have been 24 colonies on the plate. This
number represents the number of CFU in only 0.1 mL of the dilution plated. Therefore, to calculate the CFU/ml in the sample it is
necessary to multiply the number of colonies on the plate by 10 (there are ten 0.1 mL units in 1.0 mL) and then by the dilution
factor (100) to arrive at the final answer: 24 CFU x 10 x 100 = 24000 or 2.4 x 104 CFU/mL.

The only way to understand dilution theory well is to practice it, so you should work practice problems until you feel confident in
using dilution factors and calculating CFU/mL in original samples. You should also be able to determine the proper dilutions to use
to obtain 30-300 colonies on a plate if the original number of CFU/mL in a sample is known.

Watch Video 1 on how to perform a serial dilution using "pour plates" and the associated calculations:

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 Serial dilutions and pour plate technique

Watch Video 1: Serial dilutions and pour plate technique. The example here using a "pour plate" technique to spread the dilutions
out instead of the "spread plate" discussed above, but the outcome of both techniques of spreading the dilution sample out is the
same. (10:48) Video by Microbial Zoo. URL:https://www.youtube.com/watch?v=nViO9Y4Yxfk

Watch video 2 on how to perform a serial dilution and make spread plates.

Lab 3: Dilutions and Plating

Watch Video 2: Serial dilutions with a bacterial sample and the 'spread plating' technique at NC State Microbiology labs. (10:30)
URL: https://youtu.be/IJcw4fRsYnU

References
1. Contributed by Joan Petersen & Susan McLaughlin Associate Professors (Biological Sciences and Geology) at Queensborough
Community College

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5.2: Lab Procedures- How to operate a Pipettor
Getting to Know Your Pipette
A pipet is a commonly used laboratory piece of equipment used to transfer a measured volume of liquid. A mechanical
pipettor, shown in Fig. 1, can come in range of volumes it can transfer. Careful attention to its use, operation, and practice is needed
to be proficient.
1. Find the following parts on your pipette: Fig. 1 Pipettor
Volume adjustment dial
Tip ejector button
Plunger button
Stainless steel micrometer
Digital volume indicator
Stainless steel ejector arm (removable)
Plastic shaft
Disposable yellow or blue tip
2. Practice holding your pipette correctly, placing a tip on our pipette, and ejected the
tip. Do this at least three times.
3. The total volume a pipette can hold is stated on the top of the plunger. It is listed as
"μl" or microliter volumes. We will be working with the following three volume
pipettes:
P-20: 0.02 μl – 20 μl
P-200: 20 μl – 200 μl
P-1000: 200 μl – 1000 μl
4. Based on the volume pipette you have the numbers in the digital display have a different meaning.

5. Rotate the volume adjustment knob until the digital indicator reaches the desired volume, then place a disposable tip on the shaft
of the pipette (practice all three volumes min, int, max)
6. Press down on the plunger to the First Stop. (You will be able to push past this point, but there is enough resistance to stop the
movement if you try to be aware of it.)
7. Hold the pipette vertically and immerse the disposable tip into the sample. Use the colored water and the microcentrifuge tubes
provided to you.
8. Allow the plunger button to return slowly to its original position. Do not allow the button to snap up.
9. To dispense the sample: place the tip against the side wall of the receiving tube and push the plunger down to the first stop. Wait
2-3 seconds, then depress the plunger to the second stop in order to expel any residual sample in the tip.
10. While the plunger is still pushed down, remove the pipette from the tube and allow the plunger to slowly return to its original
position.
11. Practice.

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 Warning
Never rotate the volume adjustment knob past the upper or lower range of the pipetman.
Never lay the pipetman down on its side or hold it horizontally when it contains liquid.
Never immerse the shaft of the pipetman into the fluid.

Watch this video 1: Micropipetting

Micropipetting

Watch Video 1: how to use a micropipettor URL: https://youtu.be/NgosWmRjjAo (5:02)

This page titled 5.2: Lab Procedures- How to operate a Pipettor is shared under a CC BY-SA license and was authored, remixed, and/or curated by
Nazzy Pakpour & Sharon Horgan.
Lab 5: Pipette and Environmental Requirements by Nazzy Pakpour & Sharon Horgan is licensed CC BY-SA 4.0.

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5.3: Lab Procedures- Viable Plate count
Learning Outcomes
Learn microbiological skills such as pipetting, performing serial dilutions, prepare spread plates for a viable plate count,
and performing a colony count.
Estimate the number of microbes in a sample using serial dilution techniques, including: a. correctly choosing and using
pipettes and pipetting devices b. correctly spreading diluted samples for counting c. estimating appropriate dilutions d.
extrapolating plate counts to obtain the correct CFU in the starting sample.

Materials:
Cultures: Stationary phase broth culture of Serratia marcescens
Media: Dilution tubes of sterile water
Supplies: Nutrient agar plates, P-1000 Pipetman, sterile tips, Sterile L-shaped blue cell spreaders ("hockey stick” or
“spreader”)

Procedure:
A. Sample Dilution and Spread Plating
1. Label one plate on the bottom for each of the following dilutions: 10-5,10-6 , 10-7, 10-8,and 10-9. See Image 1.
2. Label the dilution tubes as follows: label the two tubes (Navy blue caps) containing 9.9 mL sterile water as 10-2 and 10-4; label
the four tubes (Green caps) containing 9.0 mL sterile water as 10-5, 10-6, 10-7, and 10-8.
3. Carefully and aseptically remove 0.1 mL (100µL) of the Serratia marcescens culture and pipette it into the tube marked 10-2.
Mix the tube completely, being careful not to spill any of the contents. The vortex mixer will help you mix the contents of the tube.
• You have now prepared a 10-2 (1/100) dilution. Why is it 10-2? Because 0.1 mL of undiluted culture was diluted into 9.9 mL of
water, giving a total volume of 10.0 mL in the dilution tube. That makes this a 10-2 dilution (0.1/0.1 + 9.9 = 0.1/10.0= 1/100= 10-2).
4. Change the pipette tip, and take 100µL (0.1 mL) from the 10-2 dilution and pipette it into the next 9.9 mL dilution tube marked
10-4. Mix well. You have now prepared a successive 1/100 dilution, resulting in 10-4 dilution of the original culture (1/100
multiplied by 1/100 = 1/10,000 = 10-4, which is the same as 10-2 x 10-2=10-4).
5. Change your pipette tip again.
• Why keep changing pipettes? Because any fluid left in the pipette tip from the previous dilution will contain many more cells
per mL than any successive dilution and, if used, will grossly confuse the final results by indicating a higher number of cells than
were actually present in the original sample.
Now we will start doing a series of 1/10 dilutions. Set your Pipetman to 1,000µL and remove a 1,000µL (1.0 mL) aliquot from the
10-4 dilution tube. Transfer it to the 9.0 mL dilution tube marked 10-5 and mix well. The original culture has now been diluted
1/100,000, or 10-5 (10-4 x 10-1 = 10-5),
• You have just prepared a 10-1 (1/10) dilution of the previously diluted culture. Why is it 10-1? Because 1.0 mL of diluted
culture was further diluted into 9.0 mL of water, giving a total volume of 10.0 mL in the dilution tube. (1.0/1.0 + 9.0 = 1.0/10.0 =
1/10 = 10-1). Now you know why these series of dilutions are referred to as serial dilutions.
Continue your dilution series, as indicated in Image 1, through to the 10-8 dilution tube.

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Image 1: Serial dilution and plating

6. Using a new pipette tip, transfer 100µL (0.1 mL) of the 10-8 dilution onto the center of the agar surface of the plate marked 10-
9
.
Consider why this is a 10-9 plate after you put 100uL (0.1 mL) of inoculum from the 10-8 dilution tube on it. Remember that you
are trying to determine the number of viable cells in each 1.0 mL aliquot of the original Serratia marcescens sample, and you only
put 10% of 1.0 mL (0.1 mL) on the nutrient agar plate.
Repeat with the rest of the dilutions, transferring 100µL (0.1 mL) of each dilution tube onto the appropriate agar surface, using a
new pipette tip between each dilution tube.
7. Spread plates: Using good aseptic technique, take one sterile blue L-shaped cell spreader out of the bag and reseal the bag.
Starting with the plate marked 10-9 , using the spreader, gently push the liquid inoculum applied to the center of the plate, two or
three times clockwise around the dish, then several times counterclockwise, turning the plate on the turn table as needed to obtain
complete coverage.
Continue with the rest of the spread plates using the same cell spreader. Make sure you are continuing to work backwards (from
10- 9 , then 10-8 , then 10-7, then 10-6 etc.) from the most dilute suspension to the most concentrated suspension to minimize the
amount of carryover from plate to plate. Again, use good aseptic technique, work quickly, do not touch the cell spreader on
surfaces other than the agar plate you are using. If you accidentally “contaminate” the spreader by touching a surface (table or
other), then dispose of it and get a new spreader. We are trying to minimize the use of the spreaders to reduce waste, but if it gets
compromised, then replace it with a new sterile spreader.
Dispose of the cell spreader in the small orange biohazard bin on your bench when you are done with your spread plates.
Remember that the plates should be labeled as a ten-fold higher dilution than the dilution tube of the 0.1 mL sample being plated.
For example, 0.1 mL of the 10-6 dilution tube should be plated on the agar plate marked 10-7. Again, if you need help visualizing
this, see Figure 6-1.
It is generally desirable to make duplicate or triplicate plantings of each dilution and to average the resulting counts. However,
since your lab sample comes from the same stock culture, the class average should give an accurate enumeration of the original
stock culture.
8. After the spread plating, leave plates agar side down for at least 30mins. in order for the inoculum to absorb onto the agar, then
invert the plates and incubate at 30°C.

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B. Counting colonies on plates
1. Looking at your dilution plates prepared last period, choose the plates that have from 30-300 colonies on them. As this
might take some practice in plate counting, you might need to choose all plates with what looks like a reasonable number of
colonies to count.
a. Those plates that have no microbial growth can be recorded as 0 or NG, No Growth.
b. Those plates on which colonies are not individually distinct (their edges run together) can be recorded as TNTC, Too
Numerous To Count.
c. Those plates on which you cannot distinguish any individual colonies, the entire surface is covered with microbial growth,
can be recorded as confluent.
2. Count each colony to give a total colony count for each plate chosen. You will avoid counting a colony twice by marking off
the colonies on the bottom of the plate as you count them. This requires, of course, that the plate be upside down. Be sure to count
any small colonies. Record your results on the report sheet.

C. Calculation of number viable cells/mL in the original sample

• Choose the plate containing between 30 and 300 colonies.
• Multiply the number of colonies on the plate by the final dilution factor. This gives the total viable cells/mL in the original
sample.
• Calculate the colony-forming units, CFU, per mL for the Serratia marcescens culture.

D. Watch this video on how to perform a serial dilution and make spread plates.

Lab 3: Dilutions and Plating

Watch Video 1: Dilutions and Plating at NC State Microbiology labs. URL: https://youtu.be/IJcw4fRsYnU

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5.4: Results
Enumeration and Dilution
1. Read lab procedure section on how to obtain colony counts and CFU/mL in the original Serratia marcescens sample.
2. Record data from your Serratia marcescens plates here:

final dilution colony count

10-5

10-6

10-7

10-8

10-9

CFU/mL of original Serratia marcescens sample =____________________

3. Record the class data here for the Serratia marcescens broth culture:

Individual Dilution with Number of colonies on CFU/mL in original Serratia

Student 30-300 plate marcescens sample
data colonies

10

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 11

12

Class average:_____________________

4. Practice question

Final sample dilution Colony Count* CFU/mL in original sample

1/1000 135

10-6 48

10-8 6.5 x 109

99 9.9 x l06

*Remember the 30-300 colonies per plate rule.

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5.5: Review Questions
1. Why do we report bacterial counts as CFUs/mL?
2. A viable plate count was performed on a river sample. Using the table below, how many bacteria were present in the original
river sample?

Dilution Amount plated Number of colonies counted

10-4 1.0mL 310

10-5 1.0mL 28

10-6 1.0mL 7

2. How would you prepare a series of dilutions to get a final dilution of 10-10? outline each step.
3. When determining the number of bacteria from a sample using a viable plant count, why do you often have to do a 'serial'
dilution of the sample first? Why don't you just plate out 1ml or 0.1ml of the sample on a spread plate?
4. Why is it called a "viable" plate count? what does that mean?

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 CHAPTER OVERVIEW

6: Microbial Physiology
6.1: Introduction to Oxygen Requirements
6.1.1: Determining Oxygen Requirements and Anaerobes
6.2: Temperature, pH, and Osmotic Requirements
6.3: Bacterial Growth Dynamics
6.4: Bacteriophages
6.5: Lab Procedures- Testing Oxygen requirements
6.6: Lab Procedures- Plaque Assay
6.7: Results
6.8: Review Questions

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1
6.1: Introduction to Oxygen Requirements
Learning Outcomes
Recognize the effects of Oxygen on bacteria
Explain the various oxygen requirements of the microbes, observe and interpret the growth of microbes in thioglycollate
agar deep media
Discuss methods of culturing anaerobic bacteria

Environmental Requirements: Oxygen requirements

How does Oxygen affect bacterial growth?
Bacteria can differ dramatically in their ability to utilize oxygen (O2). Under aerobic conditions, oxygen acts as the final
electron acceptor for the electron transport chain located in the plasma membrane of prokaryotes. Bacteria use this process to
generate ATP, the energy source for most cellular processes. In the absence of oxygen (O2), some bacteria can use alternative
metabolic pathways including anaerobic respiration and/or fermentation. During anaerobic respiration, other alternative
molecules are used as the final electron acceptor for the electron transport chain such as nitrate (NO3), sulfate (SO4), and
carbonate (CO3).

Bacteria and many microorganisms are very sensitive to oxygen concentrations. Some will only grow in its presence and are
called obligate aerobes. Facultative aerobes will grow either aerobically or in the absence of oxygen (anaerobic conditions), but
they generally do better with oxygen. Aerotolerant anaerobes don't require oxygen, but can grow in its presence, while
strict obligate anaerobes cannot use oxygen and cannot grow or survive in its presence. Microaerophiles use oxygen, but at
lower concentrations than atmospheric oxygen levels (which is ~20%).
One can determine a bacterium's oxygen requirements by cultivating them in a special medium called thioglycollate agar
tubes. The bottom of the tube of medium is kept anaerobic by cystine and thioglycollic acid, which chemically react with, and tie
up any oxygen that diffuses in. Any un-reacted oxygen in the tube will be indicated by resazurin, a dye that turns pink in the
presence of oxygen. It is common for the top centimeter or so to be pink. One can inoculate a thioglycollate tube with your
bacterium and observe where the bacterium grows in the tube to determine its oxygen requirements (see Image 1)

Image 1: Microbial oxygen requirements determined using thioglycollate agar tubes. Green dots represent bacterial
colonies within in the agar or on its surface. The surface of the agar tube is directly exposed to atmospheric oxygen, and will be
aerobic. The oxygen content of the thioglycollate medium decreases with depth until the medium becomes anaerobic towards the
bottom of the tube.

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Cultivation of Anaerobes
The cultivation of anaerobes can be done in anaerobic chamber (image 2). This is a special chamber where you can work with and
cultivate strict obligate anaerobes without exposing them to oxygen. Anaerobic chambers contain a hydrogen (H2) gas mixture that
is circulated through a heated palladium catalyst to remove oxygen (O2) by forming water (H2O). Anaerobic chambers use a gas
mixture of H2 and nitrogen gas (N2) (5/95%) or N2/carbon dioxide (CO2)/H2 (85/10/5 %) to remove oxygen. An airlock is used to
reduce O2 levels prior to the transfer of samples in and out of the chamber.
Another way of culturing bacteria anaerobically on plates is to use a GasPak anaerobic system. In these systems, hydrogen and
carbon dioxide are generated by a GasPak envelope after the addition of water. A palladium catalyst in the chamber of the GasPak
system catalyzes the formation of water from hydrogen and oxygen, thereby removing oxygen from the sealed chamber (image 3
and 4). These systems are compact, easy to use, and less expensive than an anaerobic chamber. They come in jars (image 3) or in
a box format (image 4).

Image 2:Anaerobic chamber. https://coylab.com/products/anaerobi...robic-chamber/

Image 3: GasPak system jars Image 4: GasPak system boxes.

https://www.fishersci.com/shop/produ...rs-3/p-4902079

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Watch Video 1: Basics of thioglycollate media

Basics of Fluid Thioglycollate Media (FT…

(FT…

Watch Video 1: explanation on how thioglycollate media works and examples. (9:33) URL: https://youtu.be/AJG18sQd8mU

Watch Video 2: how to prepare an anaerobic jar

How to prepare an anaerobic jar

Watch Video 2: how to set up an anaerobic jar. The process is similar for an anaerobic box. (3:03) URL: https://youtu.be/aFDYx-
7ceS8

This page titled 6.1: Introduction to Oxygen Requirements is shared under a CC BY-SA license and was authored, remixed, and/or curated by
Nazzy Pakpour & Sharon Horgan.
Lab 5: Pipette and Environmental Requirements by Nazzy Pakpour & Sharon Horgan is licensed CC BY-SA 4.0.

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6.1.1: Determining Oxygen Requirements and Anaerobes

Learning Objectives
Identify the 3 major categories of microbes based on oxygen requirements.
Learn different ways to culture anaerobic bacteria.

HOW TO DETERMINE OXYGEN REQUIREMENTS

An excellent way to determine the oxygen needs of your bacterium is to grow it in different oxygen environments---atmospheric
oxygen of 22%, no oxygen at all (GasPak jarbox or anaerobic chamber), and reduced oxygen at less than 10% (candle jar)--and
compare the quality and quantity of growth.

TYPES OF OXYGEN ENVIRONMENTS

In image 1, the candle jar on the right has 3-5% CO2 and 8-10% O2 (0.3% and 21% in the
atmosphere, respectively). This is a handy way to determine if you have an aerobe which is
microaerophilic, since they grow optimally under reduced (but present) oxygen conditions as
in the candle jar. Many microaerophilic bacteria will grow poorly at 22% O2, whereas some
will not grow at all (e.g. Neisseria gonorrhoea). Possibly the by-products of aerobic
respiration, superoxide radicals and hydrogen peroxide, make it difficult for the
microaerophiles to do well in 22% O2. Some microaerophiles are actually capnophilic
(requiring elevated CO2 levels to grow). Strict aerobes may not grow well in a candle jar,
depending on the species. The Gram-positive genus Bacillus and Gram-negative genus
Pseudomonas include aerobic bacillus-shaped bacteria.

Image 1: On the left is a GasPak jar, with a GasPak generator envelope inside. The environment
is 0% O2. On the right is a candle jar with reduced atmospheric O2 concentrations and CO2 .
The newer anaerobic system (image 2) consists of a plastic container or box (for the agar plates)
and a GasPak paper generating sachet. The sachet contains ascorbic acid and activated carbon
which reacts on exposure to air, when removed from the enclosed envelope. Oxygen is rapidly
absorbed and CO2 is produced. When the GasPak paper sachet is placed in a sealed plastic
pouch, this reaction will create ideal atmospheric conditions for the growth of anaerobes—
anaerobic within 2.5 hours.
Because a GasPak jars and boxes looks the same, whether it has oxygen inside or not, an
indicator strip, containing methylene, is included in the jar. Methylene blue is blue when
oxidized, colorless when reduced. The carbon within the pouch reacts with free oxygen in the jar, producing 10-15% CO2.

Image 2: Anaerobic boxes

Quite a few human pathogens are strict anaerobes, exemplified by the bacillus-shaped genera---Gram-negative Bacteroides,
Bacillus (anthracis), and Gram-positive Clostridium (tetani, botulinum).
Aerotolerants are anaerobes that can grow in the presence of O2 (compared to the strict anaerobes which would likely die), but
they do not use it. And last, but very common, are the facultative anaerobes which prefer to use O2 when present but will grow
without it.
Another way to culture and grow anaerobes is the use of reduced media--media without oxygen. Thioglycollate broth/agar has a
reducing agent in it---the chemical thioglycollate---which binds any free oxygen within the medium. You will also notice that these
tubes have screw caps, allowing a tight closure, to reduce oxygen entry. However, some oxygen will be in the tube between the cap
and the broth and there is no way to get rid of it. So there will be some diffusion of oxygen into the top portion of the broth, and

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that is where any aerobic bacteria may grow. An indicator, resazurin, in the medium will be a light pink in the area of
higher oxygen. You can determine whether the bacterium is an anaerobe, facultative anaerobe, or an aerobe by
checking out where the organism grows in the column of media. DO NOT SHAKE IT!

Note
Oxygen will permeate the broth when this medium sits around for a while.

Check for the pink color: if so, boil the broth for 5 minutes (removes the oxygen).
growth is indicated by gray area

PROCEDURE
Thioglycollate broth
1. The thioglycollate broth should be either boiled first before
inoculation OR recently made so that the oxygen content is
very low. (Your instructor will tell you if it needs to be
boiled).
2. Inoculate a tube of thioglycollate broth with your unknown bacterium: make sure that the loop or needle goes down
to the BOTTOM of the broth (do not get metal holder in the sterile broth).
3. Incubate at 25 or 37 degrees C as directed.

TSA plates in 3 different oxygen environments

1. Label 3 plates for the table---candle jar, ambient air, and GasPak anaerobic jar.
2. Divide the 3 plates into sections, one for each organism—your unknown, the strict aerobe, the strict anaerobe.
3. Inoculate the section by streaking a straight line or a zigzag (as seen below). HOWEVER, be sure that you
inoculate all 3 plates using the same technique.
4. Be sure that the jar has a methylene blue indicator strip (seen above) inside. The methylene blue is blue when
oxidized, but colorless when reduced. Before the jar is opened, the strip should be checked to make sure that it is
COLORLESS.
5. Incubate at 30 or 37 degrees C

INTERPRETATION: after incubation

TSA plates
Compare the presence/absence of growth, as well as the quantity of growth on the 3 plates. Determine whether aerobic,
anaerobic, or facultatively anaerobic.
To the right:
A is an facultative anaerobe
B is an aerobe (microaerophilic)
C is an anaerobe

Thioglycollate broth
Determine WHERE the most amount of growth occurs in the column of liquid---the top, the bottom, top to bottom. DO NOT
SHAKE IT! How can you determine if the bacterium is aerobic, anaerobic, or facultatively anaerobic?

Contributors
Jackie Reynolds, Professor of Biology (Richland College)

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6.1.1: Determining Oxygen Requirements and Anaerobes is shared under a not declared license and was authored, remixed, and/or curated by
LibreTexts.
6: Oxygen Requirements and Anaerobes has no license indicated.

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6.2: Temperature, pH, and Osmotic Requirements

Learning Outcomes
Recognize the cardinal temperatures of growth for bacteria
State the conditions for classification of psychrophiles, mesophiles, thermophiles, and hyperthermophiles
Recognize the pH requirements for bacteria
Recognize the osmotic requirements for bacteria

Environmental Requirements: Temperature

How does temperature affect bacterial growth?
Organisms grow best over a certain temperature range, and this range has restrictions. The cardinal temperatures are the
range of temperatures over which an organism can grow. Every organism has evolved to live at a particular optimum
temperature.
Minimum: lowest temp where reproduction occurs
Maximum: highest temp where reproduction occurs
Optimum: highest rate of reproduction
Organisms are classified based on the temperature ranges they live in:
Psychrophiles: less than zero
Psychrotrophs: 0-30°C
Mesophiles: middle temperatures 15-45°C
Thermophiles: 40-80°C
Hyperthermophiles: above 65°C

Microorganisms require a temperature growth range dictated by the heat sensitivity of its cellular components. As a result,
microbial growth has a characteristic temperature dependence with distinct cardinal temperatures---the minimum, optimum, and
maximum, temperatures at which it can grow. The optimum temperature is usually correlated to its natural habitat.

Image 1 and 2: General temperature ranges compared to growth rate

Environmental Requirements: pH
How does pH affect bacterial growth?
Hydrogen ions in a solution = pH. Organisms grow best at a specific pH range based, in part, on the environment they have
evolved to live in. If bacteria are outside their optimal pH range their proteins can become denatured. Ranges of pH over which
an organism can live place them in groups:

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 Acidophiles: below pH 5.5
Neutrophiles: pH 5.5 -8.5
Alkaliphiles: pH above 8.5

The pH is another environmental condition that dictates microbial growth. pH impacts the activities of enzymes and each
microbial species has a pH growth range. Acidophiles have a growth range between pH 0.0-5.5, neutrophiles grow btween 5.5
and 8.5, while alkalophiles do best between 8.5-11.5 (or higher). Generally, different microbial genera have characteristic pH
optima ranges. The majority of bacteria are neutrophiles while molds and yeasts tend to prefer slightly acidic environments
with a pH range of 4-6. Many bacteria produce acids as part of their metabolism, and this can lower the pH of their
environment. One excellent example of this are the Lactic Acid Bacteria (LAB); a large and diverse group of Gram-positive
bacteria that produce lactic acid as the major end product of the fermentation of carbohydrates. The lactic acid can inhibit the
growth of pathogenic and food spoilage microorganisms in food. Thus the LAB play a significant role in food fermentation,
contributing to a wide variety of fermented products (ie. cheese, yogurt, meat, fish, fruit, vegetable and cereal products). Their
breakdown of various carbohydrates, proteins, and lipids contribute to the flavor, texture and nutritional value of the fermented
foods.

Image 3: pH Classification for microorganisms.

Environmental Requirements: Salinity

How does osmotic pressure affect bacterial growth?
Water is essential to all organisms. The ability to control the movement of water across a membrane is necessary for the
survival of all cells. Osmotic pressure is the minimum pressure which needs to be applied to a solution to prevent the inward
flow of water across a semi-permeable membrane. The movement of water is controlled by the concentration of solutes
contained within the water (usually salt). Bacteria can be classified based upon the salinity they can tolerate:
Halophiles (prefer NaCl concentrations of 3% or higher)
Extreme halophiles (prefer NaCl concentrations of 15%-25%)
Xerophile (prefer low salt concentrations)

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 Image 4: Impact of various salt concentrations on movement of water into/out of a cell.

Quantifying Bacterial Growth:

How do we quantify bacterial growth?
Often in microbiology, we need to determine the number of bacterial cells in a broth. We can do this directly through spread
plates (Chapter 5: Enumeration of bacteria) or indirectly by assessing the turbidity (cloudiness) of broth tubes. We measure
turbidity using a spectrophotometer which gives us a reading of the light absorbance:
more bacteria = more cloudy = higher absorbance
less bacteria = less cloudy = lower absorbance

This page titled 6.2: Temperature, pH, and Osmotic Requirements is shared under a CC BY-SA license and was authored, remixed, and/or curated
by Nazzy Pakpour & Sharon Horgan.

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Lab 5: Pipette and Environmental Requirements by Nazzy Pakpour & Sharon Horgan is licensed CC BY-SA 4.0.

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6.3: Bacterial Growth Dynamics
Learning Outcomes
Discuss the growth dynamics of a bacterial culture
Identify phases of bacterial growth curve

Bacterial Growth Dynamics

Bacterial growth refers to an increase in bacterial numbers, not an increase in the size of the individual cells. In most bacteria,
growth first involves increase in cell mass and number of ribosomes, then duplication of the bacterial chromosome, synthesis of
new cell wall and plasma membrane, partitioning of the two chromosomes, septum formation, and cell division. This asexual
process of reproduction is called binary fission and results in two daughter cells that are genetically identical. This is
accomplished by the process of binary fission, where a single bacterial cell divides into two.

Watch Video 1: Bacterial Growth

Bacteria Growth

Watch Video 1: Bacterial cell division (00:15). URL: https://youtu.be/gEwzDydciWc

The dynamics of bacterial growth follow a predictable pattern visualized as a bacterial growth curve. This growth curve is
generated by plotting the increase of cell number versus time. The curve can then be used to determine the generation time, the
time required for a microbial population to double in cell number. There are typically four growth phases in a closed bacterial
culture vessel, like a flask or tube. The phases are lag, log/exponential, stationary, and death phases.
Lag Phase: immediately after inoculation of the cells into fresh medium, the population remains temporarily unchanged (notice the
line here is flat, no change in cell number). Although there is no apparent cell division occurring, the cells may be growing in
volume or mass, synthesizing enzymes, proteins, RNA, etc., and increasing in metabolic activity. The cells are also adapting and
adjusting to this media and growth condition, different genes may be turned on to start metabolizing different substrates. There is
some repair processes going in, cell is re-synthesizing damaged cell constituents in preparation for binary fission. The length of the
lag phase is dependent on a wide variety of factors, including the size of the inoculum; time necessary to recover from physical
damage or shock in the transfer; time required for synthesis of essential coenzymes or division factors; and time required for
synthesis of new (inducible) enzymes that are necessary to metabolize the substrates present in the medium, the age of the
inoculum (microbe introduced into a culture medium to initiate growth), an “old” culture will probably a lot of dead/aged cells and
may take longer to adjust to this medium.

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The Log (Exponential) Phase. The exponential phase of growth is a pattern of balanced growth wherein all the cells are dividing
regularly by binary fission, and are growing by geometric progression. The cells divide at a constant rate depending upon the
composition of the growth medium and the conditions of incubation. The rate of exponential growth of a bacterial culture is
expressed as generation time, also the doubling time of the bacterial population. This phase is usually relatively short in the
scheme of the entire growth curve. Cells in this phase are most active metabolically, and is preferred for industrial purposes where,
for example a product needs to be produced efficiently. Exponentially growing cells are typically at their healthiest and are thus
most desirable for studies of their enzymes or other cell components. Because the generation time is constant, a logarithmic plot of
growth during the log phase is a straight line.
Exponential growth cannot be continued forever in a batch culture. Population growth is limited by one of three factors: 1.
exhaustion of available nutrients; 2. accumulation of inhibitory metabolites or end products; 3. exhaustion of space, in this case
called a lack of "biological space". Eventually the growth rate slows, the number of microbial deaths balances the number of new
cells, and the population stabilizes. This period of equilibrium is called the Stationary phase. Bacteria that produce secondary
metabolites, such as antibiotics, often do so during the stationary phase of the growth cycle (Secondary metabolites are defined as
metabolites produced after the active stage of growth).
It is during the stationary phase that spore-forming bacteria have to induce or unmask the activity of dozens of genes that may be
involved in sporulation process to prepare for a dormant period. If incubation continues after the population reaches stationary
phase, a death phase follows, in which the viable cell population declines. During the death phase, the number of viable cells
decreases geometrically (exponentially), essentially the reverse of growth during the log phase. This phase continues until the
population is diminished to a tiny fraction of the number of cells in the previous phase or until the population dies out entirely.

Image 1: Bacterial growth curve showing 4 phases. Image by Michał

Komorniczak (Poland). https://upload.wikimedia.org/wikiped..._growth_en.svg

6.3: Bacterial Growth Dynamics is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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6.4: Bacteriophages
Learning Objectives
Learn how to culture viruses in a host cell
Quantitate viruses in a specimen
Identify viral plaques in a bacterial lawn

Viruses are obligate intracellular parasites that multiple within the host cytoplasm. Bacteriophages are viruses which infect
bacteria. PHAGE (as in phagocytosis) means "to eat", and generally refers to a virus. Viruses multiply within host cells and rely
upon the host's metabolic machinery for replication.
Most bacteria have phages that are able to parasitize them. In fact, the ability to be infected with a known phage type is used to
identify some strains of bacteria (like Staph), known as phage typing. As the virus infects bacterial cells that it has been mixed
with, the lytic infection destroys the bacteria. The bacteria have been poured into what is called a bacterial lawn on the agar plate.
As the surrounding cells are infected and killed by the released viruses, a clear spot on the agar---in the bacterial lawn--develops,
called a plaque.The plaques can be counted and the number of virus particles or virions in the original specimen, can be quantified
as viruses/ ml or plaque-forming units/ml (PFUs).
One common phage is called "T4" and it is capable of infecting its host, Escherichia coli. This type of bacteriophage is called a
"coliphage. " Viruses have high specificity for its host, and will only infect a specific bacterium host.

Watch this video animation on T4 phage infecting E. coli

T4 Phage attacking E.coli

Watch Video 1: T4 phage infecting E. coli. URL: https://youtu.be/V73nEGXUeBY

Method for estimating the number of bacteriophages

Knowing how to determine the number of microorganisms in a sample is extremely important in microbiology, and requires
accurate pipetting, aseptic technique, and calculation skills. Similar to enumeration of bacteria, one has to prepare serial dilutions of
a sample and plate these samples out. Although the principles are the same, you will be enumerating viruses instead of bacteria and
conserving on materials by using micropipettes and smaller volumes in your dilutions.
The number of viruses in a sample can be determined by direct count using electron microscopy or by determining the number of
infectious virus particles using a plaque assay. Viruses are obligate intracellular parasites. Therefore, they require a host cell in
which to grow. Some viruses lyse the cells in which they have replicated while others appear to cause little cell damage.
A plaque assay can be used to enumerate viruses that lyse their host cells. In a plaque assay the host cells and virus are incubated
together for a short time to allow the virus to attach to and enter the host cell. Then the mixture in plated within a semi-solid agar.

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This semi-solid agar is poured onto a "bottom agar" that serves to supply adequate nutrients for the host cell. At the end of one
cycle of virus replication, a cell infected with a single virus particle will lyse, releasing hundreds of new viruses.
In the semi-solid medium these newly released viruses can only infect neighboring cells; after a second cycle of replication these
neighboring cells will be lysed. Those cells that escape infection will continue to grow. After 24 to 48 hours plates that were not
infected with a virus will contain a confluent layer of cells (they will resemble the too numerous to count/TNTC plates from
bacterial standard/viable plate counts). Those plates that were infected with several hundred viruses may actually appear clear- the
viruses will have infected and lysed all of the host cells. Those plates that contain an intermediate number of viruses will have
plaques, clear or partially clear circular areas in an otherwise turbid background of cellular growth. Each plaque represents the
result of one infectious virus, called a plaque forming unit, or PFU. Many animal and bacterial viruses can be enumerated using a
plaque assay. Bacterial viruses are also referred to as phage; in our lab, we typically use a well-characterized bacterial phage, such
as T4, and its host cell, Escherichia coli.

General procedure
1. The phage specimen you will use is already diluted to 1/ 1000, and you will dilute further.
2. Bacteria and phage are mixed together in tubes of soft agar. The mix is incubated in the water bath.
3. After incubation the mix is added to the soft agar and poured over the tryptone agar plates.
4. Be SURE to mix the dilutions.
5. Change pipettes between dilutions.
6. Each table will use a different combination of a phage and an E. coli host.

Detailed procedure with diagram

Image 1: Plaque Assay diagram

Set up 5 saline (0.85% NaCl) dilution tubes labeled 10-4, 10-5,10-6, 10-7, and 10-8. Into each tube, place 9ml pf into which you will
dilute the viral solution. You will be making 1/10 dilutions.
1. Starting with the 10-3 dilution of the virus that you picked up (or were given by your instructor), transfer 1 ml to the dilution
tube marked 10-4 and mix.
2. Make 4 more dilutions out to 10-8.
3. Into 6 microtubes, add 100 microliters of each viral dilution, plus 300 microliters of E. coli. Let sit at room temperature for
10 minutes while the virus infects the bacteria. Mix these well.
4. Take the tubes over to the water bath and transfer the entire contents of E. coli - phage tubes into 6 soft agar tubes, using a
sterile plastic transfer pipet. Mix well. KEEP SOFT AGARS INSIDE OF WATER BATH SO THEY DO NOT SOLIDIFY.
5. Remove 1 soft agar tube at a time and pour it onto the TSA agar plates, gently rotating the plate WELL so as to distribute the
phage - bacteria all over the agar.
6. Allow the plates to harden and incubate at 37º C right side up.

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INTERPRETATION

Image 2: Determination of bacteriophage T4 titer by serial dilution and plating on Escherichia coli B host. These series of plates
show viral plaques--note the round, clear zones on the agar bacterial lawn on each plate (see arrow pointing to one). Image by
Anh-Hue T. Tu, Georgia Southwestern State University, Americus, GA.

1. Lay the 6 plates right side up, from lowest dilution towards highest dilution.
2. Pick each plate up, hold it up to the light, and determine which one has between 30 - 300 plaques (you can also use the Quebec
colony counters---good backlighting!)
3. Get an accurate count of that plate. Fill in the formula for viral counts.

4. Calculate the number of viruses per ml. of original specimen.

Watch Video 2: Plaque Assay

In this video, the scientist has already completed the serial dilutions and is demonstrating the mixing of the phage/bacterium
solution with the soft top agar and pouring this mixture onto the bottom agar plate.

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 Protocol 5.3 Plaque Assay

Watch Video 2: Plaque assay. URL: https://youtu.be/uAlRSB6iCt0

Contributors and Attributions

Jackie Reynolds, Professor of Biology (Richland College)

6.4: Bacteriophages is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
49: Bacteriophages (Experiment) has no license indicated.

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6.5: Lab Procedures- Testing Oxygen requirements
Learning Outcomes
Inoculating thioglycollate tubes and TSA plates for incubation

Procedure
Thioglycollate broth
1. The thioglycollate broth should be either boiled first before inoculation OR recently made so that the oxygen content is very
low. (Your instructor will tell you if it needs to be boiled).
2. Inoculate a tube of thioglycollate broth with your unknown bacterium: make sure that the loop or needle goes down to the
BOTTOM of the broth (do not get metal holder in the sterile broth).
3. Incubate at 25 or 37 degrees C as directed.

Watch Video 1: Deep stab agar slant inoculation

BIO2205_Deep Stab Agar Slant

Watch video 1: This procedure is showing you how to inoculate a deep stab agar slant. A similar procedure can be used for
inoculating thioglycollate tubes, except that the media is semi-solid agar and there is typically no slant, so you don't have to do that

6.5.1 https://bio.libretexts.org/@go/page/52333
 last zig-zagging streak on the top of the slant. (3:10) Video by Sinclair College eCourse Design &
Development. URL: https://youtu.be/p4awvOVGZXA

TSA plates in 3 different oxygen environments

1. Label 3 plates for the table---candle jar, ambient air, and GasPak anaerobic jar.
2. Divide the 3 plates into sections, one for each organism—your unknown, the strict aerobe, the strict anaerobe.
3. Inoculate the section by streaking a straight line or a zigzag (as seen below). HOWEVER, be sure that you inoculate all 3 plates
using the same technique.
4. Be sure that the jar has a methylene blue indicator strip (seen above) inside. The methylene blue is blue when oxidized, but
colorless when reduced. Before the jar is opened, the strip should be checked to make sure that it is COLORLESS.
5. Incubate at 30 or 37 degrees C

INTERPRETATION: after incubation

TSA plates
Compare the presence/absence of growth, as well as the quantity of growth on the 3 plates. Determine whether aerobic, anaerobic,
or facultatively anaerobic.

To the right:
A is an facultative anaerobe
B is an aerobe (microaerophilic)
C is an anaerobe

Thioglycollate broth

Determine WHERE the most amount of growth occurs in the column of liquid---the top, the bottom, top to bottom. DO NOT
SHAKE IT! Can you determine if the bacterium is aerobic, anaerobic, or facultatively anaerobic?

Contributors
1. Jackie Reynolds, Professor of Biology (Richland College)

6.5: Lab Procedures- Testing Oxygen requirements is shared under a not declared license and was authored, remixed, and/or curated by
LibreTexts.

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6.6: Lab Procedures- Plaque Assay
Learning Outcomes
Practice serial dilutions
Perform a plaque assay
Determine PFUs

Plaque Assay
Knowing how to determine the number of microorganisms in a sample is extremely important in microbiology, and requires
accurate pipetting, aseptic technique, and calculation skills. In this exercise, you will again prepare dilutions and enumerate the
microorganisms in a sample. Although the principles are the same, you will be enumerating viruses instead of bacteria and
conserving on materials by using micropipettes and smaller volumes in your dilutions.
The number of viruses in a sample can be determined by direct count using electron microscopy or by determining the number of
infectious virus particles using a plaque assay. Viruses are obligate intracellular parasites. Therefore, they require a host cell in
which to grow. Some viruses lyse the cells in which they have replicated while others appear to cause little cell damage. A plaque
assay can be used to enumerate viruses that lyse their host cells. In a plaque assay the host cells and virus are incubated together for
a short time to allow the virus to attach to and enter the host cell. Then the mixture in plated within a semi-solid agar. This semi-
solid agar is poured onto a "bottom agar" that serves to supply adequate nutrients for the host cell. At the end of one cycle of virus
replication a cell infected with a single virus particle will lyse, releasing hundreds of new viruses. In the semi-solid medium these
newly released viruses can only infect neighboring cells; after a second cycle of replication these neighboring cells will be lysed.
Those cells that escape infection will continue to grow. After 24 to 48 hours plates that were not infected with a virus will contain a
confluent layer of cells (they will resemble the TNTC plates of the preceding exercise). Those plates that were infected with several
hundred viruses may actually appear clear- the viruses will have infected and lysed all of the host cells. Those plates that contain an
intermediate number of viruses will have plaques, clear or partially clear circular areas in an otherwise turbid background of
cellular growth. Each plaque represents the result of one infectious virus, called a plaque forming unit, or PFU. Many animal and
bacterial viruses can be enumerated using a plaque assay. Bacterial viruses are also referred to as phage; in this exercise you will be
using a well-characterized bacterial phage, T4, and its host cell, Escherichia coli.
In this exercise you will also be setting up your own dilution tubes and using micropipetters in this laboratory. Your laboratory
instructor will go over the proper use of these pipetters and maintenance of aseptic technique.

Materials:
Cultures Escherichia coli strain B culture
Phage sample T4
Media 4 petri plates containing "bottom agar"
4 tubes containing 5 mL of "top agar" - these tubes will be in the 50°C water bath
Supplies Sterile Tryptic Soy broth diluent and 10 sterile microcentrifuge tubes
Micropipetters and sterile tips

Procedure:
A. Sample Dilution and Plating
1. Prepare 10-fold serial dilutions of the virus through 10-6
a. To do this, first prepare 6 dilution tubes by aseptically pipetting 900 µL of
Tryptic Soy broth diluent to each tube - use one pipette tip.

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 b. Add 100 µL of the T4 phage sample to the first dilution tube, close the
cap, and vortex to mix thoroughly. This is a 10-1 dilution
(100 µL/100 µL + 900 µL = 100 µL/1,000 µL = 1/10 = 10-1).
c. Use a new pipette tip to transfer 100 µL from the 10-1 dilution to the next
dilution tube, mix thoroughly, this is your 10-2 dilution.
d. Continue making dilutions of the phage until you have used all 6 dilution
tubes and have a 10-6 dilution of the phage in the 6th tube.

2. Label your remaining 4 sterile tubes 10-4, 10-5, 10-6, and 10-7, and pipette 100 µL from the appropriate phage dilutions into
these labeled tubes (use a new pipette tip for each transfer).
3. Add 100 µL of the Escherichia coli culture to each of the 4 labeled tubes. (Use the same pipette tip; add Escherichia coli to the
tube with the most diluted phage first and work back.)
4. Incubate bacteria with virus for 10 minutes to allow for adsorption (attachment) of the virus to the bacteria.
5. While you are waiting, label the agar plates with your name, lab section, and the virus dilution that will be plated on it: one
plate for each 10-4, 10-5, 10-6, and 10-7. Reset the micropipette for 200 µL.
6. After the 10 minutes, get the tubes of top agar from the 50°C water bath; working quickly, wipe off the tubes. You may want to
get one top agar tube at a time so you won't have to rush; top agar solidifies within a few minutes once it is removed from the 50°C
bath.
7. Pipette 200 µL from a labeled tube into a top agar tube, vortex for about 2 seconds, pour onto the appropriately labeled bottom
agar plate. Do this for all four labeled tubes.
8. Allow the top agar to solidify (about 5 minutes) before moving the plates. Invert the plates and incubate at 30°C.

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6.7: Results
Plaque Assay
Count the number of plaques
Look at all of your plates prepared last period. Record the number of plaques following the same procedure used in counting
bacterial colonies . Calculate the PFU/mL of the original phage sample. Remember, your plated 100 µL (0.1 mL) of the phage
dilutions.

1. Record data from your phage plates here:

Total dilution Plaque Counts

10-4

10-5

10-6

10-7

PFU/mL of original phage sample:______________________

2. Record phage enumeration data for the class here:

Student pairs Dilution with 30-300 plaques Number of plaques on plate PFU/mL in original T4 phage
sample.

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 9

10

11

12

13

Class Average:

Testing Oxygen Requirements

Illustrate the growth pattern of each bacterial species inoculated into the tube of thioglycollate agar using the pictures below.
Record any other distinguishing characteristics of the growth of each species. Name the classification of the organism based on its
oxygen requirements, aerobe, anaerobe, of facultative, in the space below.

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6.8: Review Questions
1. How does a thioglycollate medium work to determine the oxygen requirements of bacteria?
2. You isolated a new bacterium from a local lake. how can you determine it's temperature, salinity, pH, and oxygen requirements?
3. Describe the 4 growth phases in a bacterial growth curve. At which phase is the growth rate equal to the death rate?
4. Bacteriophages are highly specific to their hosts. Explain this statement
5. How do you determine PFUs/mL?

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 CHAPTER OVERVIEW

7: Microbial Metabolism
7.1: Introduction to Biochemical Tests Part I
7.2: Introduction to Biochemical Tests Part II
7.3: Lab Procedures- Biochemical Tests
7.4: Results
7.5: Review Questions

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1
7.1: Introduction to Biochemical Tests Part I
Learning Outcomes
Observe and interpret the fermentation reactions of representative bacteria in phenol red sugar broths, distinguish between
respiration and fermentation, discuss the conditions in which these reactions occur.
Observe and interpret sugar fermentation and hydrogen sulfide formation in TSI agar slants, discuss the purpose of critical
ingredients in TSI agar slants, distinguish between different sugar fermentations, interpret TSI reactions.
Learn about the role of extracellular enzymes in bacteria, observe the hydrolysis of casein hydrolysis

A. Carbohydrate Fermentation
Fermentation is a metabolic process that some microorganisms use to break down substrates such as glucose and other sugars
when O2 is not available or could not be used by the microorganism. Fermentation includes the reactions of glycolysis (where a
single molecule of glucose is broken down into 2 molecules of pyruvate), as well as additional reactions that produce a variety of
end products (acids, alcohols, gases). The end products are characteristic of individual bacterial species. Keep in mind, microbes
are very versatile, the fermentation substrate does not have to be sugars, it can include even unusual compounds like aromatics
(benzoate), glycerol (sugar-alcohol), and acetylene (hydrocarbons)!
Much of the original energy in the substrate remains tin the chemical bonds of organic end products, like lactic acid or ethanol. For
example, one fermentation waste product is ethanol, its got so much stored energy it can be used in gasoline solutions to be
combusted/burned to release that energy stored in its chemical bonds.
Note that fermentation is mainly a mechanism for regenerating NAD+ when respiratory process do not occur. Fermentation also
tends to produce waste products that can accumulate in the extracellular environment. By contrast, the waste left over after ATP
production by aerobic respiration are limited to CO2 and H2O. There can be numerous end products from fermentation, many of
which is useful for us, but not necessarily the microbes. We use many fermentation products--as diverse as antibiotics, alcohols,
and a variety of foods. Microbes such as yeast and bacteria are genetically engineered to produce valuable fermentation products.

Figure 1: Carbohydrate fermentation

Although the ultimate substrate molecule for fermentation is always glucose, some bacteria use additional chemical reactions to
convert other monosaccharides as well as disaccharides into glucose. Therefore bacteria can be differentiated both based on their

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ability to ferment various carbohydrates, as well as the end products that result from the fermentation process.
The medium used to test carbohydrate fermentation is a nutrient broth that contains a fermentable carbohydrate (usually a
monosaccharide or a disaccharide), peptone (amino acids) as well as a pH indicator. The pH of the medium is adjusted to
approximately 7.5, so it appears orange/red when using phenol red pH indicator. These types of carbohydrate fermentation tubes
are therefore called Phenol red (sugar) broths. If the carbohydrate in the medium is fermented and acidic end products are
formed, a color change to yellow will result (see image 1 tubes A and C). Occasionally, bacteria will not ferment the carbohydrate,
but instead will break down proteins producing ammonia (NH3) in the growth medium. In this case, the medium will become more
alkaline and appear red (see image 1 tube B).
Some bacteria will produce gases when fermenting a carbohydrate. To detect these gases, a Durham tube is used. This is a small
inverted glass tube that is placed within the larger glass tube containing the fermentation medium (see image 1). If gases (typically
CO2) are produced during the fermentation process, a bubble will form at the top of the Durham tube (see tube A). If you see a
bubble in the Durham tube, the medium will also be acidic. Carbohydrate fermentation media are often used to differentiate
members of the family Enterobacteriaceae (e.g., Escherichia coli, Enterobacter aerogenes) from each other.

Image 1: Fermentation Reactions Produced by Escherichia coli in Phenol Red Sugar Broths Containing Dextrose, Sucrose, and
Lactose sugars. Image by Janie Sigmon, York Technical College, Rock Hill, SC.

In many metabolic tests, end products are produced that change the pH of the medium. To measure this pH change, pH indicators
(chemicals that change color depending on pH) are included in the medium. Some common pH indicators are phenol red,
bromocresol purple, and bromothymol blue. Each pH indicator has a range of pH values over which it changes color (see below).

pH Indicator

phenol red < pH 6.8 = yellow pH 6.8 – 7.4 = red pH >7.4 = pink/magenta

bromocresol purple < pH 6.8 = yellow > 6.8 pH = purple

bromothymol blue < pH 6.0 = yellow pH 6.1 – 7.5 = green pH >7.5 = blue

Table 1: pH indicators

Watch Video 1: Phenol red sugar broth tests

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 Phenyl red broth test : Carbohydrate fer…
fer…

Watch Video 1: how to perform phenol red sugar tests. Video by Microbial zoo (3:40). URL: https://youtu.be/W8JWInjlXqQ

B. Triple Sugar Iron (TSI) Agar Slants

Triple Sugar Iron (TSI) agar is a medium used for differentiating enteric bacteria. These bacteria typically reside in the
gut/intestines of mammals. Some are major bacterial pathogens, such as certain strains of toxigenic Escherichia coli, Salmonella,
Shigella, and Campylobacter species. The TSI medium can differentiate enterics based on their ability to ferment carbohydrates
and reduce sulfur. The TSI medium contains three carbohydrates--glucose, lactose, and sucrose-- and iron ions, sodium thiosulfate,
and the pH indicator phenol red. The medium is usually made as a 'slant' agar in a glass tube. Bacteria are inoculated into the slant
of medium and into the deep portion (called the butt), where it is anaerobic.
There are 3 reactions possible in the TSI agar. First, if it only ferments glucose, then the slant and the butt will turn yellow due to
the production of acidic by-products, but after a few hours, the butt remains yellow but the slant itself may will revert back to red as
alkaline conditions reappear from the digestion of peptones and the production of ammonium compounds. Second, if lactose or
sucrose or both, are fermented, there will be sufficient acid produced to cause both slant and butt to remain yellow. Third, if no
carbohydrates are fermented, the slant and butt will remain a red alkaline color.
Gas (CO2) production from carbohydrate fermentation is noted by the presence of cracks or fissures in the medium. If there is a lot
of gas, portions of the medium may even be pushed up the tube (Image 2, middle tube/tube 3, notice small gap/space at bottom of
tube).
Another thing TSI agar tests is hydrogen sulfide production because it contains the iron ions and sodium thiosulfate. Some bacteria
use sodium thiosulfate in their metabolism and release hydrogen sulfide. The hydrogen sulfide reacts with the iron, yielding iron
sulfide, which is a black precipitate, the medium will appear black (Image 3 and 4).

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Image 2 : Triple sugar iron (TSI) agar was used to grow and differentiate various bacteria. Tube 1 (far left) is the uninoculated
control. Tube 2 (second from left) was inoculated with Pseudomonas aeruginosa and displays a red slant with no color change in
the butt, indicative of a lack of fermentation. Tube 3 (center) was inoculated with Escherichia coli and displays a yellow slant and a
yellow butt, which indicates glucose and lactose and/or sucrose fermentation. It also exhibits cracks in the agar and lifting of the
butt, which is indicative of gas production. Tube 4 (second from right) was inoculated with an unidentified culture and displays a
red slant and a yellow butt, which indicates that glucose was fermented with acid production. Tube 5 (far right) was inoculated with
Gram-positive Staphylococcus aureus and displays a yellow slant and a yellow butt, indicative of glucose and lactose and/or
sucrose fermentation. Unlike tube 3, there is no evidence of gas production. All tubes were incubated at 37°C for 24 hours. Image
by Clarissa Kaup and J. L. Henriksen, Bellevue University, Bellevue, NE.

Image 3: Proteus mirabilis in a triple sugar iron (TSI) slant. This organism ferments only glucose, indicated by the red coloring of
the agar. The slant is red due to depletion of glucose and the subsequent digestion of proteins in the agar. There is a large carbon
dioxide bubble in the bottom right area of the tube, and the black precipitate indicates hydrogen sulfide was produced. Image by
Diane Hartman, Baylor University, Waco, TX.
Image 4: Proteus vulgaris in a triple sugar iron (TSI) slant. This organism ferments glucose and sucrose. Acid causes the phenol
red indicator in the agar to turn yellow. There is a small carbon dioxide bubble in the bottom right area of the tube. The black
precipitate indicates hydrogen sulfide was produced. Image by Diane Hartman, Baylor University, Waco, TX.
Image 5: Alcaligenes faecalis in a triple sugar iron (TSI) slant. This organism does not ferment sugars so the medium remains red
(no acids are produced in the slant or butt). The slant becomes a deeper shade of red indicating the organism uses the protein in the
medium and produces alkaline waste products. There is no carbon dioxide and no hydrogen sulfide (no black precipitate)
production. Image by Diane Hartman, Baylor University, Waco, TX.

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Watch Video: how to inoculate & interpret TSI agar slants

How to Inoculate & Interpret a TSI Slant …

Watch Video: how to inoculate & interpret a TSI agar slant. Video by MCCC Microbiology (1:35)
URL: https://youtu.be/FuOcN3wB0VM

C. Extracellular enzymes
An exoenzyme, or extracellular enzyme, is an enzyme that is secreted by a cell into the environment and functions outside of that
cell. Exoenzymes are produced by both prokaryotic and eukaryotic cells. Most often these enzymes are involved in the breakdown
of larger macromolecules. The breakdown of these larger macromolecules is critical for allowing their smaller components to pass
through the cell membrane and enter into the cell. Bacteria and fungi also produce exoenzymes to digest nutrients in their
environment, and these organisms can be used to conduct laboratory assays to identify the presence and function of such
exoenzymes. Some pathogenic species also use exoenzymes as virulence factors to assist in their spread.

i. Casein Hydrolysis
Some bacteria secrete extracellular enzymes called proteinases that break down proteins. Milk contains large proteins called
casein. Some bacteria secrete caseinases that break down casein outside of the bacterial cell so the smaller products (e.g., amino
acids) can be transported inside the cell and further metabolized.
Milk agar (which contains powdered milk) is used to detect the presence of bacterial caseinases. This medium (Image 6) is cloudy
because when milk is mixed with agar, the casein forms a colloid through which light cannot pass. The presence of caseinases can
be detected by observing a clearing in the agar around the bacterial growth, which indicates that the caseins have been broken down
into transparent end products (amino acids and peptides), which are then taken up by the cells (image 7).

Image 6 (left plate): Milk agar contains skim milk (lactose and casein), peptone, and agar. Many organisms can grow on this
medium. This medium is used to detect the production of proteases/caseinases that digest casein to soluble peptides. This results

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in a clear zone. Soluble peptides can then be absorbed by the cell. Casein is responsible for the white color of milk. When digested
by exoenzymes, the white agar turns clear and colorless.
Image 7 (right plate): Milk Agar inoculated with (A) Pseudomonas aeruginosa, where casein hydrolysis is indicated by a zone of
clearing around the growing colony (green color masking clearing in agar is the diffusable bacterial pigment pyocyanin);
(B) Serratia marcescens, where casein hydrolysis is indicated by a zone of clearing around the growing colony (red pigment of
bacterium is due to prodigiosin production); (C) Escherichia coli, no casein hydrolysis, notice there is no clearing zone around the
culture streak. Images by Tasha Sturm, Cabrillo College, Aptos, CA.

ii. Starch hydrolysis test

Some bacteria produce exoenzymes called hydrolases, which will use water to break apart organic molecules such as the
carbohydrate starch. The large polysaccharide molecule starch contains two parts, amylose and amylopectin, these are rapidly
hydrolyzed using a hydrolase called alpha-amylase to produce smaller molecules: dextrins, maltose, and glucose. Reaction:

To test for the presence of alpha amylase, a starch hydrolysis test can be performed. Gram's iodine can be used to indicate the
presence of starch, when it contacts starch, it forms a blue to brown complex. If the starch has been broken down/hydrolyzed, then
there is a clear area that appears in the medium upon addition of Gram's iodine. This clearing zone indicates the presence of alpha
amylase.

Image 8: Starch agar incubated for 24 hours at 37°C with Bacillus cereus (left) and Escherichia coli (right). After adding iodine,
the iodine binds to starch if it is still present in the agar. A clear zone can be seen around the growth of Bacillus cereus indicating
the production of the exoenzyme amylase, which digests starch to glucose leaving nothing behind in the agar for the iodine to bind.
Compare his to Escherichia coli, which has no large clearing around the streaked culture area. Image by Tasha Sturm, Cabrillo
College, Aptos, CA.

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Image 9: Growth of Bacillus subtilis on a starch agar plate before the addition of iodine solution (A) and after the addition of
iodine solution (B). After the addition of iodine, the clearing surrounding the bacterial growth indicates starch hydrolysis. Image
by Archana Lal, Independence Community College, Independence, KS.

Contributors and Attributions

1. Contributed by Nazzy Pakpour & Sharon Horgan Assistant Professor (Biological Sciences) at California State University
2. Jackie Reynolds, Professor of Biology (Richland College)

This page titled 7.1: Introduction to Biochemical Tests Part I is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated
by Joan Petersen & Susan McLaughlin.
5.1: Introduction by Joan Petersen & Susan McLaughlin is licensed CC BY-NC-SA 4.0.

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7.2: Introduction to Biochemical Tests Part II
Learning Outcomes
Observe and interpret the reactions of catalase positive and catalase negative bacteria using catalase reagent, explain the
function of the enzyme catalase in cells.
Observe and interpret the reactions of oxidase positive and oxidase negative bacteria using the oxidase reagent, discuss the
role of the enzyme cytochrome c oxidase and respiratory pigment cytochrome c in cell respiration.
Observe reactions of bacteria in SIM/Sulfur Indole Motility media, describe the purpose of critical ingredients in SIM
media, Interpret SIM reactions

A. Catalase Activity
Byproducts of aerobic metabolism include two toxic compounds: superoxide free radicals (O2 -) and hydrogen peroxide (H2O2).
These toxic compounds can cause intracellular damage, such as damage to DNA, lipids, and proteins. To remove these
compounds, cells produce enzymes to break them down. Cells can convert superoxide free radicals to hydrogen peroxide by using
the enzyme superoxide dismutase (SOD); catalase breaks down hydrogen peroxide into water and oxygen.

Figure 1: Superoxide dismutase and Catalase reactions

A simple test to determine if bacteria produce catalase is to add hydrogen peroxide to bacteria on an agar slant or to bacteria spread
on a slide (image 1). If catalase is present, the hydrogen peroxide will be broken down into water and oxygen gas, resulting in the
production of bubbles (+ test). This test does not require any special type of medium, however it should never be performed on
organisms that have been grown on blood agar (a medium that contains blood). This is because there is a catalase activity in blood
that would produce a false positive result. Most aerobic and facultatively anaerobic organisms produce SOD and catalase (note:
some species use peroxidase rather than catalase to break down hydrogen peroxide). Obligate anaerobes lack these enzymes, which
is why they cannot survive in an atmosphere containing oxygen. However, some of them have modified versions of these enzymes
to deal with any possible exposure to oxygen. The archaeon, Pyrococcus furiosus, is an obligate anaerobe that lives on and near
hydrothermal vents. Certain segments of these habitats are anoxic and P. furiosus occupies these niches. Some anaerobes have
a superoxide-reducing system based on a different enzyme, called superoxide reductase (SOR), which reduces O2− rather than
dismutating it.

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Image 1: Slide catalase test results. Hydrogen peroxide was added directly to the culture on a microscope slide. A positive reaction
produced by Staphylococcus aureus is indicated by bubbling; a negative reaction produced by Streptococcus pyogenes is indicated
by lack of bubbling. Image by Karen Reiner, Andrews University, Berrien Springs, MI.

Watch Video 1: Catalase test

How to Perform a Catalase Slide Test - …

Watch video 1: Catalase test. (1:08) Video by MCCC Microbiology. URL:https://youtu.be/r3p4jHjw9o8

B. Oxidase test
Cytochrome oxidase, also known as complex IV, is the terminal, or final, enzyme of the electron transport system/ETS (this does
not include ATP synthase). Cytochrome oxidase is a transmembrane molecule found in the mitochondria of eukaryotes and in the
cellular space of aerobic prokaryotes. This molecule is a proton pump that plays a vital role in producing energy, in the form of
ATP, via the ETS. In the last steps of the energy production process, cytochrome oxidase oxidizes the waste products from the end
of the energy making process, converting reactive species, H+ and dioxygen (O2), to a more stable molecule, water (H2O).
The oxidase test is a key test to differentiate between the families of Pseudomonadaceae (ox +) and Enterobacteriaceae (ox -), and
is useful for speciation and identification of many other bacteria, those that have to use oxygen as the final electron acceptor in
aerobic respiration. The enzyme cytochrome oxidase is involved with the reduction of oxygen at the end of the electron transport
chain.
A cytochrome c oxidase test utilizes a special reagent called oxidase reagent, which is a 1% solution of the chemical tetramethyl-
para-phenylenediamine (TMDPD) dihydrochloride. The reduced form of this reagent is colorless, but donates electrons to the
cell’s cytochrome c oxidase forming an oxidized colored form.
Oxidase positive bacteria change the color of the reagent from colorless to colored and finally black.
Oxidase negative bacteria do not contain the cytochrome c oxidase and do not change the color of oxidase reagent from
colorless to black.

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There are two ways to do the oxidase test, one is using a filter paper (see image 2 below) and the oxidase reagent and the second is
doing a ‘plate’ oxidase test (image 3).

Image 2: Oxidase test on filter paper. A positive oxidase result given by Pseudomonas aeruginosa (left) is indicated by a purple
color. A negative oxidase result given by Escherichia coli (right) is indicated by the lack of color change. Both organisms were
rubbed onto a filter that was dipped in oxidase reagent and allowed to dry. Image by Laura Cathcart, University of Maryland,
College Park, MD; Sabrina Kramer, University of Maryland, College Park, MD; Patricia Shields, University of Maryland, College
Park, MD.

Image 3: Oxidase test on an agar plate with bacterial colonies. This close up view of an agar plate has a mixed culture of oxidase-
positive Vibrio cholerae, indicated by purple colonies, and oxidase-negative Escherichia coli, indicated by lack of color change
(they are the white colonies), demonstrate how the plate oxidase test differentiates between the two. In this test, the oxidase
reagent was added directly to the colonies which were grown on trypticase soy agar at 37°C for 24 hours. Image by Laura Cathcart,
University of Maryland, College Park, MD; Sabrina Kramer, University of Maryland, College Park, MD; Patricia Shields,
University of Maryland, College Park, MD.
Oxidase test is most helpful in screening colonies suspected of being one of the Enterobacteriaceae (all negative) and in identifying
colonies suspected of belonging to other genera such as Aeromonas, Pseudomonas, Neisseria, Campylobacter, and
Pasteurella (positive).

Watch Video 2: Oxidase Test

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 oxidase test

Watch Video 2: how to perform an oxidase test. (3:23) Video by URMICRO1. URL: https://youtu.be/7Aa1xO2cC1M

C. Sulfide Indole Motility (SIM) Medium

The Sulfide-Indole-Motility (SIM) medium was devised for use as a routine medium in the cultural identification of members of
the Salmonella and Shigella groups, showing hydrogen sulfide production, indole production, and motility in the same tube. These
characteristics, along with other biochemical reactions, are of prime importance in the clinical identification of members of the
Gram-negative enteric group, many of which are bacterial pathogens. This enteric group is named after the Greek word for
intestine - enteron.
Sulfide production is tested by the presence of a black precipitate. Microorganisms are capable of producing sulfide and hydrogen
sulfide in several ways. One way is when sulfur containing organic compounds, such as the amino acid cysteine, are metabolized,
they excrete the sulfide ion (S2-) or hydrogen sulfide (H2S) as a waste product, which can then combine with the ferrous iron (Fe2+)
that is present in the medium to produce ferrous sulfide, which appears as a black precipitate. Bacteria capable of producing the
enzyme cysteine desulfhydrase are able to remove the sulfhydryl group (- SH) from cysteine to produce sulfide ions (which may
combine with hydrogen ions to produce hydrogen sulfide), ammonia and pyruvic acid.

Figure 2: Chemical reaction of cysteine desulfhydrase and formation of ferrous sulfide

Another common way for bacteria to produce hydrogen sulfide is through the use of sulfate (SO42-) as a terminal electron acceptor.
Anaerobic respiration is the use of an inorganic compound (other than oxygen) as a terminal electron acceptor. You will recall that
in aerobic respiration, O2 is the final electron acceptor, and H2O is produced as an end product. In anaerobic respiration,
SO42- would be reduced to H2S. Anaerobic respiration most commonly involves NO3-, SO32-, and CO32-. When the bacteria

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produce hydrogen sulfide, it reacts with ferrous ions present in the culture medium to form the insoluble, black iron/ferrous sulfide
precipitate.
Indole production is indicative of the intracellular enzyme tryptophanase. Tryptophanase is an intracellular enzyme, which
catalyzes the breakdown of the amino acid tryptophan to pyruvate and indole. The pyruvate is used by the cell as a carbon and
energy source; the indole is excreted as a waste product. To test for tryptophanase, a culture is grown in the SIM medium, which
contains high levels of tryptophan. After incubation and growth, several drops of Kovac's reagent are added. Kovac's reagent
contains para-dimethyl-aminobenzaldehyde, which reacts with indole to produce a reddish pink compound (rosindole). The
development of a red ring at the top of the tube is a positive test, see Image 2, tube A and E.
Motility is tested by growth in a semi-solid, soft agar. Motile bacteria can swim through the medium and will show diffuse growth
and turbidity away from the line of inoculation.

Image 3: Sulfur-indole-motility (SIM) test results from various microbes. From left to right: (A) Escherichia coli,
(B) Staphylococcus aureus, (C) Salmonella arizonae, (D) Enterobacter aerogenes, and (E) Proteus vulgaris. After addition of
Kovács reagent, a pink ring at the top of the tube indicates a positive indole result (A and E). Blackening of the media indicates
hydrogen sulfide production (C and E). Growth feathering away from the stab line creating a cloudy appearance in the media
indicates motility (A, C, D, and E). Growth strictly along the stab line indicates a nonmotile organism (B). Image by Tasha L.
Sturm, Cabrillo College, Aptos, CA.

Watch Video 3: SIM medium

SIM Medium: Detection of Indole and H…

H…

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 Watch Video 3: SIM medium inoculation and interpretation. Video by Dr. Gary Kaiser (4:30)
URL: https://youtu.be/zzBhhVp0qvU

Contributors and Attributions

1. Contributed by Nazzy Pakpour & Sharon Horgan Assistant Professor (Biological Sciences) at California State University
2. Jackie Reynolds, Professor of Biology (Richland College)

7.2: Introduction to Biochemical Tests Part II is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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7.3: Lab Procedures- Biochemical Tests
Make sure you follow aseptic procedures and label everything carefully! Use the inoculation method indicated for each type of
medium—these methods may differ. Make sure to thoroughly sterilize your loop or needle between inoculations to ensure that you
are only introducing one bacterial species into your medium. If a medium is inoculated with more than one kind of bacterium, a
positive result cannot be attributed to a single bacterial species. Be sure to use the correct bacterial species for each test. Follow
directions carefully so that you do not waste media.
For comparison purposes, you will be provided with negative controls (media that have not been inoculated) in the next lab when
you are analyzing your results.

Note
All media that you inoculate today will be incubated until the next lab, when you will analyze your results .

A. Carbohydrate Fermentation
Each student: 1 tube each of the following broths: Lactose + phenol red (green cap), Sucrose + phenol red (yellow cap), Glucose +
phenol red (red cap)
Instructions: Choose 1 of the following bacteria: Proteus vulgaris, Escherichia coli, Bacillis subtilis, or Streptococcus faecalis
(each person at the table should choose a different species)
Inoculate the 3 types of fermentation broth with your chosen bacteria. Prior to inoculating the broths, make note of any small
bubbles that might be present in the Durham tubes, so these are not read as evidence of gas formation during fermentation.

B. Triple sugar iron (TSI) slant/deep

It tests the ability of bacteria to ferment sugars and to produce H2S, often used to identify Salmonella and Shigella. The medium
contains sugars (lactose, sucrose, and glucose) and thiosulfate. Slant/deep allows for aerobic and anaerobic growth conditions.

1. Inoculate your TSI slant/deep with your assigned bacteria using a needle by stabbing fully into the butt ONCE and only ONCE.
2. Then, streak across the slant WITHOUT re-dipping your needle in your plate. KEEP CAPS LOOSE and place it on the rack at
the end of the table to be incubated at 37°C

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C. Casein Hydrolysis
Each student: 1 milk agar plate
Instructions: Use both these bacteria: Bacillus subtilis and Enterobacter aerogenes
Divide your milk agar plate into 3 areas using a wax pencil or a sharpie marker. Label the plate to indicate which bacterium will be
inoculated into each area. One area is left as a negative control. Using a loop, you will do spot inoculations of each bacterial species
in the areas, just as you did on the starch agar plate.

Figure 5.2.2: Spot inoculation technique for casein hydrolysis

D. Catalase Activity
Procedure:
1. Transfer a loopful of cells of the species to be tested onto a microscope slide. Bacillus megaterium should be used as a positive
control and your unknown should be tested.
2. Add a drop of hydrogen peroxide.
3. Look closely for the evolution of bubbles.

E. Oxidase test
Procedure for BD BBL DrySlide: (each pair of students need 1 slide)
1. Open the BD BBL DrySlide Oxidase pouch and remove a slide by grabbing the edge of the slide, do not grab paper slide areas.
After removing a slide, fold the top of the pouch over and seal tightly with a self-adhesive sticker (provided).
2. Using a sterile toothpick, pick a portion of the colony to be tested and apply the growth on ONE quadrant of the dry slide. To
ensure a proper reaction, spread the inoculum on the slide reaction area to a 3-4mm size. Roll the toothpick over the slide reaction
area to transfer the cells.
3. On one oxidase slide, there are 4 quadrants: perform this test on Bacillus megaterium as a negative control, Pseudomonas
fluorescens as a positive control, your unknown, and your partner’s unknown. Examine the reaction area for appearance of a dark
purple/blue color within 20sec. Disregard color development after 20 sec.
For Gibson Bioscience Swabs: (1 swab per sample used)
1. Open the Gibson Bioscience Swabs package, ensuring that you open only at the end where you can grab the handle of the swab.
Touch the swab to a (control(s) or unknown sample) colony on your plate. Examine for purple/blue coloration after 10 sec.
Disregard any color development occurring after 60 sec.

F. SIM Tubes
Procedure:

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1. Label SIM tubes; one for Klebsiella aerogenes, one for Staphylococcus epidermidis, one for Proteus vulgaris, and one for your
unknown.
2. Using your loop, inoculate the tubes with the appropriate cultures.
To inoculate, stab the center of the agar deep continuing down into the agar about 3/4 of the way to the bottom.
3. Incubate at 30°C for 48 hours (your TA will remove from incubator).
4. Following incubation, FIRST observe results for motility and sulfide production, THEN test each tube for the presence of
indole by adding five drops of Kovac's reagent.

Contributions and Attributions

1. Contributed by Nazzy Pakpour & Sharon Horgan Assistant Professor (Biological Sciences) at California State University

This page titled 7.3: Lab Procedures- Biochemical Tests is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by
Joan Petersen & Susan McLaughlin.
5.2: Procedures by Joan Petersen & Susan McLaughlin is licensed CC BY-NC-SA 4.0.

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7.4: Results
Record your results for the metabolic tests in the tables on the following pages.

A. Carbohydrate Fermentation
Observe the results of your own carbohydrate fermentation test, as well as the tests done by your table partners. You can compare
your inoculated tubes with the negative controls in the front of the class at the instructor’s table. Record the results in the table
below.
The following convention is used when noting the results of fermentation experiments.
A = acid
G = gas
AG means that both acid and gas are present
If neither acid nor gas is present, you can write “negative”

Bacteria Glucose Lactose Sucrose

Proteus vulgaris

Escherichia coli

Bacillus subtilis

Streptococcus faecalis

B. TSI
Bacterium Glucose Lactose Sucrose Gas production H2S production

C. Casein Hydrolysis
Observe your casein plate. It is helpful to hold it up to the light so you can detect the clear zones. Make a drawing of your results
the circle below. Indicate the location of the bacterial growth and draw any clear zones that are present. Record your results in the
table below.

Bacteria Clear zone? Result (+/-)

A. Enterobacter aerogenes

B. Bacillus subtilis

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 C. Negative control

D. Catalase Activity
Add a dropper full of H2O2 to the surface of the slant. Record your results below.

Bacteria Presence of bubbles Result (+/-)

Bacillus megaterium

Unknown

E. Oxidase
Bacteria Color Oxidase Result (+/-)

Bacillus megaterium

Pseudomonas fluorescens

F. SIM Tubes
NOTE: Be sure to look on the surface of the agar as well as within the deep stab for evidence of motility.
A. SIM agar deep tubes

Culture Motility Sulfide Indole

Klebsiella aerogenes

Staphylococcus epidermidis

Proteus vulgaris

Unknown

This page titled 7.4: Results is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by Joan Petersen & Susan
McLaughlin.
5.3: Results by Joan Petersen & Susan McLaughlin is licensed CC BY-NC-SA 4.0.

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7.5: Review Questions
1. Define the process of fermentation. What are some common metabolic end products produced by different microorganisms
during fermentation?
2. What is the purpose of phenol red in a carbohydrate fermentation tube?
3. What is the function of the durham tube in a fermentation tube?
4. What is the purpose of the TSI agar test? What is the purpose of iron and sodium thiosulfate in the TSI agar? what is the pH
indicator in TSI agar?
5. How is the SIM medium used to detect motility?
6. What substrates are acted on in SIM medium in order for hydrogen sulfide/H2S to be produced?
7. What does cysteine desulfurase catalyze?
8. What is the component in the SIM tube that makes this medium suitable to detect the production of indole by bacteria?
9. What are exoenzymes? why are they important to bacteria?
10. Why is the enzyme catalase important? Do anaerobic bacteria require catalase? explain your answer.
11. What is the importance of cytochrome oxidase to bacteria that possess it?
12. What is the function of the oxidase reagent in the oxidase test?

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 CHAPTER OVERVIEW

8: Bacterial Identification
8.1: Introduction to Bacterial Identification using Culture Media
8.2: Introduction to Bacterial Identification using Enterotube test
8.3: Introduction to Bacterial Identification using Genotypic methods
8.4: Lab Procedures- Enterotube inoculation
8.5: Lab Procedures- PCR and Gel Electrophoresis
8.6: Results
8.7: Review Questions

8: Bacterial Identification is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

1
8.1: Introduction to Bacterial Identification using Culture Media
Learning Outcomes
Identify and describe culture media for the growth and identification of bacteria, including examples of selective and/or
differential media.

Bacterial Identification with Culture media

One of the common methods to identify bacteria is through the use of specialized media. Back in Module 2, you were introduced
to this idea. Here’s a recap: In clinical microbiology, it is often important to detect the presence of specific microbes associated
with disease or poor sanitation, for this task, selective and/or differential media are used. Selective media suppresses the growth of
unwanted bacteria and encourage the growth of desired microbes. For example, bismuth sulfite agar can be used to isolate
Salmonella typhi from feces. Bismuth sulfite inhibits Gram positive bacteria and most Gram negative intestinal bacteria (other than
S. typhi).

typhi, coli, proteus, bacteria, cultured, bismuth, sulfite, agar, 48hrs, incubation

Image 1: Bismuth Sulfite agar

Differential media makes it easier to distinguish colonies of your desired microorganism from other colonies growing on the same
plate. Blood agar (which contains red blood cells/RBCs) is a medium often used to identify bacterial species that destroy RBCs.
These species, such as Streptococcus pyogenes, that causes strep throat, will show a clear ring around their colonies where they
have lysed the surrounding blood cells.

Image 2: Normal Upper respiratory flora mixed with Streptococcus species. The presence of beta-hemolytic colonies (clear zones
around small colonies) indicates the possibility of Streptococcus pyogenes infection. Image by Rebecca Buxton, University of
Utah, Salt Lake City, UT.

Selective and Differential Media types

A. Mannitol Salt Agar
In some cases, selective and differential characteristics are combined into a single medium. If you wanted to isolate the common
bacterium, Staphylococcus aureus and know that it has a tolerance for high concentrations of sodium chloride and can ferment the
carbohydrate mannitol to form acids, you can use a selective-differential media called “Mannitol Salt Agar or MSA” which

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contains 7.5% sodium chloride, and will discourage the growth of competing microbes and thus select for (or favor the growth of)
S. aureus. MSA is too salty for many microbes. The medium also contains the pH indicator, phenol red, when the pH drops, such
as when mannitol in the medium is fermented to acids, it will change color from red to yellow. Thus, the mannitol-fermenting
colonies of S. aureus are differentiated from colonies of bacteria that do not ferment mannitol. Bacteria that can grow at high salt
concentration and ferment mannitol to acid can be identified on MSA by color change, such as shown on this image 3-S. aureus
streak in the left half of the plate shows growth of the bacterium and the yellow color indicating mannitol fermentation, while on
the right half of the plate, Streptococcus durans is not capable of growing on this media (because it cannot tolerate high salt
concentration) and thus there are no colonies and the media remains the same color, a pinkish red. If a bacterium is able to grow on
MSA (has visible colonies) but the medium stays pinkish-red, then it is not capable of fermenting mannitol since the medium
doesn't change color.

Image 3: Mannitol salt agar inoculated with Staphylococcus aureus on the left side of the plate and showing fermentation of
mannitol (yellow medium) and inoculated with Streptococcus durans on the right side of the plate, which shows no growth (no
colonies visible, medium remains reddish pink). Image by Anne Y. Tsang and Patricia Shields, University of Maryland, College
Park, MD.

Watch Video 1: Mannitol Salt Agar explained

Mannitol Salt Agar

Watch Video 1: Mannitol Salt Agar explained and showing plate examples. Video by Dr. Gary Kaiser (CCCB ). (1:38)
URL: https://youtu.be/kG1_Tf5Vpc0

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B. MacConkey agar
MacConkey agar is another example of a Selective & differential medium, it is used to isolate & distinguish between Gram-
negative enteric rods. MacConkey agar contains bile salts and crystal violet that inhibit Gram positive bacteria but allow the
growth of Gram negative bacteria. In this way, these chemicals act selectively, to inhibit one group but promote the growth of
another group.
MacConkey also has the sugar lactose and a pH indicator neutral red it turns pink/red under acid conditions. In this way, it
distinguishes between lactose fermenters from non-lactose fermenters.

Image 4: MacConkey agar plate inoculated with the Gram-negative lactose fermenter (pink colonies/streak) Escherichia coli and
the Gram-negative non-lactose fermenter (off yellow colonies) Serratia marcescens. Image by David Miller and Patrick Hanley,
Hartwick College, Oneonta, NY)

Watch video 2: MacConkey agar explained

MacConkey Agar

Watch video 2: MacConkey agar explained and showing plate examples. Video by Dr. Gary Kaiser (CCCB ). (4:32)
URL: https://youtu.be/yInQ9jApAlU

C. Eosin-Methylene Blue (EMB) agar

Eosin-Methylene Blue (EMB) agar is a selective & differential medium used to isolate Gram-negative enteric bacteria and
distinguish between them. EMB contains 2 dyes--Eosin and methylene blue--which act as selective agents to inhibit Gram-positive
bacteria but allow for the growth of Gram-negative bacteria.

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EMB also contains the sugars lactose and sucrose--and it distinguishes or differentiates between lactose or sucrose fermenters from
non-fermenters. The fermenters form colored colonies and the non-fermenters form colorless colonies, similar to the MacConkey
agar.

Image 5: Eosin-methylene blue ( EMB) agar plate inoculated with Escherichia coli (a Gram-negative coliform bacterium) showing
good growth of dark blue-black colonies with metallic green sheen indicating vigorous fermentation of lactose and acid production
which precipitates the green metallic pigment. Image by Naowarat Cheeptham, Thompson Rivers University, Kamloops, BC,
Canada.

D. Hektoen Enteric (HE) agar

Hektoen Enteric (HE) agar is a selective & differential medium that is used to isolate and distinguish between the enteric
pathogens Salmonella and Shigella. HE medium contains high concentrations of bile salts as selective agents that inhibit Gram-
positive bacteria but also slow the growth of normal intestinal microbiota. HE contains sugars lactose and sucrose, the pH indicator
bromothymol blue, sodium thiosulfate and ferric salts. E. coli and related coliforms ferment lactose (and sucrose) forming bright
orange to salmon pink colonies. Salmonella and Shigella are non-lactose fermenters and form green or blue green colonies.
Salmonella colonies produce Hydrogen sulfide (H2S) which reacts with the iron in the medium to form iron sulfide (FeS) forming
colonies with black centers.
All of the media we discussed are for isolating and differentiating common enteric pathogens that can cause disease in humans.

Image 6: Hektoen enteric agar sterile, uninoculated

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Image 7: Salmonella enterica on Hektoen enteric agar. Note the black center of the transparent colonies, indicating H2S production
in the absence of carbohydrate fermentation. All serotypes of Salmonella have this appearance on Hektoen enteric agar except for
serotype typhi, which is a weak H2S producer. Image by Jan Hudzicki, University of Kansas Medical Center, Kansas City, KS

Image 8: Enterobacter aerogenes on Hektoen enteric agar. Note the yellow-orange colonies, indicating the fermentation of at least
one of the carbohydrates present in the medium. The lack of black colonies indicates no H2S production. The orange haze around
the colonies is due to the precipitation of the bile salts by the organism. The appearance of E. aerogenes on Hektoen enteric agar is
typical of most nonpathogenic enteric Gram-negative rods. Image by Jan Hudzicki, University of Kansas Medical Center, Kansas
City, KS.

8.1: Introduction to Bacterial Identification using Culture Media is shared under a not declared license and was authored, remixed, and/or curated
by LibreTexts.

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8.2: Introduction to Bacterial Identification using Enterotube test
Learning Outcomes
Observe, interpret, and identify bacteria using the Enterotubes/Enteropluri test

Bacterial Identification
The identification of microorganisms is an important part of what many microbiologists do. As you can imagine, clinical
microbiologists would need to identify the pathogen that is causing disease in patients. A microbial ecologist is interested in what
microbes are contributing to environmental change or they might want to identify new species in the field. Perhaps you are working
in a lab and have a contaminant and want to know where it is coming from and what it is. We have already learned some ways to
identify microbes, in the last module, you learned about the many biochemical tests available to microbiologists that aid in their
identification of bacteria. We’ll continue with some of these biochemical tests, focusing on ones that are capable of combining
multiple biochemical tests into one, and the use of selective and differential media to isolate and identify bacteria. Then we’ll
move into bacterial genetics and how we can use molecular methods to identify bacteria.

Enteropluri/Enterotubes
A number of techniques can be used for the identification of specific species and subspecies of Enterobacteriaceae.
Speciation is important because it provides data regarding patterns of susceptibility to antimicrobial agents and
changes that occur over a period of time. It is also essential for epidemiological studies such as determination of
nosocomial infections and their spread.
In an effort to simplify the speciation of the Enterobacteriaceae and reduce the amount of prepared media and
incubation space needed by the clinical lab, a number of self-contained multi-test systems have been commercially
marketed. Some of these multi-test systems have been combined with a computer-prepared manual to provide
identification based on the overall probability of occurrence for each of the biochemical reactions. In this way, a large
number of biochemical tests can economically be performed in a short period of time, and the results can be accurately
interpreted with relative ease and assurance.
The EnteroPluri-Test /Enterotube is a self-contained, compartmented plastic tube containing 12 different agars
(enabling the performance of a total of 15 standard biochemical tests) and an enclosed inoculating wire. After
inoculation and incubation, the resulting combination of reactions, together with a Computer Coding and Identification
System (CCIS), allows for easy identification. The various biochemical reactions of the EnteroPluri-Test and their
correct interpretation are discussed below. Although it is designed to identify members of the bacterial
family Enterobacteriaceae, it will sometimes also identify common biotypes of Pseudomonas and other non-
fermentative Gram-negative bacilli. It does not identify Pseudomonas aeruginosa.
IDENTIFYING MEMBERS OF THE ENTEROBACTERIACEAE WITH THE ENTEROPLURI-TEST
The EnteroPluri-Test contains 12 different agars that can be used to carry out 15 standard biochemical test. Interpret
the results of your EnteroPluri-Test is based on a coding chart included with the test.
The enterotube is a self-contained, compartmented plastic tube containing twelve different media that allow determination of 15
biochemical reactions (glucose, gas production from glucose, lysine decarboxylase, ornithine decarboxylase, hydrogen sulfide
(H2S), indole, adonitol, lactose, arabinose, sorbitol, Voges-Proskauer (VP), dulcitol, phenylalanine deaminase (PA), urea, and
citrate). The enclosed inoculating wire allows inoculation of all compartments in one step from one or a few single colonies of
your unknown microorganism. The resulting combination of enterotube reactions, together with other metabolism tests can help
you to identify unknown organisms.

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Image 1: Four Enterotubes shown. Uninoculated control tube and 3 tubes inoculated with various bacteria. 24 hr incubation.

Image 2: Enterotube chambers

Interpretation of Enterotube chamber Results:

A. Fermentation of Sugars
Among the common products of carbohydrate breakdown by microorganisms using fermentative pathways are organic acids
(acetic, lactic, etc.), alcohols, and gases (carbon dioxide and hydrogen). The types of product formed, and the proportion of each,
depends on the species of microorganism as well as the particular carbohydrate being fermented.
The ability to ferment different sugar compounds will be tested by inoculating a single enterotube. The 5 carbohydrates tested in 1
enterotube are: glucose, adonitol, lactose, arabinose, and sorbitol. The formation of acids can be readily detected by including a pH
indicator in the microbial growth medium. Acid production will lower the pH of the medium, resulting in a color change of the
indicator, creosol red, from red (alkaline) to yellow (acidic).

End products of bacterial fermentation of glucose are either acid, or acid and gas. Gas production will be indicated by the definite
and complete separation of the wax overlay from the surface of the glucose chamber. The glucose chamber medium is covered with
wax to provide anaerobic conditions to allow detection of gas formation. Fermentation of adonitol, lactose, arabinose, and
sorbitol will also result in formation of acidic end products indicated by a change in color of indicator present in the medium from
red to yellow. Any sign of yellow is interpreted as a positive reaction; red should be considered negative. Some strains will give
slightly variable reactions, refer to the manufacturer's chart for more details.

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B. Urease
Many bacteria are able to use urea as a nitrogen source by splitting it into ammonia and carbon dioxide through the hydrolysis
reaction catalyzed by the enzyme urease:
O
ǁ urease
NH2 — C—NH2 + H20 ------------------ ► 2NH3 + CO2
urea Ammonia Carbon dioxide
The ammonia reacts in solution to form ammonium carbonate, which results in an increase in the pH of the medium. Urease
activity is detected by inoculating a medium containing urea and a pH indicator, phenol red (yellow/beige/light amber at acid pH
and red-purple at alkaline pH). Initially the urea media chamber is mostly yellow. After incubation, a red-purple color throughout
the medium indicates a rapid urea splitter, a positive urease result. No color change, (the agar remains yellow/beige/light amber) is
a negative urease result. The urease test is included in the enterotube, see Image 1, chamber 11. Escherichia coli and Enterobacter
aerogenes does not normally have the enzyme urease. Proteus vulgaris is a rapid urea splitter, as indicated by the bright purple
chamber 11.

C. Lysine and Ornithine Decarboxylation

Decarboxylase tests are useful for differentiating bacteria. Microorganisms that have the enzyme decarboxylase can
remove the carboxyl group from an amino acid. Certain bacteria can decarboxylate the amino acid lysine using the enzyme lysine
decarboxylase, which results in the formation of the alkaline end product, cadaverine. Some bacteria can decarboxylate ornithine
(a product of arginine hydrolysis) using the enzyme ornithine decarboxylase (ODC), which results in the formation of the alkaline
end product putrescine. The presence of these decarboxylation byproducts, cadaverine and putrescine, are indicated by a change in
the color of bromcresol purple, the pH indicator in the enterotube medium, from pale yellow (acidic) to purple (alkaline). The
medium is covered with wax to provide anaerobic conditions. Any degree of purple should be interpreted as a positive reaction.
The medium remains yellow, a negative reaction, if decarboxylation of lysine or ornithine does not occur. These tests are included
in the enterotube

Image 3 Lysine and ornithine decarboxylation reactions. The enzymatic reaction catalyzed by ornithine decarboxylase.The
pyridoxal phosphate (PLP)-dependent ODC enzyme catalyzes decarboxylation of ornithine and produces putrescine.

D. Voges-Proskauer
Different bacteria convert dextrose and glucose to pyruvate using different metabolic pathways. Some of these pathways
produce unstable acidic products which quickly convert to neutral compounds. Some organisms use the butylene glycol pathway,

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which produces neutral end products, including acetylmethylcarbinol (acetoin) and 2,3-butanediol. The Voges-Proskauer (VP) test
detects organisms that utilize the butylene glycol pathway and produce acetoin during glucose metabolism. After inoculation and
incubation of the enterotube, the production of acetoin is detected using Barritt’s reagent (potassium hydroxide, and alpha-
naphthol) in the VP chamber. The acetoin product is oxidized in the presence of KOH to diacetyl. The diacetyl then reacts to
produce a red color. The presence of acetoin, a positive result, is indicated by the development of a red color within 20 minutes, a
negative reaction will appear colorless or light amber. The use of Barritt’s reagent in the VP chamber will be performed after
all the results are read for the other chambers in the enterotube.

E. Citrate Utilization
This test detects those organisms which are capable of utilizing citrate, in the form of its sodium salt, as the sole source of
carbon. Organisms capable of utilizing citrate produce alkaline metabolites which change the color of the indicator from green
(acidic) to deep blue (alkaline). Any degree of blue should be considered positive. Certain microorganisms will not always
produce the ideal “strong” positive color change. Lighter shades of the same basic color should be considered positive here. The
citrate utilization is tested in the enterotube.

How to Inoculate & Interpret an Enterotube

Watch video 1: how to inoculate an Enterotube with your bacterial sample

Lab 8: Enterotube Inoculation

Watch Video 1: how to inoculate an enterotube performed in Microbiology labs at NC State. (5:08)
URL: https://youtu.be/3pmaDdZPLJg

Watch Video 2: how to interpret Enterotube results

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 Enteropluri

Watch Video 2: how to interpret Enterotube results. Video by Professor B (5:23). URL: https://youtu.be/CwxvUq4lTZ4

8.2: Introduction to Bacterial Identification using Enterotube test is shared under a not declared license and was authored, remixed, and/or curated
by LibreTexts.

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8.3: Introduction to Bacterial Identification using Genotypic methods
Learning Outcomes
Discuss the characterization of microbes based on phenotypic and genotypic methods
Discuss how PCR is used to identify bacterial species. Describe the process of PCR.
Explain the theory of PCR, its purpose, and applications
Discuss how to visualize an agarose gel
Interpret a DNA gel

Bacterial identification and characterization

Phenotypic methods
Throughout this semester, we have learned about many methods to characterize and identify bacteria. These methods include
characterizing cell shape (cellular morphology), identifying Gram status or specialized cellular features through staining, growth
requirements (oxygen, pH, temperature, etc), appearance of colonies (colony morphology), and through biochemical reactions
(enterotubes, selective and/or differential media types, etc.). All of these are primarily Phenotypic methods of analysis and
characterization, that is, the results are a product of the expression of their genes.
Cellular morphology: cell shape--through microscopy
Staining characteristics: Gram status, cell structures such as flagella, endospores---microscopy
Growth characteristics: culturing requirements such as oxygen, osmotic pressure, temperature, colony morphology----
culturing techniques
Biochemical characteristics: biochemical tests such as enterotubes, oxidase, catalase tests, selective/differential media.

Genotypic methods
The last method used for the identification of bacteria is Genetic analysis through the use of nucleic acid probes or other molecular
techniques.
The application of molecular techniques for detecting and identifying pathogens is widely used. In particular, in surveillance
studies these methods provide reliable epidemiological data for tracing the source of human infections, such as a foodborne illness
outbreak. A wide range of molecular techniques (including pulsed field gel electrophoresis, multilocus sequence typing, random
amplified polymorphism deoxyribonucleic acid, repetitive extragenic palindromic, deoxyribonucleic acid sequencing, multiplex
polymerase chain reaction and many more) have been used for detecting, speciating, typing, classifying and/or characterizing
pathogens of great significance to humans.
The advent of the “molecular biology age” has provided a plethora of tools and techniques for the detection, identification,
characterization, and typing of bacteria for a range of clinical and research purposes. Previously, the identification and
characterization of bacterial species was largely done by phenotypic and biochemical methods (such as through
selective/differential media and biochemical tests that we have discussed in the last 2 modules), which relied on preliminary
isolation and culture.
While these methods continue to hold place in certain settings, molecular-based techniques have provided unprecedented insights
into bacterial identification and typing. To name a few examples, genotypic methods have enabled the identification of a large
diversity of previously unknown taxa, the characterization of uncultivable bacteria, and facilitated metagenomics studies on large
and diverse bacterial communities. Both clinical and research setting have provided in depth insights into bacterial virulence,
pathogenesis, antibiotic resistance, and epidemiological typing, as well as identification of novel, emerging, and re-emerging
species. In addition, the widespread use and availability of molecular tools for bacterial genotyping has resulted in high throughput

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analysis, more sensitive and discriminatory results, and rapid turn-around-times, which are only likely to get better with automated
tools and data analysis pipelines.
Most molecular methods for bacterial identification are based on some variation of DNA analysis, either amplification or
sequencing based. These methods range from relatively simple DNA amplification-based approaches (PCR, real-time PCR, RAPD-
PCR) towards more complex methods based on restriction fragment analysis, targeted gene and whole-genome sequencing, and
mass spectrometry. In addition to this, approaches based on unique protein signatures such as matrix-assisted laser
desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and similar variations have also been explored.

Polymerase Chain Reaction

Many of these molecular techniques utilize the polymerase chain reaction or PCR. A technique you have probably heard of in
other classes. Polymerase chain reaction (PCR) enables researchers to produce millions of copies of a specific DNA sequence in
approximately two hours. This automated process bypasses the need to use bacteria for amplifying DNA. During the course of a
bacterial infection, the rapid identification of the causative agent(s) is necessary for the determination of effective treatment
options, thus molecular methods such as PCR is a popular option due to its speed. You may already know that for detection of the
SARS-CoV2 virus, RT-PCR is widely used.
PCR allows DNA amplification so that specific segments of DNA can be copied numerous times, and then separated and analyzed
by gel electrophoresis. The presence of a specific fragment of amplified DNA can be used to either identify an organisms or a
particular characteristic such as antibiotic resistance. We often use the 16S rRNA gene for bacterial identification purposes
because it is present in all bacteria, it is highly conserved sequences (large regions of nucleotide similarity) which are interspersed
with variable regions that are genus- or species-specific. Bacteria can be identified by nucleotide sequence analysis of the 16S
rRNA PCR product and comparing it to a database with known sequences.

Figure 1: Schematic PCR primers binding to the 16S rRNA gene for amplification from a bacterial chromosome.

In a PCR reaction, the is a series of steps that occur. Usually the dsDNA is denatured to ssDNA. At 55-58degC, a pair of
synthesized oligonucleotide primers anneal to the ssDNA that flank the sequence of interest. At 72degC, a thermostable DNA
polymerase will replicate the ssDNA to dsDNA sequences. The cycle repeats itself 20-40x to amplify the DNA.

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Figure 2: PCR reaction. Image by Erica Suchman, Colorado State University, Ft. Collins, CO.
The sequence of events in the PCR is as follows. The temperature is raised to 92-98oC, causing the DNA strands to separate. Two
primer sequences of approximately 20 nucleotides each are annealed to opposite strands of DNA. (RNA requires an initial reverse
transcription step to create a double-stranded cDNA template.) The temperature is raised to the optimum for a polymerase from a
thermophylic bacterium; usually Thermus aquaticus (Taq) is used at 72oC. Replication continues from the 3' OH of the primers,
producing two copies of the DNA. The temperature is again raised to 92-98oC, causing the DNA strands to separate. Then the
temperature is lowered to allow new primers to attach to each of the four strands created in the previous reaction. The temperature
used during the annealing of primers must be optimized for each individual primer set. The Taq polymerase fortunately is stable
during the DNA melting step and is able to begin a new cycle of synthesis. The process is repeated for 20 to 40 cycles so that
additional copies arise exponentially, i.e., in a chain reaction.

Watch Video 1: how to set up a PCR reaction

Setting up the PCR reaction

Watch Video 1: how to set up a PCR reaction. Video by Hands-on DNA. (4:38) URL:https://youtu.be/95qOSslefMM

Visualizing PCR products

After amplification, the PCR product, sometimes called an amplicon, is visualized and analyzed on an agarose gel and is abundant
enough to be detected with an ethidium bromide or SYBR safe stain (see image below). The amplicon is compared to known sized

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molecular markers for production of bands of the correct size.

Image 1: Agarose gel electrophoresis of 16S rRNA PCR products. Note the 4 bands at the 1600 bp marker.

The 16S rRNA gene is frequently a target for those who are interested in identifying the genera or species of a bacterium. If you
amplify the entire gene (~1500 bp), that is more than sufficient for a sequencing results that will tell you the identity of the
bacterium.

Watch video 2: how to run an agarose gel

How To Load and Run Agarose Gel Elec…

Elec…

Watch video 2: how to load and run an agarose gel. Video by Bio-Rad Explorer. (4:06) URL: https://youtu.be/uAttNVEEEwY

Targeting other genes

In some cases, you don’t need to identify the genus or species of the bacterium, but rather some other characteristics, such as
antibiotic resistance. In which case, you design your primers to target a specific antibiotic gene. In the gel below, the mecA gene
for methicillin resistance was targeted.

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Image 2: Ethidium bromide-stained agarose mini-gel visualizing the products of multiple PCR reactions amplifying a portion of
the mecA gene that encodes for methicillin resistance in Staphylococcus aureus ("MRSA"). Distinct 533 base-pair bands are clearly
visible in the samples containing the resistance gene. Less distinct bands, indicating smaller primer dimers and unincorporated
primers, are also visible . (Labeled view) (Rebecca Buxton, University of Utah, Salt Lake City, UT)

Watch video 3: how to interpret a DNA gel

Determining DNA Fragment Length in a …

Watch video 3: how to interpret a DNA gel. Video by Nicole Lantz. (2:30) URL: https://youtu.be/eDmaBtxym30

8.3: Introduction to Bacterial Identification using Genotypic methods is shared under a not declared license and was authored, remixed, and/or
curated by LibreTexts.

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8.4: Lab Procedures- Enterotube inoculation
Learning Outcome
Learn how to inoculate an enterotube

Enterotube Inoculation Procedure:

1. Take one enterotube, record your initials, and unknown number on the label.
2. Remove both caps. The tip of the inoculating wire is under the white cap, it is already sterile. Do not heat sterilize this wire.
Using your NA plate of your unknown culture, pick a well isolated colony directly with the tip of the enterotube inoculating wire
(Figure 1). A visible amount of inoculum should be seen at the tip and side of the wire. Avoid touching agar with wire.
3. Inoculate enterotube by first twisting wire, then withdrawing wire through all 12 compartments applying a turning motion
(Figure 2). Reinsert wire (without sterilizing) into enterotube, using a turning motion through all 12 compartments, until the notch
of the wire is aligned with the opening of the tube (Figure 3). The tip of the wire should be seen in the citrate compartment. Break
wire at the notch by bending. The portion of the wire remaining in the tube maintains anaerobic conditions necessary for the true
fermentation of glucose, production of gas, and decarboxylation of lysine and ornithine.
4. With the broken off part of the wire, punch holes through the foil covering the air inlets of the last 8 compartments (adonitol,
lactose, arabinose, sorbitol, Voges-Proskauer, dulcitol/PA, urea, and citrate) in order to support aerobic growth in these
compartments (Figure 4). Replace both caps.
5. Incubate at 30ºC for 18-24hrs with enterotube lying on its flat surface or in an upright position. Allow air circulation between
incubated tubes.
6. Interpret and record all reactions with exception of Voges-Proskauer. All other tests must be read before the Voges-Proskauer
test is performed as the reagents added for these tests may alter the remainder of the enterotube reactions. The Dulcitol/PA and
H2S/Indole compartment results will not be used since they are not reliable if read after 2 days. After all reactions are
recorded, follow directions below for completion of VP test.

Voges-Proskauer Test Reagent Addition:

1. Place enterotube horizontally on the bench with glucose compartment pointing downward. By using a toothpick, punch a
hole about 3-4mm in diameter in the plastic film above the VP chamber.
2. Add two drops of 40% KOH solution and three drops of 5% alpha-naphthol. A positive test is indicated by the development
of a red color within 20 minutes. Do not wait longer than 20 minutes before reading the results!

Watch this video 1 on Enterotube Inoculation

Lab 8: Enterotube Inoculation

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Watch Video 1: Enterotube inoculation performed in our Microbiology laboratories at NC State.
URL:https://youtu.be/3pmaDdZPLJg

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8.5: Lab Procedures- PCR and Gel Electrophoresis
Learning Outcomes
Perform a colony PCR
Run an agarose gel on PCR products

Colony PCR (For 16S rRNA Sequence Analysis)

Polymerase chain reaction (PCR) is molecular technique used to amplify specific regions of DNA for applications such as
sequencing and genetic analysis. Typically, there is a limited amount of DNA in the sample to study and amplification is required.
PCR is carried out in a test tube with the DNA template, primers specific for the region that is desired, DNA polymerase, and
reagents that stabilize the reaction. Once the reaction is put together, it will go into a thermocycler (PCR machine) that will create
the conditions for DNA replication to occur. Each round of PCR requires three steps, denaturation, annealing, and elongation, each
of which doubles the amount of DNA template present in the reaction. By repeating this process multiple times, usually 30, this
will amplify the DNA exponentially.

PCR bead method

Materials:
· 27F primer (20uM stock)
· 1492R primer (20uM stock)
· GE Illustra PuReTaq Ready to go PCR bead and tube
· Sterile nuclease-free deionized water (molecular grade)
· T-Streak plate with bacterial isolate
· Micropipettors and tips (P10, P100)

Procedures
Adapted from “GE Illustra PuRe Taq Ready to go PCR beads” guide
1. Obtain PCR bead tubes, which contain Taq polymerase (heat resistant enzyme) and other necessary reagents. Using a sharpie,
label the top of the tubes with PCR reaction number assigned in class. Make sure not to accidentally rub this off when handling
the tube and double check when you put the tube into the PCR machine that your labeling is still visible.
2. Add 25 μL of Master mix (contains molecular grade water + 16S rRNA primers) into the PCR bead tube. The bead will start to
dissolve and slightly effervesce.
3. As you dispense the Master mix, insert the micropipette tip into the mix so that you actually see the small volume go directly
into the mix.
4. Using a micropipette tip, carefully touch the colony on the streak plate. A small, visible dab of cells that barely fill the very end
of the pipette tip will provide enough DNA template for the reaction.
5. Dip pipette tip into reaction mix and gently swirl for 5-10 seconds to dislodge cells. Cap the tubes. Avoid forming bubbles.
6. Transfer tubes to thermal cycler.
7. Select appropriate program† to start cycling (about 2 hours).
8. Once cycling is complete, remove tubes and incubate on ice. Follow your instructor’s instructions about storage, and follow up
protocols to quality test the PCR products and prepare them for sequencing.

***Protocol adapted from “puRe Taq Ready-To-Go PCR Beads” guide*

16S rRNA Primers:

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Forward Primer (27F)
5’ – AGA GTT TGA TCC TGG CTC AG – 3’

Reverse Primer (1492R)

5’ – ACG GCT ACC TTG TTA CGA CTT – 3’

PCR Cycle Protocol:

1. 94oC for 10 min
2. 94oC 30 sec – Denaturation step
3. 58oC 30 sec - Annealing step
4. 72oC 1 min 50 sec (1 min per kb of DNA template) – Elongation step
5. Repeat Steps 2-4 30X
6. 72oC for 10min – Final extension step

Agarose Gel Electrophoresis

For visualizing and analysis, we will have to "run" the PCR products out on an agarose gel. Invitrogen’s E-gel system will be used.
This system is a complete buffer-less system for agarose gel electrophoresis. There is a pre-cast agarose gel (E-gel) that is a self-
contained gel that includes electrodes packaged inside a dry, disposable, UV-transparent cassette. The gel contains either Sybr-safe
or ethidium bromide for visualization of DNA. The E-gel runs in a single device that is both a base and a power supply, called the
E-gel Powerbase.
Protocol and images below is adapted from Invitrogen’s E-gel Technical Guide.
Materials
· DNA sample (from PCR reaction)
· 1KB Molecular weight markers
· Loading dye Mix

General guidelines
· Run gels stored at room temperature
· Keep samples uniform and load deionized water into empty wells
· Load gel within 15 mins of opening the pouch
· E-gel can only be used once

Procedure
Sample preparation and Loading gel:
Prepare your DNA samples by adding deionized water to the required amount of DNA to bring the total sample volume to 20ul.
1. The Lab Instructor will add the 1Kb Ladder to the gel.
2. Add 4ul of PCR reaction to new microcentrifuge tube.

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3. Add 16ul of Loading dye Mix to this microcentrifuge tube.
4. Once you set up the E-gel powerbase (below), load the entire 20ul volume to the correct gel well. Make sure to note which
gel well you loaded your sample into.

Setting up the E-gel Powerbase:

1. Plug the Powerbase into an electrical outlet using the adaptor plug.
2. Open the package containing the gel and insert the gel (with the come in place) into the apparatus right edge first. Press firmly at
the top and bottom to seat the gel in the base. You should hear a snap when it is in place. The Invitrogen logo should be located at
the bottom of the base, close to the positive pole. See diagram below. A steady, red light, indicates the E-gel is correctly inserted
(Ready Mode).

PCR Clean-Up
The PCR clean-up process is performed using a commercial product. Depending on the availability of the different commercial
kits, your TA will determine and provide the kit to use in lab. Directions will be provided with the kit.

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52: DNA Restriction and Electrophoresis has no license indicated.

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8.6: Results
Genotypic Analysis
16S rRNA PCR Results
After a 16SrRNA colony PCR on your unknown, a DNA sequencing reaction on the PCR products, and analysis of the sequence
via BLAST, what is the closest genus of our unknown organism?

Phenotypic Analysis
Culturing Results
Explain any culturing results here. Did you use any selective and/or differential media types to determine characteristics of your
unknown?

Biochemical Tests
Explain any biochemical tests results here. Tests could include enterotube results, carbohydrate fermentation, casein hydrolysis,
oxidase, catalase, tests etc.
Does the phenotypic results align with your genotypic results?

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8.7: Review Questions
1. Explain how a selective and differential media works.
2. MSA/mannitol salt agar is selective for what bacteria? how does the medium select for this population?
3. A MacConkey plate inoculated with an unknown bacterium does not grow. What can this tell you?
4. How does HE/Hektoen agar work to select and differentiate bacterial groups?
5. What is the advantage to a multi-test system like the Enterotubes?
6. Why is a combination of both phenotypic and genotypic methods ideal for identifying and characterizing a bacterium?

8.7: Review Questions is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

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Index
B C P
Bacterial Smear Capsule Staining Pipette
4.3: Lab Procedures- Bacterial Smear, Simple and 4.1: Introduction to Staining 5.2: Lab Procedures- How to operate a Pipettor
Gram Staining 6.1: Introduction to Oxygen Requirements
Bacteriophages 6.2: Temperature, pH, and Osmotic Requirements
G
6.4: Bacteriophages
Gram staining S
4.1: Introduction to Staining
growth media Silver staining
4.1: Introduction to Staining
2.1: Introduction Growth Media

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Glossary
Sample Word 1 | Sample Definition 1

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Detailed Licensing
Overview
Title: MB352 General Microbiology Laboratory 2021 (Lee)
Webpages: 65
Applicable Restrictions: Noncommercial
All licenses found:
Undeclared: 75.4% (49 pages)
CC BY-NC-SA 4.0: 20% (13 pages)
CC BY-SA 4.0: 4.6% (3 pages)

By Page
MB352 General Microbiology Laboratory 2021 (Lee) - 4.2: Specialized Bacterial Staining Techniques - CC
Undeclared BY-NC-SA 4.0
Front Matter - Undeclared 4.3: Lab Procedures- Bacterial Smear, Simple and
TitlePage - Undeclared Gram Staining - CC BY-NC-SA 4.0
InfoPage - Undeclared 4.4: Results - CC BY-NC-SA 4.0
Table of Contents - Undeclared 4.5: Review Questions - CC BY-NC-SA 4.0
Licensing - Undeclared 5: Enumeration of Bacteria - Undeclared
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5.2: Lab Procedures- How to operate a Pipettor - CC
Laboratory - Undeclared
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5.3: Lab Procedures- Viable Plate count - Undeclared
1.3: Review Questions - Undeclared
5.4: Results - Undeclared
Review Questions II - Undeclared
5.5: Review Questions - Undeclared
Review questions III - Undeclared
2: Cultivation of Microbes - Undeclared 6: Microbial Physiology - Undeclared

2.1: Introduction Growth Media - CC BY-NC-SA 4.0 6.1: Introduction to Oxygen Requirements - CC BY-
2.2: Introduction to Bacterial Growth and Aseptic SA 4.0
Techniques - Undeclared 6.1.1: Determining Oxygen Requirements and
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Broths, Slants and Plates - CC BY-NC-SA 4.0 6.2: Temperature, pH, and Osmotic Requirements -
2.4: Lab Procedures- Prepare solid media, Aseptic CC BY-SA 4.0
Technique, T-streaking - CC BY-NC-SA 4.0 6.3: Bacterial Growth Dynamics - Undeclared
2.5: Results - CC BY-NC-SA 4.0 6.4: Bacteriophages - Undeclared
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3.1: Introduction to the Microscope - Undeclared 6.6: Lab Procedures- Plaque Assay - Undeclared
3.2: Comparison of Sizes and Shapes of 6.7: Results - Undeclared
Microorganisms - Undeclared 6.8: Review Questions - Undeclared
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 7.5: Review Questions - Undeclared 8.5: Lab Procedures- PCR and Gel Electrophoresis -
8: Bacterial Identification - Undeclared Undeclared
8.1: Introduction to Bacterial Identification using 8.6: Results - Undeclared
Culture Media - Undeclared 8.7: Review Questions - Undeclared
8.2: Introduction to Bacterial Identification using Back Matter - Undeclared
Enterotube test - Undeclared Index - Undeclared
8.3: Introduction to Bacterial Identification using Glossary - Undeclared
Genotypic methods - Undeclared Detailed Licensing - Undeclared
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