Chapter 1: Introduction to

Environmental Microbiology

Environmental Microbiology (EnEg2102)// By : Dr. Tsedekech G/mesekel// Year:2024/25

 Outline
• Microbiology and Environmental microbiology

• Biology of microbes
– Classification of microorganisms
– Internal and external cellular structures of microorganisms
– Ecological importance of major microorganisms

• Microbial ecology
 Learning outcomes
At the end of this lecture, students will be able to
• Define what environmental microbiology is
• Describe how microorganism are classified
• Differentiate between prokaryotic and eukaryotic
microorganisms
• Characterize major internal and external structures of
prokaryotes
• Discuss the ecological importance of major microorganisms
• Portray the types of ecological interactions among microbes
 Overview of Environmental Microbiology
• Microbiology: is a discipline which deals with microorganisms
• Microorganisms: living things that cannot be seen with our
naked eye
• Include:
• Cellular microbes: bacteria, archaea, fungi, protists (e.g.
algae, protozoa, slime molds, and water molds), and
• Acellular: virus and other infectious agents, such as prions
and viroids.
• Cellular microbes can be unicellular or multicellular
• So, the above traditional definition is modified to describe
microbes as fairly simple agents/organisms that are not highly
differentiated
Overview of Environmental Microbiology
 Overview of Environmental Microbiology
• Environmental microbiology:- is the study of the composition
and physiology of microbial communities in the environment
(soil, water, air , and sediments and other artificial environments)

• Environmental microbiology basically concentrates on the

application of microbes in resolving environmental problems.
– Water and Wastewater treatment
– Biogas production
– Solid waste management
 Overview of Environmental Microbiology
The field of environmental microbiology interfaces with a number of
different subspecialties, including;
• soil, aquatic, and aeromicrobiology
• bioremediation, water quality, occupational health and infection
control
• food safety, and industrial microbiology
 The mission of Environmental microbiologist:
To pursue the goal of environmental sustainability, which
defined as “ the utilization of environmental resources for the
benefit of human health and welfare without deterioration of the
physical environment or the biological communities contained
therein”.
Critical components of these biological communities are the
microbial communities housed within the environment.
The challenge for the environmental microbiologists is to enhance
the understanding of these communities in order to achieve
environmental sustainability
 Classification of Organisms
• Taxonomy: (Carl Linnaeus, Swedish) is a branch of biology that
names and classifies organisms based on their similarities and
dissimilarities.

Rank of taxonomic hierarchy

 Classification of Organisms
 Phenetic classification System: Groups do not necessarily
reflect genetic similarity or evolutionary relatedness. Instead,
groups are based on convenient, observable characteristics .
• Example: morphology and metabolism

 Phylogenetic Classification System: A system of classification

that groups organisms according to their evolutionary history.
– Phylogeny– studies the evolutionary tie between organisms by
comparing genetic (rRNA) materials
Classification of Organisms

Phylogenetic tree
 Classification of microorganisms

 Prokaryotes–have a free floating

chromosome (nucleoid), which is not
membrane bounded.
• They also lack other membrane
bonded organelles such as ;
mitochondria, endoplasmic
reticulum.

 Microbes under this class are;

• Bacteria
• Archaea
Prokaryotes
Small, 10-6 m = 1 μm
 Unicellular (∴self-sufficient)
• each cell is capable of independently caring out metabolism
for growth and reproduction
Diverse metabolism, physiology (20 million organic substrates)
• Produce energy in different ways (heterotrophic and autotrophic
 Adaptability → physiological
→ genetic
 Ubiquitous
• 106 cells/mL (natural waters)
• 109 cells/g (soils + sediments)
Prokaryotes

 The domain contains a wide variety of pathogenic and non

pathogenic organisms.

Cell Morphology
Bacterial shapes: coccus, rod, spirillum, spirochete, stalk, hypha,
filamentous
• Can not use cell morphology to identify a cell because some types take many
shapes.
Cell Morphology

Size:
• Bacteria and archaea (size varies with nutritional state): 0.1-600 μm (~ 1
μm avg.)
• Eukarya: 2-200 μm

Smaller cells have a higher surface volume ratio than larger cells, so
they (small) can take up nutrients more efficiently than big cells
because more surface per unit volume.

Starved cells shrink to increase Surface Area: Volume ratio so that they
can take up more nutrients relative to their size.
Chemical Composition
Bacteria/archaea:
Dry weight (DW):wet weight (WW) = 0.2-0.4
DW:WW ≅ 0.3 (avg). So, 70% H2O
Bacteria: DW (composition):
C: 50% P: 3%
C:N ≅ 5:1 O: 20% K: 2%
N: 14% S: 1%
H: 8% Ca, Mg, Cl: 0.05%
C, N, P are ~ constant because need a certain ratio to grow
Eukaryotes: DW:WW ~ 0.1 (90% H2O)
Bacterial Cell Walls

• Bactria's are further classified into two based on their cell wall
1. Gram Negative
First discovered by the Danish physician Hans Christian Gram F
2. Gram positive
 The primary component of bacterial cell walls is peptidoglycan.
• Peptidoglycan is a macromolecule composed of sugars and amino
acids that are assembled structurally like woven material.
 The cell walls of Gram positive bacteria differ structurally
from the cell walls of Gram negative bacteria on the bases of
peptidoglycan content.
 Bacterial Cell Walls

Gram positive (G+)

Peptidoglycan can represent up to 90% of the cell wall

The cell wall has additional component, teichoic acid, a

glycopolymer, which is embedded within the peptidoglycan layers

The thick layers also enable Gram positive bacteria to retain most
of the crystal violet dye during Gram Staining causing them to
appear purple.
 Bacterial Cell Walls

Gram negative (G-)

More complex than that of gram positive bacteria, with more
ingredients overall
Peptidoglycan represents 5-10% of the total cell wall
This thin layer does not retain the initial crystal violet dye but picks up
the pink color of the counter stain during Gram staining
Cell wall is covered by plasma membrane located outside of the
peptidoglycan layers, known as the outer membrane.
Cell wall is resistant to hydrophobic substances & desiccation.
Abundant in soil because can withstand drying up & hydrocarbons
released by plants.
`
 Surface Structures
Capsules:
is a polysaccharide layer that completely envelopes the cell
it is well organized and tightly packed
offers protection from a variety of different threats to the cell, such as
desiccation, hydrophobic toxic materials (i.e., detergents), and bacterial
viruses
can enhance the ability of bacterial pathogens to cause disease and can
provide protection from phagocytosis (engulfment by white blood cells
known as phagocytes)
Slime Layer
is a loose, unorganized layer that is easily stripped from the cell that
made it.
Serve the same function as Capsule
Surface Structures
 Surface Structures
Endospores:
Produced by some species of gram-positive bacteria such as Bacillus and
Clastridium spp.
Endurance stages: allows bacteria to withstand adverse conditions including
radiation, UV light, heat, desiccation, low nutrients, and chemicals
Some endospores have remained viable for 100,000 years!
 Appendages

Flagella (singular flagellum):

1 or more/cell, different from eukaryotic whip
Flagella allows bacteria to quickly move towards a point source of nutrient so they
can grow stronger than their competitors
Fimbriae (singular fimbria)
Numerous short surface appendages
Aids in attachment of cells to surface
• Important for initial colonization for biofilm formation and initiate an infection
process
Pili (singular pilus)
Normally less numerous than fimbriae but are longer
Only found in gram negative bacteria and involved in a mating process
Appendages
 Internal Structure
Ribosomes
Turn mRNA into proteins (translation)
Evolutionary significance: highly conserved structure & function!
Numbers of ribosomes in a cell are tightly linked to growth rate:
When cell lacks nutrients, it eats its own ribosomes to survive
(shrinks) because ribosomes make up much of all volume.
Cytoplasm
The gel-like fluid that fills each cell, providing an aqueous
environment for the chemical reactions that take place in a cell
 It is composed of mostly water, with some salts and proteins
 Internal Structure
DNA – deoxyribonucleic acid or DNA
 The genetic material of the cell, the instructions for the cell’s abilities and
characteristics.
Complete set of genes, referred to as a genome, is localized in an irregularly-
shaped region known as the nucleoid in bacterial and archaeal cells, and
enclosed into a membrane-bound nucleus in eukaryotic cells.
Plasmids: Extra chromosomal DNA that often confers a comitative
advantage to the cell e.g., antibiotic resistance

Typical Prokaryotic Cell. Typical Eukaryotic Cell

 Ecological importance of bacteria

• Bacteria’s are used to remove pollutants from contaminated water,

soil and subsurface material.
• Bacteria, in particular, are the only living things that can fix
nitrogen for use in plants.
• They increase the fertility of the soil and increase crop yields,
• Nutrient cycling and the cycles of elements that make up Living
systems (C,H,N,P, and S)
• They sustain aquatic life: Primary producers in marine environment
are phytoplankton's
Archaea

Archaea– many of them are extremophiles (extreme

temperature, pH, and in high salt concentration
– Some live in the presence of O2 others strict anaerobes
Archaea cell wall lacks peptidoglycan
Ecological importance of Archaea: they have grate role
in
• Nutrient Cycling
• Decomposition of organic matter
 Eukaryotes

Microorganisms grouped under this group are:

• Protozoa,
• molds and yeasts
• Microscopic algae
Protozoa
 Are unicellular organisms
 They vary in size: some are as small as bacteria (2-6 µm) some
can be observed by the naked eye (mm in size).
 Eukaryotes
They are found in
• Varity of Fresh water
• Marine
• Some can grow in soil and
wastewater sludge.
Vorticella ciliate in compost heap
• some can survive and reproduce in
extreme environment
They can be
• Free living
• Parasitic
Paramecium in fresh water
 Eukaryotes

Ecological importance of protozoans

• Protozoa have an important role in nutrient recycling
• Help to sustain bacterial populations and stimulate the
mineralization of compounds.
• They aid in particulate removal and reduction of bacteria via
flocculation and grazing (WWT)
• Environmental quality indicators (euglena in water )
 Eukaryotes
Fungi
Fungi belong to a group of eucaryotic organisms which are the
absolute heterotrophs
They generally have rigid, polysaccharide-rich cell walls.
They produce spores by means of sexual and asexual reproduction
They absorb nutrients through their cell membranes
 Eukaryotes
Ecological importance of fungi
Fungi can be able to decompose recalcitrant organic compounds →
degrade complex polymers, important in waste degradation and
recycling
Yeast generally ferment sugars → produce a variety of useful by-
products such as ethanol, acetic acid, and lactic acid.
Pharmaceutical importance: penicillin produced by Penicillium
notatum
They enhance plant biodiversity and help to control pests such as
nematodes and fungal pathogens.
They supply nutrients (phosphate) to plants in case of unfertile soil
(mycorrhizas)
 Eukaryotes
Algae
Algae are a group of eukaryotic oxygenic photosynthetic
microorganisms that contain chlorophyll a
Can grow as single cells, in colonies or filaments.
all algae's are not microorganisms.
They live both in terrestrial and aqueous environment
 Eukaryotes

Environmental importance of microbial algae

 They are used as of environmental monitoring tools (Diatoms in
water quality studies)
 They form the bases of aquatic food chains (phytoplankton's –
floating communities of microbial algae in water )
 They are important in the initial colonization of disturbed
terrestrial environment.
 Eukaryotes

Environmental importance of microbial algae

 They are used as of environmental monitoring tools (Diatoms in
water quality studies)
 They form the bases of aquatic food chains (phytoplankton's –
floating communities of microbial algae in water )
 They are important in the initial colonization of disturbed
terrestrial environment
 Eukaryotes

Negative effect (Eutrophication in aqueous environment

and some species produce toxins)
 Microbial ecology
 Microorganisms interact with other communities, populations
and species and also with a-biotic environment
Microbial Ecology – Studies the interactions between microbes
& their environments
 Microbial ecology
Types of microbial interaction
Positive interaction: (symbiosis )
• mutualism,
• commensalism
Negative interaction:
• Ammensalism (antagonism),
• parasitism,
• predation,
• competition
 Microbial ecology
 Mutualism
• When the two different population /species interact in such a
manner that it is beneficial to each other.
• Lichens are a classic example of mutualism in between fungi and
algae.
• The alga can be either a green alga or a blue-green alga
(cyanobacteria).
• Algae provide nutrient to the fungi
• Fungi provides the algae water and minerals and creates a firm
substratum within which the algae can grow protected from
environmental stress , excess light intensity.
 Microbial ecology
 Lichens are very important organisms for air quality monitoring
 One of the ways lichens directly benefit humans is through their
ability to absorb everything in their atmosphere, especially
pollutants.
 One can extract these toxins and determine the levels that are
present in our atmosphere.
 Microbial ecology
• Rhizobium: Relation of nitrogen fixing bacteria and legume
plant (require host plant)
• Mycorrhiza: Relation between fungus and root of higher
plants
 Microbial ecology
 Commensalistic relationships between microorganisms
include situations in which the waste product of one
microorganism is the substrate for another species ( when
one microbial group modifies the environment to make it
more suited for another organism )
• Microbial succession during spoilage of milk – fermenting bacteria
promote growth of acid tolerant species
• Formation of biofilms – initial colonizer helps other
microorganisms attach
 Microbial ecology
 Competition arises when different microorganisms within a
population or community try to acquire the same resource,
whether this is a physical location or a particular limiting
nutrient.
• Competition inhibits both population from occupying exactly same
ecological niche because one will win the competition and the other one
is eliminated.
• When competition between species results in the elimination of one
species from a given habitat or region (competitive exclusion)
 Microbial ecology
 Predation
• This interaction is a very important one as it ensures that there is stability
in the ecosystem. The two main populations interacting in predation are
the predators and the prey.
• Without the predators, the prey population will go out of control. The
species diversity in a community is also maintained by the predators.
• They reduce the intensity of the competition between prey species. The
prey species have also evolved several mechanisms to lessen the impact
of predation
 Microbial ecology
 Amensalism (antagonism)
• When one microbial population produces substances that are inhibitory to
other microbial population then this inter population relationship is
known as Ammensalism or Antagonism.
• The first population which produces inhibitory substances are unaffected
or may gain competition and survive in the habitat while other
populations get inhibited. This chemical inhibition is known as antibiosis
• E.g. Thiobacillus thioxidant produces sulfuric acid by oxidation of sulfur
which is responsible to lowering of pH in the culture media which
inhibits the growth of most other bacteria.