Microbial Ecology- Part I

1. Definition of Microbial ecology

Microbial ecology is the study of relationship between microbes

and their surrounds (environments).

2. Importance of microbial ecology

Biased image of the role of microbes in nature obtained from

laboratory studies of pure culture cultures ie data leads to
inappropriate conclusions about their relevance. Eg. E. coli
grows in animals intestinal tracts but merely survive in aquatic
environments ie E. coli are transients and not residents of
aquifers from which they can be isolated.
Misconception that as microbes are small, they are irrelevant
and do not have important and significant roles to play in the
environment. Another misconception is that if they are found
in an environment that are nusiance rather than of any
importance. Eg importance on skin, in the gut, in the rumen
and in the rhizosphere.(see topic B for details)
Importance in biotechnology: Studies in microbial ecology leads
to knowledge of bidiversity. Microbial diversity can be
exploited for biotechnology.
Microbial ecology studies entail the use of conventional
microbiological techniques (cultural / enumeration procedures,
EM, radioactive tracer methods) and modern molecular
techniques (gene analysis, nuclei acid probes, sequencing) (see
topic C for details).

3. Structure of Microbial Communities in an Environment

A typical ecosystem is dynamic. Environmental (abiotic) and

biotic interactions are an ongoing occurrence (Figure).
4. Organisation of the Microbial Community in an
Environment

Microbes have developed strategies which enable them to survive:

Survival and growth by structural adaptation. eg alkaline soda
lakes, saline lakes, hot springs, desert soils.
Nutrient adaptation in case of r strategists & k strategists
 

r-strategists k-strategists

High reproduction rate allows survival Low reproduction rates

High nutrients enables rapid growth to Low nutrients available ie nutrient limiting
outcompete other cells conditions.
Crowded conditions exist Less crowded
Subject to extreme population fluctuations when More permenant and stable members of the
nutrients are depleted community
Ex: Cyanobacterial blooms due to PO4,
Ex: Spirilla and vibrios in marine environments,
Pseudomonas responds to increased carbon prostecate bacteria in oligotrophic lakes
source

5. Colonization & succession within microbial communities

 Community structures evolves with time. Its stability depends
on the interactions or interrelationships amongst populations
and the adaptaion of these populations to the environment as
seen in the figure above.
Gastrointestinal (GI) tract of new born is sterile. "Pioneer"
microbes colonise first (primary succession) --- grow to change
or alter the environment, "secondary" succession, (usually
replace the pioneers). The final stable community forms,
"climax" community.
Mice: Flavobacterium, Lactobacillus & enterococci are the
pioneers. Flavobacterium disappear in 8 days and
lactobacilli in 18 days.; Bacteroides (strict anaerobes)
increase and dominate the climax community.
Humans: Lactobacillus is the pioneer, which leads to
succession by facultative anaerobes (E. coli & S. faecalis);
Bacteroides dominate the climax community (after solid
food ingestion).
Ruminants: Climax communities include cellulose
decomposers (Bacteroides, Ruminococcus), protein
degraders (Veillonella), starch degraders (Selenomonas), and
methane producers (Methanobacterium).
 

6. Interactions within a single microbial population

Positive interactions (cooperation):

extended lag phase or failure to grow if small inoculum is
used (10% inoculum used). Cells leak low molecular weight
essential biosynthesis metabolite/ High density means loss is
counteracted by reabsorption. Low density means loss
exceeds replacement. May lead to problems in isolating
pure cultures. "95% of microbes elude cultivation" Use of
filter sterilized spent culture filterate containing the
essential metabolite can be used in preparing media for
such work.
Pathogenicity associated with "minimum infectious dose"
 (MID). A single cell rarely overcomes host defenses.
In nature, microcolonies rather than individual cells are
observed.
An inhibitor is less effective on a dense culture rather than
a sparse culture.
Transformation, transduction conjugation occurs more
efficiently at high densities than at low densities (genetic
exchange of antibiotic ressistance genes, heavy metal
ressistance genes, genes which provide ability to utilize
unusual organic sustrates).
Negtive Interaction (competition)
High densities can lead to accumulation of toxic products.
 

7. Interactions between diverse microbial populations

 Intearction between two microbial populations can positively or

negatively affect one or both populations; a neutral outcome is also
possible.

(a) Synergism:

Synergism (protocooperation): Both populatiosn benefit but the

association is not obligatory and both populations can survive
on their own. However, the association provides some mutual
benefits.
It can be difficult to judge whether the relationship is
mutualistic (mutualism is an obligatory association), synergistic
(not obligatory) or a commensalistic one (one population can
replace the other).
Some examples of synergism.
Synthesis of a product which neither populations can
perform on their own: For example, completion of a
pathway. This type of synergism is known as syntrophy.
(Figure)
 Close spatial relationships between microorganisms: For
example bacteria are often seen on surfaces of algae due to
chemotaxis.
Metabolism of toxic end-products: Pseudomonas produces
organic end-products compounds from orcinol which are
utilized by secondary microbes for  growth. These end-
products would have otherwise inhibited growth of 
Pseudomonas.
Production of degradative enzymes: Arthrobacter and
Streptomyces (soil flora) produces enzymes which
collectively degrade diazinon, an organophosphate pesticide
(useful in the degradation of xnobiotics or recalciterant
compounds).

(b) Mutualism (Symbiosis):

Obligatory relationship in which both partherners act as if they

were one (endosymbiotic theory)
Highly specific & cannot be replaced by another partner
Requires physical proximity
Some examples:
 Lichens: Association of algae or cyanobacteria with fungi.
Found as green adhesive material on rock surfaces. enables
tolerance to low humidity.
Protozoal endosymbiononts: Association of Paramecium
(amoeba) and Chlorella (green algae but red algae can also
work);  Chlorella allows Paramecium (aerobic) to enter
anaerobic zones provided there is light during which
Chlorella generates O2 for the Paramecium. Paramecium
provides protection, motility and CO2 for food production.
Rumen produce propionic acid and termite GI tract
microbes produce acetate which are adsorbed and
converted to glucose and used as an energy source (animals
adsorb ingested glucose). Coevolution of host and symbiotic
microbes
Specialised organs beneath each eye of flash light fishes are
packed (1010 cells/ml fluid) with  luminiscent
Photobacterium or Vibrio species.
   FMNH2 (Flavin mononucleotide) + RCHO (long chain
aliphatic aldehyde) is oxidised (ie in the presence of O2)
to  FMN (Flavin mononucleotide) + H20 + RCOOH in the
presence of bacterial luciferase enzyme and as a
consequence, light is emitted. The light can be turned off
by a black shutter which can be lowered or raised by the
fish.
Used for protection or for luring a prey.
Mycorrhizae (fungus root): Fungi + roots of higher vascular
plants. Increases root surface area for adsorption
Endomycorrhizae (fungus inside roots): in 80% of the
roots of vascular plants
Ectomycorrhizae (surround the roots)
Root nodulating bacteria: Rhizobium and Bradyrhizobium
associated with leguminous plants fix nitrogen (Symbiotic
nitrogen fixation).

 
  (c) Amensalism (Antagonism):

When one microbial population produces a substance that is

inhibitory to another population is known as amensalism. The
population producing the inhibitor is not affected and therfore
gains a competitive edge.
E. coli cannot grow in the rumen due to presence of high
amounts of  lactic acid produced by rumen anaerobes.
Fatty acids produced on the skin by skin microflora restrict
growth of unwanted pathogens.
O 2 production by algae precludes growth of anaerobes.
High concentrations of ethanol (eg wine production)
precludes most microbes other than the yeasts. However,
Acetobacter converts ethanol to acetate if O2 is present.
Lactate and propionate production in cheese manufacturing
and acetic acid in vinegar inhibit spoilage causing microbes.
A fungus, Trichophyton mentagrophytes, is the normal flora
of NZ hedgehogs and produces penicillin. The only other
population on the hedgehog skin surface are penicillin-
ressistant Staphylococcus.
Bacteriocins are bacterial defenses that  help in preserving
food:
Bacteriocins are heat stable peptides, are readily
digested in the GI tract, are non-toxic, non-allergic and
are already consumed in food (eg cheese).
Nisin is a bacterocin produced by Lactococcus lactis and
is an approved food preservative in cheese
manufacturing.  It inhibits Clostridium sporogenes
endospore germination and kills Salmonella.
Nisin and other antibiotics act by attaching themselves
to plasma membrane therebye destabilising membrane
permeability and decreases the proton motive force
required to make ATP.
The operon that codes for the gene also carries a gene
for resistance and hence the cells producing the
bacteriocins do not get inhibited.
 Some bacteriocins that show promise against pathogens
are listed in the table
 
Bacteriocin Produced by Bactericidal against

Lactocin S Lactobacillus sake Gram-positive bacteria

Propioncin Propionibacterium thoenii Gram-negative bacteria

Plantacin Lactobacillus plantarum Inhibits endospore germination