Microbial Ecology- Part I

• Microbial ecology is the study of relationship between microbes and their surrounds (environments).

• 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).

• A typical ecosystem is dynamic. Environmental (abiotic) and biotic interactions are an ongoing occurrence (Figure).

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

• 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).

• 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.

 Intearction between two microbial populations can positively or negatively affect one or both populations; a neutral outcome is also possible.

• 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).

• 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).

• 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.
• O₂ 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