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Microbial ecology
The study of the interactions of microorganisms with each other
and their nonliving physical environment
Environmental microbiology relates to the broad-scale effects
microorganisms and their activities have on the planet
Microbial interactions
Some interactions can be beneficial
for both participants
(mutualism and cooperation)
Some interactions benefit one
participant but do not affect the
other (commensalism)
Some interactions benefit one
participant at the expense of the
other (predation and parasitism)
Mutualism
An obligatory relationship in which the mutualist and the host are
metabolically dependent on each other
Examples include the tube worm-bacterial relationship and the
rumen ecosystem
The tube worm-bacterial relationship
Tube worm hemoglobin transports H2S to bacteria
Bacteria fix CO2 using reducing power of H2S
Tube worm supplied with organic molecules by bacteria
The rumen ecosystem
Ruminants are herbivorous
animals (cattle, deer, sheep, etc.)
Require microorganisms to
degrade cellulose
Anaerobic process produces CO2,
H2 and CH4
Cooperation
Both organisms benefit but the
interaction is not obligatory
Organisms can exist separately if
required nutrients are supplied in
the growth environment
Commensalism
A relationship in which one symbiont (the commensal) benefits
while the other (the host) is not harmed
The commensal feeds on substances captured or ingested by the
host
Commensals can become pathogens under certain circumstances
Predation
Relationship in which a predator
attacks or engulfs a prey
Predator may be larger or smaller
than the prey
Predation may have beneficial
results for the prey (protection or
enhancement of virulence)
Parasitism
One organism benefits and the other is harmed
The line between parasitism and predation is hard to define
(parasitism may eventually lead to predation)
Parasitism usually is a long-term relationship whereas predation
tends to end abruptly
Amensalism
One organism produces a
compound that has a negative
effect on another organism
Production of antibiotics by
certain bacteria is an example of
amensalism
Competition
Microorganisms can compete for a
physical location or a limiting
nutrient  2 possible outcomes
1. One organism may outcompete
the other
2. Both organisms may co-exist at
lower levels
Biogeochemical cycling
Cycling of nutrients in the
environment involving both
biological and chemical processes
Nutrients are transformed (often
by oxidation-reduction reactions)
and cycled
Biogeochemical cycling
Influence of oxygen on organic matter decomposition
Oxidized products will
accumulate when decomposition
occurs under aerobic conditions
Reduced products will
accumulate when decomposition
occurs under anaerobic
conditions
Mineralization
The release of excess nitrogen and other minerals into the
environment as a result of the decomposition of organic matter
The carbon cycle
Carbon exists in reduced forms (CH4 and organic matter) and
oxidized forms (CO and CO2)
Photosynthetic organisms fix carbon (reduced form)
The carbon cycle
Respiration produces oxidized form  CO2
Methane is generated under anaerobic conditions
(eventually oxidized to CO2)
The sulfur cycle
H2S can serve as an electron donor
for photosynthetic bacteria
H2S(ide)  Sº, SO32-(ite), SO42-(ate)
Different oxidized forms of sulfur
diffuse into a reduced environment
Other bacteria perform dissimilatory
and assimilatory reductions
The nitrogen cycle
Requires several different processes including:
Nitrification
Denitrification
Nitrogen assimilation
Nitrogen fixation
Nitrification
Involves the aerobic oxidation of ammonium ion to nitrite and
then to nitrate
NH4+  NO2-  NO3Can occur anaerobically by coupling oxidation of NH4+ with
reduction of NO2- to produces nitrogen gas (N2)
Commercial process referred to as the anamox process
(anoxic ammonium oxidation)
Denitrification
Use of nitrate as an electron acceptor in anaerobic respiration
(dissimilatory reduction)
NO3-  NO2 -  N2O  N2
Nitrogen assimilation
NH4+ can be directly incorporated into organic matter
NO3- assimilation is much more energetically expensive
Nitrogen fixation
Carried out by both aerobic and anaerobic prokaryotes
Cannot be carried out by eukaryotes
Nitrogen fixation
Involves a sequence of reduction steps that require major
expenditures of energy
Produces ammonia which is immediately incorporated into
organic matter
The iron cycle
Cycling between ferrous (2+) and ferric (3+) forms of iron
Iron reduction occurs under anaerobic conditions
Other cycles
Manganese and other metals cycle between oxidized and reduced
forms
Cycling of different elements may be metabolically linked
(e.g. Desulfobulbus propionicus oxidation of sulfate is linked to
the reduction of manganese)
The physical environment
Microorganisms occupy specific
environments in nature referred to
as microenvironments
Fluxes and gradients of nutrients,
reductants and oxidants and waste
products will influence the rate of
growth and create a unique niche
The physical environment
Biofilms and microbial mats are microenvironments or niches
created by microorganisms
Microorganisms and ecosystems
Microorganisms play two complementary roles in ecosystems
Primary production - the synthesis of organic matter from CO2
and other inorganic molecules
Microorganisms and ecosystems
Consumption and decomposition - the breakdown of organic
matter with the release of energy and inorganic molecules
Extremophiles
Some microorganisms have evolved to survive in extreme
environments  extremophiles
Extreme environments include:
High sodium concentrations
High pressure
Extreme acidic or alkaline conditions
High temperature
Microorganisms existing in such environments must possess
unique adaptations
Extremophiles
Methods used in microbial ecology
Isolation of organisms from environmental samples
Standard media does not support the growth of many
microorganisms
PCR amplification and sequencing of extracted DNA
Extracted DNA may not be representative of living
microorganisms
Methods used in microbial ecology
Direct observation - slides or EM grids placed in location,
recovered and observed
Methods used in microbial ecology
Microbial activity and turnover rates at which nutrients are
incorporated into organic matter can give an indication of the
metabolic activity of a microbial population
Often make use of radioactive isotopes
Methods used in microbial ecology
Recovery or addition of individual microorganisms - individual
microorganism may be removed and DNA analyzed after PCR
Methods used in microbial ecology
Microorganisms with reporter genes may be placed into
environments to monitor specific changes
(e.g. oxygen availability or UV radiation exposure)