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), SO4

2-(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

- NO3-

Can 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)