Advanced Microbiology

MICROBIAL ECOLOGY

Population, Guilds, andCommunitiesIn nature, individual microbialcells grow to formpopulations. Metabolicallyrelated populations are calledguilds, and sets of guildsinteract in microbialcommunities. Microbialcommunities in turn interactwith communities ofmicroorganism and theenvironment to define theentire ecosystem.

Microbial Ecology

Microbial Ecosystems

Environments and MicroenvironmentMicroorganism are very small and their habitats are

likewise very small. The microenvironment is the place in whichthe microorganism actually lives. Microorganism in nature oftenlive a feast-or-famine existence such that only the best-adaptedspecies thrive in a given niche. Cooperation among microorganismis also important in many microbial relationships.

Major resources and conditions that govern microbial growth in nature

Resources

Carbon (organic, CO2)Nitrogen (organic, inorganic)

Other macronutrients (S, P, K, Mg)

Micronutrients (Fe, Mn, Co, Cu, Zn, Mn, Ni)

O2 and other electron acceptor (NO3-, SO42-, etc)

Inorganic electron donors (H2, H2S, Fe2+, etc)

Conditions

Temperature: cold – warm - hot

Water potential: dry – moist – wet

pH: 0 – 7 – 14

O2: oxic – microoxic – anoxic

Light: bright light – dim light - dark

Osmotic conditions: freshwater – marine -hypersaline

Microbial Ecology

Microbial Growth on Surface and Biofilms• Oftentimes microorganism grow on surfaces enclosed in biofilms-

assemblages of bacterial cells attached to a surface and enclosedin adhesive polysacharides excreted by the cells. Biofilms trapnutrients for growth of the microbial population and help preventdetachment of cells on surfaces present in flowing system.

Why do bacteria form biofilms?1. Type of defense2. Allows cells to remain in a favourable niche3. Allow bacterial cells to love in close association with

each other4. The typical way bacterial cells grow in nature

Microbial Ecology

Microbial Ecology

Formation of a Bacterial Biofilm

Microbial Ecology

A biofilm of iron oxidizingprokaryotes on thesurface of rocks in theiron-rich Rio Tinto,Spain.

Photomicrograph of aDAPI-stained biofilm thatdeveloped on a stainless

steel pipe. Note thewater channels.

Terrestrial EnvironmentsThe soil is a complex habitat with numerousmicroenvironments and niches. Microorganisms are present inthe soil primarily attached to soil particles. The most importantfactor influencing microbial activity in surface soil is theavailability of water, whereas in deep soil (the subsurfaceenvironment) nutrient availability plays a major role.

Microbial Ecology

Soil and Freshwater Microbial Habitats

A soil aggregate composed ofmineral and organic components,showing the localization of soilmicroorganisms.

Freshwater Environments

•Typical freshwater environments are lakes, ponds, rivers,and springs.

•The predominant phototrophic organisms in most aquaticenvironments are microorganisms. In oxic areascyanobacteria and algae prevail, and in anoxic areasanoxygenic phototrophic bacteria dominate.

•Most of the organic matter produced is consumed bybacteria, which can lead to depletion of oxygen in theenvironment.

•BOD is a measure of the oxygen-consuming properties ofa water sample.

Microbial Ecology

Marine Habitats and Microbial Distribution

•Marine waters are more nutrient deficient than manyfreshwaters, yet substantial numbers of microorganismsexist there. Many of these use light to drive ATP synthesis.•In terms of prokaryotes, species of the domain Bacteria tendto predominate in oceanic surface water whereas Archaeaare more prevalent in deeper water.•The dominant phototroph in subtropical open oceanicwaters are prochlorophytes.

Microbial Ecology

Marine Microbiology

Percentage of totalprokaryotes belonging toeither the Archaea or theBacteria in North PasificOcean Water.

Microbial Ecology

Deep-Sea-Microbiology• The deep sea is a cold, dark habitat where high hydrostatic

pressure and low nutrient availability prevails.• Bacteria isolated from depths below 100 m are Psychrophilic

(cold-loving) 2-3oC. Some are extreme Psychrophiles.• Deep-sea microorganism must also be able withstand the

enormous hydrostatic pressures associated with great depths.Some organisms simply tolerate high pressure; they are calledbarotolerant. By contrast, others actually grow best underpressure; these are called barophilic.

• In even deeper water (10,000 m) extreme (obligate)barophiles can be found. For example, the bacteriumMoritella, isolated from the Mariana Trench (Pasific ocean,>10,000 m depth), 700-800 atm.

Microbial Ecology

Hydrothermal Vents• Hydrothermal vents are deep-sea hot springs where volcanic

activity generate fluids containing large amounts of inorganicenergy sources that can be used by chemolithotrophicbacteria.

• Two major types of vents have been found. Warm vents emithydrothermal fluid at temperature of 6-23oC. Hot vents,referred to as black smokers because the mineral-rich hotwater forms a dark cloud precipitated material upon mixingseawater, emit hydrothermal fluid at 270-380oC.

• Deep-sea hydrothermal vents are habitats where primaryproducers are chemolitotrophic rather than phototrophic.

• Some vents contain nitrifiying, hydrogen-oxidizing, iron-, andmanganase-oxidizing bacteria, or methilotrophic bacteria.

Microbial Ecology

Deep Sea Hot Springs: Hydrothermal Vents

Microbial Ecology

Microbials Leaching of Ores

•Oxidation of copper ores by bacteria can lead to thesolublelization of copper, a process called microbial leaching.•Leaching is important in the recovery of copper, uranium, andgold from low-grade ores.•Bacterial oxidation of iron in the iron sulfide mineral pyrite is alsoan important part of the microbial-leaching process because theferric iron produced is itself an oxidant of ores.

Microbial Ecology

Microbial Bioremediation

Arrangement of a leaching pile and reactions involved in themicrobial leaching of copper sulfide minerals to yield Cuo

Mercury and Heavy MetalTransformation•A major toxic form of mercuryis methylmercury. The lattercan yield Hg2+, which is reducedby bacteria to Hgo.•The ability of bacteria to resistthe toxicity of heavy metals isoften due to the presence ofspecific plasmid that encodeenzymes capable of detoxifyingor pumping out the metals.

Microbial Ecology

Mechanism of Hg2+ reduction toHg0 in Pseudomonas aeruginosa

Microbial Ecology

Biogeochemical Cycling of Mercury

Biodegradation of Xenobiotics• Xenobiotics are synthetic chemicals that are not naturally

occuring subtance.• Many chemically synthesized compounds such as insectiside,

herbicides, and plastics are completely foreign tomicroorganisms but can often be degraded by one or anotherprokaryote nonetheless.

Microbial Ecology

Pathway of aerobic 2,4,5-T biodegradation

The Plant Environment

•Key microbial habitats on plants include the rhizoplane/rhizosphere and the phyllosphere.

– Rhizosphere is the region immediately outside the root; it is azone where microbial activity usually high.

– Rhizoplane is the actual root surface.– Phyllosphere is the surface of the plant leaf.– Phylloplane is the actual plant leaf surface

Microbial Ecology

Microbial Interaction With Plants

Lichen structurec

A Lichen growing on a branch of a dead tree

Microbial Ecology

Lichens and Mycorrhizae• Lichens are symbiotic associations between a fungus and an

alga or corynobacterium.

bLichens coating the surface of a large rock

a

• Miccorrhizae are formed from fungi that associate with plantroots and improve their ability to absorb nutrient.Mycorrhizae have a great beneficial effect on plant health andcompetitiveness. ectomyorrhizae: fungal cells form an extensive sheath around the

outside of the root with only little penetration into the root tissue itself. endomycorrhizae: the fungal mycelium becomes deeply embedded

within the root tissue.

Typical ectomycorrhizal root of the pine.Pinus rigida with Thelophora terrestis

Seeding of Pinus contorta , showing extensivedevelopment of the absorptive mycelium.

Agrobacterium and Crown GallDisease•The crown gall bacteriumAgrobacterium enters into a uniquerelationship with higher plants.•A plasmid in the bacterium (the Tiplasmid) is able to transfer part ofitself into the genome of the plant,in this way bringing about theproduction of crown gall disease.•The crown gall plasmid has alsofound extensive use in the geneticengineering of crop plant.

Microbial Ecology

Crown Gall

Root Nodule Bacteria and Symbiosis With Legumes

• One of the most widespread and important plant-microbialsymbioses is that between legumes and certain nitrogen fixingbacteria.

• The bacteria induce the formation of root nodules within whichthe nitrogen-fixing process occurs.

• The plant provides the energy source needed by the root nodulebacteria, and the bacteria provide fixed nitrogen for the growthof the plant.

• Legume root nodule bacteria play an important agricultural rolebecause many important crop plants are legumes.

• Other nitrogen-fixing symbioses include the water fern Azollaand the nodule-forming Frankia.

Microbial Ecology

Soybean root nodules. Thenodules develop by infection withBradyrhizobium japonicum.

Microbial Ecology

Effect of nodulation on plantgrowth. A field of unnodulated (left)and nodulated (right) soybeansplants growing in nitrogen-poor soil.

Stages in Root Nodule Formation

1.

2.3.4.

5.

6.

Recognition of the correct partner on thepart of both plant and bacterium andattachment of the bacterium to root hairs.Excretion of nod factors by the bacterium.Bacterial invasion of the root hair.Travel to the main root via the infectionthread.Formation of modified bacterial cells,bacteroids, within the plant cells anddevelopment of the nitrogen fixing state.Continued plant and bacterial division andformation of the mature root nodule.

Microbial Ecology

Microbial Ecology

The Infection Thread and Formation of Root Nodules

An infection thread formed by cellsof Rhizobium leguminosarum

Nodules from alfafa roots infected with with cells of Sinorhizobium meliloti