Microbial Ecology

• Ecology: interactions among living things and their environments– Think globally act locally: microbes metabolize in

microenvironments, resulting in global changes– Microbes interact with each other– Microbes interact with eukaryotes, metazoans

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Microbial Communities

• Pure cultures are laboratory artifacts– Habitats support mixed groups of microbes

• Microbes both compete and cooperate– Nutrients in short supply, many used by most microbes– Sugars, amino acids rapidly consumed– Cooperation a result of adaptation to particular niches

• Niche: more role than location

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Cooperation and niches3

Oxygen diffusing into pond supplies aerobes.

Diffusion limited in pond sediment; facultative anaerobes consume oxygen, maintaining anaerobic environment for strict anaerobes.

Fermentation products (e.g. lactic acid) diffuse to aerobic zone; acids are good nutrient sources for aerobes.

Cooperation and biogeochemical cycling4

Based on: www.soils.umn.edu/.../soil2125/doc/s9chap2.htm

Degradation of organic N from biomass releases ammonia;Ammonia oxidized to nitrite for energy (e.g. Nitrosomonas)Nitrite oxidized to nitrate for energy (e.g. Nitrobacter)Nitrate N can be used by plants.

Assimilation vs. Dissimilation

• Bacteria require elements to grow (assimilation)– Sulfate reduced to sulfide for amino acids– Ammonium released from organics for amino acids– Reactions occur to the extent needed for biomass

• Other chemicals needed as electron sources or sinks– Sulfate serves as electron sink, converted to sulfide– Ammonium serves as energy source, is oxidized– Amino acids broken down for carbon, excess N excreted– Dissimilation: much larger quantities of chemicals

converted into different forms.

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Bacteria Environment

• Bacteria are adapted to their environment– Anaerobes can’t grow where there is oxygen– Acidophiles require low pH– Thermophiles require heat

• But bacteria can change the environment– Fermenting bacteria maintain low pH for themselves– Ecological succession

• Aerobic bacteria use up O2, anaerobes begin to grow

• Degradation in compost raises temperature; thermophiles take over

• Fermentation lowers pH

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Biogeochemical cycles

• Carbon– Photoautotrophic bacteria fix CO2, heterotrophs release it

– Large geological reservoirs; carbons moves quickly through living things

• Nitrogen– Multiple redox states of N, moves through soil, water, air

• Phosphorous– Mostly as phosphate; removed from rocks and cycled

• Various other nutrients and other elements:– Sulfur, iron, even mercury

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Bacteria frequently attached

• Bacteria in nature are attached to soil particles, polymeric debris (decaying leaf litter), other bacteria– Seek, associate with nutrient sources– Use fimbriae, slime to attach– Form pellicles at water surface– Grow clumped in lab

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http://publications.nigms.nih.gov/insidethecell/images/ch3_wbc.jpg

http://ec.europa.eu/research/headlines/news/images/19_11_07_small.jpg

Biofilms

• Communities of microbes attached to a surface– Surface may be a nutrient source

• Organic molecules absorb to surfaces, also– Multiple species with different niches represented– Cells use fimbriae and slime to adhere– Channels allow diffusion of nutrients (in) and waste (out)– Quorum sensing helps direct remodeling of structure– Cells move within biofilm; cells and pieces of biofilm

can leave and colonize new areas– Part of food web; provide nutrients for protozoa

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Biofilms can be problems

• Industrially– Plug pipes, stimulate corrosion, impair heat exchangers– Biocides less effective; only surface layers killed.

• Medically– Infections can lead to colonization of artificial structures– Heart valves; seed infections elsewhere in the body– Difficult for antibiotics to completely rid infection

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http://prometheus.mse.uiuc.edu/glossary/biofilms/lifecycle.png

Finding a bacterium from a niche

• Enrichment culture– Increasing the size of a specific population by specifying

what nutrients it can use– To find a bacterium in a mixed population that can:

• Use phenol: supply phenol as sole carbon source

• Use N2 as N source: provide no other N.

• Enrichment conditions can be provided– To get an anaerobe, grow without oxygen– To get a psychrophile, grow in the cold– Starting material should reflect desired properties

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