Download Microbial Ecology

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 niches
Oxygen diffusing into
pond supplies aerobes.
Fermentation products (e.g.
lactic acid) diffuse to aerobic
zone; acids are good nutrient
sources for aerobes.
Diffusion limited in
pond sediment;
facultative anaerobes
consume oxygen,
maintaining anaerobic
environment for strict
anaerobes.
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Cooperation and biogeochemical cycling
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.
Based on: www.soils.umn.edu/.../soil2125/doc/s9chap2.htm
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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
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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
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• 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
Bacteria frequently attached
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• Bacteria in nature are attached to soil particles,
polymeric debris (decaying leaf litter), other bacteria
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–
–
–
Seek, associate with nutrient sources
Use fimbriae, slime to attach
Form pellicles at water surface
Grow clumped in lab
http://ec.europa.eu/research/headlines/news/images/19
_11_07_small.jpg
http://publications.nigms.nih.gov/i
nsidethecell/images/ch3_wbc.jpg
Biofilms
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• 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
Biofilms can be problems
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• 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
http://prometheus.mse.uiuc.edu/
glossary/biofilms/lifecycle.png
Finding a bacterium from a niche
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• 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