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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 1 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 2 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. 3 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 4 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. 5 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 6 Biogeochemical cycles 7 • 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 8 • 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 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 9 • 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 10 • 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 11 • 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