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
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
Cooperation and niches 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 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
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.
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
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
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 http://ec.europa.eu/research/headlines/news/images/19_11_07_small.jpg http://publications.nigms.nih.gov/insidethecell/images/ch3_wbc.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
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 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