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

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 For 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