1. 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

2. 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

3. 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.

4. 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:

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
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

7. 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

8. 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

9. 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

10. 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