1. Microbial ecology The study of the interactions of microorganisms with each other and their nonliving physical environment Environmental microbiology relates to the broad-scale effects microorganisms and their activities have on the planet

2. Microbial interactions Some interactions can be beneficial for both participants (mutualism and cooperation) Some interactions benefit one participant but do not affect the other (commensalism) Some interactions benefit one participant at the expense of the other (predation and parasitism)

3. Mutualism An obligatory relationship in which the mutualist and the host are metabolically dependent on each other Examples include the tube worm-bacterial relationship and the rumen ecosystem

4. The tube worm-bacterial relationship Tube worm hemoglobin transports H 2 S to bacteria Bacteria fix CO 2 using reducing power of H 2 S Tube worm supplied with organic molecules by bacteria

5. The rumen ecosystem Ruminants are herbivorous animals (cattle, deer, sheep, etc.) Require microorganisms to degrade cellulose Anaerobic process produces CO 2, H 2 and CH 4

6. Cooperation Both organisms benefit but the interaction is not obligatory Organisms can exist separately if required nutrients are supplied in the growth environment

7. Commensalism A relationship in which one symbiont (the commensal) benefits while the other (the host) is not harmed The commensal feeds on substances captured or ingested by the host Commensals can become pathogens under certain circumstances

8. Predation Relationship in which a predator attacks or engulfs a prey Predator may be larger or smaller than the prey Predation may have beneficial results for the prey (protection or enhancement of virulence)

9. Parasitism One organism benefits and the other is harmed The line between parasitism and predation is hard to define (parasitism may eventually lead to predation) Parasitism usually is a long-term relationship whereas predation tends to end abruptly

10. Amensalism One organism produces a compound that has a negative effect on another organism Production of antibiotics by certain bacteria is an example of amensalism

11. Competition Microorganisms can compete for a physical location or a limiting nutrient  2 possible outcomes 1. One organism may outcompete the other 2. Both organisms may co-exist at lower levels

12. Biogeochemical cycling Cycling of nutrients in the environment involving both biological and chemical processes Nutrients are transformed (often by oxidation-reduction reactions) and cycled

13. Biogeochemical cycling

14. Influence of oxygen on organic matter decomposition Oxidized products will accumulate when decomposition occurs under aerobic conditions Reduced products will accumulate when decomposition occurs under anaerobic conditions

15. Mineralization The release of excess nitrogen and other minerals into the environment as a result of the decomposition of organic matter

16. The carbon cycle Carbon exists in reduced forms (CH 4 and organic matter) and oxidized forms (CO and CO 2 ) Photosynthetic organisms fix carbon (reduced form)

17. The carbon cycle Respiration produces oxidized form  CO 2 Methane is generated under anaerobic conditions (eventually oxidized to CO 2 )

18. The sulfur cycle H 2 S can serve as an electron donor for photosynthetic bacteria H 2 S(ide)  Sº, SO 3 2- (ite), SO 4 2- (ate) Different oxidized forms of sulfur diffuse into a reduced environment Other bacteria perform dissimilatory and assimilatory reductions

19. The nitrogen cycle Requires several different processes including: Nitrification Denitrification Nitrogen assimilation Nitrogen fixation

20. Nitrification Involves the aerobic oxidation of ammonium ion to nitrite and then to nitrate NH 4 +  NO 2 -  NO 3 - Can occur anaerobically by coupling oxidation of NH 4 + with reduction of NO 2 - to produces nitrogen gas (N 2 ) Commercial process referred to as the anamox process (anoxic ammonium oxidation)

21. Denitrification Use of nitrate as an electron acceptor in anaerobic respiration (dissimilatory reduction) NO 3 -  NO 2 -  N 2 O  N 2

22. Nitrogen assimilation NH 4 + can be directly incorporated into organic matter NO 3 - assimilation is much more energetically expensive

23. Nitrogen fixation Carried out by both aerobic and anaerobic prokaryotes Cannot be carried out by eukaryotes

24. Nitrogen fixation Involves a sequence of reduction steps that require major expenditures of energy Produces ammonia which is immediately incorporated into organic matter

25. The iron cycle Cycling between ferrous (2+) and ferric (3+) forms of iron Iron reduction occurs under anaerobic conditions

26. Other cycles Manganese and other metals cycle between oxidized and reduced forms Cycling of different elements may be metabolically linked (e.g. Desulfobulbus propionicus oxidation of sulfate is linked to the reduction of manganese)

27. The physical environment Microorganisms occupy specific environments in nature referred to as microenvironments Fluxes and gradients of nutrients, reductants and oxidants and waste products will influence the rate of growth and create a unique niche

28. The physical environment Biofilms and microbial mats are microenvironments or niches created by microorganisms

29. Microorganisms and ecosystems Microorganisms play two complementary roles in ecosystems Primary production - the synthesis of organic matter from CO 2 and other inorganic molecules

30. Microorganisms and ecosystems Consumption and decomposition - the breakdown of organic matter with the release of energy and inorganic molecules

31. Extremophiles Some microorganisms have evolved to survive in extreme environments  extremophiles Extreme environments include: High sodium concentrations High pressure Extreme acidic or alkaline conditions High temperature Microorganisms existing in such environments must possess unique adaptations

32. Extremophiles

33. Methods used in microbial ecology Isolation of organisms from environmental samples Standard media does not support the growth of many microorganisms PCR amplification and sequencing of extracted DNA Extracted DNA may not be representative of living microorganisms

34. Methods used in microbial ecology Direct observation - slides or EM grids placed in location, recovered and observed

35. Methods used in microbial ecology Microbial activity and turnover rates at which nutrients are incorporated into organic matter can give an indication of the metabolic activity of a microbial population Often make use of radioactive isotopes

36. Methods used in microbial ecology Recovery or addition of individual microorganisms - individual microorganism may be removed and DNA analyzed after PCR

37. Methods used in microbial ecology Microorganisms with reporter genes may be placed into environments to monitor specific changes (e.g. oxygen availability or UV radiation exposure)