1. Microbial Biogeochemistry Chemical reactions occurring in the environment mediated by microbial communities Outline Metabolic Classifications. Winogradsky columns, Microenvironments. Redox Reactions. Microbes and Processes in Winogradsky column. Competition and Redox cascade Winogradsky column biogeochemistry. Lab work

2. Metabolic Classification of Life “Autotrophs” “Heterotrophs” Note, organisms that exhibit both autotrophy and heterotrophy are also called mixotrophs

3. Winogradsky Column Water Sediment Cyanobacteria Algae; Bacteria Purple nonsulfur bacteria Purple S bacteria Sulfur bacteria Green S bacteria Desulfovibrio Clostridium O2O2 H2SH2S Conc. Chemoorganoheterotrophy Fermentation Photoautotrophy: PS II Chemoorganoheterotrophy Chemolithoautotrophy Chemolithoheterotrophy Photoheterotrophy Photoautotrophy: PS I Chemoorganoheterotrophy sulfate reducers Microenvironments generated by chemical gradients.

4. Transport Limitations; Advection Advective transport: u : Fluid velocity [m s -1 ] u

5. Transport Limitations; Diffusion Fickian Diffusion: D : Diffusion Coefficient [m 2 s -1 ]

6. Transport Limitations; Advection-Diffusion Transport by advection and diffusion: Must also account for reactions! u

7. Redox Reactions Reduction and Oxidation: A  B + + e - Oxidation C + e -  D - Reduction Half Reactions Complete Reaction A + C  B + + D - AC e-e- B+B+ D-D- Redox Potential, Eº` -500 -400 -300 -200 -100 0 +100 +200 +300 +400 +500 +600 +700 +800 +900 Eº` (mV) ½O 2 + 2H + + 2e -  H 2 O Reference Half Reaction: H 2  2e - + 2H + NO 3 - + 6H + + 5e -  ½N 2 + 3H 2 O Electron Tower (pH 7) SO 4 2- + 10H + + 8e -  H 2 S + 4H 2 O NO 3 - + 2H + + 2e -  NO 2 - + H 2 O CO 2 + 8H + + 8e -  CH 4 + 2H 2 O 2H + + 2e -  H 2 Fe 3+ + e -  Fe 2+ 2H + + 2e -  H 2 (pH 0) Reactions proceed in forward directions m = no. of H + consumed n = no. of electrons in rx. F = faraday (96493 coulombs/mol) R = gas const (8.314 j/K/mol) Ref. cell at pH 0

8. Oxidation states Some (many) elements have more than one stable electron configuration. Consequently, an element can exist in reduced or oxidized states; e.g., Fe 3+ or Fe 2+. Carbon and Nitrogen both have several (assume H: +1; O: -2) CH 4 -4N 2 0 CO 2 +4NO 3 - +5NH 3 -3 Fermentation Organic carbon present, but no electron acceptors: O 2, NO 3 -, SO 2 2-, etc. Use organic carbon as both electron acceptor and donor: C 6 H 12 O 6  2 CO 2 + 2 C 2 H 6 O Autotrophy 6CO 2 + 24H + + 24e -  C 6 H 12 O 6 + 6H 2 O Oxidation States and Fermentation H 2 S  2 H + + S + 2 e - PS I H 2 O  2 H + + ½ O 2 + 2 e - PS II

9. Microbes and Processes in Winogradsky column. Aerobic Environment Algae and cyanobacteria (photoautotrophy using PS II) Bacteria and eukaryotes respiring (chemoorganoheterotrophy). Sulfide oxidizers (or sulfur bacteria): H 2 S + O 2  S or SO 4 2- Some use CO 2 (chemolithoautotrophs), others use organic compounds (chemolithoheterotrophs) Examples, Thiobacillus sp. And Beggiatoa sp. Methanotrophs: CH 4 + O 2  CO 2 + 2H 2 O (chemoorganoheterotrophs) Example, Ralstonia sp., Pseudomonas sp. Anaerobic Environment Fermentors (chemoorganoheterotrophs) Break down cellulose, etc. and ferment sugars into: alcohols acetate organic acids hydrogen Many bacterial groups can conduct fermentation, but not all of these have the ability to decompose polymeric compounds such as cellulose. Example, Clostridium species

10. Anaerobic Environments, Continued Sulfur Compounds Sulfate reducers: use sulfate, SO 4 2- + e -  S or H 2 S, to oxidize organic compounds produced by fermentors. (chemoorganoheterotrophs). Many genera of bacteria. Example, Desulfovibrio sp. Phototrophic bacteria: Use light and H 2 S as electron donor (PS I) (photoautotrophs). Examples, purple and green sulfur bacteria. Methanogens and Acetogens Methanogens:CO 2 + 4H 2  CH 4 + 2H 2 O (chemolithoautotrophs) Acetate - + H 2 O  CH 4 + HCO 3 - (chemoorganoheterotrophs) Example: Methanobacterium (Archaea) Acetogens: 2CO 2 + 4H 2  CH 3 COOH + 2H 2 O (chemolithoautotrophs) Example: Homoacetogens

11. Other possible microbes Aerobic Environments Hydrogen Hydrogen oxidizers: H 2 + ½O 2  H 2 O (both chemolithoheterotrophs and chemolithoautotrophs). However, it is unlikely that H 2 will make it to the aerobic interface (it will be used in the anaerobic environment first) Example, Ralstonia eutrophus Iron Iron oxidizers: Fe 2+ + H + + ¼O 2  Fe 3+ + ½H 2 O (chemolithoautotrophs) Occurs only at low pH (~2) Example: Thiobacillus ferrooxidans Ammonium Nitrifiers:NH 3 + 1½ O 2  NO 2 - + H + + H 2 O NO 2 - + ½ O 2  NO 3 - Example: Nitrosomonas and Nitrobacter, respectively. Both chemolithoautotrophs. Anaerobic Environments Nitrate Denitrifiers: NO 3 - + 6H + + 5e -  ½N 2 + 3H 2 O Reaction combined with oxidation of organic matter. Iron Iron reducers: Many organisms can utilize Fe 3+ as electron acceptor.

12. Chemical Potential Exploitation Schulz et al. 1999: Thiomargarita namibiensis Boetius et al. 2000: H 2 S oxidation by NO 3 - CH 4 oxidation by SO 4 2- 1 mm Strous et al. 1999: Planctomycete Anammox NH 4 + + NO 2 - = N 2 + 2H 2 O CH 4 oxidation by NO 3 - (Raghoebarsing et al. 2006) 5CH 4 + 8NO 3 - + 8H +  5CO 2 + 4N 2 + 14H 2 O

13. Competition and Redox cascade How do the chemical gradients arise in the Winogradsky column, or in natural environments? Bacteria that are able to use the most energetic reactions in their surrounding environment will dominate that microenvironment. Transport combined with the microbial sources and sinks will determine the resulting chemical gradients. Chemical gradients can be transient as substrates are exhausted or products become toxic. This leads to succession. Energetics are governed by the redox potentials of the possible reactions: Electron acceptors: O 2 > NO 3 - > Mn 4+ > Fe 3+ > SO 4 2- > CO 2 > Fermentation

14. Winogradsky column biogeochemistry O2O2 H 2 S CH 4 Conc. Water Sediment With SO 4 2- Cellulose Sugars Organics, H 2, Acetate CO 2  CH 2 O + O 2 CH 2 O + O 2  CO 2 SO 4 2- H2SH2S S Light SO 4, S O2O2 Without SO 4 2- Cellulose Sugars CO 2, H 2, Acetate CO 2  CH 2 O + O 2 CH 2 O + O 2  CO 2 CH 4 Light CO 2 O2O2 FeS Organics

15. Laboratory Work Tuesday:Measure hydrogen sulfide profiles in columns using spectrometer assay. Thursday: Measure methane profiles in columns using gas chromatogram.

16. Winogradsky Column from 1999 Class