Microbial Biogeochemistry

Transcription

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 Energy Source Classification Carbon Source Light (Phototrophs) PS I: anaerobic, H 2 S PS I+II: aerobic, H 2 O Photoautotrophs Autotrophs Photoheterotrophs CO 2 (Autotrophs) Chemolithoautotrophs Chemical (Chemotrophs) Inorganic (Chemolithotrophs) Aerobic (majority) Anaerobic (few) Chemolithoheterotrophs (or Mixotrophs) Organic (Heterotrophs) Organic (Chemoorganotrophs) Aerobic respiration Anaerobic respiration Fermentation Chemoorganoheterotrphs Heterotrophs Chemoorganoautotrophs Note, organisms that exhibit both autotrophy and heterotrophy are also called mixotrophs

3 Some Microbial Metabolic Redox Reactions Nitrifiers NH + 4 O 2 h Autotrophs Heterotrophs Oxidizing Reducing N 2 NO 2 - NO 3 - OM OM Fe 3+ CO 2 Fe 2+ FeS 2 O 2 O 2 CH 4 h OM OM Methanotrophs Sulfate reducers SO 4 O 2 CO 2 NO 2 - NH 4 + CO 2 Iron cyclers OM Pyrite Syn. H 2 CO 2 H 2 S Sulfur bacteria Denitrifiers DNRA N 2 Anammox Methanogens Fermentors Anoxygenic phototrophs

4 Winogradsky Column Microenvironments generated by chemical gradients. Conc. Water Cyanobacteria Algae; Bacteria Photoautotrophy: PS I+II Chemoorganoheterotrophy H 2 S O 2 Sulfur bacteria Purple nonsulfur bacteria Purple S bacteria Green S bacteria Chemolithoautotrophy Chemolithoheterotrophy Photoheterotrophy Photoautotrophy: PS I or PS II Sediment Desulfovibrio Chemoorganoheterotrophy sulfate reducers Clostridium Chemoorganoheterotrophy Fermentation

5 Transport Limitations; Advection Advective transport: g Flux uc 2 m s u: Fluid velocity [m s -1 ] C t z uc u

6 Transport Limitations; Diffusion Fickian Diffusion: dc g Flux D 2 dz m s D: Diffusion Coefficient [m 2 s -1 ] C t C D z z

7 Transport Limitations; Advection-Diffusion Transport by advection and diffusion: dc g Flux D uc 2 dz m s C t C D z z uc u

8 Simulations Advection Diffusion Advection & Diffusion

9 Transport Limitations; Advection-Diffusion Transport by advection and diffusion: dc g Flux D uc 2 dz m s Must also account for reactions! C t C D z z uc + r

10 Redox Reactions Electron Tower (at ph 0) Eº (mv) Reduction and Oxidation: Half Reactions A B + + e - Oxidation C + e - D - Reduction Complete Reaction ZnO(s) + H 2 O + 2e - Zn + 2OH Reactions always run at standard conditions, (1 M concentration and 1 atm, 25C) A + C B + + D - 2H + + 2e - H 2 0 Redox Potential, Eº e - A C B + D - 2MnO 2 (s) + H 2 O + 2e - Mn 2 O 3 + 2OH - Fe 3+ + e - Fe Reactions proceed in forward directions +900 Reference Half Reaction: H 2 (g) 2e - + 2H + ½O 2 + 2H + + 2e - H 2 O Reference cell always at ph 0 Alkaline Battery: Zn(s) + 2MnO 2 (s) ZnO(s) + Mn 2 O 3 (s): E = 1.43 V

11 Redox Reactions-2 E h = E RT nf ln ς β i Products i i α ς j Reactents j j E = E 2.303RT nf m ph F = faraday (96493 Coulombs/mol) R = gas const (8.314 J/K/mol) m = no. of H + consumed in ½ rxn n = no. of electrons in rxn. Volt = J/(A s)=j/c; CCoulomb G = ne F Gibbs Free Energy (kj/mol) Reference Half Reaction: H 2 (g) 2e - + 2H + Reference cell at ph 0 Electron Tower (at ph 7) 6CO H e - C 6 H 12 O 6 + 6H 2 O 2H + + 2e - H 2 (g) CO 2 + 8H + + 8e - CH 4 + 2H 2 O SO H + + 8e - H 2 S + 4H 2 O NO H + + 2e - NO + H 2 O NO H + + 5e - ½N 2 + 3H 2 O Fe 3+ + e - Fe 2+ ½O 2 + 2H + + 2e - H 2 O Eº (mv) ½O 2 + 2H + + 2e - H 2 O (ph 0) Note, the number of electrons transferred does NOT change the potential or voltage

12 Oxidation States and Fermentation 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, Nitrogen and Sulfur have several (assume H: +1; O: -2) CH 4-4 N 2 0 NH 3-3 S 2 O 3 +2 CO 2 +4 NO H 2 S -2 SO 4 +6 Fermentation and/or Disproportionation Organic carbon present, but no electron acceptors: O 2, NO 3-, SO 2, etc. Use organic carbon as both electron acceptor and donor: C 6 H 12 O 6 2 CO C 2 H 6 O 4 S + 4 H 2 O 3 H 2 S + SO H + Autotrophy 6CO H e - C 6 H 12 O 6 + 6H 2 O H 2 S 2 H + + S + 2 e - PS I or PS II Anoxygenic Photosynthesis H 2 O 2 H + + ½ O e - PS I and PS II Oxygenic Photosynthesis

13 Photosystem I Only Energy production only (cyclic photophosphorylation) NADPH production only needed to reduce CO 2 These occur in the green and purple sulfur bacteria (i.e., your Winogradsky columns) (Principles of Modern Microbiology, M. Wheelis)

14 Photosystem II Only These occur in the green and purple non-sulfur bacteria Energy production only (cyclic photophosphorylation) NADPH production only needed to reduce CO 2 (Principles of Modern Microbiology, M. Wheelis)

15 Photosystem I+II These occur in the cyanobacteria, algae and plants. NADPH production only needed to reduce CO 2 Energy production only (cyclic photophosphorylation) (Principles of Modern Microbiology, M. Wheelis)

16 Phylogeny of PS I and II Schubert et al. (1998) J. Mol. Biol. 280,

17 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 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

18 Anaerobic Environments, Continued Sulfur Compounds Sulfate reducers: use sulfate, SO 4 + 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

19 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 + H + + H 2 O NO + ½ O 2 NO 3 - Example: Nitrosomonas and Nitrobacter, respectively. Both chemolithoautotrophs. Anaerobic Environments Nitrate Denitrifiers: NO H + + 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.

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

21 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 > CO 2 > Fermentation

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

23 Laboratory Work Tuesday: Measure methane profiles in columns using gas chromatogram. Thursday: Measure hydrogen sulfide profiles in columns using spectrometer assay. Success?WT.mc_id= _Firmenich_BG-TW&WT.tsrc=BGTW&linkId=

24 Winogradsky Column from 1999 Class

25 Winogradsky Column from 2011 Class Note inversion of green and purple sulfur bacteria Saltwater with rice as carbon