Lecture 9a

1. Lecture 9a Biogeochemical Cycling Chapter 14 Text

2. Cycling Carbon, Nitrogen, Sulfur, Phosphorus • Autotrophs use photosynthesis incorporates abiotic CO2, NO3, SO4, and PO4 into biotic cell compounds • polysaccharides • proteins • lipids • nucleic acids • organic acids • Heterotrophs use respiration to mineralize the biotic cell components back to inorganic compounds CO2, NO3, SO4, and PO4

3. Sometimes the products formed by microbes are detrimental to the biosphere • sulfuric acid from acid mine drainage • nitrous oxide from soil denitrification

4. The environment of the Earth has changed since life first appeared • Early Earth before life evolved • CO2 contributed 98% of atmospheric gases • surface temperature was 290o C • reducing conditions • CO2 + uv reduced organic compounds • anaerobic thermophilic heterotrophs (archaea) • Photosynthesis evolved 3.7-3.9 billion years ago • CO2 + sunlight CH2O • O2 produced from photosynthesis 2 billion years ago. CO2 + sunlight CH2O + O2

5. Molecular nitrogen was abundant in atmosphere of early Earth • Nitrogen was a limiting nutrient for early life forms • Nitrogen-fixation metabolism developed before oxygen-producing photosynthesis • nitrogen-fixing nitrogenase enzyme is sensitive to the presence of O2 N2-fixing heterocyst Photosynthetic cells

6. Earth’s environment today • CO2 is 0.03% of atmospheric gases • O2 is 20% of atmospheric gases • N2 has increased from 1.9% before life appeared to 9% when N-fixation pathway evolved to 69% today • temperature is 13oC • So, over long time scales, the evolution of life has led to evolution of the environment

7. Carbon • largest reservoir or sink or source is in form of calcium carbonate rock found in Earth’s crust • 1.2 x 1017 metric tons • 2nd largest reservoir of carbon is as dissolved calcium carbonate in world’s oceans • 3.8 x 1013 metric tons • 3rd largest reservoir is buried fossil fuel • 1.0 x 1013 metic tons • 4th largest reservoir is dissolved and particulate organic matter in the oceans • 2.1 x 1012 metric tons • Atmospheric CO2 is relatively small source of carbon 6.7 x 1011 metric tons

8. The carbon reservoir (atmospheric CO2) most available for photosynthesis is relatively small compared to calcium carbonate reservoirs • Humans have affected several of the smaller carbon reservoirs • atmospheric CO2 • fossil fuel • land biomass (deforestation) • burning fossil fuel and deforestation have reduced organic C in land biomass and in subsurface

9. Reduction of C in these reservoir results in increase in C in atm.

10. CO2 atmosphere ocean Transformations occurring on a contemporary time scale • The increase in atmospheric CO2 from burning fossil fuels and deforestation has not been as great as expected because the reservoir of calcium carbonate in ocean acts as a buffer between the atmospheric and sediment carbon reservoirs CaCO3 H2CO3 HCO3- CO2 limestone sediments

11. Ocean as a CO2 sink atmosphere • Some of the CO2 released into atmosphere has been taken up by ocean • Since CO2 is in equilibrium with bicarbonate and carbonate, more calcium carbonate is formed and deposited in ocean sediments CO2 CaCO3 HCO3- CO2 ocean sediment

12. plants algae bacteria cyanobacteria protozoa >50% bacteria protozoa Aquatic and terrestrial environments contribute equally to global primary production. Plants predominant in terrestrial, microbes in aquatic

14. Detritus

15. stopped

16. Common forms of organic carbon Single, most abundant compound

17. Second most abundant compound Plant storage product

18. How are fungal, plant & animal polysaccharides degraded? • Polysaccharides are too large to get into cell • extracellular and cell surface enzymes are used • Polysaccharidase enzymes • cellulases • chitinase • amylase

19. Cellulases • b-1,4-endoglucanase • cleaves internal linkages between glucose subunits creating shorter glucan chains • b-1,4-exoglucanase • cleaves two glucose subunits from reducing end of chain liberating disaccharide • Cellobiase • hydrolyzes disaccharide into single glucose subunits

21. Relative rates of degradation

23. Cross-section of plant tissue

24. Lignin subunits

25. Lignin: phenylpropene-based polymer

26. Lignin is the 3rd most abundant plant polymer • Basic building blocks are the aromatic amino acids tyrosine and phenylalanine • These are converted to phenylpropene subunits • 500-600 subunits are randomly polymerized

27. Lignin degradation • Non-specific enzyme: peroxide-dependent lignin peroxidase • Produce oxygen-based free radicals that react with lignin polymer to release phenylpropene residues • Since oxygen radicals are involved, lignin degradation is strictly an aerobic process. • The degradation of aromatic pollutants such as toluene, benzene, and xylenes proceeds through pathways similar to lignin degradation.

28. Lignin degradation pathway

29. Methane • Methane production is mediated primarily by microbial processes. • Environments where methanogenesis is carried out microbiologically • Rice paddies • Wetlands • Rumen • Landfills • Termite gut • Methane is formed when CO2 serves as a terminal electron acceptor during anaerobic respiration • 4H2 + CO2 CH4 +2H2O (autotrophic metabolism)

31. Methane can also be produced by heterotrophic metabolism of acetate, methanol and formate, which are formed as by-products of fermentations carried out by other populations of microbes growing close-by. H2 + CH3COOH CH4 + CO2

32. Methane oxidation • Group of microbes called methanotrophs have the ability to use methane as a carbon and energy source CH4 + O2 CH3OH HCHO HCOOH CO2 methanol formaldehyde formic acid carbon dioxide Methane monooxygenase: can also cometabolize chlorinated organic compds such as TCE under aerobic conditions

33. Methylotrophs • Microbes that can utilize other C1 compounds besides methane • Carbon monoxide (CO) CO + H2O CO2 + H2 H2 + O2 2H2O Pseudomonas carboxydoflava (chemoautotroph) • Carbon cycling by methanogens, methanotrophs and methylotrophs CO2 CH4 CH3OH HCHO HCOOH CO2

34. Common pollutant Breakdown product of hemi- cellulose Plant and animal tissues Formed from plant cyanides Industrial pollutant Generated by plants, fungi, bacteria; industrial pollutant Most common organic S compound in environment- algal origin

35. N2O NO Nitrogen cycling nitrogen fixation N2 -3 valence state anaerobic ammonia oxidation ammonia assimilation N2H4 NH4+ amino acids ammonification assimilatory nitrate reduction Proteins nitrification NH2OH denitrification NO2- aerobic nitrite oxidation NO3- +5 valence state

36. Nitrogen • Usually limiting nutrient for microbes and plants • bacteria need a C/N of 4-5 • fungi need a C/N of 10 • balance point C/N is 20 because N is better conserved than C • 4th most abundant element in biosphere • Makes up 12% of cell dry weight

38. N-fixation • Ultimately, all forms of nitrogen come from atmospheric N Table 14.11

39. N fixation • Atmospheric N is fixed into NH3 by over 100 different free-living bacteria, actinomycetes, and cyanobacteria • Highly conserved nifH gene encodes iron-containing reductase component of nitrogenase enzyme compled • N-fixation is an energy-intensive process N2 + 16ATP + 8 e- + 8H+ 2NH3 + 16ADP +16Pi + H2

40. Rates of N-fixation N-fixing system N fixation (kg N/hectare/year Rhizobium-legume 200-300 Anabaena-Axolla 100-120 Cyanobacteria-moss 30-40 Rhizosphere associations 2-25 Free-living 1-2

41. Nitrogen cycling N2O NO nitrogen fixation N2 -3 valence state anaerobic ammonia oxidation ammonia assimilation N2H4 NH4+ amino acids ammonification assimilatory nitrate reduction Proteins nitrification NH2OH denitrification NO2- aerobic nitrite oxidation NO3- +5 valence state

42. Ammonification or ammonia assimilation? • Ammonification (mineralization) refers to the release of free ammonia from N-containing organic compounds • occurs when C/N < 20 • Ammonia assimilation (immobilization) refers to the incorporation of free ammonia into organic compounds • occurs when C/N > 20

43. Nitrogen cycling N2O NO nitrogen fixation N2 -3 valence state anaerobic ammonia oxidation ammonia assimilation N2H4 NH4+ amino acids ammonification assimilatory nitrate reduction nitrification Proteins NH2OH denitrification NO2- aerobic nitrite oxidation NO3- +5 valence state

44. Nitrification • Catalyzed conversion of ammonia to nitrate • Predominantly, an aerobic chemoautotrophic process • amoA gene encoding ammonia monooxygenase is highly conserved STEP 1 NH4+ + 1/2 O2 NH2OH + H+ ammonia monooxygenase NH2OH + O2 NO2 +H2O + H+ DG = -66 kcal/mol • Both Bacterial and Archaeal domains of life carry out this process

45. Nitrification Step 2 NO2-+ 1/2O2 NO3-DG = -18 kcal/mol 100 mols NO2 required to fix 1 mol CO2

46. Nitrogen cycling N2O NO nitrogen fixation N2 -3 valence state anaerobic ammonia oxidation ammonia assimilation N2H4 NH4+ amino acids ammonification assimilatory nitrate reduction Proteins nitrification NH2OH denitrification NO2- aerobic nitrite oxidation NO3- +5 valence state

47. Anaerobic ammonia oxidation • Anammox reaction NH4+ NO2- N2H2 (hydrazine) • Carried out by a monophyletic cluster of bacteria named Brocadiales related to the order Planctomycetales • anammoxosome is organelle in which hydrazine is confined • Anammox bacteria have not yet been obtained in pure culture, but they are routinely grown in enrichment cultures

48. Anammox reaction NH4+ + 1.32NO2-+ 0.066HCO3- + 0.13H+→ 1.02N2 + 0.26NO3- + 2.03H2O+ 0.066CH2O0.5N0.15

49. Anaerobic ammonia oxidation pathway ATP production PMF-driven reverse electron transport Generates ferrodoxin for CO2 reduction in acetyl-CoA pathway J. Gijs Kuenen, Nature Reviews Microbiology 6, 320-326 (April 2008)

50. Nitrogen cycling N2O NO nitrogen fixation N2 -3 valence state anaerobic ammonia oxidation ammonia assimilation N2H4 NH4+ amino acids ammonification assimilatory nitrate reduction Proteins nitrification NH2OH denitrification NO2- aerobic nitrite oxidation NO3- +5 valence state