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Microbial Biogeochemistry

  • Christopher S. Cronan
Chapter
First Online:
Part of the Springer Textbooks in Earth Sciences, Geography and Environment book series (STEGE)

Abstract

The biogeochemical cycles of carbon, nitrogen, and sulfur are characterized by important gaseous pathways, biochemical transformations, immobilization processes, and mineralization reactions associated with microbial metabolism. Microbial organisms are thus important regulators of the source-sink behavior and cycling rates of these key elements in terrestrial and aquatic ecosystems. In addition, numerous other elements such as mercury, iron, and even phosphorus are affected directly or indirectly by microbial exudation, respiration, assimilation, oxidation-reduction, methylation, and acidification processes. Taken as a whole, microscopic bacteria and fungi have critical roles in controlling element cycles in the biosphere. The primary focus of this chapter is to explore the major microbial processes and associated environmental conditions influencing the biogeochemical behavior of nitrogen, sulfur, and carbon in the forest landscape.

Keywords

Controlling Element Cycles Dissimilatory Nitrate Reduction To Ammonium (DNRA) Microbial Nitrogen Transformations Gaseous Nitrogen Species Final Oxidation State 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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References

  1. Aber JD, Goodale CL, Ollinger SV, Smith ML, Magill AH, Martin ME, Hallett RA, Stoddard JL (2003) Is nitrogen deposition altering the nitrogen status of northeastern forests? Bioscience 53:375–389CrossRefGoogle Scholar
  2. Adams MWW, Stiefel EI (1998) Biological hydrogen production: not so elementary. Science 282:1842–1843CrossRefGoogle Scholar
  3. Anderson TR, Groffman PM, Walter MT (2015) Using a soil topographic index to distribute denitrification fluxes across a northeastern headwater catchment. J Hydrol 522:123–134CrossRefGoogle Scholar
  4. Bardgett RD, Streeter TC, Bol R (2003) Soil microbes compete effectively with plants for organic nitrogen inputs to temperate grasslands. Ecology 84:1277–1287CrossRefGoogle Scholar
  5. Barkmann J, Schwintzer CR (1998) Rapid N2 fixation in pines? Results of a Maine field study. Ecology 79:1453–1457CrossRefGoogle Scholar
  6. Barnes RT, Raymond PA, Casciotti KL (2008) Dual isotope analyses indicate efficient processing of atmospheric nitrate by forested watersheds in the northeastern U.S. Biogeochemistry 90:15–27Google Scholar
  7. Binkley D (1981) Nodule biomass and acetylene reduction rates of red alder and Sitka alder on Vancouver Island, B.C. Can J For Res 11:281–286Google Scholar
  8. Booth MS, Stark JM, Rastetter E (2005) Controls on nitrogen cycling in terrestrial ecosystems: a synthetic analysis of literature data. Ecol Monogr 75:139–157CrossRefGoogle Scholar
  9. Bormann FH, Likens GE, Siccama TG, Pierce RS, Eaton JS (1974) The export of nutrients and recovery of stable conditions following deforestation at Hubbard Brook. Ecol Monogr 44:255–277CrossRefGoogle Scholar
  10. Bowden RD, Nadelhoffer KJ, Boone RD, Melillo JM, Garrison JB (1993) Contributions of aboveground litter, belowground litter, and root respiration to total soil respiration in a temperate mixed hardwood forest. Can J For Res 23:1402–1407CrossRefGoogle Scholar
  11. Bowden RD, Rullo G, Stevens GR, Steudler PA (2000) Soil fluxes of carbon dioxide, nitrous oxide, and methane at a productive temperate deciduous forest. J Environ Qual 29:268–276CrossRefGoogle Scholar
  12. Boyer EW, Alexander RB, Parton WJ, Li C, Butterbach-bahl K, Donner SD, Skaggs W, DelGrosso SJ (2006) Modeling denitrification in terrestrial and aquatic ecosystems at regional scales. Ecol Appl 16:2123–2142CrossRefGoogle Scholar
  13. Brady NC (1984) The nature and properties of soils. Macmillan Publishing Co., New York, 750 pGoogle Scholar
  14. Bremner JM (1997) Sources of nitrous oxide in soils. Nutr Cycl Agroecosyst 49:7–16CrossRefGoogle Scholar
  15. Crill PM, Bartlett B, Harriss RC, Gorham E, Verry ES, Sebacher DI, Mazdar L, Sanner W (1988) Methane flux from Minnesota peatlands. Glob Biogeochem Cycles 2:317–384CrossRefGoogle Scholar
  16. Cronan, C.S. 1985b. Chemical weathering and solution chemistry in acid forest soils: differential influence of soil type, biotic processes, and H+ deposition. pp. 175–195 in J.I. Drever (ed) Chemistry of Weathering. D. Reidel Publ. Co., BostonGoogle Scholar
  17. Davidson EA, Hart SC, Shanks CA, Firestone MK (1991) Measuring gross nitrogen mineralization, immobilization, and nitrification by 15N isotopic pool dilution in intact soil cores. J Soil Sci 42:335–349CrossRefGoogle Scholar
  18. Davidson EA, Hart SC, Firestone MK (1992) Internal cycling of nitrate in soils of a mature coniferous forest. Ecology 73:1148–1156CrossRefGoogle Scholar
  19. Davidson EA, Matson PA, Vitousek PM, Riley R, Dunkin K, Garcia-Mendez G, Maass JM (1993) Processes regulating soil emissions of NO and N2O in a seasonally dry tropical forest. Ecology 74:130–139CrossRefGoogle Scholar
  20. Davidson EA, Potter CS, Schlesinger P, Klooster SA (1998) Model estimates of regional nitric oxide emissions from soils of the southeastern United States. Ecol Appl 8:748–759CrossRefGoogle Scholar
  21. DeBoer W, Kowalchuck GA (2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol Biochem 33:853–866CrossRefGoogle Scholar
  22. Firestone MK, Firestone RB, Tiedje JM (1980) Nitrous oxide from soil denitrification: factors controlling its biological production. Science 208:749–751CrossRefGoogle Scholar
  23. Galloway, J.N., J.D. Aber, J.W. Erisman, S.P. Seitzinger, R.W. Howarth, E.B. Cowling, and B.J. Cosby. 2003. The nitrogen cascade. BioScience 53:341–356Google Scholar
  24. Gilmour CC, Henry EA, Mitchell R (1992) Sulfate stimulation of mercury methylation in freshwater sediments. Environ Sci Technol 26:2281–2287CrossRefGoogle Scholar
  25. Hart SC (1999) Nitrogen transformations in fallen tree boles and mineral soil of an old-growth forest. Ecology 80:1385–1394CrossRefGoogle Scholar
  26. Hart SC, Firestone MK (1989) Evaluation of three in situ soil nitrogen availability assays. Can J For Res 19:185–191CrossRefGoogle Scholar
  27. Hedin LO, von Fischer JC, Ostrom NE, Kennedy BP, Brown MG, Robertson GP (1998) Thermodynamic constraints on nitrogen transformations and other biogeochemical processes at soil-stream interfaces. Ecology 79:684–703Google Scholar
  28. Heilman P, Ekuan G (1982) Nodulation and nitrogen fixation by red alder and Sitka alder on coal mine spoils. Can J For Res 12:992–997CrossRefGoogle Scholar
  29. Holmes WE, Zak DR (1994) Soil microbial biomass dynamics and net nitrogen mineralization in northern hardwoods. Soil Sci Soc Am J 58:238–243CrossRefGoogle Scholar
  30. Holmes WE, Zak DR (1999) Soil microbial control of nitrogen loss following clear-cut harvest in northern hardwood ecosystems. Ecol Appl 9:202–215CrossRefGoogle Scholar
  31. IPCC (1992) Climate change 1992 – supplemental report. Cambridge University Press, New YorkGoogle Scholar
  32. Jacinthe PA, Groffman PM, Gold AJ, Mosier A (1998) Patchiness in microbial nitrogen transformations in groundwater in a riparian forest. J Environ Qual 27:156–164CrossRefGoogle Scholar
  33. Kaye JP, Burke IC, Mosier AR, Guerschman JP (2004) Methane and nitrous oxide fluxes from urban soils to the atmosphere. Ecol Appl 14:975–981CrossRefGoogle Scholar
  34. Kerin EJ, Gilmour CC, Roden E, Suzuki MT, Coates JD, Mason RP (2006) Mercury methylation by dissimilatory iron-reducing bacteria. Appl Environ Microbiol 72:7919–7921CrossRefGoogle Scholar
  35. King GM (1996) In situ analyses of methane oxidation associated with the roots and rhizomes of a bur reed, Sparganium eurycarpum, in a Maine wetland. Appl Environ Microbiol 62:4548–4555Google Scholar
  36. Kulkarni MV, Burgin AJ, Groffman PM, Yavitt JB (2014) Direct flux and 15N tracer methods for measuring denitrification in forest soils. Biogeochemistry 117:359–373CrossRefGoogle Scholar
  37. Matson PA, Naylor R, Ortiz-Monasterio I (1998) Integration of environmental, agronomic, and economic aspects of fertilizer management. Science 280:112–115CrossRefGoogle Scholar
  38. Moore TR, Knowles R (1989) The influence of water table levels on methane and carbon dioxide emissions from peatland soils. Can J Soil Sci 69:33–38CrossRefGoogle Scholar
  39. Morse JL, Durán J, Groffman PM (2015) Soil denitrification fluxes in a northern hardwood forest: the importance of snowmelt and implications for ecosystem N budgets. Ecosystems 18:520–532CrossRefGoogle Scholar
  40. Olson RK, Reiners WA (1983) Nitrification in subalpine balsam fir soils: tests for inhibitory factors. Soil Biol Biochem 15:413–418CrossRefGoogle Scholar
  41. Panek JA, Matson PA, Ortiz-Monasterio I, Brooks P (2000) Distinguishing nitrification and denitrification sources of N2O in a Mexican wheat system using 15N. Ecol Appl 10:506–514Google Scholar
  42. Perakis SS, Hedin LO (2001) Fluxes and fates of nitrogen in soil of an unpolluted old-growth temperate forest, southern Chile. Ecology 82:2245–2260CrossRefGoogle Scholar
  43. Peterjohn WT, Melillo JM, Steudler PA, Newkirk KM, Bowles FP, Aber JD (1994) Responses of trace gas fluxes and N availability to experimentally elevated soil temperatures. Ecol Appl 4:617–625CrossRefGoogle Scholar
  44. Pulliam WM (1993) Carbon dioxide and methane exports from a southeastern floodplain swamp. Ecol Monogr 63:29–53CrossRefGoogle Scholar
  45. Reich PB, Grigal DF, Aber JD, Gower ST (1997) Nitrogen mineralization and productivity in 50 hardwood and conifer stands on diverse soils. Ecology 78:335–347CrossRefGoogle Scholar
  46. Roskowski JP (1975) Differential nitrogen fixation in wood litter. Bull Ecol Soc Am 56(2):12Google Scholar
  47. Rudd JWM (1995) Sources of methyl mercury to freshwater ecosystems: a review. Water Air Soil Pollut 80:697–713CrossRefGoogle Scholar
  48. Santoro AE (2016) The do-it-all nitrifier. Science 351:342–343CrossRefGoogle Scholar
  49. Schwintzer CR, Tjepkema JD (1994) Factors affecting the acetylene to 15N2 conversion ratio in root nodules of Myrica gale L. Plant Physiol 106:1041–1047CrossRefGoogle Scholar
  50. Sexstone AJ, Revsbech NP, Parkin TB, Tiedje JM (1985) Direct measurement of oxygen profiles and denitrification rates in soil aggregates. Soil Sci Soc Am J 49:645–651CrossRefGoogle Scholar
  51. Silver WL, Herman DJ, Firestone MK (2001) Dissimilatory nitrate reduction to ammonium in upland tropical forest soils. Ecology 82:2410–2416CrossRefGoogle Scholar
  52. Stevenson FJ (1986) Cycles of soil. Wiley, New YorkGoogle Scholar
  53. Strader RH, Binkley D, Wells CG (1989) Nitrogen mineralization in high-elevation forests of the Appalachians. I Regional patterns in southern spruce-fir forests. Biogeochemistry 7:131–145CrossRefGoogle Scholar
  54. Sullivan BW, Smith WK, Townsend AR, Nasto MK, Reed SC, Chazdon RL, Cleveland CC (2014) Spatially robust estimates of biological nitrogen (N) fixation imply substantial human alteration of the tropical N cycle. PNAS 111:8101–8106CrossRefGoogle Scholar
  55. Sun B, Griffin BM, Ayala-del-Rio HL, Hashsham SA, Tiedje JM (2002) Microbial dehalorespiration with 1,1,1-trichloroethane. Science 298:1023–1025CrossRefGoogle Scholar
  56. Tiedje JM, Sexstone AJ, Myrold DD, Robinson JA (1982) Denitrification: ecological niches, competition, and survival. Antonie van Leeuwenhock 48:569–583Google Scholar
  57. Venterea RT, Lovett GM, Groffman PM, Schwarz PA (2003) Landscape patterns of net nitrification in a northern hardwood-conifer forest. Soil Sci Soc Am J 67:527–539CrossRefGoogle Scholar
  58. Vitousek PM, Walker LR (1989) Biological invasion by Myrica faya in Hawaii: plant demography, nitrogen fixation, ecosystem effects. Ecol Monogr 59:247–265Google Scholar
  59. Vitousek PM, Aber JD, Howarth RW, Likens GE, Matson PA, Schindler DW, Schlesinger WH, Tilman DG (1997) Human alteration of the global nitrogen cycle: sources and consequences. Ecol Appl 7:737–750Google Scholar
  60. Weintraub SR, Russell AE, Townsend AR (2014) Native tree species regulate nitrous oxide fluxes in tropical plantations. Ecol Appl 24:750–758CrossRefGoogle Scholar
  61. Zogg GP, Zak DR, Pregitzer KS, Burton AJ (2000) Microbial immobilization and the retention of anthropogenic nitrate in a northern hardwood forest. Ecology 81:1858–1866CrossRefGoogle Scholar

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© Springer International Publishing AG 2018

Authors and Affiliations

  • Christopher S. Cronan
    • 1
  1. 1.School of Biology and EcologyUniversity of MaineOronoUSA

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