Skip to main content

Microbial Biogeochemistry

  • Chapter
  • First Online:

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.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   54.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   69.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • 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 53:375–389

    Article  Google Scholar 

  • Adams MWW, Stiefel EI (1998) Biological hydrogen production: not so elementary. Science 282:1842–1843

    Article  Google Scholar 

  • Anderson TR, Groffman PM, Walter MT (2015) Using a soil topographic index to distribute denitrification fluxes across a northeastern headwater catchment. J Hydrol 522:123–134

    Article  Google Scholar 

  • Bardgett RD, Streeter TC, Bol R (2003) Soil microbes compete effectively with plants for organic nitrogen inputs to temperate grasslands. Ecology 84:1277–1287

    Article  Google Scholar 

  • Barkmann J, Schwintzer CR (1998) Rapid N2 fixation in pines? Results of a Maine field study. Ecology 79:1453–1457

    Article  Google Scholar 

  • 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 90:15–27

    Google Scholar 

  • Binkley D (1981) Nodule biomass and acetylene reduction rates of red alder and Sitka alder on Vancouver Island, B.C. Can J For Res 11:281–286

    Google Scholar 

  • Booth MS, Stark JM, Rastetter E (2005) Controls on nitrogen cycling in terrestrial ecosystems: a synthetic analysis of literature data. Ecol Monogr 75:139–157

    Article  Google Scholar 

  • 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 44:255–277

    Article  Google Scholar 

  • 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 23:1402–1407

    Article  Google Scholar 

  • 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 29:268–276

    Article  Google Scholar 

  • 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 16:2123–2142

    Article  Google Scholar 

  • Brady NC (1984) The nature and properties of soils. Macmillan Publishing Co., New York, 750 p

    Google Scholar 

  • Bremner JM (1997) Sources of nitrous oxide in soils. Nutr Cycl Agroecosyst 49:7–16

    Article  Google Scholar 

  • 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 2:317–384

    Article  Google Scholar 

  • 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., Boston

    Google Scholar 

  • 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 42:335–349

    Article  Google Scholar 

  • Davidson EA, Hart SC, Firestone MK (1992) Internal cycling of nitrate in soils of a mature coniferous forest. Ecology 73:1148–1156

    Article  Google Scholar 

  • 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 74:130–139

    Article  Google Scholar 

  • 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 8:748–759

    Article  Google Scholar 

  • DeBoer W, Kowalchuck GA (2001) Nitrification in acid soils: micro-organisms and mechanisms. Soil Biol Biochem 33:853–866

    Article  Google Scholar 

  • Firestone MK, Firestone RB, Tiedje JM (1980) Nitrous oxide from soil denitrification: factors controlling its biological production. Science 208:749–751

    Article  Google Scholar 

  • 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 53:341–356

    Google Scholar 

  • Gilmour CC, Henry EA, Mitchell R (1992) Sulfate stimulation of mercury methylation in freshwater sediments. Environ Sci Technol 26:2281–2287

    Article  Google Scholar 

  • Hart SC (1999) Nitrogen transformations in fallen tree boles and mineral soil of an old-growth forest. Ecology 80:1385–1394

    Article  Google Scholar 

  • Hart SC, Firestone MK (1989) Evaluation of three in situ soil nitrogen availability assays. Can J For Res 19:185–191

    Article  Google Scholar 

  • 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 79:684–703

    Google Scholar 

  • Heilman P, Ekuan G (1982) Nodulation and nitrogen fixation by red alder and Sitka alder on coal mine spoils. Can J For Res 12:992–997

    Article  Google Scholar 

  • Holmes WE, Zak DR (1994) Soil microbial biomass dynamics and net nitrogen mineralization in northern hardwoods. Soil Sci Soc Am J 58:238–243

    Article  Google Scholar 

  • Holmes WE, Zak DR (1999) Soil microbial control of nitrogen loss following clear-cut harvest in northern hardwood ecosystems. Ecol Appl 9:202–215

    Article  Google Scholar 

  • IPCC (1992) Climate change 1992 – supplemental report. Cambridge University Press, New York

    Google Scholar 

  • Jacinthe PA, Groffman PM, Gold AJ, Mosier A (1998) Patchiness in microbial nitrogen transformations in groundwater in a riparian forest. J Environ Qual 27:156–164

    Article  Google Scholar 

  • Kaye JP, Burke IC, Mosier AR, Guerschman JP (2004) Methane and nitrous oxide fluxes from urban soils to the atmosphere. Ecol Appl 14:975–981

    Article  Google Scholar 

  • Kerin EJ, Gilmour CC, Roden E, Suzuki MT, Coates JD, Mason RP (2006) Mercury methylation by dissimilatory iron-reducing bacteria. Appl Environ Microbiol 72:7919–7921

    Article  Google Scholar 

  • 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 62:4548–4555

    Google Scholar 

  • Kulkarni MV, Burgin AJ, Groffman PM, Yavitt JB (2014) Direct flux and 15N tracer methods for measuring denitrification in forest soils. Biogeochemistry 117:359–373

    Article  Google Scholar 

  • Matson PA, Naylor R, Ortiz-Monasterio I (1998) Integration of environmental, agronomic, and economic aspects of fertilizer management. Science 280:112–115

    Article  Google Scholar 

  • Moore TR, Knowles R (1989) The influence of water table levels on methane and carbon dioxide emissions from peatland soils. Can J Soil Sci 69:33–38

    Article  Google Scholar 

  • 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 18:520–532

    Article  Google Scholar 

  • Olson RK, Reiners WA (1983) Nitrification in subalpine balsam fir soils: tests for inhibitory factors. Soil Biol Biochem 15:413–418

    Article  Google Scholar 

  • 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 10:506–514

    Google Scholar 

  • Perakis SS, Hedin LO (2001) Fluxes and fates of nitrogen in soil of an unpolluted old-growth temperate forest, southern Chile. Ecology 82:2245–2260

    Article  Google Scholar 

  • 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 4:617–625

    Article  Google Scholar 

  • Pulliam WM (1993) Carbon dioxide and methane exports from a southeastern floodplain swamp. Ecol Monogr 63:29–53

    Article  Google Scholar 

  • Reich PB, Grigal DF, Aber JD, Gower ST (1997) Nitrogen mineralization and productivity in 50 hardwood and conifer stands on diverse soils. Ecology 78:335–347

    Article  Google Scholar 

  • Roskowski JP (1975) Differential nitrogen fixation in wood litter. Bull Ecol Soc Am 56(2):12

    Google Scholar 

  • Rudd JWM (1995) Sources of methyl mercury to freshwater ecosystems: a review. Water Air Soil Pollut 80:697–713

    Article  Google Scholar 

  • Santoro AE (2016) The do-it-all nitrifier. Science 351:342–343

    Article  Google Scholar 

  • Schwintzer CR, Tjepkema JD (1994) Factors affecting the acetylene to 15N2 conversion ratio in root nodules of Myrica gale L. Plant Physiol 106:1041–1047

    Article  Google Scholar 

  • 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 49:645–651

    Article  Google Scholar 

  • Silver WL, Herman DJ, Firestone MK (2001) Dissimilatory nitrate reduction to ammonium in upland tropical forest soils. Ecology 82:2410–2416

    Article  Google Scholar 

  • Stevenson FJ (1986) Cycles of soil. Wiley, New York

    Google Scholar 

  • 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 7:131–145

    Article  Google Scholar 

  • 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 111:8101–8106

    Article  Google Scholar 

  • Sun B, Griffin BM, Ayala-del-Rio HL, Hashsham SA, Tiedje JM (2002) Microbial dehalorespiration with 1,1,1-trichloroethane. Science 298:1023–1025

    Article  Google Scholar 

  • Tiedje JM, Sexstone AJ, Myrold DD, Robinson JA (1982) Denitrification: ecological niches, competition, and survival. Antonie van Leeuwenhock 48:569–583

    Google Scholar 

  • 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 67:527–539

    Article  Google Scholar 

  • Vitousek PM, Walker LR (1989) Biological invasion by Myrica faya in Hawaii: plant demography, nitrogen fixation, ecosystem effects. Ecol Monogr 59:247–265

    Google Scholar 

  • 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 7:737–750

    Google Scholar 

  • Weintraub SR, Russell AE, Townsend AR (2014) Native tree species regulate nitrous oxide fluxes in tropical plantations. Ecol Appl 24:750–758

    Article  Google Scholar 

  • Zogg GP, Zak DR, Pregitzer KS, Burton AJ (2000) Microbial immobilization and the retention of anthropogenic nitrate in a northern hardwood forest. Ecology 81:1858–1866

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG

About this chapter

Cite this chapter

Cronan, C.S. (2018). Microbial Biogeochemistry. In: Ecosystem Biogeochemistry. Springer Textbooks in Earth Sciences, Geography and Environment. Springer, Cham. https://doi.org/10.1007/978-3-319-66444-6_3

Download citation

Publish with us

Policies and ethics