Skip to main content

Advertisement

Log in

Linking soil process and microbial ecology in freshwater wetland ecosystems

  • Published:
Plant and Soil Aims and scope Submit manuscript

Abstract

Soil microorganisms mediate many processes such as nitrification, denitrification, and methanogenesis that regulate ecosystem functioning and also feed back to influence atmospheric chemistry. These processes are of particular interest in freshwater wetland ecosystems where nutrient cycling is highly responsive to fluctuating hydrology and nutrients and soil gas releases may be sensitive to climate warming. In this review we briefly summarize research from process and taxonomic approaches to the study of wetland biogeochemistry and microbial ecology, and highlight areas where further research is needed to increase our mechanistic understanding of wetland system functioning. Research in wetland biogeochemistry has most often been focused on processes (e.g., methanogenesis), and less often on microbial communities or on populations of specific microorganisms of interest. Research on process has focused on controls over, and rates of, denitrification, methanogenesis, and methanotrophy. There has been some work on sulfate and iron transformations and wetland enzyme activities. Work to date indicates an important process level role for hydrology and soil nutrient status. The impact of plant species composition on processes is potentially critical, but is as yet poorly understood. Research on microbial communities in wetland soils has primarily focused on bacteria responsible for methanogenesis, denitrification, and sulfate reduction. There has been less work on taxonomic groups such as those responsible for nitrogen fixation, or aerobic processes such as nitrification. Work on general community composition and on wetland mycorrhizal fungi is particularly sparse. The general goal of microbial research has been to understand how microbial groups respond to the environment. There has been relatively little work done on the interactions among environmental controls over process rates, environmental constraints on microbial activities and community composition, and changes in processes at the ecosystem level. Finding ways to link process-based and biochemical or gene-based assays is becoming increasingly important as we seek a mechanistic understanding of the response of wetland ecosystems to current and future anthropogenic perturbations. We discuss the potential of new approaches, and highlight areas for further research.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Ambus P, Christensen S (1993) Denitrification variability and control in a riparian fen irrigated with agricultural drainage water. Soil Biol Biochem 25:915–923

    Google Scholar 

  • Anupam B (2003) Mycorrhizae in wetlands: a review. Int J For Manage 4:34–40

    Google Scholar 

  • Bachand PAM, Horne AJ (2000) Denitrification in constructed free-water surface wetlands: II. Effects of vegetation and temperature. Ecol Eng 14:17–32

    Google Scholar 

  • Bagwell CE, Lovell CR (2000) Persistence of selected Spartina alterniflora rhisosphere diazotrophs exposed to natural and manipulated environmental variability. Appl Environ Microbiol 66:4625–4633

    PubMed  CAS  Google Scholar 

  • Bahr M, Crump BC, Klepac-Ceraj V, Teske A, Sogin ML, Hobbie JE (2005) Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environ Microbiol 7:1175–1185

    PubMed  CAS  Google Scholar 

  • Balser TC, Firestone MK (2005) Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest. Biogeochemistry 73:395–415

    CAS  Google Scholar 

  • Balser TC, Kinzig A, Firestone M K (2001) Linking soil microbial communities and ecosystem functioning. In: Kinzig A et al. (eds) The functional consequences of biodiversity. p 392

  • Balser TC, McMahon KD, Bronson D, Coyle DR, Crage N, Flores-Mangual ML, Forshay K, Jones SE, Kent AE, Shade AL (2006) Briding the gap between micro- and macro- scale perspectives on the role of microbial communities in global change biology. Plant Soil (this issue)

  • Banat IM, Lindstrom EB, Nedwell DB, Balba MT (1981) Evidence for coexistence of two distinct functional groups of sulfate reducing bacteria in saltmarsh sediment. Appl Environ Microbiol 42:985–992

    PubMed  CAS  Google Scholar 

  • Bardgett RD, Shine A (1999) Linkages between plant litter diversity, soil microbial biomass and ecosystem function in temperate grasslands. Soil Biol Biochem 31:317–321

    CAS  Google Scholar 

  • Basiliko N, Yavitt JB (2001) Influence of Ni, Co, Fe, and Na additions on methane production in Sphagnum-dominated Northern American peatlands. Biogeochemistry 52:133–153

    CAS  Google Scholar 

  • Bellisario LM, Bubier JL, Moore TR, Chanton JP (1999) Controls on CH4 emissions from a northern peatland. Global Biogeochem Cyc 13:81–91

    CAS  Google Scholar 

  • Bergholz PW, Bagwell CE, Lovell CR (2001) Physiological diversity of rhizoplane diazotrophs of the salt meadow cordgrass Spartina patens: implications for host specific ecotypes. Microb Ecol 42:466–473

    PubMed  CAS  Google Scholar 

  • Bhat PR, Kavrappa KM (2003) Occurance of vesicular arbuscular mycorrhizal fungi in Marsilea minuta L. Mycorrhiza News 15:11–13

    Google Scholar 

  • Blodau C, Roehm CL, Moore TR (2002) Iron, sulfur, and dissolved carbon dynamics in a northern peatland Arch. Hydrobiol 154:561–583

    CAS  Google Scholar 

  • Bohrer KE, Friese CF, Amon JP (2004) Seasonal dynamics of arbuscular mycorrhizal fungi in differing wetland habitats. Mycorrhiza 14:329–337

    PubMed  Google Scholar 

  • Boon PI, Virtue P, Nichols PD (1996) Microbial consortia in wetland sediments: a biomarker analysis of the effects of hydrological regime, vegetation and season on benthic microorganisms. Mar Freshwater Res 47:27–41

    CAS  Google Scholar 

  • Borga P, Nilsson M, Tunlid A (1994) Bacterial communities in peat in relation to botanical composition as revealed by phospholipid fatty acid analysis. Soil Biol Biochem 26:841–848

    CAS  Google Scholar 

  • Borneman J (1999) Culture-independent identification of microorganisms that respond to specified stimuli. Appl Environ Microbiol 65:3398–3400

    PubMed  CAS  Google Scholar 

  • Brauer S, Yavitt J, Zinder S (2004) Methanogenesis in McLean bog, an acidic peat bog in upstate New York: stimulation by H2/CO2 in the presence of rifampicin, or by low concentrations of acetate. Geomicrobiol J 21:433–443

    Google Scholar 

  • Brundrett MC, Ashwath N, Jasper DA (1996) Mycorrhizas in the Kakadu region of tropical Australia: Propagules of mycorrhizal fungi and soil properties in natural habitats. Plant Soil 184:159–171

    CAS  Google Scholar 

  • Brusse LB, Gunkel G (2002) Riparean alder fens- source or sink for nutrients and dissolved organic carbon? Major sources and sinks. Limnologica 32:44–53

    Google Scholar 

  • Burns A, Ryder DS (2001) Response of bacterial extracellular enzymes to inundation of floodplain sediments. Freshwater Biol 46:1299–1307

    CAS  Google Scholar 

  • Butler JL, Williams MA, Bottomley PJ, Myrold DD (2003) Microbial community dynamics associated with rhizosphere carbon flow. Appl Environ Microbiol 69:6793–6800

    PubMed  CAS  Google Scholar 

  • Calhoun A, King GM (1998) Characterization of root-associated methanotrophs from three freshwater macrophytes: Ponterderia cordata, Sparganium eucarpum, and Sagittaria latifolia. Appl Environ Microbiol 64:1099–1105

    PubMed  CAS  Google Scholar 

  • Casamatta DA, Collier AB, Jenerette GD, Verb RG (1999) Spatial heterogeny of the bacterial community in a newly rehabilitated wetland. J Freshwater Ecol 14:371–378

    Google Scholar 

  • Casey RE, Klaine SJ (2001) Nutrient attenuation by a riparian wetland during natural and artificial runoff events. J Environ Qual 30:1720–1731

    PubMed  CAS  Google Scholar 

  • Castro H, Reddy KR, Ogram A (2002) Composition and function of sulfate-reducing prokaryotes in eutrophic and pristine areas of the Florida Everglades. Appl Environ Microbiol 68:6129–6137

    PubMed  CAS  Google Scholar 

  • Cavigelli MA, Robertson GP (2000) The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology 81:1404–1414

    Google Scholar 

  • Chang TC, Yang SS (2003) Methane emission from wetlands in Taiwan. Atmos Environ 37:4551–4558

    CAS  Google Scholar 

  • Chelius MK, Lepo JE (1999) Restriction fragment length polymorphism analysis PCR-amplified nifH sequences from wetland plant rhizosphere communities. Environ Tech 20:883–889

    CAS  Google Scholar 

  • Clement JC, Pinay G, Marmonier P (2002) Seasonal dynamics of denitrification along topotydrosequences in three different riparian wetlands. J Environ Qual 31:1025–1037

    PubMed  CAS  Google Scholar 

  • Coles JRP, Yavitt JB (2002) Control of methane metabolism in a forested northern wetland, New York State, by aeration, substrates, and peat size fractions. Geomicrobiol J 193:293–315

    Google Scholar 

  • Coles JRP, Yavitt JB (2004) Linking belowground carbon allocation to anaerobic CH4 and CO2 production in a forested peatland, New York State. Geomicrobiol J 21:445–455

    CAS  Google Scholar 

  • Colmer TD (2003) Long-distance transport of gases in plants; a perspective on internal aeration and radial oxygen loss from roots. Plant Cell Environ 26:17–36

    CAS  Google Scholar 

  • Conrad R (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol Rev 60:609–643

    PubMed  CAS  Google Scholar 

  • Cornwell WK, Bedford BL, Chapin CT (2001) Occurence of arbuscular mycorrhizal fungi in a phosphorus-poor wetland and mycorrhizal response to phosphorus fertilization. Am J Bot 88:1824–1829

    Google Scholar 

  • Corstanje R, Reddy KR (2004) Response of biogeochemical indicators to a drawdown and subsequent reflood. J Environ Qual 33:2357–2366

    PubMed  CAS  Google Scholar 

  • D’Angelo EM, Reddy KR (1999) Regulators of heterotrophic microbial potentials in wetland soils. Soil Biol Biochem 31:815–830

    CAS  Google Scholar 

  • Davidsson TE, Stepanauskas R, Leonardson L (1997) Vertical patterns in nitrogen transformations during infiltration in two wetland soils. Appl Environ Microbiol 63:3648–3656

    PubMed  CAS  Google Scholar 

  • Davidsson TE, Leonardson L (1997) Seasonal dynamics of denitrification activity in two water meadows. Hydrobiologia 364:189–198

    CAS  Google Scholar 

  • Davidsson TE, Stahl M (2000) The influence of organic carbon on nitrogen transformations in five wetlands soils. Soil Sci Soc Am J 64:1129–1136

    Article  CAS  Google Scholar 

  • Davidsson TE, Trepel M, Schrautzer J (2002) Denitrification in drained and rewetted minerotrophic peat soils in Northern Germany (Pohnsdorfer Stauung). J Plant Nutr Soil Sci–Z Pflanzenernahr Bodenkd 165:199–204

    CAS  Google Scholar 

  • Dedysh SN, Panikov NS (1997a) Effect of methane concentration on the rate of its oxidation by bacteria in sphagnum peat. Microbiol NY 66:470–475

    CAS  Google Scholar 

  • Dedysh SN, Panikov NS (1997b) Effect of pH, temperature, and concentration of salts on methane oxidation kinetics in sphagnum peat. Microbiol NY 66:476–479

    CAS  Google Scholar 

  • Dedysh SN, Panikov NS, Liesack W, Grosskopf R, Jizong Z, Tiedje JM (1998a) Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands. Science 282:281–284

    CAS  Google Scholar 

  • Dedysh SN, Panikov NS, Tiedje JM (1998b) Acidophilic methanotropic communities from Sphagnum peat bogs. Appl Environ Microbiol 64:922–929

    CAS  Google Scholar 

  • Dedysh SN, Liesack W, Khmelenina VN, Suzina NE, Trotsenko YA, Semrau JD, Bares AM, Panikov NS, Tiedje JM (2000) Methylocella palustris gen. nov., sp. nov., a new methane oxidizing acidophilic bacterium from peat bogs representing a novel sub-type of serine pathway methanotrophs. Int J Syst Evol Microbiol 50:955–969

    PubMed  CAS  Google Scholar 

  • Dedysh SN (2002) Methanotrophic bacteria of acidic Sphagnum peat bogs. Microbiol Moscow 71:638–650

    CAS  Google Scholar 

  • Dedysh SN, Dunfield PF, Derakshani M, Stubner S, Heyer J, Liesack W (2003) Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes. FEMS Microbiol Ecol 433:299–308

    Google Scholar 

  • Delaune RD, Lindau CW, Sulaeman E, Jugsujinda A (1998) Nitrification and denitrification estimates in a Louisiana swamp forest soil as assessed BY N-15 isotope dilution and direct gaseous measurements. Water Air Soil Pollut 106:149–161

    CAS  Google Scholar 

  • Devito KJ, Hill AR (1999) Sulfate mobilization and pore water chemistry in relation to groundwater hydrology and summer drought in two conifer swamps on the Canadian Shield. Water Air Soil Pollut 113:97–114

    CAS  Google Scholar 

  • Dick WA, Tabatabai MA (1992) Significance and potential uses of soil enzymes. In: Metting F Blain, (ed) Soil microbial ecology. Marcel Dekker, New York, pp 95–127

    Google Scholar 

  • Duncan CP, Groffman P (1994) Comparing microbial parameters in natural and constructed wetlands. J Environ Qual 23:298–305

    Google Scholar 

  • Eaton WD (2001) Microbial and nutrient activity in soils from three different subtropical forest habitats in Belize, Central America before and during the transition from dry to wet season. App Soil Ecol 16: 219–227

    Google Scholar 

  • Edgcomb VP, McDonald JH, Devereux R, Smith DW (1999) Estimation of bacterial cell numbers in humic acid-rich saltmarsh sediments with probes to 16S ribosomal RNA. Appl Environ Microbiol 65:1516–1523

    PubMed  CAS  Google Scholar 

  • Emerson D, Wiess JV, Megonigal JP (1999) Iron oxidizing bacteria are associated with ferric hydroxide precipitates (Fe-plaque) on the roots of wetland plants. Appl Environ Microbiol 65:2758–2761

    PubMed  CAS  Google Scholar 

  • Engelaar WMHG, Symens JC, Laanbroek HJ, Blom CWPM (1995) Preservation of nitrifying capacity and nitrate availability in waterlogged soils by radial oxygen loss from roots of wetland plants. Biol Fert Soils 20:243–248

    Google Scholar 

  • Eriksson PG, Andersson JL (1999) Potential nitrification and cation exchange on litter of emergent, freshwater macrophytes. Freshwater Biol 42:479–486

    Google Scholar 

  • Feng JN, Hsieh YP (1998) Sulfate reduction in freshwater wetland soils and the effects of sulfate and substrate loading. J Environ Qual 27:968–972

    CAS  Google Scholar 

  • Flite OP, Shannon RD, Schnabel RR, Parizek RR (2001) Nitrate removal in a riparian wetland of the Appalachian Valley and ridge physiographic province. J Environ Qual 30:254–261

    PubMed  CAS  Google Scholar 

  • Fortin D, Goulet R, Roy M (2000) Seasonal cycling of Fe and S in a constructed wetland: the role of sulfate-reducing bacteria. Geomicrobiol J 17:221–235

    CAS  Google Scholar 

  • Freeman C, Liska G, Ostle NJ, Lock MA, Reynolds B, Hudson J (1996) Microbial activity and enzymic decomposition processes following peatland water table drawdown. Plant Soil 180:121–127

    CAS  Google Scholar 

  • Freeman C, Liska G, Ostle NJ, Lock MA, Hughes S, Reynolds B, Hudson J (1997) Enzymes and biogeochemical cycling in wetlands during a simulated drought. Biogeochemistry 39: 177–187

    CAS  Google Scholar 

  • Freeman C, Nevison GB, Hughes S, Reynolds B, Hudson J (1998) Enzymic involvement in the biogeochemical responses of a Welsh peatland to a rainfall enhancement manipulation. Biol Fertil Soils 27:173–178

    CAS  Google Scholar 

  • Freeman C, Ostle N, Kang H (2001) An enzymic ‘latch’ on a global carbon store. Nature 409:149

    PubMed  CAS  Google Scholar 

  • Freeman C, Nevison GB, Kang H, Hughes S, Reynolds B, Hudson J (2002) Contrasted effects of simulated drought on the production and oxidation of methane in a mid-Wales wetland. Soil Biol Biochem 34:61–67

    CAS  Google Scholar 

  • Frischer ME, Danforth JM, Healy MAN, Saunders FM (2000) Whole cell versus total RNA extraction for analysis of microbial community structure with 16S rRNA-targeted oligonucleotide probes in salt marsh sediments. Appl Environ Microbiol 66:3037–3043

    PubMed  CAS  Google Scholar 

  • Gandy EL, Yoch DC (1988) Relationship between nitrogen-fixing sulfate reducers and fermenters in salt marsh sediments and roots of Spartina alterniflora. Appl Environ Microbiol 54:2031–2036

    PubMed  CAS  Google Scholar 

  • Gauci V, Fowler D, Chapman SJ, Dise NB (2004) Sulfate deposition and temperature controls on methane emission and sulfur forms in peat. Biogeochemistry 71:141–162

    CAS  Google Scholar 

  • Gilliam JW (1994) Riparian wetlands and water quality. J Environ Qual 23:896–900

    Google Scholar 

  • Glenn MG, Wagner WS, Webb SL (1991) Mycorrhizal status of mature Red Spruce (Picea-Rubens) mesic wetlands sites of northwestern New Jersey. Can J For Res (Revue Canadiennne Ce Recherche Forestiere) 21:741–749

    Google Scholar 

  • Goodroad LL, Keeny DR (1984) Nitrous oxide emission from forest, marsh, and prairie ecosystems. J Environ Qual 13:448–452

    CAS  Google Scholar 

  • Graham PH (2005) Biological dinitrogen fixation: symbiotic. In: Sylvia DM, Fuhrman J, Hartel PG, Zuberer DA (eds) Principles and applications of soil microbiology, 2nd edn. Prentice Hall, Upper Saddle River NJ, pp 405–432

  • Granberg G, Sundh I, Svensson BH, Nilsson M (2001) Effects of temperature, and nitrogen and sulfur deposition, on methane emission from a boreal mire. Ecology 82:1982–1998

    Google Scholar 

  • Groffman PM, Hanson GC, Kivat E, Stevens G (1996) Variation in microbial biomass and activity in four different wetland types. Soil Sci Soc Am J 60:622–629

    Article  CAS  Google Scholar 

  • Groffman PM, Hanson G (1997) Wetland denitrification: influence of site quality and relationships with wetland delineation protocols. Soil Sci Soc Am J 61:323–329

    Article  CAS  Google Scholar 

  • Groffman PM, Crawford MK (2003) Denitrification potential in urban riparian zones. J Environ Qual 32:1144–1149

    PubMed  CAS  Google Scholar 

  • Gusewell S, Freeman C (2003) Enzyme activity during N and P limited decomposition of wetland plant litter. Bulletin of the Geobotanical institute ETH 69:95–106

    Google Scholar 

  • Halbritter A, Mogyorossy T (2002) Phospholipid fatty acid (PLFA) analysis of rhizosphere bacterial communities in a peat soil. Agrokemia et Talajtan 51:123–128

    CAS  Google Scholar 

  • Hanson GC, Groffman PM, Gold AJ (1994) Denitrification in riparian wetlands receiving high and low groundwater nitrate inputs. J Environ Qual 23:917–922

    CAS  Google Scholar 

  • Hargreaves KJ, Fowler D (1998) Quantifying the effects of water table and soil temperature on the emission of methane from peat wetland at the field scale. Atmos Environ 32:3275–3282

    CAS  Google Scholar 

  • Hines ME, Evans RS, Genthner BRS, Willis SG, Friedman S, Rooney-Varga JN, Devereux R (1999) Molecular Phylogenetic and biochemical studies of sulfate-reducing bacteria in the rhizosphere of Spartina alterniflora. Appl Environ Microbiol 65:2209–2216

    PubMed  CAS  Google Scholar 

  • Horz HP, Raghubanshi AS, Heyer E, Kammann C, Conrad R, Dunfield PF (2002) Activity and community structure of methane-oxidizing bacteria in a wet meadow soil. FEMS Microbiol Ecol 41:247–257

    CAS  PubMed  Google Scholar 

  • Huang G, Li X, Hu Y, Shi Y, Xiao D, Blove B, Mander U (2005) Methane CH4 emission from a natural wetland in northern China. J Environ Sci Health 40:1227–1238

    CAS  Google Scholar 

  • Hume NP, Fleming MS, Horne AJ (2002) Denitrification potential and carbon quality of four aquatic plants in wetland microcosms. Soil Sci Soc Am J 66:1706–1712

    Article  CAS  Google Scholar 

  • Hunter RG, Faulkner SP (2001) Denitrification potentials in restored and natural bottomland hardwood wetlands. Soil Sci Soc Am J 65:1865–1872

    Article  CAS  Google Scholar 

  • Huttunen JT, Nykanen H, Turunen J, Martikainen PJ (2003) Methane emissions from natural peatlands in the northern boreal zone in Finland, Fennoscandia. Atmos Environ 37:147–151

    CAS  Google Scholar 

  • Ingham ER, Wilson MV (1999) The mycorrhizal colonization of six wetland plant species at sites differing in land use history. Mycorrhiza 9:233–235

    Google Scholar 

  • Jayachandran K, Shetty KG (2003) Growth response and phosphorus uptake by arbuscular mycorrhizae of wet prairie sawgrass. Aquat Bot 76:281–290

    CAS  Google Scholar 

  • Johnston CA, Bridgham SD, Schubauer-Berigan JP (2001) Nutrient dynamics in relation to geomorphology of riverine wetlands. Soil Sci Soc Am J 65:557–577

    Article  CAS  Google Scholar 

  • Jordan TE, Weller DE, Correll DL (1998) Denitrification in surface soils of a riparian forest: effects of water, nitrate, and sucrose additions. Soil Biol Biochem 30:833–843

    CAS  Google Scholar 

  • Kang HJ, Freeman C, Lee D, Mitsch WJ (1998) Enzyme activities in constructed wetlands: implication for water quality amelioration. Hydrobiologia 368:231–235

    CAS  Google Scholar 

  • Kang HJ, Freeman C (1999) Phosphatase and arylsulfatase activities in wetland soils: annual variation and controlling factors. Soil Biol Biochem 31:449–454

    CAS  Google Scholar 

  • Kao JT, Titus JE, Zhu WX (2003) Differential nitrogen and phosphorus retention by five wetland plant species. Wetlands 23:979–987

    Google Scholar 

  • Kao-Kniffin J, Balser TC Elevated CO2 differetially alters belowground plant and soil microbial community structure in reed canary grass-invaded experimental wetlands. Soil Biol Biochem (in press)

  • Kemnitz D, Chin K, Bodelier P, Conrad R (2004) Community analysis of methanogenic archaea within a riparian flooding gradient. Environ Microbiol 6:449–461

    PubMed  CAS  Google Scholar 

  • Kercher SM, Zedler JB (2004) Multiple disturbances accelerate invasion of reed canary grass (Phalaris arundinacea L.) in a mesocosm study. Oecologia 138:455–464

    PubMed  Google Scholar 

  • Kim J, Verma SB, Billesbach DP (1998) Seasonal variation in methane emission from a temperate Phragmites-dominated marsh: effect of growth stage and plant-mediated transport. Global Change Biol 5:433–440

    Google Scholar 

  • King GM (1996) Regulation by light of methane emissions from a wetland. Nature 345:513–515

    Google Scholar 

  • Kirkham FW, Wilkins RJ (1993) Seasonal fluctuations in the mineral nitrogen-content of an undrained wetland peat soil following differing rates of fertilizer nitrogen application. Agric Ecosyst Environ 43:11–29

    CAS  Google Scholar 

  • Klepac-Ceraj V, Bahr M, Crump BC, Teske AP, Hobbie JE, Polz MF (2004) High overall diversity and dominance of microdiverse relationships in salt marsh sulphate reducing bacteria. Environ Microbiol 6:686–698

    PubMed  CAS  Google Scholar 

  • Koretsky CM, Moore CM, Lowe KL, Meile C, DiChristina TJ, Van Cappellen P (2003) Seasonal oscillation of microbial iron and sulfate reduction in salt marsh sediments (Sapelo island USA). Biogeochemistry 64:179–203

    CAS  Google Scholar 

  • Kristensen E, Jensen MH, Banta GT, Hansen K, Holmer M, King JM (1998) Transformation and transport of inorganic nitrogen in sediments of a southeast Asian mangrove forest. Aquat Microbiol Ecol 15:165–175

    Google Scholar 

  • Kuschk P, Wiessner A, Kappelmeyer U, Weissbrodt E, Kastner M, Stottmeister U (2003) Annual cycle of nitrogen removal by a pilot-scale subsurface horizontal flow in a constructed wetland under moderate climate. Water Res 37:4236–4242

    PubMed  CAS  Google Scholar 

  • Kusel K, Chabbi A, Trinkwalter T (2003) Microbial processes associated with roots of bulbous rush coated with iron plaques. Microb Ecol 46:302–311

    PubMed  CAS  Google Scholar 

  • Leloup J, Quillet L, Oger C Boust D, Petit F (2004) Molecular quantification of sulfate-reducing microorganisms (Carrying dsr AB genes) by competetive PCR in estuarine sediments. FEMS Microbiol Ecol 47:207–214

    CAS  PubMed  Google Scholar 

  • Le Mer J, Roger P (2001) Production, oxidation, emission and consumption of methane by soils: a review. Eur J Soil Biol 37: 25–50

    CAS  Google Scholar 

  • Lowe KL, DiChristina TJ, Roychoundhury AN, Van Cappellen V (2000) Microbial and geochemical characterization of microbial Fe(III) reduction in salt marsh sediments. Geomicrob J 17:163–178

    CAS  Google Scholar 

  • Lowrance R, Vellidis G, Hubbard RK (1995) Denitrification in a restored riparian forest wetland. J Environ Qual 24:808–815

    CAS  Google Scholar 

  • Macdonald JA, Fowler D, Hargreaves KJ, Skiba U, Leith ID, Murray MB (1998) Methane emission rates from a northern wetland; response to temperature, water, table and transport. Atmos Environ 32:3219–3227

    CAS  Google Scholar 

  • MacGregor BJ, Bruchert V, Fleischer S, Amann R (2002) Isolation of smallsubunit rRNA for stable isotopic characterization. Environ Microbiol 4:451–464

    PubMed  CAS  Google Scholar 

  • Matheson FE, Nguyen ML, Cooper AB, Burt TP (2003) Short-term nitrogen transformation rates in riparian wetland soil determined with nitrogen-15. Biol Fert Soil 38:129–136

    CAS  Google Scholar 

  • Mausbach MJ, Parker WB (2001) Background and history of the concept of hydric soils. In: Richardson JL, Vepraskas MJ (eds) Wetland soils. Lewis, New York, pp 19–34

    Google Scholar 

  • Megonigal JP, Schlesinger WH (2002) Methane-limited methanotrophy in tidal freshwater swamps. Global Biogeochem Cycles 16:1088–1098

    Google Scholar 

  • Mentzer JL, Goodman R, Balser TC (2006) Microbial seasonal response to hydrologic and fertilization treatments in a simulated wet prairie. Plant Soil 284:85–100

    CAS  Google Scholar 

  • Miller SP, Bever JD (1999) Distribution of arbuscular mycorrhizal fungi in stands of the wetland grass Panicum hemitomon along a wide hydrologic gradient. Oecologia 119:586–592

    Google Scholar 

  • Myrold DD (2005) Transformations of nitrogen. In: Sylvia DM, Fuhrman J, Hartel PG, Zuberer DA (eds) Principles and applications of soil microbiology, 2nd edn. Prentice Hall, Upper Saddle River, pp 333–372

    Google Scholar 

  • Nedwell DB, Embley TM, Purdy KJ (2004) Sulphate reduction, methanogenesis, and phylogenetics of the sulphate reducing communities along an estuarine gradient. Aquat Microb Ecol 37:209–217

    Google Scholar 

  • Neubauer SC, Emerson D, Megonigal JP (2002) Life at the energetic edge: kinetics circumneutral iron oxidation by lithotrophic iron-oxidizing bacteria isolated from the wetland-plant rhizosphere. Appl Environ Microbiol 68:3988–3995

    PubMed  CAS  Google Scholar 

  • Otto S, Groffman PM, Findlay SEG, Arreola AE (1999) Invasive plant species and microbial processes in a tidal freshwater marsh. J Environ Qual 28:1252–1257

    CAS  Google Scholar 

  • Pavel EW, Reneau RB, Berry DF, Smith EP, Mostaghimi S (1996) Denitrification potential of nontidal riparian wetland soils in the Virginia coastal plain. Water Res 30:2798–2804

    CAS  Google Scholar 

  • Prieme A, Braker G, Tiedje JM (2002) Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl Environ Microbiol 68:1893–1900

    PubMed  CAS  Google Scholar 

  • Qiu S, McComb AJ (1996) Drying-induced stimulation of ammonium release and nitrification in reflooded lake sediment. Mar Freshwater Res 47:531–536

    CAS  Google Scholar 

  • Radajewski S, McDonald IR, Murrell JC (2003) Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms. Curr Opin Biotechnol 14:296–302

    PubMed  CAS  Google Scholar 

  • Rask H, Schoenau J, Anderson D (2002) Factors influencing methane flux from a boreal forest wetland in Saskatchewan, Canada. Soil Biol Biochem 34:435–443

    CAS  Google Scholar 

  • Ravit B, Ehrenfeld JG, Haggblom MM (2003) A comparison of sediment microbial communities associated with Phragmites australis and Spartina alterniflora in two brackish wetlands of New Jersey. Estuaries 26:465–474

    Article  Google Scholar 

  • Rickerl DH, Sancho SO, Anath S (1994) Vesicular-arbuscular endomycorrhizal colonization of wetland plants. J Environ Qual 23:913–916

    Google Scholar 

  • Roden EE, Wetzel RG (1996) Organic carbon oxidation and suppression of methane production by microbial Fe(III) oxide reduction in vegetated and unvegetated freshwater wetland sediments. Limnol Oceanogr 41:1733–1748

    Article  CAS  Google Scholar 

  • Roden EE, Wetzel RG (2002) Kinetics of microbial Fe(III) oxide reduction in freshwater wetland sediments. Limnol Oceanogr 47:198–211

    Article  CAS  Google Scholar 

  • Roden EE, Wetzel RG (2003) Competition between Fe(III)-reducing and methanogenic bacteria for acetate in iron-rich freshwater sediments. Microb Ecol 45:252–258

    PubMed  CAS  Google Scholar 

  • Roden EE (2003) Diversion of electron flow from methanogenesis to crystalline Fe(III) oxide reduction in carbon-limited cultures of wetland sediment microorganisms. Appl Environ Microbiol 69:5702–5706

    PubMed  CAS  Google Scholar 

  • Schimel J, Balser TC, Wallenstein M Stress effects on microbial communities and the implications for ecosystem function. Ecology (in press)

  • Schimel J (2004) Playing scales in the methane cycle: from microbial ecology to the globe. Proc Natl Acad Sci 101:12400–12401

    PubMed  CAS  Google Scholar 

  • Schimel J.P., Gulledge J. (1998) Microbial community structure and global trace gases. Global Change Biol 4:745–758

    Google Scholar 

  • Schipper LA, Cooper AB, Harfoot CG, Dyck WJ (1993) Regulators of denitrification in an organic riparian soil. Soil Biol Biochem 25:925–933

    CAS  Google Scholar 

  • Segers R (1998) Methane production and methane consumption: a review of processes underlying wetland methane fluxes. Biogeochemistry 41:23–51

    CAS  Google Scholar 

  • Seitzinger SP (1994) Linkages between organic-matter mineralization and denitrification in 8 riparian wetlands. Biogeochemistry 25:19–39

    CAS  Google Scholar 

  • Shackle VJ, Freeman C, Reynolds B (2000) Carbon supply and the regulation of enzyme activity in constructed wetlands. Soil Biol Biochem 32:1935–1940

    CAS  Google Scholar 

  • Sizova MV, Panikov NS, Tourova TP, Flanagan PW (2003) Isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a Sphagnum peat bog. FEMS Microbiol Ecol 45:301–315

    CAS  PubMed  Google Scholar 

  • Smith CJ, Delaune RD (1984) Influence of the rhizosphere of Spartina alterniflora Loisel. on nitrogen loss from a Louisiana gulf coast salt marsh. Environ Exp Bot 24:91–93

    Google Scholar 

  • Smith MS, Tiedje JM (1979) Phases of denitrification following oxygen depletion in soil. Soil Biol Biochem 11:261–267

    CAS  Google Scholar 

  • Sobolev D, Roden EE (2002) Evidence for rapid microscale bacterial redox cycling of iron in circum neutral environments. Antonie van Leeuwenhoek 81:587–597

    PubMed  CAS  Google Scholar 

  • Sparks DL (2003) Environmental soil chemistry, 2nd edn. Crumly CR et al. (eds) Academic Press, San Diego, pp 269–270

  • Stenlund DL, Charvat ID (1994) Vesicular-arbuscular mycorrhizae in floating wetland mat communities dominated by Typha. Mycorrhiza 4:131–137

    Google Scholar 

  • Stepanauskas R, Davidsson ET, Leonardson L (1996) Nitrogen transformations in wetland soil cores measure by (sup15)N isotope pairing and dilution at four infiltration rates. Appl Environ Microbiol 62:2345–2351

    PubMed  CAS  Google Scholar 

  • Stevens KJ, Spender SW, Peterson RL (2002) Phosphorus, arbuscular mycorrhizal fungi and performance of the wetland plant Lythrum salicaria L. under inundated conditions. Mycorrhiza 12:277–283

    PubMed  CAS  Google Scholar 

  • Strom L, Ekberg A, Mastepanov M, Christensen TR (2003) The effect of vascular plants on carbon turnover and methane emissions from a tundra wetland. Global Change Biol 9:1185–1192

    Google Scholar 

  • Sundh I, Nilsson M, Borga P (1997) Variation in microbial community structure in two boreal peatlands as determined by analysis of phospholipids fatty acid profiles. Appl Environ Microbiol 63:1476–1482

    PubMed  CAS  Google Scholar 

  • Tanner CC, D’Eugenio J, McBride GB, Sukias JPS(1999) Effect of water level fluctuation on nitrogen removal from constructed wetland mesocosms. Ecol Eng 12:67–92

    Google Scholar 

  • Tiedje JM, Amsung-Brempong S, Nusslein K, Marsh TL, Flynn SJ (1999) Opening the black box of microbial diversity. Appl Soil Ecol 13:109–122

    Google Scholar 

  • Tobias CR, Anderson IC, Canuel EA, Macho SA (2001) Nitrogen cycling through a fringing marsh-aquifer ectone. Mar Ecol Prog Ser 210:25–39

    CAS  Google Scholar 

  • Tomaszek JA, Gardner WS, Johengen TH (1997) Denitrification in sediments of a Lake Erie coastal wetland (Old Woman Creek, Huron, Ohio, USA). J Great Lakes Res 23:403–415

    Article  CAS  Google Scholar 

  • Treseder KK, Allen MF (2000) Mycorrhizal fungi have a potential role in soil carbon storage under elevated CO2 and nitrogen deposition. New Phytol 147:189–200

    CAS  Google Scholar 

  • Turner SD, Friese CF (1998) Plant-mycorrhizal community dynamics associated with a moisture gradient within a rehabilitated fen. Restor Ecol 6:44–51

    Google Scholar 

  • Turner SD, Amon JP, Schneble RM, Friese CF (2000) Mycorrhizal fungi associated with plants in ground-water fed wetlands. Wetlands 20:200–204

    Google Scholar 

  • Updegraff K, Bridgham SD, Pastor J, Weishampel P (1998) Hysteresis in the temperature response of carbon dioxide and methane production in peat soils. Biogeochemistry 43:253–272

    CAS  Google Scholar 

  • Utsumi M, Belova SE, King GM, Uchiyama H (2003) Phylogenetic comparison of methanogen diversity in different wetland soils. J Gen Appl Microbiol 49:75–83

    PubMed  CAS  Google Scholar 

  • Van den Pol-Van Dasselaar A, Van Beusichem ML, Oenema O (1999) Methane emissions from wet grasslands on peat soil in a nature preserve. Biogeochemistry 44:205–220

    Article  Google Scholar 

  • VanderNat F, DeBrouwer JFC, Middelburg JJ, Laanbroek HJ (1997) Spatial distribution and inhibition by ammonium of methane oxidation in intertidal freshwater marshes. Appl Environ Microbiol 63:4734–4740

    CAS  Google Scholar 

  • Van Hoewyk D, Groffman PM, Kiviat E, Mihocko G, Stevens G (2000) Soil nitrogen dynamics in organic and mineral soil calcareous wetlands in eastern New York. Soil Sci Soc Am J 64:2168–2173

    Article  Google Scholar 

  • Venterink HO, Davidsson TE, Kiehl K, Leonardson L (2002) Impact of drying and re-wetting on N, P and K dynamics in a wetland soil. Plant Soil 243:119–130

    CAS  Google Scholar 

  • Verhoeven JTA, Keuter A, VanLogtestijn R, VanKerkhoven MB, Wassen M (1996) Control of local nutrient dynamics is mired by regional and climatic factors: a comparison of Dutch and Polish sites. J Ecol 84:647–656

    Google Scholar 

  • Vile MA, Bridgham SD, Wieder RK (2003a) Response of anaerobic carbon mineralization rates to sulfate amendments in a boreal peatland. Ecol Appl 13:720–734

    Google Scholar 

  • Vile MA, Bridgham SD, Wieder RK, Novak M (2003b) Atmospheric sulfur deposition alters pathways of gaseous carbon production in peatlands. Global Biogeochem Cycles 17:1058–1065

    Google Scholar 

  • Wartiainen I, Hestness AG, Svenning MM (2003) Methanotrophic diversity in high arctic wetlands on the islands of Svalbard (Norway)-denaturing gradient gel electrophoresis analysis of soil DNA and enrichment cultures. Can J Microbiol 49:602–612

    PubMed  Google Scholar 

  • Weider RK, Yavitt JB (1991) Assessment of site differences in anaerobic carbon mineralization using reciprocal peat transplants. Soil Biol Biochem 23:1093–1095

    Google Scholar 

  • Weiss JV, Emerson D, Backer SM, Megonigal JP (2003) Enumeration of Fe(II)-oxidizing and Fe(III)-reducing bacteria in the root zone of wetland plants: implications for a rhizosphere iron cycle. Biogeochemistry 64:77–96

    CAS  Google Scholar 

  • Weiss JV, Emerson D, Megonigal JP (2004) Geochemical control of microbial Fe (III) reduction potential in wetlands: comparison of the rhizosphere to non-rhizosphere soil. FEMS Microbiol Ecol 48:89–100

    CAS  PubMed  Google Scholar 

  • Westermann P, Ahring BK (1987) Dynamics of methane production, sulfate reduction, and dentrification in a permanently waterlogged alter swamp. Appl Environ Microbiol 53:2554–2559

    PubMed  CAS  Google Scholar 

  • Westermann P (1993) Temperature regulation of methanogenesis in wetlands. Chemosphere 26:321–328

    CAS  Google Scholar 

  • Wetzel PR, VanderValk AG (1996) Vesicular-arbuscular mycorrhizae in prairie pothole wetland vegetation in Iowa and North Dakota. Can J Bot (Revue Canadiennne De Botanique) 74:883–890

    Google Scholar 

  • White JA, Charvat I (1999) The mycorrhizal status of an emergent aquatic, Lythrum salicaria L., at different levels of phosphorus availability. Mycorrhiza 9:191–197

    CAS  Google Scholar 

  • White JR, Reddy KR (1999) Influence of nitrate and phosphorus loading on denitrifying enzyme activity in Everglades wetland soils. Soil Sci Soc Am J 63:1945–1954

    Article  CAS  Google Scholar 

  • Wickland KP, Striegl RG, Schmidt SK, Mast MA (1999) Methane flux in subalpine wetland and unsaturated soils in the southern Rocky Mountains. Global Biogeochem Cycles 13:101–113

    CAS  Google Scholar 

  • Willems HPL, Rotelli MD, Berry DF, Smith EP, Reneau RB, Mostaghimi S (1997) Nitrate removal in riparian wetland soils: effects of flow rate, temperature, nitrate concentration and soil depth. Water Res 31:841–849

    CAS  Google Scholar 

  • Williams CJ, Shingara EA, Yavit JB (2000) Phenol oxidase activity in peatlands in New York State: response to summer drought and peat type. Wetlands 20:416–421

    Google Scholar 

  • Wirsel SGR (2004) Homogenous stands of wetland grass harbour diverse consortia of arbuscular mycorrhizal fungi. FEMS Microbiol Ecol 48:129–138

    CAS  PubMed  Google Scholar 

  • Wolf DC, Wagner GH (2005) Carbon transformations and soil organic matter formation. In: Sylvia DM, Fuhrman J, Hartel PG, Zuberer DA (eds) Principles and applications of soil microbiology, 2nd edn. Prentice Hall, Upper Saddle River pp 285–332

    Google Scholar 

  • Wolters V, Silver WL, Bignell DE, Coleman DC, Lavelle P, Van Der Putten WH, Ruiter DEP, Rusek J, Wall DH, Wardle DA, Brussard L, Dangerfield JM, Brown VK, Giller KE, Hooper DU, Sala O, Tiedje J, Van Veen JA (2000) Effects of global changes on above- and below ground biodiversity in terrestrial ecosystems: implications for ecosystem functioning. BioScience 50:1089–1098

    Google Scholar 

  • Wright AL, Reddy KR (2001) Phosphorus loading effects on extracellular enzyme activity in everglades wetland soils. Soil Sci Soc Am J 65:588–595

    Article  CAS  Google Scholar 

  • Yavitt JB, Lang GE (1990) Methane production in contrasting wetland sites—response to organic-chemical components of peat and to sulfate reduction. Geomicrobiol J 8:27–46

    Article  CAS  Google Scholar 

  • Yavitt JB, Williams CJ, Wieder RK (2000) Controls on microbial production of methane and carbon dioxide in three Sphagnum-dominated peatland ecosystems as revealed by a reciprocal field peat transplant experiment. Geomicrobiol J 17:61–88

    CAS  Google Scholar 

  • Yavitt JB, Wright SJ, Weider RK (2004) Seasonal drought and dry-season irrigation influence leaf litter nutrients and soil enzymes in a moist, lowland forest in Panama. Austral Ecol 29:177–188

    Google Scholar 

  • Yavitt JB, Williams CJ, Weider RK (2005) Soil chemistry versus environmental controls on production of CH4 and CO2 in northern peatlands. Eur J Soil Sci 56:169–178

    CAS  Google Scholar 

  • Zak DR, Grigal DF (1991) Nitrogen mineralization, nitrification and denitrification in upland and wetland ecosystems. Oecologia 88:189–196

    Google Scholar 

  • Zhu WX, Ehrenfeld JG (1999) Nitrogen mineralization and nitrification in suburban and undeveloped Atlantic white cedar wetlands. J Environ Qual 28:523–529

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank the Balser lab for general support and the Andrew W. Mellon Foundation and NSF DEB–45652 for funding. Dr. Erica Smithwick and Ann Curtis provided editorial input. We thank Dr. David Bart for stimulating discussion of wetland ecosystems and processes. Comments from two anonymous reviewers and subject editor Chris Neill helped to substantially improve the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Teri C. Balser.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gutknecht, J.L.M., Goodman, R.M. & Balser, T.C. Linking soil process and microbial ecology in freshwater wetland ecosystems. Plant Soil 289, 17–34 (2006). https://doi.org/10.1007/s11104-006-9105-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11104-006-9105-4

Keywords

Navigation