Ecological Aspects of Microbes and Microbial Communities Inhabiting the Rhizosphere of Wetland Plants

  • Paul L. E. Bodelier
  • Peter Frenzel
  • Harold L. Drake
  • Thomas Hurek
  • Kirsten Küsel
  • Charles Lovell
  • Patrick Megonigal
  • Barbara Reinhold-Hurek
  • Brian Sorrell
Part of the Ecological Studies book series (ECOLSTUD, volume 190)


Salt Marsh Rice Field Paddy Soil Wetland Plant Biological Nitrogen Fixation 
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  1. Armstrong W, Beckett PM (1987) Internal aeration and the development of stelar anoxia in submerged roots. A multishelled mathematical model combining axial diffusion of oxygen in the cortex with radial losses to the stele, the wall layers and the rhizosphere. New Phytol 105:221–245CrossRefGoogle Scholar
  2. Armstrong J, Armstrong W, Beckett PM (1992) Phragmites australis: venturi-and humidity-induced pressure flows enhance rhizome aeration and rhizosphere oxidation. New Phytol 120:197–207CrossRefGoogle Scholar
  3. Armstrong W, Justin SHFW, Beckett PM, Lythe S (1991) Root adaptation to soil waterlogging. Aquat Bot 39:57–73CrossRefGoogle Scholar
  4. Armstrong W, Brändle R, Jackson MB (1994) Mechanisms of flood tolerance in plants. Acta Bot Neerl 43:307–358Google Scholar
  5. Armstrong W, Cousins D, Armstrong J, Turner DW, Beckett PM (2000) Oxygen distribution in wetland plant roots and permeability barriers to gas-exchange with the rhizosphere: a microelectrode and modelling study with Phragmites australis. Ann Bot 86:687–703CrossRefGoogle Scholar
  6. Bagwell CE, Lovell CR (2000) Persistence of selected Spartina alterniflora rhizoplane diazotrophs exposed to natural and manipulated environmental variability. Appl Environ Microbiol 66:4625–4633CrossRefGoogle Scholar
  7. Bagwell CE, Lovell CR (2004) A DNA-DNA hybridization method for the detection and quantification of specific bacterial taxa in natural environments. In: Spencer JFT, Ragout de Spencer AL (eds) Environmental microbiology, Humana, Totowa, pp 169–174Google Scholar
  8. Bagwell CE, Dantzler M, Bergholz, PW, Lovell CR (2001) Host specific ecotypic diversity of rhizoplane diazotrophs of the perennial glasswort, Salicornia virginica and selected salt marsh grasses. Aquat Microb Ecol 23:293–300Google Scholar
  9. Blom CWPM, Voesenek LACJ (1996) Flooding: the survival strategies of plants Trends Evol Ecol 11:290–295CrossRefGoogle Scholar
  10. Boddey RM (1995) Biological nitrogen fixation in sugar cane: a key to energetically viable biofuel production. Critical Rev Plant Sci 14:263–279Google Scholar
  11. Bodelier PLE, Laanbroek HJ (2004) Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiol Ecol 47:265–277CrossRefGoogle Scholar
  12. Bodelier PLE, Roslev P, Henckel T, Frenzel P (2000) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403:421–424CrossRefGoogle Scholar
  13. Boschker HTS, Nold SC, Wellsbury P, Bos D, DeGraaf W, Pel R, Parkes RJ, Cappenberg TE (1998) Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392:801–805CrossRefGoogle Scholar
  14. Bosse U, Frenzel P (1997) Activity and distribution of methane-oxidizing bacteria in flooded rice soil microcosms and in rice plants (Oryza sativa). Appl Environ Microbiol 63:1199–1207Google Scholar
  15. Bouma TJ, Nielsen KL, Hal B van, Koudstaal B (2001) Root system topology and diameter distribution of species from habitats differing in inundation frequency. Funct Ecol 15: 360–369CrossRefGoogle Scholar
  16. Brown MM, Friez MJ, Lovell CR (2003) Expression of nifH genes by diazotrophic bacteria in the rhizosphere of short form Spartina alterniflora. FEMS Microbiol Ecol 43:411–417CrossRefGoogle Scholar
  17. Cassman KG, De Datta SK, Olk DC, Alcantara JM, Samson MI, Descalsota JP, Dizon MA (1995) Yield decline and the nitrogen economy of long-term experiments on continuous, irrigated rice systems in the tropics. In: Lal R, Stewart BA (eds) Soil management: experimental basis for sustainability and environmental quality, Lewis/CRC, Boca Raton, pp 181–222Google Scholar
  18. Conrad R, Frenzel P (2002) Flooded soils. In: Britton G (ed) Encyclopedia of environmental microbiology. Wiley, New York, pp 1316–1333Google Scholar
  19. Conrad R, Rothfuss F (1991) Methane oxidation in the soil surface layer of a flooded ride field and the effect of ammonium. Biol Fertil Soils 12:28–32CrossRefGoogle Scholar
  20. Conrad R, Bak F, Seitz H.J Thebrath B, Mayer HP Schütz H (1989) Hydrogen turnover by psychrotrophic homoacetogenic and mesophilic methanogenic bacteria in anoxic paddy soil and lake sediment. FEMS Microbiol Ecol 62:285–294CrossRefGoogle Scholar
  21. Conrad R, Klose M, Claus P (2002) Pathway of CH4 formation in anoxic rice field soil and rice roots determined by 13C-stable isotope fractionation. Chemosphere 47:797–806CrossRefGoogle Scholar
  22. Cypionka, H (2000) Oxygen respiration by Desulfovibrio species. Annu Rev Microbiol 54:827–848CrossRefGoogle Scholar
  23. Dannenberg S, Conrad R (1999) Effect of rice plants on methane production and rhizospheric metabolism in paddy soil. Biogeochemistry 45:53–71Google Scholar
  24. Das A, Coulter ED, Kurtz DM Jr, Ljungdahl LG (2001) Five-gene cluster in Clostridium thermoaceticum consisting of two divergent operons encoding rubredoxin oxidoreductase — rubredoxin and rubrerythrin-type flavodoxin — high-molecular-weight rubredoxin. J Bacteriol 183:1560–1567CrossRefGoogle Scholar
  25. Dedysh SN, Ricke P, Liesack W (2004) NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria. Mikrobiologia 48:592–598Google Scholar
  26. Denier van der Gon HAC, Bodegom PM van, Houweling S, Verburg PH, Breemen N van (2000) Combining upscaling and downscaling of methane emissions from rice fields: Methodologies and preliminary results. Nutr Cycl Agroecosyst 58:285–301CrossRefGoogle Scholar
  27. Drake HL, Küsel K, Matthies C (2002) Ecological consequences of the phylogenetic and physiological diversities of acetogens. Antonie van Leeuwenhoek 81:203–213CrossRefGoogle Scholar
  28. Drake HL, Küsel K, Matthies C (2004) Acetogenic prokaryotes. In: Dworkin M, et al. (eds) The prokaryotes, 3rd edn: an evolving electronic resource for the microbiological community, rel 3.17. Springer, New York,, accessed August 2004Google Scholar
  29. Eller G, Stubner S, Frenzel P (2001) Group specific 16S rRNA targeted probes for the detection of type I and type II methanotrophs by fluorescence in situ hybridisation. FEMS Microbiol Lett 198:91–97CrossRefGoogle Scholar
  30. Eller G, Krüger M, Frenzel P (2005) Comparing field and microcosm experiments: A case study on methano-and methylotrophic bacteria in paddy soil. FEMS Microbiol Ecol 51:279–291CrossRefGoogle Scholar
  31. Emerson D (2000) Microbial oxidation of Fe(II) and Mn(II) at circumneutral pH. In: Lovley DR (ed) Environmental microbe-metal interactions. ASM, Washington, D.C., pp 31–52Google Scholar
  32. Emerson D, Moyer C (1997) Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH. Appl Environ Microbiol 63:4784–4792Google Scholar
  33. Emerson D, Weiss JV, Megonigal JP (1999) Iron-oxidizing bacteria are associated with ferric hydroxide precipitates (Fe-plaque) on the roots of wetland plants. Appl Environ Microbiol 65:2758–2761Google Scholar
  34. Engelhard M, Hurek T, Reinhold-Hurek B (2000) Preferential occurrence of diazotrophic endophytes, Azoarcus spp, in wild rice species and land races of Oryza sativa in comparison with modern races. Environ Microbiol 2:131–141CrossRefGoogle Scholar
  35. FAO (2004) FAOstat data. FAO, RomeGoogle Scholar
  36. Flessa H, Fischer WR (1992) Redox processes in the rhizosphere of terrestrial and paludal plants. Z Pflanzenernaehr Bodenk 155:373–378Google Scholar
  37. Frenzel P (2000) Plant-associated methane oxidation in ricefields and wetlands. Adv Microb Ecol 16:85–114Google Scholar
  38. Frenzel P, Rothfuss F, Conrad R (1992) Oxygen profiles and methane turnover in a flooded rice microcosm. Biol Fertil Soils 14:84–89CrossRefGoogle Scholar
  39. Frenzel P, Bosse U, Janssen PH (1999) Rice roots and methanogenesis in a paddy soil: ferric iron as an alternative electron acceptor in the rooted soil. Soil Biol Biochem 31:421–430CrossRefGoogle Scholar
  40. Galloway JN, Schlesinger WH, Levy HI, Michaels AF, Schnoor JL (1995) Nitrogen fixation: anthropogenic enhancement-environmental response. Global Biogeochem Cycles 9:235–252CrossRefGoogle Scholar
  41. Giblin AE, Howarth RW (1984) Pore water evidence for a dynamic sedimentary iron cycle in salt marshes. Limnol Oceanogr 29:47–63Google Scholar
  42. Gilbert B, Aßmus B, Hartmann A, Frenzel P (1998) In situ localization of two methanotrophic strains in the rhizosphere of rice plants by combined use of fluorescently labeled antibodies and 16S rRNA signature probes. FEMS Microbiol Ecol 25:117–128CrossRefGoogle Scholar
  43. Gößner A, Devereux R, Ohnemüller N, Acker G, Stackebrandt E, Drake HL (1999) Thermicanus aegyptius gen. nov., sp. nov., isolated from oxic soil, a facultative microaerophile that grows commensally with the thermophilic acetogen Moorella thermoacetica. Appl Environ Microbiol 65:5124–5133Google Scholar
  44. Gribsholt B, Kostka JE, Kristensen E (2003) Impact of fiddler crabs and plant roots on sediment biogeochemistry in a Georgia saltmarsh. Mar Ecol Prog Ser 259:237–251Google Scholar
  45. Hamelin J, Fromin N, Tarnawski S, Teyssier-Cuvelle S, Aragno M (2002) NifH gene diversity in the bacterial community associated with the rhizosphere of Molinia coerulea, an oligonitrophilic perennial grass. Environ Microbiol 4:477–481CrossRefGoogle Scholar
  46. Hauck S, Benz M, Brune A, Schink B (2001) Ferrous iron oxidation by denitrifying bacteria in profundal sediments of a deep lake (Lake Constance). FEMS Microbiol Ecol 37:127–134CrossRefGoogle Scholar
  47. Henckel T, Friedrich M, Conrad R (1999) Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl Environ Microbiol 65:1980–1990Google Scholar
  48. Heyer J, Galchenko VF, Dunfield PF (2002) Molecular phylogeny of type II methane-oxidizing bacteria isolated from various environments. Microbiol SGM 48:592–598; 148:2831–2846Google Scholar
  49. Hines ME, Evans RS, Sharak Genthner BR, Willis SG, Friedman S, Rooney-Varga JN, Devereux R (1999) Molecular phylogenetic and biogeochemical studies of sulfate-reducing bacteria in the rhizosphere of Spartina alterniflora. Appl Environ Microbiol 65:2209–2216Google Scholar
  50. Holzapfel-Pschorn A, Conrad R, Seiler W (1985) Production, oxidation and emission of methane in rice paddies. FEMS Microbiol Ecol 31:343–351CrossRefGoogle Scholar
  51. Horz HP, Rotthauwe JH, Lukow T, Liesack W (2000) Identification of major subgroups of ammonia-oxidizing bacteria in environmental samples by T-RFLP analysis of amoA PCR products. J Microbiol Methods 39:197–204CrossRefGoogle Scholar
  52. Howard JB, Rees DC (1996) Structural basis of biological nitrogen fixation. Chem Rev 96:2965–2982CrossRefGoogle Scholar
  53. Howes BL, Dacey JWH, Goehringer DD (1986) Factors controlling the growth form of Spartina alterniflora: feedbacks between above-ground production, sediment oxidation, nitrogen and salinity. J Ecol 74:881–898CrossRefGoogle Scholar
  54. Hurek T, Reinhold-Hurek B (1998) Interactions of Azoarcus sp. with rhizosphere fungi. In: Varma A, Hock B (eds) Mycorrhiza, 2nd edn. Springer, Berlin Heidelberg New York, pp 595–614Google Scholar
  55. Hurek T, Reinhold-Hurek B (2006) Molecular ecology of N2-fixing microbes associated with graminaceous plants. In: Werner D, Newton WE (eds) Agriculture, forestry, ecology and the environment. Kluwer, Dordrecht, pp 173–198Google Scholar
  56. Hurek T, Egener T, Reinhold-Hurek B (1997) Divergence in nitrogenases of Azoarcus spp, Proteobacteria of the α-subclass. J Bacteriol 179:4172–4178Google Scholar
  57. Hurek T, Handley L, Reinhold-Hurek B, Piché Y (2002) Azoarcus grass endophytes contribute fixed nitrogen to the plant in an unculturable state. Mol Plant Microb Interact 15:233–242Google Scholar
  58. Karl D, Bergman B, Capone D, Carpenter E, Letelier R, Lipschultz F, Paerl H, Sigman D, Stal L (2002). Dinitrogen fixation in the world’s oceans. Biogeochemistry 57/58:47–98CrossRefGoogle Scholar
  59. Kamura T, Takai Y, Ishikawa K (1963) Microbial reduction mechanism of ferric iron in paddy soils (part 1). Soil Sci Plant Nutr 9:171–175Google Scholar
  60. Karnholz A, Küsel K, Gößner A, Schramm A, Drake HL (2002) Tolerance and metabolic response of acetogenic bacteria toward oxygen. Appl Environ Microbiol 68:1005–1009CrossRefGoogle Scholar
  61. Kimura M (2000) Anaerobic microbiology in waterlogged rice fields. In: Bollag JM, Stotzky G (eds) Soil biochemistry. Dekker, New York, pp 35–138Google Scholar
  62. Knief C, Lipski A, Dunfield PF (2003) Diversity and activity of methanotrophic bacteria in different upland soils. Appl Environ Microbiol 69:6703–6714CrossRefGoogle Scholar
  63. Kolb S, Knief C, Stubner S, Conrad R (2003) Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl Environ Microbiol 69:2423–2429CrossRefGoogle Scholar
  64. Koretsky CM, Moore CM, Lowe KL, Meile C, DiChristina TJ, Van Cappellen P (2003) Seasonal oscillation of microbial iron and sulfate reduction in saltmarsh sediments (Sapelo Island, GA, USA). Biogeochemistry 64:179–203CrossRefGoogle Scholar
  65. Kostka JE, Luther GWI (1995) Seasonal cycling of Fe in saltmarsh sediments. Biogeochemistry 29:159–181CrossRefGoogle Scholar
  66. Kostka JE, Gribsholt B, Petrie E, Dalton D, Skelton H, Kristensen E (2002) The rates and pathways of carbon oxidation in bioturbated saltmarsh sediments. Limnol Oceanogr 47:230–240CrossRefGoogle Scholar
  67. Koyama T (1955) Gaseous metabolism in lake muds and paddy soils. J Earth Sci 3:65–76Google Scholar
  68. Krüger M, Frenzel P (2003) Effects of N-fertilisation on CH4 oxidation and production, and consequences for CH4 emissions from microcosms and rice fields. Global Change Biol 9:773–784CrossRefGoogle Scholar
  69. Krüger M, Frenzel P, Conrad R (2001) Microbial processes influencing methane emission from rice fields. Global Change Biol 7:49–63CrossRefGoogle Scholar
  70. Krüger M, Eller G, Conrad R, Frenzel P (2002) Seasonal variation in pathways of CH4 production and in CH4 oxidation in rice fields determined by stable carbon isotopes and specific inhibitors. Global Change Biol 8:265–280CrossRefGoogle Scholar
  71. Krüger M, Frenzel P, Kemnitz D, Conrad R (2005) Activity, structure and dynamics of the methanogenic archaeal community in a flooded Italian rice field. FEMS Microbiol Ecol 51:323–331CrossRefGoogle Scholar
  72. Kurtz DM (2003) Oxygen and anaerobes. In: Ljungdahl LG, Adams M, Barton L, Ferry JG, Johnson M (eds) Biochemistry and physiology of anaerobic bacteria. Springer, Berlin Heidelberg New York, pp 128–142CrossRefGoogle Scholar
  73. Küsel K, Pinkart HC, Drake HL, Devereux R (1999) Acetogenic and sulfate-reducing bacteria inhabiting the rhizoplane and deep cortex cells of the sea grass Halodule wrightii. Appl Environ Microbiol 65:5117–5123Google Scholar
  74. Küsel K, Karnholz A, Trinkwalter T, Devereux R, Acker G, Drake HL (2001) Physiological ecology of Clostridium glycolicum RD-1, an aerotolerant acetogen isolated from sea grass roots. Appl Environ Microbiol 67:4734–4741CrossRefGoogle Scholar
  75. Leaphart AB, Friez MJ, Lovell CR (2003) Formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups. Appl Environ Microbiol 69:693–696.CrossRefGoogle Scholar
  76. Lee N, Nielsen PH, Andreasen KH, Juretschenko S, Nielsen JP, Schleifer KH, Wagner M (1999) Combination of fluorescent in situ hybridization and micro-autoradiography — a new tool for structure-function analyses in microbial ecology. Appl Environ Microbiol 65:1289–1297Google Scholar
  77. Lenssen JPM, Menting FBJ, Putten WH van der, Blom CWPM (1999) Effects of sediment type and water level on biomass production of wetland plant species. Aquat Bot 64:151–165CrossRefGoogle Scholar
  78. Liles MR, Manske BF, Bintrim SB, Handelsman J, Goodman RM (2003) A census of rRNA genes linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 69:2684–2691CrossRefGoogle Scholar
  79. Lovell CR (2002) Plant-microbe interactions in the marine environment. In: Bitton G (ed) Encyclopedia of environmental microbiology, vol 5. Wiley, New York, pp 2539–2554Google Scholar
  80. Lovell CR, Piceno YM, Quattro JM, Bagwell CE (2000) Molecular analysis of diazotrophic diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora. Appl Environ Microbiol 66:3814–3822CrossRefGoogle Scholar
  81. Lovell CR, Friez MJ, Longshore JW, Bagwell CE (2001a) Recovery and phylogenetic analysis of nifH sequences from diazotrophic bacteria associated with dead aboveground biomass of Spartina alterniflora. Appl Environ Microbiol 67:5308–5314CrossRefGoogle Scholar
  82. Lovell CR, Bagwell CE, Czákó M, Márton L, Piceno YM, Ringelberg DB (2001b) Stability of a rhizosphere microbial community exposed to natural and manipulated environmental variability. FEMS Microbiol Ecol 38:69–76CrossRefGoogle Scholar
  83. Lovley DR (2000) Fe(III) and Mn(IV) reduction. In: Lovley DR (ed) Environmental microbe-metal interactions. ASM, Washington, D.C., pp 3–30Google Scholar
  84. Lüders T, Manefield M, Friedrich MW (2003) Enhanced sensitivity of DNA-and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6:73–78CrossRefGoogle Scholar
  85. Luther GW III, Kostka JE, Church TM, Sulzberger B, Stumm W (1992) Seasonal iron cycling in a salt marsh sedimentary environment: the importance of ligand complexes with Fe(II) and Fe(III) in the dissolution of Fe(III) minerals and pyrite, respectively. Mar Chem 40:81–103CrossRefGoogle Scholar
  86. Marik T, Fischer H, Conen F, Smith K (2002) Seasonal variations in stable carbon and hydrogen isotopes ratios in methane from rice fields. Global Biogeochem Cycles 16:1094CrossRefGoogle Scholar
  87. Megonigal JP, Hines ME, Visscher PT (2004) Anaerobic metabolism: linkages to trace gases and aerobic processes. In: Schlesinger WH (ed) Biogeochemistry. Elsevier-Pergamon, Oxford, pp 317–424CrossRefGoogle Scholar
  88. Mendelssohn IA (1979) The influence of nitrogen level, form, and application method on the growth response of Spartina alterniflora in North Carolina. Estuaries 2:106–112CrossRefGoogle Scholar
  89. Mendelssohn IA, Kleiss BA, Wakeley JS (1995) Factors controlling the formation of oxidized root channels: a review. Wetlands 15:37–46Google Scholar
  90. Müller V, Inkamp F, Rauwolf A, Küsel K, Drake HL (2004) Molecular and cellular biology of acetogenic bacteria. In: Nakano MM, Zuber P (eds) Strict and facultative anaerobes: medical and environmental aspects. Horizon Bioscience, Norfolk, pp 251–281Google Scholar
  91. Neubauer SC, Emerson D, Megonigal JP (2002) Life at the energetic edge: kinetics of circumneutral iron oxidation by lithotrophic iron-oxidizing bacteria isolated from the wetland-plant rhizophere. Appl Environ Microbiol 68:3988–3995CrossRefGoogle Scholar
  92. Noll M, Matthies D, Frenzel P, Derakshani M, Liesack W (2005) Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environ Microbiol 7:382–395CrossRefGoogle Scholar
  93. Pernthaler A, Amann R (2004) Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl Environ Microbiol 70:5426–5433CrossRefGoogle Scholar
  94. Piceno YM, Lovell CR (2000a) Stability in natural bacterial communities. I. Nutrient addition effects on rhizosphere diazotroph assemblage composition. Microb Ecol 39:32–40CrossRefGoogle Scholar
  95. Piceno YM, Lovell CR (2000b) Stability in natural bacterial communities. II. Plant resource allocation effects on rhizosphere diazotroph assemblage composition. Microb Ecol 39:41–48CrossRefGoogle Scholar
  96. Piceno YM, Noble PA, Lovell CR (1999) Spatial and temporal assessment of diazotroph assemblage composition in vegetated salt marsh sediments using denaturing gradient gel electrophoresis analysis. Microb Ecol 38:157–167CrossRefGoogle Scholar
  97. Poly F, Ranjard L, Nazaret S, Gourbière F, Monrozier LJ (2001) Comparison of gene pools in soils and soil microenvironments with contrasting properties. Appl Environ Microbiol 67:2255–2262CrossRefGoogle Scholar
  98. Ponnamperuma FN (1984) Effects of flooding on soils. In: Kozlowski TT (ed) Flooding and plant growth. Academic, New York, pp 9–45Google Scholar
  99. Powell SW, Day FP (1991) Root production in four communities in the Great Dismal Swamp. Am J Bot 78:288–297CrossRefGoogle Scholar
  100. Reinhold B, Hurek T, Niemann E-G, Fendrik I (1986) Close association of Azospirillum and diazotrophic rods with different root zones of Kallar grass. Appl Environ Microbiol 52:520–526Google Scholar
  101. Ribbe M, Gadkari D, Meyer O (1997) N-2 fixation by Streptomyces thermoautotrophicus involves a molybdenum-dinitrogenase and a manganese-superoxide oxidoreductase that couple N-2 reduction to the oxidation of superoxide produced from O-2 by a molybdenum-CO dehydrogenase. J Biol Chem 272:26627–26633CrossRefGoogle Scholar
  102. Roden EE (2003) Fe(III) oxide reactivity toward biological versus chemical reduction. Environ Sci Technol 37:1319–1324CrossRefGoogle Scholar
  103. Roden EE, Wetzel RG (1996) Organic carbon oxidation and suppression of methane production by microbial Fe(III) oxide reduction in vegetated freshwater wetland sediments. Limnol Oceanogr 41:1733–1748CrossRefGoogle Scholar
  104. Roden EE, Wetzel RG (2002) Kinetics of microbial Fe (III) oxide reduction in freshwater wetland sediments. Limnol Oceanogr 47:198–211CrossRefGoogle Scholar
  105. Roslev P, King GM (1995) Aerobic and anaerobic starvation metabolism in methanotrophic bacteria. Appl Environ Microbiol 61:1563–1570Google Scholar
  106. Schippers A, Jorgensen BB (2002) Biogeochemistry of pyrite and iron sulfide oxidation in marine sediments. Geochim Cosmochim Acta 66:85–92CrossRefGoogle Scholar
  107. Schubauer JP, Hopkinson CS (1984) Above-and belowground emergent macrophyte production and turnover in a coastal marsh ecosystem, Georgia. Limnol Oceanogr 29:1052–1065Google Scholar
  108. Shearer MJ, Khalil MAK (2000) Rice agriculture: emissions. In: Atmospheric methane: its role in the global environment. Springer, Berlin Heidelberg New York, pp 170–189Google Scholar
  109. Silaghi-Dumitrescu R, Coulter ED, Das A, Ljungdahl LG, Jameson GNL, Huynh BH, Kurtz DM Jr (2003) A flavodiiron protein and high molecular weight rubredoxin from Moorella thermoacetica with nitric oxide reductase activity. Biochemistry 42:2806–2815CrossRefGoogle Scholar
  110. Singer PC, Stumm W (1970) Acid mine drainage: the rate-determining step. Science 167:1121–1123CrossRefGoogle Scholar
  111. Sobolev D, Roden EE (2001) Suboxic deposition of ferric iron by bacteria in opposing gradients of Fe(II) and oxygen at circumneutral pH. Appl Environ Microbiol 67:1328–1334CrossRefGoogle Scholar
  112. Sobolev D, Roden EE (2004) Characterization of a neutrophilic, chemolithotrophic Fe(II)-oxidizing B-proteobacterium from freshwater wetland sediments. Geomicrobiol J 21:1–10CrossRefGoogle Scholar
  113. Sorrell BK (1994) Airspace structure and mathematical modelling of oxygen diffusion, aeration and anoxia in Eleocharis sphacelata R. Br. roots. Aust J Mar Freshwater Res 45:1529–1541CrossRefGoogle Scholar
  114. Sorrell BK, Mendelssohn IA, McKee KL, Woods RA (2000) Ecophysiology of wetland plant roots: a modeling comparison of aeration in relation to species distribution. Ann Bot 86:675–685CrossRefGoogle Scholar
  115. Straub KL, Buchholz-Cleven BEE (1998) Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse European sediments. Appl Environ Microbiol 64:4846–4856Google Scholar
  116. Straub KL, Benz M, Schink B, Widdel F (1996) Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Appl Environ Microbiol 62:1458–1460Google Scholar
  117. Straub KL, Rainey FA, Widdel F (1999) Rhodovulum iodosum sp. nov. and Rhodovulum robiginosum sp. nov., two new marine phototrophic ferrous-iron-oxidizing purple bacteria. Int J Syst Bacteriol 49:729–735CrossRefGoogle Scholar
  118. Summers JE, Ratcliffe RG, Jackson MB (2000) Anoxia tolerance in the aquatic monocot Potamogeton pectinatus: absence of oxygen stimulates elongation in association with an unusually large Pasteur effect. J Exp Bot 51:1413–1422CrossRefGoogle Scholar
  119. Tan Z, Hurek T, Reinhold-Hurek B (2003) Effect of N-fertilization, plant genotype and environmental conditions on nifH gene pools in roots of rice. Environ Microbiol 2:1009–1015CrossRefGoogle Scholar
  120. Thamdrup B (2000) Bacterial manganese and iron reduction in aquatic sediments. Adv Microb Ecol 16:41–84Google Scholar
  121. Tiquia SM, Liyou W, Chong SC, Passovets S, Xu D, Xu Y, Zhou J (2004) Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. BioTechniques 36:664–675Google Scholar
  122. Turner RE (1976) Geographic variations in salt marsh macrophyte production: a review. Contrib Mar Sci 20:47–68Google Scholar
  123. Van Bodegom P, Stams F, Mollema L, Boeke S, Leffelaar P (2001) Methane oxidation and the competition for oxygen in the rice rhizosphere. Appl Environ Microbiol 67:3586–3597CrossRefGoogle Scholar
  124. Wang MX, Li J (2002) CH4 emission and oxidation in Chinese rice paddies. Nutr Cycl Agroecosyst 64:43–55CrossRefGoogle Scholar
  125. Weber KA, Picardal FW, Roden EE (2001) Microbially catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds. Environ Sci Technol 35:1644–1650CrossRefGoogle Scholar
  126. 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 64:77–96CrossRefGoogle Scholar
  127. 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 48:89–100CrossRefGoogle Scholar
  128. Widdel F, Schnell S, Heising S, Ehrenreich A, Assmus B, Schink B (1993) Ferrous iron oxidation by anoxygenic phototrophic bacteria. Nature 362:834–836CrossRefGoogle Scholar
  129. Yao H, Conrad R, Wassmann R, Neue HU (1999) Effect of soil characteristics on sequential reduction and methane production in sixteen rice paddy soils from China, the Philippines, and Italy. Biogeochemistry 47:269–295CrossRefGoogle Scholar
  130. Zani S, Mellon MT, Collier JL, Zehr JP (2000). Expression of nifH genes in natural microbial assemblages in Lake George, New York, detected by reverse transcriptase PCR. Appl Environ Microbiol 66:3119–3124CrossRefGoogle Scholar
  131. Zehr JP, McReynolds LA (1989) Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 55:2522–2526Google Scholar
  132. Zehr JP, Jenkins BD, Short SM, Steward GF (2003) Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol 5:539–554CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Paul L. E. Bodelier
    • 1
  • Peter Frenzel
    • 2
  • Harold L. Drake
    • 3
  • Thomas Hurek
    • 4
  • Kirsten Küsel
    • 5
  • Charles Lovell
    • 6
  • Patrick Megonigal
    • 7
  • Barbara Reinhold-Hurek
    • 4
  • Brian Sorrell
    • 8
  1. 1.Centre for Limnology, Department of Microbial EcologyNetherlands Institute of Ecology (NIOO-KNAW)MaarssenThe Netherlands
  2. 2.Max Planck Institut für terrestrische MikrobiologieMarburgGermany
  3. 3.Department of Ecological MicrobiologyUniversity of BayreuthBayreuthGermany
  4. 4.Laboratory for General Microbiology, Faculty of BiologyUniversity of BremenGermany
  5. 5.Limnology Research Group, Institute of EcologyUniversity of JenaJenaGermany
  6. 6.Department of Biological SciencesUniversity of South CarolinaColumbiaUSA
  7. 7.Smithsonian Environmental Research CenterEdgewaterUSA
  8. 8.National Institute of Water and Atmospheric ResearchChristchurchNew Zealand

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