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Phylogenetic diversity of Fe(III)-reducing microorganisms in rice paddy soil: enrichment cultures with different short-chain fatty acids as electron donors - Journal of Soils and Sediments

  • ️Zhu, Yongguan
  • ️Wed May 11 2011

  • Aulakh MS, Wassmann R, Bueno C, Kreuzwieser J, Rennenberg H (2001) Characterization of root exudates at different growth stages of ten rice (Oryza sativa L.) cultivars. Plant Biol 3:139–148

    Article  CAS  Google Scholar 

  • Boga HI, Ji R, Ludwig W, Brune A (2007) Sporotalea propionica gen. nov sp nov., a hydrogen-oxidizing, oxygen-reducing, propionigenic Firmicute from the intestinal tract of a soil-feeding termite. Arch Microbiol 187:15–27

    Article  CAS  Google Scholar 

  • Boonchayaanant B, Nayak D, Du X, Criddle CS (2009) Uranium reduction and resistance to reoxidation under iron-reducing and sulfate-reducing conditions. Water Res 43:4652–4664

    Article  CAS  Google Scholar 

  • Boone DR, Liu YT, Zhao ZJ, Balkwill DL, Drake GR, Stevens TO, Aldrich HC (1995) Bacillus infernus sp. nov, an Fe(III)-reducing and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. Int J Syst Bacteriol 45:441–448

    Article  CAS  Google Scholar 

  • Borch T, Kretzschmar R, Kappler A, Van Cappellen P, Ginder-Vogel M, Voegelin A, Campbell K (2010) Biogeochemical redox processes and their impact on contaminant dynamics. Environ Sci Technol 44:15–23

    Article  CAS  Google Scholar 

  • Bromfield SM (1954) Reduction of ferric compounds by soil bacteria. J Gen Microbiol 11:1–6

    CAS  Google Scholar 

  • Chaudhuri SK, Lovley DR (2003) Electricity generation by direct oxidation of glucose in mediatorless microbial fuel cells. Nat Biotechnol 21:1229–1232

    Article  CAS  Google Scholar 

  • Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33:D294–D296

    Article  CAS  Google Scholar 

  • Dittmar J, Voegelin A, Roberts LC, Hug SJ, Saha GC, Ali MA, Badruzzaman ABM, Kretzschmar R (2010) Arsenic accumulation in a paddy field in Bangladesh: seasonal dynamics and trends over a three-year monitoring period. Environ Sci Technol 44:2925–2931

    Article  CAS  Google Scholar 

  • Dobbin PS, Carter JP, San Juan CGS, von Hobe M, Powell AK, Richardson DJ (1999) Dissimilatory Fe(III) reduction by Clostridium beijerinckii isolated from freshwater sediment using Fe(III) maltol enrichment. FEMS Microbiol Lett 176:131–138

    Article  CAS  Google Scholar 

  • Fredrickson JK, Zachara JM, Kennedy DW, Dong HL, Onstott TC, Hinman NW, Li SM (1998) Biogenic iron mineralization accompanying the dissimilatory reduction of hydrous ferric oxide by a groundwater bacterium. Geochim Cosmochim Acta 62:3239–3257

    Article  CAS  Google Scholar 

  • Guan SY (2007) Characterization and phylogenetic analysis of ferric reducing microorganism. Dissertation, Northwest A & F University

  • Hammann R, Ottow JCG (1974) Reductive dissolution of Fe2O3 by saccharolytic Clostridia and Bacillus polymyxa under anaerobic conditions. Z Pflanz Bodenkunde 137:108–115

    Article  CAS  Google Scholar 

  • He JZ, Liu XZ, Zheng Y, Shen JP, Zhang LM (2010) Dynamics of sulfate reduction and sulfate-reducing prokaryotes in anaerobic paddy soil amended with rice straw. Biol Fertil Soils 46:283–291

    Article  CAS  Google Scholar 

  • Hoffland E, Wei CZ, Wissuwa M (2006) Organic anion exudation by lowland rice (Oryza sativa L.) at zinc and phosphorus deficiency. Plant Soil 283:155–162

    Article  CAS  Google Scholar 

  • Hori T, Muller A, Igarashi Y, Conrad R, Friedrich MW (2010) Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing. ISME J 4:267–278

    Article  CAS  Google Scholar 

  • Islam FS, Gault AG, Boothman C, Polya DA, Charnock JM, Chatterjee D, Lloyd JR (2004) Role of metal-reducing bacteria in arsenic release from Bengal delta sediments. Nature 430:68–71

    Article  CAS  Google Scholar 

  • Kim JJ, Cummings TE, Cox JA (1972) Effect of pyruvate on the redox behavior of the iron (III)-(II) couple. Anal Lett 5:703–715

    CAS  Google Scholar 

  • Kögel-Knabner I, Amelung W, Cao ZH, Fiedler S, Frenzel P, Jahn R, Kalbitz K, Kolbl A, Schloter M (2010) Biogeochemistry of paddy soils. Geoderma 157:1–14

    Article  Google Scholar 

  • Kostka JE, Dalton DD, Skelton H, Dollhopf S, Stucki JW (2002) Growth of iron(III)-reducing bacteria on clay minerals as the sole electron acceptor and comparison of growth yields on a variety of oxidized iron forms. Appl Environ Microbiol 68:6256–6262

    Article  CAS  Google Scholar 

  • Krylova NI, Janssen PH, Conrad R (1997) Turnover of propionate in methanogenic paddy soil. FEMS Microbiol Ecol 23:107–117

    Article  CAS  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175

    Google Scholar 

  • Lin B, Hyacinthe C, Bonneville S, Braster M, Van Cappellen P, Roling WFM (2007) Phylogenetic and physiological diversity of dissimilatory ferric iron reducers in sediments of the polluted Scheldt estuary, Northwest Europe. Environ Microbiol 9:1956–1968

    Article  CAS  Google Scholar 

  • Lovley DR (1995) Microbial reduction of iron, manganese, and other metals. Adv Agron 54:175–231

    Article  CAS  Google Scholar 

  • Lovley DR (2000) Fe(III)- and Mn(IV)-reducing prokaryotes. Springer, New York

    Google Scholar 

  • Lovley DR, Phillips EJP (1988) Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl Environ Microbiol 54:1472–1480

    CAS  Google Scholar 

  • Lovley DR, Woodward JC, Chapelle FH (1994) Stimulated anoxic biodegradation of aromatic-hydrocarbons using Fe(III) ligands. Nature 370:128–131

    Article  CAS  Google Scholar 

  • Lovley DR, Holmes DE, Nevin KP (2004) Dissimilatory Fe(III) and Mn(IV) reduction. Adv Microb Physiol 49:219–286

    Article  CAS  Google Scholar 

  • Lu RK (1999) Analytical methods for soil and agricultural chemistry. Agricultural Science and Technology, Beijing

    Google Scholar 

  • Park HS, Kim BH, Kim HS, Kim HJ, Kim GT, Kim M, Chang IS, Park YK, Chang HI (2001) A novel electrochemically active and Fe(III)-reducing bacterium phylogenetically related to Clostridium butyricum isolated from a microbial fuel cell. Anaerobe 7:297–306

    Article  CAS  Google Scholar 

  • Pollock J, Weber KA, Lack J, Achenbach LA, Mormile MR, Coates JD (2007) Alkaline iron(III) reduction by a novel alkaliphilic, halotolerant, Bacillus sp isolated from salt flat sediments of Soap Lake. Appl Microbiol Biotechnol 77:927–934

    Article  CAS  Google Scholar 

  • Rhee SK, Jeon CO, Bae JW et al (2002) Characterization of Symbiobacterium toebii, an obligate commensal thermophile isolated from compost. Extremophiles 6:57–64

    Article  Google Scholar 

  • Rui JP, Peng JJ, Lu YH (2009) Succession of bacterial populations during plant residue decomposition in rice field soil. Appl Environ Microbiol 75:4879–4886

    Article  CAS  Google Scholar 

  • Scala DJ, Hacherl EL, Cowan R, Young LY, Kosson DS (2006) Characterization of Fe(III)-reducing enrichment cultures and isolation of Fe(III)-reducing bacteria from the Savannah River site, South Carolina. Res Microbiol 157:772–783

    Article  CAS  Google Scholar 

  • Schwertmann U, Cornell RM (1996) Iron oxides in the laboratory preparation and characteriazation. Wiley, Weinheim

    Google Scholar 

  • Su JQ, Yang XR, Zheng TL, Hong HS (2007) An efficient method to obtain axenic cultures of Alexandrium tamarense—a PSP-producing dinoflagellate. J Microbiol Meth 69:425–430

    Article  CAS  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  CAS  Google Scholar 

  • Ueda K, Yamashita A, Ishikawa J, Shimada M, Watsuji T, Morimura K, Ikeda H, Hattori M, Beppu T (2004) Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. Nucleic Acids Res 32:4937–4944

    Article  CAS  Google Scholar 

  • Wang XJ, Yang J, Chen XP, Sun GX, Zhu YG (2009) Phylogenetic diversity of dissimilatory ferric iron reducers in paddy soil of Hunan, South China. J Soils Sediments 9:568–577

    Article  Google Scholar 

  • Weber KA, Picardal FW, Roden EE (2001) Microbially catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds. Environ Sci Technol 35:1644–1650

    Article  CAS  Google Scholar 

  • Yao H, Conrad R (2001) Thermodynamics of propionate degradation in anoxic paddy soil from different rice-growing regions. Soil Biol Biochem 33:359–364

    Article  CAS  Google Scholar 

  • Ye Q, Roh Y, Carroll SL, Blair B, Zhou JZ, Zhang CL, Fields MW (2004) Alkaline anaerobic respiration: isolation and characterization of a novel alkaliphilic and metal-reducing bacterium. Appl Environ Microbiol 70:5595–5602

    Article  Google Scholar 

  • Zhu YG, Williams PN, Meharg AA (2008) Exposure to inorganic arsenic from rice: a global health issue? Environ Pollut 154:169–171

    Article  CAS  Google Scholar