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Soil biology

Metatranscriptomic insights into microbial consortia driving methane metabolism in paddy soils

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Pages 455-464 | Received 05 Oct 2017, Accepted 21 Mar 2018, Published online: 29 Mar 2018

References

  • Baba R, Asakawa S, Watanabe T 2016: H2-producing bacterial community during rice straw decomposition in paddy field soil: estimation by an analysis of [FeFe]-hydrogenase gene transcripts. Microbes Environ., 31, 226–233. doi:10.1264/jsme2.ME16036
  • Baba R, Kimura M, Asakawa S, Watanabe T 2014: Analysis of [FeFe]-hydrogenase genes for the elucidation of a hydrogen-producing bacterial community in paddy field soil. FEMS Microbiol. Lett., 350, 249–256. doi:10.1111/fml.2014.350.issue-2
  • Bao Q, Huang Y, Wang F, Nie S, Nicol GW, Yao H, Ding L 2016: Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil. Appl. Microbiol. Biotechnol., 100, 5989–5998. doi:10.1007/s00253-016-7377-z
  • Bräuer SL, Cadillo-Quiroz H, Ward RJ, Yavitt JB, Zinder SH 2011: Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog. Int. J. Syst. Evol. Microbiol., 261, 45–52. doi:10.1099/ijs.0.021782-0
  • Bräuer SL, Cadillo-Quiroz H, Yashiro E, Yavitt JB, Zinder SH 2006: Isolation of a novel acidiphilic methanogen from an acidic peat bog. Nature, 442, 192–194. doi:10.1038/nature04810
  • Breidebach B, Conrad R 2014: Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage. Front. Microbiol., 5, 752.
  • Conrad R 2007: Microbial ecology of methanogens and methanotrophs. Adv. Agron., 96, 1–63.
  • Conrad R, Klose M 2006: Dynamics of the methanogenic archaeal community in anoxic rice soil upon addition of straw. Eur. J. Soil Sci., 57, 476–484. doi:10.1111/j.1365-2389.2006.00791.x
  • Coppi MV 2005: The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective. Microbiology, 151, 1239–1254. doi:10.1099/mic.0.27535-0
  • Coppi MV, O’Neil RA, Lovley DR 2004: Identification of an uptake hydrogenase required for hydrogen-dependent reduction of Fe (III) and other electron acceptors by Geobacter sulfurreducens. J. Bacteriol, 186, 3022–3028. doi:10.1128/JB.186.10.3022-3028.2004
  • Drake HL, Küsel K, Matthies C 2006: Acetogenic Prokaryotes. In The Prokaryotes, Eds. Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E, 3rd ed., Vol. 2, pp. 354–420. Ecophysiology and Biochemistry Springer SBM, New York.
  • 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, 91–97. doi:10.1111/j.1574-6968.2001.tb10624.x
  • Falz KZ, Holliger C, Großkopf R, Liesack W, Nozhevnikova AN, Müller B, Wehrli B, Hahn D 1999: Vertical distribution of methanogens in the anoxic sediment of Rotsee (Switzerland). Appl. Environ. Microbiol., 65, 2402–2408.
  • Fazli P, Man HC, Shah UK, Idris A 2013: Characteristics of methanogens and methanotrophs in rice fields: a review. As. Pac. J. Mol. Biol. Biotechnol., 1, 3–17.
  • Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, DeLong EF 2008: Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. U. S. A., 105, 3805–3810. doi:10.1073/pnas.0708897105
  • Fukui M, Suwa Y, Urushigawa Y 1996: High survival efficiency and ribosomal RNA decaying pattern of Desulfobacter latus, a highly specific acetate-utilizing organism, during starvation. FEMS Microbiol. Ecol., 19, 17–25. doi:10.1111/j.1574-6941.1996.tb00194.x
  • Galagan JE, Nusbaum C, Roy A et al. 2002: The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res., 12, 532–542. doi:10.1101/gr.223902
  • Geymonat E, Ferrando L, Tarlera SE 2011: Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph from a rice paddy field. Int. J. Syst. Evol. Microbiol., 61, 2568–2572. doi:10.1099/ijs.0.028274-0
  • Großkopf R, Janssen PH, Liesack W 1998: Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol., 64, 960–969.
  • Hanson RS, Hanson TE 1996: Methanotrophic bacteria. Microbiol. Mol. Biol. Rev., 60, 439–471.
  • Hattori M, Tanaka N, Kanehisa M, Goto S 2010: SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. Nucleic Acid Res., 38, 652–656. doi:10.1093/nar/gkq367
  • Hoffman BM, Lukoyanov D, Yang ZY, Dean DR, Seefeldt LC 2014: Mechanism of nitrogen fixation by nitrogense: the next stage. Chem. Rev., 114, 4041–4062. doi:10.1021/cr400641x
  • Holmes DE, Shrestha PM, Walker DJF, Dnag Y, Nevin KP, Woodard TL, Lovley DR 2017: Metatranscriptomic evidence for direct interspecies electron transfer between Geobacter and Methanothrix species in methanogenic rice paddy soils. Appl. Environ. Microbiol., 83, e00223–17. doi:10.1128/AEM.00223-17
  • Hori T, Müller 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. doi:10.1038/ismej.2009.100
  • Hou AX, Wang ZP, Chen GX, Patrick WH 2000: Effects of organic and N fertilizers on methane production in a Chinese rice soil and its microbiological aspect. Nutr. Cycl. Agroecosyst., 58, 333–338. doi:10.1023/A:1009875509876
  • IPCC Climate Change 2013: the Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. T.F. Stocker, D. Qin, G.K. Plattner, M. Tignor, S.K. Allen, J. Boschung, A. Nauels, Y. Xia, V. Bex, P.M. Midgley (eds). Cambridge University Press, Cambridge, UK.
  • Ishii S, Yamamoto M, Kikuchi M, Oshima K, Hattori M, Otsuka S, Senoo K 2009: Microbial populations responsive to denitrification-inducing conditions in paddy soil, as revealed by comparative 16S rRNA gene analysis. Appl. Environ. Microbiol., 75, 7070–7078. doi:10.1128/AEM.01481-09
  • Islam T, Larsen Ø, Torsvik V, Øvreås L, Panosyan H, Murrell JC, Birkeland NK, Bodrossy L 2015: Novel methanotrophs of the family methylococcaceae from different geographical regions and habitats. Microorganisms, 3, 484–499. doi:10.3390/microorganisms3030484
  • Itoh H, Ishii S, Shiratori Y, Oshima K, Osuka S, Hattori M, Senoo K 2013: Seasonal transition of active bacterial and archaeal communities in relation to water management in paddy soils. Micobes Environ., 28, 370–380. doi:10.1264/jsme2.ME13030
  • Jewell TN, Karaoz U, Bill M, Chakraborty R, Brodie EL, Williams KH, Beller HR 2017: Metatranscriptomic analysis reveals unexpectedly diverse microbial metabolism in a biogeochemical hot spot in an alluvial aquifer. Front. Microbiol., 8, 40. doi:10.3389/fmicb.2017.00040
  • Kamagata Y, Mikami E 1991: Isolation and characterization of a novel thermophilic Methanosaeta strain. Int. J. Syst. Bacteriol., 41, 191–196. doi:10.1099/00207713-41-2-191
  • Kato S, Watanabe K 2010: Ecological and evolutionary interactions in syntrophic methanogenic consortia. Microbes Environ., 25, 145–151. doi:10.1264/jsme2.ME10122
  • Kato S, Yumoto I, Kamagata Y 2015: Isolation of acetogenic bacteria that induce biocorrosion by utilizing metallic iron as the sole electron donor. Appl. Environ. Microbiol., 81, 67–73. doi:10.1128/AEM.02767-14
  • Kimura M 2000: Anaerobic microbiology in waterlogged rice fields. In Soil Biochemistry, Eds. Bollarg JM, Stotzky G, Vol. 10, pp. 35–138. Marcel Dekker Inc., New York.
  • Kouzuma A, Kato S, Watanabe K 2015: Microbial interspecies interactions: recentfindings in syntrophic consortia. Front. Microbiol., 6, 477. doi:10.3389/fmicb.2015.00477
  • Krylova NI, Janssen PH, Conrad R 1997: Turnover of propionate in methanogenic paddy soil. FEMS Microbiol. Ecol., 23, 107–117. doi:10.1111/j.1574-6941.1997.tb00395.x
  • Kumarswamy S, Ramakrishnan B, Sethunathan N 2001: Methane production and oxidation in an anoxic rice soil as influenced by inorganic redox species. J. Environ. Qual., 30, 2195–2201. doi:10.2134/jeq2001.2195
  • Lärdh K, Cohen PS, Kjelleberg S 1992: Ribosomes exist in large excess over the apparent demand for protein synthesis during carbon starvation in marine Vibrio sp. strain-CCUG-15956. J. Bacteriol., 174, 6780–6788. doi:10.1128/jb.174.21.6780-6788.1992
  • Liesack W, Schnell S, Revsbech NP 2000: Microbiology of flooded rice paddies. FEMS Microbiol. Rev., 24, 625–645. doi:10.1111/j.1574-6976.2000.tb00563.x
  • Liu J, Xu H, Jiang Y, Zhang K, Hu Y, Zeng Z 2017: Methane emissions and microbial communities as influenced by dual cropping of Azolla along with early rice. Sci. Rep., 7, 40635. doi:10.1038/srep40635
  • Lu Y, Lueders T, Friedrich MW, Conrad R 2005: Detecting active methanogenic populations on rice roots using stable isotope probing. Environ. Microbiol., 7, 326–336. doi:10.1111/emi.2005.7.issue-3
  • Lu Y, Wassmann R, Neue HU, Huang C, Bueno CS 2000: Methanogenic responses to exogenous substrates in anaerobic rice soils. Soil Biol. Biochem., 32, 1683–1690. doi:10.1016/S0038-0717(00)00085-7
  • Masuda Y, Itoh H, Shiratori Y, Isobe K, Otsuka S, Keishi S 2017: Predominant but previously-overlooked prokaryotic drivers of reductive nitrogen transformation in paddy soils, revealed by metatranscriptomics. Microbes Environ., 32, 180–183. doi:10.1264/jsme2.ME16179
  • Meyer F, Paarmann D, D’Souza M et al. 2008: The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 9, 386. doi:10.1186/1471-2105-9-386
  • Min H, Zinder SH 1989: Kinetics of acetate utilization by two thermophilic acetotrophic methanogens: methanosarcina sp. strain CALS-1 and Methanothrix sp. strain CALS-1. Appl. Environ. Microbiol., 55, 488–491.
  • Nguyen SG, Guevarra RB, Kim J, Ho CT, Trinh MV, Unno T 2015: Impacts of initial fertilizers and irrigation systems on paddy methanogens and methane emission. Water Air. Soil Pollut., 226, 309. doi:10.1007/s11270-015-2501-8
  • Orellana LH, Rodriguez-R LM, Higgins S, Chee-Sanford JC, Sanford RA, Ritalahti KM, Löffler FE, Konstantinidis KT 2014: Detecting nitrous oxide reductase (nosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle. MBio, 5, e01193–14. doi:10.1128/mBio.01193-14
  • Peng J, Lü Z, Rui J, Lu Y 2008: Dynamics of methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil. Appl. Environ. Microbiol., 74, 2894–2901. doi:10.1128/AEM.00070-08
  • Qiu YL, Hanada S, Ohashi A, Harada H, Kamagata Y, Sekiguchi Y 2008: Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the first cultured anaerobe capable of degrading phenol to acetate in obligate syntrophic associations with a hydrogenotrophic methanogen. Appl. Environ. Microbiol., 74, 2051–2058. doi:10.1128/AEM.02378-07
  • Rosencrantz D, Rainey FA, Janssen PH 1999: Culturable populations of Sporomusa spp. and Desulfovibrio spp. in the anoxic bulk soil of flooded rice microcosms. Appl. Environ. Microbiol., 65, 3526–3533.
  • Sakai S, Imachi H, Sekiguchi Y, Ohashi A, Harada H, Kamagata Y 2007: Isolation of key methanogens for global methane emission from rice paddy fields: a novel isolate affiliated with the clone cluster rice cluster I. Appl. Environ. Microbiol., 73, 4326–4331. doi:10.1128/AEM.03008-06
  • Sanford RA, Cole JR, Tiedje JM 2002: Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl. Environ. Microbiol., 68, 893–900. doi:10.1128/AEM.68.2.893-900.2002
  • Schäfer T, Selig M, Schönheit P 1993: Acetyl-CoA synthetase (ADP forming) in archaea, a novel enzyme involved in acetate formation and ATP synthesis. Arch. Microbiol., 159, 72–83. doi:10.1007/BF00244267
  • Schmieder R, Edwards R 2011: Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27, 863–864. doi:10.1093/bioinformatics/btr026
  • Shieh JS, Whitman WB 1987: Pathway of acetate assimilation in autotrophic and heterotrophic methanococci. J. Bacteriol., 169, 5327–5329. doi:10.1128/jb.169.11.5327-5329.1987
  • Singh A, Dubey SK 2012: Temporal variations in methanogenic community structure and methane production potential of tropical rice ecosystems. Soil Biol. Biochem., 48, 162–166. doi:10.1016/j.soilbio.2012.01.022
  • Sugano A, Tsuchimoto H, Cho TC, Kimura M, Asakawa S 2005: Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses. Archaea, 1, 391–397. doi:10.1155/2005/582597
  • Supparattanapan S, Saenjan P, Quantin C, Maeght JL, Grunberger O 2009: Salinity and organic amendment effects on methane emission from rain-fed saline paddy field. Soil Sci. Plant Nutr., 55, 142–149. doi:10.1111/j.1747-0765.2008.00330.x
  • Takai Y 1970: The mechanism of methane fermentation in flooded paddy soil. Soil Sci. Plan Nut., 16, 238–244. doi:10.1080/00380768.1970.10433371
  • Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC 2008: Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One, 3, e2527. doi:10.1371/journal.pone.0002527
  • Vignais PM, Billoud B 2007: Occurrence, classification, and biological function of hydrogenases: an overview. Chem. Rev., 107, 4206–5801. doi:10.1021/cr050196r
  • Watanabe T, Wang G, Taki K, Ohashi Y, Kimura M, Asakawa S 2010: Vertical changes in bacterial and archaeal communities with soil depth in Japanese paddy fields. Soil Sci. Plant Nutr., 56, 705–715. doi:10.1111/j.1747-0765.2010.00511.x
  • Weber S, Lueders T, Friedrich MW, Conrad R 2001: Methanogenic populations involved in the degradation of rice straw in anoxic paddy soil. FEMS Microbiol. Ecol., 38, 11–20. doi:10.1111/j.1574-6941.2001.tb00877.x
  • Wilke A, Harrison T, Wilkening J, Field D, Glass EM, Kyrpides N, Mavrommatis K, Meyer F 2012: The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics, 13, 141. doi:10.1186/1471-2105-13-141
  • Yagi K, Minami K 1990: Effect of organic matter application on methane emission from some Japanese paddy fields. Soil Sci. Plant Nutr., 36, 599–610. doi:10.1080/00380768.1990.10416797
  • Yan X, Yagi K, Akiyama H, Akimoto H 2005: Statistical analysis of the major variables controlling methane emission from rice fields. Glob. Change Biol., 11, 1131–1141. doi:10.1111/j.1365-2486.2005.00976.x
  • Yang SS, Chang HL 2001: Effect of green manure amendment and flooding on methane emission from paddy fields. Chemosphere, 3, 41–49.
  • Yashiro Y, Ehara M, Miyazaki M, Yamaguchi T, Imachi H 2011: Methanoregula formicica sp. Nov., a methane-producing archaeon isolated from methanogenic sludge. Int. J. Syst. Evol. Microbiol., 61, 53–59. doi:10.1099/ijs.0.014811-0

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