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Soil biology

Denitrification in paddy soil as a cooperative process of different nitrogen oxide reducers, revealed by metatranscriptomic analysis of denitrification-induced soil microcosm

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Pages 342-345 | Received 06 Nov 2018, Accepted 20 May 2019, Published online: 27 May 2019

References

  • Akiyama H, Yagi K, Yan X 2005: Direct N2O emissions from rice paddy fields: summary of available data. Global Biochem. Cycles, 19(1), GB1005. doi:10.1029/2004GB002378
  • Brons HJ, Hagen WR, Zehnder AJ 1991: Ferrous iron dependent nitric oxide production in nitrate-reducing cultures of Escherichia coli. Arch. Microbiol., 155(4), 341–347. doi:10.1007/BF00243453
  • Chen Z, Liu J, Wu M, Xie X, Wu J, Wei W 2012: Differentiated response of denitrifying communities to fertilization regime in paddy soil. Microb. Ecol., 63(2), 446–459. doi:10.1007/s00248-011-9909-5
  • Francis CA, O’Mullan GD, Cornwell JC, Ward BB 2013: Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary. Front Microbiol., 4, 237. doi:10.3389/fmicb.2013.00237
  • Hallin S, Philippot L, Löffler FE, Sanford RA, Jones CM 2018: Genomics and ecology of novel N2O-reducing microorganisms. Trends Microbiol., 26(1), 53–55. doi:10.1016/j.tim.2017.07.003
  • Huang S, Chen C, Yang X, Wu Q, Zhang R 2011: Distribution of typical denitrifying functional genes and diversity of the nirS-encoding bacterial community related to environmental characteristics of river sediments. Biogeosciences, 8, 3041–3051. doi:10.5194/bg-8-3041-2011
  • Ishii S, Ikeda S, Minamisawa K, Senoo K 2011: Nitrogen cycling in rice paddy environments: past achievements and future challenges. Microbes Environ., 26(4), 282–292. doi:10.1264/jsme2.ME11293
  • Itoh H, Ishii S, Shiratori Y, Oshima K, Otsuka S, Hattori M, Senoo K 2013: Seasonal transition of active bacterial and archaeal communities in relation to water management in paddy soils. Microbes Environ., 28(3), 370–380. doi:10.1264/jsme2.ME13030
  • Jones CM, Graf DR, Bru D, Philippot L, Hallin S 2013: The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. Isme J, 7(2), 417–426. doi:10.1038/ismej.2012.125
  • Lou Y, Ren L, Li Z, Zhang T, Inubushi K 2007: Effect of rice residues on carbon dioxide and nitrous oxide emissions from a paddy soil of subtropical China. Water Air Soil Poll., 178(1), 157–168. doi:10.1007/s11270-006-9187-x
  • Masuda Y, Itoh H, Shiratori Y, Isobe K, Otsuka S, Senoo K 2017: Predominant but previously-overlooked prokaryotic drivers of reductive nitrogen transformation in paddy soils, revealed by metatranscriptomics. Microbes Environ., 32(2), 180–183. doi:10.1264/jsme2.ME16179
  • Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, 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.
  • Plate L, Marletta MA 2012: Nitric oxide modulates bacterial biofilm formation through a multicomponent cyclic-di-GMP signaling network. Mol. Cell, 46(4), 449–460. doi:10.1016/j.molcel.2012.03.023
  • Schreiber F, Wunderlin P, Udert KM, Wells GF 2012: Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies. Front Microbiol., 3, 372. doi:10.3389/fmicb.2012.00372
  • Smith CJ, Nedwell DB, Dong LF, Osborn AM 2007: Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Appl. Environ. Microbiol., 73(11), 3612–3622. doi:10.1128/AEM.02894-06
  • Tago K, Ishii S, Nishizawa T, Otsuka S, Senoo K 2011: “Phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice-soybean rotation fields. Microbes Environ., 26(1), 30–35. doi:10.1264/jsme2.ME10167
  • Wei W, Isobe K, Nishizawa T, Zhu L, Shiratori Y, Ohte N, Koba K, Otsuka S, Senoo K 2015: Higher diversity and abundance of denitrifying microorganisms in environments than considered previously. Isme J, 9(9), 1954–1965. doi:10.1038/ismej.2015.9
  • Xiong ZQ, Huang TQ, Ma YC, Xing GX, Zhu ZL 2010: Nitrate and ammonium leaching in variable- and permanent- charge paddy soils. Pedosphere, 20(2), 209–216. doi:10.1016/S1002-0160(10)60008-2
  • Yoshida M, Ishii S, Fujii D, Otsuka S, Senoo K 2012: Identification of active denitrifiers in rice paddy soil by DNA- and RNA-based analyses. Microbes Environ., 27(4), 456–461. doi:10.1264/jsme2.ME12076
  • Yoshida M, Ishii S, Otsuka S, Senoo K 2009: Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy fields. Soil Biol. Biochem., 41(10), 2044–2051. doi:10.1016/j.soilbio.2009.07.012
  • Zhou K, Qiao K, Edgar S, Stephanopoulos G 2015: Distributing metabolic pathway among a microbial consortium enhances production of natural products. Nat. Biotechnol., 33(4), 377–383. doi:10.1038/nbt.3095
  • Zumft WG 1997: Cell biology and molecular basis of denitrification. Microbiol. Mol. Biol. Rev., 61(4), 533–616.

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