Denitrification process in agricultural fields is a large source of nitrous oxide (N2O) emitted to the atmosphere. The rhizosphere soils tend to be the hotspots of denitrification in agricultural soils. Recent studies have reported the important role of nosZ II in eliminating N2O. However, little was known about how these more recently discovered N2O-reducing microorganisms together with other N2O-producers affected the N2O emission in agricultural rhizosphere soils.
Materials and methods
Here, we compared the potential N2O production rate, the denitrification end-product ratio, and the denitrifier communities between rhizosphere and non-rhizosphere soils of two types of crops in winter and summer. The potential activities were measured by acetylene inhibition technique. QPCR analysis was used to quantify the functional genes. High-throughput sequencing and clone library were conducted to analyze the community structure of denitrifiers.
Results and discussion
The rhizosphere soils had a higher N2O production potential but lower denitrification end-product ratio (N2O/(N2O+N2)) than the non-rhizosphere soils. The potential N2O production rate was correlated to the nirS-bacteria abundance, especially in terms of the genus Azospirillum. The N2O/(N2O+N2) ratio showed a negative correlation with both the diversity and abundance of the nosZ II-type N2O-reducers.
Altogether, we propose that nirS-type N2O-producers and nosZ II-type N2O-reducers can affect the N2O emission in agricultural rhizosphere soils, and enhancement of diversity and abundance of nosZ II-type N2O-reducers may help with the N2O mitigation from upland crops.
This is a preview of subscription content, log in to check access.
Buy single article
Instant unlimited access to the full article PDF.
Price includes VAT for USA
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
This is the net price. Taxes to be calculated in checkout.
Abell GC, Revill AT, Smith C, Bissett AP, Volkman JK, Robert SS (2010) Archaeal ammonia oxidizers and nirS-type denitrifiers dominate sediment nitrifying and denitrifying populations in a subtropical macrotidal estuary. ISME J 4:286–300
Ai C, Liang G, Wang X, Sun J, He P, Zhou W (2017) A distinctive root-inhabiting denitrifying community with high N2O/(N2O+N2) product ratio. Soil Biol Biochem 109:118–123
Bao S (2000) Soil and agricultural chemistry analysis. China Agriculture Press, Beijing
Bardon C, Piola F, Bellvert F, Haichar F, Comte G, Meiffren G, Pommier T, Puijalon S, Tsafack N, Poly F (2014) Evidence for biological denitrification inhibition (BDI) by plant secondary metabolites. New Phytol 204:620–630
Beck H, Christensen S (1987) The effect of grass maturing and root decay on N2O production in soil. Plant Soil 103:269–273
Butterbach-Bahl K, Baggs EM, Dannenmann M, Kiese R, Zechmeister-Boltenstern S (2013) Nitrous oxide emissions from soils: how well do we understand the processes and their controls? Philos Trans R Soc B Biol Sci 368:20130122
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336
Conthe M, Wittorf L, Kuenen JG, Kleerebezem R, Hallin S, van Loosdrecht MC (2018) Growth yield and selection of nosZ clade II types in a continuous enrichment culture of N2O respiring bacteria. Env Microbiol Rep 10:239–244
Di Rienzi SC, Sharon I, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield JF (2013) The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. Elife 2:e01102
Domeignoz-Horta L, Spor A, Bru D, Bizouard F, Leonard J, Philippot L (2015) The diversity of the N2O reducers matters for the N2O: N2 denitrification end-product ratio across an annual and a perennial cropping system. Front Microbiol 6:971
Domeignoz-Horta LA, Philippot L, Peyrard C, Bru D, Breuil MC, Bizouard F, Justes E, Mary B, Léonard J, Spor A (2017) Peaks of in situ N2O emissions are influenced by N2O producing and reducing microbial communities across arable soils. Glob Change Biol 24:360–370
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461
Friedl J, Scheer C, Rowlings DW, McIntosh HV, Strazzabosco A, Warner DI, Grace PR (2016) Denitrification losses from an intensively managed sub-tropical pasture-impact of soil moisture on the partitioning of N2 and N2O emissions. Soil Biol Biochem 92:58–66
Gobran GR, Clegg S (1996) A conceptual model for nutrient availability in the mineral soil-root system. Can J Soil Sci 76:125–131
Graf DR, Jones CM, Hallin S (2014) Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions. PLoS One 9:e114118
Hallin S, Philippot L, Löffler FE, Sanford RA, Jones CM (2017) Genomics and ecology of novel N2O-reducing microorganisms. Trends Microbiol 26:43–55
Henry S, Texier S, Hallet S, Bru D, Dambreville C, Cheneby D, Bizouard F, Germon J, Philippot L (2008) Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates. Environ Microbiol 10:3082–3092
Hu H-W, Chen D, He J-Z (2015) Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates. FEMS Microbiol Rev 39:729–749
Ishii S, Ohno H, Tsuboi M, Otsuka S, Senoo K (2011) Identification and isolation of active N2O reducers in rice paddy soil. ISME J 5:1936–1945
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 7:417–426
Jones CM, Spor A, Brennan FP, Breuil M-C, Bru D, Lemanceau P, Griffiths B, Hallin S, Philippot L (2014) Recently identified microbial guild mediates soil N2O sink capacity. Nat Clim Chang 4:801–805
Kong X, Duan Y, Schramm A, Eriksen J, Holmstrup M, Larsen T, Bol R, Petersen SO (2017) Mitigating N2O emissions from clover residues by 3, 4-dimethylpyrazole phosphate (DMPP) without adverse effects on the earthworm Lumbricus terrestris. Soil Biol Biochem 104:95–107
Liu XJ, Mosier AR, Halvorson AD, Reule CA, Zhang FS (2007) Dinitrogen and N2O emissions in arable soils: effect of tillage, N source and soil moisture. Soil Biol Biochem 39:2362–2370
Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963
Mounier E, Hallet S, Cheneby D, Benizri E, Gruet Y, Nguyen C, Piutti S, Robin C, Slezack-Deschaumes S, Martin-Laurent F (2004) Influence of maize mucilage on the diversity and activity of the denitrifying community. Environ Microbiol 6:301–312
Payne WJ (1981) Denitrification. John Wiley & Sons Inc, New York
Pell M, Stenberg B, Stenström J, Torstensson L (1996) Potential denitrification activity assay in soil-with or without chloramphenicol? Soil Biol Biochem 28:393–398
Philippot L, Andert J, Jones CM, Bru D, Hallin S (2011) Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil. Glob Chang Biol 17:1497–1504
Philippot L, Hallin S, Schloter M (2007) Ecology of denitrifying prokaryotes in agricultural soil. Adv Agron 96:249–305
Robertson G, Vitousek P, Matson P, Tiedje J (1987) Denitrification in a clearcut Loblolly pine (Pinus taeda L.) plantation in the southeastern US. Plant Soil 97:119–129
Søvik A, Kløve B (2007) Emission of N2O and CH4 from a constructed wetland in southeastern Norway. Sci Total Environ 380:28–37
Saarenheimo J, Rissanen AJ, Arvola L, Nykänen H, Lehmann MF, Tiirola M (2015) Genetic and environmental controls on nitrous oxide accumulation in lakes. PLoS One 10:e0121201
Samad MS, Biswas A, Bakken LR, Clough TJ, De Klein CA, Richards KG, Lanigan GJ, Morales SE (2016) Phylogenetic and functional potential links pH and N2O emissions in pasture soils. Sci Rep 6:35990
Sanford RA, Wagner DD, Wu Q, Chee-Sanford JC, Thomas SH, Cruz-García C, Rodríguez G, Massol-Deyá A, Krishnani KK, Ritalahti KM (2012) Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils. P Natl Acad Sci USA 109:19709–19714
Scheer C, Wassmann R, Butterbach-Bahl K, Lamers JP, Martius C (2009) The relationship between N2O, NO, and N2 fluxes from fertilized and irrigated dryland soils of the Aral Sea Basin, Uzbekistan. Plant Soil 314:273–283
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
Seitzinger S, Harrison JA, Böhlke J, Bouwman A, Lowrance R, Peterson B, Tobias C, Drecht GV (2006) Denitrification across landscapes and waterscapes: a synthesis. Ecol Appl 16:2064–2090
Sun L, Lu Y, Kronzucker HJ, Shi W (2016) Quantification and enzyme targets of fatty acid amides from duckweed root exudates involved in the stimulation of denitrification. J Plant Physiol 198:81–88
Syakila A, Kroeze C (2011) The global nitrous oxide budget revisited. Greenhouse Gas Meas Manage 1:17–26
Truu M, Ostonen I, Preem J-K, Lõhmus K, Nõlvak H, Ligi T, Rosenvald K, Parts K, Kupper P, Truu J (2017) Elevated air humidity changes soil bacterial community structure in the silver birch stand. Front Microbiol 8:557
Wallenstein MD, Myrold DD, Firestone M, Voytek M (2006) Environmental controls on denitrifying communities and denitrification rates: insights from molecular methods. Ecol Appl 16:2143–2152
Wang H, Marshall CW, Cheng M, Xu H, Li H, Yang X, Zheng T (2017) Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils. Sci Rep 7:44049
Wang Q, Quensen JF, Fish JA, Lee TK, Sun Y, Tiedje JM, Cole JR (2013) Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. MBio 4:e00592–e00513
Ye X, Li J, Wang Y-h, E-m L, Li R-x YQ, B-x C (2005) Characterization of emissions of nitrous oxide from soils of typical crop fields in North China Plain. JAES 24:1186–1191
Yoon S, Nissen S, Park D, Sanford RA, Löffler FE (2016) Nitrous oxide reduction kinetics distinguish bacteria harboring clade I versus clade II NosZ. Appl Environ Microbiol: AEM:00409–00416
Zhao S, Wang Q, Zhou J, Yuan D, Zhu G (2018) Linking abundance and community of microbial N2O-producers and N2O-reducers with enzymatic N2O production potential in a riparian zone. Sci Total Environ 642:1090–1099
Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol R 61:533–616
Zumft WG, Kroneck PM (2006) Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea. Adv Microb Physiol 52:107–227
Conflict of interest
The authors declare that they have no conflicts of interest.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Responsible editor: Yuan Ge
Electronic supplementary material
About this article
Cite this article
Zhao, S., Zhou, J., Yuan, D. et al. NirS-type N2O-producers and nosZ II-type N2O-reducers determine the N2O emission potential in farmland rhizosphere soils. J Soils Sediments 20, 461–471 (2020) doi:10.1007/s11368-019-02395-3
- nosZ II
- Rhizosphere soils