Abstract
Denitrifying nitrous oxide (N2O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N2O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different supplements of nitrate and glucose to simulate the varying nitrogen and carbon conditions. The results show that N2O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of nitrogen and carbon. The abundance of most denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N2O production (nirS and nirK) to the gene responsible for N2O reduction (nosZ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities, with a higher abundance of N2O-generating bacteria in BF and a higher abundance of N2O-reducing bacteria in FF. High accumulation of N2O was verified by the bacterial isolates of Rhodanobacter predominated in BF due to a lack of N2O reduction capacity. The dominance of Castellaniella and others in FF led to a rapid reduction in N2O and thus less N2O accumulation, as demonstrated when the corresponding isolate was inoculated into the studied soils. Therefore, the different phenotypes of N2O metabolism of the distinct denitrifiers predominantly colonized the two soils, causing differing N2O accumulation. This knowledge would help to develop a strategy for mitigating N2O emissions in agricultural soils by regulating the phenotypes of N2O metabolism.
Similar content being viewed by others
Data Availability
The raw Illumina sequence data generated in this study have been deposited to the GenBank Sequence Read Archive (SRA) database in the National Center for Biotechnology Information (NCBI) under the accession number PRJNA755188. 16S rRNA gene sequences for selected predominant bacterial strains were deposited in GenBank under accession numbers MZ824722–MZ824747.
References
Ishii S, Ikeda S, Minamisawa K, Senoo K (2011) Nitrogen cycling in rice paddy environments: past achievements and future challenges. Microbes Environ 26:282–292
Ravishankara AR, Daniel JS, Portmann RW (2009) Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. Science 326:123–125
Dou XL, Zhou W, Zhang QF, Cheng XL (2016) Greenhouse gas (CO2, CH4, N2O) emissions from soils following afforestation in central China. Atmos Environ 126:98–106
Lopez-Aizpun M, Horrocks CA, Charteris AF, Marsden KA, Ciganda VS, Evans JR, Chadwick DR, Cardenas LM (2020) Meta-analysis of global livestock urine-derived nitrous oxide emissions from agricultural soils. Global Change Biol 26:2002–2013
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 368:20130122
Yu Z, Yang J, Liu LM (2014) Denitrifier community in the oxygen minimum zone of a subtropical deep reservoir. PLoS One 9:e92055
Lycus P, Bothun KL, Bergaust L, Shapleigh JP, Bakken LR, Frostegard A (2017) Phenotypic and genotypic richness of denitrifiers revealed by a novel isolation strategy. ISME J 11:2219–2232
Domeignoz-Horta LA, Philippot L, Peyrard C, Bru D, Breuil MC, Bizouard F, Justes E, Mary B, Leonard J, Spor A (2018) Peaks of in situ N2O emissions are influenced by N2O-producing and reducing microbial communities across arable soils. Global Change Biol 24:360–370
Hu HW, Chen D, He JZ (2015) Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates. FEMS Microbiol Rev 39:729–749
Yan XY, Akimoto H, Ohara T (2003) Estimation of nitrous oxide, nitric oxide and ammonia emissions from croplands in East, Southeast and South Asia. Global Change Biol 9:1080–1096
Florio A, Brefort C, Gervaix J, Berard A, Le Roux X (2019) The responses of NO2– and N2O-reducing bacteria to maize inoculation by the PGPR Azospirillum lipoferum CRT1 depend on carbon availability and determine soil gross and net N2O production. Soil Biol Biochem 136:107524
Liu BB, Morkved PT, Frostegard A, Bakken LR (2010) Denitrification gene pools, transcription and kinetics of NO, N2O and N2 production as affected by soil pH. FEMS Microbiol Ecol 72:407–417
Yang LQ, Zhang XJ, Ju XT (2017) Linkage between N2O emission and functional gene abundance in an intensively managed calcareous fluvo-aquic soil. Sci Rep-UK 7:43283
Gao JM, Xie YX, Jin HY, Liu Y, Bai XY, Ma DY, Zhu YJ, Wang CY, Guo TC (2016) Nitrous oxide emission and denitrifier abundance in two agricultural soils amended with crop residues and urea in the North China Plain. PLoS One 11:e0154773
Fang WS, Yan DD, Wang XL, Huang B, Wang XN, Liu J, Liu XM, Li Y, Ouyang CB, Wang QX, Cao AC (2018) Responses of nitrogen-cycling microorganisms to dazomet fumigation. Front Microbiol 9:2529
Rich JJ, Heichen RS, Bottomley PJ, Cromack K, Myrold DD (2003) Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils. Appl Environ Microb 69:5974–5982
Ji MM, Tian H, Wu XG, Li J, Zhu Y, Wu GJ, Xu T, Wang JG, Zhang XJ (2021) Enhanced N2O emission rate in field soil undergoing conventional intensive fertilization is attributed to the shifts of denitrifying guilds. Pedosphere 31:145–156
Yin C, Fan FL, Song AL, Cui PY, Li TQ, Liang YC (2015) Denitrification potential under different fertilization regimes is closely coupled with changes in the denitrifying community in a black soil. Appl Microbiol Biot 99:5719–5729
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
Xu XZ, Xu Y, Chen SC, Xu SG, Zhang HW (2010) Soil loss and conservation in the black soil region of Northeast China: a retrospective study. Environ Sci Policy 13:793–800
Ju XT, Xing GX, Chen XP, Zhang SL, Zhang LJ, Liu XJ, Cui ZL, Yin B, Christie P, Zhu ZL, Zhang FS (2009) Reducing environmental risk by improving N management in intensive Chinese agricultural systems. Proc Natl Acad Sci USA 106:3041–3046
Zhu GD, Song XT, Ju XT, Zhang JB, Muller C, Sylvester-Bradley R, Thorman RE, Bingham I, Rees RM (2019) Gross N transformation rates and related N2O emissions in Chinese and UK agricultural soils. Sci Total Environ 666:176–186
Xu XP, He P, Pampolino MF, Li YY, Liu SQ, Xie JG, Hou YP, Zhou W (2016) Narrowing yield gaps and increasing nutrient use efficiencies using the Nutrient Expert system for maize in Northeast China. Field Crop Res 194:75–82
Shang Z, Zhou F, Smith P, Saikawa E, Ciais P, Chang J, Tian H, Del Grosso SJ, Ito A, Chen M, Wang Q, Bo Y, Cui X, Castaldi S, Juszczak R, Kasimir A, Magliulo V, Medinets S, Medinets V, Rees RM, Wohlfahrt G, Sabbatini S (2019) Weakened growth of cropland-N2O emissions in China associated with nationwide policy interventions. Global Change Biol 25:3706–3719
Zhang Y, Liu F, Wang J, Hu H, He J, Zhang L (2021) Effect of straw incorporation and nitrification inhibitor on nitrous oxide emission in various cropland soils and its microbial mechanism. Biorxiv. https://doi.org/10.1101/2021.05.26.445903
Molstad L, Dorsch P, Bakken LR (2007) Robotized incubation system for monitoring gases (O2, NO, N2O, N2) in denitrifying cultures. J Microbiol Meth 71:202–211
Paulin MM, Nicolaisen MH, Jacobsen CS, Gimsing AL, Sorensen J, Baelum J (2013) Improving Griffith’s protocol for co-extraction of microbial DNA and RNA in adsorptive soils. Soil Biol Biochem 63:37–49
Griffiths RI, Whiteley AS, O’Donnell AG, Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microb 66:5488–5491
Wu XG, Wang Y, Zhu Y, Tian H, Qin XC, Cui CZ, Zhao LP, Simonet P, Zhang XJ (2019) Variability in the response of bacterial community assembly to environmental selection and biotic factors depends on the immigrated bacteria, as revealed by a soil microcosm experiment. mSystems 4: e00496–19.
Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200
Cole JR, Wang Q, Fish JA, Chai BL, McGarrell DM, Sun YN, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM (2014) Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42:D633–D642
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Tumbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336
Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814–821
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60
Wei GF, Pan L, Du HM, Chen JY, Zhao LP (2004) ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts. J Microbiol Meth 59:91–108
Liu BB, Mao YJ, Bergaust L, Bakken LR, Frostegard A (2013) Strains in the genus Thauera exhibit remarkably different denitrification regulatory phenotypes. Environ Microbiol 15:2816–2828
Demoling F, Nilsson LO, Baath E (2008) Bacterial and fungal response to nitrogen fertilization in three coniferous forest soils. Soil Biol Biochem 40:370–379
Li J, Li YT, Yang XD, Zhang JJ, Lin ZA, Zhao BQ (2015) Microbial community structure and functional metabolic diversity are associated with organic carbon availability in an agricultural soil. J Integr Agr 14:2500–2511
Kuo J, Liu D, Wang SH, Lin CH (2021) Dynamic changes in soil microbial communities with glucose enrichment in sediment microbial fuel cells. Indian J Microbiol 61:497–505
Fanin N, Hattenschwiler S, Schimann H, Fromin N (2015) Interactive effects of C, N and P fertilization on soil microbial community structure and function in an Amazonian rain forest. Funct Ecol 29:140–150
Whalen SC (2000) Nitrous oxide emission from an agricultural soil fertilized with liquid swine waste or constituents. Soil Sci Soc Am J 64:781–789
Wu X, Liu G, Butterbach-Bahl K, Fu B, Zheng X, Bruggemann N (2013) Effects of land cover and soil properties on denitrification potential in soils of two semi-arid grasslands in Inner Mongolia, China. J Arid Environ 92:98–101
Carrino-Kyker SR, Smemo KA, Burke DJ (2012) The effects of pH change and NO3- pulse on microbial community structure and function: a vernal pool microcosm study. FEMS Microbiol Ecol 81:660–672
Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol R 61:533–616
Pan YT, Ni BJ, Yuan ZG (2013) Modeling electron competition among nitrogen oxides reduction and N2O accumulation in denitrification. Environ Sci Technol 47:11083–11091
Liang LL, Eberwein JR, Allsman LA, Grantz DA, Jenerette GD (2015) Regulation of CO2 and N2O fluxes by coupled carbon and nitrogen availability. Environ Res Lett 10:034008
Miller MN, Zebarth BJ, Dandie CE, Burton DL, Goyer C, Trevors JT (2008) Crop residue influence on denitrification, N2O emissions and denitrifier community abundance in soil. Soil Biol Biochem 40:2553–2562
Li SQ, Song LN, Gao X, Jin YG, Liu SW, Shen QR, Zou JW (2017) Microbial abundances predict methane and nitrous oxide fluxes from a windrow composting system. Front Microbiol 8:409
Li SQ, Song LN, Jin YG, Liu SW, Shen QR, Zou JW (2016) Linking N2O emission from biochar-amended composting process to the abundance of denitrify (nirK and nosZ) bacteria community. AMB Express 6:37
Cui PY, Fan FL, Yin C, Song AL, Huang PR, Tang YJ, Zhu P, Peng C, Li TQ, Wakelin SA, Liang YC (2016) Long-term organic and inorganic fertilization alters temperature sensitivity of potential N2O emissions and associated microbes. Soil Biol Biochem 93:131–141
Braker G, Matthies D, Hannig M, Brandt FB, Brenzinger K, Grongroft A (2015) Impact of land use management and soil properties on denitrifier communities of Namibian Savannas. Microb Ecol 70:981–992
Philippot L, Spor A, Henault C, Bru D, Bizouard F, Jones CM, Sarr A, Maron PA (2013) Loss in microbial diversity affects nitrogen cycling in soil. ISME J 7:1609–1619
Hu XJ, Liu JJ, Wei D, Zhu P, Cui XA, Zhou BK, Chen XL, Jin J, Liu XB, Wang GH (2020) Chronic effects of different fertilization regimes on nirS-type denitrifier communities across the black soil region of Northeast China. Pedosphere 30:73–86
Pang CM, Liu WT (2007) Community structure analysis of reverse osmosis membrane biofilms and the significance of Rhizobiales bacteria in biofouling. Environ Sci Technol 41:4728–4734
Acknowledgements
The authors would like to express their gratitude to Dr. Wei Zhang (Institute of Applied Ecology, CAS) for her help in collecting the black soil.
Funding
This work was supported by the National Natural Science Foundation of China (NSFC 31971526, 31861133018), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB40020204), and the Key R&D project of Ministry of Science and Technology (2017YFD0200102).
Author information
Authors and Affiliations
Contributions
Q.W. and X.Z. conceived and designed the study; Q.W., M. J., S.Y., J.L., X.W., and B.L. designed the methodology; Q.W. and S.Y. collected the data and performed the data analysis; X.J. and B.L. were involved in the discussion of results; Q.W. wrote the first draft of the manuscript. Q.W. and X.Z. contributed to revisions. All authors contributed to the drafts and gave the final approval for publication.
Corresponding author
Ethics declarations
Conflict of Interest
The authors declare no competing interests.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Wu, Q., Ji, M., Yu, S. et al. Distinct Denitrifying Phenotypes of Predominant Bacteria Modulate Nitrous Oxide Metabolism in Two Typical Cropland Soils. Microb Ecol 86, 509–520 (2023). https://doi.org/10.1007/s00248-022-02085-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00248-022-02085-7