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Effect of rice straw and/or nitrogen fertiliser inputs on methanogenic archaeal and denitrifying communities in a typical rice paddy soil

Published online by Cambridge University Press:  14 January 2019

Qiongli BAO ,
Long-Jun DING ,
Yizong HUANG  and
Keqing XIAO
Qiongli BAO
Affiliation:
Centre for Research in Ecotoxicology and Environmental Remediation, Institute of Agro-Environmental Protection, Ministry of Agriculture, Tianjin 300191, China.
Long-Jun DING*
Affiliation:
State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. Email: ljding@rcees.ac.cn
Yizong HUANG
Affiliation:
Centre for Research in Ecotoxicology and Environmental Remediation, Institute of Agro-Environmental Protection, Ministry of Agriculture, Tianjin 300191, China.
Keqing XIAO
Affiliation:
Department of Bioscience-Center for Geomicrobiology, University of Aarhus, 8000 Aarhus C, Denmark.
*
*Corresponding author
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Abstract

To understand better the microbial functional populations which are involved in methanogenesis and denitrification in paddy soils with rice straw (RS) and/or nitrogen fertiliser (potassium nitrate, N) application, the dynamics of methanogens and the denitrifying community were monitored simultaneously during the incubation period. The results show that the community structure of methanogens remained relatively stable among treatments based on 16S rDNA analysis, but fluctuated based on 16S rRNA. The Methanocellaceae and Methanosarcinaceae dominated all treatments at 16S rDNA and 16S rRNA level, respectively. RS+N increased the relative abundance of Methanosaetaceae at the 16S rRNA level, while there was an increasing trend in that Methanomicrobiaceae following RS addition at the 16S rDNA level. RS and/or N did not significantly change the diversity of methanogens targeting both 16S rDNA and 16S rRNA. RS and RS+N increased copy numbers of methanogens targeting both 16S rDNA and 16S rRNA analyses. The community structure and abundance of nirS and nosZ-containing denitrifiers, and the diversity of nirS-containing denitrifiers was significantly altered only by the N treatment. These results indicate that the community structure, diversity and abundance of methanogens respond differently to RS addition at the 16S rDNA and 16S rRNA levels.

Keywords

crop residuesdenitrifiersmethanogenic archaeanitrate
Type
Articles
Information
Earth and Environmental Science Transactions of The Royal Society of Edinburgh , Volume 109 , Issue 3-4: Earth Surface Processes and Environmental Sustainability in China , September 2018 , pp. 375 - 386
Copyright
Copyright © The Royal Society of Edinburgh 2019 

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References

7. References

Bañeras, L., Ruiz-Rueda, O., López-Flores, R., Quintana, X. & Hallin, S. 2012. The role of plant type and salinity in the selection for the denitrifying community structure in the rhizosphere of wetland vegetation. International Microbiology 15, 89–99.Google Scholar
Bao, Q. L., Ju, X. T., Gao, B., Qu, Z., Christie, P. & Lu, Y. H. 2011. Response of nitrous oxide and corresponding bacteria to managements in an agricultural soil. Soil Science Society of America Journal 76, 130–141.Google Scholar
Bao, Q. L., Xiao, K. Q., Chen, Z., Yao, H. Y. & Zhu, Y. G. 2014. Methane production and methanogenic archaeal communities in two types of paddy soil amended with different amounts of rice straw. FEMS Microbiology Ecology 88, 372–385.Google Scholar
Bao, Q. L., Huang, Y. Z., Wang, F. H., Nie, S. A., Graeme, W., Yao, H. Y. & Ding, L. J. 2016. Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil. Applied Microbiology and Biotechnology 100, 5989–5998.Google Scholar
Chen, X. P., Zhu, Y. G., Xia, Y., Shen, J. P. & He, J. Z. 2008. Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? Environmental Microbiology 10, 1978–1987.Google Scholar
Chen, Z., Luo, X., Hu, R., Wu, M., Wu, J. & Wei, W. 2010. Impact of long-term fertilization on the composition of denitrifier communities based on nitrite reductase analyses in a paddy soil. Microbiology Ecology 60, 850–861.Google Scholar
Chen, Z., Hou, H. J., Zheng, Y., Qin, H. L., Zhu, Y. J., Wu, J. S. & Wei, W. X. 2012. Influence of fertilization regimes on a nosZ-containing denitrifying community in a rice paddy soil. Journal of the Science of Food and Agriculture 92, 1064–1072.Google Scholar
Conrad, R. 2007. Microbial ecology of methanogens and methanotrophs. Advances in Agronomy 96, 1–63.Google Scholar
Conrad, R., Klose, M., Noll, M., Kermnitz, D. & Bodelier, P. L. E. 2008. Soil type links microbial colonization of rice roots to methane emission. Global Change Biology 14, 657–669.Google Scholar
Conrad, R., Klose, M., Lu, Y. H. & Chidthaisong, A. 2012. Methanogenic pathway and archaeal communities in three different anoxic soils amended with rice straw and maize straw. Frontier in Microbiology 3, 1–11.Google Scholar
Conrad, R. & Klose, M. 2006. Dynamics of the methanogenic archaeal community in anoxic rice soil upon addition of straw. European Journal of Soil Science 57, 476–484.Google Scholar
Cui, S. H., Shi, Y. L., Groffman, P. M., Schlesinger, W. H. & Zhu, Y. G. 2013. Centennial-scale analysis of the creation and fate of reactive nitrogen in China (1910–2010). Proceedings of the National Academy of Sciences USA 110, 2052–2057.Google Scholar
Dambreville, C., Hallet, S., Nguyen, C., Morvan, T., Germon, J. C. & Philippot, L. 2006. Structure and activity of the denitrifying community in a maize-cropped field fertilized with composted pig manure or ammonium nitrate. FEMS Microbiology Ecology 56, 119–131.Google Scholar
Devêvre, O. C. & Horwáth, W. R. 2001. Stabilization of fertilizer nitrogen-15 into humic substances in aerobic vs. Waterlogged soil following straw incorporation. Soil Science Society of American Journal 65, 499–510.Google Scholar
Ding, L. J., An, X. L., Li, S., Zhang, G. L. & Zhu, Y. G. 2014. Nitrogen loss through anaerobic ammonium oxidation coupled to iron reduction from paddy soils in a chronosequence. Environmental Science and Technology 48, 10641–47.Google Scholar
Enwall, K., Philippot, L. & Hallin, S. 2005. Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization. Applied and Environmental Microbiology 71, 8335–8343.Google Scholar
Enwall, K., Throbäck, I. N., Stenberg, M., Söderström, M. & Hallin, S. 2010. Soil resources influence spatial patterns of denitrifying communities at scales compatible with land management. Applied and Environmental Microbiology 76, 2243–2250.Google Scholar
Guo, G. X., Deng, H., Qiao, M., Mu, Y. J. & Zhu, Y. G. 2011. Effect of pyrene on denitrification activity and abundance and composition of denitrifying community in an agricultural soil. Environmental Pollution 159, 1886–1895.Google Scholar
Henderson, S. L., Dandie, C. E., Patten, C. L., Zebarth, B. J., Burton, D. L., Trevors, J. T. & Goyer, C. 2010. Changes in denitrifier abundance, denitrification gene mRNA levels, nitrous oxide emissions, and denitrification in anoxic soil microcosms amended with glucose and plant residues. Applied and Environmental Microbiology 76, 2155–2164.Google Scholar
Henry, S., Bru, D., Stres, B., Hallet, S. & Philippot, L. 2006. Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils. Applied and Environmental Microbiology 72, 5181–9.Google Scholar
Ishii, S., Yamamoto, M., Kikuchi, M., Oshima, K., Hattori, M., Otsuka, S. & Senoo, K. 2009. Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis. Applied and Environmental Microbiology 75, 7070–7078.Google Scholar
Jetten, M. S. M., Stams, A. J. M. & Zehnder, A. J. B. 1990. Acetate threshold values and acetate activating enzymes in methanogenic bacteria. FEMS Microbiology Ecology 73, 339–344.Google Scholar
Jetten, M. S. M., Stams, A. J. M. & Zehnder, A. J. B. 1992. Methanogenesis from acetate – a comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp. FEMS Microbiology Review 88, 181–197.Google Scholar
Jones, C. M. & Hallin, S. 2010. Ecological and evolutionary factors underlying global and local assembly of denitrifier communities. The ISME Journal 4, 633–641.Google Scholar
Kemnitz, D., Chin, K. J., Bodelier, P. & Conrad, R. 2004. Community analysis of methanogenic archaea within a riparian flooding gradient. Environmental Microbiology 6, 449–461.Google Scholar
Klüber, H. D. & Conrad, R. 1998a. Inhibitory effects of nitrate, nitrite, NO and N2O on methanogenesis by Methanosarcina barkeri and Methanobacterium bryantii. FEMS Microbiology Ecology 25, 331–339.Google Scholar
Klüber, H. D. & Conrad, R. 1998b. Effects of nitrate, nitrite, NO and N2O on methanogenesis and other redox processes in anoxic rice field soil. FEMS Microbiology Ecology 25, 301–318.Google Scholar
Lan, T., Han, Y. & Cai, Z. C. 2015. Denitrification and its product composition in typical Chinese paddy soils. Biology and Fertility of Soils 51, 89–98.Google Scholar
Liesack, W., Schnell, S. & Revsbech, N. P. 2000. Microbiology of flooded rice paddies. FEMS Microbiology Review 24, 625–645.Google Scholar
Lu, Y., Fu, L., Lu, Y. H., Floor, H. & Ma, K. 2015. Effect of temperature on the structure and activity of a methanogenic archaeal community during rice straw decomposition. Soil Biology and Biochemistry 81, 17–27.Google Scholar
Lu, Y. H. & Conrad, R. 2005. In situ stable isotope probing of methanogenic archaeal in the rice rhizosphere. Science 309, 1088–1090.Google Scholar
Lueders, T. & Friedrich, M. 2000. Archaeal population dynamics during sequential reduction processes in rice field soil. Applied and Environmental Microbiology 66, 2732–2742.Google Scholar
Ma, K., Conrad, R. & Lu, Y. H. 2012. Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. Applied and Environmental Microbiology 78, 445–454.Google Scholar
Ma, Y. C., Sun, L. Y., Zhang, X. Y., Yang, B., Wang, J. Y., Yin, B., Yan, X. Y. & Xiong, Z. Q. 2013. Mitigation of nitrous oxide emissions from paddy soil under conventional and no-till practices using nitrification inhibitors during the winter wheat-growing season. Biology and Fertility of Soils 49, 627–635.Google Scholar
Miller, M. N., Dandie, C. E., Zebarth, B. J., Burton, D. L., Goyer, C. & Trevors, J. T. 2012. Influence of carbon amendments on soil denitrifier abundance in soil microcosms. Geoderma 170, 48–55.Google Scholar
Morales, S. E., Cosart, T. & Holben, W. E. 2010. Bacterial gene abundances as indicators of greenhouse gas emission in soils. The ISME Journal 4, 799–808.Google Scholar
Morrissey, E. M., Jenkins, A. S., Brown, B. L. & Franklin, R. B. 2013. Resource availability effects on nitrate reducing microbial communities in a freshwater wetland. Wetlands 33, 301–310.Google Scholar
Morrissey, E. M. & Franklin, R. B. 2015. Resource effects on denitrification are mediated by community composition in tidal freshwater wetlands soils. Environmental Microbiology 17, 1520–1532.Google Scholar
Nannipieri, P. & Eldor, P. 2009. The chemical and functional characterization of soil N and its biotic components. Soil Biology and Biochemistry 41, 2357–2369.Google Scholar
Peng, J. J., Lü, Z., Rui, J. P. & Lu, Y. H. 2008. Dynamics of the methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil. Applied and Environmental Microbiology 74, 2894–2901.Google Scholar
Philippot, L. & Hallin, S. 2005. Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community. Current Opinion in Microbiology 8, 234–239.Google Scholar
Satio, T., Ishii, S., Otsuka, S., Nishiyama, M. & Senoo, K. 2008. Identification of novel betaproteobacteria in a sucdinate-assimilation population in denitrifying rice paddy soil by using stable isotope probing. Microbes and Environments 23, 192–200.Google Scholar
Scheid, D., Stubner, S. & Conrad, R. 2004. Identification of rice root associated nitrate, sulfate and ferric iron reducing bacteria during root decomposition. FEMS Microbiology Ecology 50, 101–110.Google Scholar
Smith, P., Martino, D., Cai, Z., Gwary, D., Janzen, H., Kumar, P., McCarl, B., Ogle, S., O'Mara, F., Rice, C., Scholes, B., Sirotenko, O., Howden, M., McAllister, T., Pan, G., Romanenkov, V., Schneider, U. & Towprayoon, S. 2007. Policy and technological constraints to implementation of greenhouse gas mitigation options in agriculture. Agriculture Ecosystems and Environment 118, 6–28.Google Scholar
Sun, R. B., Guo, X. S., Wang, D. Z. & Chu, H. Y. 2015. Effects of long-term application of chemical and organic fertilizers on the abundance of microbial communities involved in the nitrogen cycle. Applied Soil Ecology 95, 171–178.Google Scholar
Tang, H., Yan, K., Zhang, L., Chi, F., Li, Q., Lian, S. & Wei, D. 2010. Diversity analysis of nitrite reductase genes (nirS) in black soil under different long-term fertilization conditions. Annals of Microbiology 60, 97–104.Google Scholar
Throbäck, I. N., Enwall, K., Jarvis, Å. & Hallin, S. 2004. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiology Ecology 49, 401–417.Google Scholar
Tirol-Padre, A., Tsuchiya, K., Inubushi, K. & Ladha, J. K. 2005. Enhancing soil quality through residue management in a rice-wheat system in Fukuoka, Japan. Journal of Soil Science and Plant Nutrition 51, 849–860.Google Scholar
Töwe, S., Wallisch, S., Bannert, A., Fischer, D., Hai, B., Haesler, F., Kleineidam, K. & Schloter, M. 2011. Improved protocol for the simultaneous extraction and column-based separation of DNA and RNA from different soils. Journal of Microbiological Methods 84, 406–412.Google Scholar
Wang, W. Q., Lai, D. Y. F., Sardans, J., Wang, C., Datta, A., Pan, T., Zeng, C. S., Bartrons, M. & Peñuelas, J. 2015. Rice straw incorporation affects global warming potential differently in early vs. Late cropping seasons in Southeastern China. Field Crop Research 181, 42–51.Google Scholar
Wolsing, M. & Prieme, A. 2004. Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments. FEMS Microbiology Ecology 48, 261–271.Google Scholar
Wu, L. Q., Ma, K., Li, Q., Ke, X. B. & Lu, Y. H. 2009. Composition of archaeal community in paddy field as affected by rice cultivar and N fertilizer. Microbiology Ecology 58, 819–826.Google Scholar
Xiao, K. Q., Bao, P., Bao, Q. L., Jia, Y., Huang, F. Y., Su, J. Q. & Zhu, Y. G. 2013. Quantitative analyses of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit genes (cbbL) in typical paddy soils. FEMS Microbiology Ecology 38, 11–20.Google Scholar
Xu, Y., Ma, K., Huang, S. W., Liu, L. M. & Lu, Y. H. 2012. Diel cycle of methanogen mcrA transcripts in rice rhizosphere. Environmental Microbiology Reports 4, 655–663.Google Scholar
Yang, J. K., Cheng, Z. B., Li, J. & Miao, L. H. 2013. Community composition of nirS-type denitrifier in a shallow eutrophic lake. Microbiology Ecology 66, 796–805.Google Scholar
Yoshida, M., Ishii, S., Otsuka, S. & Senoo, K. 2009. Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil. Soil Biology and Biochemistry 41, 2044–2051.Google Scholar
Yuan, Q. & Lu, Y. H. 2009. Response of methanogenic archaeal community to nitrate addition in rice field soil. Environmental Microbiology Reports 1, 362–369.Google Scholar
Yuan, Y. L., Conrad, R. & Lu, Y. H. 2011. Transcriptional response of methanogen mcrA genes to oxygen exposure of rice field soil. Environmental Microbiology Reports 3, 320–328.Google Scholar
Zhu, J. G., Liu, G., Han, Y., Zhang, Y. L. & Xing, G. X. 2003. Nitrate distribution and denitrification in the saturated zone of paddy field under rice/wheat rotation. Chemosphere 50, 725–732.Google Scholar
Zhu, Y. G., Su, J. Q., Cao, Z. H., Xue, K., Quensen, J., Guo, G. X., Yang, Y. F., Zhou, J. Z., Chu, H. Y. & Tiedje, J. M. 2016. A buried neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation. Science Bulletin 61, 1052–1060.Google Scholar