A rice variety with a high straw biomass retained nitrogen and phosphorus without affecting soil bacterial species
Xinqiang Liang, Fayong Li, Sheng Wang, Guifen Hua, Miaomiao He, Guangming Tian, Sangar Khan, Ravin Poudel, Karen A. Garrett
A rice variety with a high straw biomass retained nitrogen and phosphorus without affecting soil bacterial species
It is well documented that rice paddy fields act as agricultural wetlands that remove or retain nutrients; however, their associated effects on soil microbial communities are rarely reported. The present study evaluates the impact of rice variety on nutrient removal via plant uptake, nutrient retention in the soil, and bacterial associations in rice paddy fields, using a network analysis that compares the soil bacterial communities of two rice varieties. We found that the high-straw rice variety (YD-1) allows uptake of a high amount of nitrogen (N) and phosphorus (P) from paddy rice fields via harvesting, but causes less residual total N and P to remain in the soil. However, both rice varieties (YD-1 and XS-134(Xiushui-134)) had non-significant effects on the dominant bacterial taxa. The short-term response of bacterial community diversity to rice variety is found to be mainly due to less frequently recovered species. A network analysis that incorporates soil nutrients as nodes, as well as bacterial taxa, found that only one node that denotes the total P related to the non-dominant species had an indirect association with the rice straw biomass. The observed short-term impact of the two rice varieties (XS-134 and YD-1) on soil bacterial diversity and nutrient surplus in these agricultural wetlands is limited under a high level of fertilization.
Agricultural wetland / Network analysis / Nutrient / Rice variety / Soil bacterial communities
[1] |
Amato, K.R., Yeoman, C.J., Kent, A., Righini, N., Carbonero, F., Estrada, A., Gaskins, H.R., Stumpf, R.M., Yildirim, S., Torralba, M., Gillis, M., Wilson, B.A., Nelson, K.E., White, B.A., Leigh, S.R., 2013. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME Journal 7, 1344–1353
CrossRef
Pubmed
Google scholar
|
[2] |
Balasooriya, W.K., Huygens, D., Rajapaksha, R.M.C.P., Boeckx, P., 2016. Effect of rice variety and fertilizer type on the active microbial community structure in tropical paddy fields in Sri Lanka. Geoderma 265, 87–95
CrossRef
Google scholar
|
[3] |
Benjamini, Y., Hochberg, Y., 1995. Controlling the false discovery rate-a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B. Methodological 57, 289–300
CrossRef
Google scholar
|
[4] |
Bhadraray, S., Purakayastha, T.J., Chhonkar, P.K., Verma, V., 2002. Phosphorus mobilization in hybrid rice rhizosphere compared to high yielding varieties under integrated nutrient management. Biology and Fertility of Soils 35, 73–78
CrossRef
Google scholar
|
[5] |
Breidenbach, B., Pump, J., Dumont, M.G., 2016. Microbial community structure in the rhizosphere of rice plants. Frontiers in Microbiology 6, 1537
CrossRef
Pubmed
Google scholar
|
[6] |
Breulmann, M., Schulz, E., Weißhuhn, K., Buscot, F., 2012. Impact of the plant community composition on labile soil organic carbon, soil microbial activity and community structure in semi-natural grassland ecosystems of different productivity. Plant and Soil 352, 253–265
CrossRef
Google scholar
|
[7] |
Brown, M.B., 1975. 400: A method for combining non-independent, one–sided tests of significance. Biometrics 31, 987
CrossRef
Google scholar
|
[8] |
Cade-Menun, B.J., Carter, M.R., James, D.C., Liu, C.W., 2010. Phosphorus forms and chemistry in the soil profile under long-term conservation tillage: a phosphorus-31 nuclear magnetic resonance study. Journal of Environmental Quality 39, 1647–1656
CrossRef
Pubmed
Google scholar
|
[9] |
Campiglia, E., Mancinelli, R., Di Felice, V., Radicetti, E., 2014. Long-term residual effects of the management of cover crop biomass on soil nitrogen and yield of endive (Cichorium endivia L.) and savoy cabbage (Brassica oleracea var. sabauda). Soil & Tillage Research 139, 1–7
CrossRef
Google scholar
|
[10] |
Chowdhury, S. P., Babin, D., Sandmann, M., Jacquiod, S., Sommermann, L., Sørensen, S.J., Fliessbach, A., Mäder, P., Geistlinger, J., Smalla, K., Rothballer, M., Grosch, R., 2019. Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce. Environmental Microbiology 21, 2426–2439
CrossRef
Pubmed
Google scholar
|
[11] |
Chen, H., Wang, G., Lu, X., Jiang, M., Mendelssohn, I.A., 2015. Balancing the needs of China’s wetland conservation and rice production. Environmental Science & Technology 49, 6385–6393
CrossRef
Pubmed
Google scholar
|
[12] |
Conrad, R., 2007. Microbial ecology of methanogens and methanotrophs. Advances in Agronomy 96, 1–63.
|
[13] |
Dass, A., Kaur, R., Choudhary, A.K., Pooniya, V., Raj, R., Rana, K.S., 2015. System of rice (Oryza sativa) intensification for enhanced productivity and resource-use-efficiency–A review. Indian Journal of Agronomy 60, 1–19.
|
[14] |
Dobermann, A., Fairhurst, T.H., 2000. Rice: Nutrient Disorders and Nutrient Management. Makati City: International Rice Research Institute, Philippines, pp.199
|
[15] |
Eisenhauer, N., Bessler, H., Engels, C., Gleixner, G., Habekost, M., Milcu, A., Partsch, S., Sabais, A.C., Scherber, C., Steinbeiss, S., Weigelt, A., Weisser, W.W., Scheu, S., 2010. Plant diversity effects on soil microorganisms support the singular hypothesis. Ecology 91, 485–496
CrossRef
Pubmed
Google scholar
|
[16] |
Faust, K., Raes, J., 2012. Microbial interactions: from networks to models. Nature Reviews Microbiology 10, 538–550
CrossRef
Pubmed
Google scholar
|
[17] |
Faust, K., Sathirapongsasuti, J.F., Izard, J., Segata, N., Gevers, D., Raes, J., Huttenhower, C., 2012. Microbial co-occurrence relationships in the human microbiome. PLoS Computational Biology 8, e1002606
CrossRef
Pubmed
Google scholar
|
[18] |
Freese, D., Vanderzee, S., Vanriemsdijk, W.H., 1992. Comparison of different models for phosphate sorption as a function of the iron an aluminum–oxides of soils. Journal of Soil Science 43, 729–738
CrossRef
Google scholar
|
[19] |
Han, S., Luo, X., Liao, H., Nie, H., Chen, W., Huang, Q., 2017. Nitrospira are more sensitive than Nitrobacter to land management in acid, fertilized soils of a rapeseed-rice rotation field trial. Science of the Total Environment 599-600, 135–144
CrossRef
Pubmed
Google scholar
|
[20] |
Harish, M.N., Choudhary, A.K., Singh, Y.V., Pooniya, V., Das, A., Varatharajan, T., 2018. Influence of promising rice (Oryza sativa) varieties and nutrient management practices on micronutrient biofortification and soil fertility in Eastern Himalayas. Indian Journal of Agronomy 63, 377–399.
|
[21] |
Jennings, P.R., 1974. Rice breeding and world food production. Science 186, 1085–1088
CrossRef
Pubmed
Google scholar
|
[22] |
Ju, X.T., Xing, G.X., Chen, X.P., Zhang, S.L., Zhang, L.J., Liu, X.J., Cui, Z.L., Yin, B., Christie, P., Zhu, Z.L., Zhang, F.S., 2009. Reducing environmental risk by improving N management in intensive Chinese agricultural systems. Proceedings of the National Academy of Sciences of the United States of America 106, 3041–3046
CrossRef
Pubmed
Google scholar
|
[23] |
Kulichevskaya, I.S., Suzina, N.E., Liesack, W., Dedysh, S.N., 2010. Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria. International Journal of Systematic and Evolutionary Microbiology 60, 301–306
CrossRef
Pubmed
Google scholar
|
[24] |
Lange, M., Eisenhauer, N., Sierra, C.A., Bessler, H., Engels, C., Griffiths, R.I., Mellado-Vázquez, P.G., Malik, A.A., Roy, J., Scheu, S., Steinbeiss, S., Thomson, B.C., Trumbore, S.E., Gleixner, G., 2015. Plant diversity increases soil microbial activity and soil carbon storage. Nature Communications 6, 6707
CrossRef
Pubmed
Google scholar
|
[25] |
Liang, X.Q., Chen, Y.X., Li, H., Tian, G.M., Zhang, Z.J., Ni, W.Z., He, M.M., 2007. Nitrogen interception in floodwater of rice field in Taihu region of China. Journal of Environmental Sciences (China) 19, 1474–1481
CrossRef
Pubmed
Google scholar
|
[26] |
Liang, X.Q., Chen, Y.X., Nie, Z.Y., Ye, Y.S., Liu, J., Tian, G.M., Wang, G.H., Tuong, T.P., 2013. Mitigation of nutrient losses via surface runoff from rice cropping systems with alternate wetting and drying irrigation and site-specific nutrient management practices. Environmental Science and Pollution Research International 20, 6980–6991
CrossRef
Pubmed
Google scholar
|
[27] |
Liang, X.Q., Harter, T., Porta, L., van Kessel, C., Linquist, B.A., 2014. Nitrate leaching in californian rice fields: a field- and regional-scale assessment. Journal of Environmental Quality 43, 881–894
CrossRef
Pubmed
Google scholar
|
[28] |
Liang, X.Q., Jin, Y., He, M.M., Liu, Y., Hua, G.F., Wang, S., Tian, G.M., 2017. Composition of phosphorus species and phosphatase activities in a paddy soil treated with manure at varying rates. Agriculture, Ecosystems & Environment 237, 173–180
CrossRef
Google scholar
|
[29] |
Lima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J.C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A.M., Coppola, L., Cornejo-Castillo, F.M., d’Ovidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M.J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sánchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S.G., Sunagawa, S., Bork, P., Sullivan, M.B., Karsenti, E., Bowler, C., de Vargas, C., Raes, J., the Tara Oceans coordinators, 2015. Ocean plankton. Determinants of community structure in the global plankton interactome. Science 348, 1262073
Pubmed
|
[30] |
Luo, X.S., Han, S., Fu, X.Q., Li, X., Wang, L., Peng, S.B., Chen, W.L., Huang, X.Y., 2019. The microbial network in naturally fertile paddy soil possibly facilitates functional recruitment in the rice mature stage. Applied Soil Ecology 135, 174–181
CrossRef
Google scholar
|
[31] |
Makarov, M.I., Haumaier, L., Zech, W., Marfenina, O.E., Lysak, L.V., 2005. Can 31P NMR spectroscopy be used to indicate the origins of soil organic phosphates? Soil Biology & Biochemistry 37, 15–25
CrossRef
Google scholar
|
[32] |
Olsen, S.R., Sommers, L.E., 1982. Phosphorus. In: Page, A.L., Miller, R.H., Keeney, D.R., eds. Methods of Soil Analysis. Part 2 Chemical and Microbiological Properties. Madison, WI:ASASSSA, pp. 403–430.
|
[33] |
Palm, C., Blanco-Canqui, H., DeClerck, F., Gatere, L., Grace, P., 2014. Conservation agriculture and ecosystem services: An overview. Agriculture, Ecosystems & Environment 187, 87–105
CrossRef
Google scholar
|
[34] |
Pittelkow, C.M., Liang, X., Linquist, B.A., van Groenigen, K.J., Lee, J., Lundy, M.E., van Gestel, N., Six, J., Venterea, R.T., van Kessel, C., 2015. Productivity limits and potentials of the principles of conservation agriculture. Nature 517, 365–368
CrossRef
Pubmed
Google scholar
|
[35] |
Poudel, R., Jumpponen, A., Schlatter, D.C., Paulitz, T.C., Gardener, B.B., Kinkel, L.L., Garrett, K.A., 2016. Microbiome networks: A systems framework for identifying candidate microbial assemblages for disease management. Phytopathology 106, 1083–1096
CrossRef
Pubmed
Google scholar
|
[36] |
Singh, K., Trivedi, P., Singh, G., Singh, B., Patra, D.D., 2016. Effect of different leaf litters on carbon, nitrogen and microbial activities of sodic soils. Land Degradation & Development 27, 1215–1226
CrossRef
Google scholar
|
[37] |
Somaweera, K.A.T.N., Suriyagoda, L.D.B., Sirisena, D.N., De Costa, W.A.J.M., 2016. Accumulation and partitioning of biomass, nitrogen, phosphorus and potassium among different tissues during the life cycle of rice grown under different water management regimes. Plant and Soil 401, 169–183
CrossRef
Google scholar
|
[38] |
Stewart, J.W.B., Tiessen, H., 1987. Dynamics of soil organic phosphorus. Biogeochemistry 4, 41–60
CrossRef
Google scholar
|
[39] |
Suriyagoda, L., De Costa, W.A.J.M., Lambers, H., 2014. Growth and phosphorus nutrition of rice when inorganic fertiliser application is partly replaced by straw under varying moisture availability in sandy and clay soils. Plant and Soil 384, 53–68
CrossRef
Google scholar
|
[40] |
Tejada, M., Benitez, C., 2014. Effects of crushed maize straw residues on soil biological properties and soil restoration. Land Degradation & Development 25, 501–509
CrossRef
Google scholar
|
[41] |
Tilman, D., Cassman, K.G., Matson, P.A., Naylor, R., Polasky, S., 2002. Agricultural sustainability and intensive production practices. Nature 418, 671–677
CrossRef
Pubmed
Google scholar
|
[42] |
Toor, G.S., Condron, L.M., Di, H.J., Cameron, K.C., Cade–Menun, B.J., 2003. Characterization of organic phosphorus in leachate from a grassland soil. Soil Biology & Biochemistry 35, 1317–1323
CrossRef
Google scholar
|
[43] |
Traina, S.J., Sposito, G., Hesterberg, D., Kafkafi, U., 1986. Effects of pH and organic acids on orthophosphate solubility in an acidic, montmorillonitic soil. Soil Science Society of America Journal 50, 45–52
CrossRef
Google scholar
|
[44] |
Walker, T.W., Adams, A.F.R., 1958. Studies on soil organic matter: 1. Influence of phosphorus contents of parent materials on accumulations of carbon, nitrogen, sulfur, and organic phosphorus in grassland soils. Soil Science 85, 307–318
CrossRef
Google scholar
|
[45] |
Wang, S.X., Liang, X.Q., Chen, Y.X., Luo, Q.X., Liang, W.S., Li, S., Huang, C.L., Li, Z.Z., Wan, L.L., Li, W., Shao, X.X., 2012. Phosphorus loss potential and phosphatase activity under phosphorus fertilization in long-term paddy wetland agroecosystems. Soil Science Society of America Journal 76, 161–167
CrossRef
Google scholar
|
[46] |
Xiong, Y., Peng, S., Luo, Y., Xu, J., Yang, S., 2015. A paddy eco-ditch and wetland system to reduce non-point source pollution from rice-based production system while maintaining water use efficiency. Environmental Science and Pollution Research International 22, 4406–4417
CrossRef
Pubmed
Google scholar
|
[47] |
Yao, L., Wang, D., Kang, L., Wang, D., Zhang, Y., Hou, X., Guo, Y., 2018. Effects of fertilizations on soil bacteria and fungi communities in a degraded arid steppe revealed by high through-put sequencing. Peer J 6, e4623
CrossRef
Pubmed
Google scholar
|
[48] |
Ye, Y., Liang, X., Chen, Y., Li, L., Ji, Y., Zhu, C., 2014. Carbon, nitrogen and phosphorus accumulation and partitioning, and C:N:P stoichiometry in late-season rice under different water and nitrogen managements. PLoS One 9, e101776
CrossRef
Pubmed
Google scholar
|
[49] |
Yin, Y., Wang, J., 2016. Changes in microbial community during biohydrogen production using gamma irradiated sludge as inoculum. Bioresource Technology 200, 217–222
CrossRef
Pubmed
Google scholar
|
[50] |
Yuan, G., Lavkulich, L.M., 1994. Phosphate sorption in relation to extractable iron and aluminum in spodosols. Soil Science Society of America Journal 58, 343–346
CrossRef
Google scholar
|
[51] |
Zhang, K.L., Chen, L., Li, Y., Brookes, P.C., Xu, J.M., Luo, Y., 2017. The effects of combinations of biochar, lime, and organic fertilizer on nitrification and nitrifiers. Biology and Fertility of Soils 53, 77–87
CrossRef
Google scholar
|
[52] |
Zhao, J., Ni, T., Li, J., Lu, Q., Fang, Z.Y., Huang, Q.W., Zhang, R.F., Li, R., Shen, B., Shen, Q.R., 2016. Effects of organic–inorganic compound fertilizer with reduced chemical fertilizer application on crop yields, soil biological activity and bacterial community structure in a rice–wheat cropping system. Applied Soil Ecology 99, 1–12
CrossRef
Google scholar
|
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