A biogeographic map of soil bacterial communities in wheats field of the North China Plain

Yu Shi, Yuntao Li, Meiqing Yuan, Jonathan M. Adams, Xianzhang Pan, Yunfeng Yang, Haiyan Chu

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Soil Ecology Letters ›› 2019, Vol. 1 ›› Issue (1-2) : 50-58. DOI: 10.1007/s42832-019-0014-x
RESEARCH ARTICLE
RESEARCH ARTICLE

A biogeographic map of soil bacterial communities in wheats field of the North China Plain

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Abstract

The vast diversity of soil bacteria provides essential ecosystem services that support agricultural production. Variation in the diversity and composition of soil biota may have predictive values for soil nutrient cycling and resilience of ecosystem services, thus providing valuable insights to improve food production. The North China Plain (NCP) is one of the world’s key agricultural regions, supplying more than 50% of the cereal consumed in Asia. However, it is unknown whether soil microbial diversity is predictable across the NCP. Using the MiSeq Illumina platform, we examined bacterial community variation in relation to spatial and environmental factors from 243 soils in wheat-maize double cropping rotation fields across the NCP, which cover nearly 0.3 million KM2. Based on observed bacterial communities and their relationships with environmental factors, we generated a map of bacterial communities across the NCP. The highest bacterial diversity was found in the middle part of the NCP, with most of the variation in diversity attributable to differences in the community similarity of Actinobacteria and Alphaproteobacteria. These findings provide important baseline information for analyzing the relationships between microbial community, soil functionality and crop yields.

Keywords

predicting map / bacteria diversity / Actinobacteria / Alphaproteobacteria

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Yu Shi, Yuntao Li, Meiqing Yuan, Jonathan M. Adams, Xianzhang Pan, Yunfeng Yang, Haiyan Chu. A biogeographic map of soil bacterial communities in wheats field of the North China Plain. Soil Ecology Letters, 2019, 1(1-2): 50‒58 https://doi.org/10.1007/s42832-019-0014-x

References

[1]
Barberán, A., Dunn, R.R., Reich, B.J., Pacifici, K., Laber, E.B., Menninger, H.L., Morton, J.M., Henley, J.B., Leff, J.W., Miller, S.L., Fierer, N., 2015. The ecology of microscopic life in household dust. Proceedings. Biological Sciences 282, 212–220
CrossRef Pubmed Google scholar
[2]
Bérdy, J., 2005. Bioactive microbial metabolites. Journal of Antibiotics 58, 1–26
CrossRef Pubmed Google scholar
[3]
Brooker, S., Singhasivanon, P., Waikagul, J., Supavej, S., Kojima, S., Takeuchi, T., Luong, T.V., Looareesuwan, S., 2003. Mapping soil-transmitted helminths in Southeast Asia and implications for parasite control. Southeast Asian Journal of Tropical Medicine and Public Health 34, 24–36
Pubmed
[4]
Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S.M., Betley, J., Fraser, L., Bauer, M., Gormley, N., Gilbert, J.A., Smith, G., Knight, R., 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME Journal 6, 1621–1624
CrossRef Pubmed Google scholar
[5]
Chu, H., Fierer, N., Lauber, C.L., Caporaso, J.G., Knight, R., Grogan, P., 2010. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environmental Microbiology 12, 2998–3006
CrossRef Pubmed Google scholar
[6]
Chu, H., Sun, H., Tripathi, B.M., Adams, J.M., Huang, R., Zhang, Y., Shi, Y., 2016. Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau. Environmental Microbiology 18, 1523–1533
CrossRef Pubmed Google scholar
[7]
Delgado-Baquerizo, M., Oliverio, A.M., Brewer, T.E., Benavent-González, A., Eldridge, D.J., Bardgett, R.D., Maestre, F.T., Singh, B.K., Fierer, N., 2018. A global atlas of the dominant bacteria found in soil. Science 359, 320–325
CrossRef Pubmed Google scholar
[8]
Faith, D.P., 1996. Conservation evaluation and phylogenetic diversity. Biological Conservation 61, 1–10
CrossRef Google scholar
[9]
Fierer, N., 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nature Reviews. Microbiology 15, 579–590
CrossRef Pubmed Google scholar
[10]
Fierer, N., Jackson, R.B., 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America 103, 626–631
CrossRef Pubmed Google scholar
[11]
Fierer, N., Ladau, J., 2012. Predicting microbial distributions in space and time. Nature Methods 9, 549–551
CrossRef Pubmed Google scholar
[12]
Fierer, N., Ladau, J., Clemente, J.C., Leff, J.W., Owens, S.M., Pollard, K.S., Knight, R., Gilbert, J.A., McCulley, R.L., 2013. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342, 621–624
CrossRef Pubmed Google scholar
[13]
Franklin, J., Miller, J.A., 2009. Mapping species distributions: Spatial Inference and Prediction. Cambridge University Press: Cambridge, UK.
[14]
Griffiths, R.I., Thomson, B.C., James, P., Bell, T., Bailey, M., Whiteley, A.S., 2011. The bacterial biogeography of British soils. Environmental Microbiology 13, 1642–1654
CrossRef Pubmed Google scholar
[15]
Hamedi, J., Mohammadipanah, F., 2015. Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria. Journal of Industrial Microbiology & Biotechnology 42, 157–171
CrossRef Pubmed Google scholar
[16]
Harris, J., 2009. Soil microbial communities and restoration ecology: facilitators or followers? Science 325, 573–574
CrossRef Pubmed Google scholar
[17]
Hubert, C., Loy, A., Nickel, M., Arnosti, C., Baranyi, C., Brüchert, V., Ferdelman, T., Finster, K., Christensen, F.M., Rosa de Rezende, J., Vandieken, V., Jørgensen, B.B., 2009. A constant flux of diverse thermophilic bacteria into the cold Arctic seabed. Science 325, 1541–1544
CrossRef Pubmed Google scholar
[18]
Jeong, S.J., Ho, C.H., Piao, S.L., Kim, J., Ciais, P., Lee, Y.B., Jhun, J.G., Park, S.K., 2014. Effects of double cropping on summer climate of the North China Plain and neighbouring regions. Nature Climate Change 4, 615–619
CrossRef Google scholar
[19]
Karimi, B., Terrat, S., Dequiedt, S., Saby, N.P.A., Horrigue, W., Lelièvre, M., Nowak, V., Jolivet, C., Arrouays, D., Wincker, P., Cruaud, C., Bispo, A., Maron, P.A., Bouré, N.C.P., Ranjard, L., 2018. Biogeography of soil bacteria and archaea across France. Science Advances 4, t1808
CrossRef Pubmed Google scholar
[20]
Ladau, J., Sharpton, T.J., Finucane, M.M., Jospin, G., Kembel, S.W., O’Dwyer, J., Koeppel, A.F., Green, J.L., Pollard, K.S., 2013. Global marine bacterial diversity peaks at high latitudes in winter. ISME Journal 7, 1669–1677
CrossRef Pubmed Google scholar
[21]
Larsen, P.E., Field, D., Gilbert, J.A., 2012. Predicting bacterial community assemblages using an artificial neural network approach. Nature Methods 9, 621–625
CrossRef Pubmed Google scholar
[22]
Lauber, C.L., Hamady, M., Knight, R., Fierer, N., 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 75, 5111–5120
CrossRef Pubmed Google scholar
[23]
Manivasagan, P., Venkatesan, J., Sivakumar, K., Kim, S.K., 2013. RETRACTED: Marine actinobacterial metabolites: current status and future perspectives. Microbiology Research 168, 311–332
CrossRef Pubmed Google scholar
[24]
Martiny, J.B.H., Bohannan, B.J.M., Brown, J.H., Colwell, R.K., Fuhrman, J.A., Green, J.L., Horner-Devine, M.C., Kane, M., Krumins, J.A., Kuske, C.R., Morin, P.J., Naeem, S., Ovreås, L., Reysenbach, A.L., Smith, V.H., Staley, J.T., 2006. Microbial biogeography: putting microorganisms on the map. Nature Reviews. Microbiology 4, 102–112
CrossRef Pubmed Google scholar
[25]
Orgiazzi, A., Bardgett, R.D., Barrios, E., Behan-Pelletier, V., Briones, M.J.I., Chotte, J.L., 2016, Global Soil Biodiversity Atlas. European Commission, Publications Office of the European Union, Luxembourg. 176 pp.
[26]
Poole, A.M., Phillips, M.J., Penny, D., 2003. Prokaryote and eukaryote evolvability. Bio Systems 69, 163–185
CrossRef Pubmed Google scholar
[27]
R Development Core Team, 2006. R, a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
[28]
Ramirez, K.S., Knight, C.G., de Hollander, M., Brearley, F.Q., Constantinides, B., Cotton, A., Creer, S., Crowther, T.W., Davison, J., Delgado-Baquerizo, M., Dorrepaal, E., Elliott, D.R., Fox, G., Griffiths, R.I., Hale, C., Hartman, K., Houlden, A., Jones, D.L., Krab, E.J., Maestre, F.T., McGuire, K.L., Monteux, S., Orr, C.H., van der Putten, W.H., Roberts, I.S., Robinson, D.A., Rocca, J.D., Rowntree, J., Schlaeppi, K., Shepherd, M., Singh, B.K., Straathof, A.L., Bhatnagar, J.M., Thion, C., van der Heijden, M.G.A., de Vries, F.T., 2018. Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature Microbiology 3, 189–196
CrossRef Pubmed Google scholar
[29]
Scholte, R.G., Schur, N., Bavia, M.E., Carvalho, E.M., Chammartin, F., Utzinger, J., Vounatsou, P., 2013. Spatial analysis and risk mapping of soil-transmitted helminth infections in Brazil, using Bayesian geostatistical models. Geospatial Health 8, 97–110
CrossRef Pubmed Google scholar
[30]
Shi, Y., Li, Y.T., Xiang, X.J., Sun, R.B., Yang, T., He, D., Zhang, K.P., Ni, Y.Y., Zhu, Y.G., Adams, J.M., Chu, H.Y., 2018. Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain. Microbiome 6. Robert, J.H., Steven, P., John, L., Jane, E., 2015. Species Distribution Modeling. dismo: Species Distribution Modeling. R package version 1.0–12. http://CRAN.R-project.org/package=dismo.
[31]
Tedersoo, L., Bahram, M., Põlme, S., Kõljalg, U., Yorou, N.S., Wijesundera, R., Villarreal Ruiz, L., Vasco-Palacios, A.M., Thu, P.Q., Suija, A., Smith, M.E., Sharp, C., Saluveer, E., Saitta, A., Rosas, M., Riit, T., Ratkowsky, D., Pritsch, K., Põldmaa, K., Piepenbring, M., Phosri, C., Peterson, M., Parts, K., Pärtel, K., Otsing, E., Nouhra, E., Njouonkou, A.L., Nilsson, R.H., Morgado, L.N., Mayor, J., May, T.W., Majuakim, L., Lodge, D.J., Lee, S.S., Larsson, K.H., Kohout, P., Hosaka, K., Hiiesalu, I., Henkel, T.W., Harend, H., Guo, L.D., Greslebin, A., Grelet, G., Geml, J., Gates, G., Dunstan, W., Dunk, C., Drenkhan, R., Dearnaley, J., De Kesel, A., Dang, T., Chen, X., Buegger, F., Brearley, F.Q., Bonito, G., Anslan, S., Abell, S., Abarenkov, K., 2014. Fungal biogeography. Global diversity and geography of soil fungi. Science 346, 1256688
CrossRef Pubmed Google scholar
[32]
Toju, H., Peay, K.G., Yamamichi, M., Narisawa, K., Hiruma, K., Naito, K., Fukuda, S., Ushio, M., Nakaoka, S., Onoda, Y., Yoshida, K., Schlaeppi, K., Bai, Y., Sugiura, R., Ichihashi, Y., Minamisawa, K., Kiers, E.T., 2018. Core microbiomes for sustainable agroecosystems. Nature Plants 4, 247–257
CrossRef Pubmed Google scholar
[33]
Wall, D.H., Nielsen, U.N., Six, J., 2015. Soil biodiversity and human health. Nature 528, 69–76
Pubmed
[34]
Whitfield, J., 2005. Biogeography. Is everything everywhere? Science 310, 960–961
CrossRef Pubmed Google scholar
[35]
Wickham, H., 2009. ggplot2: elegant graphics for data analysis. Springer New York.
[36]
Zhang, X., Xu, S., Li, C., Zhao, L., Feng, H., Yue, G., Ren, Z., Cheng, G., 2014. The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau. Research in Microbiology 165, 128–139
CrossRef Pubmed Google scholar

Acknowledgments

We thank Ruibo Sun, Xingjia Xiang, Dan He, Kaoping Zhang, Yingying Ni, Teng Yang, Hongfei Wang and Kunkun Fan for their assistance in soil sampling and laboratory analyses. This work was supported by the Strategic Priority Research Program (XDB15010101) of the Chinese Academy of Sciences, the National Key Research and Development Program of China (2017YFD0200604, 2017YFC0803803), the “135” Plan and Frontiers Projects of Institute of Soil Science (ISSASIP1641), The collaborative innovation project from the Forensic Appraisal Center of The ministry of Public Security of the People’s Republic of China (2016XTCX02), and the China Biodiversity Observation Networks (Sino BON).

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Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s42832-019-0014-x and is accessible for authorized users.

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