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Different types of agricultural land use drive distinct soil bacterial communities

  • 1.

    Marschner, P., Crowley, D. & Yang, C. H. Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type. Plant Soil 261, 199–208 (2004).

    CAS  Article  Google Scholar 

  • 2.

    Osler, G. H. R. & Sommerkorn, M. Toward a complete soil C and N cycle: Incorporating the soil fauna. Ecology 88, 1611–1621 (2007).

    PubMed  Article  PubMed Central  Google Scholar 

  • 3.

    Kennedy, A. C. Bacterial diversity in agroecosystems. Agric. Ecosyst. Environ. 74, 65–76 (1999).

    Article  Google Scholar 

  • 4.

    Mendes, R., Garbeva, P. & Raaijmakers, J. M. The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol. Rev. 37, 634–663 (2013).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 5.

    van der Heijden, M. G. A., Bardgett, R. D. & van Straalen, N. M. The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol. Lett. 11, 296–310 (2008).

    PubMed  Article  PubMed Central  Google Scholar 

  • 6.

    Drenovsky, R. E., Steenwerth, K. L., Jackson, L. E. & Scow, K. M. Land use and climatic factors structure regional patterns in soil microbial communities. Glob. Ecol. Biogeogr. 19, 27–39 (2010).

    PubMed  PubMed Central  Article  Google Scholar 

  • 7.

    Ma, B. et al. Distinct biogeographic patterns for archaea, bacteria, and fungi along the vegetation gradient at the continental scale in Eastern China. mSystems 2, e00174-e1116 (2017).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 8.

    Wang, X. B. et al. Habitat-specific patterns and drivers of bacterial beta-diversity in China’s drylands. ISME J. 11, 1345–1358 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  • 9.

    Sala, O. E. et al. Global biodiversity scenarios for the year 2100. Science 287, 1770–1774 (2000).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 10.

    Singh, J. S., Pandey, V. C. & Singh, D. P. Efficient soil microorganisms: A new dimension for sustainable agriculture and environmental development. Agric. Ecosyst. Environ. 140, 339–353 (2011).

    Article  Google Scholar 

  • 11.

    Verhulst, N. et al. Soil quality as affected by tillage-residue management in a wheat-maize irrigated bed planting system. Plant Soil 340, 453–466 (2011).

    CAS  Article  Google Scholar 

  • 12.

    Aziz, I., Mahmood, T. & Islam, K. R. Effect of long term no-till and conventional tillage practices on soil quality. Soil Tillage Res. 131, 28–35 (2013).

    Article  Google Scholar 

  • 13.

    Navarro-Noya, Y. E. et al. Relative impacts of tillage, residue management and crop-rotation on soil bacterial communities in a semi-arid agroecosystem. Soil Biol. Biochem. 65, 86–95 (2013).

    CAS  Article  Google Scholar 

  • 14.

    Meriles, J. M. et al. Soil microbial communities under different soybean cropping systems: Characterization of microbial population dynamics, soil microbial activity, microbial biomass, and fatty acid profiles. Soil Tillage Res. 103, 271–281 (2009).

    Article  Google Scholar 

  • 15.

    Chaudhry, V., Rehman, A., Mishra, A., Chauhan, P. S. & Nautiyal, C. S. Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microb. Ecol. 64, 450–460 (2012).

    PubMed  Article  PubMed Central  Google Scholar 

  • 16.

    Hartmann, M., Frey, B., Mayer, J., Mader, P. & Widmer, F. Distinct soil microbial diversity under long-term organic and conventional farming. ISME J. 9, 1177–1194 (2015).

    PubMed  Article  PubMed Central  Google Scholar 

  • 17.

    Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006).

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 18.

    Bartram, A. K. et al. Exploring links between pH and bacterial community composition in soils from the Craibstone experimental farm. FEMS Microbiol. Ecol. 87, 403–415 (2014).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 19.

    Min, W. et al. Response of soil microbial community and diversity to increasing water salinity and nitrogen fertilization rate in an arid soil. Acta Agric. Scand. B Soil Plant Sci. 66, 117–126 (2016).

    CAS  Google Scholar 

  • 20.

    Lauber, C. L., Strickland, M. S., Bradford, M. A. & Fierer, N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol. Biochem. 40, 2407–2415 (2008).

    CAS  Article  Google Scholar 

  • 21.

    Lozupone, C. A. & Knight, R. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci. USA. 104, 11436–11440 (2007).

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 22.

    Zhang, X.-Y., Sui, Y.-Y., Zhang, X.-D., Meng, K. & Herbert, S. J. Spatial variability of nutrient properties in black soil of Northeast China. Pedosphere 17, 19–29 (2007).

    Article  Google Scholar 

  • 23.

    Griffiths, R. I. et al. The bacterial biogeography of British soils. Environ. Microbiol. 13, 1642–1654 (2011).

    PubMed  Article  PubMed Central  Google Scholar 

  • 24.

    Liu, J. et al. High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China. Soil Biol. Biochem. 70, 113–122 (2014).

    CAS  Article  Google Scholar 

  • 25.

    Kim, M. et al. Highly heterogeneous soil bacterial communities around Terra Nova Bay of northern Victoria, Land Antarctica. PLoS ONE 10, e0119966 (2015).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 26.

    Hermans, S. M. et al. Bacteria as emerging indicators of soil condition. Appl. Environ. Microbiol. 83, e02826-e12816 (2017).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 27.

    Barberan, A., Bates, S. T., Casamayor, E. O. & Fierer, N. Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J. 6, 343–351 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 28.

    Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 29.

    van der Heijden, M. G. & Hartmann, M. Networking in the plant microbiome. PLoS Biol. 14, e1002378 (2016).

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 30.

    Shi, S. et al. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. Ecol. Lett. 19, 926–936 (2016).

    PubMed  Article  PubMed Central  Google Scholar 

  • 31.

    Kim, J. M. et al. Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea. J. Microbiol. 54, 838–845 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 32.

    Tripathi, B. et al. Spatial scaling effects on soil bacterial communities in Malaysian tropical forests. Microb. Ecol. 68, 247–258 (2014).

    PubMed  Article  PubMed Central  Google Scholar 

  • 33.

    Feng, M. et al. Interpreting distance-decay pattern of soil bacteria via quantifying the assembly processes at multiple spatial scales. MicrobiologyOpen 8, e00851 (2019).

    PubMed  PubMed Central  Google Scholar 

  • 34.

    Morlon, H. et al. A general framework for the distance-decay of similarity in ecological communities. Ecol. Lett. 11, 904–917 (2008).

    PubMed  PubMed Central  Article  Google Scholar 

  • 35.

    Figuerola, E. L. M. et al. Bacterial indicator of agricultural management for soil under no-till crop production. PLoS ONE 7, e51075 (2012).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 36.

    Jimenez-Bueno, N. G. et al. Bacterial indicator taxa in soils under different long-term agricultural management. J. Appl. Microbiol. 120, 921–933 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 37.

    Liesack, W., Schnell, S. & Revsbech, N. P. Microbiology of flooded rice paddies. FEMS Microbiol. Rev. 24, 625–645 (2000).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 38.

    Kang, S. S. et al. Status and change in chemical properties of polytunnel soil in Korea from 2000 to 2012. Korean J. Soil Sci. Fertil. 46, 641–646 (2013).

    CAS  Article  Google Scholar 

  • 39.

    Handley, K. M. et al. High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment. FEMS Microbiol. Ecol. 81, 188–204 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 40.

    Ma, J. C., Ibekwe, A. M., Yang, C. H. & Crowley, D. E. Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations. Sci. Total Environ. 563, 199–209 (2016).

    ADS  PubMed  Article  CAS  PubMed Central  Google Scholar 

  • 41.

    Reich, P. B. et al. Linking litter calcium, earthworms and soil properties: A common garden test with 14 tree species. Ecol. Lett. 8, 811–818 (2005).

    Article  Google Scholar 

  • 42.

    Sridevi, G. et al. Soil bacterial communities of a calcium-supplemented and a reference watershed at the Hubbard Brook experimental forest (HBEF), New Hampshire, USA. FEMS Microbiol. Ecol. 79, 728–740 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 43.

    Singh, D., Shi, L. & Adams, J. M. Bacterial diversity in the mountains of South-West China: Climate dominates over soil parameters. J. Microbiol. 51, 439–447 (2013).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 44.

    Miethling, R., Wieland, G., Backhaus, H. & Tebbe, C. C. Variation of microbial rhizosphere communities in response to crop secies, soil origin, and inoculation with Sinorhizobium meliloti L33. Microb. Ecol. 40, 43–56 (2000).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 45.

    De Caceres, M. & Legendre, P. Associations between species and groups of sites: Indices and statistical inference. Ecology 90, 3566–3574 (2009).

    PubMed  Article  PubMed Central  Google Scholar 

  • 46.

    Oyaizu, H., Debrunner-Vossbrinck, B., Mandelco, L., Studier, J. A. & Woese, C. R. The green non-sulfur bacteria: A deep branching in the eubacterial line of descent. Syst. Appl. Microbiol. 9, 47–53 (1987).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 47.

    Rappe, M. S. & Giovannoni, S. J. The uncultured microbial majority. Annu. Rev. Microbiol. 57, 369–394 (2003).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 48.

    Krzmarzick, M. J. et al. Natural niche for organohalide-respiring Chloroflexi. Appl. Environ. Microbiol. 78, 393–401 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 49.

    Speirs, L. B. M., Rice, D. T. F., Petrovski, S. & Seviour, R. J. The phylogeny, biodiversity, and ecology of the chloroflexi in activated sludge. Front. Microbiol.10 (2019).

  • 50.

    Janssen, P. H. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72, 1719–1728 (2006).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 51.

    Will, C. et al. Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl. Environ. Microbiol. 76, 6751–6759 (2010).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 52.

    Costello, E. K. & Schmidt, S. K. Microbial diversity in alpine tundra wet meadow soil: novel Chloroflexi from a cold, water-saturated environment. Environ. Microbiol. 8, 1471–1486 (2006).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 53.

    Lee, H. J., Jeong, S. E., Kim, P. J., Madsen, E. & Jeon, C. O. High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy. Front. Microbiol. 6, 639 (2015).

    PubMed  PubMed Central  Google Scholar 

  • 54.

    Ahn, J. H. et al. Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices. J. Microbiol. 54, 724–731 (2016).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 55.

    Hernández, M., Conrad, R., Klose, M., Ma, K. & Lu, Y. Structure and function of methanogenic microbial communities in soils from flooded rice and upland soybean fields from Sanjiang plain NE China. Soil Biol. Biochem. 105, 81–91 (2017).

    Article  CAS  Google Scholar 

  • 56.

    Fierer, N., Bradford, M. A. & Jackson, R. B. Toward an ecological classification of soil bacteria. Ecology 88, 1354–1364 (2007).

    PubMed  Article  PubMed Central  Google Scholar 

  • 57.

    Jones, R. T. et al. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 3, 442–453 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 58.

    Navarrete, A. A. et al. Differential response of Acidobacteria subgroups to forest-to-pasture conversion and their biogeographic patterns in the western Brazilian Amazon. Front. Microbiol. 6, 1443 (2015).

    PubMed  PubMed Central  Article  Google Scholar 

  • 59.

    Leff, J. W. et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc. Natl. Acad. Sci. USA. 112, 10967–10972 (2015).

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 60.

    Trivedi, P., Delgado-Baquerizo, M., Anderson, I. C. & Singh, B. K. Response of soil properties and microbial communities to agriculture: Implications for primary productivity and soil health indicators. Front. Plant Sci. 7, 990 (2016).

    PubMed  PubMed Central  Google Scholar 

  • 61.

    Radhakrishnan, R., Hashem, A. & Abd Allah, E. F. Bacillus: A biological tool for crop improvement through bio-molecular changes in adverse environments. Front. Physiol. 8, 667 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  • 62.

    Pujalte, M. J., Lucena, T., Ruvira, M. A., Arahal, D. R. & Macián, M. C. The Family Rhodobacteraceae. In The Prokaryotes (eds Rosenberg, E. et al.) 439–512 (Springer, Berlin, 2014).

    Google Scholar 

  • 63.

    Baldani, J. I. et al. The Family Rhodospirillaceae. In The Prokaryotes (eds Rosenberg, E. et al.) 533–618 (Springer, Berlin, 2014).

    Google Scholar 

  • 64.

    Karimi, B. et al. Biogeography of soil bacterial networks along a gradient of cropping intensity. Sci. Rep. 9, 3812 (2019).

    ADS  PubMed  PubMed Central  Article  CAS  Google Scholar 

  • 65.

    Hartman, K. et al. Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome 6, 14 (2018).

    PubMed  PubMed Central  Article  Google Scholar 

  • 66.

    Nielsen, M. N. & Winding, A. Microorganisms as indicators of soil health. National Environmental Research Institute, Denmark, Technical Report no. 388 (2002).

  • 67.

    Allison, L. E. Organic carbon in Methods of Soil Analysis, Part 2, Chemical and Microbiological Properties (ed Black, C. A.) 1367–1378 (American Society of Agronomy, 1965).

  • 68.

    National Institute of Agricultural Science and Technology (NIAST). Methods of analysis of soil and plant. (NIAST, 2000)

  • 69.

    Edgar, R. C. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 70.

    Schloss, P. D. et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 71.

    R Core Team. R: a language and environment for statistical computing. https://www.R-project.org/ (2016).

  • 72.

    Dray, S. et al. Community ecology in the age of multivariate multiscale spatial analysis. Ecol. Monogr. 82, 257–275 (2012).

    Article  Google Scholar 

  • 73.

    Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R Stat. Soc. Series B Stat. Methodol. 57, 289–300 (1995).

    MathSciNet  MATH  Google Scholar 

  • 74.

    Ogle, D. H. FSA: Fisheries stock analysis. R package version 0.8.13. (2017).

  • 75.

    Bastian, M., Heymann, S. & Jacomy, M. Gephi: an open source software for exploring and manipulating networks. International AAAI Conference on Weblogs and Social Media (2009).

  • 76.

    Deng, Y. et al. Molecular ecological network analyses. BMC Bioinform. 13, 113 (2012).

    Article  Google Scholar 


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