Crop type drives soil bacterial community and functional structure on the Loess Plateau terraces of China

References

1. ↵
   1. Amirnia, R.,
   2. M. Ghiyasi,
   3. S.S. Moghaddam,
   4. A. Rahimi,
   5. C.A. Damalas, and
   6. S. Heydarzadeh

   . 2019. Nitrogen-fixing soil bacteria plus mycorrhizal fungi improve seed yield and quality traits of lentil (Lens culinaris Medik). Journal of Soil Science and Plant Nutrition 19:592-602.

   OpenUrl
2. ↵
   1. Augusto, L.,
   2. D.L. Achat,
   3. M. Jonard,
   4. D. Vidal, and
   5. B. Ringeval

   . 2017. Soil parent material—a major driver of plant nutrient limitations in terrestrial ecosystems. Global Change Biology 23(9):3808-3824.

   OpenUrl
3. ↵
   1. Bastian, M.,
   2. S. Heymann, and
   3. M. Jacomy

   . 2009. Gephi: An open source software for exploring and manipulating networks. In Proceedings of the International AAAI Conference on Weblogs and Social Media, San Jose, California, May 17-20, 2009. Palo Alto, CA: Association for the Advancement of Artificial Intelligence.
4. ↵
   1. Chakraborty, P., and
   2. P. Tribedi

   . 2019. Functional diversity performs a key role in the isolation of nitrogen-fixing and phosphate-solubilizing bacteria from soil. Folia Microbiologica 64(3):461-470.

   OpenUrl
5. ↵
   1. Chaudhry, V.,
   2. A. Rehman,
   3. A. Mishra,
   4. P.S. Chauhan, and
   5. C.S. Nautiyal

   . 2012. Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microbial Ecology 64(2):450-460.

   OpenUrlCrossRefPubMed
6. ↵
   1. Che, R.,
   2. Y. Wang,
   3. K. Li,
   4. Z. Xu,
   5. J. Hu,
   6. F. Wang,
   7. Y. Rui,
   8. L. Li,
   9. Z. Pang, and
   10. X. Cui

   . 2019. Degraded patch formation significantly changed microbial community composition in alpine meadow soils. Soil and Tillage Research 195(December):104426.

   OpenUrl
7. ↵
   1. Deangelis, K.M.,
   2. G. Pold,
   3. B.D. Topçuoğlu,
   4. L.T.A. Van Diepen,
   5. R.M. Varney,
   6. J.L. Blanchard,
   7. J. Melillo, and
   8. S.D. Frey

   . 2015. Long-term forest soil warming alters microbial communities in temperate forest soils. Frontiers in Microbiology 6:104.

   OpenUrl
8. ↵
   1. Dong, W.,
   2. E. Liu,
   3. C. Yan,
   4. J. Tian,
   5. H. Zhang, and
   6. Y. Zhang

   . 2017. Impact of no tillage vs. conventional tillage on the soil bacterial community structure in a winter wheat cropping succession in northern China. European Journal of Soil Biology 80(May–June):35-42.

   OpenUrl
9. ↵
   1. Fierer, N., and
   2. R.B. Jackson

   . 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America 103(3):626-631.

   OpenUrlAbstract/FREE Full Text
10. ↵
    1. Fu, B.,
    2. L. Chen,
    3. K. Ma,
    4. H. Zhou, and
    5. J. Wang

    . 2000. The relationships between land use and soil conditions in the hilly area of the loess plateau in northern Shaanxi, China. Catena 39(1):69-78.

    OpenUrlCrossRefGeoRef
11. ↵
    1. Gispert, M.,
    2. G. Pardini,
    3. M. Colldecarrera,
    4. M. Emran, and
    5. S. Doni

    . 2017. Water erosion and soil properties patterns along selected rainfall events in cultivated and abandoned terraced fields under renaturalisation. Catena 155(August):114-126.

    OpenUrl
12. ↵
    1. Goberna, M.,
    2. A. Montesinos-Navarro,
    3. A. Valiente-Banuet,
    4. Y. Colin,
    5. A. Gómez-Fernández,
    6. S. Donat,
    7. J.A. Navarro-Cano, and
    8. M. Verdú

    . 2019. Incorporating phylogenetic metrics to microbial co-occurrence networks based on amplicon sequences to discern community assembly processes. Molecular Ecology Resources 19(6):1552-1564.

    OpenUrl
13. ↵
    1. Goldfarb, K.C.,
    2. U. Karaoz,
    3. C.A. Hanson,
    4. C.A. Santee,
    5. M.A. Bradford,
    6. K.K. Treseder,
    7. M.D. Wallenstein, and
    8. E.L. Brodie

    . 2011. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Frontiers in Microbiology 2:94.

    OpenUrl
14. ↵
    1. Hou, J.,
    2. B. Fu,
    3. Y. Liu,
    4. N. Lu,
    5. G. Gao, and
    6. J. Zhou

    . 2014. Ecological and hydrological response of farmlands abandoned for different lengths of time: Evidence from the Loess Hill Slope of China. Global and Planetary Change 113(February):59-67.

    OpenUrlGeoRef
15. ↵
    1. Hua, W.,
    2. C. Peng,
    3. B. Yang,
    4. H. Song, and
    5. W. Meng

    . 2018. Contrasting soil bacterial community, diversity, and function in two forests in China. Frontiers in Microbiology 9:1693.

    OpenUrl
16. ↵
    1. Ishaq, S.L.,
    2. S.P. Johnson,
    3. Z.J. Miller,
    4. E.A. Lehnhoff,
    5. S. Olivo,
    6. C.J. Yeoman, and
    7. F.D. Menalled

    . 2017. Impact of cropping systems, soil inoculum, and plant species identity on soil bacterial community structure. Microbial Ecology 73:417-434.

    OpenUrl
17. ↵
    1. Koyama, A.,
    2. M.D. Wallenstein,
    3. R.T. Simpson, and
    4. J.C. Moore

    . 2014. Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils. Frontiers in Microbiology 5:516.

    OpenUrl
18. ↵
    1. Leff, J.W.,
    2. S.E. Jones,
    3. S.M. Prober,
    4. A. Barberán,
    5. E.T. Borer,
    6. J.L. Firn,
    7. W.S. Harpole,
    8. S.E. Hobbie,
    9. K.S. Hofmockel, and
    10. J.M. Knops

    . 2015. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proceedings of the National Academy of Sciences of the United States of America 112(35):10967-10972.

    OpenUrlAbstract/FREE Full Text
19. ↵
    1. Li, B.Q.,
    2. G.L. Li,
    3. Y. Fu, and
    4. K. Wang

    . 2019. Distribution of soil organic carbon within aggregate size fractions following the conversion of cropland to black locust forest on the southern Loess Plateau, China. Journal of Soil and Water Conservation 74(1):59-66. https://doi.org/10.2489/jswc.74.1.59.

    OpenUrlAbstract/FREE Full Text
20. ↵
    1. Li, R.,
    2. R. Tao,
    3. N. Ling, and
    4. G. Chu

    . 2017. Chemical, organic and bio-fertilizer management practices effect on soil physicochemical property and antagonistic bacteria abundance of a cotton field: Implications for soil biological quality. Soil and Tillage Research 167(April):30-38.

    OpenUrl
21. ↵
    1. Li, Y., and
    2. M.J. Lindstrom

    . 2001. Evaluating soil quality-soil redistribution relationship on terraces and steep hillslope. Soil Science Society of America Journal 65(5):1500-1508.

    OpenUrlGeoRefWeb of Science
22. ↵
    1. Liu, W.,
    2. W. An,
    3. E. Jeppesen,
    4. J. Ma,
    5. M. Yang, and
    6. D. Trolle

    . 2019. Modelling the fate and transport of Cryptosporidium, a zoonotic and waterborne pathogen, in the Daning River watershed of the Three Gorges Reservoir Region, China. Journal of Environmental Management 232(February):462-474.

    OpenUrl
23. ↵
    1. Ma, B.,
    2. H. Wang,
    3. M. Dsouza,
    4. J. Lou,
    5. Y. He,
    6. Z. Dai,
    7. P.C. Brookes,
    8. J. Xu, and
    9. J.A. Gilbert

    . 2016. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. The ISME Journal 10:1891-1901.

    OpenUrl
24. ↵
    1. Molinaro, F.,
    2. O. Tyc,
    3. J. Beekwilder,
    4. K. Cankar,
    5. C.M. Bertea,
    6. M. Negre, and
    7. P. Garbeva

    . 2018. The effect of isabelin, a sesquiterpene lactone from Ambrosia artemisiifolia on soil microorganisms and human pathogens. FEMS Microbiology Letters 365(4):fny001.

    OpenUrl
25. ↵
    1. Nemergut, D.N.,
    2. C.C. Cleveland,
    3. W.R. Wieder,
    4. C.L. Washenberger, and
    5. A.R. Townsend

    . 2010. Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest. Soil Biology & Biochemistry 42(12): 2153-2160.

    OpenUrl
26. ↵
    1. Nielsen, U.N.,
    2. G.H.R. Osler,
    3. C.D. Campbell,
    4. D.F.R.P. Burslem, and
    5. R. van der Wal

    . 2010. The influence of vegetation type, soil properties and precipitation on the composition of soil mite and microbial communities at the landscape scale. Journal of Biogeography 37(7):1317-1328.

    OpenUrlCrossRefWeb of Science
27. ↵
    1. A.L. Page

    1. Olsen, S.R., and
    2. L.E. Sommers

    . 1982. Phosphorus. In Methods of Soil Analysis. Part 2. Chemical and Microbiological Properties, ed. A.L. Page, 403-430. Madison, WI: American Society of Agronomy and Soil Science Society of America.
28. ↵
    1. Poulsen, P.H.B.,
    2. J. Magid,
    3. J. Luxhøi, and
    4. A.D. Neergaard

    . 2013. Effects of fertilization with urban and agricultural organic wastes in a field trial—Waste imprint on soil microbial activity. Soil Biology and Biochemistry 57 (February):794-802.

    OpenUrl
29. ↵
    1. Riggs, C.E.,
    2. S.E. Hobbie,
    3. E.M. Bach,
    4. K.S. Hofmockel, and
    5. C.E. Kazanski

    . 2015. Nitrogen addition changes grassland soil organic matter decomposition. Biogeochemistry 125:203-219.

    OpenUrlCrossRef
30. ↵
    1. Singh, R.J.,
    2. B. Ghosh,
    3. N. Sharma,
    4. S. Patra,
    5. K. Dadhwal,
    6. V.S. Meena,
    7. J. Deshwal, and
    8. P. Mishra

    . 2017. Effect of seven years of nutrient supplementation through organic and inorganic sources on productivity, soil and water conservation, and soil fertility changes of maize-wheat rotation in north-western Indian Himalayas. Agriculture, Ecosystems & Environment 249 (November):177-186.

    OpenUrl
31. ↵
    1. Spain, A.M.,
    2. L.R. Krumholz, and
    3. M.S. Elshahed

    . 2009. Abundance, composition, diversity and novelty of soil Proteobacteria. The ISME Journal 3:992-1000.

    OpenUrl
32. ↵
    1. Sparks, D.L.,
    2. A.L. Page,
    3. P.A. Helmke,
    4. R.H. Loeppert,
    5. P.N. Soltanpour,
    6. M.A. Tabatabai,
    7. C.T. Johnston, and
    8. M.E. Sumner

    , eds. 1996. Methods of Soil Analysis. Part 3. Chemical Methods. Madison, WI: Soil Science Society of America and American Society of Agronomy.
33. ↵
    1. Sparling, G., and
    2. A. West

    . 1988. Modifications to the flmigation-extraction technique to permit simultaneous extraction and estimation of soil microbial C and N. Communications in Soil Science and Plant Analysis 19(3):327-344.

    OpenUrl
34. ↵
    1. Su, Z.,
    2. J. Zhang,
    3. D. Xiong, and
    4. G. Liu

    . 2012. Assessment of soil erosion by compensatory hoeing tillage in a purple soil. Journal of Mountain Science 9:59-66.

    OpenUrl
35. ↵
    1. Tscherko, D.,
    2. U. Hammesfahr,
    3. G. Zeltner,
    4. E. Kandeler, and
    5. R. Böcker

    . 2005. Plant succession and rhizosphere microbial communities in a recently deglaciated alpine terrain. Basic and Applied Ecology 6(4):367-383.

    OpenUrl
36. ↵
    1. Uuml, H.,
    2. Y. Zhu,
    3. T.H. Skaggs, and
    4. Z. Yu

    . 2009. Comparison of measured and simulated water storage in dryland terraces of the Loess Plateau, China. Agricultural Water Management 96(2):299-306.

    OpenUrl
37. ↵
    1. Vance, E.,
    2. P. Brookes, and
    3. D. Jenkinson

    . 1987. An extraction method for measuring soil microbial biomass C. Soil Biology and Biochemistry, 19, 703-707.

    OpenUrl
38. ↵
    1. Veum, K.S.,
    2. K.W. Goyne,
    3. R.J. Kremer,
    4. R.J. Miles, and
    5. K.A. Sudduth

    . 2014. Biological indicators of soil quality and soil organic matter characteristics in an agricultural management continuum. Biogeochemistry 117:81-99.

    OpenUrl
39. ↵
    1. Wakelin, S.A.,
    2. M.J. Colloff,
    3. P.R. Harvey,
    4. M. Petra,
    5. A.L. Gregg, and
    6. S.L. Rogers

    . 2007. The effects of stubble retention and nitrogen application on soil microbial community structure and functional gene abundance under irrigated maize. FEMS Microbiology Ecology 59(3):661-670.

    OpenUrlCrossRefPubMed
40. ↵
    1. Wang, D.,
    2. B. Fu,
    3. W. Zhao,
    4. H. Hu, and
    5. Y. Wang

    . 2008. Multifractal characteristics of soil particle size distribution under different land-use types on the Loess Plateau, China. Catena 72(1): 29-36.

    OpenUrlGeoRef
41. ↵
    1. Wang, X.,
    2. J.D. Van Nostrand,
    3. Y. Deng,
    4. X. Lü,
    5. C. Wang,
    6. J. Zhou, and
    7. X. Han

    . 2015. Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China’s grasslands. FEMS Microbiology Ecology 91(12):fiv133.

    OpenUrlCrossRefPubMed
42. ↵
    1. Xiao, L.,
    2. Y. Huang,
    3. Q. Zeng,
    4. J. Zhao, and
    5. J. Zhou

    . 2018. Soil enzyme activities and microbial biomass response to crop types on the terraces of the Loess Plateau, China. Journal of Soils and Sediments 18:1971-1980.

    OpenUrl
43. ↵
    1. Xu, S.,
    2. M.L. Silveira,
    3. K.S. Inglett,
    4. L.E. Sollenberger, and
    5. S. Gerber

    . 2017. Soil microbial community responses to long-term land use intensification in subtropical grazing lands. Geoderma 293(May):73-81.

    OpenUrl
44. ↵
    1. Xue, X.,
    2. J. Liao,
    3. Y. Hsing,
    4. C. Huang, and
    5. F. Liu

    . 2015. Policies, land use, and water resource management in an arid oasis ecosystem. Environmental Management 55:1036-1051.

    OpenUrl
45. ↵
    1. Yadav, S.,
    2. B. Reddy, and
    3. S.K. Dubey

    . 2020. De novo genome assembly and comparative annotation reveals metabolic versatility in cellulolytic bacteria from cropland and forest soils. Functional & Integrative Genomics 20(1):89-101.

    OpenUrl
46. ↵
    1. Yuan, Y.,
    2. G. Si,
    3. W. Jian,
    4. T. Luo, and
    5. G. Zhang

    . 2014. Bacterial community in alpine grasslands along an altitudinal gradient on the Tibetan Plateau. FEMS Microbiology Ecology 87(1):121-132.

    OpenUrlCrossRefPubMedWeb of Science
47. ↵
    1. Zeng, Q.,
    2. S. An, and
    3. Y. Liu

    . 2017. Soil bacterial community response to vegetation succession after fencing in the grassland of China. Science of the Total Environment 609(December):2-10.

    OpenUrlCrossRef
48. ↵
    1. Zeng, Q.,
    2. Y. Dong, and
    3. S. An

    . 2016a. Bacterial community responses to soils along a latitudinal and vegetation gradient on the loess plateau, China. PLOS ONE 11(4):e0152894.

    OpenUrl
49. ↵
    1. Zeng, Q.,
    2. X. Li,
    3. Y. Dong,
    4. S. An, and
    5. F. Darboux

    . 2016b. Soil and plant components ecological stoichiometry in four steppe communities in the Loess Plateau of China. Catena 147(December):481-488.

    OpenUrl
50. ↵
    1. Zhang, C.,
    2. G. Liu,
    3. S. Xue, and
    4. G. Wang

    . 2016. Soil bacterial community dynamics reflect changes in plant community and soil properties during the secondary succession of abandoned farmland in the Loess Plateau. Soil Biology & Biochemistry 97(June):40-49.

    OpenUrl
51. ↵
    1. Zhang, H.,
    2. X. Song,
    3. C. Wang,
    4. H. Liu,
    5. J. Zhang,
    6. Y. Li,
    7. G. Li,
    8. D. Yang, and
    9. S. Zhao

    . 2013. The effects of different vegetation restoration patterns on soil bacterial diversity for sandy land in Hulunbeier. Acta Ecologica Sinica 33(4):211-216.

    OpenUrl
52. ↵
    1. Zhao, C.,
    2. M.A. Shao,
    3. X. Jia, and
    4. Y. Zhu

    . 2017. Estimation of spatial variability of soil water storage along the south–north transect on China’s Loess Plateau using the state-space approach. Journal of Soils and Sediments 17:1009-1020.

    OpenUrl
53. ↵
    1. Zhou, Y.,
    2. F. Bastida,
    3. B. Zhou,
    4. Y. Sun,
    5. T. Gu,
    6. S. Li, and
    7. Y. Li

    . 2020. Soil fertility and crop production are fostered by micro-nano bubble irrigation with associated changes in soil bacterial community. Soil Biology and Biochemistry 141:107663.

    OpenUrl
54. ↵
    1. Zhu, B.,
    2. G. van Dijk,
    3. C. Fritz,
    4. A.J.P. Smolders,
    5. A. Pol,
    6. M.S.M. Jetten, and
    7. K.F. Ettwig

    . 2012. Anaerobic oxidization of methane in a minerotrophic peatland: Enrichment of nitrite-dependent methane-oxidizing bacteria. Applied and Environmental Microbiology 78(24):8657-8665.

    OpenUrlAbstract/FREE Full Text
55. ↵
    1. Zhu, X.,
    2. W. Liu,
    3. J. Chen,
    4. L.A. Bruijnzeel,
    5. Z. Mao,
    6. X. Yang,
    7. R. Cardinael, et al.

    2019. Reductions in water, soil and nutrient losses and pesticide pollution in agroforestry practices: A review of evidence and processes. Plant and Soil 453:45-86.

    OpenUrl