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Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing

Archives of Microbiology volume 200, pages 653–662 (2018)Cite this article

Abstract

The present study aimed to identify the structural succession of the bacteria community in soil during long-term continuous cotton cropping and its relationship with continuous cropping obstacles in Xinjiang, China. High-throughput sequencing was used to analyze and compare the composition of the bacterial community in the soil at the cotton root zone after years of continuous cotton cropping and crop rotation over 30 years of cultivation. Cotton cultivation increased the structural diversity of the bacterial community, among which the populations of Actinobacteria, Acidobacteria, Firmicutes, Nitrospirae, and Chloroflexi changed considerably. A 0-year sample and samples after continuous short- and long-term cropping, along with some with crop rotation, were gathered into three individual clusters. The findings of the rotation sample were similar to those of the sample of continuous long-term cropping. Cropping is the main cause of changes in the structure of the bacteria community; however, the new structure formed under continued duress of both long-term cotton cultivation and the associated farming methods gradually stabilizes after 10 years of repeated fluctuations. Crop rotation can lead to the rapid recovery of some species of soil bacteria.

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References

  • Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5:908–917

    CAS  Article  PubMed  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Method 7(5):335–336

    CAS  Article  Google Scholar 

  • Davenport CF, Tümmler B (2013) Advances in computational analysis of metagenome sequences. Environ Microbiol 15:1–5

    CAS  Article  PubMed  Google Scholar 

  • Garbeva P, van Veen JA, van Elsas JD (2004) Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol 42:243–270

    CAS  Article  PubMed  Google Scholar 

  • Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microb 69:1800–1809

    CAS  Article  Google Scholar 

  • Han CL, Liu J, Zhang WF, Liu M, Huang WJ, Gao XM, Zhang HZ (2010) Biocycling of nine mineral elements of soil-cotton system in Xinjiang oasis. Acta Ecol Sin 30(22):6234–6241

    CAS  Google Scholar 

  • He JZ, Zheng Y, Chen CR (2010) Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches. J Soil Sediment 8:349–358

    Article  Google Scholar 

  • Huang JW, Yang JK, Duan YQ (2010) Bacterial diversities on unaged and aging flue-cured tobacco leaves estimated by 16S rRNA sequence analysis. Appl Microbiol Biot 88(2):553–562

    CAS  Article  Google Scholar 

  • Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNAgenes. Appl Environ Microbiol 72(3):1719–1728

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Joshua PS, Braddock JF, Gulledge JM, Clein-Curley JS, Lindstrom JE (1999) Moisture effects on microbial activity and community structure in decomposing birch litter in the Alaskan taiga. Soil Biol Biochem 31(6):831–838

    Article  Google Scholar 

  • Ma K, Zhang L, Du Q, Song NP (2004) Effect of potato continuous cropping on soil microorganism community structure and function. J Soil Water Conserv 24(4):229–233

    Google Scholar 

  • Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21):2957–2963

    Article  PubMed  PubMed Central  Google Scholar 

  • Meriles JM, Vargas GS, Haro R, March GJ, Guzman CA (2008) Selected soil-borne fungi under glyphosate application and crop residues from a long-term field experiment. Biol Agric Hortic 26(2):193–205

    Article  Google Scholar 

  • Ndaw SM, Gama-Rodrigues AC, Gama-Rodrigues EF, Sals KR, Rosado AS (2009) Relationships between bacterial diversity, microbial biomass, and litter quality in soils under different plant covers in northern Rio de Janeiro State, Brazil. Can J Microbiol 55(9):1089–1095

    CAS  Article  PubMed  Google Scholar 

  • Noah F, Joshua PS, Patricia AH (2003) Variations in microbial community composition through two soil depth profiles. Soil Biol Biochem 35(1):167–176

    Article  Google Scholar 

  • Noah F, Jonathan WL, Byron JA, Uffe NN, Scott TB, Christian LL, Sarah O, Jack AG, Diana HW, Gregory JC (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109:21390–21395

    Article  Google Scholar 

  • Pimental D, Stachow U, Takacs DA, Burbaker HW, Dumas AR, Meaney JJ, ONeil JAS, Onsi DE, Corzilius DB (1992) Conserving biological diversity in agricultural /forest systems. Biosphere 42:354–362

    Google Scholar 

  • Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38:525–552

    CAS  Article  PubMed  Google Scholar 

  • Sarathchandra SU, Ghani A, Yeates GW, Burch G, Cox NR (2001) Effect of nitrogen and phosphate fertilisers on microbial and nematode diversity in pasture soils. Soil Biol Biochem 33:953–964

    CAS  Article  Google Scholar 

  • Sessitsch A, Weilhater A, Gerzabek M, Kirchmann H, Kandeler E (2001) Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67(9):4215–4224

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer H, Berg G (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67:4742–4751

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Steven B, Gallegos-Graves L, Starkenburg SR, Chain PS, Kuske CR (2012) Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Env Microbiol Rep 4:248–256

    Article  Google Scholar 

  • Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6:805–814

    CAS  Article  PubMed  Google Scholar 

  • Vargas GS, Meriles J, Conforto C, Figoni G, Basanta M, Lovera E, March GJ (2009) Field assessment of soil biological and chemical quality in response to crop management practices. World J Microb Biot 25(3):439–448

    Article  Google Scholar 

  • von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315:1126–1130

    Article  Google Scholar 

  • Waid JS (1999) Does soil biodiversity depend upon metabiotic activity and influences. Appl Soil Ecol 13:151–158

    Article  Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73(16):5261–5267

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Wang WF, Ma YT, Ma X, Wu F, Ma XJ, An LZ, Feng HY (2010) Seasonal variations of airborne bacteria in the Mogao Grottoes, Dunhuang, China. Int Biodeterior Biodegradation 64(4):309–315

    CAS  Article  Google Scholar 

  • Wei XR, Hao MD, Shao MA (2006) Changes in soil properties and the availability of soil micronutrients after 18 years of cropping and fertilization. Soil Till Res 91:120–130

    Article  Google Scholar 

  • Yan QY, Bi YH, Deng Y, He ZL, Wu LY, Joy D, Nostrand V, Shi Z, Li JJ, Wang X, Hu ZY, Yu YH, Zhou JZ (2015) Impacts of the Three Gorges Dam on microbial structure and potential function. Sci Rep 5:8605

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Yu YH, Yan QY, Feng WS (2008) Spatiotemporal heterogeneity of plankton communities in Lake Donghu, China, as revealed by PCR-denaturing gradient gel electrophoresis and its relation to biotic and abiotic factors. FEMS Microbiol Ecol 63:328–337

    CAS  Article  PubMed  Google Scholar 

  • Zhang XL, Li X, Zhan CG (2011a) Ecological risk of long-term chlorimuron-ethyl application to soil microbial community:an in situ investigation in a continuously cropped soybean field in north-east china. Environ Sci Pollut R 18:407–415

    CAS  Article  Google Scholar 

  • Zhang Y, Du BH, Jin ZG, Li ZH, Song HN, Ding YQ (2011b) Analysis of bacterial communities in rhizosphere soil of healthy and diseased cotton (Gossypium sp.) at different plant growth stages. Plant Soil 339:447–455

    CAS  Article  Google Scholar 

  • Zhang W, Long XQ, Huo XD, Chen YF, Lou K (2013) 16S rRNA-based PCR-DGGE analysis of actinomycete communities in fields with continuous cotton cropping in Xinjiang, China. Microb Ecol 66:385–393

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (Project No. 30460108).

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Affiliations

  1. Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Xinjiang Normal University, Xinyi Road, Urumqi, 830054, China

    Zhang Wei & Du Yu

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  1. Zhang Wei
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  2. Du Yu
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Correspondence to Zhang Wei.

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Communicated by Shuang-Jiang Liu.

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Wei, Z., Yu, D. Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing. Arch Microbiol 200, 653–662 (2018). https://doi.org/10.1007/s00203-018-1476-4

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  • DOI: https://doi.org/10.1007/s00203-018-1476-4

Keywords

  • Bacterial community structure
  • Continuous cotton cropping
  • Bacterial diversity
  • High-throughput sequencing