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Community structure and co-occurrence network analysis of bacteria and fungi in wheat fields vs fruit orchards

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Abstract

Soil microorganisms play a vital role in biogeochemical processes and nutrient turnover in agricultural ecosystems. However, the information on how the structure and co-occurrence patterns of microbial communities response to the change of planting methods is still limited. In this study, a total of 34 soil samples were collected from 17 different fields of 2 planting types (wheat and orchards) along the Taige Canal in Yangtze River Delta. The structure of bacterial and fungal communities in soil were determined by 16S rRNA gene and ITS gene, respectively. The dominated bacteria were Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Bacteroidota, and Firmicutes. The relative abundances of Actinobacteriota and Firmicutes were higher in the orchards, while Chloroflexi and Nitrospirota were more abundant in wheat fields. Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungus in both soil types. Diversity of bacterial and fungal communities were greater in the wheat fields than in orchards. Statistical analyses showed that pH was the main factor shaping the community structure, and parameters of water content (WC), total organic carbon (TOC) and total nitrogen (TN) had great influences on community structure. Moreover, high co-occurrence patterns of bacterial and fungal were confirmed in both wheat fields and orchards. Network analyses showed that both wheat fields and orchards occurred modular structure, including nodes of Acidobacteriota, Chloroflexi, Gemmatimonadota, Nitrospirota and Ascomycota. In summary, our work showed the co-occurrence network and the convergence/divergence of microbial community structure in wheat fields and orchards, giving a comprehensive understanding of the microbe–microbe interaction during planting methods’ changes.

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Data availability

Nucleotide sequence data of this study are deposited in NODE (The National Omics Data Encyclopedia) public available database for full access under the accession number OEP002256.

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Funding

This work was supported by National Science Foundation of China (No. 41907202, 91951112, 41877336), National Water Pollution Control and Governance of Science and Technology Major Special (No. 2017ZX07202-004), Project funded by China Postdoctoral Science Foundation (No. 2019M651877), Natural Science Found of Jiangsu Province (No. SBK2019043965), High-level Innovation and Entrepreneurship Talents Introduction Program of Jiangsu Province of China.

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  1. Xinyu Cui and Huan He contributed equally to this research.

Authors and Affiliations

  1. School of Environment, Nanjing Normal University, Nanjing, 210023, People’s Republic of China

    Xinyu Cui, Huan He, Fengxiao Zhu, You Ma, Wenming Xie, Han Meng & Limin Zhang

  2. Green Economy Development Institute, Nanjing University of Finance and Economics, Nanjing, 210023, People’s Republic of China

    Limin Zhang

  3. Environmental Science and Engineering Research Group, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, 515063, Guangdong, People’s Republic of China

    Xiaobo Liu

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  1. Xinyu Cui
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Contributions

XC sampling, methodology, data analysis, writing–original draft. HH Data analysis, supervision, writing–review and editing. FZ supervision, review and editing. XL writing and review. YM sampling, methodology. HM conceptualization, supervision, methodology, investigation, writing–review and editing. LZ supervision, review and editing.

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Correspondence to Han Meng.

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Cui, X., He, H., Zhu, F. et al. Community structure and co-occurrence network analysis of bacteria and fungi in wheat fields vs fruit orchards. Arch Microbiol 204, 453 (2022). https://doi.org/10.1007/s00203-022-03074-7

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