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

Xinyu Cui; Huan He; Fengxiao Zhu; Xiaobo Liu; You Ma; Wenming Xie; Han Meng; Limin Zhang

doi:10.1007/s00203-022-03074-7

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

Xinyu Cui, Huan He, Fengxiao Zhu, Xiaobo Liu, You Ma, Wenming Xie, Han Meng^*, Limin Zhang

^*Corresponding author for this work

Environmental Science and Engineering

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

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.

Original language	English
Article number	453
Journal	Archives of Microbiology
Volume	204
Issue number	8
DOIs	https://doi.org/10.1007/s00203-022-03074-7
State	Published - Aug 2022

Keywords

Bacteria
Co-occurrence network
Fungi
High-throughput sequencing
Soil

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10.1007/s00203-022-03074-7

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

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{\textquoteright} changes.",

keywords = "Bacteria, Co-occurrence network, Fungi, High-throughput sequencing, Soil",

author = "Xinyu Cui and Huan He and Fengxiao Zhu and Xiaobo Liu and You Ma and Wenming Xie and Han Meng and Limin Zhang",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.",

year = "2022",

month = aug,

doi = "10.1007/s00203-022-03074-7",

language = "英语",

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T1 - Community structure and co-occurrence network analysis of bacteria and fungi in wheat fields vs fruit orchards

AU - Cui, Xinyu

AU - He, Huan

AU - Zhu, Fengxiao

AU - Liu, Xiaobo

AU - Ma, You

AU - Xie, Wenming

AU - Meng, Han

AU - Zhang, Limin

PY - 2022/8

Y1 - 2022/8

N2 - 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.

AB - 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.

KW - Bacteria

KW - Co-occurrence network

KW - Fungi

KW - High-throughput sequencing

KW - Soil

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U2 - 10.1007/s00203-022-03074-7

DO - 10.1007/s00203-022-03074-7

M3 - 文章

C2 - 35786781

AN - SCOPUS:85133221796

SN - 0302-8933

VL - 204

JO - Archives of Microbiology

JF - Archives of Microbiology

IS - 8

M1 - 453

ER -

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

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