Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

Ma, Bin; Wang, Haizhen; Dsouza, Melissa; Lou, Jun; He, Yan; Dai, Zhongmin; Brookes, Philip C.; Xu, Jianming; Gilbert, Jack A.

doi:10.1038/ismej.2015.261

Title: Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

Journal Article · Fri Jan 15 00:00:00 EST 2016 · The ISME Journal

DOI:https://doi.org/10.1038/ismej.2015.261· OSTI ID:1623772

Ma, Bin ^[1]; Wang, Haizhen ^[1]; Dsouza, Melissa ^[2]; Lou, Jun ^[3]; He, Yan ^[1]; Dai, Zhongmin ^[3]; Brookes, Philip C. ^[3]; Xu, Jianming ^[1]; Gilbert, Jack A. ^[4]

College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, China
Univ. of Chicago, IL (United States). Department of Ecology and Evolution, Department of Surgery
College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
Univ. of Chicago, IL (United States); Department of Ecology and Evolution, Department of Surgery; ; Argonne National Lab. (ANL), Argonne, IL (United States) Bioscience Division

Soil microbiota play a critical role in soil biogeochemical processes and have a profound effect on soil functions. Recent studies have revealed microbial co-occurrence patterns in soil microbial communities, yet the geographic pattern of topological features in soil microbial co-occurrence networks at the continental scale are largely unknown. Here, we investigated the shifts of topological features in co-occurrence networks inferred from soil microbiota along a continental scale in eastern China. Integrating archaeal, bacterial and fungal community datasets, we inferred a meta-community co-occurrence network and analyzed node-level and network-level topological shifts associated with five climatic regions. Both node-level and network-level topological features revealed geographic patterns wherein microorganisms in the northern regions had closer relationships but had a lower interaction influence than those in the southern regions. We further identified topological differences associated with taxonomic groups and demonstrated that co-occurrence patterns were random for archaea and non-random for bacteria and fungi. Given that microbial interactions may contribute to soil functions more than species diversity, this geographic shift of topological features provides new insight into studying microbial biogeographic patterns, their organization and impacts on soil-associated function.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE; National Natural Science Foundation of China (NSFC); 111 Project; Fundamental Research Funds for the Central Universities

Grant/Contract Number:: AC02-06CH11357; 41520104001; 41130532; B06014

OSTI ID:: 1623772

Journal Information:: The ISME Journal, Vol. 10, Issue 8; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence Hakim, Joseph; Schram, Julie; Galloway, Aaron Microorganisms, Vol. 7, Issue 2 https://doi.org/10.3390/microorganisms7020035	journal	January 2019
Nutrients Drive the Structures of Bacterial Communities in Sediments and Surface Waters in the River-Lake System of Poyang Lake Ren, Ze; Qu, Xiaodong; Peng, Wenqi Water, Vol. 11, Issue 5 https://doi.org/10.3390/w11050930	journal	May 2019
Feed Types Driven Differentiation of Microbial Community and Functionality in Marine Integrated Multitrophic Aquaculture System Deng, Yale; Zhou, Fan; Ruan, Yunjie Water, Vol. 12, Issue 1 https://doi.org/10.3390/w12010095	journal	December 2019
Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification Lou, Jun; Yang, Li; Wang, Haizhen PeerJ, Vol. 6 https://doi.org/10.7717/peerj.4514	journal	January 2018
Soil pH and temperature regulate assembly processes of abundant and rare bacterial communities in agricultural ecosystems Jiao, Shuo; Lu, Yahai Environmental Microbiology, Vol. 22, Issue 3 https://doi.org/10.1111/1462-2920.14815	journal	August 2019
Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils Jiao, Shuo; Chen, Weimin; Wei, Gehong Molecular Ecology, Vol. 26, Issue 19 https://doi.org/10.1111/mec.14218	journal	September 2017
Progressive Microbial Community Networks with Incremental Organic Loading Rates Underlie Higher Anaerobic Digestion Performance Wu, Linwei; Shan, Xiaoyu; Chen, Si mSystems, Vol. 5, Issue 1 https://doi.org/10.1128/msystems.00357-19	journal	January 2020
Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women Dugas, Lr; Bernabé, Bp; Priyadarshini, Medha University of Illinois at Chicago https://doi.org/10.25417/uic.14888316	text	January 2021
Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau Guo, Wei; Wang, Weiwei; Bi, Sisi Animals, Vol. 10, Issue 1 https://doi.org/10.3390/ani10010144	journal	January 2020
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming Hartman, Kyle; Van Der Heijden, Marcel G. A.; Wittwer, Raphaël A. BioMed Central https://doi.org/10.5167/uzh-168385	text	January 2018
Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting Mussaenda shikokiana along an elevation gradient Qian, Xin; Chen, Liang; Guo, Xiaoming PeerJ, Vol. 6 https://doi.org/10.7717/peerj.5767	journal	January 2018
Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning Wagg, Cameron; Schlaeppi, Klaus; Banerjee, Samiran Nature Publishing Group https://doi.org/10.7892/boris.134558	text	January 2019
Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women Dugas, Lr; Bernabé, Bp; Priyadarshini, Medha University of Illinois at Chicago https://doi.org/10.25417/uic.14888316.v1	text	January 2021
Linking microbial co-occurrences to soil ecological processes across a woodland-grassland ecotone Banerjee, Samiran; Thrall, Peter H.; Bissett, Andrew Wiley Open Access https://doi.org/10.5167/uzh-168387	text	January 2018
Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning Wagg, Cameron; Schlaeppi, Klaus; Banerjee, Samiran Nature Publishing Group https://doi.org/10.5167/uzh-182853	text	January 2019
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming Hartman, Kyle; Van Der Heijden, Marcel G. A.; Wittwer, Raphaël A. ETH Zurich https://doi.org/10.3929/ethz-b-000237418	text	January 2018
Long-term inorganic fertilizer use influences bacterial communities in Mollisols of Northeast China based on high-throughput sequencing and network analyses Yu, Zhenhua; Hu, Xiaojing; Wei, Dan Taylor & Francis https://doi.org/10.6084/m9.figshare.7546445.v1	text	January 2019
Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp Dong, Xiaoli; Kleiner, Manuel; Sharp, Christine E. bioRxiv https://doi.org/10.1101/131631	posted_content	April 2017
Long-term inorganic fertilizer use influences bacterial communities in Mollisols of Northeast China based on high-throughput sequencing and network analyses Yu, Zhenhua; Hu, Xiaojing; Wei, Dan Taylor & Francis https://doi.org/10.6084/m9.figshare.7546445	text	January 2019
Mainland and island populations of Mussaenda kwangtungensis differ in their phyllosphere fungal community composition and network structure Qian, Xin; Li, Shengchun; Wu, Binwei Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-57622-6	journal	January 2020
Relating network analyses to phylogenetic relatedness to infer protistan co-occurrences and co-exclusions in marine and terrestrial environments Lentendu, Guillaume; Dunthorn, Micah bioRxiv https://doi.org/10.1101/2020.04.27.063685	journal	April 2020
Geospatial variation in co‐occurrence networks of nitrifying microbial guilds Jones, Christopher M.; Hallin, Sara Molecular Ecology, Vol. 28, Issue 2 https://doi.org/10.1111/mec.14893	journal	November 2018
Gestational Diabetes Mellitus Is Associated with Reduced Dynamics of Gut Microbiota during the First Half of Pregnancy Zheng, Wei; Xu, Qian; Huang, Wenyu mSystems, Vol. 5, Issue 2 https://doi.org/10.1128/msystems.00109-20	journal	April 2020
Conservation of Species- and Trait-Based Modeling Network Interactions in Extremely Acidic Microbial Community Assembly Kuang, Jialiang; Cadotte, Marc W.; Chen, Yongjian Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01486	journal	August 2017
Microbiome of Total Versus Live Bacteria in the Gut of Rex Rabbits Fu, Xiangchao; Zeng, Bo; Wang, Ping Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00733	journal	April 2018
Dynamics of Sediment Microbial Functional Capacity and Community Interaction Networks in an Urbanized Coastal Estuary Dai, Tianjiao; Zhang, Yan; Ning, Daliang Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02731	journal	November 2018
Variations in Soil Bacterial Composition and Diversity in Newly Formed Coastal Wetlands Li, Wenbing; Lv, Xiaofei; Ruan, Junchao Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03256	journal	January 2019
Diurnal Temperature Variation and Plants Drive Latitudinal Patterns in Seasonal Dynamics of Soil Microbial Community Hu, Ang; Nie, Yanxia; Yu, Guirui Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00674	journal	April 2019
Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere Qian, Xin; Li, Hanzhou; Wang, Yonglong Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01015	journal	May 2019
Characterization of a nifH-Harboring Bacterial Community in the Soil-Limited Gotjawal Forest Lee, Tae Kwon; Han, Il; Kim, Min Sung Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01858	journal	August 2019
Anthropogenic Pollution Intervenes the Recovery Processes of Soil Archaeal Community Composition and Diversity From Flooding Wang, Yu; Hong, Yiguo; Ma, Maohua Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02285	journal	October 2019
Soil Bacterial and Fungal Communities Exhibit Distinct Long-Term Responses to Disturbance in Temperate Forests Osburn, Ernest D.; McBride, Steven G.; Aylward, Frank O. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02872	journal	December 2019
Rare Species Shift the Structure of Bacterial Communities Across Sphagnum Compartments in a Subalpine Peatland Tian, Wen; Xiang, Xing; Ma, Liyuan Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.03138	journal	January 2020
Distinct Assembly Mechanisms Underlie Similar Biogeographic Patterns of Rare and Abundant Bacterioplankton in Cascade Reservoirs of a Large River Chen, Juan; Wang, Peifang; Wang, Chao Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00158	journal	February 2020
Sowing Methods Influence Soil Bacterial Diversity and Community Composition in a Winter Wheat-Summer Maize Rotation System on the Loess Plateau Huang, Chunguo; Han, Xiaoli; Yang, Zhenping Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.00192	journal	February 2020
The Nexus Between Plant and Plant Microbiome: Revelation of the Networking Strategies Babalola, Olubukola Oluranti; Fadiji, Ayomide E.; Enagbonma, Ben J. Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.548037	journal	September 2020
The Structure and Species Co-Occurrence Networks of Soil Denitrifying Bacterial Communities Differ Between A Coniferous and A Broadleaved Forests Chen, Jie; Li, Jiajia; Shen, Weijun Microorganisms, Vol. 7, Issue 9 https://doi.org/10.3390/microorganisms7090361	journal	September 2019
External bacterial diversity on bats in the southwestern United States: Changes in bacterial community structure above and below ground Winter, Ara S.; Kimble, Jason C.; Young, Jesse M. PeerJ Preprints https://doi.org/10.7287/peerj.preprints.2493v1	journal	October 2016
Improvement of subsoil physicochemical and microbial properties by short-term fallow practices Li, Guangyu; de Vries, Walter Timo; Wu, Cifang PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7501	journal	August 2019

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