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Title: Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

Abstract

Microbial interactions shape the structure and function of microbial communities; microbial association networks in specic environments have been widely developed to explore these complex systems, but their wired pattern across microbiomes in various environments at the global scale remains unexplored. Here we have inferred an Earth microbial association network from a communal catalogue with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset. Results: This non-random scale-free Earth microbial association network consisted of 8 taxonomy distinct modules linked with dierent environments, which featured environment specic microbial associations. Dierent topological features of subnetworks inferred from datasets trimmed into uniform size indicate distinct association patterns in the microbiomes of various environments. The proportions of specialist edges, which ranged from 43.0% to 65.7%, highlight that environmental specic microbial associations are essential features of microbiomes in various environments. Based on edge-overlap similarity, the microbiomes of various environments were clustered into two groups, which were mainly bridged by the microbiomes of plant and animal surface. Acidobacteria Gp2 and Nisaea were identied as hubs in most of subnetworks. Negative edges proportions ranged from 1.9% in the soil subnetwork to 48.9% the non-saline surface subnetwork, suggesting various environments experience distinctmore » intensities of competition or niche dierentiation. Conclusion: This investigation provides a new resource for examining Earth microbial association patterns across environments and emphasizes the network perspective for comprehensively understanding unique microbiome features. Keywords: Association pattern; Earth microbiomes; Genelist edges; Network hubs; Negative associations; Specialist edges; Topological properties« less

Authors:
 [1];  [2];  [2];  [2];  [1];  [3];  [4];  [5];  [6];  [7];  [4]; ORCiD logo [1]
  1. Zhejiang Univ., Hangzhou (China). Inst. of Soil and Water Resources and Environmental Science; Zhejiang Provincial Key Lab. of Agricultural Resources and Environment, Hangzhou (China)
  2. Zhejiang Univ., Hangzhou (China). Inst. of Soil and Water Resources and Environmental Science
  3. Univ. of California San Diego, La Jolla, CA (United States). Dept. of Pediatrics and Scripps Inst. of Oceanography
  4. KU Leuven (Belgium). Rega Inst.
  5. Univ. of California San Diego, La Jolla, CA (United States)
  6. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  7. Univ. of Chicago, IL (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE; National Natural Science Foundation of China (NSFC); Zhejiang Provincial Natural Science Foundation of China; 111 Project
OSTI Identifier:
1642385
Report Number(s):
PNNL-SA-153001
Journal ID: ISSN 2049-2618
Grant/Contract Number:  
AC05-76RL01830; B17039; LD19D060001; 41721001; 41991334
Resource Type:
Accepted Manuscript
Journal Name:
Microbiome
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2049-2618
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; association pattern, earth microbiomes, genelist edges, network hubs, negative associations, specialist edges, topological properties; co-occurrence patterns; microbial network topology

Citation Formats

Ma, Bin, Wang, Yiling, Ye, Shudi, Liu, Shan, Stirling, Erinne, Gilbert, Jack A., Faust, Karoline, Knight, Rob, Jansson, Janet K., Cardona, Cesar, Röttjers, Lisa, and Xu, Jianming. Earth microbial co-occurrence network reveals interconnection pattern across microbiomes. United States: N. p., 2020. Web. https://doi.org/10.1186/s40168-020-00857-2.
Ma, Bin, Wang, Yiling, Ye, Shudi, Liu, Shan, Stirling, Erinne, Gilbert, Jack A., Faust, Karoline, Knight, Rob, Jansson, Janet K., Cardona, Cesar, Röttjers, Lisa, & Xu, Jianming. Earth microbial co-occurrence network reveals interconnection pattern across microbiomes. United States. https://doi.org/10.1186/s40168-020-00857-2
Ma, Bin, Wang, Yiling, Ye, Shudi, Liu, Shan, Stirling, Erinne, Gilbert, Jack A., Faust, Karoline, Knight, Rob, Jansson, Janet K., Cardona, Cesar, Röttjers, Lisa, and Xu, Jianming. Thu . "Earth microbial co-occurrence network reveals interconnection pattern across microbiomes". United States. https://doi.org/10.1186/s40168-020-00857-2. https://www.osti.gov/servlets/purl/1642385.
@article{osti_1642385,
title = {Earth microbial co-occurrence network reveals interconnection pattern across microbiomes},
author = {Ma, Bin and Wang, Yiling and Ye, Shudi and Liu, Shan and Stirling, Erinne and Gilbert, Jack A. and Faust, Karoline and Knight, Rob and Jansson, Janet K. and Cardona, Cesar and Röttjers, Lisa and Xu, Jianming},
abstractNote = {Microbial interactions shape the structure and function of microbial communities; microbial association networks in specic environments have been widely developed to explore these complex systems, but their wired pattern across microbiomes in various environments at the global scale remains unexplored. Here we have inferred an Earth microbial association network from a communal catalogue with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset. Results: This non-random scale-free Earth microbial association network consisted of 8 taxonomy distinct modules linked with dierent environments, which featured environment specic microbial associations. Dierent topological features of subnetworks inferred from datasets trimmed into uniform size indicate distinct association patterns in the microbiomes of various environments. The proportions of specialist edges, which ranged from 43.0% to 65.7%, highlight that environmental specic microbial associations are essential features of microbiomes in various environments. Based on edge-overlap similarity, the microbiomes of various environments were clustered into two groups, which were mainly bridged by the microbiomes of plant and animal surface. Acidobacteria Gp2 and Nisaea were identied as hubs in most of subnetworks. Negative edges proportions ranged from 1.9% in the soil subnetwork to 48.9% the non-saline surface subnetwork, suggesting various environments experience distinct intensities of competition or niche dierentiation. Conclusion: This investigation provides a new resource for examining Earth microbial association patterns across environments and emphasizes the network perspective for comprehensively understanding unique microbiome features. Keywords: Association pattern; Earth microbiomes; Genelist edges; Network hubs; Negative associations; Specialist edges; Topological properties},
doi = {10.1186/s40168-020-00857-2},
journal = {Microbiome},
number = 1,
volume = 8,
place = {United States},
year = {2020},
month = {6}
}

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