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Title: The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

While interactions between roots and microorganisms have been intensively studied, we know little about interactions among root-associated microbes. We used random matrix theory-based network analysis of 16S rRNA genes to identify bacterial networks associated with wild oat (Avena fatua) over two seasons in greenhouse microcosms. Rhizosphere networks were substantially more complex than those in surrounding soils, indicating the rhizosphere has a greater potential for interactions and niche-sharing. Network complexity increased as plants grew, even as diversity decreased, highlighting that community organisation is not captured by univariate diversity. Covariations were predominantly positive (> 80%), suggesting that extensive mutualistic interactions may occur among rhizosphere bacteria; we identified quorum-based signalling as one potential strategy. Putative keystone taxa often had low relative abundances, suggesting low-abundance taxa may significantly contribute to rhizosphere function. Network complexity, a previously undescribed property of the rhizosphere microbiome, appears to be a defining characteristic of this habitat.
Authors:
 [1] ; ORCiD logo [2] ;  [3] ;  [3] ;  [4] ;  [5]
  1. Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy and Management; Univ. of Oklahoma, Norman, OK (United States). Dept. of Botony and Microbiology and Inst. of Environmental Genomics
  2. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Nuclear and Chemical Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy and Management
  3. Univ. of Oklahoma, Norman, OK (United States). Dept. of Botony and Microbiology and Inst. of Environmental Genomics
  4. Univ. of Oklahoma, Norman, OK (United States). Dept. of Botony and Microbiology and Inst. of Environmental Genomics; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division; Tsinghua Univ., Beijing (China). State Key Joint Lab. of Environment Simulation and Pollution Control and School of Environment
  5. Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy and Management; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division
Publication Date:
Report Number(s):
LLNL-JRNL-679806
Journal ID: ISSN 1461-023X; 803848
Grant/Contract Number:
AC52-07NA27344; AC02-05CH11231; SC0004730; SC0010570; SCW1421; 00008322
Type:
Accepted Manuscript
Journal Name:
Ecology Letters
Additional Journal Information:
Journal Volume: 19; Journal Issue: 8; Journal ID: ISSN 1461-023X
Publisher:
Wiley
Research Org:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; community ecology; keystone species; microbial ecology; microbial interactions; microbial networks; quorum sensing; random matrix theory; rhizosphere
OSTI Identifier:
1467800
Alternate Identifier(s):
OSTI ID: 1401210; OSTI ID: 1474903

Shi, Shengjing, Nuccio, Erin E., Shi, Zhou J., He, Zhili, Zhou, Jizhong, and Firestone, Mary K.. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. United States: N. p., Web. doi:10.1111/ele.12630.
Shi, Shengjing, Nuccio, Erin E., Shi, Zhou J., He, Zhili, Zhou, Jizhong, & Firestone, Mary K.. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. United States. doi:10.1111/ele.12630.
Shi, Shengjing, Nuccio, Erin E., Shi, Zhou J., He, Zhili, Zhou, Jizhong, and Firestone, Mary K.. 2016. "The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages". United States. doi:10.1111/ele.12630. https://www.osti.gov/servlets/purl/1467800.
@article{osti_1467800,
title = {The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages},
author = {Shi, Shengjing and Nuccio, Erin E. and Shi, Zhou J. and He, Zhili and Zhou, Jizhong and Firestone, Mary K.},
abstractNote = {While interactions between roots and microorganisms have been intensively studied, we know little about interactions among root-associated microbes. We used random matrix theory-based network analysis of 16S rRNA genes to identify bacterial networks associated with wild oat (Avena fatua) over two seasons in greenhouse microcosms. Rhizosphere networks were substantially more complex than those in surrounding soils, indicating the rhizosphere has a greater potential for interactions and niche-sharing. Network complexity increased as plants grew, even as diversity decreased, highlighting that community organisation is not captured by univariate diversity. Covariations were predominantly positive (> 80%), suggesting that extensive mutualistic interactions may occur among rhizosphere bacteria; we identified quorum-based signalling as one potential strategy. Putative keystone taxa often had low relative abundances, suggesting low-abundance taxa may significantly contribute to rhizosphere function. Network complexity, a previously undescribed property of the rhizosphere microbiome, appears to be a defining characteristic of this habitat.},
doi = {10.1111/ele.12630},
journal = {Ecology Letters},
number = 8,
volume = 19,
place = {United States},
year = {2016},
month = {6}
}