The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages
Abstract
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:
-
[2];
- 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
- 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
- Univ. of Oklahoma, Norman, OK (United States). Dept. of Botony and Microbiology and Inst. of Environmental Genomics
- 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
- 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:
- Research Org.:
- Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1467800
- Alternate Identifier(s):
- OSTI ID: 1401210; OSTI ID: 1474903
- Report Number(s):
- LLNL-JRNL-679806
Journal ID: ISSN 1461-023X; 803848
- Grant/Contract Number:
- AC52-07NA27344; AC02-05CH11231; SC0004730; SC0010570; SCW1421; 00008322
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Ecology Letters
- Additional Journal Information:
- Journal Volume: 19; Journal Issue: 8; Journal ID: ISSN 1461-023X
- Publisher:
- Wiley
- 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
Citation Formats
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., 2016.
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. https://doi.org/10.1111/ele.12630
Shi, Shengjing, Nuccio, Erin E., Shi, Zhou J., He, Zhili, Zhou, Jizhong, and Firestone, Mary K. Mon .
"The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages". United States. https://doi.org/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 = {Mon Jun 06 00:00:00 EDT 2016},
month = {Mon Jun 06 00:00:00 EDT 2016}
}
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- Ren, Ze; Gao, Hongkai
- PeerJ Preprints
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- Nature Publishing Group
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- Banerjee, Samiran; Thrall, Peter H.; Bissett, Andrew
- Wiley Open Access
Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning
text, January 2019
- Wagg, Cameron; Schlaeppi, Klaus; Banerjee, Samiran
- Nature Publishing Group
Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia
posted_content, August 2019
- Ren, Ze; Gao, Hongkai
- PeerJ Preprints
Keystone taxa as drivers of microbiome structure and functioning
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- Banerjee, Samiran; Schlaeppi, Klaus; Van Der Heijden, Marcel G. A.
- Springer Nature
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- Vergine, Marzia; Meyer, Joana B.; Cardinale, Massimiliano
- ETH Zurich
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- Banerjee, Samiran; Walder, Florian; Büchi, Lucie
- Nature Publishing Group
Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia
journal, January 2019
- Ren, Ze; Gao, Hongkai
- PeerJ, Vol. 7
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Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
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Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling
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Seasonal Changes in a Maize-Based Polyculture of Central Mexico Reshape the Co-occurrence Networks of Soil Bacterial Communities
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Succession of Composition and Function of Soil Bacterial Communities During Key Rice Growth Stages
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Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere
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Soil Microbial Networks Shift Across a High-Elevation Successional Gradient
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Challenges and Approaches in Microbiome Research: From Fundamental to Applied
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Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia
posted_content, August 2019
- Ren, Ze; Gao, Hongkai
- PeerJ Preprints