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Title: Functional Molecular Ecological Networks

Abstract

Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2more » dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change.« less

Authors:
 [1];  [2];  [3];  [4];  [4];  [4]
  1. Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division; Tsinghua Univ., Beijing (China). Dept. of Environmental Science and Engineering
  2. Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology; Glomics Inc., Norman, OK (United States)
  3. Clemson Univ., SC (United States). School of Computing
  4. Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of Oklahoma, Norman, OK (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division
OSTI Identifier:
1626091
Grant/Contract Number:  
AC02-05CH11231; SC0004601
Resource Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 1; Journal Issue: 4; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology (ASM)
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Microbiology

Citation Formats

Zhou, Jizhong, Deng, Ye, Luo, Feng, He, Zhili, Tu, Qichao, and Zhi, Xiaoyang. Functional Molecular Ecological Networks. United States: N. p., 2010. Web. doi:10.1128/mbio.00169-10.
Zhou, Jizhong, Deng, Ye, Luo, Feng, He, Zhili, Tu, Qichao, & Zhi, Xiaoyang. Functional Molecular Ecological Networks. United States. https://doi.org/10.1128/mbio.00169-10
Zhou, Jizhong, Deng, Ye, Luo, Feng, He, Zhili, Tu, Qichao, and Zhi, Xiaoyang. Tue . "Functional Molecular Ecological Networks". United States. https://doi.org/10.1128/mbio.00169-10. https://www.osti.gov/servlets/purl/1626091.
@article{osti_1626091,
title = {Functional Molecular Ecological Networks},
author = {Zhou, Jizhong and Deng, Ye and Luo, Feng and He, Zhili and Tu, Qichao and Zhi, Xiaoyang},
abstractNote = {Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2 dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change.},
doi = {10.1128/mbio.00169-10},
journal = {mBio (Online)},
number = 4,
volume = 1,
place = {United States},
year = {Tue Oct 05 00:00:00 EDT 2010},
month = {Tue Oct 05 00:00:00 EDT 2010}
}

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Initial soil microbiome composition and functioning predetermine future plant health
journal, September 2019


The Seasonal Dynamics and the Influence of Human Activities on Campus Outdoor Microbial Communities
journal, July 2019


An integrated insight into the response of sedimentary microbial communities to heavy metal contamination
journal, September 2015

  • Yin, Huaqun; Niu, Jiaojiao; Ren, Youhua
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep14266

Variations in phyllosphere microbial community along with the development of angular leaf-spot of cucumber
journal, May 2019


Molecular ecological network analysis of the response of soil microbial communities to depth gradients in farmland soils
journal, January 2020

  • Yu, Hang; Xue, Dongmei; Wang, Yidong
  • MicrobiologyOpen, Vol. 9, Issue 3
  • DOI: 10.1002/mbo3.983

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover
journal, May 2015


Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria
journal, February 2020


Pseudomonas spp. are key players in agricultural biogas substrate degradation
journal, September 2019


Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland
journal, December 2019


Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession
journal, May 2015

  • Cong, Jing; Yang, Yunfeng; Liu, Xueduan
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep10007

Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling
journal, September 2015

  • Wang, Feng; Liang, Yuting; Jiang, Yuji
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep14345

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system
journal, October 2016

  • Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep34744

Plant–microbe networks in soil are weakened by century‐long use of inorganic fertilizers
journal, July 2019

  • Huang, Ruilin; McGrath, Steve P.; Hirsch, Penny R.
  • Microbial Biotechnology, Vol. 12, Issue 6
  • DOI: 10.1111/1751-7915.13487

Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea
journal, April 2014

  • Zhang, Yao; Zhao, Zihao; Dai, Minhan
  • Molecular Ecology, Vol. 23, Issue 9
  • DOI: 10.1111/mec.12739

Initial soil microbiome composition and functioning predetermine future plant health
journal, September 2019


The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome
journal, October 2015

  • Hannigan, Geoffrey D.; Meisel, Jacquelyn S.; Tyldsley, Amanda S.
  • mBio, Vol. 6, Issue 5
  • DOI: 10.1128/mbio.01578-15

Elevated CO2 influences microbial carbon and nitrogen cycling
journal, January 2013


Revisiting the variation of clustering coefficient of biological networks suggests new modular structure
journal, January 2012


Microevolution from shock to adaptation revealed strategies improving ethanol tolerance and production in Thermoanaerobacter
journal, July 2013


The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria
journal, October 2011


Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste
journal, July 2017


Above and belowground community strategies respond to different global change drivers
text, January 2019


Toward Understanding, Managing, and Protecting Microbial Ecosystems
journal, January 2011


Use of functional gene arrays for elucidating in situ biodegradation
journal, January 2012


Conservation of Species- and Trait-Based Modeling Network Interactions in Extremely Acidic Microbial Community Assembly
journal, August 2017


An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease
journal, November 2017


Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams
journal, November 2017


Distribution of Archaeal Communities along the Coast of the Gulf of Finland and Their Response to Oil Contamination
journal, January 2018


A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill
journal, March 2018


Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach
journal, October 2018


Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach
journal, November 2018

  • De Anda, Valerie; Zapata-Peñasco, Icoquih; Blaz, Jazmín
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.02606

Succession of Composition and Function of Soil Bacterial Communities During Key Rice Growth Stages
journal, March 2019


The Seasonal Dynamics and the Influence of Human Activities on Campus Outdoor Microbial Communities
journal, July 2019


Vineyard Soil Microbiome Composition Related to Rotundone Concentration in Australian Cool Climate ‘Peppery’ Shiraz Grapes
journal, July 2019

  • Gupta, Vadakattu V. S. R.; Bramley, Robert G. V.; Greenfield, Paul
  • Frontiers in Microbiology, Vol. 10
  • DOI: 10.3389/fmicb.2019.01607

Enhanced Microbial Interactions and Deterministic Successions During Anoxic Decomposition of Microcystis Biomass in Lake Sediment
journal, October 2019


Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil
journal, November 2019

  • Gupta, Vadakattu V. S. R.; Zhang, Bangzhou; Penton, Christopher Ryan
  • Frontiers in Molecular Biosciences, Vol. 6
  • DOI: 10.3389/fmolb.2019.00115

Cracks Reinforce the Interactions among Soil Bacterial Communities in the Coal Mining Area of Loess Plateau, China
journal, December 2019

  • Luo, Zhanbin; Ma, Jing; Chen, Fu
  • International Journal of Environmental Research and Public Health, Vol. 16, Issue 24
  • DOI: 10.3390/ijerph16244892

Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances
journal, October 2018

  • Taketani, Rodrigo G.; Moitinho, Marta A.; Mauchline, Tim H.
  • PeerJ, Vol. 6
  • DOI: 10.7717/peerj.5710