Molecular ecological network analyses

Deng, Ye; Jiang, Yi-Huei; Yang, Yunfeng; He, Zhili; Luo, Feng; Zhou, Jizhong

doi:10.1186/1471-2105-13-113

Molecular ecological network analyses

Journal Article · Sun Jan 01 00:00:00 EST 2012 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-13-113· OSTI ID:1626287

Deng, Ye ^[1]; Jiang, Yi-Huei ^[2]; Yang, Yunfeng ^[3]; He, Zhili ^[2]; Luo, Feng ^[4]; Zhou, Jizhong ^[5]

Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology; Glomics Inc, Norman, OK (United States); DOE/OSTI
Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology
Tsinghua Univ., Beijing (China). State Key Joint Lab. of Environment Simulation and Pollution Control. School of Environment
Clemson Univ., SC (United States). School of Computing
Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology; Tsinghua Univ., Beijing (China). State Key Joint Lab. of Environment Simulation and Pollution Control. School of Environment; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division

Background: Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Results: Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA). Conclusions: The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.

View Accepted Manuscript (DOE)

Research Organization:: Glomics, Inc., Norman, OK (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of Oklahoma, Norman, OK (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231; SC0004601; SC0004613

OSTI ID:: 1626287

Journal Information:: BMC Bioinformatics, Journal Name: BMC Bioinformatics Journal Issue: 1 Vol. 13; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 1 of Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome Huang, Zhijian; Zeng, Shenzheng; Xiong, Jinbo figshare https://doi.org/10.6084/m9.figshare.11967030	dataset	January 2020
Additional file 1 of High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome Wen, Tao; Zhao, Mengli; Liu, Ting figshare https://doi.org/10.6084/m9.figshare.12135162	image	January 2020
Additional file 4 of Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China Tang, Xiangming; Xie, Guijuan; Shao, Keqiang figshare https://doi.org/10.6084/m9.figshare.12197373	dataset	January 2020
Additional file 3 of Low-dosage ozonation in gas-phase biofilter promotes community diversity and robustness Yeung, Marvin; Saingam, Prakit; Xu, Yang figshare https://doi.org/10.6084/m9.figshare.13566101.v1	dataset	January 2021
Additional file 5 of Low-dosage ozonation in gas-phase biofilter promotes community diversity and robustness Yeung, Marvin; Saingam, Prakit; Xu, Yang figshare https://doi.org/10.6084/m9.figshare.13566107.v1	dataset	January 2021
Additional file 3 of Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop Ceja-Navarro, Javier A.; Wang, Yuan; Ning, Daliang figshare https://doi.org/10.6084/m9.figshare.14509590	dataset	January 2021
Additional file 2 of Archaeal and bacterial communities assembly and co-occurrence networks in subtropical mangrove sediments under Spartina alterniflora invasion Chen, Weidong; Wen, Donghui figshare https://doi.org/10.6084/m9.figshare.14532299	dataset	January 2021
Additional file 1 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615537.v1	image	January 2023
Additional file 2 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615540	image	January 2023
Additional file 3 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615543	image	January 2023
Additional file 4 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615549.v1	image	January 2023
Additional file 5 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615552.v1	image	January 2023
Additional file 6 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615555	image	January 2023
Additional file 7 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615558	image	January 2023
Additional file 8 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615564	image	January 2023
Additional file 9 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615567	image	January 2023
Additional file 10 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615570	dataset	January 2023
Additional file 11 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615573.v1	dataset	January 2023
Additional file 12 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615576.v1	dataset	January 2023
Additional file 13 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615579	dataset	January 2023
Additional file 14 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615582.v1	dataset	January 2023
Additional file 15 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615585	dataset	January 2023
Additional file 16 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615588	dataset	January 2023
Additional file 17 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615591.v1	dataset	January 2023
Additional file 18 of Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes Zhang, Xiaoxia; Ma, Yi-Nan; Wang, Xing figshare https://doi.org/10.6084/m9.figshare.22615594	dataset	January 2023
Additional file 1 of Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome Ji, Niuniu; Liang, Di; Clark, Lindsay V. figshare https://doi.org/10.6084/m9.figshare.24225193	dataset	January 2023
Additional file 1 of A coral-associated actinobacterium mitigates coral bleaching under heat stress Li, Jie; Zou, Yiyang; Li, Qiqi figshare https://doi.org/10.6084/m9.figshare.24630339	dataset	January 2023
Additional file 1 of New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms Chen, Jianfei; Chen, Xiuli; Zhu, Ying figshare https://doi.org/10.6084/m9.figshare.25322900	dataset	January 2024
Additional file 1 of Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community Wu, Chong-Die; Fan, Yong-Bin; Chen, Xue figshare https://doi.org/10.6084/m9.figshare.25572580	image	January 2024
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Unifying concepts of biological function from molecules to ecosystems Farnsworth, Keith D.; Albantakis, Larissa; Caruso, Tancredi Oikos https://doi.org/10.1101/105320	journal	February 2017
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Syntrophobacteraceae -affiliated species are major propionate-degrading sulfate reducers in paddy soil : Major propionate degrading SRB in paddy soil Liu, Pengfei; Conrad, Ralf Environmental Microbiology, Vol. 19, Issue 4 https://doi.org/10.1111/1462-2920.13698	journal	March 2017
Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes Ren, Ge; Ma, Anzhou; Zhang, Yanfen Environmental Microbiology, Vol. 20, Issue 7 https://doi.org/10.1111/1462-2920.14128	journal	May 2018
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Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests Ding, Junjun; Zhang, Yuguang; Wang, Mengmeng Molecular Ecology, Vol. 24, Issue 20 https://doi.org/10.1111/mec.13384	journal	October 2015
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Unifying concepts of biological function from molecules to ecosystems Farnsworth, Keith D.; Albantakis, Larissa; Caruso, Tancredi Oikos, Vol. 126, Issue 10 https://doi.org/10.1111/oik.04171	journal	June 2017
Seed mucilage interacts with soil microbial community and physiochemical processes to affect seedling emergence on desert sand dunes: Interactions between mucilage and soil microbes Hu, Dandan; Zhang, Shudong; Baskin, Jerry M. Plant, Cell & Environment, Vol. 42, Issue 2 https://doi.org/10.1111/pce.13442	journal	September 2018
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Chemotherapy Alters the Phylogenetic Molecular Ecological Networks of Intestinal Microbial Communities Cong, Jing; Zhu, Jingjuan; Zhang, Chuantao Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01008	journal	May 2019
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Decoding Wheat Endosphere–Rhizosphere Microbiomes in Rhizoctonia solani–Infested Soils Challenged by Streptomyces Biocontrol Agents Araujo, Ricardo; Dunlap, Christopher; Barnett, Steve Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.01038	journal	August 2019
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Molecular Ecological Network Complexity Drives Stand Resilience of Soil Bacteria to Mining Disturbances among Typical Damaged Ecosystems in China Ma, Jing; Lu, Yongqiang; Chen, Fu Microorganisms, Vol. 8, Issue 3 https://doi.org/10.3390/microorganisms8030433	journal	March 2020
The Variation of the Soil Bacterial and Fungal Community Is Linked to Land Use Types in Northeast China Ma, Jincai; Nergui, Sumiya; Han, Ziming Sustainability, Vol. 11, Issue 12 https://doi.org/10.3390/su11123286	journal	June 2019
Distribution and Abundance of Antibiotic Resistance Genes in Sand Settling Reservoirs and Drinking Water Treatment Plants across the Yellow River, China Lu, Junying; Tian, Zhe; Yu, Jianwei Water, Vol. 10, Issue 3 https://doi.org/10.3390/w10030246	journal	February 2018
Aquatic Macrophytes and Local Factors Drive Bacterial Community Distribution and Interactions in a Riparian Zone of Lake Taihu Lyu, Yuanjiao; Huang, Rui; Zeng, Jin Water, Vol. 12, Issue 2 https://doi.org/10.3390/w12020432	journal	February 2020
Interactive network configuration maintains bacterioplankton community structure under elevated CO 2 in a eutrophic coastal mesocosm experiment Lin, Xin; Huang, Ruiping; Li, Yan Biogeosciences, Vol. 15, Issue 2 https://doi.org/10.5194/bg-15-551-2018	journal	January 2018

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59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
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