Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

Zhou, Jizhong; Deng, Ye; Luo, Feng; He, Zhili; Yang, Yunfeng

doi:10.1128/mbio.00122-11

Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO₂

Journal Article · Tue Jul 26 04:00:00 EDT 2011 · mBio (Online)

DOI:https://doi.org/10.1128/mbio.00122-11· OSTI ID:1626086

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

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

Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO₂, is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual framework to discern phylogenetic molecular ecological networks using metagenomic sequencing data of 16S rRNA genes from grassland soil microbial communities, which were sampled from a long-term free-air CO₂ enrichment experimental facility at the Cedar Creek Ecosystem Science Reserve in Minnesota. Our experimental results demonstrated that an RMT-based network approach is very useful in delineating phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data. The structure of the identified networks under ambient and elevated CO₂ levels was substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher-order organization, topological roles of individual nodes, and network hubs, suggesting that the network interactions among different phylogenetic groups/populations were markedly changed. Also, the changes in network structure were significantly correlated with soil carbon and nitrogen contents, indicating the potential importance of network interactions in ecosystem functioning. In addition, based on network topology, microbial populations potentially most important to community structure and ecosystem functioning can be discerned. The novel approach described in this study is important not only for research on biodiversity, microbial ecology, and systems microbiology but also for microbial community studies in human health, global change, and environmental management.

View Accepted Manuscript (DOE)

Research Organization:: 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

OSTI ID:: 1626086

Journal Information:: mBio (Online), Journal Name: mBio (Online) Journal Issue: 4 Vol. 2; ISSN 2150-7511

Publisher:: American Society for Microbiology (ASM)Copyright Statement

Country of Publication:: United States

Language:: English

References (54)

Interactive Effects of Time, CO2, N, and Diversity on Total Belowground Carbon Allocation and Ecosystem Carbon Storage in a Grassland Community Carol Adair, E.; Reich, Peter B.; Hobbie, Sarah E. Ecosystems, Vol. 12, Issue 6 https://doi.org/10.1007/s10021-009-9278-9	journal	September 2009
Plant diversity enhances ecosystem responses to elevated CO2 and nitrogen deposition Reich, Peter B.; Knops, Jean; Tilman, David Nature, Vol. 410, Issue 6830 https://doi.org/10.1038/35071062	journal	April 2001
The contribution of species richness and composition to bacterial services Bell, Thomas; Newman, Jonathan A.; Silverman, Bernard W. Nature, Vol. 436, Issue 7054 https://doi.org/10.1038/nature03891	journal	August 2005
Nitrogen limitation constrains sustainability of ecosystem response to CO2 Reich, Peter B.; Hobbie, Sarah E.; Lee, Tali Nature, Vol. 440, Issue 7086 https://doi.org/10.1038/nature04486	journal	April 2006
Diversity and dispersal interactively affect predictability of ecosystem function France, Kristin E.; Duffy, J. Emmett Nature, Vol. 441, Issue 7097 https://doi.org/10.1038/nature04729	journal	June 2006
Ecological networks and their fragility Montoya, José M.; Pimm, Stuart L.; Solé, Ricard V. Nature, Vol. 442, Issue 7100 https://doi.org/10.1038/nature04927	journal	July 2006
Habitat modification alters the structure of tropical host–parasitoid food webs Tylianakis, Jason M.; Tscharntke, Teja; Lewis, Owen T. Nature, Vol. 445, Issue 7124 https://doi.org/10.1038/nature05429	journal	January 2007
Terrestrial ecosystem carbon dynamics and climate feedbacks Heimann, Martin; Reichstein, Markus Nature, Vol. 451, Issue 7176 https://doi.org/10.1038/nature06591	journal	January 2008
An Earth-system perspective of the global nitrogen cycle Gruber, Nicolas; Galloway, James N. Nature, Vol. 451, Issue 7176 https://doi.org/10.1038/nature06592	journal	January 2008
Microbial community structure and its functional implications Fuhrman, Jed A. Nature, Vol. 459, Issue 7244 https://doi.org/10.1038/nature08058	journal	May 2009
A human gut microbial gene catalogue established by metagenomic sequencing Qin, Junjie; Li, Ruiqiang; Raes, Jeroen Nature, Vol. 464, Issue 7285 https://doi.org/10.1038/nature08821	journal	March 2010
Enterotypes of the human gut microbiome Arumugam, Manimozhiyan; Raes, Jeroen; Pelletier, Eric Nature, Vol. 473, Issue 7346 https://doi.org/10.1038/nature09944	journal	April 2011
Functional organization of the transcriptome in human brain Oldham, Michael C.; Konopka, Genevieve; Iwamoto, Kazuya Nature Neuroscience, Vol. 11, Issue 11 https://doi.org/10.1038/nn.2207	journal	October 2008
Network biology: understanding the cell's functional organization Barabási, Albert-László; Oltvai, Zoltán N. Nature Reviews Genetics, Vol. 5, Issue 2 https://doi.org/10.1038/nrg1272	journal	February 2004
Altered soil microbial community at elevated CO2 leads to loss of soil carbon Carney, K. M.; Hungate, B. A.; Drake, B. G. Proceedings of the National Academy of Sciences, Vol. 104, Issue 12 https://doi.org/10.1073/pnas.0610045104	journal	March 2007
The modularity of pollination networks Olesen, J. M.; Bascompte, J.; Dupont, Y. L. Proceedings of the National Academy of Sciences, Vol. 104, Issue 50 https://doi.org/10.1073/pnas.0706375104	journal	December 2007
Food-web structure and network theory: The role of connectance and size Dunne, J. A.; Williams, R. J.; Martinez, N. D. Proceedings of the National Academy of Sciences, Vol. 99, Issue 20 https://doi.org/10.1073/pnas.192407699	journal	September 2002
Finding community structure in very large networks Clauset, Aaron; Newman, M. E. J.; Moore, Cristopher Physical Review E, Vol. 70, Issue 6 https://doi.org/10.1103/physreve.70.066111	journal	December 2004
What have we learned from 15 years of free-air CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2: Tansley review Ainsworth, Elizabeth A.; Long, Stephen P. New Phytologist, Vol. 165, Issue 2 https://doi.org/10.1111/j.1469-8137.2004.01224.x	journal	November 2004
Biodiversity and Ecosystem Functioning: Current Knowledge and Future Challenges Loreau, M. Science, Vol. 294, Issue 5543 https://doi.org/10.1126/science.1064088	journal	October 2001
Specificity and Stability in Topology of Protein Networks Maslov, S. Science, Vol. 296, Issue 5569 https://doi.org/10.1126/science.1065103	journal	May 2002
Biological Networks: The Tinkerer as an Engineer Alon, U. Science, Vol. 301, Issue 5641 https://doi.org/10.1126/science.1089072	journal	September 2003
PRESIDENTIAL ADDRESS: Grand Challenges and Great Opportunities in Science, Technology, and Public Policy Omenn, G. S. Science, Vol. 314, Issue 5806 https://doi.org/10.1126/science.1135003	journal	December 2006
A General Model for Food Web Structure Allesina, S.; Alonso, D.; Pascual, M. Science, Vol. 320, Issue 5876 https://doi.org/10.1126/science.1156269	journal	May 2008
Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans Muegge, B. D.; Kuczynski, J.; Knights, D. Science, Vol. 332, Issue 6032 https://doi.org/10.1126/science.1198719	journal	May 2011
Functional Molecular Ecological Networks Zhou, Jizhong; Deng, Ye; Luo, Feng mBio, Vol. 1, Issue 4 https://doi.org/10.1128/mbio.00169-10	journal	October 2010
Understanding network concepts in modules Dong, Jun; Horvath, Steve BMC Systems Biology, Vol. 1, Issue 1 https://doi.org/10.1186/1752-0509-1-24	journal	June 2007
Eigengene networks for studying the relationships between co-expression modules Langfelder, Peter; Horvath, Steve BMC Systems Biology, Vol. 1, Issue 1 https://doi.org/10.1186/1752-0509-1-54	journal	November 2007
Compilation and Network Analyses of Cambrian Food Webs Dunne, Jennifer A.; Williams, Richard J.; Martinez, Neo D. PLoS Biology, Vol. 6, Issue 4 https://doi.org/10.1371/journal.pbio.0060102	journal	April 2008
Geometric Interpretation of Gene Coexpression Network Analysis Horvath, Steve; Dong, Jun PLoS Computational Biology, Vol. 4, Issue 8 https://doi.org/10.1371/journal.pcbi.1000117	journal	August 2008
ELEVATED CO ₂ STIMULATES NET ACCUMULATIONS OF CARBON AND NITROGEN IN LAND ECOSYSTEMS: A META-ANALYSIS Luo, Yiqi; Hui, Dafeng; Zhang, Deqiang Ecology, Vol. 87, Issue 1 https://doi.org/10.1890/04-1724	journal	January 2006
A global network of coexisting microbes from environmental and whole-genome sequence data Chaffron, S.; Rehrauer, H.; Pernthaler, J. Cold Spring Harbor Laboratory Press https://doi.org/10.5167/uzh-34788	text	January 2010
Networks in ecology Bascompte, Jordi Basic and Applied Ecology, Vol. 8, Issue 6 https://doi.org/10.1016/j.baae.2007.06.003	journal	November 2007
Application of random matrix theory to biological networks Luo, Feng; Zhong, Jianxin; Yang, Yunfeng Physics Letters A, Vol. 357, Issue 6 https://doi.org/10.1016/j.physleta.2006.04.076	journal	September 2006
Application of random matrix theory to biological networks Luo, F.; Zhong, J.; Yang, Y. Physics Letters A https://doi.org/10.1016/j.physleta.2006.04.085	journal	May 2006
Collective dynamics of ‘small-world’ networks Watts, Duncan J.; Strogatz, Steven H. Nature, Vol. 393, Issue 6684 https://doi.org/10.1038/30918	journal	June 1998
Biodiversity and ecosystem stability in a decade-long grassland experiment Tilman, David; Reich, Peter B.; Knops, Johannes M. H. Nature, Vol. 441, Issue 7093 https://doi.org/10.1038/nature04742	journal	June 2006
Hierarchical structure and the prediction of missing links in networks Clauset, Aaron; Moore, Cristopher; Newman, M. E. J. Nature, Vol. 453, Issue 7191 https://doi.org/10.1038/nature06830	journal	May 2008
The architecture of mutualistic networks minimizes competition and increases biodiversity Bastolla, Ugo; Fortuna, Miguel A.; Pascual-García, Alberto Nature, Vol. 458, Issue 7241 https://doi.org/10.1038/nature07950	journal	April 2009
Classes of complex networks defined by role-to-role connectivity profiles Guimerà, Roger; Sales-Pardo, Marta; Amaral, Luís A. N. Nature Physics, Vol. 3, Issue 1 https://doi.org/10.1038/nphys489	journal	December 2006
Molecular eco-systems biology: towards an understanding of community function Raes, Jeroen; Bork, Peer Nature Reviews Microbiology, Vol. 6, Issue 9 https://doi.org/10.1038/nrmicro1935	journal	June 2008
Invariant properties in coevolutionary networks of plant-animal interactions: Invariant properties in coevolutionary networks Jordano, Pedro; Bascompte, Jordi; Olesen, Jens M. Ecology Letters, Vol. 6, Issue 1 https://doi.org/10.1046/j.1461-0248.2003.00403.x	journal	December 2002
A global network of coexisting microbes from environmental and whole-genome sequence data Chaffron, S.; Rehrauer, H.; Pernthaler, J. Genome Research, Vol. 20, Issue 7 https://doi.org/10.1101/gr.104521.109	journal	May 2010
Finding community structure in very large networks Clauset, Aaron; Newman, M. E. J.; Moore, Cristopher Physical Review E, Vol. 70, Issue 6 https://doi.org/10.1103/PhysRevE.70.066111	journal	December 2004
Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2: Changes in the soil microbial community at elevated CO2 He, Zhili; Xu, Meiying; Deng, Ye Ecology Letters, Vol. 13, Issue 5 https://doi.org/10.1111/j.1461-0248.2010.01453.x	journal	April 2010
Rising Atmospheric CO2 Reduces Sequestration of Root-Derived Soil Carbon Heath, J. Science, Vol. 309, Issue 5741 https://doi.org/10.1126/science.1110700	journal	September 2005
Functional Molecular Ecological Networks Zhou, Jizhong; Deng, Ye; Luo, Feng mBio, Vol. 1, Issue 4 https://doi.org/10.1128/mBio.00169-10	journal	October 2010
Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory Luo, Feng; Yang, Yunfeng; Zhong, Jianxin BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-299	journal	January 2007
Long-Term and Large-Scale Perspectives on the Relationship between Biodiversity and Ecosystem Functioning Symstad, Amy J.; Chapin, F. Stuart; Wall, Diana H. BioScience, Vol. 53, Issue 1 https://doi.org/10.1641/0006-3568(2003)053[0089:LTALSP]2.0.CO;2	journal	January 2003
Effects of Biodiversity on Ecosystem Functioning: a Consensus of Current Knowledge Hooper, D. U.; Chapin, F. S.; Ewel, J. J. Ecological Monographs, Vol. 75, Issue 1 https://doi.org/10.1890/04-0922	journal	February 2005
Community structure of marine bacterioplankton: patterns, networks, and relationships to function Fuhrman, Ja; Steele, Ja Aquatic Microbial Ecology, Vol. 53 https://doi.org/10.3354/ame01222	journal	September 2008
Finding community structure in very large networks Clauset, Aaron; Newman, M. E. J.; Moore, Cristopher arXiv https://doi.org/10.48550/arxiv.cond-mat/0408187	text	January 2004
Classes of complex networks defined by role-to-role connectivity profiles Guimera, R.; Sales-Pardo, M.; Amaral, L. A. N. arXiv https://doi.org/10.48550/arxiv.physics/0701149	text	January 2007
Effects of biodiversity on ecosystem functioning: a consensus of current knowledge Hooper, D. U.; S., Chapin III, F.; Ewel, J. J. Ecological Society of America https://doi.org/10.5167/uzh-2060	text	January 2005

Cited By (107)

Contrasting soil microbial community functional structures in two major landscapes of the Tibetan alpine meadow Chu, Houjuan; Wang, Shiping; Yue, Haowei MicrobiologyOpen, Vol. 3, Issue 5 https://doi.org/10.1002/mbo3.190	journal	July 2014
Molecular ecological network analysis of the response of soil microbial communities to depth gradients in farmland soils Yu, Hang; Xue, Dongmei; Wang, Yidong MicrobiologyOpen, Vol. 9, Issue 3 https://doi.org/10.1002/mbo3.983	journal	January 2020
Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover Liang, Yuting; Jiang, Yuji; Wang, Feng The ISME Journal, Vol. 9, Issue 12 https://doi.org/10.1038/ismej.2015.78	journal	May 2015
Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation Siles, José A.; Margesin, Rosa Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-02363-2	journal	May 2017
Molecular ecological network analysis reveals the effects of probiotics and florfenicol on intestinal microbiota homeostasis: An example of sea cucumber Yang, Gang; Peng, Mo; Tian, Xiangli Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-05312-1	journal	July 2017
Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland Yang, Jie; Wang, Yanfen; Cui, Xiaoyong Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-55940-y	journal	December 2019
Integrated metagenomics and network analysis of soil microbial community of the forest timberline Ding, Junjun; Zhang, Yuguang; Deng, Ye Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep07994	journal	January 2015
Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling Wang, Feng; Liang, Yuting; Jiang, Yuji Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep14345	journal	September 2015
Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms Shiba, Takahiko; Watanabe, Takayasu; Kachi, Hirokazu Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep30997	journal	August 2016
Characterising the interspecific variations and convergence of gut microbiota in Anseriformes herbivores at wintering areas Yang, Yuzhan; Deng, Ye; Cao, Lei Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep32655	journal	September 2016
Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient Monard, C.; Gantner, S.; Bertilsson, S. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep37719	journal	November 2016
From hairballs to hypotheses–biological insights from microbial networks Röttjers, Lisa; Faust, Karoline FEMS Microbiology Reviews, Vol. 42, Issue 6 https://doi.org/10.1093/femsre/fuy030	journal	July 2018
Unique bacterial assembly, composition, and interactions in a parasitic plant and its host Fitzpatrick, Connor R.; Schneider, Adam C. Journal of Experimental Botany, Vol. 71, Issue 6 https://doi.org/10.1093/jxb/erz572	journal	January 2020
Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea Zhang, Yao; Zhao, Zihao; Dai, Minhan Molecular Ecology, Vol. 23, Issue 9 https://doi.org/10.1111/mec.12739	journal	April 2014
Initial soil microbiome composition and functioning predetermine future plant health Wei, Zhong; Gu, Yian; Friman, Ville-Petri Science Advances, Vol. 5, Issue 9 https://doi.org/10.1126/sciadv.aaw0759	journal	September 2019
DNA Stable-Isotope Probing Delineates Carbon Flows from Rice Residues into Soil Microbial Communities Depending on Fertilization Kong, Yali; Kuzyakov, Yakov; Ruan, Yang Applied and Environmental Microbiology, Vol. 86, Issue 7 https://doi.org/10.1128/aem.02151-19	journal	January 2020
Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities Zhou, Jizhong; Jiang, Yi-Huei; Deng, Ye mBio, Vol. 4, Issue 3 https://doi.org/10.1128/mbio.00324-13	journal	June 2013
Progressive Microbial Community Networks with Incremental Organic Loading Rates Underlie Higher Anaerobic Digestion Performance Wu, Linwei; Shan, Xiaoyu; Chen, Si mSystems, Vol. 5, Issue 1 https://doi.org/10.1128/msystems.00357-19	journal	January 2020
Molecular ecological network analyses Deng, Ye; Jiang, Yi-Huei; Yang, Yunfeng BMC Bioinformatics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2105-13-113	journal	January 2012
The core populations and co-occurrence patterns of prokaryotic communities in household biogas digesters Rui, Junpeng; Li, Jiabao; Zhang, Shiheng Biotechnology for Biofuels, Vol. 8, Issue 1 https://doi.org/10.1186/s13068-015-0339-3	journal	September 2015
Responses of phyllosphere microbiota and plant health to application of two different biocontrol agents Qin, Chong; Tao, Jiemeng; Liu, Tianbo AMB Express, Vol. 9, Issue 1 https://doi.org/10.1186/s13568-019-0765-x	journal	March 2019
Model-based quantification of metabolic interactions from dynamic microbial-community data Hanemaaijer, Mark; Olivier, Brett G.; Röling, Wilfred F. M. PLOS ONE, Vol. 12, Issue 3 https://doi.org/10.1371/journal.pone.0173183	journal	March 2017
Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste Shaw, Grace Tzun-Wen; Liu, An-Chi; Weng, Chieh-Yin PLOS ONE, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pone.0181395	journal	July 2017
Network topology reveals high connectance levels and few key microbial genera within soils Lupatini, Manoeli; Suleiman, Afnan K. A.; Jacques, Rodrigo J. S. Frontiers in Environmental Science, Vol. 2 https://doi.org/10.3389/fenvs.2014.00010	journal	May 2014
Conservation of Species- and Trait-Based Modeling Network Interactions in Extremely Acidic Microbial Community Assembly Kuang, Jialiang; Cadotte, Marc W.; Chen, Yongjian Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01486	journal	August 2017
An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease Yang, Hongwu; Li, Juan; Xiao, Yunhua Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02179	journal	November 2017
Distribution of Archaeal Communities along the Coast of the Gulf of Finland and Their Response to Oil Contamination Yan, Lijuan; Yu, Dan; Hui, Nan Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00015	journal	January 2018
A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill Zhang, Shuangfei; Hu, Zhong; Wang, Hui Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00520	journal	March 2018
Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach Chen, Wen; Wilkes, Graham; Khan, Izhar U. H. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02301	journal	October 2018
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
Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere Qian, Xin; Li, Hanzhou; Wang, Yonglong Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01015	journal	May 2019
Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System Zhu, Hai-Zhen; Zhang, Zhi-Feng; Zhou, Nan Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01726	journal	August 2019
Soil Property and Plant Diversity Determine Bacterial Turnover and Network Interactions in a Typical Arid Inland River Basin, Northwest China Wang, Wenjuan; Wang, Jianming; Ye, Ziqi Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02655	journal	November 2019
Soil Microbial Networks Shift Across a High-Elevation Successional Gradient Farrer, Emily C.; Porazinska, Dorota L.; Spasojevic, Marko J. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02887	journal	December 2019
Cracks Reinforce the Interactions among Soil Bacterial Communities in the Coal Mining Area of Loess Plateau, China Luo, Zhanbin; Ma, Jing; Chen, Fu International Journal of Environmental Research and Public Health, Vol. 16, Issue 24 https://doi.org/10.3390/ijerph16244892	journal	December 2019
Inhibition of Tumor Growth by Dietary Indole-3-Carbinol in a Prostate Cancer Xenograft Model May Be Associated with Disrupted Gut Microbial Interactions Wu, Yanbei; Li, Robert; Huang, Haiqiu Nutrients, Vol. 11, Issue 2 https://doi.org/10.3390/nu11020467	journal	February 2019
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
Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances Taketani, Rodrigo G.; Moitinho, Marta A.; Mauchline, Tim H. PeerJ, Vol. 6 https://doi.org/10.7717/peerj.5710	journal	October 2018
Taking insight into the gut microbiota of three spider species: No characteristic symbiont was found corresponding to the special feeding style of spiders Hu, Guowen; Zhang, Lihua; Yun, Yueli Ecology and Evolution, Vol. 9, Issue 14 https://doi.org/10.1002/ece3.5382	journal	June 2019
Continuous-cropping tobacco caused variance of chemical properties and structure of bacterial network in soils Chen, Shu; Qi, Gaofu; Luo, Tian Land Degradation & Development, Vol. 29, Issue 11 https://doi.org/10.1002/ldr.3167	journal	October 2018
Soil bacterial communities in grasslands revegetated using Elymus nutans are largely influenced by soil pH and total phosphorus across restoration time Hu, Lei; Zi, Hongbiao; Wu, Pengfei Land Degradation & Development, Vol. 30, Issue 18 https://doi.org/10.1002/ldr.3414	journal	August 2019
Sediment microbiomes associated with the rhizosphere of emergent macrophytes in a shallow, subtropical lake Huang, Rui; Zeng, Jin; Zhao, Dayong Limnology and Oceanography, Vol. 65, Issue S1 https://doi.org/10.1002/lno.11325	journal	January 2020
Distinct shifts in bacterioplankton community composition and functional gene structure between macrophyte‐ and phytoplankton‐dominated regimes in a large shallow lake Wang, Yujing; Cao, Xinyi; Zeng, Jin Limnology and Oceanography, Vol. 65, Issue S1 https://doi.org/10.1002/lno.11373	journal	January 2020
Malvidin 3‐Glucoside Modulated Gut Microbial Dysbiosis and Global Metabolome Disrupted in a Murine Colitis Model Induced by Dextran Sulfate Sodium Liu, Fang; Wang, Thomas T. Y.; Tang, Qingjuan Molecular Nutrition & Food Research, Vol. 63, Issue 21 https://doi.org/10.1002/mnfr.201900455	journal	August 2019
Illumina MiSeq sequencing and network analysis the distribution and co-occurrence of bacterioplankton in Danjiangkou Reservoir, China Chen, Zhao-Jin; Xu, Ge; Ding, Chuan-Yu Archives of Microbiology, Vol. 202, Issue 4 https://doi.org/10.1007/s00203-019-01798-7	journal	January 2020
Contrasting Network Features between Free-Living and Particle-Attached Bacterial Communities in Taihu Lake Xu, Huimin; Zhao, Dayong; Huang, Rui Microbial Ecology, Vol. 76, Issue 2 https://doi.org/10.1007/s00248-017-1131-7	journal	January 2018
Integrated network analysis reveals the importance of microbial interactions for maize growth Tao, Jiemeng; Meng, Delong; Qin, Chong Applied Microbiology and Biotechnology, Vol. 102, Issue 8 https://doi.org/10.1007/s00253-018-8837-4	journal	March 2018
Alterations in soil fungal community composition and network assemblage structure by different long-term fertilization regimes are correlated to the soil ionome Xue, Chao; Ryan Penton, C.; Zhu, Chen Biology and Fertility of Soils, Vol. 54, Issue 1 https://doi.org/10.1007/s00374-017-1241-x	journal	September 2017
Sugars altered fungal community composition and caused high network complexity in a Fusarium wilt pathogen-infested soil Ren, Gaidi; Meng, Tianzhu; Ma, Yan Biology and Fertility of Soils, Vol. 56, Issue 3 https://doi.org/10.1007/s00374-019-01424-0	journal	January 2020
Isolation and characterization from solar salterns of North Algeria of a haloarchaeon producing a new halocin Mazguene, Souhila; Rossi, Mosè; Gogliettino, Marta Extremophiles, Vol. 22, Issue 2 https://doi.org/10.1007/s00792-017-0994-3	journal	December 2017
Following legume establishment, microbial and chemical associations facilitate improved productivity in degraded grasslands Zhou, Jiqiong; Zhang, Fengge; Huo, Yunqian Plant and Soil, Vol. 443, Issue 1-2 https://doi.org/10.1007/s11104-019-04169-9	journal	August 2019
Characterization and comprehensive analysis of the ecological interaction networks of bacterial communities in Paullinia cupana var. sorbilis by 16S rRNA gene metabarcoding Liotti, Rhavena Graziela; da Silva, Rafael Correia; Pinheiro, Daniel Guariz World Journal of Microbiology and Biotechnology, Vol. 35, Issue 12 https://doi.org/10.1007/s11274-019-2758-y	journal	November 2019
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision Weiss, Sophie; Van Treuren, Will; Lozupone, Catherine The ISME Journal, Vol. 10, Issue 7 https://doi.org/10.1038/ismej.2015.235	journal	February 2016
Soil protist communities form a dynamic hub in the soil microbiome Xiong, Wu; Jousset, Alexandre; Guo, Sai The ISME Journal, Vol. 12, Issue 2 https://doi.org/10.1038/ismej.2017.171	journal	October 2017
Belowground biodiversity and ecosystem functioning Bardgett, Richard D.; van der Putten, Wim H. Nature, Vol. 515, Issue 7528 https://doi.org/10.1038/nature13855	journal	November 2014
Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy Chen, Casey; Hemme, Chris; Beleno, Joan The ISME Journal, Vol. 12, Issue 5 https://doi.org/10.1038/s41396-017-0037-1	journal	January 2018
Soil bacterial networks are less stable under drought than fungal networks de Vries, Franciska T.; Griffiths, Rob I.; Bailey, Mark Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05516-7	journal	August 2018
Keystone taxa as drivers of microbiome structure and functioning Banerjee, Samiran; Schlaeppi, Klaus; van der Heijden, Marcel G. A. Nature Reviews Microbiology, Vol. 16, Issue 9 https://doi.org/10.1038/s41579-018-0024-1	journal	May 2018
Wheat dwarfing influences selection of the rhizosphere microbiome Kavamura, Vanessa N.; Robinson, Rebekah J.; Hughes, David Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-58402-y	journal	January 2020
An integrated insight into the response of sedimentary microbial communities to heavy metal contamination Yin, Huaqun; Niu, Jiaojiao; Ren, Youhua Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep14266	journal	September 2015
Temporal Variation and Co-occurrence Patterns of Bacterial Communities in Eutrophic Lake Taihu, China Peng, Yuke; Yue, Dongmei; Xiao, Lin Geomicrobiology Journal, Vol. 35, Issue 3 https://doi.org/10.1080/01490451.2017.1348406	journal	December 2017
Long-term inorganic fertilizer use influences bacterial communities in Mollisols of Northeast China based on high-throughput sequencing and network analyses Yu, Zhenhua; Hu, Xiaojing; Wei, Dan Archives of Agronomy and Soil Science, Vol. 65, Issue 10 https://doi.org/10.1080/03650340.2018.1563685	journal	January 2019
Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils Khan, M. A. Wadud; Bohannan, Brendan J. M.; Nüsslein, Klaus FEMS Microbiology Ecology, Vol. 95, Issue 2 https://doi.org/10.1093/femsec/fiy230	journal	November 2018
Co-occurrence analysis reveal that biotic and abiotic factors influence soil fungistasis against Fusarium graminearum Legrand, Fabienne; Chen, Wen; Cobo-Díaz, José Francisco FEMS Microbiology Ecology, Vol. 95, Issue 5 https://doi.org/10.1093/femsec/fiz056	journal	April 2019
Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis Wang, Yu; Zhang, Rui; Zheng, Qiang ICES Journal of Marine Science, Vol. 73, Issue 3 https://doi.org/10.1093/icesjms/fsv187	journal	November 2015
Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states Bardgett, Richard D.; Caruso, Tancredi Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 375, Issue 1794 https://doi.org/10.1098/rstb.2019.0112	journal	January 2020
Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters: Network analysis of microbial community structure de Menezes, Alexandre B.; Prendergast-Miller, Miranda T.; Richardson, Alan E. Environmental Microbiology, Vol. 17, Issue 8 https://doi.org/10.1111/1462-2920.12559	journal	August 2014
Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation: Competition in bioremediation system Deng, Ye; Zhang, Ping; Qin, Yujia Environmental Microbiology, Vol. 18, Issue 1 https://doi.org/10.1111/1462-2920.12981	journal	August 2015
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
Lime and ammonium carbonate fumigation coupled with bio‐organic fertilizer application steered banana rhizosphere to assemble a unique microbiome against Panama disease Shen, Zongzhuan; Wang, Beibei; Zhu, Jiaxin Microbial Biotechnology, Vol. 12, Issue 3 https://doi.org/10.1111/1751-7915.13391	journal	March 2019
Plant–microbe networks in soil are weakened by century‐long use of inorganic fertilizers Huang, Ruilin; McGrath, Steve P.; Hirsch, Penny R. Microbial Biotechnology, Vol. 12, Issue 6 https://doi.org/10.1111/1751-7915.13487	journal	July 2019
Interactome‐based abiotic and biotic impacts on biodiversity of plankton communities in disturbed wetlands Yang, Yuzhan; Gao, Yangchun; Chen, Yiyong Diversity and Distributions, Vol. 25, Issue 9 https://doi.org/10.1111/ddi.12949	journal	June 2019
The effects of straw incorporation with plastic film mulch on soil properties and bacterial community structure on the loess plateau Li, Yüze; Hu, Yingchun; Song, Duanpu European Journal of Soil Science https://doi.org/10.1111/ejss.12912	journal	December 2019
Microbial community responses to anthropogenically induced environmental change: towards a systems approach Bissett, Andrew; Brown, Mark V.; Siciliano, Steven D. Ecology Letters, Vol. 16 https://doi.org/10.1111/ele.12109	journal	May 2013
The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages Shi, Shengjing; Nuccio, Erin E.; Shi, Zhou J. Ecology Letters, Vol. 19, Issue 8 https://doi.org/10.1111/ele.12630	journal	June 2016
Higher precipitation strengthens the microbial interactions in semi-arid grassland soils Wang, Shang; Wang, Xiaobo; Han, Xingguo Global Ecology and Biogeography, Vol. 27, Issue 5 https://doi.org/10.1111/geb.12718	journal	January 2018
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
Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes Guo, Junjie; Ling, Ning; Chen, Zhaojie New Phytologist, Vol. 226, Issue 1 https://doi.org/10.1111/nph.16345	journal	December 2019
Microbial Network and Soil Properties Are Changed in Bacterial Wilt-Susceptible Soil Qi, Gaofu; Ma, Gaoqiang; Chen, Shu Applied and Environmental Microbiology, Vol. 85, Issue 13 https://doi.org/10.1128/aem.00162-19	journal	April 2019
Fungal Communities Respond to Long-Term CO ₂ Elevation by Community Reassembly Tu, Qichao; Yuan, Mengting; He, Zhili Applied and Environmental Microbiology, Vol. 81, Issue 7 https://doi.org/10.1128/aem.04040-14	journal	January 2015
High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats Zhou, Jizhong; He, Zhili; Yang, Yunfeng mBio, Vol. 6, Issue 1 https://doi.org/10.1128/mbio.02288-14	journal	January 2015
The succession pattern of soil microbial communities and its relationship with tobacco bacterial wilt Niu, Jiaojiao; Rang, Zhongwen; Zhang, Chao BMC Microbiology, Vol. 16, Issue 1 https://doi.org/10.1186/s12866-016-0845-x	journal	October 2016
Inferring microbial interaction network from microbiome data using RMN algorithm Tsai, Kun-Nan; Lin, Shu-Hsi; Liu, Wei-Chung BMC Systems Biology, Vol. 9, Issue 1 https://doi.org/10.1186/s12918-015-0199-2	journal	September 2015
The mutated tegument protein UL7 attenuates the virulence of herpes simplex virus 1 by reducing the modulation of α-4 gene transcription Xu, Xingli; Fan, Shengtao; Zhou, Jienan Virology Journal, Vol. 13, Issue 1 https://doi.org/10.1186/s12985-016-0600-9	journal	September 2016
The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism Liu, Fang; Horton-Sparks, Kayla; Hull, Vanessa Molecular Autism, Vol. 9, Issue 1 https://doi.org/10.1186/s13229-018-0251-3	journal	December 2018
Variations in phyllosphere microbial community along with the development of angular leaf-spot of cucumber Luo, Luyun; Zhang, Zhuo; Wang, Pei AMB Express, Vol. 9, Issue 1 https://doi.org/10.1186/s13568-019-0800-y	journal	May 2019
Root ethylene mediates rhizosphere microbial community reconstruction when chemically detecting cyanide produced by neighbouring plants Chen, Yan; Bonkowski, Michael; Shen, Yi Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-019-0775-6	journal	January 2020
Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome Huang, Zhijian; Zeng, Shenzheng; Xiong, Jinbo Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00802-3	journal	March 2020
Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics Maus, Irena; Klocke, Michael; Derenkó, Jaqueline Environmental Microbiome, Vol. 15, Issue 1 https://doi.org/10.1186/s40793-020-00354-x	journal	March 2020
Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica Ramírez-Fernández, Lía; Trefault, Nicole; Carú, Margarita PLOS ONE, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pone.0209887	journal	January 2019
An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa Jordaan, K.; Comeau, A. M.; Khasa, D. P. PLOS ONE, Vol. 14, Issue 5 https://doi.org/10.1371/journal.pone.0216758	journal	May 2019
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 Research Square https://doi.org/10.21203/rs.2.22872/v1	journal	February 2020
The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes Myrold, David D.; Zeglin, Lydia H.; Jansson, Janet K. Soil Science Society of America Journal, Vol. 78, Issue 1 https://doi.org/10.2136/sssaj2013.07.0287dgs	journal	January 2014
Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases Rebollar, Eria A.; Antwis, Rachael E.; Becker, Matthew H. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00068	journal	February 2016
Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies Gopal, Murali; Gupta, Alka Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01971	journal	December 2016
Distinct Network Interactions in Particle-Associated and Free-Living Bacterial Communities during a Microcystis aeruginosa Bloom in a Plateau Lake Yang, Caiyun; Wang, Qi; Simon, Paulina N. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01202	journal	June 2017
Vineyard Soil Microbiome Composition Related to Rotundone Concentration in Australian Cool Climate ‘Peppery’ Shiraz Grapes Gupta, Vadakattu V. S. R.; Bramley, Robert G. V.; Greenfield, Paul Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01607	journal	July 2019
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
Impacts of Elevated CO2 Levels on the Soil Bacterial Community in a Natural CO2-Enhanced Oil Recovery Area Ma, Jing; Luo, Zhanbin; Chen, Fu Diversity, Vol. 11, Issue 5 https://doi.org/10.3390/d11050077	journal	May 2019
Flooding Irrigation Weakens the Molecular Ecological Network Complexity of Soil Microbes during the Process of Dryland-to-Paddy Conversion Li, Xiaoxiao; Zhang, Qi; Ma, Jing International Journal of Environmental Research and Public Health, Vol. 17, Issue 2 https://doi.org/10.3390/ijerph17020561	journal	January 2020
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
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
Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids Purkamo, Lotta; Bomberg, Malin; Kietäväinen, Riikka Biogeosciences, Vol. 13, Issue 10 https://doi.org/10.5194/bg-13-3091-2016	journal	January 2016
Temporal Variation and Co-occurrence Patterns of Bacterial Communities in Eutrophic Lake Taihu, China Peng, Yuke; Yue, Dongmei; Xiao, Lin Taylor & Francis https://doi.org/10.6084/m9.figshare.5198548	text	January 2017
Long-term inorganic fertilizer use influences bacterial communities in Mollisols of Northeast China based on high-throughput sequencing and network analyses Yu, Zhenhua; Hu, Xiaojing; Wei, Dan Taylor & Francis https://doi.org/10.6084/m9.figshare.7546445	text	January 2019
Keystone taxa as drivers of microbiome structure and functioning Banerjee, Samiran; Schlaeppi, Klaus; Van Der Heijden, Marcel G. A. Springer Nature https://doi.org/10.7892/boris.117151	text	January 2018

Similar Records

Functional Molecular Ecological Networks

Journal Article · Tue Oct 05 00:00:00 EDT 2010 · mBio (Online) · OSTI ID:1626091

Molecular ecological network analyses

Journal Article · Sat Dec 31 23:00:00 EST 2011 · BMC Bioinformatics · OSTI ID:1626287

Functional Ecological Gene Networks to Reveal the Changes Among Microbial Interactions Under Elevated Carbon Dioxide Conditions

Technical Report · Mon May 17 00:00:00 EDT 2010 · OSTI ID:985926

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Microbiology