skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation: Competition in bioremediation system

Abstract

When trying to discern network interactions among different species/populations in microbial communities interests have been evoked in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. We modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the network interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140–269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. In particular, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations.

Authors:
 [1];  [2];  [2];  [2];  [3];  [2];  [4];  [5]
  1. Chinese Academy of Sciences (CAS), Beijing (China). CAS Key Lab. of Environmental Biotechnology; Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics and Dept. of Microbiology and Plant Biology
  2. Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics and Dept. of Microbiology and Plant Biology
  3. Tsinghua Univ., Beijing (China). State Key Joint Lab. of Environment Simulation and Pollution Control
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioSciences Division
  5. Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics and Dept. of Microbiology and Plant Biology; Tsinghua Univ., Beijing (China). State Key Joint Lab. of Environment Simulation and Pollution Control; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1325419
Grant/Contract Number:  
AC05-00OR22725; FG02-07ER64398; AC02-05CH11231; SC0004613
Resource Type:
Accepted Manuscript
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Deng, Ye, Zhang, Ping, Qin, Yujia, Tu, Qichao, Yang, Yunfeng, He, Zhili, Schadt, Christopher Warren, and Zhou, Jizhong. Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation: Competition in bioremediation system. United States: N. p., 2015. Web. doi:10.1111/1462-2920.12981.
Deng, Ye, Zhang, Ping, Qin, Yujia, Tu, Qichao, Yang, Yunfeng, He, Zhili, Schadt, Christopher Warren, & Zhou, Jizhong. Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation: Competition in bioremediation system. United States. doi:10.1111/1462-2920.12981.
Deng, Ye, Zhang, Ping, Qin, Yujia, Tu, Qichao, Yang, Yunfeng, He, Zhili, Schadt, Christopher Warren, and Zhou, Jizhong. Tue . "Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation: Competition in bioremediation system". United States. doi:10.1111/1462-2920.12981. https://www.osti.gov/servlets/purl/1325419.
@article{osti_1325419,
title = {Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation: Competition in bioremediation system},
author = {Deng, Ye and Zhang, Ping and Qin, Yujia and Tu, Qichao and Yang, Yunfeng and He, Zhili and Schadt, Christopher Warren and Zhou, Jizhong},
abstractNote = {When trying to discern network interactions among different species/populations in microbial communities interests have been evoked in recent years, but little information is available about temporal dynamics of microbial network interactions in response to environmental perturbations. We modified the random matrix theory-based network approach to discern network succession in groundwater microbial communities in response to emulsified vegetable oil (EVO) amendment for uranium bioremediation. Groundwater microbial communities from one control and seven monitor wells were analysed with a functional gene array (GeoChip 3.0), and functional molecular ecological networks (fMENs) at different time points were reconstructed. Our results showed that the network interactions were dramatically altered by EVO amendment. Dynamic and resilient succession was evident: fairly simple at the initial stage (Day 0), increasingly complex at the middle period (Days 4, 17, 31), most complex at Day 80, and then decreasingly complex at a later stage (140–269 days). Unlike previous studies in other habitats, negative interactions predominated in a time-series fMEN, suggesting strong competition among different microbial species in the groundwater systems after EVO injection. In particular, several keystone sulfate-reducing bacteria showed strong negative interactions with their network neighbours. These results provide mechanistic understanding of the decreased phylogenetic diversity during environmental perturbations.},
doi = {10.1111/1462-2920.12981},
journal = {Environmental Microbiology},
number = 1,
volume = 18,
place = {United States},
year = {2015},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 18 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Microbial diversity and the genetic nature of microbial species
journal, May 2008

  • Achtman, Mark; Wagner, Michael
  • Nature Reviews Microbiology, Vol. 6, Issue 6
  • DOI: 10.1038/nrmicro1872

Stimulating the In Situ Activity of Geobacter Species To Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer
journal, October 2003


Network biology: understanding the cell's functional organization
journal, February 2004

  • Barabási, Albert-László; Oltvai, Zoltán N.
  • Nature Reviews Genetics, Vol. 5, Issue 2
  • DOI: 10.1038/nrg1272

Networks in ecology
journal, November 2007


Plant-Animal Mutualistic Networks: The Architecture of Biodiversity
journal, December 2007


Microbial community responses to anthropogenically induced environmental change: towards a systems approach
journal, May 2013

  • Bissett, Andrew; Brown, Mark V.; Siciliano, Steven D.
  • Ecology Letters, Vol. 16
  • DOI: 10.1111/ele.12109

Microbial Communities in Contaminated Sediments, Associated with Bioremediation of Uranium to Submicromolar Levels
journal, May 2008

  • Cardenas, E.; Wu, W. -M.; Leigh, M. B.
  • Applied and Environmental Microbiology, Vol. 74, Issue 12
  • DOI: 10.1128/AEM.02308-07

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists
journal, November 2013

  • Chow, Cheryl-Emiliane T.; Kim, Diane Y.; Sachdeva, Rohan
  • The ISME Journal, Vol. 8, Issue 4
  • DOI: 10.1038/ismej.2013.199

The microbial ocean from genomes to biomes
journal, May 2009


Molecular ecological network analyses
journal, January 2012


Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities
journal, February 2012

  • Deng, Ye; He, Zhili; Xu, Meiying
  • Applied and Environmental Microbiology, Vol. 78, Issue 8
  • DOI: 10.1128/AEM.06924-11

Understanding network concepts in modules
journal, June 2007


Microbial interactions: from networks to models
journal, July 2012

  • Faust, Karoline; Raes, Jeroen
  • Nature Reviews Microbiology, Vol. 10, Issue 8
  • DOI: 10.1038/nrmicro2832

Microbial Co-occurrence Relationships in the Human Microbiome
journal, July 2012


Inferring Correlation Networks from Genomic Survey Data
journal, September 2012


Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
journal, November 2001

  • Ge, Hui; Liu, Zhihua; Church, George M.
  • Nature Genetics, Vol. 29, Issue 4
  • DOI: 10.1038/ng776

A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer
journal, July 2011

  • Gihring, Thomas M.; Zhang, Gengxin; Brandt, Craig C.
  • Applied and Environmental Microbiology, Vol. 77, Issue 17
  • DOI: 10.1128/AEM.00220-11

Energetics and Topology of CzcA, a Cation/Proton Antiporter of the Resistance-Nodulation-Cell Division Protein Family
journal, September 1999

  • Goldberg, Martina; Pribyl, Thomas; Juhnke, Susanne
  • Journal of Biological Chemistry, Vol. 274, Issue 37
  • DOI: 10.1074/jbc.274.37.26065

Cartography of complex networks: modules and universal roles
journal, February 2005


GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
journal, May 2007

  • He, Zhili; Gentry, Terry J.; Schadt, Christopher W.
  • The ISME Journal, Vol. 1, Issue 1
  • DOI: 10.1038/ismej.2007.2

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity
journal, April 2010


Geometric Interpretation of Gene Coexpression Network Analysis
journal, August 2008


Making sense of microarray data distributions
journal, April 2002


Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths
journal, September 2008

  • Hwang, Chiachi; Wu, Weimin; Gentry, Terry J.
  • The ISME Journal, Vol. 3, Issue 1
  • DOI: 10.1038/ismej.2008.77

Sparse and Compositionally Robust Inference of Microbial Ecological Networks
journal, May 2015

  • Kurtz, Zachary D.; Müller, Christian L.; Miraldi, Emily R.
  • PLOS Computational Biology, Vol. 11, Issue 5
  • DOI: 10.1371/journal.pcbi.1004226

Eigengene networks for studying the relationships between co-expression modules
journal, November 2007


Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients
journal, March 2014


Biodiversity and Ecosystem Functioning: Current Knowledge and Future Challenges
journal, October 2001


Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory
journal, January 2007


Ecological networks and their fragility
journal, July 2006

  • Montoya, José M.; Pimm, Stuart L.; Solé, Ricard V.
  • Nature, Vol. 442, Issue 7100
  • DOI: 10.1038/nature04927

Metagenomics and the global ocean survey: what's in it for us, and why should we care?
journal, June 2007


Functional organization of the transcriptome in human brain
journal, October 2008

  • Oldham, Michael C.; Konopka, Genevieve; Iwamoto, Kazuya
  • Nature Neuroscience, Vol. 11, Issue 11
  • DOI: 10.1038/nn.2207

The modularity of pollination networks
journal, December 2007

  • Olesen, J. M.; Bascompte, J.; Dupont, Y. L.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 50
  • DOI: 10.1073/pnas.0706375104

Predation on prokaryotes in the water column and its ecological implications
journal, June 2005


Detecting Novel Associations in Large Data Sets
journal, December 2011


Dominant species maintain ecosystem function with non-random species loss
journal, June 2003


CPx-type ATPases: a class of P-type ATPases that pump heavy metals
journal, July 1996


Complete Genome Sequence of Nitrobacter hamburgensis X14 and Comparative Genomic Analysis of Species within the Genus Nitrobacter
journal, March 2008

  • Starkenburg, S. R.; Larimer, F. W.; Stein, L. Y.
  • Applied and Environmental Microbiology, Vol. 74, Issue 9
  • DOI: 10.1128/AEM.02311-07

Marine bacterial, archaeal and protistan association networks reveal ecological linkages
journal, March 2011

  • Steele, Joshua A.; Countway, Peter D.; Xia, Li
  • The ISME Journal, Vol. 5, Issue 9
  • DOI: 10.1038/ismej.2011.24

U(VI) Bioreduction with Emulsified Vegetable Oil as the Electron Donor – Model Application to a Field Test
journal, March 2013

  • Tang, Guoping; Watson, David B.; Wu, Wei-Min
  • Environmental Science & Technology, Vol. 47, Issue 7
  • DOI: 10.1021/es304643h

ATP-dependent cadmium transport by the cadA cadmium resistance determinant in everted membrane vesicles of Bacillus subtilis.
journal, January 1992


Collective dynamics of ‘small-world’ networks
journal, June 1998

  • Watts, Duncan J.; Strogatz, Steven H.
  • Nature, Vol. 393, Issue 6684
  • DOI: 10.1038/30918

Acetate Availability and its Influence on Sustainable Bioremediation of Uranium-Contaminated Groundwater
journal, June 2011


Pilot-Scale in Situ Bioremediation of Uranium in a Highly Contaminated Aquifer. 1. Conditioning of a Treatment Zone
journal, June 2006

  • Wu, Wei-Min; Carley, Jack; Fienen, Michael
  • Environmental Science & Technology, Vol. 40, Issue 12
  • DOI: 10.1021/es051954y

Pilot-Scale in Situ Bioremedation of Uranium in a Highly Contaminated Aquifer. 2. Reduction of U(VI) and Geochemical Control of U(VI) Bioavailability
journal, June 2006

  • Wu, Wei-Min; Carley, Jack; Gentry, Terry
  • Environmental Science & Technology, Vol. 40, Issue 12
  • DOI: 10.1021/es051960u

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
journal, January 2011


Efficient statistical significance approximation for local similarity analysis of high-throughput time series data
journal, November 2012


Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction
journal, April 2015

  • Zhang, Ping; Wu, Wei-Min; Van Nostrand, Joy D.
  • Applied and Environmental Microbiology, Vol. 81, Issue 12
  • DOI: 10.1128/AEM.00043-15

Spatial scaling of functional gene diversity across various microbial taxa
journal, May 2008

  • Zhou, J.; Kang, S.; Schadt, C. W.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 22
  • DOI: 10.1073/pnas.0709016105

Functional Molecular Ecological Networks
journal, October 2010


Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2
journal, July 2011


Microbial mediation of carbon-cycle feedbacks to climate warming
journal, December 2011

  • Zhou, Jizhong; Xue, Kai; Xie, Jianping
  • Nature Climate Change, Vol. 2, Issue 2
  • DOI: 10.1038/nclimate1331

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem
journal, February 2014

  • Zhou, Jizhong; Deng, Ye; Zhang, Ping
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 9
  • DOI: 10.1073/pnas.1324044111

High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats
journal, January 2015


    Works referencing / citing this record:

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


    Integrated network analysis reveals the importance of microbial interactions for maize growth
    journal, March 2018

    • Tao, Jiemeng; Meng, Delong; Qin, Chong
    • Applied Microbiology and Biotechnology, Vol. 102, Issue 8
    • DOI: 10.1007/s00253-018-8837-4

    Responses of phyllosphere microbiota and plant health to application of two different biocontrol agents
    journal, March 2019