Metagenomic applications in environmental monitoring and bioremediation
Abstract
With the rapid advances in sequencing technology, the cost of sequencing has dramatically dropped and the scale of sequencing projects has increased accordingly. This has provided the opportunity for the routine use of sequencing techniques in the monitoring of environmental microbes. While metagenomic applications have been routinely applied to better understand the ecology and diversity of microbes, their use in environmental monitoring and bioremediation is increasingly common. In this review we seek to provide an overview of some of the metagenomic techniques used in environmental systems biology, addressing their application and limitation. We will also provide several recent examples of the application of metagenomics to bioremediation. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities.
- Authors:
-
- Michigan Technological Univ., Houghton, MI (United States)
- Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering
- Publication Date:
- Research Org.:
- Univ. of Tennessee, Knoxville, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1329773
- Alternate Identifier(s):
- OSTI ID: 1480739
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Industrial Microbiology and Biotechnology
- Additional Journal Information:
- Journal Volume: 43; Journal Issue: 10; Journal ID: ISSN 1367-5435
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; 60 APPLIED LIFE SCIENCES; Bioremediation; Metagenomics; Microbial community structure; Environmental systems biology
Citation Formats
Techtmann, Stephen M., and Hazen, Terry C. Metagenomic applications in environmental monitoring and bioremediation. United States: N. p., 2016.
Web. doi:10.1007/s10295-016-1809-8.
Techtmann, Stephen M., & Hazen, Terry C. Metagenomic applications in environmental monitoring and bioremediation. United States. https://doi.org/10.1007/s10295-016-1809-8
Techtmann, Stephen M., and Hazen, Terry C. Wed .
"Metagenomic applications in environmental monitoring and bioremediation". United States. https://doi.org/10.1007/s10295-016-1809-8. https://www.osti.gov/servlets/purl/1329773.
@article{osti_1329773,
title = {Metagenomic applications in environmental monitoring and bioremediation},
author = {Techtmann, Stephen M. and Hazen, Terry C.},
abstractNote = {With the rapid advances in sequencing technology, the cost of sequencing has dramatically dropped and the scale of sequencing projects has increased accordingly. This has provided the opportunity for the routine use of sequencing techniques in the monitoring of environmental microbes. While metagenomic applications have been routinely applied to better understand the ecology and diversity of microbes, their use in environmental monitoring and bioremediation is increasingly common. In this review we seek to provide an overview of some of the metagenomic techniques used in environmental systems biology, addressing their application and limitation. We will also provide several recent examples of the application of metagenomics to bioremediation. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities.},
doi = {10.1007/s10295-016-1809-8},
journal = {Journal of Industrial Microbiology and Biotechnology},
number = 10,
volume = 43,
place = {United States},
year = {Wed Aug 24 00:00:00 EDT 2016},
month = {Wed Aug 24 00:00:00 EDT 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 52 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Describing microbial communities and performing global comparisons in the ‘omic era
journal, June 2012
- Delmont, Tom O.; Simonet, Pascal; Vogel, Timothy M.
- The ISME Journal, Vol. 6, Issue 9
The biogeochemistry and bioremediation of uranium and other priority radionuclides
journal, January 2014
- Newsome, Laura; Morris, Katherine; Lloyd, Jonathan R.
- Chemical Geology, Vol. 363
High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment
journal, April 2012
- Handley, Kim M.; Wrighton, Kelly C.; Piceno, Yvette M.
- FEMS Microbiology Ecology, Vol. 81, Issue 1
Beyond the Venn diagram: the hunt for a core microbiome: The hunt for a core microbiome
journal, October 2011
- Shade, Ashley; Handelsman, Jo
- Environmental Microbiology, Vol. 14, Issue 1
Evaluation of Slow Release Substrates for Anaerobic Bioremediation
journal, July 2006
- Borden, Robert C.; Rodriguez, B. Ximena
- Bioremediation Journal, Vol. 10, Issue 1-2
Tracking Hydrocarbon Plume Transport and Biodegradation at Deepwater Horizon
journal, August 2010
- Camilli, Richard; Reddy, Christopher M.; Yoerger, Dana R.
- Science, Vol. 330, Issue 6001
Microbial reduction of uranium
journal, April 1991
- Lovley, Derek R.; Phillips, Elizabeth J. P.; Gorby, Yuri A.
- Nature, Vol. 350, Issue 6317
Microbial Responses to the Deepwater Horizon Oil Spill: From Coastal Wetlands to the Deep Sea
journal, January 2015
- King, G. M.; Kostka, J. E.; Hazen, T. C.
- Annual Review of Marine Science, Vol. 7, Issue 1
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
Cleaning up with genomics: applying molecular biology to bioremediation
journal, October 2003
- Lovley, Derek R.
- Nature Reviews Microbiology, Vol. 1, Issue 1
Field-Scale Demonstration of Enhanced MTBE Bioremediation through Aquifer Bioaugmentation and Oxygenation
journal, October 2000
- Salanitro, Joseph P.; Johnson, Paul C.; Spinnler, Gerard E.
- Environmental Science & Technology, Vol. 34, Issue 19
Postbiostimulation microbial community structure changes that control the reoxidation of uranium: Postbiostimulation microbial community structure
journal, September 2010
- N'Guessan, Adeola Lucie; Moon, Hee Sun; Peacock, Aaron D.
- FEMS Microbiology Ecology, Vol. 74, Issue 1
Phase Preference by Active, Acetate-Utilizing Bacteria at the Rifle, CO Integrated Field Research Challenge Site
journal, February 2011
- Kerkhof, Lee J.; Williams, Ken H.; Long, Philip E.
- Environmental Science & Technology, Vol. 45, Issue 4
Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization
journal, January 2014
- Lancaster, W. Andrew; Menon, Angeli Lal; Scott, Israel
- Metallomics, Vol. 6, Issue 5
Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles
journal, December 2010
- Callister, Stephen J.; Wilkins, Michael J.; Nicora, Carrie D.
- Environmental Science & Technology, Vol. 44, Issue 23
Evidence for multiple modes of uranium immobilization by an anaerobic bacterium
journal, May 2011
- Ray, Allison E.; Bargar, John R.; Sivaswamy, Vaideeswaran
- Geochimica et Cosmochimica Acta, Vol. 75, Issue 10
Ecosystem processes and interactions in a morass of diversity
journal, July 2012
- Prosser, James I.
- FEMS Microbiology Ecology, Vol. 81, Issue 3
Nitrate removal using Brevundimonas diminuta MTCC 8486 from ground water
journal, July 2009
- Kavitha, S.; Selvakumar, R.; Sathishkumar, M.
- Water Science and Technology, Vol. 60, Issue 2
Enhanced Reductive Dechlorination of Polychlorinated Biphenyl Impacted Sediment by Bioaugmentation with a Dehalorespiring Bacterium
journal, October 2011
- Payne, Rayford B.; May, Harold D.; Sowers, Kevin R.
- Environmental Science & Technology, Vol. 45, Issue 20
Phylogenetic and Functional Biomakers as Indicators of Bacterial Community Responses to Mixed-Waste Contamination
journal, April 2006
- Fields, M. W.; Bagwell, C. E.; Carroll, S. L.
- Environmental Science & Technology, Vol. 40, Issue 8
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities: Metagenomic and rRNA diversity characterization
journal, February 2013
- Shakya, Migun; Quince, Christopher; Campbell, James H.
- Environmental Microbiology, Vol. 15, Issue 6
Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community
journal, February 2010
- Hemme, Christopher L.; Deng, Ye; Gentry, Terry J.
- The ISME Journal, Vol. 4, Issue 5
In Situ Bioreduction of Technetium and Uranium in a Nitrate-Contaminated Aquifer
journal, January 2004
- Istok, J. D.; Senko, J. M.; Krumholz, L. R.
- Environmental Science & Technology, Vol. 38, Issue 2
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
journal, August 2012
- Klindworth, Anna; Pruesse, Elmar; Schweer, Timmy
- Nucleic Acids Research, Vol. 41, Issue 1
Microbial Incorporation of 13 C-Labeled Acetate at the Field Scale: Detection of Microbes Responsible for Reduction of U(VI)
journal, December 2005
- Chang, Yun-Juan; Long, Philip E.; Geyer, Roland
- Environmental Science & Technology, Vol. 39, Issue 23
Composition and fate of gas and oil released to the water column during the Deepwater Horizon oil spill
journal, July 2011
- Reddy, C. M.; Arey, J. S.; Seewald, J. S.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 50
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
Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors
journal, May 2015
- Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.
- mBio, Vol. 6, Issue 3
Acetate Availability and its Influence on Sustainable Bioremediation of Uranium-Contaminated Groundwater
journal, June 2011
- Williams, Kenneth H.; Long, Philip E.; Davis, James A.
- Geomicrobiology Journal, Vol. 28, Issue 5-6
Functional Gene Array-Based Analysis of Microbial Community Structure in Groundwaters with a Gradient of Contaminant Levels
journal, May 2009
- Waldron, Patricia J.; Wu, Liyou; Nostrand, Joy D. Van
- Environmental Science & Technology, Vol. 43, Issue 10
Metagenomics meets time series analysis: unraveling microbial community dynamics
journal, June 2015
- Faust, Karoline; Lahti, Leo; Gonze, Didier
- Current Opinion in Microbiology, Vol. 25
Monitoring Microbial Community Structure and Dynamics during in situ U(VI) Bioremediation with a Field-Portable Microarray Analysis System
journal, July 2010
- Chandler, Darrell P.; Kukhtin, Alexander; Mokhiber, Rebecca
- Environmental Science & Technology, Vol. 44, Issue 14
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies
journal, October 2015
- Parada, Alma E.; Needham, David M.; Fuhrman, Jed A.
- Environmental Microbiology, Vol. 18, Issue 5
Magnitude of the 2010 Gulf of Mexico Oil Leak
journal, September 2010
- Crone, Timothy J.; Tolstoy, Maya
- Science, Vol. 330, Issue 6004
Genomes from Metagenomics
journal, November 2013
- Sharon, I.; Banfield, J. F.
- Science, Vol. 342, Issue 6162
Succession of Hydrocarbon-Degrading Bacteria in the Aftermath of the Deepwater Horizon Oil Spill in the Gulf of Mexico
journal, September 2013
- Dubinsky, Eric A.; Conrad, Mark E.; Chakraborty, Romy
- Environmental Science & Technology, Vol. 47, Issue 19
In situ mobility of uranium in the presence of nitrate following sulfate-reducing conditions
journal, April 2016
- Paradis, Charles J.; Jagadamma, Sindhu; Watson, David B.
- Journal of Contaminant Hydrology, Vol. 187
Systems biology approach to bioremediation
journal, June 2012
- Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.
- Current Opinion in Biotechnology, Vol. 23, Issue 3
Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota
journal, May 2015
- Xiong, Weili; Abraham, Paul E.; Li, Zhou
- PROTEOMICS, Vol. 15, Issue 20
Disturbance and temporal partitioning of the activated sludge metacommunity
journal, August 2014
- Vuono, David C.; Benecke, Jan; Henkel, Jochen
- The ISME Journal, Vol. 9, Issue 2
16S rRNA Gene Microarray Analysis of Microbial Communities in Ethanol-Stimulated Subsurface Sediment
journal, January 2011
- Mohanty, Santosh R.; Kollah, Bharati; Brodie, Eoin L.
- Microbes and Environments, Vol. 26, Issue 3
Marine Oil Biodegradation
journal, February 2016
- Hazen, Terry C.; Prince, Roger C.; Mahmoudi, Nagissa
- Environmental Science & Technology, Vol. 50, Issue 5
GroopM: an automated tool for the recovery of population genomes from related metagenomes
journal, January 2014
- Imelfort, Michael; Parks, Donovan; Woodcroft, Ben J.
- PeerJ, Vol. 2
A unified initiative to harness Earth's microbiomes
journal, October 2015
- Alivisatos, A. P.; Blaser, M. J.; Brodie, E. L.
- Science, Vol. 350, Issue 6260
Metaproteomics : Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities
journal, March 2013
- Hettich, Robert L.; Pan, Chongle; Chourey, Karuna
- Analytical Chemistry, Vol. 85, Issue 9
StressChip as a High-Throughput Tool for Assessing Microbial Community Responses to Environmental Stresses
journal, August 2013
- Zhou, Aifen; He, Zhili; Qin, Yujia
- Environmental Science & Technology, Vol. 47, Issue 17
Sizing up metatranscriptomics
journal, August 2012
- Moran, Mary Ann; Satinsky, Brandon; Gifford, Scott M.
- The ISME Journal, Vol. 7, Issue 2
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
journal, January 2014
- Mason, Olivia U.; Scott, Nicole M.; Gonzalez, Antonio
- The ISME Journal, Vol. 8, Issue 7
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes
journal, October 2015
- Hemme, Christopher L.; Tu, Qichao; Shi, Zhou
- Frontiers in Microbiology, Vol. 6
Advances in monitoring environmental microbes
journal, June 2013
- Hazen, Terry C.; Rocha, Andrea M.; Techtmann, Stephen M.
- Current Opinion in Biotechnology, Vol. 24, Issue 3
Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria
journal, August 2010
- Hazen, Terry C.; Dubinsky, Eric A.; DeSantis, Todd Z.
- Science, Vol. 330, Issue 6001
Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013
- Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
- Nature, Vol. 499, Issue 7459
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
Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site
journal, December 2011
- Green, Stefan J.; Prakash, Om; Jasrotia, Puja
- Applied and Environmental Microbiology, Vol. 78, Issue 4
Oil Biodegradation and Bioremediation: A Tale of the Two Worst Spills in U.S. History
journal, August 2011
- Atlas, Ronald M.; Hazen, Terry C.
- Environmental Science & Technology, Vol. 45, Issue 16, p. 6709-6715
Marine microorganisms make a meal of oil
journal, March 2006
- Head, Ian M.; Jones, D. Martin; Röling, Wilfred F. M.
- Nature Reviews Microbiology, Vol. 4, Issue 3
Obligate oil-degrading marine bacteria
journal, June 2007
- Yakimov, Michail M.; Timmis, Kenneth N.; Golyshin, Peter N.
- Current Opinion in Biotechnology, Vol. 18, Issue 3
Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill
journal, October 2011
- Redmond, M. C.; Valentine, D. L.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 50
Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP
journal, June 2013
- Gutierrez, Tony; Singleton, David R.; Berry, David
- The ISME Journal, Vol. 7, Issue 11
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
journal, June 2012
- Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon
- The ISME Journal, Vol. 6, Issue 9
Health effects of uranium: new research findings
journal, January 2011
- Brugge, Doug; Buchner, Virginia
- Reviews on Environmental Health, Vol. 26, Issue 4
Stimulating the In Situ Activity of Geobacter Species To Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer
journal, October 2003
- Anderson, R. T.; Vrionis, H. A.; Ortiz-Bernad, I.
- Applied and Environmental Microbiology, Vol. 69, Issue 10
Molecular Analysis of the In Situ Growth Rates of Subsurface Geobacter Species
journal, December 2012
- Holmes, Dawn E.; Giloteaux, Ludovic; Barlett, Melissa
- Applied and Environmental Microbiology, Vol. 79, Issue 5
Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation
journal, August 2009
- Wilkins, M. J.; VerBerkmoes, N. C.; Williams, K. H.
- Applied and Environmental Microbiology, Vol. 75, Issue 20
Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during In Situ Uranium Reduction
journal, February 2012
- Liang, Yuting; Van Nostrand, Joy D.; N′Guessan, Lucie A.
- Applied and Environmental Microbiology, Vol. 78, Issue 8
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
Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach
journal, August 2010
- Cardenas, E.; Wu, W. -M.; Leigh, M. B.
- Applied and Environmental Microbiology, Vol. 76, Issue 20
Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology
journal, September 2014
- Brown, S. D.; Utturkar, S. M.; Magnuson, T. S.
- Genome Announcements, Vol. 2, Issue 5
Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP
text, January 2013
- David, Berry,; D., Aitken, Michael; Tony, Gutierrez,
- The University of North Carolina at Chapel Hill University Libraries
Works referencing / citing this record:
Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation
journal, August 2019
- Júlio, Aline Daniela Lopes; de Cássia Mourão Silva, Ubiana; Medeiros, Julliane Dutra
- Scientific Reports, Vol. 9, Issue 1
Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches
journal, June 2018
- Malla, Muneer A.; Dubey, Anamika; Yadav, Shweta
- Frontiers in Microbiology, Vol. 9
Microbial Community Dynamics During Lake Ice Freezing
journal, April 2019
- Butler, Timothy M.; Wilhelm, Anna-Catharina; Dwyer, Amber C.
- Scientific Reports, Vol. 9, Issue 1
Anaerobic Biodegradation of Hydrocarbons: Metagenomics and Metabolomics
book, January 2016
- Gieg, Lisa M.; Toth, Courtney R. A.
- Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation
A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining
journal, February 2019
- Gastauer, Markus; Vera, Mabel Patricia Ortiz; de Souza, Kleber Padovani
- Scientific Data, Vol. 6, Issue 1
Anaerobic Biodegradation of Hydrocarbons: Metagenomics and Metabolomics
book, January 2019
- Gieg, Lisa M.; Toth, Courtney R. A.
- Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation
Microbial Community Dynamics During Lake Ice Freezing
journal, April 2019
- Butler, Timothy M.; Wilhelm, Anna-Catharina; Dwyer, Amber C.
- Scientific Reports, Vol. 9, Issue 1
Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation
journal, August 2019
- Júlio, Aline Daniela Lopes; de Cássia Mourão Silva, Ubiana; Medeiros, Julliane Dutra
- Scientific Reports, Vol. 9, Issue 1
A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining
journal, February 2019
- Gastauer, Markus; Vera, Mabel Patricia Ortiz; de Souza, Kleber Padovani
- Scientific Data, Vol. 6, Issue 1
Water quality assessments and metagenomic analysis of the polluted river Apatlaco, Mexico
journal, January 2019
- Breton-Deval, Luz; Juárez, Katy; Sánchez-Flores, Alejandro
- bioRxiv
One step towards bioremediating a heavily polluted river: Metagenomic insights on the function of microbial community
journal, June 2019
- Breton-Deval, Luz; Sanchez-Reyes, Ayixon; Sánchez-Flores, Alejandro
- bioRxiv
A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill
journal, March 2018
- Zhang, Shuangfei; Hu, Zhong; Wang, Hui
- Frontiers in Microbiology, Vol. 9
Unconventional Oil and Gas Energy Systems: An Unidentified Hotspot of Antimicrobial Resistance?
journal, October 2019
- Campa, Maria Fernanda; Wolfe, Amy K.; Techtmann, Stephen M.
- Frontiers in Microbiology, Vol. 10
Concepts and Methods to Access Novel Antibiotics from Actinomycetes
journal, May 2018
- Hug, Joachim; Bader, Chantal; Remškar, Maja
- Antibiotics, Vol. 7, Issue 2