The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; Hammack, Richard W.; Gregory, Kelvin B.; Forster, Robert J.

doi:10.1371/journal.pone.0107682

Title: The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

Journal Article · Wed Oct 22 00:00:00 EDT 2014 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0107682· OSTI ID:1168804

Mohan, Arvind Murali ^[1]; Bibby, Kyle J. ^[2]; Lipus, Daniel ^[2]; Hammack, Richard W. ^[3]; Gregory, Kelvin B. ^[1]; Forster, Robert J. ^[4]

National Energy Technology Lab., Pittsburgh, PA (United States); Carnegie Mellon Univ., Pittsburgh, PA (United States)
National Energy Technology Lab., Pittsburgh, PA (United States); Univ. of Pittsburgh, Pittsburgh, PA (United States)
National Energy Technology Lab., Pittsburgh, PA (United States)
Agriculture and Agri-Food Canada (Canada)

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. Thus, the metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: National Energy Technology Laboratory (NETL), Pittsburgh, PA, Morgantown, WV (United States)

Sponsoring Organization:: USDOE Office of Fossil Energy (FE)

OSTI ID:: 1168804

Report Number(s):: NETL-PUB-1113

Journal Information:: PLoS ONE, Vol. 9, Issue 10; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 36 works

Citation information provided by
Web of Science

References (40)

Spatial and Temporal Correlation of Water Quality Parameters of Produced Waters from Devonian-Age Shale following Hydraulic Fracturing Barbot, Elise; Vidic, Natasa S.; Gregory, Kelvin B. Environmental Science & Technology, Vol. 47, Issue 6 https://doi.org/10.1021/es304638h	journal	February 2013
BLAT---The BLAST-Like Alignment Tool Kent, W. J. Genome Research, Vol. 12, Issue 4 https://doi.org/10.1101/gr.229202	journal	March 2002
The Impact of Corrosion on Oil and Gas Industry Kermani, M. B.; Harrop, D. SPE Production & Facilities, Vol. 11, Issue 03 https://doi.org/10.2118/29784-PA	journal	August 1996
Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome Urich, Tim; Lanzén, Anders; Qi, Ji PLoS ONE, Vol. 3, Issue 6 https://doi.org/10.1371/journal.pone.0002527	journal	June 2008
Bacterial Communities Associated with Production Facilities of Two Newly Drilled Thermogenic Natural Gas Wells in the Barnett Shale (Texas, USA) Davis, James P.; Struchtemeyer, Christopher G.; Elshahed, Mostafa S. Microbial Ecology, Vol. 64, Issue 4 https://doi.org/10.1007/s00248-012-0073-3	journal	May 2012
Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas Murali Mohan, Arvind; Hartsock, Angela; Hammack, Richard W. FEMS Microbiology Ecology, Vol. 86, Issue 3 https://doi.org/10.1111/1574-6941.12183	journal	August 2013
Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common An, Dongshan; Caffrey, Sean M.; Soh, Jung Environmental Science & Technology, Vol. 47, Issue 18 https://doi.org/10.1021/es4020184	journal	September 2013
The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses Yergeau, Etienne; Hogues, Hervé; Whyte, Lyle G. The ISME Journal, Vol. 4, Issue 9 https://doi.org/10.1038/ismej.2010.41	journal	April 2010
Bioenergetics of marine bacteria Kogure, Kazuhiro Current Opinion in Biotechnology, Vol. 9, Issue 3 https://doi.org/10.1016/S0958-1669(98)80059-1	journal	June 1998
Water Management Challenges Associated with the Production of Shale Gas by Hydraulic Fracturing Gregory, K. B.; Vidic, R. D.; Dzombak, D. A. Elements, Vol. 7, Issue 3 https://doi.org/10.2113/gselements.7.3.181	journal	June 2011
Metagenomic analysis of the microbial community associated with the coral Porites astreoides Wegley, Linda; Edwards, Robert; Rodriguez-Brito, Beltran Environmental Microbiology, Vol. 9, Issue 11 https://doi.org/10.1111/j.1462-2920.2007.01383.x	journal	November 2007
Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge Yu, Ke; Zhang, Tong PLoS ONE, Vol. 7, Issue 5 https://doi.org/10.1371/journal.pone.0038183	journal	May 2012
I will survive: protecting and repairing spore DNA. Setlow, P. Journal of Bacteriology, Vol. 174, Issue 9 https://doi.org/10.1128/jb.174.9.2737-2741.1992	journal	May 1992
Microbial Iron Acquisition: Marine and Terrestrial Siderophores Sandy, Moriah; Butler, Alison Chemical Reviews, Vol. 109, Issue 10 https://doi.org/10.1021/cr9002787	journal	October 2009
Order and Disorder during Escherichia coli Divergence Hendrickson, Heather PLoS Genetics, Vol. 5, Issue 1 https://doi.org/10.1371/journal.pgen.1000335	journal	January 2009
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models Brady, Arthur; Salzberg, Steven L. Nature Methods, Vol. 6, Issue 9 https://doi.org/10.1038/nmeth.1358	journal	August 2009
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Goecks, Jeremy; Nekrutenko, Anton; Taylor, James Genome Biology, Vol. 11, Issue 8 https://doi.org/10.1186/gb-2010-11-8-r86	journal	January 2010
H alomonas sulfidaeris -dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir : Microbial community inhabits 1.8 km-deep Sandstone Dong, Yiran; Kumar, Charu Gupta; Chia, Nicholas Environmental Microbiology, Vol. 16, Issue 6 https://doi.org/10.1111/1462-2920.12325	journal	December 2013
Functional metagenomic profiling of nine biomes Dinsdale, Elizabeth A.; Edwards, Robert A.; Hall, Dana Nature, Vol. 452, Issue 7187 https://doi.org/10.1038/nature06810	journal	March 2008
A critical assessment of the efficacy of biocides used during the hydraulic fracturing process in shale natural gas wells Struchtemeyer, Christopher G.; Morrison, Michael D.; Elshahed, Mostafa S. International Biodeterioration & Biodegradation, Vol. 71 https://doi.org/10.1016/j.ibiod.2012.01.013	journal	July 2012
Microbial diversity in production waters of a low-temperature biodegraded oil reservoir Grabowski, A.; Nercessian, O.; Fayolle, F. FEMS Microbiology Ecology, Vol. 54, Issue 3 https://doi.org/10.1016/j.femsec.2005.05.007	journal	November 2005
Microbial diversity of an oil-water processing site and its associated oil field: the possible role of microorganisms as information carriers from oil-associated environments van der Kraan, Geert M.; Bruining, Johannes; Lomans, Bart P. FEMS Microbiology Ecology, Vol. 71, Issue 3 https://doi.org/10.1111/j.1574-6941.2009.00813.x	journal	March 2010
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets Schmieder, Robert; Lim, Yan Wei; Rohwer, Forest BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-341	journal	June 2010
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes Overbeek, R. Nucleic Acids Research, Vol. 33, Issue 17 https://doi.org/10.1093/nar/gki866	journal	September 2005
Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean Shi, Yanmei; Tyson, Gene W.; Eppley, John M. The ISME Journal, Vol. 5, Issue 6 https://doi.org/10.1038/ismej.2010.189	journal	December 2010
Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods Pham, Vinh D.; Hnatow, Linda L.; Zhang, Shiping Environmental Microbiology, Vol. 11, Issue 1 https://doi.org/10.1111/j.1462-2920.2008.01751.x	journal	January 2009
Bacterial communities associated with hydraulic fracturing fluids in thermogenic natural gas wells in North Central Texas, USA Struchtemeyer, Christopher G.; Elshahed, Mostafa S. FEMS Microbiology Ecology, Vol. 81, Issue 1 https://doi.org/10.1111/j.1574-6941.2011.01196.x	journal	November 2011
Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior DeLong, E. F. Science, Vol. 311, Issue 5760 https://doi.org/10.1126/science.1120250	journal	January 2006
Comparative fecal metagenomics unveils unique functional capacity of the swine gut Lamendella, Regina; Santo Domingo, Jorge W.; Ghosh, Shreya BMC Microbiology, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2180-11-103	journal	January 2011
Microbial Community Changes in Hydraulic Fracturing Fluids and Produced Water from Shale Gas Extraction Murali Mohan, Arvind; Hartsock, Angela; Bibby, Kyle J. Environmental Science & Technology, Vol. 47, Issue 22 https://doi.org/10.1021/es402928b	journal	October 2013
Galaxy: A platform for interactive large-scale genome analysis Giardine, B. Genome Research, Vol. 15, Issue 10 https://doi.org/10.1101/gr.4086505	journal	September 2005
Structure, fluctuation and magnitude of a natural grassland soil metagenome Delmont, Tom O.; Prestat, Emmanuel; Keegan, Kevin P. The ISME Journal, Vol. 6, Issue 9 https://doi.org/10.1038/ismej.2011.197	journal	February 2012
Microbial community structure analysis of produced water from a high-temperature North Sea oil-field Dahle, Håkon; Garshol, Frøydis; Madsen, Marit Antonie van Leeuwenhoek, Vol. 93, Issue 1-2 https://doi.org/10.1007/s10482-007-9177-z	journal	June 2007
Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities Gilbert, Jack A.; Field, Dawn; Huang, Ying PLoS ONE, Vol. 3, Issue 8 https://doi.org/10.1371/journal.pone.0003042	journal	August 2008
Molecular biomarkers of oxidative stress in aquatic organisms in relation to toxic environmental pollutants Valavanidis, Athanasios; Vlahogianni, Thomais; Dassenakis, Manos Ecotoxicology and Environmental Safety, Vol. 64, Issue 2 https://doi.org/10.1016/j.ecoenv.2005.03.013	journal	June 2006
Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies Zerbino, Daniel R. Current Protocols in Bioinformatics, Vol. 31, Issue 1 https://doi.org/10.1002/0471250953.bi1105s31	journal	September 2010
Metagenomics: DNA sequencing of environmental samples Tringe, Susannah Green; Rubin, Edward M. Nature Reviews Genetics, Vol. 6, Issue 11 https://doi.org/10.1038/nrg1709	journal	October 2005
Selenoproteins Lu, Jun; Holmgren, Arne Journal of Biological Chemistry, Vol. 284, Issue 2 https://doi.org/10.1074/jbc.r800045200	journal	August 2008
Prokaryotic Community Structure and Sulfate Reducer Activity in Water from High-Temperature Oil Reservoirs with and without Nitrate Treatment Gittel, A.; Sorensen, K. B.; Skovhus, T. L. Applied and Environmental Microbiology, Vol. 75, Issue 22 https://doi.org/10.1128/aem.01123-09	journal	October 2009
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes Meyer, F.; Paarmann, D.; D'Souza, M. BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-386	journal	September 2008

Cited By (10)

Oil and Gas Produced Water, High‐Salinity Brines, and Associated Cost Modeling Sullivan Graham, Enid J. Encyclopedia of Water: Science, Technology, and Society https://doi.org/10.1002/9781119300762.wsts0041	book	January 2019
Anaerobic Biodegradation of Hydrocarbons: Metagenomics and Metabolomics Gieg, Lisa M.; Toth, Courtney R. A. Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation https://doi.org/10.1007/978-3-319-44535-9_16-1	book	January 2016
Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale Vikram, Amit; Lipus, Daniel; Bibby, Kyle Microbial Ecology, Vol. 72, Issue 3 https://doi.org/10.1007/s00248-016-0811-z	journal	July 2016
Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales Daly, Rebecca A.; Borton, Mikayla A.; Wilkins, Michael J. Nature Microbiology, Vol. 1, Issue 10 https://doi.org/10.1038/nmicrobiol.2016.146	journal	September 2016
Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales Borton, Mikayla A.; Hoyt, David W.; Roux, Simon Proceedings of the National Academy of Sciences, Vol. 115, Issue 28 https://doi.org/10.1073/pnas.1800155115	journal	June 2018
Microbial communities in Bakken region produced water Lipus, Daniel; Roy, Dhritikshama; Khan, Eakalak FEMS Microbiology Letters, Vol. 365, Issue 12 https://doi.org/10.1093/femsle/fny107	journal	April 2018
Draft Genome Sequences of Marinobacter Strains Recovered from Utica Shale-Produced Fluids Tummings, Shantal; Panescu, Jenny; Daly, Rebecca A. Genome Announcements, Vol. 6, Issue 14 https://doi.org/10.1128/genomea.00155-18	journal	April 2018
Metabolic Capability of a Predominant Halanaerobium sp. in Hydraulically Fractured Gas Wells and Its Implication in Pipeline Corrosion Liang, Renxing; Davidova, Irene A.; Marks, Christopher R. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00988	journal	June 2016
Anaerobic Biodegradation of Hydrocarbons: Metagenomics and Metabolomics Gieg, Lisa M.; Toth, Courtney R. A. Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation https://doi.org/10.1007/978-3-319-50433-9_16	book	January 2019
Unconventional Oil and Gas Energy Systems: An Unidentified Hotspot of Antimicrobial Resistance? Campa, Maria Fernanda; Wolfe, Amy K.; Techtmann, Stephen M. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02392	journal	October 2019

Similar Records

Microbial Community Changes in Hydraulic Fracturing Fluids and Produced Water from Shale Gas Extraction

Journal Article · Tue Nov 19 00:00:00 EST 2013 · ENVIRONMENTAL SCIENCE & TECHNOLOGY · OSTI ID:1168804

Mohan, Arvind Murali; Hartsock, Angela; Bibby, Kyle J; +3 more

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

Journal Article · Tue Jul 22 00:00:00 EDT 2014 · Frontiers in Microbiology · OSTI ID:1168804

Piao, Hailan; Lachman, Medora; Malfatti, Stephanie; +7 more

Final Technical Report: Optimization and Directed, Natural Evolution of Biologically-Mediated Chromate Reduction in Subsurface Soil Microcosms

Technical Report · Fri Jul 27 00:00:00 EDT 2012 · OSTI ID:1168804

Thompson, Dorothea K; Wickham, Gene S; Layton, Alice C

Related Subjects

54 ENVIRONMENTAL SCIENCES
carbohydrate metabolism
sulfur
ribosomal RNA
sequence assembly tools
metagenomics
gene mapping
natural gas
sequence analysis

Title: The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

Citation Formats

References (40)

Cited By (10)

Similar Records

Related Subjects