Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico
Abstract
Oil and gas percolate profusely through the sediments of the Gulf of Mexico, leading to numerous seeps at the seafloor, where complex microbial, and sometimes animal communities flourish. Sediments from three areas (two cold seeps with contrasting hydrocarbon composition and a site outside any area of active seepage) of the Gulf of Mexico were investigated and compared. Consistent with the existence of a seep microbiome, a distinct microbial community was observed in seep areas compared to sediment from outside areas of active seepage. The microbial community from sediments without any influence from hydrocarbon seepage was characterized by Planctomycetes and the metabolic potential was consistent with detrital marine snow degradation. By contrast, in seep samples with methane as the principal hydrocarbon, methane oxidation by abundant members of ANME-1 was likely the predominant process. Seep samples characterized by fluids containing both methane and complex hydrocarbons, were characterized by abundant Chloroflexi (Anaerolinaceae) and deltaproteobacterial lineages and exhibited potential for complex hydrocarbon degradation. These different metabolic capacities suggested that microorganisms in cold seeps can potentially rely on other processes beyond methane oxidation and that the hydrocarbon composition of the seep fluids may be a critical factor structuring the seafloor microbial community composition and function.
- Authors:
-
[1];
[4]
- Newcastle Univ., Newcastle Upon Tyne (United Kingdom); Shell International Exploration and Production Inc., Houston, TX (United States)
- Shell International Exploration and Production Inc., Houston, TX (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Institut national de la recherche agronomique (INRA), Montferrier-sur-Lez (France). Centre de Biologie et de Gestion des Populations (CBGP)
- Shell International Exploration and Production Inc., Houston, TX (United States)
- Shell Global Solutions International B.V., Rijswijk (Netherlands)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Newcastle Univ., Newcastle Upon Tyne (United Kingdom)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1543776
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Vigneron, Adrien, Alsop, Eric B., Cruaud, Perrine, Philibert, Gwenaelle, King, Benjamin, Baksmaty, Leslie, Lavallée, David, P. Lomans, Bartholomeus, Kyrpides, Nikos C., Head, Ian M., and Tsesmetzis, Nicolas. Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico. United States: N. p., 2017.
Web. doi:10.1038/s41598-017-16375-5.
Vigneron, Adrien, Alsop, Eric B., Cruaud, Perrine, Philibert, Gwenaelle, King, Benjamin, Baksmaty, Leslie, Lavallée, David, P. Lomans, Bartholomeus, Kyrpides, Nikos C., Head, Ian M., & Tsesmetzis, Nicolas. Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico. United States. doi:10.1038/s41598-017-16375-5.
Vigneron, Adrien, Alsop, Eric B., Cruaud, Perrine, Philibert, Gwenaelle, King, Benjamin, Baksmaty, Leslie, Lavallée, David, P. Lomans, Bartholomeus, Kyrpides, Nikos C., Head, Ian M., and Tsesmetzis, Nicolas. Wed .
"Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico". United States. doi:10.1038/s41598-017-16375-5. https://www.osti.gov/servlets/purl/1543776.
@article{osti_1543776,
title = {Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico},
author = {Vigneron, Adrien and Alsop, Eric B. and Cruaud, Perrine and Philibert, Gwenaelle and King, Benjamin and Baksmaty, Leslie and Lavallée, David and P. Lomans, Bartholomeus and Kyrpides, Nikos C. and Head, Ian M. and Tsesmetzis, Nicolas},
abstractNote = {Oil and gas percolate profusely through the sediments of the Gulf of Mexico, leading to numerous seeps at the seafloor, where complex microbial, and sometimes animal communities flourish. Sediments from three areas (two cold seeps with contrasting hydrocarbon composition and a site outside any area of active seepage) of the Gulf of Mexico were investigated and compared. Consistent with the existence of a seep microbiome, a distinct microbial community was observed in seep areas compared to sediment from outside areas of active seepage. The microbial community from sediments without any influence from hydrocarbon seepage was characterized by Planctomycetes and the metabolic potential was consistent with detrital marine snow degradation. By contrast, in seep samples with methane as the principal hydrocarbon, methane oxidation by abundant members of ANME-1 was likely the predominant process. Seep samples characterized by fluids containing both methane and complex hydrocarbons, were characterized by abundant Chloroflexi (Anaerolinaceae) and deltaproteobacterial lineages and exhibited potential for complex hydrocarbon degradation. These different metabolic capacities suggested that microorganisms in cold seeps can potentially rely on other processes beyond methane oxidation and that the hydrocarbon composition of the seep fluids may be a critical factor structuring the seafloor microbial community composition and function.},
doi = {10.1038/s41598-017-16375-5},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {2017},
month = {11}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 14 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:
Microbial sulfate reduction rates and sulfur and oxygen isotope fractionations at oil and gas seeps in deepwater Gulf of Mexico
journal, January 2000
- Aharon, Paul; Fu, Baoshun
- Geochimica et Cosmochimica Acta, Vol. 64, Issue 2
Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of Mexico
journal, October 2006
- Martinez, Robert J.; Mills, Heath J.; Story, Sandra
- Environmental Microbiology, Vol. 8, Issue 10
Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes
journal, August 2007
- Woebken, Dagmar; Teeling, Hanno; Wecker, Patricia
- The ISME Journal, Vol. 1, Issue 5
Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink
journal, October 2006
- Niemann, Helge; Lösekann, Tina; de Beer, Dirk
- Nature, Vol. 443, Issue 7113
Diversity and Spatial Distribution of Prokaryotic Communities Along A Sediment Vertical Profile of A Deep-Sea Mud Volcano
journal, May 2011
- Pachiadaki, Maria G.; Kallionaki, Argyri; Dählmann, Anke
- Microbial Ecology, Vol. 62, Issue 3
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
journal, October 2015
- Evans, P. N.; Parks, D. H.; Chadwick, G. L.
- Science, Vol. 350, Issue 6259
Microbial and Isotopic Evidence for Methane Cycling in Hydrocarbon-Containing Groundwater from the Pennsylvania Region
journal, April 2017
- Vigneron, Adrien; Bishop, Andrew; Alsop, Eric B.
- Frontiers in Microbiology, Vol. 8
Thermogenic gas hydrates and hydrocarbon gases in complex chemosynthetic communities, Gulf of Mexico continental slope
journal, July 1999
- Sassen, Roger; Joye, Samantha; Sweet, Stephen T.
- Organic Geochemistry, Vol. 30, Issue 7
Global dispersion and local diversification of the methane seep microbiome
journal, March 2015
- Ruff, S. Emil; Biddle, Jennifer F.; Teske, Andreas P.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 13
Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane : The partner bacterium in thermophilic methanotrophy
journal, April 2016
- Krukenberg, Viola; Harding, Katie; Richter, Michael
- Environmental Microbiology, Vol. 18, Issue 9
Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi
journal, August 2013
- Wasmund, Kenneth; Schreiber, Lars; Lloyd, Karen G.
- The ISME Journal, Vol. 8, Issue 2
Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics
journal, June 2015
- Nobu, Masaru K.; Dodsworth, Jeremy A.; Murugapiran, Senthil K.
- The ISME Journal, Vol. 10, Issue 2
Chemosynthetic bacterial mats at cold hydrocarbon seeps, Gulf of Mexico continental slope
journal, January 1993
- Sassen, Roger; Roberts, Harry H.; Aharon, Paul
- Organic Geochemistry, Vol. 20, Issue 1
High abundance of JS-1- and Chloroflexi -related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR
journal, May 2010
- Blazejak, Anna; Schippers, Axel
- FEMS Microbiology Ecology, Vol. 72, Issue 2
Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014
- Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern
- Bioinformatics, Vol. 30, Issue 15
Asphalt Volcanism and Chemosynthetic Life in the Campeche Knolls, Gulf of Mexico
journal, May 2004
- MacDonald, I. R.
- Science, Vol. 304, Issue 5673
Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria
journal, September 2007
- Kniemeyer, Olaf; Musat, Florin; Sievert, Stefan M.
- Nature, Vol. 449, Issue 7164
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
journal, January 2015
- Li, Dinghua; Liu, Chi-Man; Luo, Ruibang
- Bioinformatics, Vol. 31, Issue 10
Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi ) in Sulfur Cycling
journal, May 2016
- Wasmund, Kenneth; Cooper, Myriel; Schreiber, Lars
- mBio, Vol. 7, Issue 3
Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
journal, January 2017
- Vollmers, John; Wiegand, Sandra; Kaster, Anne-Kristin
- PLOS ONE, Vol. 12, Issue 1
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
journal, May 2011
- Miller, Christopher S.; Baker, Brett J.; Thomas, Brian C.
- Genome Biology, Vol. 12, Issue 5
Microbial communities associated with benthic faunal assemblages at cold seep sediments of the Sonora Margin, Guaymas Basin
journal, August 2015
- Cruaud, Perrine; Vigneron, Adrien; Pignet, Patricia
- Frontiers in Marine Science, Vol. 2
Anaerolineaceae and Methanosaeta turned to be the dominant microorganisms in alkanes-dependent methanogenic culture after long-term of incubation
journal, June 2015
- Liang, Bo; Wang, Li-Ying; Mbadinga, Serge Maurice
- AMB Express, Vol. 5, Issue 1
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
journal, January 2015
- Kang, Dongwan D.; Froula, Jeff; Egan, Rob
- PeerJ, Vol. 3
Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps
journal, September 2005
- Orcutt, Beth!; Boetius, Antje; Elvert, Marcus
- Geochimica et Cosmochimica Acta, Vol. 69, Issue 17
The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes: Syntrophaceae in methanogenic oil degrading consortia
journal, September 2011
- Gray, N. D.; Sherry, A.; Grant, R. J.
- Environmental Microbiology, Vol. 13, Issue 11
Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps
journal, April 2014
- Kleindienst, Sara; Herbst, Florian-Alexander; Stagars, Marion
- The ISME Journal, Vol. 8, Issue 10
Distribution and in situ abundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments : Sulfate-reducing bacteria at marine hydrocarbon seeps
journal, August 2012
- Kleindienst, Sara; Ramette, Alban; Amann, Rudolf
- Environmental Microbiology, Vol. 14, Issue 10
Petroleum degradation and associated microbial signatures at the Chapopote asphalt volcano, Southern Gulf of Mexico
journal, August 2011
- Schubotz, Florence; Lipp, Julius S.; Elvert, Marcus
- Geochimica et Cosmochimica Acta, Vol. 75, Issue 16
Metabolic Capabilities of Microorganisms Involved in and Associated with the Anaerobic Oxidation of Methane
journal, February 2016
- Wegener, Gunter; Krukenberg, Viola; Ruff, S. Emil
- Frontiers in Microbiology, Vol. 7
Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi
journal, April 2012
- Loffler, F. E.; Yan, J.; Ritalahti, K. M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 2
Anaerobic Oxidation of Methane: Progress with an Unknown Process
journal, October 2009
- Knittel, Katrin; Boetius, Antje
- Annual Review of Microbiology, Vol. 63, Issue 1
Bacterial communities and syntrophic associations involved in anaerobic oxidation of methane process of the Sonora Margin cold seeps, Guaymas Basin: AOM involved bacteria at Sonora Margin
journal, December 2013
- Vigneron, Adrien; Cruaud, Perrine; Pignet, Patricia
- Environmental Microbiology, Vol. 16, Issue 9
IMG/M: a data management and analysis system for metagenomes
journal, December 2007
- Markowitz, V. M.; Ivanova, N. N.; Szeto, E.
- Nucleic Acids Research, Vol. 36, Issue Database
Thickness of the gas hydrate stability zone, Gulf of Mexico continental slope
journal, November 2000
- Milkov, A. V.; Sassen, R.
- Marine and Petroleum Geology, Vol. 17, Issue 9
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007
- Pruesse, E.; Quast, C.; Knittel, K.
- Nucleic Acids Research, Vol. 35, Issue 21
A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses
journal, November 2014
- Buttigieg, Pier Luigi; Ramette, Alban
- FEMS Microbiology Ecology, Vol. 90, Issue 3
VSEARCH: a versatile open source tool for metagenomics
journal, January 2016
- Rognes, Torbjørn; Flouri, Tomáš; Nichols, Ben
- PeerJ, Vol. 4
An Anaerobic Methane-Oxidizing Community of ANME-1b Archaea in Hypersaline Gulf of Mexico Sediments
journal, September 2006
- Lloyd, K. G.; Lapham, L.; Teske, A.
- Applied and Environmental Microbiology, Vol. 72, Issue 11
Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments: Genomic content of uncultured benthic Bathyarchaeota
journal, January 2016
- Lazar, Cassandre Sara; Baker, Brett J.; Seitz, Kiley
- Environmental Microbiology, Vol. 18, Issue 4
Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics
journal, May 2008
- Pernthaler, A.; Dekas, A. E.; Brown, C. T.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 19
Characterization of Microbial Community Structure in Gulf of Mexico Gas Hydrates: Comparative Analysis of DNA- and RNA-Derived Clone Libraries
journal, June 2005
- Mills, H. J.; Martinez, R. J.; Story, S.
- Applied and Environmental Microbiology, Vol. 71, Issue 6
A marine microbial consortium apparently mediating anaerobic oxidation of methane
journal, October 2000
- Boetius, Antje; Ravenschlag, Katrin; Schubert, Carsten J.
- Nature, Vol. 407, Issue 6804
Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group
journal, February 2010
- Meyerdierks, Anke; Kube, Michael; Kostadinov, Ivaylo
- Environmental Microbiology, Vol. 12, Issue 2
QIIME allows analysis of high-throughput community sequencing data
journal, April 2010
- Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
- Nature Methods, Vol. 7, Issue 5
Anaerobic oxidation of methane associated with sulfate reduction in a natural freshwater gas source
journal, December 2015
- Timmers, Peer HA; Suarez-Zuluaga, Diego A.; van Rossem, Minke
- The ISME Journal, Vol. 10, Issue 6
Thermophilic anaerobic oxidation of methane by marine microbial consortia
journal, June 2011
- Holler, Thomas; Widdel, Friedrich; Knittel, Katrin
- The ISME Journal, Vol. 5, Issue 12
Methanogenic archaea: ecologically relevant differences in energy conservation
journal, June 2008
- Thauer, Rudolf K.; Kaster, Anne-Kristin; Seedorf, Henning
- Nature Reviews Microbiology, Vol. 6, Issue 8
Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California)
journal, February 2013
- Vigneron, Adrien; Cruaud, Perrine; Pignet, Patricia
- The ISME Journal, Vol. 7, Issue 8
Archaea in coastal marine environments.
journal, June 1992
- DeLong, E. F.
- Proceedings of the National Academy of Sciences, Vol. 89, Issue 12
Bacteria and Archaea Physically Associated with Gulf of Mexico Gas Hydrates
journal, November 2001
- Lanoil, B. D.; Sassen, R.; La Duc, M. T.
- Applied and Environmental Microbiology, Vol. 67, Issue 11
Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments: Proteogenomics of ANME-1 in cold seep sediments
journal, March 2012
- Stokke, Runar; Roalkvam, Irene; Lanzen, Anders
- Environmental Microbiology, Vol. 14, Issue 5
Energy Metabolism during Anaerobic Methane Oxidation in ANME Archaea
journal, January 2017
- McGlynn, Shawn E.
- Microbes and environments, Vol. 32, Issue 1
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
Predominant archaea in marine sediments degrade detrital proteins
journal, March 2013
- Lloyd, Karen G.; Schreiber, Lars; Petersen, Dorthe G.
- Nature, Vol. 496, Issue 7444
Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep
journal, January 2010
- Lloyd, Karen G.; Albert, Daniel B.; Biddle, Jennifer F.
- PLoS ONE, Vol. 5, Issue 1
Seafloor oxygen consumption fuelled by methane from cold seeps
journal, August 2013
- Boetius, Antje; Wenzhöfer, Frank
- Nature Geoscience, Vol. 6, Issue 9
Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases
journal, October 2014
- Müller, Albert Leopold; Kjeldsen, Kasper Urup; Rattei, Thomas
- The ISME Journal, Vol. 9, Issue 5
Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages
journal, July 1993
- DeLong, Edward F.; Franks, Diana G.; Alldredge, Alice L.
- Limnology and Oceanography, Vol. 38, Issue 5
DNA recovery from soils of diverse composition.
journal, January 1996
- Zhou, J.; Bruns, M. A.; Tiedje, J. M.
- Applied and environmental microbiology, Vol. 62, Issue 2
Works referencing / citing this record:
Mud volcanoes and the presence of PAHs
journal, January 2020
- Remizovschi, Alexei; Carpa, Rahela; Forray, Ferenc L.
- Scientific Reports, Vol. 10, Issue 1
Methane-fuelled biofilms predominantly composed of methanotrophic ANME-1 in Arctic gas hydrate-related sediments
journal, July 2019
- Gründger, Friederike; Carrier, Vincent; Svenning, Mette M.
- Scientific Reports, Vol. 9, Issue 1
On the maverick Planctomycetes
journal, July 2018
- Wiegand, Sandra; Jogler, Mareike; Jogler, Christian
- FEMS Microbiology Reviews, Vol. 42, Issue 6
Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments
journal, February 2019
- Vigneron, Adrien; Alsop, Eric B.; Cruaud, Perrine
- mSystems, Vol. 4, Issue 1
Anaerobic hydrocarbon degradation in candidate phylum ‘Atribacteria’ (JS1) inferred from genomics
journal, June 2019
- Liu, Yi-Fan; Qi, Zhen-Zhen; Shou, Li-Bin
- The ISME Journal, Vol. 13, Issue 9
Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments
journal, April 2019
- Dong, Xiyang; Greening, Chris; Rattray, Jayne E.
- Nature Communications, Vol. 10, Issue 1
Methane-fuelled biofilms predominantly composed of methanotrophic ANME-1 in Arctic gas hydrate-related sediments
journal, July 2019
- Gründger, Friederike; Carrier, Vincent; Svenning, Mette M.
- Scientific Reports, Vol. 9, Issue 1
On the maverick Planctomycetes
journal, July 2018
- Wiegand, Sandra; Jogler, Mareike; Jogler, Christian
- FEMS Microbiology Reviews, Vol. 42, Issue 6