Metabolic capability and in situ activity of microorganisms in an oil reservoir
Abstract
Background: Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. Results: Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondarymore »
- Authors:
-
- Chinese Academy of Sciences (CAS), Shanghai (China). Shanghai Inst. of Ceramics, Key Lab. for Bioreactor Engineering and Inst. of Applied Chemistry; Univ. of California, San Diego, CA (United States). Dept. of Pediatrics
- Univ. of California, San Diego, CA (United States). Dept. of Pediatrics
- Chinese Academy of Sciences (CAS), Shanghai (China). Shanghai Inst. of Ceramics, Key Lab. for Bioreactor Engineering and Inst. of Applied Chemistry; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai (China)
- Univ. of Hong Kong (China). School of Biological Sciences
- Univ. of California, San Diego, CA (United States). Dept. of Pediatrics and Center for Microbiome Innovation,
- Publication Date:
- Research Org.:
- Univ. of California, San Diego, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1510971
- Grant/Contract Number:
- SC0012586
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Microbiome
- Additional Journal Information:
- Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2049-2618
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Auxotrophy; Hydrocarbon degradation; Metagenomics and metatranscriptomics; Microbial community; Oil reservoir
Citation Formats
Liu, Yi-Fan, Galzerani, Daniela Domingos, Mbadinga, Serge Maurice, Zaramela, Livia S., Gu, Ji-Dong, Mu, Bo-Zhong, and Zengler, Karsten. Metabolic capability and in situ activity of microorganisms in an oil reservoir. United States: N. p., 2018.
Web. doi:10.1186/s40168-017-0392-1.
Liu, Yi-Fan, Galzerani, Daniela Domingos, Mbadinga, Serge Maurice, Zaramela, Livia S., Gu, Ji-Dong, Mu, Bo-Zhong, & Zengler, Karsten. Metabolic capability and in situ activity of microorganisms in an oil reservoir. United States. https://doi.org/10.1186/s40168-017-0392-1
Liu, Yi-Fan, Galzerani, Daniela Domingos, Mbadinga, Serge Maurice, Zaramela, Livia S., Gu, Ji-Dong, Mu, Bo-Zhong, and Zengler, Karsten. Fri .
"Metabolic capability and in situ activity of microorganisms in an oil reservoir". United States. https://doi.org/10.1186/s40168-017-0392-1. https://www.osti.gov/servlets/purl/1510971.
@article{osti_1510971,
title = {Metabolic capability and in situ activity of microorganisms in an oil reservoir},
author = {Liu, Yi-Fan and Galzerani, Daniela Domingos and Mbadinga, Serge Maurice and Zaramela, Livia S. and Gu, Ji-Dong and Mu, Bo-Zhong and Zengler, Karsten},
abstractNote = {Background: Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. Results: Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondary recovery. Conclusion: Our data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.},
doi = {10.1186/s40168-017-0392-1},
journal = {Microbiome},
number = 1,
volume = 6,
place = {United States},
year = {Fri Jan 05 00:00:00 EST 2018},
month = {Fri Jan 05 00:00:00 EST 2018}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 55 works
Citation information provided by
Web of Science
Web of Science
Figures / Tables:
Fig. 1: Taxonomic analysis of metagenomes evaluated from unassembled reads by MetaPhlAn2 and Metaxa2 and from assembled 16S rRNA gene sequences. Bar graph is showing the percent abundance of the different members at order level, and only members with more than 0.1% abundance in either sample is showed here. Archaealmore »
All figures and tables
(5 total)
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:
Networks of energetic and metabolic interactions define dynamics in microbial communities
journal, November 2015
- Embree, Mallory; Liu, Joanne K.; Al-Bassam, Mahmoud M.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 50
AliView: a fast and lightweight alignment viewer and editor for large datasets
journal, August 2014
- Larsson, Anders
- Bioinformatics, Vol. 30, Issue 22
Quality control and preprocessing of metagenomic datasets
journal, January 2011
- Schmieder, R.; Edwards, R.
- Bioinformatics, Vol. 27, Issue 6
Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community
journal, October 2013
- Embree, Mallory; Nagarajan, Harish; Movahedi, Narjes
- The ISME Journal, Vol. 8, Issue 4
Thermodynamic constraints on methanogenic crude oil biodegradation
journal, December 2007
- Dolfing, Jan; Larter, Stephen R.; Head, Ian M.
- The ISME Journal, Vol. 2, Issue 4
A protein trisulfide couples dissimilatory sulfate reduction to energy conservation
journal, December 2015
- Santos, A. A.; Venceslau, S. S.; Grein, F.
- Science, Vol. 350, Issue 6267
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria
journal, April 2015
- Baker, Brett J.; Lazar, Cassandre Sara; Teske, Andreas P.
- Microbiome, Vol. 3, Issue 1
Identification of ribosomal RNA genes in metagenomic fragments
journal, April 2009
- Huang, Ying; Gilna, Paul; Li, Weizhong
- Bioinformatics, Vol. 25, Issue 10
Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities
journal, October 2009
- Duncan, Kathleen E.; Gieg, Lisa M.; Parisi, Victoria A.
- Environmental Science & Technology, Vol. 43, Issue 20
Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common
journal, September 2013
- An, Dongshan; Caffrey, Sean M.; Soh, Jung
- Environmental Science & Technology, Vol. 47, Issue 18
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997
- Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
- Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
Anaerobic alkane-degrading strain AK-01 contains two alkylsuccinate synthase genes
journal, February 2008
- Callaghan, Amy V.; Wawrik, Boris; Ní Chadhain, Sinéad M.
- Biochemical and Biophysical Research Communications, Vol. 366, 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
Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs
journal, September 2004
- Aitken, Carolyn M.; Jones, D. M.; Larter, S. R.
- Nature, Vol. 431, Issue 7006
Growth- and substrate-dependent transcription of formate dehydrogenase and hydrogenase coding genes in Syntrophobacter fumaroxidans and Methanospirillum hungatei
journal, September 2010
- Worm, P.; Stams, A. J. M.; Cheng, X.
- Microbiology, Vol. 157, Issue 1
Anaerobic Biodegradation of Aromatic Hydrocarbons: Pathways and Prospects
journal, January 2008
- Foght, Julia
- Journal of Molecular Microbiology and Biotechnology, Vol. 15, Issue 2-3
CD-HIT: accelerated for clustering the next-generation sequencing data
journal, October 2012
- Fu, Limin; Niu, Beifang; Zhu, Zhengwei
- Bioinformatics, Vol. 28, Issue 23
Streaming fragment assignment for real-time analysis of sequencing experiments
journal, November 2012
- Roberts, Adam; Pachter, Lior
- Nature Methods, Vol. 10, Issue 1
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions
journal, October 2017
- Hubalek, Valerie; Buck, Moritz; Tan, BoonFei
- mSystems, Vol. 2, Issue 5
DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences
journal, November 2011
- Wright, Erik S.; Yilmaz, L. Safak; Noguera, Daniel R.
- Applied and Environmental Microbiology, Vol. 78, Issue 3
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
journal, August 2013
- Segata, Nicola; Börnigen, Daniela; Morgan, Xochitl C.
- Nature Communications, Vol. 4, Issue 1
Ribosomal Database Project: data and tools for high throughput rRNA analysis
journal, November 2013
- Cole, James R.; Wang, Qiong; Fish, Jordan A.
- Nucleic Acids Research, Vol. 42, Issue D1
Methane formation from long-chain alkanes by anaerobic microorganisms
journal, September 1999
- Zengler, Karsten; Richnow, Hans H.; Rosselló-Mora, Ramon
- Nature, Vol. 401, Issue 6750
Insights into the Anaerobic Biodegradation Pathway of n-Alkanes in Oil Reservoirs by Detection of Signature Metabolites
journal, May 2015
- Bian, Xin-Yu; Maurice Mbadinga, Serge; Liu, Yi-Fan
- Scientific Reports, Vol. 5, Issue 1
KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 1999
- Ogata, H.; Goto, S.; Sato, K.
- Nucleic Acids Research, Vol. 27, Issue 1
Novel Type of ADP-Forming Acetyl Coenzyme A Synthetase in Hyperthermophilic Archaea: Heterologous Expression and Characterization of Isoenzymes from the Sulfate Reducer Archaeoglobus fulgidus and the Methanogen Methanococcus jannaschii
journal, February 2002
- Musfeldt, M.; Schonheit, P.
- Journal of Bacteriology, Vol. 184, Issue 3
Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill
journal, May 2016
- Dombrowski, Nina; Donaho, John A.; Gutierrez, Tony
- Nature Microbiology, Vol. 1, Issue 7
The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008
- Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
- BMC Genomics, Vol. 9, Issue 1, Article No. 75
Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples
journal, March 2015
- Tan, Boonfei; Jane Fowler, S.; Laban, Nidal Abu
- The ISME Journal, Vol. 9, Issue 9
Biological activity in the deep subsurface and the origin of heavy oil
journal, November 2003
- Head, Ian M.; Jones, D. Martin; Larter, Steve R.
- Nature, Vol. 426, Issue 6964
Anaerobic oxidation of long-chain n-alkanes by the hyperthermophilic sulfate-reducing archaeon, Archaeoglobus fulgidus
journal, April 2014
- Khelifi, Nadia; Amin Ali, Oulfat; Roche, Philippe
- The ISME Journal, Vol. 8, Issue 11
Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets
journal, October 2013
- Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.
- Bioinformatics, Vol. 30, Issue 5
Microbial communities in bulk fluids and biofilms of an oil facility have similar composition but different structure: Microbial communities in produced water and biofilms
journal, January 2011
- Stevenson, Bradley S.; Drilling, Heather S.; Lawson, Paul A.
- Environmental Microbiology, Vol. 13, Issue 4
Stereochemical Investigations Reveal the Mechanism of the Bacterial Activation of n-Alkanes without Oxygen
journal, November 2011
- Jarling, René; Sadeghi, Masih; Drozdowska, Marta
- Angewandte Chemie International Edition, Vol. 51, Issue 6
A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane
journal, January 2014
- Rotaru, Amelia-Elena; Shrestha, Pravin Malla; Liu, Fanghua
- Energy Environ. Sci., Vol. 7, Issue 1
The genome sequence of Desulfatibacillum alkenivorans AK-01: a blueprint for anaerobic alkane oxidation: Genome sequence of Desulfatibacillum alkenivorans AK-01
journal, June 2011
- Callaghan, A. V.; Morris, B. E. L.; Pereira, I. A. C.
- Environmental Microbiology, Vol. 14, Issue 1
Anaerobic bacterial metabolism of hydrocarbons
journal, December 1998
- Heider, Johann; Spormann, Alfred M.; Beller, Harry R.
- FEMS Microbiology Reviews, Vol. 22, Issue 5
Identification of a novel Baeyer-Villiger monooxygenase from Acinetobacter radioresistens : close relationship to the Mycobacterium tuberculosis prodrug activator EtaA : A new BVMO from
journal, August 2012
- Minerdi, Daniela; Zgrablic, Ivan; Sadeghi, Sheila J.
- Microbial Biotechnology, Vol. 5, Issue 6
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
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
Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China
journal, February 2016
- Gao, Peike; Tian, Huimei; Wang, Yansen
- Scientific Reports, Vol. 6, Issue 1
Archaeoglobus fulgidus couples CO oxidation to sulfate reduction and acetogenesis with transient formate accumulation : The CO metabolism of
journal, April 2007
- Henstra, Anne M.; Dijkema, Cor; Stams, Alfons J. M.
- Environmental Microbiology, Vol. 9, Issue 7
metaxa 2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
journal, March 2015
- Bengtsson-Palme, Johan; Hartmann, Martin; Eriksson, Karl Martin
- Molecular Ecology Resources, Vol. 15, Issue 6
Comparison of bacterial community in aqueous and oil phases of water-flooded petroleum reservoirs using pyrosequencing and clone library approaches
journal, January 2014
- Wang, Li-Ying; Ke, Wen-Ji; Sun, Xiao-Bo
- Applied Microbiology and Biotechnology, Vol. 98, Issue 9
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
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
journal, September 2008
- Meyer, F.; Paarmann, D.; D'Souza, M.
- BMC Bioinformatics, Vol. 9, Issue 1
The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
journal, November 1997
- Klenk, Hans-Peter; Clayton, Rebecca A.; Tomb, Jean-Francois
- Nature, Vol. 390, Issue 6658
Metagenomic microbial community profiling using unique clade-specific marker genes
journal, June 2012
- Segata, Nicola; Waldron, Levi; Ballarini, Annalisa
- Nature Methods, Vol. 9, Issue 8
Growth of Pseudomonas chloritidismutans AW-1T on n-alkanes with chlorate as electron acceptor
journal, April 2009
- Mehboob, Farrakh; Junca, Howard; Schraa, Gosse
- Applied Microbiology and Biotechnology, Vol. 83, Issue 4
Alkane Hydroxylase from Acinetobactersp. Strain ADP1 Is Encoded by alkM and Belongs to a New Family of Bacterial Integral-Membrane Hydrocarbon Hydroxylases
journal, April 1998
- Ratajczak, Andreas; Geißdörfer, Walter; Hillen, Wolfgang
- Applied and Environmental Microbiology, Vol. 64, Issue 4
Diversity of Sea Star-Associated Densoviruses and Transcribed Endogenous Viral Elements of Densovirus Origin
journal, December 2020
- Jackson, Elliot W.; Wilhelm, Roland C.; Johnson, Mitchell R.
- Journal of Virology, Vol. 95, Issue 1
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
Stereochemical Investigations Reveal the Mechanism of the Bacterial Activation of n-Alkanes without Oxygen
journal, November 2011
- Jarling, René; Sadeghi, Masih; Drozdowska, Marta
- Angewandte Chemie International Edition, Vol. 51, Issue 6
Growth of Pseudomonas chloritidismutans AW-1T on n-alkanes with chlorate as electron acceptor
journal, April 2009
- Mehboob, Farrakh; Junca, Howard; Schraa, Gosse
- Applied Microbiology and Biotechnology, Vol. 83, Issue 4
Comparison of bacterial community in aqueous and oil phases of water-flooded petroleum reservoirs using pyrosequencing and clone library approaches
journal, January 2014
- Wang, Li-Ying; Ke, Wen-Ji; Sun, Xiao-Bo
- Applied Microbiology and Biotechnology, Vol. 98, Issue 9
Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment
journal, June 2021
- Kim, Minji; Lee, Ki-Eun; Cha, In-Tae
- Current Microbiology, Vol. 78, Issue 8
Anaerobic alkane-degrading strain AK-01 contains two alkylsuccinate synthase genes
journal, February 2008
- Callaghan, Amy V.; Wawrik, Boris; Ní Chadhain, Sinéad M.
- Biochemical and Biophysical Research Communications, Vol. 366, Issue 1
Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities
journal, October 2009
- Duncan, Kathleen E.; Gieg, Lisa M.; Parisi, Victoria A.
- Environmental Science & Technology, Vol. 43, Issue 20
The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
journal, November 1997
- Klenk, Hans-Peter; Clayton, Rebecca A.; Tomb, Jean-Francois
- Nature, Vol. 390, Issue 6658
Methane formation from long-chain alkanes by anaerobic microorganisms
journal, September 1999
- Zengler, Karsten; Richnow, Hans H.; Rosselló-Mora, Ramon
- Nature, Vol. 401, Issue 6750
Thermodynamic constraints on methanogenic crude oil biodegradation
journal, December 2007
- Dolfing, Jan; Larter, Stephen R.; Head, Ian M.
- The ISME Journal, Vol. 2, Issue 4
Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community
journal, October 2013
- Embree, Mallory; Nagarajan, Harish; Movahedi, Narjes
- The ISME Journal, Vol. 8, Issue 4
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
Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples
journal, March 2015
- Tan, Boonfei; Jane Fowler, S.; Laban, Nidal Abu
- The ISME Journal, Vol. 9, Issue 9
Tritagonist as a new term for uncharacterised microorganisms in environmental systems
journal, June 2015
- Freimoser, Florian M.; Pelludat, Cosima; Remus-Emsermann, Mitja N. P.
- The ISME Journal, Vol. 10, Issue 1
Biological activity in the deep subsurface and the origin of heavy oil
journal, November 2003
- Head, Ian M.; Jones, D. Martin; Larter, Steve R.
- Nature, Vol. 426, Issue 6964
Anaerobic hydrocarbon biodegradation in deep subsurface oil reservoirs
journal, September 2004
- Aitken, Carolyn M.; Jones, D. M.; Larter, S. R.
- Nature, Vol. 431, Issue 7006
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
journal, August 2013
- Segata, Nicola; Börnigen, Daniela; Morgan, Xochitl C.
- Nature Communications, Vol. 4, Issue 1
Streaming fragment assignment for real-time analysis of sequencing experiments
journal, November 2012
- Roberts, Adam; Pachter, Lior
- Nature Methods, Vol. 10, Issue 1
Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill
journal, May 2016
- Dombrowski, Nina; Donaho, John A.; Gutierrez, Tony
- Nature Microbiology, Vol. 1, Issue 7
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens
journal, March 2021
- Papalexi, Efthymia; Mimitou, Eleni P.; Butler, Andrew W.
- Nature Genetics, Vol. 53, Issue 3
Insights into the Anaerobic Biodegradation Pathway of n-Alkanes in Oil Reservoirs by Detection of Signature Metabolites
journal, May 2015
- Bian, Xin-Yu; Maurice Mbadinga, Serge; Liu, Yi-Fan
- Scientific Reports, Vol. 5, Issue 1
Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China
journal, February 2016
- Gao, Peike; Tian, Huimei; Wang, Yansen
- Scientific Reports, Vol. 6, Issue 1
Networks of energetic and metabolic interactions define dynamics in microbial communities
journal, November 2015
- Embree, Mallory; Liu, Joanne K.; Al-Bassam, Mahmoud M.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 50
Identification of ribosomal RNA genes in metagenomic fragments
journal, April 2009
- Huang, Ying; Gilna, Paul; Li, Weizhong
- Bioinformatics, Vol. 25, Issue 10
Quality control and preprocessing of metagenomic datasets
journal, January 2011
- Schmieder, R.; Edwards, R.
- Bioinformatics, Vol. 27, Issue 6
CD-HIT: accelerated for clustering the next-generation sequencing data
journal, October 2012
- Fu, Limin; Niu, Beifang; Zhu, Zhengwei
- Bioinformatics, Vol. 28, Issue 23
AliView: a fast and lightweight alignment viewer and editor for large datasets
journal, August 2014
- Larsson, Anders
- Bioinformatics, Vol. 30, Issue 22
KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 1999
- Ogata, H.; Goto, S.; Sato, K.
- Nucleic Acids Research, Vol. 27, Issue 1
Ribosomal Database Project: data and tools for high throughput rRNA analysis
journal, November 2013
- Cole, James R.; Wang, Qiong; Fish, Jordan A.
- Nucleic Acids Research, Vol. 42, Issue D1
Growth- and substrate-dependent transcription of formate dehydrogenase and hydrogenase coding genes in Syntrophobacter fumaroxidans and Methanospirillum hungatei
journal, September 2010
- Worm, P.; Stams, A. J. M.; Cheng, X.
- Microbiology, Vol. 157, Issue 1
metaxa 2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
journal, March 2015
- Bengtsson-Palme, Johan; Hartmann, Martin; Eriksson, Karl Martin
- Molecular Ecology Resources, Vol. 15, Issue 6
Archaeoglobus fulgidus couples CO oxidation to sulfate reduction and acetogenesis with transient formate accumulation : The CO metabolism of
journal, April 2007
- Henstra, Anne M.; Dijkema, Cor; Stams, Alfons J. M.
- Environmental Microbiology, Vol. 9, Issue 7
The genome sequence of Desulfatibacillum alkenivorans AK-01: a blueprint for anaerobic alkane oxidation: Genome sequence of Desulfatibacillum alkenivorans AK-01
journal, June 2011
- Callaghan, A. V.; Morris, B. E. L.; Pereira, I. A. C.
- Environmental Microbiology, Vol. 14, Issue 1
A protein trisulfide couples dissimilatory sulfate reduction to energy conservation
journal, December 2015
- Santos, A. A.; Venceslau, S. S.; Grein, F.
- Science, Vol. 350, Issue 6267
The Genes rubA and rubB for Alkane Degradation in Acinetobacter sp. Strain ADP1 Are in an Operon with estB, Encoding an Esterase, andoxyR
journal, July 1999
- Geißdörfer, Walter; Kok, Ruben G.; Ratajczak, Andreas
- Journal of Bacteriology, Vol. 181, Issue 14
Comparative Genetic Diversity of Pseudomonas stutzeri Genomovars, Clonal Structure, and Phylogeny of the Species
journal, August 2004
- Cladera, A. M.; Bennasar, A.; Barcelo, M.
- Journal of Bacteriology, Vol. 186, Issue 16
Anaerobic Biodegradation of Aromatic Hydrocarbons: Pathways and Prospects
journal, January 2008
- Foght, Julia
- Journal of Molecular Microbiology and Biotechnology, Vol. 15, Issue 2-3
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
journal, September 2008
- Meyer, F.; Paarmann, D.; D'Souza, M.
- BMC Bioinformatics, Vol. 9, Issue 1
The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008
- Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
- BMC Genomics, Vol. 9, Issue 1, Article No. 75
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
Commentary: Microbial Small Talk: Volatiles in Fungal–Bacterial Interactions
journal, January 2017
- Hacquard, Stéphane
- Frontiers in Microbiology, Vol. 8
Works referencing / citing this record:
Developing an l‐ threonine‐producing strain from wild‐type Escherichia coli by modifying the glucose uptake, glyoxylate shunt, and l ‐threonine biosynthetic pathway
journal, September 2019
- Zhu, Lifei; Fang, Yu; Ding, Zhixiang
- Biotechnology and Applied Biochemistry, Vol. 66, Issue 6
Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures
journal, October 2019
- Révész, Fruzsina; Figueroa-Gonzalez, Perla Abigail; Probst, Alexander J.
- Archives of Microbiology, Vol. 202, Issue 2
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
Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands
journal, April 2018
- Ridley, Christina M.; Voordouw, Gerrit
- FEMS Microbiology Ecology, Vol. 94, Issue 6
Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism
journal, October 2018
- Hidalgo‐Ahumada, Catalina A. P.; Nobu, Masaru K.; Narihiro, Takashi
- Environmental Microbiology, Vol. 20, Issue 12
Characteristics of crude oil-degrading bacteria Gordonia iterans isolated from marine coastal in Taean sediment
journal, October 2018
- Kim, Hyun-Sook; Dong, Ke; Kim, Jinsoo
- MicrobiologyOpen, Vol. 8, Issue 6
Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation
journal, October 2018
- Beckmann, Sabrina; Luk, Alison W. S.; Gutierrez-Zamora, Maria-Luisa
- The ISME Journal, Vol. 13, Issue 3
The social network of microorganisms — how auxotrophies shape complex communities
journal, March 2018
- Zengler, Karsten; Zaramela, Livia S.
- Nature Reviews Microbiology, Vol. 16, Issue 6
Characteristics of crude oil-degrading bacteria Gordonia iterans isolated from marine coastal in Taean sediment
journal, October 2018
- Kim, Hyun-Sook; Dong, Ke; Kim, Jinsoo
- MicrobiologyOpen, Vol. 8, Issue 6
Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures
journal, October 2019
- Révész, Fruzsina; Figueroa-Gonzalez, Perla Abigail; Probst, Alexander J.
- Archives of Microbiology, Vol. 202, Issue 2
Oil reservoirs, an exceptional habitat for microorganisms
journal, March 2019
- Pannekens, Mark; Kroll, Lisa; Müller, Hubert
- New Biotechnology, Vol. 49
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
Composition of Bacterial and Archaeal Communities in an Alkali-Surfactant-Polyacrylamide-Flooded Oil Reservoir and the Responses of Microcosms to Nutrients
journal, September 2019
- Gao, Peike; Li, Yu; Tan, Lijie
- Frontiers in Microbiology, Vol. 10
Figures / Tables found in this record:
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.