Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf...

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Published inNature communications Vol. 10; no. 1; p. 1816
Main Authors Dong, Xiyang, Greening, Chris, Rattray, Jayne E., Chakraborty, Anirban, Chuvochina, Maria, Mayumi, Daisuke, Dolfing, Jan, Li, Carmen, Brooks, James M., Bernard, Bernie B., Groves, Ryan A., Lewis, Ian A., Hubert, Casey R. J.
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Published London Nature Publishing Group UK 18.04.2019
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Abstract The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism. Little is known about the microbial ecology of the deep seabed. Here, Dong et al. predict metabolic capabilities and microbial interactions in deep seabed petroleum seeps using shotgun metagenomics, sediment geochemistry, metabolomics, and thermodynamic modelling.
AbstractList The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.
The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.Little is known about the microbial ecology of the deep seabed. Here, Dong et al. predict metabolic capabilities and microbial interactions in deep seabed petroleum seeps using shotgun metagenomics, sediment geochemistry, metabolomics, and thermodynamic modelling.
The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism. Little is known about the microbial ecology of the deep seabed. Here, Dong et al. predict metabolic capabilities and microbial interactions in deep seabed petroleum seeps using shotgun metagenomics, sediment geochemistry, metabolomics, and thermodynamic modelling.
Little is known about the microbial ecology of the deep seabed. Here, Dong et al. predict metabolic capabilities and microbial interactions in deep seabed petroleum seeps using shotgun metagenomics, sediment geochemistry, metabolomics, and thermodynamic modelling.
ArticleNumber 1816
Author Chuvochina, Maria
Bernard, Bernie B.
Brooks, James M.
Dolfing, Jan
Li, Carmen
Hubert, Casey R. J.
Rattray, Jayne E.
Lewis, Ian A.
Groves, Ryan A.
Chakraborty, Anirban
Mayumi, Daisuke
Dong, Xiyang
Greening, Chris
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Snippet The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate...
Little is known about the microbial ecology of the deep seabed. Here, Dong et al. predict metabolic capabilities and microbial interactions in deep seabed...
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SubjectTerms 631/158/855
631/326/2565/2142
631/326/26
631/326/41/2535
Acetates - metabolism
Acetic acid
Aliphatic compounds
Archaea
Archaea - genetics
Archaea - isolation & purification
Archaea - metabolism
Aromatic compounds
Bacteria - genetics
Bacteria - isolation & purification
Bacteria - metabolism
Communities
Deep sea
Deep sea environments
Ecological monitoring
Genomes
Geochemistry
Geologic Sediments - chemistry
Geologic Sediments - microbiology
Harbors
Humanities and Social Sciences
Hydrocarbons
Hydrocarbons - metabolism
Hydrogen - metabolism
Metabolism
Metabolomics
Metagenome
Metagenomics - methods
Mexico
Microbial activity
Microbial Interactions - physiology
Microbiota - physiology
Microorganisms
multidisciplinary
Ocean floor
Oxidation
Petroleum
Petroleum - metabolism
Phylogeny
Science
Science (multidisciplinary)
Sediments
Seepage
Thermodynamic models
Water depth
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Title Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments
URI https://link.springer.com/article/10.1038/s41467-019-09747-0
https://www.ncbi.nlm.nih.gov/pubmed/31000700
https://www.proquest.com/docview/2211321024
https://search.proquest.com/docview/2211946266
https://pubmed.ncbi.nlm.nih.gov/PMC6472368
https://doaj.org/article/dd16be85002e482586ec2d3303aa6171
Volume 10
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