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Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes

Karthikeyan, Smruthi and Rodriguez-R, Luis M. and Heritier-Robbins, Patrick and Hatt, Janet K. and Huettel, Markus and Kostka, Joel E. and Konstantinidis, Konstantinos T. (2020) Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes. Environmental Microbiology, 22 (6). pp. 2094-2106. ISSN 1462-2912. doi:10.1111/1462-2920.14966.

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Microbial communities ultimately control the fate of petroleum hydrocarbons (PHCs) that enter the natural environment, but the interactions of microbes with PHCs and the environment are highly complex and poorly understood. Genome-resolved metagenomics can help unravel these complex interactions. However, the lack of a comprehensive database that integrates existing genomic/metagenomic data from oil environments with physicochemical parameters known to regulate the fate of PHCs currently limits data analysis and interpretations. Here, we curated a comprehensive, searchable database that documents microbial populations in natural oil ecosystems and oil spills, along with available underlying physicochemical data, geocoded via geographic information system to reveal their geographic distribution patterns. Analysis of the ~2000 metagenome-assembled genomes (MAGs) available in the database revealed strong ecological niche specialization within habitats. Over 95% of the recovered MAGs represented novel taxa underscoring the limited representation of cultured organisms from oil-contaminated and oil reservoir ecosystems. The majority of MAGs linked to oil-contaminated ecosystems were detectable in non-oiled samples from the Gulf of Mexico but not in comparable samples from elsewhere, indicating that the Gulf is primed for oil biodegradation. The repository should facilitate future work toward a predictive understanding of the microbial taxa and their activities that control the fate of oil spills.

Item Type:Article
Related URLs:
URLURL TypeDescription
Karthikeyan, Smruthi0000-0001-6226-4536
Rodriguez-R, Luis M.0000-0001-7603-3093
Heritier-Robbins, Patrick0000-0002-6905-0191
Hatt, Janet K.0000-0002-5666-0994
Huettel, Markus0000-0003-4844-7525
Kostka, Joel E.0000-0003-3051-1330
Konstantinidis, Konstantinos T.0000-0002-0954-4755
Additional Information:This research was made possible by grants from The Gulf of Mexico Research Initiative (RFP V Grant No 321611-00 as well as grants to the C-IMAGE II, C-IMAGE III, and Deep-C consortia). Data are publicly available at Associated NCBI accession numbers have also been provided where applicable (Supporting Information Table S1 as well as in the MiGA webserver). The authors would also like to thank Ramachandra Sivakumar from the Center for Spatial Planning Analytics and Visualization (CSPAV) at Georgia Institute of Technology for his valuable input with the incorporation of GIS layers into the webserver. The authors declare no conflict of interest.
Funding AgencyGrant Number
Gulf of Mexico Research Initiative321611-00
Issue or Number:6
Record Number:CaltechAUTHORS:20221215-540530000.27
Persistent URL:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:118359
Deposited By: George Porter
Deposited On:16 Dec 2022 16:21
Last Modified:16 Dec 2022 16:21

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