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

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Title: Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes.
Authors: Karthikeyan, Smruthi1 (AUTHOR), Rodriguez‐R, Luis M.1 (AUTHOR), Heritier‐Robbins, Patrick1 (AUTHOR), Hatt, Janet K.1 (AUTHOR), Huettel, Markus2 (AUTHOR), Kostka, Joel E.3,4 (AUTHOR), Konstantinidis, Konstantinos T.1,3 (AUTHOR) kostas@ce.gatech.edu
Source: Environmental Microbiology. Jun2020, Vol. 22 Issue 6, p2094-2106. 13p.
Subjects: Oil spill cleanup, Geographic information systems, Petroleum, Ecological niche, Petroleum reservoirs
Geographic Terms: Gulf of Mexico
Abstract: Summary: 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. [ABSTRACT FROM AUTHOR]
Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes.
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  Data: <searchLink fieldCode="JN" term="%22Environmental+Microbiology%22">Environmental Microbiology</searchLink>. Jun2020, Vol. 22 Issue 6, p2094-2106. 13p.
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  Data: <searchLink fieldCode="DE" term="%22Oil+spill+cleanup%22">Oil spill cleanup</searchLink><br /><searchLink fieldCode="DE" term="%22Geographic+information+systems%22">Geographic information systems</searchLink><br /><searchLink fieldCode="DE" term="%22Petroleum%22">Petroleum</searchLink><br /><searchLink fieldCode="DE" term="%22Ecological+niche%22">Ecological niche</searchLink><br /><searchLink fieldCode="DE" term="%22Petroleum+reservoirs%22">Petroleum reservoirs</searchLink>
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  Data: <searchLink fieldCode="DE" term="%22Gulf+of+Mexico%22">Gulf of Mexico</searchLink>
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  Data: Summary: 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. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1111/1462-2920.14966
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      – SubjectFull: Petroleum
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      – TitleFull: Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil‐associated microbes.
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              Text: Jun2020
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