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

Autor: Karthikeyan S; School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA., Rodriguez-R LM; School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA., Heritier-Robbins P; School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA., Hatt JK; School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA., Huettel M; Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA., Kostka JE; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.; School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA., Konstantinidis KT; School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA.; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
Jazyk: angličtina
Zdroj: Environmental microbiology [Environ Microbiol] 2020 Jun; Vol. 22 (6), pp. 2094-2106. Date of Electronic Publication: 2020 Mar 16.
DOI: 10.1111/1462-2920.14966
Abstrakt: 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.
(© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)
Databáze: MEDLINE
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