The Crude-Oil Microbiome Webserver: An Interactive, Searchable (Meta-)Genome Repository That Expands The Catalogued Diversity Of Crude-Oil-Associated Microbes

Smruthi Karthikeyan1, Luis M Rodriguez-R2, Patrick Heritier-Robbins2, Markus H Huettel3, Joel E Kostka4 and Konstantinos Konstantinidis4, (1)Georgia Institute of Technology Main Campus, School of Civil and Environmental Engineering, Atlanta, GA, United States, (2)Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, United States, (3)Florida St Univ, Department of Earth, Ocean and Atmospheric Sciences, Tallahassee, FL, United States, (4)Georgia Institute of Technology Main Campus, Atlanta, GA, United States
Abstract:
Oil spills can have pronounced impacts on natural ecosystems and the microbial community dynamics following such spills have only recently been documented, especially for the Deepwater Horizon (DWH) spill in the Gulf of Mexico, one of the largest marine oil spills. The microbial interactions that ultimately dictate the fate of oil are highly complex and remain poorly understood but genome-revolved metagenomics can help unravel these complex interactions. Public repositories host a plethora of sequence data from a diverse array of environments in the form of raw-reads or assembled MAGs (metagenome-assembled genomes). However, lack of environmental context in the form of in situ physicochemical data and comparative MAG analysis capabilities in these repositories have severely limited the interpretation of the data and progress. Here, we curated a comprehensive and searchable database documenting microbial populations that responded to accidental or natural oil spills across a range of global ecosystems along with their underlying physicochemical data, geocoded via GIS to reveal their biogeographic distribution patterns. Analysis of the ~2,000 MAGs available in the database revealed ecological niche specialization within specific habitats (e.g., specialization to coastal sediments vs. water-column vs. deep-sea sediments) as well as distinct biogeographic distribution of MAGs associated with the DWH spill. Over 95% of the recovered MAGs belong to novel/uncultured taxa underscoring the limited representation of cultured or characterized organisms associated with response to oil contamination. Whole genome comparisons identified a total of 1,536 unique clades at the species level (average nucleotide identity >95%) among these MAGs, revealing extensive species diversity. Our interactive metagenomics repository will help provide a predictive understanding of the microbial response to oil perturbations and identify biomarkers that can universally predict ecosystem recovery.
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