Abstract
Modeling crude-oil biodegradation in sediments remains a challenge due in part to the lack of appropriate model organisms. Here we report the metagenome-guided isolation of a novel organism that represents a phylogenetically narrow (>97% 16S rRNA gene identity) group of previously uncharacterized, crude-oil degraders. Analysis of available sequence data showed that these organisms are highly abundant in oiled sediments of coastal marine ecosystems across the world, often comprising ~30% of the total community, and virtually absent in pristine sediments or seawater. The isolate genome encodes functional nitrogen fixation and hydrocarbon degradation genes together with putative genes for biosurfactant production that apparently facilitate growth in the typically nitrogen-limited, oiled environment. Comparisons to available genomes revealed that this isolate represents a novel genus within the Gammaproteobacteria, for which we propose the provisional name “Candidatus Macondimonas diazotrophica” gen. nov., sp. nov. “Ca. M. diazotrophica” appears to play a key ecological role in the response to oil spills around the globe and could be a promising model organism for studying ecophysiological responses to oil spills.
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Data availability
The data reported in this paper are publicly available through the Gulf of Mexico Research Initiative Information & Data Cooperative (GRIIDC), under the accession numbers R5.x278.000:0014 and R5.x278.000:0002 (NCBI accession MH795143). The metagenome sequences as well as the assembled genome sequences are also available at http://enve-omics.ce.gatech.edu/data/.
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Acknowledgements
The authors would like to thank Dr. Aharon Oren for his valuable input on the naming of the new type species. This research was made possible by a grant from The Gulf of Mexico Research Initiative (Grant No 321611-00; RFP V). Data are publicly available through the Gulf of Mexico Research Initiative Information & Data Cooperative (GRIIDC) at https://data.gulfresearchinitiative.org (UDI: R5.x278.000:0014, UDI: R5.x278.000:0002). RR-M acknowledges the financial support for his sabbatical stay at Georgia Tech from the Spanish Ministry of Sciences, Innovation and Universities (Grant No. PRX18/00048).
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Karthikeyan, S., Rodriguez-R, L.M., Heritier-Robbins, P. et al. “Candidatus Macondimonas diazotrophica”, a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments. ISME J 13, 2129–2134 (2019). https://doi.org/10.1038/s41396-019-0400-5
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DOI: https://doi.org/10.1038/s41396-019-0400-5
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