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Research article - Peer-reviewed, 2022

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Somee, Maryam Rezaei; Amoozegar, Mohammad Ali; Dastgheib, Seyed Mohammad Mehdi; Shavandi, Mahmoud; Maman, Leila Ghanbari; Bertilsson, Stefan; Mehrshad, Maliheh


Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. Results Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria. Conclusion Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.


Aerobic hydrocarbon degradation; Alkane mono-oxygenase; Ring-hydroxylating oxygenase; Archaea; Bacteria

Published in

BMC Genomics
2022, volume: 23, number: 1, article number: 690
Publisher: BMC

Authors' information

Somee, Maryam Rezaei
University of Tehran
Amoozegar, Mohammad Ali
University of Tehran
Dastgheib, Seyed Mohammad Mehdi
Research Institute of Petroleum Industry
Shavandi, Mahmoud
Research Institute of Petroleum Industry
Maman, Leila Ghanbari
University of Tehran
Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment
Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment

UKÄ Subject classification

Biocatalysis and Enzyme Technology

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