Abstract
Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.
Highlights
Hydrocarbons are diverse compounds consisting of carbon and hydrogen atoms that differ in size, structure, and reactivity
Anaerobic hydrocarbon degradation genes were only detected in the genomes of anaerobes, further showing the prediction accuracy of CANT-HYD Hidden Markov Model (HMM)
Ethyl Benzene (Toluene)-benzene monooxygenase beta subunit (TmoB_BmoB) was found adjacent to TmoA_BmoA gene on the Pseudoxanthomonas spadix BD-a59 genome with a score above the noise cutoff, which indicates that it likely is a TmoB_BmoB gene divergent from the seed sequences that were used to make the HMM. These results show that CANT-HYD reliably identifies hydrocarbon degradation marker genes and can be used to predict the hydrocarbon degradation potential of genomes and in metagenomes
Summary
Hydrocarbons are diverse compounds consisting of carbon and hydrogen atoms that differ in size, structure, and reactivity. They can be the product of geological processes as well as produced biogenically by organisms in all domains of life (Tornabene et al, 1969; Lerdau et al, 1997; LeaSmith et al, 2015). Microorganisms employ a range of enzymes to use hydrocarbons (Rabus et al, 2016; Xu et al, 2018) in oxic and anoxic conditions. Catabolism of these hydrocarbons is coupled with
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