CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation

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.

Geological processes mediate a microbial dispersal loop in the deep biosphere

“…3 and table S7) and encoded glycyl radical enzymes related to alkylsuccinate synthases proposed to mediate anaerobic alkane biodegradation via addition to fumarate ( 34 , 35 ). Using newly developed hidden Markov models for annotating alkylsuccinate synthases ( 36 ), putative assA gene sequences in thermophilic spores are shown here to diverge from canonical assA found in mesophilic Proteobacteria (fig. S5).…”

“…Metabolic pathways were identified using KEGG Decoder ( 69 ) to parse genes annotated with KEGG Orthology using BlastKOALA ( 70 ). Hydrocarbon degradation genes were additionally annotated using CANT-HYD ( 36 ) following gene predictions made using Prodigal version 2.6.3 ( 71 ). MAGs were classified with GTDB-Tk version 1.3.0 ( 72 ) and by alignment with Silva database version 138 ( 62 ) using mothur version 1.39.5 ( 73 ) in instances where 16 S rRNA gene was recovered by rRNAFinder ( 68 ).…”

Environmental Selection and Biogeography Shape the Microbiome of Subsurface Petroleum Reservoirs

“…Hydrocarbon activation genes detected in metagenome libraries. Genes were identified using CANT-HYD HMMs ( 27 ). Download .…”

“…To identify the potential for microbial degradation of crude oil, functional marker genes encoding enzymes that initiate aerobic or anaerobic hydrocarbon biodegradation, by activating either alkane or aromatic compounds, were examined using a set of 37 hidden Markov models (reference 27 ; Fig. 4 ; Table S7 ).…”

Natural and oil surface slicks as microbial habitats in marine systems: A mini review

“…Apparently, microbial communities and marine oil snow production vary according to environmental conditions related to seasonal changes (temperature and light dependent) (Ziervogel et al, 2014;Ortmann et al, 2020). In general, microorganisms are capable of utilizing hydrocarbons under oxic, microaerophilic, and anoxic conditions as carbon source (Khot et al, 2021), but in marine oil slicks, microbial oil degradation dominantly occurs aerobically (Kimes et al, 2014;Gutierrez et al, 2016). Surprisingly, obligately anaerobic and potential hydrocarbonoclastic Fusobacteria have been isolated from DWH oil slicks.…”