Next-Generation Sequencing of Functional Marker Genes for Anaerobic Degraders of Petroleum Hydrocarbons in Contaminated Environments

Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams

“… Benzoyl-CoA pathway genes and subunits, from 4-hydroxybenzoyl-CoA and benzoate to 3-hydroxypimeloyl-CoA, and their presence in the selected contig bins (MAGs). Benzoyl-CoA reductase genes for two enzyme systems are displayed: the class-I, ATP-dependent bcrABCD (associated with facultative anaerobes), as well as the class-II, ATP-independent bamB (associated with obligate anaerobes) ( 15 , 32 ). See Table S2 for number of occurrences of each gene in the MAGs and metagenomes.…”

“…The most commonly detected benzoyl-CoA reductase gene subunits were those of bcrABCD from the class-I enzyme system, associated with facultative anaerobes such as Magnetospirillum and Thauera spp. ( 15 , 32 ). The Prokka ( 31 ) annotations contained the highest number of these; however, the BlastKOALA ( 38 ) annotations included an additional enzyme system ( Table 2 ; Table S2 ).…”

“…This additional enzyme system, found in S. aromaticivorans bin 2.2, was the ATP-independent class-II benzoyl-CoA reductase gene subunit, bamB , associated with obligate anaerobes ( Fig. 1 ) ( 32 ).…”

“…Unlike the novel Krumholzibacteriota MAG, S. aromaticivorans has been identified within the coal seam environment on numerous previous occasions. Indeed, the CSMB reference set presently lists six distinct taxa from the Syntrophorhabdus genus, and one or more of these have been identified from coal-bearing basins of eastern Australia on 23 different occasions (Table S5) ( 8 , 32 ). Recently, Syntrophorhabdus have also been detected in the Powder River Basin, USA, and implicated as a potential primary degrader of organic matter in coal based on both their increase in abundance after algal-amendment and on the published syntrophic degradative abilities for monoaromatic compounds by the type species when grown in coculture with a methanogen ( 23 ).…”

“…Resultant contigs were annotated using prokkaMeta v1.14.5 ( 31 ), and these annotation descriptions were then searched for any class-I enzyme system benzoyl-CoA reductase subunits, which are associated with facultative anaerobes such as Magnetospirillum and Thauera spp. ( 15 , 32 ). Contigs with benzoyl-CoA reductase gene subunits were then also explored, using the Prokka annotations, for other genes in the benzoyl-CoA pathway.…”