Identity and hydrocarbon degradation activity of enriched microorganisms from natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI)

A previous cultivation-independent investigation of the microbial community structure of natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI) revealed the dominance of uncultured bacterial taxa belonging to the phyla Deferribacterota and Coprothermobacterota and the orders Thermodesulfobacteriales, Thermales, and Burkholderiales. Here we report on a cultivation-dependent approach to identify members of these groups involved in hydrocarbon degradation in the KRI oil and asphalt seeps. For this purpose, we set up anoxic crude oil-degrading enrichment cultures based on cultivation media known to support the growth of members of the above-mentioned taxonomic groups. During 100–200 days incubation periods, nitrate-reducing and fermentative enrichments showed up to 90% degradation of C–C alkanes and up to 28% degradation of C–C alkanes along with aromatic hydrocarbons. Community profiling of the enrichment cultures showed that they were dominated by diverse bacterial taxa, which were rare in situ community members in the investigated seeps. Groups initially targeted by our approach were not enriched, possibly because their members are slow-growing and involved in the degradation of recalcitrant hydrocarbons. Nevertheless, the enriched taxa were taxonomically related to phylotypes recovered from hydrocarbon-impacted environments as well as to characterized bacterial isolates not previously known to be involved in hydrocarbon degradation. Marker genes (assA and bssA), diagnostic for fumarate addition-based anaerobic hydrocarbon degradation, were not detectable in the enrichment cultures by PCR. We conclude that hydrocarbon biodegradation in our enrichments occurred via unknown pathways and synergistic interactions among the enriched taxa. We suggest, that although not representing abundant populations in situ, studies of the cultured close relatives of these taxa will reveal an unrecognized potential for anaerobic hydrocarbon degradation, possibly involving poorly characterized mechanisms.