Potential hydrocarbon-degrading microorganisms in Baltic Sea sediments

The spill of crude oil and other petroleum derivatives comprises the majority of ocean pollution and leads to acute and chronic damage to exposed marine organisms and coastal ecosystems. Some bacteria and fungi are known to biodegrade petroleum hydrocarbons in terrestrial and aquatic environments. In this study, sediment samples from the Baltic Sea, collected near an oil terminal, and from the Curonian Lagoon strait, an area under high anthropogenic and shipping pressure, were explored as a source of microorganisms with potential for hydrocarbon degradation. Next-generation sequencing showed the presence of 25 prokaryotic phyla with relative abundances over 1 % in Baltic Sea and Curonian Lagoon sediments, including hydrocarbon-associated taxa such as Thalassolituus, Alcanivorax, and Marinomonas, alongside 5 fungal phyla and 9 classes over 1 % relative abundance, including diverse members of Chytridiomycota, Ascomycota and Rozellomycota, suggesting exposure to petroleum compounds in the sediments. The BLASTn comparison of the obtained ASVs with 16S rRNA gene and ITS region sequences of hydrocarbon degrading bacteria and fungi available at GeneBank database showed a high sequence similarity of bacterial and fungal ASVs with multiple hydrocarbon-degrading taxa. The bacterial ASVs were closely related to Bacillus subtilis and other hydrocarbon-degrading Bacilli, as well as diesel-degrading Flavobacterium petrolei, petroleum-degrading Polaribacter dokdonensis, phenantrene-degrading Pseudomonas guineae and diesel-degrading P. aeruginosa, and Rhodobacter sphaeroides. The fungal ASVs showed a 100 % identity with hydrocarbon-degrading Penicillium rubens. Through the enrichment of sediment samples with crude oil, marine diesel oil and lubricating oil, strains belonging to the genera Pseudomonas and Priestia were isolated, as well as fungi from the genera Yarrowia, Cyberlindnera, Geotrichum, Pichia, Candida and Fusarium. The results suggest that bacterial and fungal communities present in sediments demonstrate potential for future application in the bioremediation of petroleum hydrocarbons and other pollutants.