An assessment of the microbial community in an urban fringing tidal marsh with an emphasis on petroleum hydrocarbon degradative genes

Highlights: • A fringing tidal marsh microbial community is dominated by Beta- and Gammaproteobacteria. • Pseudomonad and Rhizobiales type alkB and CYP 153A1 alkane hydroxylase genes were detected. • Pseudomonads dominated communities enriched with shorter chain n-alkanes. • Rhodococci dominated a community enriched with dodecane. • AlkB alkane hydroxylases were more abundant than CYP 153A1 hydroxylases in marsh sediments. - Abstract: Small fringing marshes are ecologically important habitats often impacted by petroleum. We characterized the phylogenetic structure (16S rRNA) and petroleum hydrocarbon degrading alkane hydroxylase genes (alkB and CYP 153A1) in a sediment microbial community from a New Hampshire fringing marsh, using alkane-exposed dilution cultures to enrich for petroleum degrading bacteria. 16S rRNA and alkB analysis demonstrated that the initial sediment community was dominated by Betaproteobacteria (mainly Comamonadaceae) and Gammaproteobacteria (mainly Pseudomonas), while CYP 153A1 sequences predominantly matched Rhizobiales. 24 h of exposure to n-hexane, gasoline, dodecane, or dilution culture alone reduced functional and phylogenetic diversity, enriching for Gammaproteobacteria, especially Pseudomonas. Gammaproteobacteria continued to dominate for 10 days in the n-hexane and no alkane exposed samples, while dodecane and gasoline exposure selected for gram-positive bacteria. The data demonstrate that small fringing marshes in New England harbor petroleum-degrading bacteria, suggesting that petroleum degradation may be an important fringing marsh ecosystem function.