Oil pollution drives microbial community and remendiation potential in Ancona harbor sediments

Every year, a high amount of hydrocarbon pollutants enters in the Mediterranean Sea waters because of the high oil related traffic and the high urbanization of its coastline. Marine environments exposed to hydrocarbons are often subjected to co-contamination by heavy metals that make them particularly difficult to clean up. Autochthonous bioaugmentation (ABA) is a bioremediation practice based on the use of autochthonous microbial populations, previously enriched under laboratory conditions, which could be useful for oil remediation in co-contaminated environments. In this perspective, we studied by cultivation dependent and independent approaches the Ancona harbor sediments comparing polluted stations inside the harbor and five stations located offshore considered pristine. The aims of this work were to i) investigate which environmental parameters are the main driving factors influencing the bacterial communities inhabiting the Ancona harbor’s sediments, ii) establish enrichment cultures using different hydrocarbons as the sole carbon source aiming to evaluate their direct effects on the bacterial communities composition and iii) establish a collection of hydrocarbon degrading bacterial isolates potentially exploitable in ABA. Microbial abundance, evaluated through DAPI staining, showed typical values of coastal sediments with high organic load in all sites. The bacterial communities composition inhabiting both the Ancona harbor sediments and microcosm enrichments set up with the contaminated sediments were investigated using different molecular techniques, including DNA-based fingerprinting and 16S rRNA pyrosequencing. The analysis of bacterial diversity by means of DNA-based fingerprinting unveiled different phylogenetic richness in the bacterial communities colonizing contaminated and not contaminated sediments. A distance-based multivariate analysis for a linear model was used to investigate possible links between bacterial richness and the wide array of environmental data collected in each station, including the content of different classes of pollutants. This analysis identified the hydrocarbons and heavy metals’ concentration as the main drivers of the bacterial communities’ richness. On the other side, the study of enriched bacterial communities showed the selection of different and specialized bacterial populations driven by different hydrocarbons added as unique carbon source. Crude oil and diesel oil selected mainly -proteobacteria of the genera Alcanivorax and Marinobacter while Bacilli was the dominant phylum in the naphthalene enrichment, which  -proteobacterial community was represented primarily by Halomonas. Finally, a strain collection was obtained from the established enrichments and was screened for metabolic traits of interest for oil degradation (e.g. biosurfactants production, cell hydrophobicity, uric acid and catechol degradation, biofilm formation and presence of genes for heavy metals resistance). The results showed the selection of bacterial isolates, belonging to different species, potentially exploitable for ABA application. Overall, this work improved the knowledge about environmental drivers that influence the enrichment of sediment-dwelling microbial communities involved in the degradation of oil pollutants, an important step towards the implementation of successful bioremediation strategies.