A new molecular approach based on qPCR for the quantification of fecal bacteria in contaminated marine sediments

Harbour sediments are periodically subjected to dredging operations and their management is mainly based on the assessment of the chemical contamination levels, but the potential risks posed by the presence of pathogenic microorganisms have been largely neglected. Here we first developed new molecular protocols based on the use of Real Time Quantitative PCR (qPCR), targeting both bacterial DNA and the transcription product (rRNA), for the identification and quantification of bacteria of fecal origin (Escherichia coli, Enterococcus spp. and Salmonella spp.) in contaminated harbour sediments. Then, we assessed the effects of bioremediation treatments, conventionally utilized for abating the hydrocarbon contamination in the sediment, on the abundance of fecal bacteria (FB). The qPCR technique was highly specific, sensitive and reproducible, and detected a number of fecal bacteria significantly higher than the classical cultivation techniques. Sediments subjected to bioremediation experiments by biostimulation with inorganic nutrients at different temperatures displayed a significant increase of the abundance of E. coli and Enterococcus spp. These findings suggest the risk of a potential increase of the contamination by pathogenic microorganisms of fecal origin during bioremediation and, as such, highlight the importance of careful monitoring this biological component in harbour sediments when subjected to bio-treatments.

► Harbour sediments can host high numbers of fecal bacteria (FB).
► Need of new molecular tools for the analysis of FB in harbour sediments.
► DNA- and RNA-based qPCR analyses are more effective than cultivation.
► Biotreatments to reduce chemical contamination increase numbers of FB in sediments.