Harbour dredging – effective transport for faecal bacteria.

A review of: Gian Marco Lunaa, Antonio Dell’Annoa, Biancamaria Pietrangelib, Roberto Danovaroa. (2012). A new molecular approach based on qPCR for the quantification of fecal bacteria in contaminated marine sediments. Journal of Biotechnology. 157 (1), 446–453

Marine sediments can be a reservoir for pathogenic and virulent strains of microorganisms by providing protection against environmental pressures. Disturbance of these sediments has been suggested to significantly increase the risk of harmful faecal bacteria contaminating marine systems. The need for harbour environments to be routinely dredged is a key example of anthropogenic re-suspension of these marine sediments. Sediments are removed to maintain the depth of harbours areas to allow access for marine vessels. The sediment is often redistributed to adjacent areas which can have detrimental effects on the chemical-physical and biological characteristics of the marine systems. Therefore it is critical to maintain the microbiological quality of these marine systems through accurate quantification approaches.

Modern molecular approaches of bacterial quantification, based on real time PCR assays, are capable of identifying bacteria that more traditional (culture based) approaches are not capable of. Similar procedure can also be applied to identify rRNA of the bacteria which can help to increase understanding the potential risk associated with faecal bacteria by providing information on metabolic activity. These molecular approaches are commonly used in areas like the food industry however have never been utilised to monitor harbour sediments. The aim of this investigation was to develop molecular tools to improve the identification and quantification of faecal bacteria in the marine harbour environment.

The sediments samples used in this investigation were collected from two harbours located in the Adriatic Sea. Enumeration of cultivable faecal bacteria was carried out on two different types of agar and quantified using colony forming units. Enumeration of total faecal bacteria by Real Time Quantitative PCR was determined by extracting DNA from sediment samples and staining them by using a mixture of specific primer sets that were designed to identify pathogenic regions of faecal bacteria. To determine number ribosomal RNA, extracted RNA from the bacteria was tested for potential DNA carryover by performing a conventional PCR procedure and using the products electrophoresis to indicate the absence of carryover DNA. (The paper did not explain what was meant by “DNA carryover” however I assume that this refers to the products of the extracted rRNA after they were run through the PCR procedure.)

The use of both traditional and modern methods to quantify faecal bacteria on the same sediment samples allowed the authors to directly compare the effectiveness of the techniques. The modern molecular method identified 65–1571 times higher E. coli abundance and 11-57 times higher enterococcus abundance in comparison to the traditional culture based method. Due to the ability to design primers the molecular quantification was specific and sensitive to known problematic bacteria. The use of the reverse-transcription real time PCR assay showed that there was significantly high number of rRNA in the faecal bacteria indicating that there was high metabolic activity in the sediments.

This was a very interesting study that represents a promising step forward in the development of techniques used to monitor contaminated marine environments. It is evident from the results that these new molecular methods are incredibly valuable to allow the accurate detection of very low levels of bacterial indicators. This is incredibly important as infections of humans can be triggered when faecal bacteria are present in numbers as low as 10 to 100 cells. Not only will these molecular methods allow us to identify the source of the contamination which will further help management efforts. I found it surprising that despite these marine environments are obviously high risk areas these new molecular methods have not been utilised sooner.