Plasmids are extrachromosomal DNA molecules, typically circular, commonly found in bacteria and other unicellular organisms. Plasmids are regularly used in molecular biology and biotechnology as cloning and expression vectors, and are infamous as carriers and spreaders of antibiotic resistance genes. However, they also play an important environmental role as major drivers of horizontal gene transfer, providing a pool of functional genes which can be transferred to different microorganisms and provide them with additional “superpowers”.
Our knowledge about plasmids comes mostly from several model plasmids which were extensively studied and from hospital and agriculture-related isolates. In recent years, with the increasing availability of metagenomic data, there are more and more studies of overall plasmid populations (plasmidome) from different environments, such as soil, wastewater, bovine guts etc., but still very little is known about marine plasmids. To date, only ~1.4% of the plasmids deposited in the NCBI nucleotide database are from marine origin. Moreover, from the available studies about marine plasmids we learn that marine plasmids are different from the known terrestrial plasmids. Therefore, there is a large gap in our knowledge about plasmids from marine origin.
In my talk I will present our study of plasmids from the Red Sea. We developed a pipeline for plasmid detection from available metagenomic data, and used it to identify 362 plasmid candidates from 45 samples from the Red Sea. We characterized the candidates, studied their genetic arsenal, and identified correlations between the plasmid population and environmental parameters. From the 362 candidates, only 1 is a known plasmid. 37 candidates contain ORFs which are clearly plasmid-related (therefore defined as probably novel plasmids), and 90 candidates contain ORFs which may be plasmid-related (therefore defined as putative novel plasmids). Yet, most of the candidates are unknown, containing ORFs with unknown function, and experimental validation is needed. Our study provides another example for the uniqueness of marine plasmids and emphasizes the need for further studies and characterization of marine plasmids.