Comparative whole-genome analysis of novel marine Vibrio campbellii from pure and non-axenic cultures reveals a unique plasmid

Abstract

Background Vibrio spp. is ubiquitously present in the marine environment. Numerous Vibrio species are known pathogens affecting animal welfare and ecosystem function, causing significant economic losses. Hence, monitoring their presence accurate taxonomic identification and understanding their functional potential are important for disease control. All of this information is contained in the microorganism’s genome, which is easiest obtained from bacterial culture. Whole-genome sequencing in combination with new bioinformatics tools enables high phylogenetic resolution and provides insights into the full genetic potential of the microorganism, beyond traditional microbiological approaches. Results We assembled a complete genome of Vibrio campbellii isolated from the coastal Adriatic Sea. We showed that comparable genome sequences could be assembled from pure and non-axenic cultures (Average Nucleotide Identity value 99.98%) using a set of different bioinformatics tools, overcoming the problems of culture contamination frequently encountered in environmental microbiology. Based on the complete genome, we were able to accurately determine taxonomy, which often cannot be reliably determined with commonly applied genetic markers (e.g., 16S rRNA sequences). Pangenomic analyses with 10 reference genomes suggested that our newly assembled genome clusters in the sublineages of V. campbellii associated with diseases of marine organisms (e.g., Acute Hepatopancreatic Necrosis Disease in shrimps). Furthermore, our analysis revealed unique genomic features mainly associated with a new unique plasmid connected to bacterial defense (e.g., type I restriction-modification systems, CRISPR Csa3 proteins) and with the propagation of genetic material (e.g., transposases associated with horizontal gene transfer, ardC genes increasing plasmids host range). Conclusions Our completed genome assembly from a non-axenic culture highlights the possibility of obtaining complete genomic information when encountering contamination events, or beyond our study, even in the case of co-cultures. With this new complete V. campbellii genome we are contributing novel insights into the genomic characteristics and functional potential of this potential pathogen. In the light of projected human pressures on coastal regions and associated marine ecosystem services, pathogen surveillance and control of possible disease outbreaks are crucial. Our study reveals a novel, unique mobile element associated with V. campbellii that could potentially ease the propagation of its associated genetic material across different microbes.