Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies

Abstract

Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P. baetica strain a390T was sequenced using a unique combination of Ion Torrent semiconductor and Oxford Nanopore methods as part of a collaborative community-led project. The use of high-quality Ion Torrent sequences with long Nanopore reads gave rapid, high-contiguity and -quality, 16-contig genome sequence. Whole genome phylogenetic analysis places P. baetica within the P. koreensis clade of the P. fluorescens group. Comparison of the main genomic features of P. baetica with a variety of other Pseudomonas spp. suggests that it is a highly adaptable organism, typical of the genus. This strain was originally isolated from the liver of a diseased wedge sole fish, and genotypic and phenotypic analyses show that it is tolerant to osmotic stress and to oxytetracycline.

Reliable Identification of Environmental Pseudomonas Isolates Using the rpoD Gene

“…Pseudomonas species are ubiquitous bacteria present in terrestrial, aquatic, and marine environments [ 1 , 2 ]. While several species are a threat to human health or food industry, with detrimental impacts on crops and aquaculture, the large majority of the species are commensals [ 3 , 4 , 5 ]. In fact, several species have been described as potential biocontrol agents to fight against diverse plant pathogens but also for bioaccumulation or biodegradation of pollutants [ 6 , 7 ].…”

A Rare Case of Mixed Infectious Keratitis Caused by <b><i>Pseudomonas koreensis</i></b> and <b><i>Aspergillus fumigatus</i></b>

“…We believe that the environmental niches of this species have not been fully characterized. It has been isolated from soil in Northern France [13] and related species such as P. baetica have been isolated from other parts of Europe, notably Spain [14]. There was a 3-week delay in identification of the causative organism in our case and it required multiple corneal scrapes for microbiological investigation.…”

Lectin-Like Bacteriocins

“…With few exceptions, Pseudomonas isolates only host one L-type bacteriocin gene in their genome, if any ( Ghequire and De Mot, 2014 ). The latter observation strongly contrasts with modular S-type bacteriocins for which usually multiple representatives, albeit with different receptor-binding/toxin domain combinations, are present within a single Pseudomonas genome ( Loper et al, 2012 ; Ghequire and De Mot, 2014 ; Sharp et al, 2017 ; Beaton et al, 2018 ). Bacteriocin sequences from strains encoding two LlpAs are usually dissimilar (30–52% pairwise AA id), arguing against a duplication event.…”