Complete genome sequence of a marine Pseudoalteromonas bacterial strain

Pseudoalteromonas species are a group of gamma proteobacteria exclusively isolated from marine waters worldwide (1). These species are often found in extreme environments, including cold habitats and deep-sea sediments (2–4). Interestingly, Pseudoalteromonas species are frequently associated with eukaryotic organisms such as sponges, tunicates, and various marine algae, and play a role in controlling harmful dinoflagellate blooms (5–9). This genus forms biofilm and produces active compounds (10, 11). The ecological success and diverse associations of this genus reveal its potential as a vast reservoir of active metabolites, making it highly relevant for both fundamental and applied research. The genus Pseudoalteromonas is classified into pigmented and non-pigmented clades, with pigmented species often linked to a higher propensity for natural product synthesis (12–14). Despite the identification of over 2,000 species, the full extent of the genus diversity remains largely unexplored.

Here, we report the complete genome sequences of a pigmented Pseudoalteromonas sourced from the National Collection of Industrial Microorganisms (NCIMB_1079) as Pseudomonas fluorescens. This discrepancy has been reported to NCIMB. Pseudoalteromonas (1,079 NCIMB) was isolated on 12 October 1962, from sea water, 16 km East South East of Aberdeen in the United Kingdom (latitude 57°6′15″N, longitude 1°44′15″W). The salinity of sea water at the sampling site was 34.7‰ (15). Upon isolation, the strain was plated on Anderson’s marine medium (16). Upon purchase in October 2019, the strain was stored as a glycerol stock at −80°C. Cells were cultured in liquid Luria–Bertani (LB) medium at 30°C with shaking at 180 rpm for 48 h. DNA was extracted using the MagAttract High Molecular Weight DNA Kit (Cat. no. 67563) following the manufacturer’s instructions. Genomic DNA was sheared with Covaris g-TUBES at 4,000 RPM. The DNA libraries were prepared without size selection using SMRTbell Express Template Prep Kit 2.0 protocol following the Pacific Biosciences Procedure. DNA was sequenced by Genome Quebec using the Pacific Biosciences Sequel platform with Circular Consensus Sequencing (CCS). SmrtLink v8.0 was used to monitor run QC, demultiplex reads, remove adapter sequences, and generate subreads filtered for minimum read quality. CCS reads were generated from subreads with CCS 6.4.0 and assembled with Canu (v2.2) (17). Genome coverage was 118.11×, with an estimated size of 4.5 Mb (Table 1, Fig. 1). Among the three contigs, two were identified as chromosomes and the third as a plasmid. The large chromosome, small chromosome, and plasmid display overlaps at their ends measuring 15.4, 14.2, and 16.4 kb, respectively. The identification of plasmids was performed using two plasmid prediction tools: PlasmidHunter (v1.4) (18) and PLASMe (v1.1) (19). These tools predicted a plasmid with a length of 86,689 bp (Fig. 1). Gene annotation and functional assignment were performed using anvi'o v7.1 (20). Additional gene annotations were performed with DFAST 1.2.20 (21), Prokka (v1.14.6) (22) with compliant parameter and EggNOG (v2.1.12) (23). For all softwares, default parameters were used except where otherwise noted. The parameters -m [diamond] and pfam_realign [realign] were used for EggNOG. The assembled genome is available on BacBrowse (https://BacBrowse.univ-nantes.fr).

This study was supported by Connect Talent EpiAlg grant from Région Pays de la Loire to L.T. The authors thank Udita Chandola for DNA extraction. We are grateful to the Genomics Core Facility GenoA, member of Biogenouest and France Genomique and to the Bioinformatics Core Facility BiRD, member of Biogenouest and Institut Français de Bioinformatique (IFB) (ANR-11-INBS-0013) for the use of their resources and their technical support.

L.T. conceived, designed, and supervised the study. E.M. performed the bioinformatics analysis. T.C. contributed to the bioinformatics analysis. L.T. wrote the manuscript with input from E.M. and T.C. All authors read and approved the manuscript.