AUTHOR=Girard Léa , Lood Cédric , De Mot René , van Noort Vera , Baudart Julia 

TITLE=Genomic diversity and metabolic potential of marine Pseudomonadaceae

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1071039

DOI=10.3389/fmicb.2023.1071039

ISSN=1664-302X

ABSTRACT=<p>Recent changes in the taxonomy of the <italic>Pseudomonadaceae</italic> family have led to the delineation of three new genera (<italic>Atopomonas</italic>, <italic>Halopseudomonas</italic> and <italic>Stutzerimonas</italic>). However, the genus <italic>Pseudomonas</italic> remains the most densely populated and displays a broad genetic diversity. <italic>Pseudomonas</italic> are able to produce a wide variety of secondary metabolites which drives important ecological functions and have a great impact in sustaining their lifestyles. While soilborne <italic>Pseudomonas</italic> are constantly examined, we currently lack studies aiming to explore the genetic diversity and metabolic potential of marine <italic>Pseudomonas</italic> spp. In this study, 23 <italic>Pseudomonas</italic> strains were co-isolated with <italic>Vibrio</italic> strains from three marine microalgal cultures and <italic>rpoD</italic>-based phylogeny allowed their assignment to the <italic>Pseudomonas oleovorans</italic> group (<italic>Pseudomonas chengduensis</italic>, <italic>Pseudomonas toyotomiensis</italic> and one new species). We combined whole genome sequencing on three selected strains with an inventory of marine <italic>Pseudomonas</italic> genomes to assess their phylogenetic assignations and explore their metabolic potential. Our results revealed that most strains are incorrectly assigned at the species level and half of them do not belong to the genus <italic>Pseudomonas</italic> but instead to the genera <italic>Halopseudomonas</italic> or <italic>Stutzerimonas</italic>. We highlight the presence of 26 new species (<italic>Halopseudomonas</italic> (<italic>n</italic> = 5), <italic>Stutzerimonas</italic> (<italic>n</italic> = 7) and <italic>Pseudomonas</italic> (<italic>n</italic> = 14)) and describe one new species, <italic>Pseudomonas chaetocerotis</italic> sp. nov. (type strain 536<sup>T</sup> = LMG 31766<sup>T</sup> = DSM 111343<sup>T</sup>). We used genome mining to identify numerous BGCs coding for the production of diverse known metabolites (i.e., osmoprotectants, photoprotectants, quorum sensing molecules, siderophores, cyclic lipopeptides) but also unknown metabolites (e.g., ARE, hybrid ARE-DAR, siderophores, orphan NRPS gene clusters) awaiting chemical characterization. Finally, this study underlines that marine environments host a huge diversity of <italic>Pseudomonadaceae</italic> that can drive the discovery of new secondary metabolites.</p>