AUTHOR=Rudra Bashudev , Gupta Radhey S. 

TITLE=Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2024

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1273665

DOI=10.3389/fmicb.2023.1273665

ISSN=1664-302X

ABSTRACT=<p>Genus <italic>Pseudomonas</italic> is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 <italic>Pseudomonadaceae</italic> genomes. In phylogenomic trees, <italic>Pseudomonas</italic> species formed 12 main clusters, apart from the “Aeruginosa clade” containing its type species, <italic>P. aeruginosa</italic>. In parallel, our detailed analyses on protein sequences from <italic>Pseudomonadaceae</italic> genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the “Aeruginosa clade,” provide reliable demarcation of this clade corresponding to the genus <italic>Pseudomonas sensu stricto</italic> in molecular terms. The remaining 92 identified CSIs are specific for nine other <italic>Pseudomonas</italic> species clades and the genera <italic>Azomonas</italic> and <italic>Azotobacter</italic> which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed <italic>Pseudomonas</italic> species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade – <italic>Aquipseudomonas</italic> gen. nov.; Fluvialis clade – <italic>Caenipseudomonas</italic> gen. nov.; Linyingensis clade – <italic>Geopseudomonas</italic> gen. nov.; Oleovorans clade – <italic>Ectopseudomonas</italic> gen. nov.; Resinovorans clade – <italic>Metapseudomonas</italic> gen. nov.; Straminea clade – <italic>Phytopseudomonas</italic> gen. nov.; and Thermotolerans clade – <italic>Zestomonas</italic> gen. nov. In addition, descriptions of the genera <italic>Azomonas</italic>, <italic>Azotobacter</italic>, <italic>Chryseomonas, Serpens</italic>, and <italic>Stutzerimonas</italic> are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for <italic>Pseudomonas</italic> species.</p>