The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group

Abstract

The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is constantly evolving. In this study, whole genome sequencing enabled us to define 43 new Pseudomonas species and provide an update of the Pseudomonas evolutionary and taxonomic relationships. Phylogenies based on the rpoD gene and whole genome sequences, including, respectively, 316 and 313 type strains of Pseudomonas, revealed sixteen groups of Pseudomonas and, together with the distribution of cyclic lipopeptide biosynthesis gene clusters, enabled the partitioning of the P. putida group into fifteen subgroups. Pairwise average nucleotide identities were calculated between type strains and a selection of 60 genomes of non-type strains of Pseudomonas. Forty-one strains were incorrectly assigned at the species level and among these, 19 strains were shown to represent an additional 13 new Pseudomonas species that remain to be formally classified. This work pinpoints the importance of correct taxonomic assignment and phylogenetic classification in order to perform integrative studies linking genetic diversity, lifestyle, and metabolic potential of Pseudomonas spp.

Pseudomonas 1-Aminocyclopropane-1-carboxylate (ACC) Deaminase and Its Role in Beneficial Plant-Microbe Interactions

“…The ACC deaminase gene is present in 2591 Pseudomonas genomes (accessed in August 2021), including 39 Pseudomonas type strain genomes (Table 1). ACC deaminase was mostly detected in members of the following Pseudomonas genomic groups/subgroups (previously determined in Girard et al [64]): P. syringae group (P. syringae, P. amygdali, P. avellanae, P. asturiensis, P. cannabina, P. capsici, P. caricapapayae, P. caspiana, P. cichorii, P. congelans, P. ficuserectae, P. floridensis, P. foliumensis, P. tremae, P. triticumensis, P. viridiflava); P. fluorescens subgroup (P. grimontii, P. marginalis, P. palleroniana, P. panacis), P. corrugata subgroup (P. bijieensis, P. brassicacearum, P. kilonensis, P. ogarae, P. tehranensis, P. thivervalensis, P. viciae; P. zarinae); P. mandelii subgroup (P. farris, P. migulae); P. massiliensis group (P. typographi); P. gessardii group (P. gessardii); P. asplenii subgroup (P. fuscovaginae); P. straminea group (P. flavescens); P. anguilliseptica group (P. benzenivorans); P. oryzihabitans group (P. oryzihabitans, P. psychrotolerans, P. rhizoryzae).…”

Transporter Gene-Mediated Typing for Detection and Genome Mining of Lipopeptide-Producing Pseudomonas

“…3 ) were selected for chemical characterization. Two of these taxonomically distinct strains belong to the P. fluorescens group, namely, P. prosekii LMG 26867 T (Bananamide; Pseudomonas mandelii subgroup) and P. zeae OE 48.2 T (Amphisin; P. koreensis subgroup), whereas Pseudomonas xantholysigenes RW9S1A T (Xantholysin; Pseudomonas mosselii subgroup) and P. fulva LMG 11722 T (Putisolvin; P. putida subgroup) are affiliated with the P. putida group ( 40 ).…”

Lipopeptide Interplay Mediates Molecular Interactions between Soil Bacilli and Pseudomonads

“…According to data available so far, sessilin/tolaasin-type CLPs are formed by a limited number of species, such as P. tolaasii , P. costantinii, and P. sessilinigenes isolates, as illustrated by CMR12a. This isolate has recently been taxonomically positioned as P. sessilinigenes ( 55 ) and has certain similarities with strains belonging to the P. protegens subgroup containing many soil Pseudomonas biocontrol strains ( 56 – 59 ). Considering the ever-growing number of new CLP producers discovered in recent years and the diversity/modularity of Pseudomonas NR secondary metabolites, we suspect that the potential to form CLPs from the tolaasin family could be more widespread among environmental Pseudomonas ( 54 ).…”