Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera

Abstract

The evolutionary relationships among species of the family Pseudomonadaceae were examined based on 255 available genomes representing >85 % of the species from this family. In a phylogenetic tree based on concatenated sequences of 118 core proteins, most species of the genus Pseudomonas grouped within one large cluster which also included members of the genera Azotobacter and Azomonas . Within this large cluster 18–30 clades/subclades of species of the genus Pseudomonas consisting of between 1 and 36 species, were observed. However, a number of species of the genus Pseudomonas branched outside of this main cluster and were interspersed among other genera of the family Pseudomonadaceae . This included a strongly supported clade (Pertucinogena clade) consisting of 19 mainly halotolerant species. The distinctness of this clade from all other members of the family Pseudomonadaceae is strongly supported by 24 conserved signature indels (CSIs) in diverse proteins that are exclusively found in all members of this clade. Nine uncharacterized members of the genus Pseudomonas also shared these CSIs and they branched within the Pertucinogena clade, indicating their affiliation to this clade. On the basis of the strong evidence supporting the distinctness of the Pertucinogena clade, we are proposing transfer of species from this clade into a novel genus Halopseudomonas gen. nov. Pseudomonas caeni also branches outside of the main cluster and groups reliably with Oblitimonas alkaliphila and Thiopseudomonas denitrificans . Six identified CSIs are uniquely shared by these three species and we are proposing their integration into the emended genus Thiopseudomonas , which has priority over the name Oblitimonas . We are also proposing transfer of the deep-branching Pseudomonas hussainii , for which 22 exclusive CSIs have been identified, into the genus Atopomonas gen. nov. Lastly, we present strong evidence that the species Pseudomonas cissicola and Pseudomonas geniculata are misclassified into the genus Pseudomonas and that they are specifically related to the genera Xanthomonas and Stenotrophomonas , respectively. In addition, we are also reclassifying ‘Pseudomonas acidophila’ as Paraburkholderia acidicola sp. nov. (Type strain: G-6302=ATCC 31363=BCRC 13035).

Oil-degrading bacterial consortium from Gulf of Mexico designed by a factorial method, reveals stable population dynamics

“…In consortium, the selected isolates presumably removed light crude oil through metabolic complementarity and/or cooperative interactions. Pseudomonas, related to Halopseudomonas (Rudra and Gupta, 2021) and Arthrobacter, closely related to Paenarthrobacter (Busse, 2016) are two of the genera most frequently employed in patented bioremediation strategies, as they are versatile bacteria, capable of degrading recalcitrant compounds and different types of HCs (Villela et al, 2019). There are many reports describing HC degradation by the ubiquitous Pseudomonas.…”

International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021

“…Paraburkholderia acidicola G-6302 T (=ATCC 31363 T =BCRC 13035 T ) Soil, Japan GCF_002362315.1 [53] Paraburkholderia acidiphila 7Q-K02 T (=KCTC 62472 T =LMG 29209 T ) Forest soil, PR China GCF_009789655.1 [25] Paraburkholderia acidisoli DHF22 T (=GDMCC 1.1448 T =LMG 30262 T ) Forest soil, PR China GCF_009789675.1 [25] Table 1. Continued Continued oryzae, which had an uncertain position in previous studies [10,12].…”

Pseudomonas oligotrophica sp. nov., a Novel Denitrifying Bacterium Possessing Nitrogen Removal Capability Under Low Carbon–Nitrogen Ratio Condition

“…The genus Pseudomonas was first proposed with the description of P. aeruginosa JCM 5962 T by Migula ( 1894 ) and belongs to the family Pseudomonadaceae within the class Gammaproteobacteria . Recently, Lalucat et al ( 2021 ) proposed the division of Pseudomonas into five new genera: “ Halopseudomonas ,” “ Linyingimonas ,” “ Stutzerimonas ,” “ Alcaligenimonas ,” and “ Ubiquimonas ” based on the phylogenetic and phylogenomic analyses, and the genus Halopseudomonas published by Rudra and Gupta ( 2021 ) has been validated. Pseudomonas strains displayed some potential roles, such as the high biodegradation capability of polycyclic aromatic hydrocarbons, sulfide oxidation, phosphate accumulation, and denitrification (Xie et al, 2016 , 2021 ; Sun et al, 2019 ; Zhang R. C. et al, 2020 ).…”