Reclassification of Brevibacterium frigoritolerans as Peribacillus frigoritolerans comb. nov. based on phylogenomics and multiple molecular synapomorphies

Abstract

The taxonomic assignment of Brevibacterium frigoritolerans together with the in-house environmental isolate EB93 was reassessed in this study using phylogenetic and phylogenomic approaches, and the detection of multiple molecular synapomorphies. Results from the reconstructed phylogenetic trees based on the 16S rRNA gene sequences, the concatenated protein sequences of GyrA-GyrB-RpoB-RpoC, and the whole-genome sequences revealed the consistent exclusion of B. frigoritolerans and the environmental isolate EB93 from the cluster formed by the type strains of the genus Brevibacterium . In addition, B. frigoritolerans and the environmental isolate EB93 were both observed to form a clade together with the type strains of the genus Peribacillus . The results from the analysis of the digital DNA–DNA hybridization, average nucleotide identity, average amino acid identity and the difference in the G+C content also corroborated with the phylogenetic inference, and that B. frigoritolerans and the environmental isolate EB93 were of the same species. Furthermore, the presence of the molecular synapomorphies in the protein sequences noted in the description of the genus Peribacillus were also observed in B. frigoritolerans , further strengthening its taxonomic affiliation in the genus. Based on the evidence from the multiple lines of analyses, we propose the reclassification of Brevibacterium frigoritolerans as a member of the genus Peribacillus and assume the name Peribacillus frigoritolerans comb. nov. (type strain DSM 8801 T=ATCC 25097T=CCUG 43489T=CIP 67.20T=JCM 11681T).

AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species

“…Due to their group (taxon)-specificity and predictive ability to be found in other members of the indicated group, the identified CSIs have provided important means for the demarcation of prokaryotic taxa of different ranks in molecular terms, thus aiding in the development of more robust classification schemes for prokaryotic organisms [38, 39, 47, 48, 50, 52, 53, 58]. The CSIs have now been identified for numerous prokaryotic taxa [38, 39, 47, 48, 50, 52, 53, 58, 63, 93, 94] and several investigators have used them for the classification of newly described species into specific taxa [54–56, 62, 67–74]. However, the lack of a convenient method for determining the presence or absence of known CSIs in genome sequences has limited the use of these molecular markers for taxonomic and diagnostic studies.…”

“…In the new classification scheme for Bacillus species, all newly described genera were reliably distinguished from each other (and other prokaryotic taxa) based on multiple identified CSIs which were specific for each of these genera [52,58]. Because of the predictive ability of the CSIs to be present in other members of these genera, the described CSIs have also been used by other investigators to assign newly described Bacillaceae species, as well as other species, into different genera [54][55][56][67][68][69][70][71][72][73][74]. Although the CSIs provide a very useful means for the circumscription of taxa of different ranks (specifically the genus-level clades), and for the assignment of new species into these genera based on the shared presence of CSIs, there is no convenient method available for determining the presence or absence of known taxon-specific CSIs in genome sequences.…”

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

“…All newly proposed genera and other studied genera/clades in this work have been circumscribed based on their harboring multiple uniquely shared CSIs. One notable characteristic of the CSIs, which is of much importance for classification purposes, is that these markers exhibit high degree of predictive ability to be found in other (uncharacterized or unidentified) members of a given group/taxon (Bhandari et al, 2013;Gupta, 2014Gupta, , 2016Dobritsa and Samadpour, 2019;Patel and Gupta, 2020;Montecillo and Bae, 2022). Thus, the CSIs specific for the genus Halopseudomonas identified in our earlier work (Rudra and Gupta, 2021) are also present in all newly described species from this genus (Supplementary Figure S2).…”

Isolation and Degradation Characteristics of PBAT Film Degrading Bacteria

“…The PBAT-degrading bacterium we isolated from the soil sample in our research was first defined as Brevibacterium frigoritolerans in 1953 [ 29 ] and reclassified as Peribacillus frigoritolerans later [ 30 ]. This bacterium has been reported to effectively degrade organophosphorus pesticide phorate [ 31 , 32 , 33 , 34 ] in soil and paracetamol [ 35 ] in the liquid mineral salt medium. This is the first study that reports the degradation of the PBAT mulch film by Peribacillus frigoritolerans .…”