Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots

Abstract

A Gram-stain-positive, facultatively anaerobic, rod-shaped, endospore-forming, oxidase-positive, and catalase-negative strain designated as BRMEA1T was isolated from the surface-sterilized Selaginella involvens roots. Growth of strain BRMEA1T was found to occur at pH 6.0–8.0 (optimum, pH 7.0), 15–50 °C (optimum, 25–30 °C) and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BRMEA1T formed a lineage within the genus Neobacillus (family Bacillaceae ) and showed the highest sequence similarity to Neobacillus drentensis DSM 15600T (98.3 %) and Neobacillus fumarioli KCTC 13885T (98.2 %), and less than 98.2 % 16S rRNA gene sequence similarity to the other members of the genus Neobacillus . Whole-genome analysis of strain BRMEA1T comprised a circular chromosome (5 632 809 bp in size) with 38.5 mol% G+C content. Digital DNA–DNA hybridization analyses revealed that strain BRMEA1T showed 20.5 and 22.0% genomic DNA relatedness with the closest species, N. drentensis DSM 15600T and N. fumarioli KCTC 13885T, respectively. The whole-genome sequence of strain BRMEA1T showed the presence of 11 specific conserved signature indels for the genus Neobacillus . The major cellular fatty acids (>10 %) of strain BRMEA1T were found to be iso-C15 : 0 and anteiso-C15 : 0, while the major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Polyphasic analysis results revealed that BRMEA1T represents a novel species of the genus Neobacillus , with the proposed name Neobacillus endophyticus sp. nov. The type strain is BRMEA1T (=KCTC 43208T=CCTCC AB 2020071T).

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

“…With the exception of these species/strains, this CSI was not present in any other Bacillota or other bacteria in the top 500 hits. The observed results demonstrate the specificity of this CSI for Neobacillus and provide further evidence of the predictive ability of the CSIs to be present in other members of a specific taxon [67,68].…”

“…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.…”

Neobacillus rhizosphaerae sp. nov., isolated from the rhizosphere, and reclassification of Bacillus dielmonensis as Neobacillus dielmonensis comb. nov.

“…At the time of writing, the genus Neobacillus contained 19 species with validated names (https://lpsn.dsmz.de/search?word=Neobacillus). The majority of these were represented by type strains isolated from the soil, root and rhizosphere environment, including root endophytes [2][3][4][5][6][7][8][9][10]. In addition other type strains were found in compost material [11], deep sea sediment samples [12], and also human faeces [13].…”

Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., isolated from maize root rhizosphere

“…At the time of writing, 16 species were allocated to this genus. Most of the type strains of Neobacillus species were isolated from soil [2][3][4][5][6], including root-associated [7] and specifically rhizosphere soil [8], as well as root endophytes [9,10]. Single type strains were also isolated from compost [11], deep sea sediment [12], and human faeces [13].…”