Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons

Abstract

The whole-genome-sequenced rhizobacterium Bacillus amyloliquefaciens FZB42T (Chen et al., 2007) and other plant-associated strains of the genus Bacillus described as belonging to the species Bacillus amyloliquefaciens or Bacillus subtilis are used commercially to promote the growth and improve the health of crop plants. Previous investigations revealed that a group of strains represented a distinct ecotype related to B. amyloliquefaciens; however, the exact taxonomic position of this group remains elusive (Reva et al., 2004). In the present study, we demonstrated the ability of a group of Bacillus strains closely related to strain FZB42T to colonize Arabidopsis roots. On the basis of their phenotypic traits, the strains were similar to Bacillus amyloliquefaciens DSM 7T but differed considerably from this type strain in the DNA sequences of genes encoding 16S rRNA, gyrase subunit A (gyrA) and histidine kinase (cheA). Phylogenetic analysis performed with partial 16S rRNA, gyrA and cheA gene sequences revealed that the plant-associated strains of the genus Bacillus, including strain FZB42T, formed a lineage, which could be distinguished from the cluster of strains closely related to B. amyloliquefaciens DSM 7T. DNA–DNA hybridizations (DDH) performed with genomic DNA from strains DSM 7T and FZB42T yielded relatedness values of 63.7–71.2 %. Several methods of genomic analysis, such as direct whole-genome comparison, digital DDH and microarray-based comparative genomichybridization (M-CGH) were used as complementary tests. The group of plant-associated strains could be distinguished from strain DSM 7T and the type strain of B. subtilis by differences in the potential to synthesize non-ribosomal lipopeptides and polyketides. Based on the differences found in the marker gene sequences and the whole genomes of these strains, we propose two novel subspecies, designated B. amyloliquefaciens subsp. plantarum subsp. nov., with the type strain FZB42T ( = DSM 23117T = BGSC 10A6T), and B. amyloliquefaciens subsp. amyloliquefaciens subsp. nov., with the type strain DSM 7T( = ATCC 23350T = Fukumoto Strain FT), for plant-associated and non-plant-associated representatives, respecitvely. This is in agreement with results of DDH and M-CGH tests and the MALDI-TOF MS of cellular components, all of which suggested that the ecovars represent two different subspecies.

Bacillus velezensis is not a later heterotypic synonym of Bacillus amyloliquefaciens; Bacillus methylotrophicus, Bacillus amyloliquefaciens subsp. plantarum and ‘Bacillus oryzicola’ are later heterotypic synonyms of Bacillus velezensis based on phylogenomics

“…plantarum FZB42 T and 'B oryzicola' KACC 18228 are consistent with the strains belonging to the same species (Borriss et al, 2011;Chung et al, 2015;Madhaiyan et al, 2010;Ruiz-García et al, 2005). The previously published fatty acid methyl ester data are slightly variable, but the primary fatty acid components are the same.…”

“…Because the valid publication of B. velezensis (Ruiz-García et al, 2005) predates the publication of B. methylotrophicus (Madhaiyan et al, 2010), B. amyloliquefaciens subsp. plantarum (Borriss et al, 2011) and 'B. oryzicola' (Chung et al, 2015), we propose that B. methylotrophicus, B. amyloliquefaciens subsp.…”

Bacillus nakamurai sp. nov., a black-pigment-producing strain

“…The cell-wall peptidoglycan contained meso-diaminopimelic acid. The total cellular fatty acid profiles showed a large amount of branched fatty acids; the major components (>5.0 %) were anteiso-C 15 : 0 (34.8 %), iso-C 15 : 0 (21.9 %), iso-C 17 : 0 (15.7 %), anteiso-C 17 : 0 (11.4 %) and C 16 : 0 (9.7 %) ( the close relatives B. amyloliquefaciens, B. atrophaeus and B. velezensis determined in this study were consistent with previously reported profiles (Borriss et al, 2011;Nakamura, 1989;Ruiz-García et al, 2005). B. nakamurai could not be distinguished from its closest related species on the basis of fatty acid profiles.…”

The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics

“…In this way W23 more closely resembles the Gram-positive pathogen Staphylococcus aureus (Qian et al, 2006). Understanding the enzymology (Brown et al, 2010) and regulation (Minnig et al, 2005) of W23 wall synthesis remains an ongoing concern. W23 also remains a useful comparison to 168 for the study of B. subtilis taxonomy, ecology and evolution, since W23 is the best-characterized member of the subspecies spizizenii and 168 of subspecies subtilis (Nakamura et al, 1999).…”