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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

Dunlap, Christopher A., Kim, Soo-Jin, Kwon, Soon-Wo, Rooney, Alejandro P.
International Journal of Systematic and Evolutionary Microbiology 2016 v.66 pp. 1212-1217
Bacillus amyloliquefaciens, Oryza sativa, antagonists, antibiosis, chemotaxonomy, endophytes, genes, genomics, genotype, greenhouses, nucleic acid hybridization, phenotype, phylogeny, plant pathogens, ribosomal RNA, rice, sequence homology, strains, taxonomic revisions
Bacillus velezensis was previously reported to be a later heterotypic synonym of Bacillus amyloliquefaciens, based primarily on DNA–DNA relatedness values. We have sequenced a draft genome of B. velezensis NRRL B-41580(T). Comparative genomics and DNA–DNArelatedness calculations show that it is not a synonym of B. amyloliquefaciens. It was instead synonymous with Bacillus methylotrophicus. ‘Bacillus oryzicola’ is a recently described species that was isolated as an endophyte of rice (Oryza sativa). The strain was demonstrated to have plant-pathogen antagonist activity in greenhouse assays, and the 16S rRNA gene was reported to have 99.7 % sequence similarity with Bacillus siamensis andB. methylotrophicus , which are both known for their plant pathogen antagonism. To better understand the phylogenetics of these closely related strains, we sequenced the genome of ‘B. oryzicola ’ KACC 18228. Comparative genomic analysis showed only minor differences between this strain and the genomes of B. velezensis NRRL B-41580(T), B. methylotrophicus KACC 13015(T) and Bacillus amyloliquefaciens subsp. plantarum FZB42(T). The pairwisein silico DNA–DNA hybridization values calculated in comparisons between the strains were all greater than 84 %, which is well above the standard species threshold of 70 %. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the strains share phenotype and genotype coherence. Therefore, we propose that B. methylotrophicus KACC 13015(T), B. amyloliquefaciens subsp. plantarum FZB42(T), and ‘B. oryzicola’ KACC 18228 should be reclassified as later heterotypic synonyms of B. velezensis NRRL B-41580(T), since the valid publication date of B. velezensis precedes the other three strains.