Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/22/2016
Publication Date: 6/1/2016
Publication URL: https://handle.nal.usda.gov/10113/5695397
Citation: Dunlap, C.A., Bowman, M.J., Schisler, D.A., Rooney, A.P. 2016. Genome analysis shows Bacillus axarquiensis is not a later heterotypic synonym of Bacillus mojavensis; Reclassification of Bacillus malacitensis and Brevibacterium halotolerans as heterotypic synonyms of Bacillus axarquiensis. International Journal of Systematic and Evolutionary Microbiology. 66:2438-2443. doi: 10.1099/ijsem.0.001048.
Interpretive Summary: This study compares four important species of plant associated bacteria and demonstrates that three species should be considered the same species based on genomic data. These results will simplify further studies and regulatory activities with the organisms accurately identified. This group of species comprises a large group of strains that have been commercially developed as plant growth promoters and for control of fungal pathogens.
Technical Abstract: Bacillus axarquiensis and Bacillus malacitensis were previously reported to be later heterotypic synonyms of Bacillus mojavensis, based primarily on DNA-DNA relatedness values. We have sequenced draft genomes of Bacillus axarquiensis NRRL B-41617**T and Bacillus malacitensis NRRL B-41618**T. Comparative genomics and DNA-DNA relatedness calculations show that while Bacillus axarquiensis and Bacillus malacitensis are synonymous with each other, they are not synonymous with Bacillus mojavensis. In addition, a draft genome was completed for Brevibacterium halotolerans, a strain long suspected of being a Bacillus subtilis group member based on 16S rRNA similarities (99.8 % with Bacillus mojavensis). Phylogenomics and DNA-DNA relatedness calculations show that Brevibacterium halotolerans should be reclassified as Bacillus halotolerans comb. nov. In addition, the analyses show Bacillus halotolerans is synonymous with Bacillus axarquiensis and Bacillus malacitensis. The pairwise in silico DNA-DNA hybridization values calculated in comparisons between the three conspecific strains were all greater than 92%, which is well above the standard species threshold of 70%. While the pairwise in silico DNA-DNA hybridization values calculated in comparisons of the three conspecific strains with Bacillus mojavensis were all less than 65%. The combined results of our genotype and phenotype studies show Bacillus axarquiensis, Bacillus malacitensis and Bacillus halotolerans are conspecific and distinct from Bacillus mojavensis. Because the valid publication of Bacillus halotolerans predates the publication of Bacillus axarquiensis and Bacillus malacitensis, we propose Bacillus axarquiensis and Bacillus malacitensis be reclassified as a synonym of Bacillus halotolerans.