Bacillus amyloliquefaciens, Bacillus velezensis, andBacillus siamensisForm an "Operational GroupB. amyloliquefaciens" within theB. subtilisSpecies Complex.
The plant growth promoting model bacterium FZB42Twas proposed as the type strain ofBacillus amyloliquefacienssubsp.plantarum(Borriss et al., 2011), but has been recently recognized as being synonymous toBacillus velezensisdue to phylogenomic analysis (Dunlap C. et al., 2016). However, until now, majority of publications consider plant-associated close relatives of FZB42 still as "B. amyloliquefaciens." Here, we reinvestigated the taxonomic status of FZB42 and related strains in its context to the free-living soil bacterium DSM7T, the type strain ofB. amyloliquefaciens. We identified 66 bacterial genomes from the NCBI data bank with high similarity to DSM7T. Dendrograms based on completerpoBnucleotide sequences and on core genome sequences, respectively, clustered into a clade consisting of three tightly linked branches: (1)B. amyloliquefaciens, (2)Bacillus siamensis, and (3) a conspecific group containing the type strains ofB. velezensis, Bacillus methylotrophicus, andB. amyloliquefacienssubsp.plantarum. The three monophyletic clades shared a common mutation rate of 0.01 substitutions per nucleotide position, but were distantly related toBacillus subtilis(0.1 substitutions per nucleotide position). The tight relatedness of the three clusters was corroborated by TETRA, dDDH, ANI, and AAI analysis of the core genomes, but dDDH and ANI values were found slightly below species level thresholds whenB. amyloliquefaciensDSM7Tgenome sequence was used as query sequence. Due to these results, we propose that theB. amyloliquefaciensclade should be considered as a taxonomic unit above of species level, designated here as "operational groupB. amyloliquefaciens" consisting of the soil borneB. amyloliquefaciens, and plant associatedB. siamensisandB. velezensis, whose members are closely related and allow identifying changes on the genomic level due to developing the plant-associated life-style.
Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University Nanjing, China.
Ben
B
Fan
Bioinformatics and Systems Biology, Justus-Liebig-Universität Giessen Giessen, Germany.
Jochen
J
Blom
School of Biology, Newcastle University Newcastle upon Tyne, UK.
Hans-Peter
HP
Klenk
Fachgebiet Phytomedizin, Institut für Agrar- und Gartenbauwissenschaften, Humboldt Universität zu BerlinBerlin, Germany; Nord Reet UGGreifswald, Germany.
Rainer
R
Borriss
Bacillus amyloliquefaciens; Bacillus subtilis group; Bacillus taxonomy; average amino acid identity (AAI); average nucleotide identity (ANI); digital DNA–DNA hybridization; phylogenomics