AUTHOR=Fan Ben , Blom Jochen , Klenk Hans-Peter , Borriss Rainer 

TITLE=Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an “Operational Group B. amyloliquefaciens” within the B. subtilis Species Complex

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.00022

DOI=10.3389/fmicb.2017.00022

ISSN=1664-302X

ABSTRACT=<p>The plant growth promoting model bacterium FZB42<sup>T</sup> was proposed as the type strain of <italic>Bacillus amyloliquefaciens</italic> subsp. <italic>plantarum</italic> (Borriss et al., <xref ref-type="bibr" rid="B6">2011</xref>), but has been recently recognized as being synonymous to <italic>Bacillus velezensis</italic> due to phylogenomic analysis (Dunlap C. et al., <xref ref-type="bibr" rid="B16">2016</xref>). However, until now, majority of publications consider plant-associated close relatives of FZB42 still as “<italic>B. amyloliquefaciens</italic>.” Here, we reinvestigated the taxonomic status of FZB42 and related strains in its context to the free-living soil bacterium DSM7<sup>T</sup>, the type strain of <italic>B. amyloliquefaciens</italic>. We identified 66 bacterial genomes from the NCBI data bank with high similarity to DSM7<sup>T</sup>. Dendrograms based on complete <italic>rpoB</italic> nucleotide sequences and on core genome sequences, respectively, clustered into a clade consisting of three tightly linked branches: (1) <italic>B. amyloliquefaciens</italic>, (2) <italic>Bacillus siamensis</italic>, and (3) a conspecific group containing the type strains of <italic>B. velezensis, Bacillus methylotrophicus</italic>, and <italic>B. amyloliquefaciens</italic> subsp. <italic>plantarum</italic>. The three monophyletic clades shared a common mutation rate of 0.01 substitutions per nucleotide position, but were distantly related to <italic>Bacillus subtilis</italic> (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 when <italic>B. amyloliquefaciens</italic> DSM7<sup>T</sup> genome sequence was used as query sequence. Due to these results, we propose that the <italic>B. amyloliquefaciens</italic> clade should be considered as a taxonomic unit above of species level, designated here as “operational group <italic>B. amyloliquefaciens</italic>” consisting of the soil borne <italic>B. amyloliquefaciens</italic>, and plant associated <italic>B. siamensis</italic> and <italic>B. velezensis</italic>, whose members are closely related and allow identifying changes on the genomic level due to developing the plant-associated life-style.</p>