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.
The whole-genome-sequenced rhizobacterium Bacillus amyloliquefaciens FZB42(T) (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 FZB42(T) to colonize Arabidopsis roots. On the basis of their phenotypic traits, the strains were similar to Bacillus amyloliquefaciens DSM 7(T) 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 FZB42(T), formed a lineage, which could be distinguished from the cluster of strains closely related to B. amyloliquefaciens DSM 7(T). DNA-DNA hybridizations (DDH) performed with genomic DNA from strains DSM 7(T) and FZB42(T) 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 7(T) 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 FZB42(T) ( = DSM 23117(T) = BGSC 10A6(T)), and B. amyloliquefaciens subsp. amyloliquefaciens subsp. nov., with the type strain DSM 7(T)( = ATCC 23350(T) = Fukumoto Strain F(T)), 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.
Borriss
Rainer
R
Bakteriengenetik, Institut für Biologie, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany.
Chen
Xiao-Hua
XH
Bakteriengenetik, Institut für Biologie, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany.
Rueckert
Christian
C
Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
Blom
Jochen
J
Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
Becker
Anke
A
Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
Baumgarth
Birgit
B
Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
Fan
Ben
B
Bakteriengenetik, Institut für Biologie, Humboldt Universität Berlin, Chausseestrasse 117, 10115 Berlin, Germany.
Pukall
Rüdiger
R
DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
Schumann
Peter
P
DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
Spröer
Cathrin
C
DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
Junge
Helmut
H
ABiTEP, Glienicker Weg 185, 12489 Berlin, Germany.
Vater
Joachim
J
Institut für Chemie, Technische Universität Berlin, Franklinstrasse 29, 10587 Berlin, Germany.
Pühler
Alfred
A
Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
Klenk
Hans-Peter
HP
DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
D001407:Bacillus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S