Genome Sequence of Lysinibacillus sphaericus Strain KCTC 3346T

Lysinibacillus mangiferihumi, Lysinibacillus tabacifolii and Lysinibacillus varians are later heterotypic synonyms of Lysinibacillus sphaericus

The current study evaluates the taxonomic positions of Lysinibacillusmangiferihumi, Lysinibacillus sphaericus, Lysinibacillustabacifolii and Lysinibacillus varians. Phylogenomic and genomic comparisons show the four strains are conspecific based on standard species thresholds for this genus (monophyletic and pairwise average nucleotide identities >96 %). Analysis of the 16S rRNA gene sequences provided in original descriptions with genome-derived 16S rRNA gene sequences from the current study showed significant differences in three of the four strains. Variant analysis of the 16S rRNA gene sequences using the genomic data showed that the 16S rRNA gene copies are polyallelic for these species. Previously reported distinguishing phenotypes were re-examined and the strains show phenotype congruence, with the exception of a few variable traits. Based on the rules of priority, L. mangiferihumi, L. tabacifolii and L. varians are later heterotypic synonyms of L. sphaericus.

Comparative genomics reveals Lysinibacillus sphaericus group comprises a novel species

Background

Early in the 1990s, it was recognized that Lysinibacillus sphaericus, one of the most popular and effective entomopathogenic bacteria, was a highly heterogeneous group. Many authors have even proposed it comprises more than one species, but the lack of phenotypic traits that guarantee an accurate differentiation has not allowed this issue to be clarified. Now that genomic technologies are rapidly advancing, it is possible to address the problem from a whole genome perspective, getting insights into the phylogeny, evolutive history and biology itself.

Results

The genome of the Colombian strain L. sphaericus OT4b.49 was sequenced, assembled and annotated, obtaining 3 chromosomal contigs and no evidence of plasmids. Using these sequences and the 13 other L. sphaericus genomes available on the NCBI database, we carried out comparative genomic analyses that included whole genome alignments, searching for mobile elements, phylogenomic metrics (TETRA, ANI and in-silico DDH) and pan-genome assessments. The results support the hypothesis about this species as a very heterogeneous group. The entomopathogenic lineage is actually a single and independent species with 3728 core genes and 2153 accessory genes, whereas each non-toxic strain seems to be a separate species, though without a clear circumscription. Toxin-encoding genes, binA, B and mtx1, 2, 3 could be acquired via horizontal gene transfer in a single evolutionary event. The non-toxic strain OT4b.31 is the most related with the type strain KCTC 3346.

Conclusions

The current L. sphaericus is actually a sensu lato due to a sub-estimation of diversity accrued using traditional non-genomics based classification strategies. The toxic lineage is the most studied with regards to its larvicidal activity, which is a greatly conserved trait among these strains and thus, their differentiating feature. Further studies are needed in order to establish a univocal classification of the non-toxic strains that, according to our results, seem to be a paraphyletic group.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3056-9) contains supplementary material, which is available to authorized users.

Complete genome sequence of Lysinibacillus varians GY32, a bacterium with filament-to-rod cell cycle

The complete genome sequence of Lysinibacillus varians GY32 was determined to be 4,662,822 base pairs in a single circular chromosome. Genes in cell division, cell cycle, surface layer and cell wall synthesis are foundation of its unique cell morphology. The genome contains multiple clusters of transcriptional regulator, two-component system and sigma factors, providing the organism with the ability to regulate a filament-to-rod cell cycle progression. L. varians GY32 was, to our knowledge, the first bacterium with a filament-to-rod cell cycle to be sequenced and its annotated genome might provide new insights into our understanding of bacterial cell cycle regulation.

Genome comparison provides molecular insights into the phylogeny of the reassigned new genus Lysinibacillus

BACKGROUND

Lysinibacillus sphaericus (formerly named Bacillus sphaericus) is incapable of polysaccharide utilization and some isolates produce active insecticidal proteins against mosquito larvae. Its taxonomic status was changed to the genus Lysinibacillus in 2007 with some other organisms previously regarded as members of Bacillus. However, this classification is mainly based on physiology and phenotype and there is limited genomic information to support it.

RESULTS

In this study, four genomes of L. sphaericus were sequenced and compared with those of 24 representative strains belonging to Lysinibacillus and Bacillus. The results show that Lysinibacillus strains are phylogenetically related based on the genome sequences and composition of core genes. Comparison of gene function indicates the major difference between Lysinibacillus and the two Bacillus species is related to metabolism and cell wall/membrane biogenesis. Although L. sphaericus mosquitocidal isolates are highly conserved, other Lysinibacillus strains display a large heterogeneity. It was observed that mosquitocidal toxin genes in L. sphaericus were in close proximity to genome islands (GIs) and mobile genetic elements (MGEs). Furthermore, different copies and varying genomic location of the GIs containing binA/binB was observed amongst the different isolates. In addition, a plasmid highly similar to pBsph, but lacking the GI containing binA/binB, was found in L. sphaericus SSII-1.

CONCLUSIONS

Our results confirm the taxonomy of the new genus Lysinibacillus at the genome level and suggest a new species for mosquito-toxic L. sphaericus. Based on our findings, we hypothesize that (1) Lysinibacillus strains evolved from a common ancestor and the mosquitocidal L. sphaericus toxin genes were acquired by horizontal gene transfer (HGT), and (2) capture and loss of plasmids occurs in the population, which plays an important role in the transmission of binA/binB.