Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons

Abstract

In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database were performed. The genome of B. velezensis UFLA258 consisted of a single circular chromosome of 3.95 Mb in length, with a mean GC content of 46.69%. It contained 3,949 genes encoding proteins and 27 RNA genes. Analyses based on Average Nucleotide Identity and Digital DNA–DNA Hybridization and a phylogeny with complete sequences of the rpoB gene confirmed that 19 strains deposited in the database as Bacillus amyloliquefaciens were in fact B. velezensis. In total, 115 genomes were analyzed and taxonomically classified as follows: 105 were B. velezensis, 9 were B. amyloliquefaciens, and 1 was Bacillus siamensis. Although these species are phylogenetically close, the combined analyses of several genomic characteristics, such as the presence of biosynthetic genes encoding secondary metabolites, CRISPr/Cas arrays, Average Nucleotide Identity and Digital DNA–DNA Hybridization, and other information on the strains, including isolation source, allowed their unequivocal classification. This genomic analysis expands our knowledge about the closely related species, B. velezensis, B. amyloliquefaciens, and B. siamensis, with emphasis on their taxonomical status.

The combination of two Bacillus strains suppresses Meloidogyne incognita and fungal pathogens, but does not enhance plant growth

“…Additionally, through a PCR‐based screening, we verified that the strains under study have the genes encoding for the synthesis of bacillomycin (Supplementary Text). The fact that these strains are closely related to B. velezensis corroborates the production of the antibiotic bacillomycin, which may be present in B. velezensis 65 . However, zwittermicin A has never been reported in B. velezensis and related species, but was found in B. cereus 73 .…”

“…Sequence analysis of the gene16S rRNA indicated that the Bacillus strains BMH and INV are phylogenetically related and belong in the B. velezensis clade 65 . Species of this clade are known for their association with plants, especially with the rhizosphere, acting as agents of growth promotion and in the suppression of pathogens, 66 and for these reasons are frequently used in commercial formulations 23,67 .…”

Characteristics of Genome of Bacillus velezensis ONU 553 Strain Isolated from the Bottom Sediments of the Black Sea

“…It seems like present determinants of biosynthesis of macrolactin and difficidin are slightly less distributed (they are absent in 1 strain from 105 according to the study [27]). From five known for this species bacteriocins -subtilin, mersacidin, planthazolicin, LCI, and amylocyclicin -only the last two were found, and they are known generally for species B. amyloliquefaciens and different species of B. subtilis group, respectively [27]. Bacteriocin LCI even is a part of B. velezensis core genome [28].…”

Аеробні Споротвірні Бактерії Глибоководних Осадів Чорного Моря

“…4.20 Кільцева карта геному B. velezensis ONU 553 з локалізацією профагових елементів, виявлених PHASTER Також наявні детермінанти біосинтезу макролактину та дифіцидину, лише трохи менш поширені (відсутні в одному штамі з 105) [115]. З семи відомих для даного виду бактеріоцинівсубтілін, мерсацидин, бациломіцин, плантазоліцин, лоциломіцин, аміноцикліцин та LCIвиявлено лише два останніх, які відомі переважно для виду B. amyloliquefaciens та ряду видів групи Bacillus subtilis, відповідно [115]. Бактеріоцин LCI взагалі є таким, що входить до корового геному B. velezensis [29,114].…”