Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis

Abstract

Background Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. paralicheniformis and B. licheniformis. Results A comparative genomics analysis based on B. paralicheniformis MDJK30 and 55 other previously reported Bacillus strains was performed. The evolutionary position of MDJK30 and the evolutionary relationship between B. paralicheniformis and B. licheniformis were evaluated by studying the phylogeny of the core genomes, a population structure analysis and ANI results. Comparative genomic analysis revealed various features of B. paralicheniformis that contribute to its commensal lifestyle in the rhizosphere, including an opening pan genome, a diversity of transport and the metabolism of the carbohydrates and amino acids. There are notable differences in the numbers and locations of the insertion sequences, prophages, genomic islands and secondary metabolic synthase operons between B. paralicheniformis and B. licheniformis . In particular, we found most gene clusters of Fengycin, Bacitracin and Lantipeptide were only present in B. paralicheniformis and were obtained by horizontal gene transfer (HGT), and these clusters may be used as genetic markers for distinguishing B. paralicheniformis and B. licheniformis . Conclusions This study reveals that MDJK30 and the other strains of lineage paralicheniformis present plant growth-promoting traits at the genetic level and can be developed and commercially formulated in agriculture as PGPR. Core genome phylogenies and population structure analysis has proven to be a powerful tool for differentiating B. paralicheniformis and B. licheniformis . Comparative genomic analyses illustrate the genetic differences between the paralicheniformis-licheniformis group with respect to rhizosphere adaptation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5646-9) contains supplementary material, which is available to authorized users.

Bacillus Responses to Plant-Associated Fungal and Bacterial Communities

“…In the comparative genomic era, numerous adjustments have been done in the last years to clarify the phylogeny of the B. subtilis complex, which includes, among others, species, such as B. velezensis, B. amyloliquefaciens, B. atrophaeus, B. subtilis subspecies subtilis, B. licheniformis, B. pumilus, and B. siamensis with potential as biocontrol agents (Expósito et al, 2017;Fira et al, 2018;Maksimov et al, 2020), and which led to some confusion in species names but also to misassignments (Dunlap et al, 2016;Fan et al, 2017;Harwood et al, 2018;Du, 2019;Torres Manno et al, 2019). Many isolates, such as strains FZB42, QST713, or SQR9 formerly assigned to the B. subtilis or B. amyloliquefaciens species have been reclassified as B. velezensis representing the model species for plant-associated bacilli (Dunlap et al, 2016;Fan et al, 2017).…”

“…The siderophore bacillibactin is highly conserved in the B. subtilis group (Figure 1) FIGURE 1 | Main non-ribosomal BSMs produced by the various species in the B. subtilis complex. The BSMs production is indicated for the following species B. subtilis, B. siamensis, B. velezensis, B. atrophaeus, B. amyloliquefaciens, B. pumilus, and B. licheniformis by a green square whereas red square indicates an absence of production of the BSMs in this species (Zhao and Kuipers, 2016;Fan et al, 2017;Harwood et al, 2018;Du, 2019;Torres Manno et al, 2019). The surfactins, iturins, and fengycins groups include lichenycin (1;AA1:L-Gln) and pumilacidin (1;AA4: L-Leu, AA7 = I-Ile); mycosubtilin (2;AA6: D-Ser, AA7 = L-Thr) and bacillomycin (2; AA6: D-Ser, AA7 = L-Asn); maltacin (4;AA1: L-Ser), agrastatin (4;AA10: L-Val) and plipastatin (4;AA9: D-Tyr), respectively.…”

Effects of Bacillus velezensis FKM10 for Promoting the Growth of Malus hupehensis Rehd. and Inhibiting Fusarium verticillioides

“…Analysis of Antagonistic Activities (Du et al, 2019) The pathogenic hyphae were taken as a rondure of 6-mm diameter and then placed on the center of a potato dextrose agar (PDA) plate. The plate was then incubated for 2 days at 28 • C. Strains were then streaked at a distance of 1 cm from the edge of the pathogenic fungal hyphae and cultured at 28 • C for another 2 days.…”

Isolation and Molecular Profiling Of Thermoresistant Bacteria From Chimneys Of Baking Industries Of Madurai, Tamilnadu, India

“…The identification of these isolates as Bacillus species is in agreement with the findings of previous study 9 . It was also observed previously that the accurate taxonomic assignment depends upon the region of 16S rRNA gene that it targeted during sequencing 10,11 . Phylogenetic research showed that thermophiles are abundant in many more extreme environments 12,13&14 .…”