Bacillus velezensis is a novel species of Bacillus that has been widely investigated and used because of its direct or indirect growth improvement effect for many plants. B. velezensis FKM10 was previously isolated from rhizosphere soil of apple trees and shows potential as a plant growth-promoting and biocontrol bacterium. In this study, strain FKM10 was verified to inhibit some fungal pathogens of soil-borne plant diseases, produce siderophores to absorb ferric iron for plants, and degrade proteins. Pot experiments showed that the application of strain FKM10 could directly promote the growth of Malus hupehensis Rehd. by increasing biomass, promoting the absorption of nutrients, improving soil fertility, changing the soil microbial community structure, and reducing fungal diversity. The results of this study provided a basis for using strain FKM10 to improve crop yield and overcome diseases of plants. The mechanism of strain FKM10 to control the phytopathogenic fungus Fusarium verticillioides was studied by interoperation with RNA sequencing. Strain FKM10 can destroy the cell wall and cell membrane of F. verticillioides. The secretion of glucosidases, such as β-glucanase, might be one of the causes of the destruction of the fungal cell wall. The regulation of amino acid metabolism might also play an important role in the antibacterial process of strain FKM10. During the antibacterial process, strain FKM10 attacks F. verticillioides and strain FKM10 itself is also affected: the expression of spores is increased, the number of viable cells is decreased, and the ribonucleoprotein complex and flagellar assembly-related genes are downregulated. The results of this study indicate that both strain FKM10 and F. verticillioides have mutually inhibitory activities in a liquid environment. Comparative genome analysis of B. velezensis FKM10 reveals that the general features of their genomes are similar overall and contain the core genome for this species. The results of this study further reveal that B. velezensis can also serve as a basis for developing new biocontrol agents or microbial fertilizers.

Paenibacillus polymyxa is an important member of the plant growth-promoting rhizobacteria. P. polymyxa YC0136 inoculation had beneficial effect on growth promotion and biological control of tobacco (Nicotiana tabacum L.) under field conditions. This study aimed to reveal the growth-promoting mechanisms of strain YC0136. In growth-promotion assays, tobacco plant height was increased by 8.42% and 8.25% at 60 and 90 days, respectively, after inoculation with strain YC0136. Strain YC0136 also promoted the accumulation of tobacco biomass in varying degrees. Following inoculation with strain YC0136, 3,525 and 4,368 tobacco genes were up-regulated and down-regulated, respectively. Strain YC0136 induced the expression of plant hormone-related genes in tobacco, including auxin, cytokinin, and gibberellin, as well as transcription factors related to stress resistance such as WRKY and MYB. In addition, strain YC0136 induced the up-regulation of genes in the phenylpropanoid biosynthesis pathway by 1.51–4.59 times. Interaction with tobacco also induced gene expression changes in strain YC0136, with 286 and 223 genes up-regulated and down-regulated, respectively. Tobacco interaction induced up-regulation of the ilvB gene related to auxin biosynthesis in strain YC0136 by 1.72 times and induced expression of some nutrient transport genes. This study contributes to our understanding of the growth-promoting mechanisms of strain YC0136 on tobacco and provides a theoretical basis for the application of P. polymyxa YC0136 as a biological fertilizer.

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. 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. 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.