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.

This study aimed to explore the effects of two siderophore-producing bacterial strains on iron absorption and plant growth of peanut in calcareous soil. Two siderophore-producing bacterial strains, namely, YZ29 and DZ13, isolated from the rhizosphere soil of peanut, were identified as Paenibacillus illinoisensis and Bacillus sp., respectively. In potted experiments, YZ29 and DZ13 enhanced root activity, chlorophyll and active iron content in leaves, total nitrogen, phosphorus and potassium accumulation of plants and increased the quality of peanut kernels and plant biomass over control. In the field trial, the inoculated treatments performed better than the controls, and the pod yields of the three treatments inoculated with YZ29, DZ13, and YZ29+DZ13 (1:1) increased by 37.05%, 13.80% and 13.57%, respectively, compared with the control. Based on terminal restriction fragment length polymorphism analysis, YZ29 and DZ13 improved the bacterial community richness and species diversity of soil surrounding the peanut roots. Therefore, YZ29 and DZ13 can be used as candidate bacterial strains to relieve chlorosis of peanut and promote peanut growth. The present study is the first to explore the effect of siderophores produced by P. illinoisensis on iron absorption.

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.

Background: Paenibacillus polymyxaSC2, a bacterium isolated from the rhizosphere soil of pepper (Capsicum annuumL.), promotes growth and biocontrol of pepper. However, the mechanisms of interaction betweenP. polymyxaSC2 and pepper have not yet been elucidated. This study aimed to investigate the interactional relationship ofP. polymyxaSC2 and pepper using transcriptomics.Results: P. polymyxaSC2 promotes growth of pepper stems and leaves in pot experiments in the greenhouse. Under interaction conditions, peppers stimulate the expression of genes related to quorum sensing, chemotaxis, and biofilm formation inP. polymyxaSC2. Peppers induced the expression of polymyxin and fusaricidin biosynthesis genes inP. polymyxaSC2, and these genes were up-regulated 2.93- to 6.13-fold and 2.77- to 7.88-fold, respectively. Under the stimulation of medium which has been used to culture pepper, the bacteriostatic diameter ofP. polymyxaSC2 againstXanthomonas citriincreased significantly. Concurrently, under the stimulation ofP. polymyxaSC2, expression of transcription factor genesWRKY2andWRKY40in pepper was up-regulated 1.17-fold and 3.5-fold, respectively.Conclusions: Through the interaction with pepper, the ability ofP. polymyxaSC2 to inhibit pathogens was enhanced.P. polymyxaSC2 also induces systemic resistance in pepper by stimulating expression of corresponding transcription regulators. Furthermore, pepper has effects on chemotaxis and biofilm formation ofP. polymyxaSC2. This study provides a basis for studying interactional mechanisms ofP. polymyxaSC2 and pepper.

Background: Paenibacillus polymyxais a typical plant growth-promoting rhizobacterium (PGPR), and synthesis of indole-3-acetic acid (IAA) is one of the reasons for its growth-promoting capacity. The synthetic pathways of IAA inP. polymyxamust be identified and modified.Results: P. polymyxaSC2 and its spontaneous mutant SC2-M1 could promote plant growth by directly secreting IAA. Through metabonomic and genomic analysis, the genespatA,ilvB3, andfusEin the native IPyA pathway of IAA synthesis in strain SC2-M1 were predicted. A novel strong promoterP₀₄₄₂₀was rationally selected, synthetically analyzed, and then evaluated on its ability to express IAA synthetic genes.Co-expression of three genes,patA,ilvB3, andfusE, increased IAA yield by 60% in strain SC2-M1. Furthermore, the heterogeneous geneiaamof the IAM pathway and two heterogeneous IPyA pathways of IAA synthesis were selected to improve the IAA yield of strain SC2-M1.The genesELJP6_14505,ipdC,andELJP6_00725of the entire IPyA pathway fromEnterobacter ludwigiiJP6 were expressed well by promoterP₀₄₄₂₀in strain SC2-M1 and increased IAA yield in the engineered strain SC2-M1 from 13 to 31 μg/mL, which was an increase of 138%.Conclusions: The results of our study help reveal and enhance the IAA synthesis pathways ofP. polymyxaand its future application.

Plant growth and yield are adversely affected by soil salinity. PGPRs can promote plant growth and enhance plant tolerance to salt stress.