Genomic and phenotypic analyses reveal Paenibacillus polymyxa PJH16 is a potential biocontrol agent against cucumber fusarium wilt.

In recent years, bacterial-based biocontrol agents (BCA) have become a new trend for the control of fungal diseases such as fusarium wilt that seriously threaten the yield and quality of cucumber, which are transmitted through infested soil and water. This study was set out with the aim of figuring the mechanism of the isolated rhizobacterial strain Paenibacillus polymyxa PJH16 in preventing Fusarium oxysporum f. sp. cucumerinum (Foc). Biocontrol and growth-promoting experiments revealed that bacterial strain causes effective inhibition of the fungal disease through a significant growth-promoting ability of plants, and had activities of ß-1,3-glucanase, cellulase, amylase and protease. It could produce siderophore and indole-3-acetic acid, too. Using the high-throughput sequencing tool PacBio Sequel II system and the database annotation, the bacterial strain was identified as P. polymyxa PJH16 and contained genes encoding for presence of biofilm formation, antimicrobial peptides, siderophores and hydrolyases. From comparing data between the whole genome of P. polymyxa PJH16 with four closely related P. polymyxa strains, findings revealed markedly the subtle differences in their genome sequences and proposed new antifungal substances present in P. polymyxa PJH16. Therefore, P. polymyxa PJH16 could be utilized in bioengineering a microbial formulation for application as biocontrol agent and bio-stimulant, in the future.

Genome sequencing and analysis of Bacillus velezensis VJH504 reveal biocontrol mechanism against cucumber Fusarium wilt.

One major issue in reducing cucumber yield is the destructive disease Cucumber (Cucumis sativus L.) wilt disease caused by Fusarium oxysporum f. sp. cucumerinum (Foc). When using the isolate VJH504 isolated from cucumber rhizosphere soil and identified as Bacillus velezensis, the growth of Foc in the double culture experiment was effectively inhibited. Phenotypic, phylogenetic, and genomic analyses were conducted to enhance understanding of its biocontrol mechanism. According to the result of the phenotype analysis, B. velezensis VJH504 could inhibit cucumber fusarium wilt disease both in vitro and in vivo, and significantly promote cucumber seed germination and seedling growth. Additionally, the tests of growth-promoting and biocontrol characteristics revealed the secretion of proteases, amylases, ß-1,3-glucanases, cellulases, as well as siderophores and indole-3-acetic acid by B. velezensis VJH504. Using the PacBio Sequel II system, we applied the complete genome sequencing for B. velezensis VJH504 and obtained a single circular chromosome with a size of 3.79 Mb. A phylogenetic tree was constructed based on the 16S rRNA gene sequences of B. velezensis VJH504 and 13 other Bacillus species, and Average Nucleotide Identity (ANI) analysis was performed using their whole-genome sequences, confirming isolateVJH504 as B. velezensis. Following this, based on the complete genome sequence od B. velezensis VJH504, specific functional analysis, Carbohydrate-Active Enzymes (CAZymes) analysis, and secondary metabolite analysis were carried out, predicting organism's abilities for biofilm formation, production of antifungal CAZymes, and synthesis of antagonistic secondary metabolites against pathogens. Afterwards, a comparative genomic analysis was performed between B. velezensis VJH504 and three other B. velezensis strains, revealing subtle differences in their genomic sequences and suggesting the potential for the discovery of novel antimicrobial substances in B. velezensis VJH504. In conclusion, the mechanism of B. velezensis VJH504 in controlling cucumber fusarium wilt was predicted to appear that B. velezensis VJH504is a promising biocontrol agent, showcasing excellent application potential in agricultural production.

Effects of Rhizosphere Microbial Communities on Cucumber Fusarium wilt Disease Suppression.

Cucumber Fusarium wilt is a worldwide soil-borne disease that seriously restricts the yield and quality of cucumber. The rhizosphere soil microbiome, as the first line of defense against pathogens invading plant roots, plays a key role in rhizosphere immune formation and function. The purpose of this study was to reveal the key microecological factors and dominant microbial flora affecting cucumber resistance and susceptibility to Fusarium wilt by analyzing the physical and chemical properties and microbial flora of rhizosphere soil with different degrees of susceptibility and resistance to cucumber Fusarium wilt, thereby laying a foundation to establish cucumber resistance to the Fusarium wilt rhizosphere core microbiome. Firstly, Illumina Miseq sequencing technology was used to evaluate the physical and chemical properties and microbial groups of cucumber rhizosphere soil at different health levels, and the key environmental factors and microbial factors related to cucumber Fusarium wilt were screened out. Subsequently, PICRUSt2 and FUNGuild were used to predict the functions of rhizosphere bacteria and fungi. Combined with functional analysis, the possible interactions among soil physical and chemical properties, cucumber rhizosphere microorganisms, and Fusarium wilt were summarized. The results showed that the available potassium content in the rhizosphere soil of healthy cucumber decreased by 10.37% and 0.56%, respectively, compared with the rhizosphere soil of severely susceptible cucumber and mildly susceptible cucumber. Exchangeable calcium content increased by 25.55% and 5.39%; the α diversity Chao1 index of bacteria and fungi in the rhizosphere soil of healthy cucumber was significantly lower than that in the rhizosphere soil of seriously infected cucumber, and the MBC content of its physical and chemical properties was also significantly lower than that in the rhizosphere soil of seriously infected cucumber. There was no significant difference in the Shannon and Simpson diversity indexes between healthy cucumber rhizosphere soil and seriously infected cucumber rhizosphere soil. The results of the ß diversity analysis showed that the bacterial and fungal community structure of healthy cucumber rhizosphere soil was significantly different from that of severely and mildly infected cucumber rhizosphere soil. At the genus level, through statistical analysis, LEfSe analysis, and RDA analysis, the key bacterial and fungal genera with potential biomarker values were screened out as SHA_26, Subgroup_22, MND1, Aeromicrobium, TM7a, Pseudorhodoplanes, Kocuria, Chaetomium, Fusarium, Olpidium, and Scopulariopsis, respectively. The bacteria SHA_26, Subgroup_22, and MND1 related to cucumber Fusarium wilt inhibition belong to Chloroflexi, Acidobacteriota, and Proteobacteria, respectively. Chaetomiacea belongs to Sordariomycates. The results of functional prediction showed that changes to the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway in the bacterial microbiota were concentrated in tetracycline biosynthesis, selenocompound metabolism, lipopolysaccharide biosynthesis, etc., which were mainly involved in the metabolism of terpenoids and polyketides, energy metabolism, metabolism of other amino acids, glycan biosynthesis and metabolism, lipid metabolism, cell growth and death, transcription, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites. The difference in fungi was mainly dung saprotroph-ectomycorrhizal-soil saprotroph-wood saprotroph. Through the correlation analysis and functional predictions of the key environmental factors, microbial flora, and cucumber health index in cucumber rhizosphere soil, we determined that the inhibition of cucumber Fusarium wilt was a synergistic effect of environmental factors and microbial flora, and a model diagram was drawn to briefly explain its mechanism. This work will provide a basis for the biological control of cucumber Fusarium wilt in the future.

Genome-Wide Analysis of the Auxin/Indoleacetic Acid Gene Family and Response to Indole-3-Acetic Acid Stress in Tartary Buckwheat (Fagopyrum tataricum).

Auxin/indoleacetic acid (Aux/IAA) family genes respond to the hormone auxin, which have been implicated in the regulation of multiple biological processes. In this study, all 25 Aux/IAA family genes were identified in Tartary buckwheat (Fagopyrum tataricum) by a reiterative database search and manual annotation. Our study provided comprehensive information of Aux/IAA family genes in buckwheat, including gene structures, chromosome locations, phylogenetic relationships, and expression patterns. Aux/IAA family genes were nonuniformly distributed in the buckwheat chromosomes and divided into seven groups by phylogenetic analysis. Aux/IAA family genes maintained a certain correlation and a certain species-specificity through evolutionary analysis with Arabidopsis and other grain crops. In addition, all Aux/IAA genes showed a complex response pattern under treatment of indole-3-acetic acid (IAA). These results provide valuable reference information for dissecting function and molecular mechanism of Aux/IAA family genes in buckwheat.

Embedding Bacillus velezensis NH-1 in Microcapsules for Biocontrol of Cucumber Fusarium Wilt.

Cucumber Fusarium wilt, caused by Fusarium oxysporum, is a devastating disease of cucumber and leads to enormous economic losses worldwide. The antagonistic bacterium Bacillus velezensis NH-1 suppresses F. oxysporum For a higher biological control effect, control-released microcapsules of NH-1 were prepared using cell immobilization technology. NH-1 cells were embedded in combinations of the biodegradable wall materials sodium alginate, chitosan, and cassava-modified starch to prepare control-released microbiological microcapsules. For the preparation of alginate single-layer microcapsules, the highest embedding rate of 72.60% was obtained by applying 3% sodium alginate and 2% calcium chloride. After the application of monolayer alginate microcapsules in soil, the number of bacterial cells corresponded to a sustained release curve, and the survival rate of NH-1 was higher than the control in which soil was directly irrigated with NH-1 broth. The use of 0.8% chitosan (pH 3.0) and 0.5% cassava-modified starch in the preparation of double-layer and triple-layer microcapsules changed the performance of the microcapsules and increased the embedding rate. After dry storage for 65 days, the number of NH-1 cells was at the highest level in the monolayer microcapsules. In the field experiment, the control efficiency of alginate-coated monolayer microcapsules on Fusarium wilt was 100%, which was significantly higher than for the NH-1 culture and double-layer and triple-layer microcapsules. Collectively, sodium alginate is an ideal wall material for preparing slow-release bacterial microcapsules to control cucumber Fusarium wilt. Monolayer alginate microcapsules retard the release of B. velezensis NH-1 in soils and significantly improve its biocontrol efficiency on cucumber Fusarium wilt.IMPORTANCEBacillus species are often used for the biocontrol of various plant pathogens, but the control efficiency of Bacillus is usually unstable in field experiments. To improve the control efficiency of Bacillus, in this study, microcapsules of Bacillus velezensis strain NH-1 were prepared using different wall materials (sodium alginate, chitosan, and cassava-modified starch). It was found that the control efficiency of alginate-coated monolayer microcapsules on Fusarium wilt was 100% in field experiments, which was higher than for NH-1 culture and double-layer and triple-layer microcapsules. This study provides a new approach for preparing a biocontrol agent against Fusarium wilt with high biocontrol efficiency.