Induced Disease Resistance and Promotion of Shallot Growth by <i>Bacillus velezensis</i> B-27

Application of Silica Nanoparticles in Combination with Bacillus velezensis and Bacillus thuringiensis for Anthracnose Disease Control in Shallot

<b>Background and Objective:</b> Anthracnose in shallot contributes to significant losses. To solve this issue, silica nanoparticles, in combination with <i>Bacillus velezensis</i> and <i>Bacillus thuringiensis</i> were used together. <b>Materials and Methods:</b> <i>In vitro</i> antagonistic test of <i>Bacillus velezensis</i> B-27 with <i>Colletotrichum gloeosporioides</i> was carried out using dual culture and co-culture methods. Treatment in greenhouse experiments was carried out using single application of silica, <i>B. thuringiensis</i>, <i>B. velezensis</i>, a combination of <i>B. thuringiensis</i> and <i>B. velezensis</i> and a combination of <i>B. thuringiensis</i>, <i>B. velezensis</i> and silica. Detection of <i>B. velezensis</i> in the roots of shallot plants was carried out by PCR using a pair of specific primers. <b>Results:</b> <i>Bacillus velezensis</i> was able to inhibit the growth of <i>C. gloeosporioides</i> mycelium <i>in vitro</i>, both in the dual culture and co-culture methods, by 62.8 and 77.17%, respectively. Treatment of <i>B. thuringiensis</i> and <i>B. velezensis</i>, either individually or in combination with silica, could reduce the intensity of anthracnose disease by 20% each and stimulate the growth of shallot plants. The PCR detection using specific primers on the roots of shallot plants showed that <i>B. velezensis</i> was detected with a DNA band length of ±576 bp. <b>Conclusion:</b> <i>Bacillus velezensis</i> can inhibit the growth of <i>C. gloeosporioides</i> mycelium <i>in vitro</i>. Applying <i>B. velezensis</i>, <i>B. thuringiensis</i> and silica can reduce the intensity of anthracnose disease, promote plant growth and increase plant productivity. Furthermore, <i>B. velezensis</i> was detected in the roots of shallot plants, revealing that the bacteria are well-established.

Genomics assisted functional characterization of Bacillus velezensis E as a biocontrol and growth promoting bacterium for lily

Lily (Lilium spp.) is one of the most famous ornamental flowers globally. Lily basal rot (also known as root rot or stem rot) and lily gray mold have seriously affected the yield and quality of lily, resulting in huge economic losses. In this study, bacterial strain E was isolated from a continuous lily cropping field. Strain E displayed high control efficiency against lily basal rot and gray mold, caused by Fusarium oxysporum and Botrytis cinerea respectively, and promoted the occurrence of scale bulblets. Strain E displayed strong inhibitory effects against several other plant pathogenic fungi and two pathogenic bacteria in dual culture and disc diffusion assays, respectively. Whole genome sequencing revealed that strain E contained a 3,929,247 bp circular chromosome with 4,056 protein-coding genes and an average GC content of 47.32%. Strain E was classified as Bacillus velezensis using genome-based phylogenetic analysis and average nucleotide identity and digital DNA–DNA hybridization analyses. A total of 86 genes and 13 secondary metabolite biosynthetic gene clusters involved in antifungal and antibacterial activity, plant growth promotion, colonization, nutrient uptake and availability were identified in the genome of strain E. In vitro biochemical assays showed that strain E produced siderophores, proteases, cellulases, biofilms, antifungal and antibacterial substances, and exhibited organic phosphate solubilization and swimming and swarming motility, which were consistent with the results of the genome analysis. Colonization analysis showed that strain E could colonize the root of the lily, but not the leaf. Overall, these results demonstrate that B. velezensis strain E can be used as a potential biofertilizer and biocontrol agent for lily production.

Comparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects

Bacillus velezensis HNA3, a potential plant growth promoter and biocontrol rhizobacterium, was isolated from plant rhizosphere soils in our previous work. Here, we sequenced the entire genome of the HNA3 strain and performed a comparative genome analysis. We found that HNA3 has a 3,929-kb chromosome with 46.5% GC content and 4,080 CDSs. We reclassified HNA3 as a Bacillus velezensis strain by core genome analysis between HNA3 and 74 previously defined Bacillus strains in the evolutionary tree. A comparative genomic analysis among Bacillus velezensis HNA3, Bacillus velezensis FZB42, Bacillus amyloliquefaciens DSM7, and Bacillus subtilis 168 showed that only HNA3 has one predicated secretory protein feruloyl esterase that catalyzes the hydrolysis of plant cell wall polysaccharides. The analysis of gene clusters revealed that whole biosynthetic gene clusters type Lanthipeptide was exclusively identified in HNA3 and might lead to the synthesis of new bioactive compounds. Twelve gene clusters were detected in HNA3 responsible for the synthesis of 14 secondary metabolites including Bacillaene, Fengycin, Bacillomycin D, Surfactin, Plipastatin, Mycosubtilin, Paenilarvins, Macrolactin, Difficidin, Amylocyclicin, Bacilysin, Iturin, Bacillibactin, Paenibactin, and others. HNA3 has 77 genes encoding for possible antifungal and antibacterial secreting carbohydrate active enzymes. It also contains genes involved in plant growth promotion, such as 11 putative indole acetic acid (IAA)-producing genes, spermidine and polyamine synthase genes, volatile compound producing genes, and multiple biofilm related genes. HNA3 also has 19 phosphatase genes involved in phosphorus solubilization. Our results provide insights into the genetic characteristics responsible for the bioactivities and potential application of HNA3 as plant growth-promoting strain in ecological agriculture.

IMPORTANCE This study is the primary initiative to identify Bacillus velezensis HNA3 whole genome sequence and reveal its genomic properties as an effective biocontrol agent against plant pathogens and a plant growth stimulator. HNA3 genetic profile can be used as a reference for future studies that can be applied as a highly effective biofertilizer and biofungicide inoculum to improve agriculture productivity. HNA3 reclassified in the phylogenetic tree which may be helpful for highly effective strain engineering and taxonomy. The genetic comparison among HNA3 and closely similar species B. velezensis FZB42, B. amyloliquefaciens DSM7, and B. subtilis 168 demonstrates some distinctive genetic properties of HNA3 and provides a basis for the genetic diversity of the Bacillus genus, which allows developing more effective eco-friendly resources for agriculture and separation of Bacillus velezensis as distinct species in the phylogenetic tree.