Whole Genome Sequence of Bacillus velezensis Strain GUMT319: A Potential Biocontrol Agent Against Tobacco Black Shank Disease

Managing tobacco black shank disease using biochar: direct toxicity and indirect ecological mechanisms

Black shank disease in tobacco, caused by Phytophthora nicotianae, can lead to yield losses of 30%-50% upon outbreak. Recently, biochar derived from agricultural waste has shown significant potential in controlling soil-borne diseases, though its mechanisms remain unclear. Over a 3-year observation period, we found that the incidence of black shank was significantly lower in plots amended with biochar compared with normal cultivation plots. To investigate the underlying mechanisms, we studied both the direct and indirect effects of biochar on black shank. Direct antifungal assays indicated that biochar reduced the total number of sporangia by 53.91%. Further pot experiments revealed a 62.34% reduction in the P. nicotianae population in the soil following biochar application. Additionally, biochar application led to notable changes in soil physicochemical properties and microbial community composition. Microbial species analysis showed that biochar promoted the aggregation of beneficial microbes such as Sphingomonas, Flavisolibacter, and Mucoromycota. Functional predictions using the PICRUSt 2 software revealed that biochar enhances bacterial functions related to antimicrobial substance synthesis (Tetracycline biosynthesis), detoxification metabolism (D-arginine and D-ornithine metabolism, arginine and proline metabolism), and lipid and fatty acid metabolism (Lipopolysaccharide biosynthesis, fatty acid biosynthesis), while fungal functions showed no significant changes. This suggests that rhizosphere bacteria play a more prominent role in the suppression of black shank by biochar, a finding supported by partial least squares path modeling analysis. Therefore, we hypothesize that biochar not only directly inhibits P. nicotianae growth but also regulates the composition of the rhizosphere microbial community, inducing the production of antimicrobial substances by rhizosphere bacteria, effectively preventing P. nicotianae invasion.IMPORTANCEBlack shank, a global soil-borne fungal disease in tobacco, currently lacks effective control methods. Notably, biochar derived from agricultural waste has shown significant potential in controlling soil-borne diseases. Over a 3-year observation period, we found that plots amended with biochar had a significantly lower incidence of black shank compared with normal cultivation plots. However, the mechanisms of disease suppression remained unclear. Through in vitro antifungal assays and pot experiments, we discovered that tobacco-derived biochar can directly inhibit the growth of the pathogen. Additionally, biochar regulates the composition of the rhizosphere microbial community, inducing rhizosphere bacteria to produce antimicrobial substances, effectively preventing pathogen invasion. This discovery reveals both the direct and indirect mechanisms by which biochar suppresses black shank in tobacco. It provides a scientific basis for developing green control technologies for black shank and offers theoretical support for the application of biochar in managing soil-borne diseases in tobacco cultivation areas.

Bacillus velezensis: a versatile ally in the battle against phytopathogens-insights and prospects

The escalating interest in Bacillus velezensis as a biocontrol agent arises from its demonstrated efficacy in inhibiting both phytopathogenic fungi and bacteria, positioning it as a promising candidate for biotechnological applications. This mini review aims to offer a comprehensive exploration of the multifaceted properties of B. velezensis, with particular focus on its beneficial interactions with plants and its potential for controlling phytopathogenic fungi. The molecular dialogues involving B. velezensis, plants, and phytopathogens are scrutinized to underscore the intricate mechanisms orchestrating these interactions. Additionally, the review elucidates the mode of action of B. velezensis, particularly through cyclic lipopeptides, highlighting their importance in biocontrol and promoting plant growth. The agricultural applications of B. velezensis are detailed, showcasing its role in enhancing crop health and productivity while reducing reliance on chemical pesticides. Furthermore, the review extends its purview in the industrial and environmental arenas, highlighting its versatility across various sectors. By addressing challenges such as formulation optimization and regulatory frameworks, the review aims to chart a course for the effective utilization of B. velezensis. KEY POINTS: • B. velezensis fights phytopathogens, boosting biotech potential • B. velezensis shapes agri-biotech future, offers sustainable solutions • Explores plant-B. velezensis dialogue, lipopeptide potential showcased.

Biocontrol manufacturing and agricultural applications of Bacillus velezensis

Many microorganisms have been reported as bioagents for producing ecofriendly, cost-effective, and safe products. Some Bacillus species of bacteria can be used in agricultural applications. Bacillus velezensis in particular has shown promising results for controlling destructive phytopathogens and in biofungicide manufacturing. Some B. velezensis strains can promote plant growth and display antibiotic activities against plant pathogen agents. In this review, we focus on the often-overlooked potential properties of B. velezensis as a bioagent for applications that will extend beyond the traditional agricultural uses. We delve into its versatility and future prospects, the challenges such uses may encounter, and some drawbacks associated with B. velezensis-based products.

A Bacillus velezensis strain isolated from oats with disease-preventing and growth-promoting properties

Endophytes have been shown to promote plant growth and health. In the present study, a Bacillus velezensis CH1 (CH1) strain was isolated and identified from high-quality oats, which was capable of producing indole-3-acetic acid (IAA) and strong biofilms, and capabilities in the nitrogen-fixing and iron carriers. CH1 has a 3920 kb chromosome with 47.3% GC content and 3776 code genes. Compared genome analysis showed that the largest proportion of the COG database was metabolism-related (44.79%), and 1135 out of 1508 genes were associated with the function "biosynthesis, transport, and catabolism of secondary metabolites." Furthermore, thirteen gene clusters had been identified in CH1, which were responsible for the synthesis of fifteen secondary metabolites that exhibit antifungal and antibacterial properties. Additionally, the strain harbors genes involved in plant growth promotion, such as seven putative genes for IAA production, spermidine and polyamine synthase genes, along with multiple membrane-associated genes. The enrichment of these functions was strong evidence of the antimicrobial properties of strain CH1, which has the potential to be a biofertilizer for promoting oat growth and disease resistance.

Complete Genome Sequence Analysis of Bacillus subtilis MC4-2 Strain That against Tobacco Black Shank Disease

The MC4-2 bacterium strain was isolated and purified from the Periplaneta americana intestine as a biocontrol agent with good antagonistic effect against the pathogens of a soil-borne disease called tobacco black shank. The MC4-2 strain was found to have good broad-spectrum inhibition by plate stand-off test. Based on 16S rRNA and gyrB genes, ANI analysis, and other comparative genomics methods, it was determined that the MC4-2 strain was Bacillus subtilis. The complete genome sequence showed that the genome size was 4,076,630 bp, the average GC content was 43.78%, and the total number of CDSs was 4,207. Genomic prediction analysis revealed that a total of 145 genes were annotated by the CAZy, containing mainly GH and CE enzymes that break down carbohydrates such as glucose, chitin, starch, and alginate, and a large number of enzymes involved in glycosylation were present. A total of ten secondary metabolite clusters were predicted, six clusters of which were annotated as surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. The present investigation found the biological control mechanism of B. subtilis MC4-2, which provides a strong theoretical basis for the best use of this strain in biological control methods and provides a reference for the subsequent development of agents of this bacterium.

Perception of the Biocontrol Potential and Palmitic Acid Biosynthesis Pathway of Bacillus subtilis H2 through Merging Genome Mining with Chemical Analysis

Bacillus has been widely studied for its potential to protect plants from pathogens. Here, we report the whole genome sequence of Bacillus subtilis H2, which was isolated from the tea garden soil of Guiyang Forest Park. Strain H2 showed a broad spectrum of antagonistic activities against many plant fungal pathogens and bacteria pathogens, including the rice blast fungus Magnaporthe oryzae, and showed a good field control effect against rice blast. The complete genome of B. subtilis H2 contained a 4,160,635-bp circular chromosome, with an average G + C content of 43.78%. Through the genome mining of strain H2, we identified 7 known antimicrobial compound biosynthetic gene clusters (BGCs) including sporulation killing factor, surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. Palmitic acid (PA), a secondary metabolite, was detected and identified in the H2 strain through genome mining analysis and gas chromatography-mass spectrometry (GC-MS). Additionally, we propose, for the first time, that the type II fatty acid synthesis (FAS) pathway in Bacillus is responsible for PA biosynthesis. This finding was confirmed by studying the antimicrobial activity of PA and conducting reverse transcription-quantitative polymerase chain reaction (RT-qPCR) experiments. We also identified numerous genes associated with plant-bacteria interactions in the H2 genome, including more than 94 colonization-related genes, more than 34 antimicrobial genes, and more than 13 plant growth-promoting genes. These findings contribute to our understanding of the biocontrol mechanisms of B. subtilis H2 and have potential applications in crop disease control.

Complete genome sequence of Bacillus cereus Z4, a biocontrol agent against tobacco black shank, isolated from the Western Pacific Ocean

Bacillus species have been considered as promising biological control agents due to their excellent antimicrobial ability. Bacillus cereus strain Z4 was isolated from 2000 m deep sea sediments of the Western Pacific Ocean, which possesses significant antifungal activity against Phytophthora nicotianae, the pathogenic fungus of tobacco black shank disease. To reveal the underlying antifungal genetic mechanisms, here, we report the complete genomic sequence of the strain Z4. The genome has one circular chromosome of 5,664,309 bp with a G + C content of 35.31%, 109 tRNAs, and 43 rRNAs. Genomic analysis identified 10 gene clusters related to the biosynthesis of biocontrol active compounds, including bacillibactin, petrobactin, fengycin, and molybdenum cofactor. Meanwhile, 6 gene clusters were responsible for the biosynthesis of metabolites with unknown functions. Strain Z4 also contains a large number of genes encoding carbohydrate-active enzymes and secreted proteins, respectively. The whole genomic analysis of Bacillus cereus Z4 may provide a valuable reference for elucidating its biocontrol mechanism against tobacco black shank.

Complete Genome Sequence of Bacillus velezensis GUAL210, a Potential Biocontrol Agent Isolated from Pepper Rhizosphere

Bacillus velezensis GUAL210 was isolated from the rhizosphere of healthy pepper plants growing in high-incidence anthracnose fields in Guizhou, China. GUAL210 could be used as a potential biocontrol agent against pepper anthracnose and other soil-borne diseases. The GUAL210 genome consisted of a single circular chromosome 4,011,788 bp in length, with an average GC content of 46.41%, and did not harbor any plasmids. A total of 4,115 protein-coding genes, 27 rRNAs, 87 tRNAs, and 12 secondary metabolite biosynthesis gene clusters were identified. The products of the gene clusters included bacilysin, surfactin, bacteriocin, bacillaene, terpene, and so on, which might help host plants inhibit pathogens. The two clusters predicted to produce terpene had not typically been found in other Bacillus spp. The findings of this study will provide valuable data to explore the biocontrol mechanisms of B. velezensis strains.

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.

Biocontrol efficacy of Bacillus velezensis strain YS-AT-DS1 against the root-knot nematode Meloidogyne incognita in tomato plants

Root-knot nematodes (RKNs; Meloidogyne spp.), one of the most economically important plant-parasitic nematodes (PPNs), cause severe yield and quality losses in agriculture annually. The application of biological control agents is an environmentally safe and effective approach to control RKNs. Here, we report the genomic characteristics of a Bacillus velezensis strain YS-AT-DS1 (Bv-DS1) isolated from the tidal soil, revealing that it has a 4.73 Mb circular chromosome with an average GC-content of 46.43%, 3,977 genes, 86 tRNAs, and 27 rRNAs, and contains secondary metabolite clusters for producing antimicrobial compounds. In vitro assays indicated that Bv-DS1 has not only antagonistic activities against fungal pathogens, but also shows nematicidal activity, with a mortality rate of 71.62% mortality rates in second-stage juvenile (J2s) Meloidogyne incognita. We then focused on the biocontrol efficiency of Bv-DS1 against M. incognita in pot assays. Preinoculation with Bv-DS1 enhanced tomato growth, and significantly reduced the infection rate of J2s, and the number of galls and egg masses on tomato roots. The underlying mechanism in Bv-DS1-induced resistance to M. incognita was further investigated through split-root experiments, and analysing the expression of the genes related to jasmonic acid (JA), salicylic acid (SA), and the tonoplast intrinsic protein (TIP). The results indicated that Bv-DS1 could not activate host systemic-induced resistance (ISR) in the split-root system of tomatoes. Additionally, the expression of JA- (LOX D and MC) and SA- (PAL2 and PR) responsive genes did not change in Bv-DS1-pretreated plants at 3 and 14 days after nematode inoculation. The presented data showed that JA-and SA-dependent pathways were not required for the biocontrol action of the Bv-DS1 against RKN. The TIP genes, responsible for transport of water and small substrates in plants, have previously been shown to negatively regulate the parasitism of PPNs. Surprisingly, Bv-DS1 compromised the downregulation of TIP1.1 and TIP1.3 by M. incognita. Together, our data suggest that Bv-DS1 exhibits a dual effect on plant growth promotion and protection against RKN, possibly related to the regulation of water and solute transport via TIPs. Thus, the Bv-DS1 strain could be used as a biocontrol agent for RKN control in sustainable agriculture.

Biological Control of Oomycete Soilborne Diseases Caused by Phytophthora capsici, Phytophthora infestans, and Phytophthora nicotianae in Solanaceous Crops

Oomycete pathogens that belong to the genus Phytophthora cause devastating diseases in solanaceous crops such as pepper, potato, and tobacco, resulting in crop production losses worldwide. Although the application of fungicides efficiently controls these diseases, it has been shown to trigger negative side effects such as environmental pollution, phytotoxicity, and fungicide resistance in plant pathogens. Therefore, biological control of Phytophthora-induced diseases was proposed as an environmentally sound alternative to conventional chemical control. In this review, progress on biological control of the soilborne oomycete plant pathogens, Phytophthora capsici, Phytophthora infestans, and Phytophthora nicotianae, infecting pepper, potato, and tobacco is described. Bacterial (e.g., Acinetobacter, Bacillus, Chryseobacterium, Paenibacillus, Pseudomonas, and Streptomyces) and fungal (e.g., Trichoderma and arbuscular mycorrhizal fungi) agents, and yeasts (e.g., Aureobasidium, Curvibasidium, and Metschnikowia) have been reported as successful biocontrol agents of Phytophthora pathogens. These microorganisms antagonize Phytophthora spp. via antimicrobial compounds with inhibitory activities against mycelial growth, sporulation, and zoospore germination. They also trigger plant immunity-inducing systemic resistance via several pathways, resulting in enhanced defense responses in their hosts. Along with plant protection, some of the microorganisms promote plant growth, thereby enhancing their beneficial relations with host plants. Although the beneficial effects of the biocontrol microorganisms are acceptable, single applications of antagonistic microorganisms tend to lack consistent efficacy compared with chemical analogues. Therefore, strategies to improve the biocontrol performance of these prominent antagonists are also discussed in this review.

Bacillus velezensis Strain GUMT319 Reshapes Soil Microbiome Biodiversity and Increases Grape Yields

Bacillus velezensis strain GUMT319 is a rhizobacteria biocontrol agent that can control tobacco black shank disease. We took GUMT319 as a biological fertilizer on Vitis vinifera L. The test group was treated with GUMT319 for one year and the control group had a water treatment. Yields of GUMT319-treated grape groups were significantly increased compared to the controls. The average length and width of single grape fruit, weight of 100 grape fruits, the sugar/acid ratio, and the content of vitamin C were all increased in the GUMT319-treated grape group. The pH of the soil was higher and the contents of alkaline hydrolyzable nitrogen and available potassium were significantly lower in the GUMT319-treated groups than the controls. The soil microbial community composition was evaluated by 16S rDNA high-throughput sequencing, and the Shannon index and Simpson index all showed that soil microbes were more abundant in the GUMT319-treated group. These results indicate that GUMT319 is not only a biocontrol agent, but also a plant growth-promoting rihizobacteria. It can increase the yield of grape by altering the physical and chemical properties and the microbial community composition of the soil.

Biocontrol Ability of the Bacillus amyloliquefaciens Group, B. amyloliquefaciens, B. velezensis, B. nakamurai, and B. siamensis, for the Management of Fungal Postharvest Diseases: A Review

The Bacillus amyloliquefaciens group, composed of B. amyloliquefaciens, B. velezensis, B. nakamurai, and B. siamensis, has recently emerged as an interesting source of biocontrol agents for the management of pathogenic fungi. In this review, all the reports regarding the ability of these species to control postharvest fungal diseases have been covered for the first time. B. amyloliquefaciens species showed various antifungal mechanisms, including production of antifungal lipopeptides and volatile organic compounds, competition for nutrients, and induction of disease resistance. Most reports discussed their use for the control of fruit diseases. Several strains were studied in combination with additives, improving their inhibitory efficacies. In addition, a few strains have been commercialized. Overall, studies showed that B. amyloliquefaciens species are a suitable environmentally friendly alternative for the control of postharvest diseases. However, there are still crucial knowledge gaps to improve their efficacy and host range.

Comparative genomics analysis of Bacillus velezensis LOH112 isolated from a nonagenarian provides insights into its biocontrol and probiotic traits

Bacillus velezensis has recently received increasing attention as a biological fungicide and a potential probiotic agent because of its broad spectrum of antibacterial and antifungal activities. Here, we evaluated the beneficial traits of a newly isolated B. velezensis strain LOH112 using comprehensive bioinformatics and comparative genomic analyses and in vitro experimental approaches. Whole genome sequencing and assembly results showed that the genome of LOH112 consists of a circular chromosome and a circular plasmid, which encodes proteins involved in important biological processes such as sporulation, quorum sensing, and antibiotic synthesis. LOH112 contains 13 secondary metabolism gene clusters responsible for the production of antimicrobial compounds. In vitro experiments showed that LOH112 effectively inhibits several fungi and Gram-positive pathogenic bacteria, hydrolyzes protein and cellulose, and is capable of forming strong adhesive biofilms. Furthermore, comparative genomics revealed that LOH112 contains 34 strain-specific orthologous gene clusters, including two caseinolytic protease P (clpP) genes responsible for proteomic homeostasis. Selective pressure analysis indicated that the transmembrane transporter and ATP-dependent alanine/valine adenylase genes were strongly positively selected, which may endow LOH112 with better biocontrol ability and potential probiotic properties. Collectively, these results not only provide insights into a deeper understanding of the genomic characterization of LOH112 but also imply the potential application of LOH112 as biocontrol and probiotic agents.