Bacillus velezensis RC 218 as a biocontrol agent to reduce Fusarium head blight and deoxynivalenol accumulation: Genome sequencing and secondary metabolite cluster profiles

Role of the beneficial phyllosphere microbiome in the defense against red clover anthracnose caused by Colletotrichum americae-borealis

Red clover (Trifolium pratense), a high-quality forage plant, faces significant threats from anthracnose in northeastern China, but the pathogen responsible remains unidentified. The phyllosphere microbiota is crucial in plantpathogen interactions, yet its role in the resistance of red clover to anthracnose is poorly understood. Using morphological, molecular, and multigene phylogenetic analyses, we identified Colletotrichum americae-borealis (Cab) as the pathogen that causes anthracnose in red clover in China. We also investigated changes in the phyllosphere microbiomes of highly resistant (XJ) and susceptible (SC) red clover materials after Cab infection, via 16S rRNA gene sequencing. The results revealed significant differences in bacterial α- and β-diversity, with novel microbial taxa and a complex microbial network emerging postinfection. Notably, after Cab inoculation, the Shannon diversity index in XJ exhibited more pronounced changes, manifested as an increase in the abundance of beneficial microorganisms such as Bacillus, Pantoea, and Pseudomonas. Network analysis revealed that the XJ microbiome was more complex and stable than the SC microbiome was, regardless of infection status. Bacillus J2, the dominant bacterium, significantly inhibited Cab growth in vitro and reduced the disease index by 33.4-47.7 % when it was reapplied to the leaf surface, suggesting its role in enhancing disease resistance. This study is the first to report that C. americae-borealis causes anthracnose in red clover in China, and demonstrates the potential of the beneficial bacterium J2 in enhancing disease resistance, providing insights into disease resistance mechanisms and the role of the phyllosphere microbiome in pathogen challenge.

An environmental isolate of Pseudomonas, 20EI1, reduces Aspergillus flavus growth in an iron-dependent manner and alters secondary metabolism

Introduction

Aspergillus flavus is an opportunistic pathogenic fungus that infects oilseed crops worldwide. When colonizing plants, it produces mycotoxins, including carcinogenic compounds such as aflatoxins. Mycotoxin contamination results in an important economic and health impact. The design of new strategies to control A. flavus colonization and mycotoxin contamination is paramount.

Methods

The biocontrol potential of a promising new isolate of Pseudomonas spp., 20EI1 against A. flavus was assessed using bioassays and microscopy. To further elucidate the nature of this bacterial-fungal interaction, we also performed chemical and transcriptomics analyses.

Results

In the present study, Pseudomonas spp., 20EI1 was able to reduce the growth of A. flavus. Furthermore, we determined that this growth inhibition is iron-dependent. In addition, Pseudomonas 20EI1 reduced or blocked the production of aflatoxin, as well as cyclopiazonic acid and kojic acid. Expression of iron-related genes was altered in the presence of the bacteria and genes involved in the production of aflatoxin were down-regulated. Iron supplementation partially reestablished their expression. Expression of other secondary metabolite (SM) genes was also reduced by the bacteria, including genes of clusters involved in cyclopiazonic acid, kojic acid and imizoquin biosynthesis, while genes of the cluster corresponding to aspergillicin, a siderophore, were upregulated. Interestingly, the global SM regulatory gene mtfA was significantly upregulated by 20EI1, which could have contributed to the observed alterations in SM.

Discussion

Our results suggest that Pseudomonas 20EI1 is a promising biocontrol against A. flavus, and provide further insight into this iron-dependent bacterial-fungal interaction affecting the expression of numerous genes, among them those involved in SM.

Bacillus velezensis CL197: a zearalenone detoxifying strain isolated from wheat with potential to be used in animal production

Zearalenone (ZEA) is a mycotoxin produced by Fusarium species, and cause contamination of food and feed, with impacts in animal production and in food production chain. Effective detoxifying methods, such as biodegradation, are therefore required. This study aimed to isolate microorganisms and screen ZEA detoxifying strains. As a result, 197 microorganisms were isolated, and six were initially selected after colorimetric screening. ZEA (1 µg/mL) was added to culture media, and after 24 h, all six microorganisms were able to degrade ZEA, without the formation of α-ZOL. One isolate eliminated ~ 99% of ZEA and was identified as Bacillus velezensis CL197. ZEA metabolites produced by the bacteria were evaluated, and no metabolites with greater or similar toxicity than ZEA were detected. This strain was applied to swine in vitro digestion, and up to 64% of ZEA was degraded. B. velezensis CL197 significantly degraded ZEA, demonstrating potential to be used as a detoxifying agent in the food production chain as a biocontrol agent.

Characterization and Biocontrol Efficacy of Bacillus velezensis GYUN-1190 against Apple Bitter Rot

The application of synthetic fungicides has resulted in environmental pollution and adverse effects on non-target species. To reduce the use of agrochemicals, crop disease management requires microbial biological control agents. Bacillus-related genera produce secondary metabolites to control fungal pathogens. Bacillus velezensis GYUN-1190, isolated from soil, showed antagonistic activity against Colletotrichum fructicola, the apple anthracnose pathogen. Volatile organic compounds and culture filtrate (CF) from GYUN-1190 inhibited C. fructicola growth in vitro, by 80.9% and 30.25%, respectively. The CF of GYUN-1190 inhibited pathogen spore germination more than cell suspensions at 10 8 cfu/ml. Furthermore, GYUN-1190 CF is effective in inhibiting C. fructicola mycelial growth in vitro, and it suppresses apple fruit bitter rot more effectively than GYUN-1190 cell suspensions and pyraclostrobin in planta. The mycelial growth of C. fructicola was completely inhibited 48 h after immersion into the CF, in compared with positive controls and GYUN-1190 cell suspensions. The genetic mechanism underlying the biocontrol features of GYUN-1190 was defined using its whole-genome sequence, which was closely compared to similar strains. It consisted of 4,240,653 bp with 45.9% GC content, with 4,142 coding sequences, 87 tRNA, and 28 rRNA genes. The genomic investigation found 14 putative secondary metabolite biosynthetic gene clusters. The investigation suggests that B. velezensis GYUN-1190 might be more effective than chemical fungicides and could address its potential as a biological control agent.

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.

Potentiality of Beneficial Microbe Bacillus siamensis GP-P8 for the Suppression of Anthracnose Pathogens and Pepper Plant Growth Promotion

This study was carried out to screen the antifungal activity against Colletotrichum acutatum, Colletotrichum dematium, and Colletotrichum coccodes. Bacterial isolate GP-P8 from pepper soil was found to be effective against the tested pathogens with an average inhibition rate of 70.7% in in vitro dual culture assays. 16S rRNA gene sequencing analysis result showed that the effective bacterial isolate as Bacillus siamensis. Biochemical characterization of GP-P8 was also performed. According to the results, protease and cellulose, siderophore production, phosphate solubilization, starch hydrolysis, and indole-3-acetic acid production were shown by the GP-P8. Using specific primers, genes involved in the production of antibiotics, such as iturin, fengycin, difficidin, bacilysin, bacillibactin, surfactin, macrolactin, and bacillaene were also detected in B. siamensis GP-P8. Identification and analysis of volatile organic compounds through solid phase microextraction/gas chromatography-mass spectrometry (SPME/GC-MS) revealed that acetoin and 2,3-butanediol were produced by isolate GP-P8. In vivo tests showed that GP-P8 significantly reduced the anthracnose disease caused by C. acutatum, and enhanced the growth of pepper plant. Reverse transcription polymerase chain reaction analysis of pepper fruits revealed that GP-P8 treated pepper plants showed increased expression of immune genes such as CaPR1, CaPR4, CaNPR1, CaMAPK4, CaJA2, and CaERF53. These results strongly suggest that GP-P8 could be a promising biocontrol agent against pepper anthracnose disease and possibly a pepper plant growth-promoting agent.

Expression of endogenous UDP-glucosyltransferase in endophyte Phomopsis liquidambaris reduces deoxynivalenol contamination in wheat

Fusarium head blight is a devastating disease that causes severe yield loses and mycotoxin contamination in wheat grain. Additionally, balancing the trade-off between wheat production and disease resistance has proved challenging. This study aimed to expand the genetic tools of the endophyte Phomopsis liquidambaris against Fusarium graminearum. Specifically, we engineered a UDP-glucosyltransferase-expressing P. liquidambaris strain (PL-UGT) using ADE1 as a selection marker and obtained a deletion mutant using an inducible promoter that drives Cas9 expression. Our PL-UGT strain converted deoxynivalenol (DON) into DON-3-G in vitro at a rate of 71.4 % after 36 h. DON inactivation can be used to confer tolerance in planta. Wheat seedlings inoculated with endophytic strain PL-UGT showed improved growth compared with those inoculated with wildtype P. liquidambaris. Strain PL-UGT inhibited the growth of Fusarium graminearum and reduced infection rate to 15.7 %. Consistent with this finding, DON levels in wheat grains decreased from 14.25 to 0.56 μg/g when the flowers were pre-inoculated with PL-UGT and then infected with F. graminearum. The expression of UGT in P. liquidambaris was nontoxic and did not inhibit plant growth. Endophytes do not enter the seeds nor induce plant disease, thereby representing a novel approach to fungal disease control.

Whole Genome Sequencing of Bacillus velezensis AMR25, an Effective Antagonist Strain against Plant Pathogens

The most serious problems for cultivated grapes are pathogenic microorganisms, which reduce the yield and quality of fruit. One of the most widespread disease of grapes is "gray mold", caused by the fungus Botrytis cinerea. Some strains of Bacillus, such as Bacillus halotolerans, Bacillus amyloliquefaciens, and Bacillus velezensis, are known to be active against major post-harvest plant rots. In this study, we showed that the endophytic bacteria B. velezensis strain AMR25 isolated from the leaves of wild grapes Vitis amurensis Rupr. exhibited antimicrobial activity against grape pathogens, including B. cinerea. The genome of B. velezensis AMR25 has one circular chromosome with a length of 3,909,646 bp. with 3689 open reading frames. Genomic analysis identified ten gene clusters involved in the nonribosomal synthesis of polyketides (macrolactin, bacillene, and difficidin), lipopeptides (surfactin, fengycin, and bacillizin), and bacteriocins (difficidin). Also, the genome under study contains a number of genes involved in root colonization, biofilm formation, and biosynthesis of phytohormones. Thus, the endophytic bacteria B. velezensis strain AMR25 shows great promise in developing innovative biological products for enhancing plant resistance against various pathogens.

Draft genome sequences of two biocontrol agents isolated from the maize phyllosphere: Bacillus subtilis strain EM-A7 and Bacillus velezensis strain EM-A8

In the present study, the genomes of B. subtilis EM-A7 and B. velezensis EM-A8 were sequenced and annotated. The Illumina sequencing platform (NovaSeq PE150) was used to sequence the genomic DNA. There were 6 277 054 raw reads for EM-A7, with a Q20 of 97.52 % and 43.78 % GC, and 8 030 262 raw reads for EM-A8, with a Q20 of 97.53 % and 46.21 % GC. Annotation was carried out by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The strains were classified taxonomically on the basis of an average nucleotide identity analysis (ANI), as well as through a dDDh analysis on the Genome-to-Genome Distance Calculator (GGDC v3.0). The pipeline predicted 4062 protein-coding sequences (CDSs) and 73 RNA genes (62 tRNA and 6 rRNA) for EM-A7, and 3797 protein-coding sequences (CDSs) and 80 RNA genes for EM-A8. These findings enhance our understanding of the two strains' potential as biocontrol agents to manage disease in maize.

Biocontrol of Fusarium head blight in rice using Bacillus velezensis JCK-7158

Fusarium head blight (FHB) is a destructive disease caused by several species of Fusarium, such as Fusarium graminearum and F. asiaticum. FHB affects cereal crops, including wheat, barley, and rice, worldwide. Fusarium-infected kernels not only cause reduced yields but also cause quality loss by producing mycotoxins, such as trichothecenes and zearalenone, which are toxic to animals and humans. For decades, chemical fungicides have been used to control FHB because of their convenience and high control efficacy. However, the prolonged use of chemical fungicides has caused adverse effects, including the emergence of drug resistance to pathogens and environmental pollution. Biological control is considered one of the most promising alternatives to chemicals and can be used for integrated management of FHB due to the rare possibility of environment pollution and reduced health risks. In this study, Bacillus velezensis JCK-7158 isolated from rice was selected as an ecofriendly alternative to chemical fungicides for the management of FHB. JCK-7158 produced the extracellular enzymes protease, chitinase, gelatinase, and cellulase; the plant growth hormone indole-3-acetic acid; and the 2,3-butanediol precursor acetoin. Moreover, JCK-7158 exhibited broad antagonistic activity against various phytopathogenic fungi and produced iturin A, surfactin, and volatile substances as active antifungal compounds. It also enhanced the expression of PR1, a known induced resistance marker gene, in transgenic Arabidopsis plants expressing β-glucuronidase (GUS) fused with the PR1 promoter. Under greenhouse conditions, treatments with the culture broth and suspension concentrate formulation of JCK-7158 at a 1,000-fold dilution inhibited the development of FHB by 50 and 66%, respectively. In a field experiment, treatment with the suspension concentrate formulation of JCK-7158 at a 1,000-fold dilution effectively controlled the development of FHB with a control value of 55% and reduced the production of the mycotoxin nivalenol by 40%. Interestingly, treatment with JCK-7158 enhanced the expression of plant defense-related genes in salicylic acid, jasmonic acid, ethylene, and reactive oxygen species (ROS) signaling pathways before and after FHB pathogen inoculation. Taken together, our findings support that JCK-7158 has the potential to serve as a new biocontrol agent for the management of FHB.

Genome sequence of the plant-growth-promoting bacterium Bacillus velezensis EU07

Many Gram-positive spore-forming rhizobacteria of the genus Bacillus show potential as biocontrol biopesticides that promise improved sustainability and ecological safety in agriculture. Here, we present a draft-quality genome sequence for Bacillus velezensis EU07, which shows growth-promotion in tomato plants and biocontrol against Fusarium head blight. We found that the genome of EU07 is almost identical to that of the commercially used strain QST713, but identified 46 single-nucleotide differences that distinguish these strains from each other. The availability of this genome sequence will facilitate future efforts to unravel the genetic and molecular basis for EU07's beneficial properties.

Bacillus velezensis RC218 and emerging biocontrol agents against Fusarium graminearum and Fusarium poae in barley: in vitro, greenhouse and field conditions

Fusarium head blight (FHB) is one of the most common diseases in Argentina, affecting the quality and yield of barley grains. Fusarium graminearum sensu stricto (ss) and Fusarium poae are causal agents of FHB and potential sources of mycotoxin contamination in barley. Conventional management strategies do not lead to a complete control of FHB; therefore, biological control emerges as an eco-friendly alternative in the integrated management of the disease. In the present work, Bacillus velezensis, Bacillus inaquosorum, Bacillus nakamurai and Lactobacillus plantarum were evaluated as potential biocontrol agents against F. graminearum ss and F. poae on barley-based media. Bacillus velezensis RC218 was selected to carry out greenhouse and field trials in order to reduce FHB and mycotoxin accumulation. This strain was able to control growth of both Fusarium species and reduced deoxynivalenol (DON) and nivalenol (NIV) production by 66 % and 79 %, respectively. Bacillus inaquosorum and B. nakamurai were more effective in controlling F. poae growth, and the mean levels of reduction in DON accumulation were 50 and 38 %, and 93 and 26 % for NIV, respectively. Lactobacillus plantarum showed variable biocontrol capacity depending on the strain, with no significant mycotoxin reduction. The biocontrol on incidence and severity of FHB in the greenhouse and field trials was effective, being more efficient against F. graminearum ss and DON accumulation than against F. poae and NIV occurrence. This study provides valuable data for the development of an efficient tool based on biocontrol agents to prevent FHB-producing Fusarium species development and mycotoxin occurrence in barley, contributing to food safety.

Bacillus subtilis NBRI-W9 simultaneously activates SAR and ISR against Fusarium chlamydosporum NBRI-FOL7 to increase wilt resistance in tomato

AIMS

The study aimed to determine the pathogenicity of Fusarium species currently prevalent in tomato fields having history of chemical fungicide applications and determine the bio-efficacy of Bacillus subtilis NBRI-W9 as a potent biological control agent.

METHODS AND RESULTS

Fusarium was isolated from surface-sterilized infected tomato plants collected from fields. Pathogenicity of 30 Fusarium isolates was determined by in vitro and in vivo assays. Following Koch's postulates, F. chlamydosporum (FOL7) was identified as a virulent pathogen. The biological control of FOL 7 by B. subtilis NBRI-W9 (W9) and the colonization potential of W9 were established using spontaneous rifampicin-resistant mutants. W9 showed 82% inhibition of FOL7 on a dual-culture plate and colonization levels in tomato plants of ∼5.5, ∼3.3, and ∼2.2 log10 CFU/g in root, stem, and leaf tissue, respectively. Antagonistic activity was shown by scanning electron microscopy (SEM) and cell-wall-degradative enzymes. W9 reduced FOL7 infection in net-house and field experiments by 60% and 41%, respectively. Biochemical investigation, defence enzymes, defence gene expression analysis, SEM, and field studies provide evidence of hyperparasitism and induced resistance as the mode of biological control. The study also demonstrates that the potent biocontrol agent W9, isolated from Piper, can colonize tomato plants, control fungal disease by inducing induced systemic resistance (ISR) and systemic acquired resistance (SAR) simultaneously, and increase crop yield by 21.58% under field conditions.

CONCLUSIONS

This study concludes that F. chlamydosporum (NBRI-FOL7) is a potent, fungicide-resistant pathogen causing wilt in tomatoes. NBRI-W9 controlled FOL7 through mycoparasitism and simultaneously activated ISR and SAR in plants, providing an attractive tool for disease control that acts at multiple levels.

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, β-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.

Screening, Identification, and Growth Promotion of Antagonistic Endophytes Associated with Chenopodium quinoa Against Quinoa Pathogens

Fungal disease is one of the important reasons for crop yield reduction. Isolation of important endophytes with biocontrol and growth-promoting effects is of great significance for the exploitation of beneficial microbial resources and the biological control of crop fungal diseases. In this study, endophytes from roots, stems, and leaves of quinoa at different growth and development stages were isolated and purified; then the antagonistic activity and growth-promoting characteristics of antagonistic endophytes were determined. Finally, the antagonistic endophytes were identified by morphological characteristics and ITS/16S rRNA sequence analysis. Our results showed that 122 endophytic fungi and 371 endophytic bacteria were isolated from quinoa, of which three endophytic fungi and seven endophytic bacteria were screened that had inhibitory activity against quinoa pathogenic fungi. Most of the antagonistic strains could produce indole-3 acetic acid and had the ability to dissolve organic phosphorus. In addition, the bacterial suspension of endophytic bacteria had the ability to promote the seed germination and plant growth of quinoa. The endophytic fungi with antagonistic activity were identified as Penicillium raperi and P. pulvillorum; the endophytic bacteria were identified as Bacillus paralicheniformis, B. tequilensis, and B. velezensis, respectively. The strains of quinoa endophytes in this study can provide rich microbial resources and a theoretical basis for biological control of plant fungal diseases and agricultural production.

A novel Bacillus sp. with antagonistic activity against a plant pathogen, Fusarium graminearum, and its potential antagonistic mechanism

Fusarium head blight (FHB) is a wheat disease caused by the plant pathogen Fusarium graminearum, which leads to crop yield losses and agricultural economic losses, as well as poses a threat to the environment and human health. Effective biocontrol of F. graminearum is urgent. An antagonistic strain HZ-5 with 59.2% antagonistic activity against F. graminearum in vitro had been isolated from sea mud of Haizhou Bay using a dual-culture assay, which was highly homologous with Bacillus halosaccharovorans according to the 16S rRNA sequence. The antagonistic activity of HZ-5 had been further studied. HZ-5 had a broad range of antagonistic activity against another six plant pathogenic fungi and was effective in controlling FHB of wheat in pot experiment. The substances with antagonistic activity were temperature insensitive, and had been purified by HPLC (High Performance Liquid Chromatography) to prove to be secreted lipopeptides. The antagonistic substances induced the biosynthesis of chitin and glycerol, while ergosterol , cholesterol, and phosphatidylcholine reduced their inhibitory effects on F. graminearum. These data would be helpful to provide a better biocontrol strain against FHB, and to provide important basis to elucidate the antagonistic mechanism of biocontrol.

Biocontrol Efficacy of Endophyte Pseudomonas poae to Alleviate Fusarium Seedling Blight by Refining the Morpho-Physiological Attributes of Wheat

Some endophyte bacteria can improve plant growth and suppress plant diseases. However, little is known about the potential of endophytes bacteria to promote wheat growth and suppress the Fusarium seedling blight pathogen Fusarium graminearum. This study was conducted to isolate and identify endophytic bacteria and evaluate their efficacy for the plant growth promotion and disease suppression of Fusarium seedling blight (FSB) in wheat. The Pseudomonas poae strain CO showed strong antifungal activity in vitro and under greenhouse conditions against F. graminearum strain PH-1. The cell-free supernatants (CFSs) of P. poae strain CO were able to inhibit the mycelium growth, the number of colonies forming, spore germination, germ tube length, and the mycotoxin production of FSB with an inhibition rate of 87.00, 62.25, 51.33, 69.29, and 71.08%, respectively, with the highest concentration of CFSs. The results indicated that P. poae exhibited multifarious antifungal properties, such as the production of hydrolytic enzymes, siderophores, and lipopeptides. In addition, compared to untreated seeds, wheat plants treated with the strain showed significant growth rates, where root and shoot length increased by about 33% and the weight of fresh roots, fresh shoots, dry roots, and dry shoots by 50%. In addition, the strain produced high levels of indole-3-acetic acid, phosphate solubilization, and nitrogen fixation. Finally, the strain demonstrated strong antagonistic properties as well as a variety of plant growth-promoting properties. Thus, this result suggest that this strain could be used as an alternate to synthetic chemicals, which can serve as an effective method of protecting wheat from fungal infection.

Biocontrol potential of bacteria belonging to the Bacillus subtilis group against pests and diseases of agricultural interest through genome exploration

The usage of microorganisms as biocontrol agents and biofertilizers has been recommended and recognized as an ecologically correct alternative to maintaining the productivity and safety of crops. Thus, the objectives of this work were to characterize twelve strains belonging to Invertebrate Bacteria Collection of Embrapa Genetic Resources and Biotechnology by molecular, morphological, and biochemical methods and to evaluate the pathogenicity of these strains against pests and diseases of agricultural interest. The morphological characteristic of the strains was performed according to the principles of Bergy's Manual of Systematic Bacteriology. The genomes of the 12 strains were sequenced in Macrogen, Inc. (Seoul, Korea) using the HiSeq2000 and GS-FLX Plus high-performance platforms. In the determination of antibiotic sensibility profiles, disc-diffusion methods (Cefar Diagnótica Ltda) were adopted©. Selective bioassays were carried out with insects of the Lepidoptera (Spodoptera frugiperda, Helicoverpa armigera, and Chrysodeixis includens), Coleoptera (Anthonomus grandis), Diptera (Aedes aegypti) and Hemiptera (Euschistus heros) orders, and with the nematode Caenorhabditis elegans. In addition, the antagonistic action of the phytopathogens Fusarium oxysporum f. sp. vasinfectum and Sclerotinia sclerotiorum against the strains under study, and in vitro assays of phosphate solubilization were also performed. Sequencing of the complete genome of the 12 strains determined that all of them belonged to the Bacillus subtilis sensu lato group. In the strains genome were detected genic clusters responsible for encoding secondary metabolites such as surfactin, iturin, fengycins/plipastatin, bacillomycin, bacillisin, and siderophores. Due to the production of these compounds, there was a survival reduction of the Lepidoptera order insects and a reduction in the phytopathogens mycelial growth. These results show that the species of group B. subtilis s.l. can become promising microbiological alternatives to pest and disease control.

Impact of Enniatin and Deoxynivalenol Co-Occurrence on Plant, Microbial, Insect, Animal and Human Systems: Current Knowledge and Future Perspectives

Fusarium mycotoxins commonly contaminate agricultural products resulting in a serious threat to both animal and human health. The co-occurrence of different mycotoxins in the same cereal field is very common, so the risks as well as the functional and ecological effects of mycotoxins cannot always be predicted by focusing only on the effect of the single contaminants. Enniatins (ENNs) are among the most frequently detected emerging mycotoxins, while deoxynivalenol (DON) is probably the most common contaminant of cereal grains worldwide. The purpose of this review is to provide an overview of the simultaneous exposure to these mycotoxins, with emphasis on the combined effects in multiple organisms. Our literature analysis shows that just a few studies on ENN-DON toxicity are available, suggesting the complexity of mycotoxin interactions, which include synergistic, antagonistic, and additive effects. Both ENNs and DON modulate drug efflux transporters, therefore this specific ability deserves to be explored to better understand their complex biological role. Additionally, future studies should investigate the interaction mechanisms of mycotoxin co-occurrence on different model organisms, using concentrations closer to real exposures.

Harnessing Native Bacillus spp. for Sustainable Wheat Production

The genus Bacillus has been widely applied in contemporary agriculture as an environmentally-friendly biological agent. However, the real effect of commercial Bacillus-based fertilizers and pesticides varies immensely in the field. To harness Bacillus for efficient wheat production, we reviewed the diversity, functionality, and applicability of wheat-associated native Bacillus for the first time. Our main findings are: (i) Bacillus spp. inhabit the rhizosphere, root, stem, leaf, and kernel of wheat; (ii) B. subtilis and B. velezensis are the most widely endophytic species that can be isolated from both below and aboveground tissues; (iii) major functions of these representative strains are promotion of plant growth and alleviation of both abiotic and biotic stresses in wheat; (iv) stability and effectiveness are 2 major challenges during field application; (v) a STVAE pipeline that includes 5 processes, namely, Screen, Test, Validation, Application, and Evaluation, has been proposed for the capture and refinement of wheat-associated Bacillus spp. In particular, this review comprehensively addresses possible solutions, concerns, and criteria during the development of native Bacillus-based inoculants for sustainable wheat production.

Profiling of Antimicrobial Metabolites Synthesized by the Endophytic and Genetically Amenable Biocontrol Strain Bacillus velezensis DMW1

The genus Bacillus is one of the most important genera for the biological control of plant diseases that are caused by various phytopathogens. The endophytic Bacillus strain DMW1 was isolated from the inner tissues of potato tubers and exhibited strong biocontrol activity. Based on its whole-genome sequence, DMW1 belongs to the Bacillus velezensis species, and it is similar to the model strain B. velezensis FZB42. 12 secondary metabolite biosynthetic gene clusters (BGCs), including two unknown function BGCs, were detected in the DMW1 genome. The strain was shown to be genetically amenable, and seven secondary metabolites acting antagonistically against plant pathogens were identified by a combined genetic and chemical approach. Strain DMW1 did significantly improve the growth of tomato and soybean seedlings, and it was able to control the Phytophthora sojae and Ralstonia solanacearum that were present in the plant seedlings. Due to these properties, the endophytic strain DMW1 appears to be a promising candidate for comparative investigations performed together with the Gram-positive model rhizobacterium FZB42, which is only able to colonize the rhizoplane. IMPORTANCE Phytopathogens are responsible for the wide spread of plant diseases as well as for great losses of crop yields. At present, the strategies used to control plant disease, including the development of resistant cultivars and chemical control, may become ineffective due to the adaptive evolution of pathogens. Therefore, the use of beneficial microorganisms to deal with plant diseases attracts great attention. In the present study, a new strain DMW1, belonging to the species B. velezensis, was discovered with outstanding biocontrol properties. It showed plant growth promotion and disease control abilities that are comparable with those of B. velezensis FZB42 under greenhouse conditions. According to a genomic analysis and a bioactive metabolites analysis, genes that are responsible for promoting plant growth were detected, and metabolites with different antagonistic activities were identified. Our data provide a basis for DMW1 to be further developed and applied as a biopesticide, which is similar to the closely related model strain FZB42.

Genome sequence and comparative analysis of fungal antagonistic strain Bacillus velezensis LJBV19

Bacillus species as fungal antagonistic agents have been widely used in the agriculture and considered as safe products for the management of plant pathogens. In this study, we reported the whole genome sequence of strain LJBV19 isolated from grapevine rhizosphere soil. Strain LJBV19 was identified as Bacillus velezensis through morphological, physicochemical, molecular analysis and genome comparison. Bacillus velezensis LJBV19 had a significant inhibitory effect on the growth of Magnaporthe oryzae with an inhibition ratio up to 75.55% and showed broad spectrum of activity against fungal phytopathogens. The 3,973,013-bp circular chromosome with an average GC content of 46.5% consisted of 3993 open reading frames (ORFs), and 3308 ORFs were classified into 19 cluster of orthologous groups of proteins (COG) categories. Genes related to cell wall degrading enzymes were predicted by Carbohydrate-Active enZYmes (CAZy) database and validated at the metabolic level, producing 0.53 ± 0.00 U/mL cellulose, 0.14 ± 0.01 U/mL chitinase, and 0.11 ± 0.01 U/mL chitosanase. Genome comparison confirmed the taxonomic position of LJBV19, conserved genomic structure, and genetic homogeneity. Moreover, 13 gene clusters for biosynthesis of secondary metabolites in LJBV19 genome were identified and two unique clusters (clusters 2 and 12) shown to direct an unknown compound were only present in strain LJBV19. In general, our results will provide insights into the antifungal mechanisms of Bacillus velezensis LJBV19 and further application of the strain.

Cell-Free Supernatant of Bacillus subtilis Reduces Kiwifruit Rot Caused by Botryosphaeria dothidea through Inducing Oxidative Stress in the Pathogen

Biological control of postharvest diseases has been proven to be an effective alternative to chemical control. As an environmentally friendly biocontrol agent, Bacillus subtilis has been widely applied. This study explores its application in kiwifruit soft rot and reveals the corresponding mechanisms. Treatment with cell-free supernatant (CFS) of Bacillus subtilis BS-1 significantly inhibits the mycelial growth of the pathogen Botryosphaeria dothidea and attenuates the pathogenicity on kiwifruit in a concentration-dependent manner. In particular, mycelial growth diameter was only 21% of the control after 3 days of treatment with 5% CFS. CFS caused swelling and breakage of the hyphae of B. dothidea observed by scanning electron microscopy, resulting in the leakage of nucleic acid and soluble protein and the loss of ergosterol content. Further analysis demonstrated that CFS significantly induces the expression of Nox genes associated with reactive oxygen species (ROS) production by 1.9-2.7-fold, leading to a considerable accumulation of ROS in cells and causing mycelial cell death. Our findings demonstrate that the biocontrol effect of B. subtilis BS-1 CFS on B. dothidea is realized by inducing oxidative damage to the mycelia cell.

Important wheat diseases in the US and their management in the 21st century

Wheat is a crop of historical significance, as it marks the turning point of human civilization 10,000 years ago with its domestication. Due to the rapid increase in population, wheat production needs to be increased by 50% by 2050 and this growth will be mainly based on yield increases, as there is strong competition for scarce productive arable land from other sectors. This increasing demand can be further achieved using sustainable approaches including integrated disease pest management, adaption to warmer climates, less use of water resources and increased frequency of abiotic stress tolerances. Out of 200 diseases of wheat, 50 cause economic losses and are widely distributed. Each year, about 20% of wheat is lost due to diseases. Some major wheat diseases are rusts, smut, tan spot, spot blotch, fusarium head blight, common root rot, septoria blotch, powdery mildew, blast, and several viral, nematode, and bacterial diseases. These diseases badly impact the yield and cause mortality of the plants. This review focuses on important diseases of the wheat present in the United States, with comprehensive information of causal organism, economic damage, symptoms and host range, favorable conditions, and disease management strategies. Furthermore, major genetic and breeding efforts to control and manage these diseases are discussed. A detailed description of all the QTLs, genes reported and cloned for these diseases are provided in this review. This study will be of utmost importance to wheat breeding programs throughout the world to breed for resistance under changing environmental conditions.

Biocontrol of the causal brown patch pathogen Rhizoctonia solani by Bacillus velezensis GH1-13 and development of a bacterial strain specific detection method

Brown patch caused by the basidiomycete fungus Rhizoctonia solani is an economically important disease of cool-season turfgrasses. In order to manage the disease, different types of fungicides have been applied, but the negative impact of fungicides on the environment continues to rise. In this study, the beneficial bacteria Bacillus velezensis GH1-13 was characterized as a potential biocontrol agent to manage brown patch disease. The strain GH1-13 strongly inhibited the mycelial growth of turf pathogens including different anastomosis groups of R. solani causing brown patch and large patch. R. solani AG2-2(IIIB) hyphae were morphologically changed, and fungal cell death resulted from exposure to the strain GH1-13. In addition, the compatibility of fungicides with the bacterial strain, and the combined application of fungicide azoxystrobin and the strain in brown patch control on creeping bentgrass indicated that the strain could serve as a biocontrol agent. To develop strain-specific detection method, two unique genes from chromosome and plasmid of GH1-13 were found using pan-genome analysis of 364 Bacillus strains. The unique gene from chromosome was successfully detected using both SYBR Green and TaqMan qPCR methods in bacterial DNA or soil DNA samples. This study suggests that application of GH1-13 offers an environmentally friendly approach via reducing fungicide application rates. Furthermore, the developed pipeline of strain-specific detection method could be a useful tool for detecting and studying the dynamics of specific biocontrol agents.

Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives

For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.

A novel of new class II bacteriocin from Bacillus velezensis HN-Q-8 and its antibacterial activity on Streptomyces scabies

Potato common scab is a main soil-borne disease of potato that can significantly reduce its quality. At present, it is still a challenge to control potato common scab in the field. To address this problem, the 972 family lactococcin (Lcn972) was screened from Bacillus velezensis HN-Q-8 in this study, and an Escherichia coli overexpression system was used to obtain Lcn972, which showed a significant inhibitory effect on Streptomyces scabies, with a minimum inhibitory concentration of 10.58 μg/mL. The stability test showed that Lcn972 is stable against UV radiation and high temperature. In addition, long-term storage at room temperature and 4°C had limited effects on its activity level. The antibacterial activity of Lcn972 was enhanced by Cu²⁺ and Ca²⁺, but decreased by protease K. The protein was completely inactivated by Fe²⁺. Cell membrane staining showed that Lcn972 damaged the cell membrane integrity of S. scabies. Scanning electron microscope (SEM) and transmission electron microscope (TEM) observations revealed that the hyphae of S. scabies treated with Lcn972 were deformed and adhered, the cell membrane was incomplete, the cytoplasm distribution was uneven, and the cell appeared hollow inside, which led to the death of S. scabies. In conclusion, we used bacteriocin for controlling potato common scab for the first time in this study, and it provides theoretical support for the further application of bacteriocin in the control of plant diseases.

Lactic Acid Bacteria as Potential Biocontrol Agents for Fusarium Head Blight Disease of Spring Barley

Fusarium head blight (FHB) is a devastating disease encountered by spring-grown barley. Traditionally, synthetic chemicals have been used to control this disease on small grain cereals. A move toward biological control agents as part of sustainable agriculture is pertinent due to the evolutionary mechanisms employed by fungal diseases to circumvent current protection strategies. This study evaluated the effect of six lactic acid bacteria isolates on the development of FHB under in vitro and glasshouse conditions. The relative expression of Fusarium marker genes and transcription factors under Fusarium infection was examined. Dual-culture assays observed inhibition zones of up to 10 and 17% of total plate area for L. amylovorus FST 2.11 and L. brevis R2Δ, respectively. Detached leaf assays validated the antifungal activity and showed the potential of all test isolates to significantly inhibit sporulation of Fusarium culmorum and Fusarium graminearum strains. Spray inoculation of lactic acid bacteria to barley spikelets prior to Fusarium spore application significantly reduced disease severity for five candidates (P < 0.05) under glasshouse conditions. Mycotoxin analysis revealed the ability of L. amylovorus DSM20552 to significantly reduce deoxynivalenol content in spikelets (P < 0.05). A preliminary gene expression study showed the positive influence of lactic acid bacteria on the expression of important defense-related marker genes and transcription factors upon FHB. These results indicate the potential of lactic acid bacteria to be included as part of an integrated pest management strategy for the management of FHB disease. This strategy will reduce FHB severity and deoxynivalenol (DON) contamination of spring barley, leading to high acceptance in the grain market.

Combination of Bacillus velezensis RC218 and Chitosan to Control Fusarium Head Blight on Bread and Durum Wheat under Greenhouse and Field Conditions

Fusarium graminearum sensu stricto is, worldwide, the main causal agent of Fusarium head blight in small cereal crops such as wheat, barley, and oat. The pathogen causes not only reductions in yield and grain quality but also contamination with type-B trichothecenes such as deoxynivalenol. Prevention strategies include the use of less susceptible cultivars through breeding programs, cultural practices, crop rotation, fungicide application, or a combination of them through an integrated pest management. Additionally, the use of more eco-friendly strategies by the evaluation of microorganisms and natural products is increasing. The effect of combining Bacillus velezensis RC218 and chitosan on Fusarium Head Blight (FHB) and deoxynivalenol accumulation under greenhouse and field conditions in bread and durum wheat was evaluated. Under greenhouse conditions, both B. velezensis RC218 and chitosan (0.1%) demonstrated FHB control, diminishing the severity by 38 and 27%, respectively, while the combined treatment resulted in an increased reduction of 54% on bread wheat. Field trials on bread wheat showed a biocontrol reduction in FHB by 18 to 53%, and chitosan was effective only during the first year (48% reduction); surprisingly, the combination of these active principles allowed the control of FHB disease severity by 39 and 36.7% during the two harvest seasons evaluated (2017/18, 2018/19). On durum wheat, the combined treatment showed a 54.3% disease severity reduction. A reduction in DON accumulation in harvested grains was observed for either bacteria, chitosan, or their combination, with reductions of 50.3, 68, and 64.5%, respectively, versus the control.

Bioflocculant produced by Bacillus velezensis and its potential application in brewery wastewater treatment

This study was designed to evaluate the potential of bioflocculant producing strains isolated from wastewater sludge. According to the Plackett–Burman design, the response surface revealed glucose, magnesium sulfate, and ammonium sulfate as critical media components of the nutritional source, whereas the central composite design affirmed an optimum concentration of the critical nutritional source as 16.0 g/l (glucose), 3.5 g/l magnesium sulfate heptahydrate (MgSO₄.7H₂O), and 1.6 g/l ammonium sulfate ( (NH₄)₂SO₄), yielding an optimal flocculation activity of 96.8%. Fourier Transformer Infrared Spectroscopy (FTIR) analysis confirmed the presence of hydroxyl, carboxyl and methoxyl in the structure of the bioflocculant. Additionally, chemical analysis affirmed the presence of mainly a polysaccharide in the main backbone of the purified bioflocculant with no detection of protein. Energy Dispersive X-ray analysis affirmed the presence of chlorine, phosphorous, oxygen and chlorine as representatives of elemental composition. Thermogravimetric (TGA) analysis revealed over 60% weight was retained at a temperature range of 700 °C. The purified bioflocculant remarkably removed chemical oxygen demand, biological oxygen demand and turbidity in brewery wastewater. This study suggested that the bioflocculant might be an alternate candidate for wastewater treatment.

Plant Beneficial Bacteria as Bioprotectants against Wheat and Barley Diseases

Wheat and barley are the main cereal crops cultivated worldwide and serve as staple food for a third of the world's population. However, due to enormous biotic stresses, the annual production has significantly reduced by 30-70%. Recently, the accelerated use of beneficial bacteria in the control of wheat and barley pathogens has gained prominence. In this review, we synthesized information about beneficial bacteria with demonstrated protection capacity against major barley and wheat pathogens including Fusarium graminearum, Zymoseptoria tritici and Pyrenophora teres. By summarizing the general insights into molecular factors involved in plant-pathogen interactions, we show to an extent, the means by which beneficial bacteria are implicated in plant defense against wheat and barley diseases. On wheat, many Bacillus strains predominantly reduced the disease incidence of F. graminearum and Z. tritici. In contrast, on barley, the efficacy of a few Pseudomonas, Bacillus and Paraburkholderia spp. has been established against P. teres. Although several modes of action were described for these strains, we have highlighted the role of Bacillus and Pseudomonas secondary metabolites in mediating direct antagonism and induced resistance against these pathogens. Furthermore, we advance a need to ascertain the mode of action of beneficial bacteria/molecules to enhance a solution-based crop protection strategy. Moreover, an apparent disjoint exists between numerous experiments that have demonstrated disease-suppressive effects and the translation of these successes to commercial products and applications. Clearly, the field of cereal disease protection leaves a lot to be explored and uncovered.

Biosurfactant-Producing Bacillus velezensis PW192 as an Anti-Fungal Biocontrol Agent against Colletotrichum gloeosporioides and Colletotrichum musae

In this study, plant-root-associated Bacillus species were evaluated as antifungal biocontrol agents by analyzing the production of surface bioactive molecules known as lipopeptide biosurfactants. This study aimed to isolate and characterize antifungal biosurfactant-producing Bacillus bacterium. Bacillusvelezensis PW192 was isolated from the rhizosphere of Lagerstroemia macrocarpa var macrocarpa and identified based on phylogenetic analysis of the 16S rRNA gene. The biosurfactant was excreted to cultured supernatant and exhibited emulsification power up to 60% and a decrease in surface tension from 72 in distilled water to 21 mN/m. The surface tension properties were stable in a broad range of pH from 6 to 10, in high temperatures up to 100 °C, and in salinities with a NaCl concentration up to 12% (w/v). Starting from 0.5 mg of acid, precipitated crude biosurfactant exhibited antifungal activity toward Anthracnose, caused by the phytopathogens Colletotrichum gloeosporioides and C. musae. The chemical structures of the biosurfactant were structurally characterized as lipopeptides fengycin A and fengycin B. The stability of the biosurfactant, as well as the antifungal properties of B. velezensis PW192, can potentially make them useful as agricultural biocontrol agents, as well as in other biotechnological applications.

Native Cultivable Bacteria from the Blueberry Microbiome as Novel Potential Biocontrol Agents

Blueberry production is affected by fungal postharvest pathogens, including Botrytis cinerea and Alternaria alternata, the causative agents of gray mold disease and Alternaria rot, respectively. Biocontrol agents adapted to blueberries and local environments are not known to date. Here, we report on the search for and the identification of cultivable blueberry epiphytic bacteria with the potential to combat the aforementioned fungi. Native, blueberry-borne bacterial strains were isolated from a plantation in Tucumán, Argentina and classified based on 16S rRNA gene sequences. Antagonistic activities directed at B. cinerea and A. alternata were studied in vitro and in vivo. The 22 bacterial strains obtained could be attributed to eleven different genera: Rosenbergiella, Fictibacillus, Bacillus, Pseudomonas, Microbacterium, Asaia, Acinetobacter, Curtobacterium, Serratia, Sphingomonas and Xylophilus. Three strains displaying antagonistic impacts on the fungal pathogens were identified as Bacillus velezensis (BA3 and BA4) and Asaia spathodeae (BMEF1). These strains are candidates for biological control agents of local blueberry production and might provide a basis for the development of eco-friendly, sustainable alternatives to synthetic pesticides.

Could Bacillus biofilms enhance the effectivity of biocontrol strategies in the phyllosphere?

Maize (Zea mays L.), a major crop in Argentina and a staple food around the world, is affected by the emergence and re-emergence of foliar diseases. Agrochemicals are the main control strategy nowadays, but they can cause resistance in insects and microbial pathogens and have negative effects on the environment and human health. An emerging alternative is the use of living organisms, i.e. microbial biocontrol agents, to suppress plant pathogen populations. This is a risk-free approach when the organisms acting as biocontrol agents come from the same ecosystem as the foliar pathogens they are meant to antagonize. Some epiphytic microorganisms may form biofilm by becoming aggregated and attached to a surface, as is the case of spore-forming bacteria from the genus Bacillus. Their ability to sporulate and their tolerance to long storage periods make them a frequently used biocontrol agent. Moreover, the biofilm that they create protects them against different abiotic and biotic factors and helps them to acquire nutrients, which ensures their survival on the plants they protect. This review analyzes the interactions that the phyllosphere-inhabiting Bacillus genus establishes with its environment through biofilm, and how this lifestyle could serve to design effective biological control strategies.

Bacillus subtilis suppresses the charcoal rot disease by inducing defence responses and physiological attributes in soybean

Endophytes can induce the defence responses and modulates physiological attributes in host plants during pathogen attacks. In the present study, 127 bacterial endophytes (BEs) were isolated from different parts of healthy soybean plant. Among them, two BEs (M-2 and M-4) resulted a significant antagonistic property against Macrophomina phaseolina, causes charcoal rot disease in soybean. The antagonistic potential was evaluated through dual culture plate assay, where M-4 expressed higher antifungal activity than M-2 against M. phaseolina. The M-4 produces cell wall degrading enzymes viz. cellulase (145.71 ± 1.34 μgmL-1), chitinase (0.168 ± 0.0009 unitmL-1) and β,1-3 endoglucanase (162.14 ± 2.5 μgmL-1), which helps in cell wall disintegration of pathogens. Additionally, M-4 also can produce siderophores, indole-3-acetic acid (IAA) (17.03 ± 1.10 μgmL-1) and had a phosphate solubilization potential (19.89 ± 0.26 μgmL-1). Further, GC-MS profiling of M-4 has been carried out to demonstrate the production of lipophilic secondary metabolites which efficiently suppress the M. phaseolina defensive compounds under co-culture conditions. Bio-efficacy study of M-4 strain shown a significant reduction in disease incidence around 60 and 80% in resistant and susceptible varieties of soybean, respectively. The inoculation of M-4 potentially enhances the physiological attributes and triggers various defence responsive enzymes viz. superoxide dismutase (SOD), phenol peroxidase (PPO), peroxidase (PO) and catalase (CAT). The histopathological study also confirmed that M-4 can reduce the persistence of microsclerotia in root and shoot tissue. Conclusively, M-4 revealed as an efficient biocontrol agent that can uses multifaceted measures for charcoal rot disease management, by suppress the M. phaseolina infection and enhance the physiological attributes of soybean.

Multi-Omics Techniques for Analysis Antifungal Mechanisms of Lipopeptides Produced by Bacillus velezensis GS-1 against Magnaporthe oryzae In Vitro

Magnaporthe oryzae is a fungal pathogen that causes rice blast, a highly destructive disease. In the present study, the bacteria strain GS-1 was isolated from the rhizosphere soil of ginseng and identified as Bacillus velezensis through 16S rRNA gene sequencing, whole genome assembly, and average nucleotide identity analysis. B. velezensis strain GS-1 exhibited significant antagonistic activity to several plant fungal pathogens. Through whole genome sequencing, 92 Carbohydrate-Active Enzymes and 13 gene clusters that encoded for secondary metabolites were identified. In addition, strain GS-1 was able to produce the lipopeptide compounds, surfactin, fengycin, and plantazolicin. The inhibitory effects of lipopeptide compounds on M. oryzae were confirmed, and the antagonistic mechanism was explored using transcriptomics and metabolomics analysis. Differential expressed genes (DEGs) and differential accumulated metabolites (DAMs) revealed that the inhibition of M. oryzae by lipopeptide produced by GS-1 downregulated the expression of genes involved in amino acid metabolism, sugar metabolism, oxidative phosphorylation, and autophagy. These results may explain why GS-1 has antagonistic activity to fungal pathogens and revealed the mechanisms underlying the inhibitory effects of lipopeptides produced by GS-1 on fungal growth, which may provide a theoretical basis for the potential application of B. velezensis GS-1 in future plant protection.

Purification and characterization of antibacterial surfactin isoforms produced by Bacillus velezensis SK

Bacillus velezensis SK having broad-spectrum antimicrobial activity has been isolated from soil. The efficient extraction of antimicrobial compounds produced in various mediums has been done using Diaion HP-20 resin. Further, characterization of an antimicrobial compound by TLC, FTIR, in-situ bioautography analysis revealed the presence of cyclic lipopeptides, which is then purified by the combination of silica gel, size exclusion, dual gradient, and RP-HPLC chromatography techniques. Growth kinetic studies showed that Bacillus velezensis SK produces a mixture of lipopeptides (1.33 gL^-1). The lipopeptide exhibits good pH (2-10) and temperature stability up to 80 °C. LC-ESI-MS analysis of partially purified lipopeptide identified variant of surfactin, further analysis of purified chromatographic fractions revealed the occurrence of most abundant C₁₅-surfactin homologues (m/z 1036.72 Da). The isolated surfactin exhibits good antimicrobial activity (1600 AU/ml) against drug-resistant food-born B. cereus and human pathogen Staphylococcus aureus. Hence, identified strain B. velezensis SK and its potent antibacterial surfactin lipopeptide could be used in various food and biomedical applications.

Microorganisms from corn stigma with biocontrol potential of Fusarium verticillioides

Abstract The mycotoxigenic fungus Fusarium verticillioides is the primary maize pathogen and causes the maize stalk and ear rot diseases with significant economic losses. Furthermore, the excessive use of fungicides to control F. verticillioides constitutes threats to the environment and human health. Thus, sustainable alternatives such as biological control are needed to minimize the hazards associated with the current method. Although much is known about the vulnerability of the maize silks as a gateway for several fungal pathogens invading the developing grains, studies on the chemical properties of silk extracts and their resident microbiota are scarce. This study isolated and characterized bacteria and fungi that colonize the maize stigma to assess new potential biocontrol agents. The samples were collected from maize fields in the Brazilian localities of Sete Lagoas-MG, Sidrolândia-MS, Sertaneja-PR, and Goiânia-GO. One hundred sixty-seven microorganisms were isolated, 46% endophytic and 54% epiphytic. First, the antagonist activity was evaluated by the agar disc diffusion method performed in triplicate, and 83% of the isolates showed antagonist activity against F. verticillioides. Then, the 42 most efficient isolates were identified based on the partial sequencing of the bacterial 16S rRNA gene and fungi ITS region. The bacteria belong to the genera Bacillus (57.1%), Burkholderia (23.8%), Achromobacter (7.1%), Pseudomonas (2.4%), and Serratia (2.4%), while the fungi are Penicillium (2.4%), Candida (2.4), and Aspergillus (2.4%). The results showed that microorganisms from maize stigma might represent new promising agents for F. verticillioides control.

Bacillus velezensis: A Treasure House of Bioactive Compounds of Medicinal, Biocontrol and Environmental Importance

Bacillus velezensis gram-positive bacterium, is frequently isolated from diverse niches mainly soil, water, plant roots, and fermented foods. B. velezensis is ubiquitous, non-pathogenic and endospore forming. Being frequently isolated from diverse plant holobionts it is considered host adapted microorganism and recognized of high economic importance given its ability to promote plant growth under diverse biotic and abiotic stress conditions. Additionally, the species suppress many plant diseases, including bacterial, oomycete, and fungal diseases. It is also able after plant host root colonization to induce unique physiological situation of host plant called primed state. Primed host plants are able to respond more rapidly and/or effectively to biotic or abiotic stress. Moreover, B. velezenis have the ability to resist diverse environmental stresses and help host plants to cope with, including metal and xenobiotic stresses. Within species B. velezensis strains have unique abilities allowing them to adopt different life styles. Strain level abilities knowledge is warranted and could be inferred using the ever-expanding new genomes list available in genomes databases. Pangenome analysis and subsequent identification of core, accessory and unique genomes is actually of paramount importance to decipher species full metabolic capacities and fitness across diverse environmental conditions shaping its life style. Despite the crucial importance of the pan genome, its assessment among large number of strains remains sparse and systematic studies still needed. Extensive knowledge of the pan genome is needed to translate genome sequencing efforts into developing more efficient biocontrol agents and bio-fertilizers. In this study, a genome survey of B. velezensis allowed us to (a) highlight B. velezensis species boundaries and show that Bacillus suffers taxonomic imprecision that blurs the debate over species pangenome; (b) identify drivers of their successful acquisition of specific life styles and colonization of new niches; (c) describe strategies they use to promote plant growth and development; (d) reveal the unlocked strain specific orphan secondary metabolite gene clusters (biosynthetic clusters with corresponding metabolites unknown) that product identification is still awaiting to amend our knowledge of their putative role in suppression of pathogens and plant growth promotion, and (e) to describe a dynamic pangenome with a secondary metabolite rich accessory genome.

Effect of cultivation media and temperature on metabolite profiles of three nematicidal Bacillus species

Globally, root-knot nematode (RKN) infestations cause great financial losses. Although agrochemicals are used to manage these pests, there is increased interest in using biocontrol agents based on natural antagonistic microorganisms, such as Bacillus. These nematicidal bacteria demonstrate antagonism towards RKN through different modes of action, including specialised metabolite production. The aim of this study was to compare metabolite profiles of nematicidal Bacillus species and assess the influence of cultivation conditions on these profiles. Two hyphenated metabolomics platforms, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QTOF-MS), were employed to profile and compare metabolite features produced during the cultivation of three nematicidal Bacillus species (Bacillus firmus, B. cereus and B. soli) in complex Luria-Bertani broth (LB) and a simpler minimal broth (MB), at three different temperatures (25, 30 and 37°C). Cultivation in complex LB as opposed to simpler MB resulted in the production of more statistically significant metabolite features. Selected temperatures in this study did not have a significant influence on metabolite profiles. Moreover, media-specific influences outweighed temperature-specific influences on metabolite profiles. Results from this study are a valuable first step in establishing suitable cultivation conditions for the production of Bacillus metabolites of interest.

Detection and characterization of a rare two-component lantibiotic, amyloliquecidin GF610 produced by Bacillus velezensis, using a combination of culture, molecular and bioinformatic analyses

AIM

To detect and characterize novel lantibiotics from a collection of Bacillus spp. using a multifaceted analytical approach.

METHODS AND RESULTS

A previously completed microassay identified 45 Bacillus isolates with anti-Listeria activity. The isolates were PCR screened using degenerate primers targeting conserved sequences in lanM-type lantibiotics. B. velezensis GF610 produced a PCR product whose sequence, along with genome mining and bioinformatics, guided the liquid chromatographic analysis of strain's cell-free extracts and the mass spectrometry of purified fractions. Results revealed a new amyloliquecidin variant (designated GF610) produced by the strain. Amyloliquecidin GF610 is a two-component lantibiotic with α and β peptides having monoisotopic masses of 3026 and 2451 Da, and molecular formulae C₁₃₀ H₁₉₁ N₃₅ O₃₉ S₅ and C₁₁₀ H₁₅₈ N₂₆ O₃₀ S₄ , respectively. Amyloliquecidin GF610 is active against Listeria monocytogenes, Clostridium sporogenes, Clostridioides difficile, Staphylococcus aureus and Alicyclobacillus acidoterrestris with minimum inhibitory concentrations (MICs) in the range of 0.5-7.0 µmol l^-1 .

CONCLUSIONS

The proposed multifaceted analytical approach was valuable to provide a deep and proper characterization of a novel bacteriocin, amyloliquecidin GF610, with high antimicrobial activity against Gram-positive bacteria.

SIGNIFICANCE AND IMPACT

The discovered Amyloliquecidin GF610 is potentially useful in food, agricultural or medical applications. The analytical approach followed may facilitate future discoveries of two-component lantibiotics, which are challenging compounds to detect and characterize.

Selection of Bacterial Strains for Control of Root-Knot Disease Caused by Meloidogyne incognita

Root-knot disease caused by Meloidogyne incognita leads to significant crop yield losses that may be aggravated by the association with pathogenic fungi and bacteria. Biological agents can be effectively used against the complex disease of root-knot nematode and pathogenic fungi. In this study, 35 bacterial strains were analyzed for their in vitro nematicidal, antagonistic and growth stimulation activities. Based on results from the in vitro assays, grow-box experiments on tomato and cucumber were carried out with the strain BZR 86 of Bacillus velezensis applied at different concentrations. Effects of B. velezensis BZR 86 on the development of root-knot disease were evaluated by recording root gall index, number of galls and number of eggs in egg masses. Application of B. velezensis BZR 86 noticeably decreased the development of root-knot disease on tomato and cucumber plants, as well as significantly increased growth and biomass of cucumber plants in accordance with bacterial concentration. This study seems to demonstrate that strain B. velezensis BZR 86 could be an additional tool for an environmentally safe control of root-knot disease on horticultural crops.

Dietary supplementation of Bacillus velezensis B8 enhances immune response and resistance against Aeromonas veronii in grass carp

The heavy use of prophylactic antibiotics in aquaculture leads to elevated antibiotic residues, posing a huge hidden danger in aquaculture products and other natural aquatic environments. Therefore, this study aims to isolate probiotics that can replace antibiotics from the gut of grass carp for disease control. Bacillus velezensis B8 was isolated from the gut of grass carp and showed broad-spectrum antimicrobial activity against several fish pathogenic bacteria, including Aeromonas hydrophilis, Aeromonas veronii, Vibrio parahaemolyticus, Escherichia coli, Edwardsiella tarda and Vibrio mimicus. The safety evaluation showed that the strain B8 was non-toxic to grass carp, had no hemolytic activity, and was sensitive to most antibiotics. In vitro study indicated that strain B8 was viable at pH 2-7, had weak tolerance to 0.1% (w/v) bile salt, and could grow at 10°C-40 °C. The grass carps were fed with diets containing 0 (control), 10⁷, and 10⁹ cfu/g of strain B8 for 4 weeks. Various immune parameters were measured at 1, 2, 3, and 4 weeks of post-feeding. The results of non-specific immunoassay showed that diets supplemented with B8 significantly increased alkaline phosphatase (AKP) and superoxide dismutase (SOD) activity in serum samples (p < 0.05). The expression levels of immune-related genes in the kidney and spleen of grass carp were measured. Among them, the expression levels of IgM and TNF-α both in spleen and kidney were significantly increased after 3 and 4 weeks of post-feeding (p < 0.05). The expression of IgD and MHCI in kidney was significantly upregulated in high-dose groups after 2 and 3 weeks of feeding, respectively (p < 0.05). In addition, after 7 days of challenging with A. veronii, the high-dose group and low-dose group had 48% and 53% survival compared to 25% survival for the control group. These results suggest that B. velezensis B8 has the potential to be developed into a microecological preparation for the alternatives of antibiotics in aquaculture.

Potential of Bacillus velezensis as a probiotic in animal feed: a review

Bacillus velezensis is a plant growth-promoting bacterium that can also inhibit plant pathogens. However, based on its properties, it is emerging as a probiotic in animal feed. This review focuses on the potential characteristics of B. velezensis for use as a probiotic in the animal feed industry. The review was conducted by collecting recently published articles from peer-reviewed journals. Google Scholar and PubMed were used as search engines to access published literature. Based on the information obtained, the data were divided into three groups to discuss the (i) probiotic characteristics of B. velezensis, (ii) probiotic potential for fish, and (iii) the future potential of this species to be developed as a probiotic for the animal feed industry. Different strains of B. velezensis isolated from different sources were found to have the ability to produce antimicrobial compounds and have a beneficial effect on the gut microbiota, with the potential to be a candidate probiotic in the animal feed industry. This review provides valuable information about the characteristics of B. velezensis, which can provide researchers with a better understanding of the use of this species in the animal feed industry.

Bacillus velezensis strain MBY2, a potential agent for the management of crown gall disease

The reduction of the use chemical pesticides in agriculture is gaining importance as an objective of decision-makers in both politics and economics. Consequently, the development of technically efficient and economically affordable alternatives as, e.g., biological control agents or practices is highly solicited. Crown gall disease of dicotyledonous plants is caused by ubiquitous soil borne pathogenic bacteria of the Agrobacterium tumefaciens species complex, that comprises the species Agrobacterium fabrum and represents a globally relevant plant protection problem. Within the framework of a screening program for bacterial Agrobacterium antagonists a total of 14 strains were isolated from Tunisian soil samples and assayed for antagonistic activity against pathogenic agrobacteria. One particularly promising isolate, termed strain MBY2, was studied more in depth. Using a Multilocus Sequence Analysis (MLSA) approach, the isolate was assigned to the taxonomic species Bacillus velezensis. Strain MBY2 was shown to display antagonistic effects against the pathogenic A. fabrum strain C58 in vitro and to significantly decrease pathogen populations under sterile and non-sterile soil conditions as well as in the rhizosphere of maize and, to a lower extent, tomato plants. Moreover, the ability of B. velezensis MBY2 to reduce C58-induced gall development has been demonstrated in vivo on stems of tomato and almond plants. The present study describes B. velezensis MBY2 as a newly discovered strain holding potential as a biological agent for crown gall disease management.

Diversity and biopotential of Bacillus velezensis strains A6 and P42 against rice blast and bacterial blight of pomegranate

Bacillus velezensis is widely known for its inherent biosynthetic potential to produce a wide range of bio-macromolecules and secondary metabolites, including polyketides (PKs) and siderophores, as well as ribosomally and non-ribosomally synthesized peptides. In the present study, we aimed to investigate the bio-macromolecules, such as proteins and peptides of Bacillus velezensis strains, namely A6 and P42 by whole-cell sequencing and highlighted the potential application in controlling phytopathogens. The bioactive compounds, specifically secondary metabolites, were characterized by whole-cell protein profiling, Thin-Layer Chromatography, Infra-Red Spectroscopy, Nuclear Magnetic Resonance, Gas Chromatograph and Electro Spray Liquid Chromatography. Gas Chromatography analysis revealed that the A6 and P42 strains exert different functional groups of compounds, such as aromatic ring, aliphatic, alkene, ketone, amine groups and carboxylic acid. Whole-cell protein profiling of A6 and P42 strains of B. velezensis by nano-ESI LC-MS/MS revealed the presence of 945 and 5303 proteins, respectively. The in vitro evaluation of crude extracts (10%) of A6 and P42 significantly inhibited the rice pathogen, Magnaporthe oryzae (MG01), whereas the cell-free culture filtrate (75%) of strain P42 showed 58.97% inhibition. Similarly, in vitro evaluation of crude extract (10%) of P42 strain inhibited bacterial blight of pomegranate pathogen, Xanthomonas axonopodis pv. punicae, which eventually resulted in a higher inhibition zone of 3 cm, whereas the cell-free extract (75%) of the same strain significantly suppressed the growth of the pathogen with an inhibition zone of 1.48 cm. From the results obtained, the crude secondary metabolites and cell-free filtrates (containing bio-macromolecules) of the strains A6 and P42 of B. velezensis can be employed for controlling the bacterial and fungal pathogens of crop plants.