Surfactin and fengycin contribute to the protection of a Bacillus subtilis strain against grape downy mildew by both direct effect and defence stimulation

Bacillus velezensis BE2 controls wheat and barley diseases by direct antagonism and induced systemic resistance

Wheat and barley rank among the main crops cultivated on a global scale, providing the essential nutritional foundation for both humans and animals. Nevertheless, these crops are vulnerable to several fungal diseases, such as Septoria tritici blotch and net blotch, which significantly reduce yields by adversely affecting leaves and grain quality. To mitigate the effect of these diseases, chemical fungicides have proven to be genuinely effective; however, they impose a serious environmental burden. Currently, biocontrol agents have attracted attention as a sustainable alternative to fungicides, offering an eco-friendly option. The study aimed to assess the efficacy of Bacillus velezensis BE2 in reducing disease symptoms caused by Zymoseptoria tritici and Pyrenophora teres. This bacterium exhibited significant antagonistic effects in vitro by suppressing fungal development when pathogens and the beneficial strain were in direct confrontation. These findings were subsequently confirmed through microscopic analysis, which illustrated the strain's capacity to inhibit spore germination and mycelial growth in both pathogens. Additionally, the study analysed the cell-free supernatant of the bacterium using UPLC-MS (ultra-performance liquid chromatography-mass spectrometry). The results revealed that strain BE2 produces, among other metabolites, different families of cyclic lipopeptides that may be involved in biocontrol. Furthermore, the beneficial effects of strain BE2 in planta were assessed by quantifying the fungal DNA content directly at the leaf level after bacterization, using two different application methods (foliar and drenching). The results indicated that applying the beneficial bacterium at the root level significantly reduced pathogens pressure. Finally, gene expression analysis of different markers showed that BE2 application induced a priming effect within the first hours after infection. KEY POINTS: • BE2 managed Z. tritici and P. teres by direct antagonism and induced systemic resistance. • Strain BE2 produced seven metabolite families, including three cyclic lipopeptides. • Application of strain BE2 at the root level triggered plant defense mechanisms.

The Utilization of Bacillus subtilis to Design Environmentally Friendly Living Paints with Anti-Mold Properties

The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into paint. "Mold" refers to the ubiquitous fungal species that generate visible multicellular filaments commonly found in household dust. The development of mold leads to severe health problems for occupants, including allergic response, hypersensitivity pneumonitis, and asthma, which have significant economic and clinical outcomes. We here demonstrate the robust effect of a commercial paint enhanced with Bacillus subtilis cells against the common mold agent, Aspergillus niger, and identify three biosynthetic clusters essential for this effect. Our results lay the foundation for bio-convergence and synthetic biology approaches to introduce renewable and environmentally friendly bio-anti-fungal agents into the built environment.

Combination of irradiated chitosan and microbial agent to reduce downy mildew on grapevine cv. Thompson seedless

Globally sustainable disease management ensuring high quality in grapes is in demand as it holds significant importance as a versatile fruit for consumption, winemaking, and production of various products such as grape juice, raisin, and grape-seed oil. The present paper reports a combination of nano-biotechnology as a promising strategy for enhancing plant health and fruit productivity in grapes combining Irradiated chitosan nanoparticles and bio-control agents. The Irradiated Chitosan with Bacillus subtilis and Trichoderma viridae and pesticides were evaluated for disease management. Percent disease index, percent disease control, and percent yield enhancement in Cymoxanil 8% + Mamcozeb 64% WP @ 0.2% treatment were as 17. 24%, 67.97% and 33.91% in 150 ppm Irradiated chitosan+B. subtilis were 19.83, 63.16, 30.41 and in Trichoderma 150 ppm Irradiated chitosan were 24.58, 54.33, and 27.40, respectively as compared to untreated crop with disease severity 53.84% PDI. Thus, irradiated chitosan and Bacillus subtilis elucidated a synergistic combination for residue-free efficient phytosanitary measures, which harnessed the strength of chitosan and bio-control agents for sustainable grape productivity. These findings will also pave the way for a deeper understanding of the synergistic interaction between Irradiated nanochitosan and bio-control agents for an eco-friendly and economically viable disease management strategy. The minimum temperature and morning relative humidity (RH I) had positive significance, with correlation coefficients of 0.484 and 0.485, respectively. The evening relative humidity (RH II) had a positive highly significant positive correlation coefficient of 0.664. Chitosan merits as a multiple stress tolerance enhancing agent that will further help in mitigating climate change adaptations in grapevines reducing reliance on chemical agro-inputs.

Toxicological evaluation of microbial secondary metabolites in the context of European active substance approval for plant protection products

Risk assessment (RA) of microbial secondary metabolites (SM) is part of the EU approval process for microbial active substances (AS) used in plant protection products (PPP). As the number of potentially produced microbial SM may be high for a certain microbial strain and existing information on the metabolites often are low, data gaps are frequently identified during the RA. Often, RA cannot conclusively clarify the toxicological relevance of the individual substances. This work presents data and RA conclusions on four metabolites, Beauvericin, 2,3-deepoxy-2,3-didehydro-rhizoxin (DDR), Leucinostatin A and Swainsonin in detail as examples for the challenging process of RA. To overcome the problem of incomplete assessment reports, RA of microbial AS for PPP is in need of new approaches. In view of the Next Generation Risk Assessment (NGRA), the combination of literature data, omic-methods, in vitro and in silico methods combined in adverse outcome pathways (AOPs) can be used for an efficient and targeted identification and assessment of metabolites of concern (MoC).

Volatilomics of Fruit Wines

Volatilomics is a scientific field concerned with the evaluation of volatile compounds in the food matrix and methods for their identification. This review discusses the main groups of compounds that shape the aroma of wines, their origin, precursors, and selected metabolic pathways. The paper classifies fruit wines into several categories, including ciders and apple wines, cherry wines, plum wines, berry wines, citrus wines, and exotic wines. The following article discusses the characteristics of volatiles that shape the aroma of each group of wine and the concentrations at which they occur. It also discusses how the strain and species of yeast and lactic acid bacteria can influence the aroma of fruit wines. The article also covers techniques for evaluating the volatile compound profile of fruit wines, including modern analytical techniques.

Endogenous cell wall degrading enzyme LytD is important for the biocontrol activity of Bacillus subtilis

Autolysins are endogenous cell wall degrading enzymes (CWDEs) in bacteria that remodel the peptidoglycan layer of its own cell wall. In the Bacillus subtilis genome, at least 35 autolysin genes have been identified. However, the study of their roles in bacterial physiology has been hampered by their complexity and functional redundancy. B. subtilis GLB191 is an effective biocontrol strain against grape downy mildew disease, the biocontrol effect of which results from both direct effect against the pathogen and stimulation of the plant defense. In this study, we show that the autolysin N-acetylglucosaminidase LytD, a major autolysin of vegetative growth in B. subtilis, plays an important role in its biocontrol activity against grape downy mildew. Disruption of lytD resulted in reduced suppression of the pathogen Plasmopara viticola and stimulation of the plant defense. LytD is also shown to affect the biofilm formation and colonization of B. subtilis on grape leaves. This is the first report that demonstrates the role of an endogenous CWDE in suppressing plant disease infection of a biological control microorganism. These findings not only expand our knowledge on the biological function of autolysins but also provide a new target to promote the biocontrol activity of B. subtilis.

A glycoside hydrolase 30 protein BpXynC of Bacillus paralicheniformis NMSW12 recognized as A MAMP triggers plant immunity response

Bacillus spp. has been widely used as a biocontrol agent to control plant diseases. However, little is known about mechanisms of the protein MAMP secreted by Bacillus spp. Herein, our study reported a glycoside hydrolase family 30 (GH30) protein, BpXynC, produced by the biocontrol bacteria Bacillus paralicheniformis NMSW12, that can induce cell death in several plant species. The results revealed that the recombinant protein triggers cell death in Nicotiana benthamiana in a BAK1-dependent manner and elicits an early defense response, including ROS burst, activation of MAPK cascades, and upregulation of plant immunity marker genes. BpXynC was also found to be a glucuronoxylanase that exhibits hydrolysis activity on xlyan. Two mutants of BpXynC which lost the glucuronoxylanase activity still retained the elicitor activity. The qRT-PCR results of defense-related genes showed that BpXynC induces plant immunity responses via an SA-mediated pathway. BpXynC and its mutants could induce resistance in N. benthamiana against infection by Sclerotinia sclerotiorum and tobacco mosaic virus (TMV). Furthermore, BpXynC-treated tomato fruits exhibited strong resistance to the infection of Phytophthora capsica. Overall, our study revealed that GH30 protein BpXynC can induce plant immunity response as MAMP, which can be further applied as a biopesticide to control plant diseases.

Lipopeptides from Bacillus: unveiling biotechnological prospects-sources, properties, and diverse applications

Bacillus sp. has proven to be a goldmine of diverse bioactive lipopeptides, finding wide-range of industrial applications. This review highlights the importance of three major families of lipopeptides (iturin, fengycin, and surfactin) produced by Bacillus sp. and their diverse activities against plant pathogens. This review also emphasizes the role of non-ribosomal peptide synthetases (NRPS) as significant enzymes responsible for synthesizing these lipopeptides, contributing to their peptide diversity. Literature showed that these lipopeptides exhibit potent antifungal activity against various plant pathogens and highlight their specific mechanisms, such as siderophore activity, pore-forming properties, biofilm inhibition, and dislodging activity. The novelty of this review comes from its comprehensive coverage of Bacillus sp. lipopeptides, their production, classification, mechanisms of action, and potential applications in plant protection. It also emphasizes the importance of ongoing research for developing new and enhanced antimicrobial agents. Furthermore, this review article highlights the need for future research to improve the production efficiency of these lipopeptides for commercial applications. It recognizes the potential for these lipopeptides to expand the field of biological pest management for both existing and emerging plant diseases.

Genome Sequencing and Characterization of Bacillus velezensis N23 as Biocontrol Agent against Plant Pathogens

The overuse of chemical fungicides against fungal pathogens adversely affects soil and plant health, resulting in environmental problems and food safety. Therefore, biocontrol is considered as an environmentally friendly and cost-effective green technique in environmental protection and agricultural production. We obtained a bacterial strain N23 from a contaminated plate which showed significant inhibition to anthracnose. The strain N23 was identified as Bacillus velezensis based on 16S rRNA gene, gyrA gene, and whole-genome sequence. The bacterium N23 was able to suppress the mycelial growth of numerous plant pathogenic fungi on solid media. Tomato seeds treated with strain N23 showed significantly higher germination levels than untreated ones. Moreover, strain N23 effectively reduced the lesion area of pepper anthracnose disease in planta. The gene clusters responsible for antifungal metabolites (fengycin, surfactin, and iturin) were identified in the genome sequence of N23 based on genome mining and PCR. Furthermore, methanol extracts of the bacterial culture caused significant inhibition in growth of the fungal Colletotrichum sp. and Botrytis cinerea. These findings suggested that B. velezensis N23 could be a potential biocontrol agent in agricultural production and a source of antimicrobial compounds for further exploitation.

Characterization and evaluation of Bacillus subtilis GYUN-2311 as a biocontrol agent against Colletotrichum spp. on apple and hot pepper in Korea

Crop plants are vulnerable to a variety of diseases, including anthracnose, caused by various species of Colletotrichum fungi that damages major crops, including apples and hot peppers. The use of chemical fungicides for pathogen control may lead to environmental pollution and disease resistance. Therefore, we conducted this research to develop a Bacillus subtilis-based biological control agent (BCA). B. subtilis GYUN-2311 (GYUN-2311), isolated from the rhizosphere soil of an apple orchard, exhibited antagonistic activity against a total of 12 fungal pathogens, including eight Colletotrichum species. The volatile organic compounds (VOCs) and culture filtrate (CF) from GYUN-2311 displayed antifungal activity against all 12 pathogens, with 81% control efficiency against Fusarium oxysporum for VOCs and 81.4% control efficacy against Botryosphaeria dothidea for CF. CF also inhibited germination and appressorium formation in Colletotrichum siamense and C. acutatum. The CF from GYUN-2311 showed antifungal activity against all 12 pathogens in different media, particularly in LB medium. It also exhibited plant growth-promoting (PGP) activity, lytic enzyme activity, siderophore production, and the ability to solubilize insoluble phosphate. In trials on apples and hot peppers, GYUN-2311 effectively controlled disease, with 75 and 70% control efficacies against C. siamense in wounded and unwounded apples, respectively. Similarly, the control efficacy of hot pepper against C. acutatum in wounded inoculation was 72%. Combined application of GYUN-2311 and chemical suppressed hot pepper anthracnose to a larger extent than other treatments, such as chemical control, pyraclostrobin, TK®, GYUN-2311 and cross-spraying of chemical and GYUN-2311 under field conditions. The genome analysis of GYUN-2311 identified a circular chromosome comprising 4,043 predicted protein-coding sequences (CDSs) and 4,096,969 bp. B. subtilis SRCM104005 was the strain with the highest average nucleotide identity (ANI) to GYUN-2311. AntiSMASH analysis identified secondary metabolite biosynthetic genes, such as subtilomycin, bacillaene, fengycin, bacillibactin, pulcherriminic acid, subtilosin A, and bacilysin, whereas BAGEL analysis confirmed the presence of competence (ComX). Six secondary metabolite biosynthetic genes were induced during dual culture in the presence of C. siamense. These findings demonstrate the biological control potential of GYUN-2311 against apple and hot pepper anthracnose.

Advances in understanding grapevine downy mildew: From pathogen infection to disease management

Plasmopara viticola is geographically widespread in grapevine-growing regions. Grapevine downy mildew disease, caused by this biotrophic pathogen, leads to considerable yield losses in viticulture annually. Because of the great significance of grapevine production and wine quality, research on this disease has been widely performed since its emergence in the 19th century. Here, we review and discuss recent understanding of this pathogen from multiple aspects, including its infection cycle, disease symptoms, genome decoding, effector biology, and management and control strategies. We highlight the identification and characterization of effector proteins with their biological roles in host-pathogen interaction, with a focus on sustainable control methods against P. viticola, especially the use of biocontrol agents and environmentally friendly compounds.

Bioherbicidal potential of Bacillus altitudinis D30202 on Avena fatua L.: a whole-genome sequencing analysis

Avena fatua L. (wild oat) is one of the most harmful gramineous weeds that can affect the yield and quality of infiltrating crops. Bacillus altitudinis D30202 exhibits an excellent biocontrol activity against wild oat. To elucidate the biocontrol mechanisms of B. altitudinis D30202, the genome structure of this strain was assessed via whole-genome sequencing analysis. We predicted and analyzed secondary metabolite synthesis gene clusters to elucidate the mechanisms underlying the biocontrol of weeds. The whole-genome sequencing data indicated that B. altitudinis D30202 had the genome size and GC content of 3,777,154 bp and 41.32%, respectively, and 3809 coding genes were identified. Moreover, this strain could generate several compounds with bioherbicidal activity, including 4-hydroxy-3-methoxycinnamic acid and two indole derivatives. Bioinformatics prediction and comparative genomic analysis revealed that the strain had 6 secondary metabolite gene clusters. Furthermore, the taxonomic position of B. altitudinis D30202 was assessed, confirming its uniqueness and novelty within the Bacillus genus. Comparative genomic analysis showed differences in gene distribution, suggesting potential adaptations to different environments. In conclusion, B. altitudinis D30202 possesses a genome with unique characteristics, encoding enzymes and pathways related to herbicidal potential and biocontrol. This study provides a reference basis for understanding the molecular mechanisms of weed inhibition.

The antifungal substance from Bacillus velezensis B-3 improved the malt quality against premature yeast flocculation induced by Fusarium graminearum infection

Malt produced from barley contaminated with Fusarium graminearum can cause premature yeast flocculation (PYF) in beer fermentation, which ultimately affects the production efficiency and flavor quality of beer. In this study, a strain of Bacillus velezensis B-3 that was isolated from soil displayed strong antifungal activity against F. graminearum. The antifungal substances were extracted and separated by ammonium sulfate fractional precipitation and semipreparative high-performance liquid chromatography to obtain fraction VI with the strongest antifungal activity. Ultra-performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry was used to identify that the fraction contained lipopeptides such as iturin A, surfactant B, and surfactant C. The minimum inhibitory concentration of the fraction was 0.2 mg/mL, and confocal laser scanning microscopy showed that the morphology of F. graminearum hyphae was obviously abnormal, with most of them were dead. Antifungal fraction VI could inhibit the growth of F. graminearum and avoid the production of PYF factor during malting but did not affect other qualities of malt. Therefore, the development of antimicrobial agents against Fusarium provides an effective potential strategy to control the production of PYF factors for malt-manufacturing enterprises. PRACTICAL APPLICATION: Antifungal fraction VI could inhibit the growth of F. graminearum and the formation of DON during malting but did not affect other qualities of malt. The levels of soluble nitrogen, free amino nitrogen, and color experienced a substantial reduction compared to the malt infected by F. graminearum. The PYF phenomenon was significantly improved, the number of suspended yeast cells and the degree of fermentation were increased, and the level of residual extract in the wort was low, close to that of control malt.

degQ associated with the degS/degU two-component system regulates biofilm formation, antimicrobial metabolite production, and biocontrol activity in Bacillus velezensis DMW1

The gram-positive bacterium Bacillus velezensis strain DMW1 produces a high level of antimicrobial metabolites that can suppress the growth of phytopathogens. We investigated the mechanism used by degQ and the degS/degU two-component system to regulate the biocontrol characteristics of DMW1. When degQ and degU were deleted, the biofilm formation, cell motility, colonization activities, and antifungal abilities of ΔdegQ and ΔdegU were significantly reduced compared to wild-type DMW1. The expression levels of biofilm-related genes (epsA, epsB, epsC, and tasA) and swarming-related genes (swrA and swrB) were all down-regulated. We also evaluated the impact on secondary metabolites of these two genes. The degQ and degU genes reduced surfactin and macrolactin production and up-regulated the production of fengycin, iturin, bacillaene, and difficidin metabolites. The reverse transcription-quantitative PCR results were consistent with these observations. Electrophoretic mobility shift assay and microscale thermophoresis revealed that DegU can bind to the promoter regions of these six antimicrobial metabolite genes and regulate their synthesis. In conclusion, we provided systematic evidence to demonstrate that the degQ and degU genes are important regulators of multicellular behaviour and antimicrobial metabolic processes in B. velezensis DMW1 and suggested novel amenable strains to be used for the industrial production of antimicrobial metabolites.

Pectic homogalacturonan sensed by Bacillus acts as host associated cue to promote establishment and persistence in the rhizosphere

Bacillus velezensis isolates are among the most promising plant-associated beneficial bacteria used as biocontrol agents. However, various aspects of the chemical communication between the plant and these beneficials, determining root colonization ability, remain poorly described. Here we investigated the molecular basis of such interkingdom interaction occurring upon contact between Bacillus velezensis and its host via the sensing of pectin backbone homogalacturonan (HG). We showed that B. velezensis stimulates key developmental traits via a dynamic process involving two conserved pectinolytic enzymes. This response integrates transcriptional changes leading to the switch from planktonic to sessile cells, a strong increase in biofilm formation, and an accelerated sporulation dynamics while conserving the potential to efficiently produce specialized secondary metabolites. As a whole, we anticipate that this response of Bacillus to cell wall-derived host cues contributes to its establishment and persistence in the competitive rhizosphere niche and ipso facto to its activity as biocontrol agent.

Bacterial and Fungal Biocontrol Agents for Plant Disease Protection: Journey from Lab to Field, Current Status, Challenges, and Global Perspectives

Plants are constantly exposed to various phytopathogens such as fungi, Oomycetes, nematodes, bacteria, and viruses. These pathogens can significantly reduce the productivity of important crops worldwide, with annual crop yield losses ranging from 20% to 40% caused by various pathogenic diseases. While the use of chemical pesticides has been effective at controlling multiple diseases in major crops, excessive use of synthetic chemicals has detrimental effects on the environment and human health, which discourages pesticide application in the agriculture sector. As a result, researchers worldwide have shifted their focus towards alternative eco-friendly strategies to prevent plant diseases. Biocontrol of phytopathogens is a less toxic and safer method that reduces the severity of various crop diseases. A variety of biological control agents (BCAs) are available for use, but further research is needed to identify potential microbes and their natural products with a broad-spectrum antagonistic activity to control crop diseases. This review aims to highlight the importance of biocontrol strategies for managing crop diseases. Furthermore, the role of beneficial microbes in controlling plant diseases and the current status of their biocontrol mechanisms will be summarized. The review will also cover the challenges and the need for the future development of biocontrol methods to ensure efficient crop disease management for sustainable agriculture.

Biosynthetic Gene Clusters in Sequenced Genomes of Four Contrasting Rhizobacteria in Phytopathogen Inhibition and Interaction with Capsicum annuum Roots

Through screening of rhizobacteria, species that effectively suppress phytopathogens and/or promote plant growth are found. Genome sequencing is a crucial step in obtaining a complete characterization of microorganisms for biotechnological applications. This study aimed to sequence the genomes of four rhizobacteria that differ in their inhibition of four root pathogens and in their interaction with chili pepper roots to identify the species and analyze differences in the biosynthetic gene clusters (BGCs) for antibiotic metabolites and to determine possible phenotype-genotype correlations. Results from sequencing and genome alignment identified two bacteria as Paenibacillus polymyxa, one as Kocuria polaris, and one that was previously sequenced as Bacillus velezensis. Analysis with antiSMASH and PRISM tools showed that B. velezensis 2A-2B, the strain with the best performance of referred characteristics, had 13 BGCs, including those related to surfactin, fengycin, and macrolactin, not shared with the other bacteria, whereas P. polymyxa 2A-2A and 3A-25AI, with up to 31 BGCs, showed lower pathogen inhibition and plant hostility; K. polaris showed the least antifungal capacity. P. polymyxa and B. velezensis had the highest number of BGCs for nonribosomal peptides and polyketides. In conclusion, the 13 BGCs in the genome of B. velezensis 2A-2B that were not present in the other bacteria could explain its effective antifungal capacity and could also contribute to its friendly interaction with chili pepper roots. The high number of other BGCs for nonribosomal peptides and polyketide shared by the four bacteria contributed much less to phenotypic differences. IMPORTANCE To advance the characterization of a microorganism as a biocontrol agent against phytopathogens, it is highly recommended to analyze the potential of the profile of secondary metabolites as antibiotics that it produces to counteract pathogens. Some specific metabolites have positive impacts in plants. By analyzing sequenced genomes with bioinformatic tools, such as antiSMASH and PRISM, outstanding bacterial strains with high potential to inhibit phytopathogens and/or promote plant growth can be quickly selected to confirm and expand our knowledge of BGCs of great value in phytopathology.

A marine lipopeptides-producing Bacillus amyloliquefaciens HY2-1 with a broad-spectrum antifungal and antibacterial activity and its fermentation kinetics study

The antagonistic Bacillus amyloliquefaciens HY2-1 was a marine microbiology that was isolated previously from the seabed silt of Beibu Gulf in China by dual culture with Penicillium digitatum. As a continuous study, the present work focused on evaluating the antimicrobial activity, identifying the produced active components, and revealing the fermentation characteristics of B. amyloliquefaciens HY2-1, respectively. It was found that B. amyloliquefaciens HY2-1 exhibited a broad-spectrum antimicrobial activity against the tested seven phytopathogenic fungi and five pathogenic bacteria by producing Bacillus lipopeptides such as fengycin A (C₁₄ to C₁₉ homologues) and surfactin (C₁₄ and C₁₅ homologues). Morphological observation of P. digitatum under light microscope, scanning electron microscopy, transmission electron microscopy, and fluorescence microscope inferred that B. amyloliquefaciens exerted the antagonistic activity by damaging the fungal cell membrane, thus inhibiting the mycelium growth and sporification of phytopathogenic fungi. As a marine microbiology, our results showed that B. amyloliquefaciens could survive and metabolize even at the culture condition with 110 g/L of NaCl concentration, and the produced antimicrobial compounds exhibited excellent thermostability and acid-alkali tolerance. The dynamic models were further constructed to theoretically analyze the fermentation process of B. amyloliquefaciens HY2-1, suggesting that the synthesis of antimicrobial compounds was coupled with both cell growth and cell biomass. In conclusion, the marine lipopeptides-producing B. amyloliquefaciens HY2-1 showed a promising prospect to be explored as a biocontrol agent for plant disease control of crops and postharvest preservation of fruits and vegetables, especially due to its outstanding stress resistance and the broad-spectrum and effective antagonist on various phytopathogenic fungi.

Fengycin produced by Bacillus subtilis XF-1 plays a major role in the biocontrol of Chinese cabbage clubroot via direct effect and defense stimulation

Bacillus subtilis XF-1 is a well-investigated biocontrol agent against the biotrophic Plasmodiophora brassicae Woron., the causal agent of clubroot disease of cruciferous crops. The present study demonstrates that XF-1 could efficiently control clubroot disease via leaf spraying and provides an understanding of the biocontrol mechanisms. High-performance thin-layer chromatography (HTPLC) analysis indicated the presence of fengycin-type cyclopeptides in the supernatant. A ppsB deletion mutant of XF-1 resulted in no fengycin production, significantly reduced the lysis rate of testing spores in vitro and the primary infection rate of root hair in vivo, and decreased the protection value against clubroot disease under the greenhouse conditions. Confocal laser scanning microscopy proved that fengycin was not required for leaf internalization and root colonization. Moreover, the expression level of the ppsB gene in XF-1 was regulated by its cell density in root during interaction with P. brassicae. In addition, the ΔppsB mutant of XF-1 could not efficiently control disease because it led to a lower activation level of the jasmonic acid and salicylic acid signaling pathways in roots, which are necessary for the plant defense reaction upon pathogen invasion. Altogether, the present study provides a new understanding of specific cues in the interaction between B. subtilis and P. brassicae as well as insights into the application of B. subtilis in agriculture.

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.

Transcriptome profiling reveals the underlying mechanism of grape post-harvest pathogen Penicillium olsonii against the metabolites of Bacillus velezensis

Introduction

Pathogen infection influences the post-harvest shelf life of grape berries. In a preliminary study, metabolites produced by Bacillus velezensis significantly inhibited the growth of the grape postharvest pathogen Penicillium olsonii.

Methods

To investigate the mechanism of interaction between B. velezensis and P. olsonii, a draft genome was generated for P. olsonii WHG5 using the Illumina NovaSeq platform, and the transcriptomic changes in WHG5 were analyzed in response to the exposure to B. velezensis metabolites (10% v/v).

Results

The expression levels of genes associated with sporulation, including GCY1, brlA, and abaA, were down-regulated compared with those of the control. In addition, spore deformation and abnormal swelling of the conidiophore were observed. The expression of crucial enzymes, including fructose 2,6-bisphosphate and mannitol-2-dehydrogenase, was down-regulated, indicating that the glycolytic pathway of WHG5 was adversely affected by B. velezensis metabolites. The KEGG pathway enrichment analysis revealed that glutathione metabolism and the antioxidant enzyme system were involved in the response to B. velezensis metabolites. The down-regulation of the pathogenesis-related genes, PG1 and POT1, suggested that B. velezensis metabolites decreased the pathogenicity of P. olsonii. B. velezensis metabolites disrupted the homeostasis of reactive oxygen species in P. olsonii by affecting glucose metabolism, resulting in spore deformation and disruption of growth. In addition, the expression of key pathogenesis-related genes was down-regulated, thereby reducing the pathogenicity of P. olsonii.

Disscusion

This study provides insights into the responses of P. olsonii to B. velezensis metabolites and identifies potential target genes that may be useful in biocontrol strategies for the suppression of post-harvest spoilage in grapes.

Multifarious Plant Probiotic Features of Bacillus sp. W11 Isolated from Vermicast and Its Promises for Biocontrol Activity Against Phytopathogens

Organic agricultural practice using vermisources is considered as one of the common sustainable strategies in agriculture. Apart from their nutrient content, beneficial microbes associated with natural vermicast serve as an efficient bioinoculant for improving agricultural productivity. Hence, studies on the identification of suitable microbial inoculants with multi-trait plant beneficial properties from these hotspots are highly promising as an ecofriendly substitute against harmful chemical fertilizers. The current study has been designed to isolate bacterial strains with various plant probiotic and biocontrol properties against various fungal phytopathogens. Among the various bacteria obtained in the study, the isolate W11 was found to have remarkable inhibitory activity against a broad range of phytopathogens like Fusarium oxysporum, Pythium myriotylum, and Rhizoctonia solani, in addition to its multiple plant growth-promoting properties. The W11 was further identified as Bacillus sp. by 16S rDNA sequence-based analysis. The W11 treatment was also found to enhance the plant growth parameters of Vigna unguiculata. In addition, the priming of Bacillus sp. W11 on potato tuber has confirmed to protect it from Fusarium wilt caused by Fusarium oxysporum. This highlights the possible protective effect of W11 during the post-harvest storage of potatoes. Also, the metabolite analysis of W11 extract by LC-QTOF-MS/MS analysis has revealed the presence of lipopeptide surfactin derivatives with m/z of 1008, 1022, and 1036 (M + H)⁺. All the results obtained in the study thus indicate the remarkable agricultural promises of Bacillus sp. W11 isolated from vermicast. Even though vermicast has been studied for its beneficial agricultural applications, the isolation of plant beneficial bacteria from it and detailed characterization of its beneficial effects make the study important.

Bio-Inspired Rhamnolipids, Cyclic Lipopeptides and a Chito-Oligosaccharide Confer Protection against Wheat Powdery Mildew and Inhibit Conidia Germination

Plant protection is mainly based on the application of synthetic pesticides to limit yield losses resulting from diseases. However, the use of more eco-friendly strategies for sustainable plant protection has become a necessity that could contribute to controlling pathogens through a direct antimicrobial effect and/or an induction of plant resistance. Three different families of natural or bioinspired compounds originated from bacterial or fungal strains have been evaluated to protect wheat against powdery mildew, caused by the biotrophic Blumeria graminis f.sp. tritici (Bgt). Thus, three bio-inspired mono-rhamnolipids (smRLs), three cyclic lipopeptides (CLPs, mycosubtilin (M), fengycin (F), surfactin (S)) applied individually and in mixtures (M + F and M + F + S), as well as a chitosan oligosaccharide (COS) BioA187 were tested against Bgt, in planta and in vitro. Only the three smRLs (Rh-Eth-C12, Rh-Est-C12 and Rh-Succ-C12), the two CLP mixtures and the BioA187 led to a partial protection of wheat against Bgt. The higher inhibitor effects on the germination of Bgt spores in vitro were observed from smRLs Rh-Eth-C12 and Rh-Succ-C12, mycosubtilin and the two CLP mixtures. Taking together, these results revealed that such molecules could constitute promising tools for a more eco-friendly agriculture.

Antifungal Activity and Plant Growth-Promoting Properties of Bacillus mojovensis B1302 against Rhizoctonia Cerealis

Rhizoctonia cerealis is a worldwide soil-borne pathogenic fungus that significantly infects wheat and causes sharp eyespot in China. However, the biocontrol strains used for the control of Rhizoctonia cerealis are insufficient. In the present study, antagonistic strain B1302 from the rhizosphere of wheat were isolated and identified as Bacillus mojovensis based on their morphological, physiological, and biochemical characteristics, and their 16S rDNA sequence. Culture filtrate of strain B1302 had a broad antifungal spectrum. In order to improve the antifungal activity of B1302, response surface methodology (RSM) was used to optimize the culture conditions. The final medium composition and culture conditions were 13.2 g/L of wheat bran, 14.1 g/L of soybean meal, 224 r/min of rotation speed, 7.50 of initial pH, and 1.5 × 10⁸ CFU/mL of inoculation amount at 35 °C for a culture duration of 72 h. B. mojavensis B1302 inhibited the hyphae growth of R.cerealis and produced hydrolytic enzymes (protease, chitinase, and glucanase), IAA, and had N-fixing potentiality and P-solubilisation capacity. It can also promote wheat seedling growth in potted plants. The disease incidence and index of wheat seedlings were consistent with the effect of commercial pesticides under treatment with culture filtrate. The biocontrol efficacy of culture filtrate was significant—up to 65.25%. An animal toxicological safety analysis suggested that culture filtrate was safe for use and could be developed into an effective microbial fungicide to control wheat sharp eyespot.

Exploration of surfactin production by newly isolated Bacillus and Lysinibacillus strains from food related sources

As a lipopeptide (LP), surfactin exhibits properties, such as emulsifying and dispersing ability, which are useful in food industry. Discovery of new LP-producing strains from food sources is an important step towards possible application of surfactin in foods. A total of 211 spore-forming, Gram-positive, and catalase-positive bacterial strains were isolated from fermented African locust beans (iru) and Palm Oil Mill Effluents in a screening process and examined for their ability to produce surfactin. This was achieved by a combination of methods, which included microbiological and molecular classification of strains, along with chemical analysis of surfactin production. Altogether, 29 isolates, positive for oil spreading and emulsification assays, were further identified with 16S rDNA analysis. The strains belonged to nine species including less commonly reported strains of Lysinibacillus, Bacillus flexus, B. tequilensis, and B. aryabhattai. The surfactin production was quantitatively and qualitatively analyzed by high-performance thin-layer chromatography (HPTLC) and liquid chromatography-mass spectrometry (LC-MS). Confirmation of surfactin by MS was achieved in all the 29 strains. Highest surfactin production capability was found in B. subtilis IRB2-A1 with a titer of 1444.1 mg L^-1 .

Quantitative High-Throughput Screening Methods Designed for Identification of Bacterial Biocontrol Strains with Antifungal Properties

Large screens of bacterial strain collections to identify potential biocontrol agents often are time-consuming and costly and fail to provide quantitative results. In this study, we present two quantitative and high-throughput methods to assess the inhibitory capacity of bacterial biocontrol candidates against fungal phytopathogens. One method measures the inhibitory effect of bacterial culture supernatant components on the fungal growth, while the other accounts for direct interaction between growing bacteria and the fungus by cocultivating the two organisms. The antagonistic supernatant method quantifies the culture components' antifungal activity by calculating the cumulative impact of supernatant addition relative to the growth of a nontreated fungal control, while the antagonistic cocultivation method identifies the minimal bacterial cell concentration required to inhibit fungal growth by coinoculating fungal spores with bacterial culture dilution series. Thereby, both methods provide quantitative measures of biocontrol efficiency and allow prominent fungal inhibitors to be distinguished from less effective strains. The combination of the two methods sheds light on the types of inhibition mechanisms and provides the basis for further mode-of-action studies. We demonstrate the efficacy of the methods using Bacillus spp. with different levels of antifungal activities as model antagonists and quantify their inhibitory potencies against classic plant pathogens. IMPORTANCE Fungal phytopathogens are responsible for tremendous agricultural losses on an annual basis. While microbial biocontrol agents represent a promising solution to the problem, there is a growing need for high-throughput methods to evaluate and quantify inhibitory properties of new potential biocontrol agents for agricultural application. In this study, we present two high-throughput and quantitative fungal inhibition methods that are suitable for commercial biocontrol screening.

Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde

The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.

Perception of Biocontrol Potential of Bacillus inaquosorum KR2-7 against Tomato Fusarium Wilt through Merging Genome Mining with Chemical Analysis

Simple Summary

Bacillus is a bacterial genus that is widely used as a promising alternative to chemical pesticides due to its protective activity toward economically important plant pathogens. Fusarium wilt of tomato is a serious fungal disease limiting tomato production worldwide. Recently, the newly isolated B. inaquosorum strain KR2-7 considerably suppressed Fusarium wilt of tomato plants. The present study was performed to perceive potential direct and indirect biocontrol mechanisms implemented by KR2-7 against this disease through genome and chemical analysis. The potential direct biocontrol mechanisms of KR2-7 were determined through the identification of genes involved in the synthesis of antibiotically active compounds suppressing tomato Fusarium wilt. Furthermore, the indirect mechanisms of this bacterium were perceived through recognizing genes that contributed to the resource acquisition or modulation of plant hormone levels. This is the first study that aimed at the modes of actions of B. inaquosorum against Fusarium wilt of tomatoes and the results strongly indicate that strain KR2-7 could be a good candidate for microbial biopesticide formulations to be used for biological control of plant diseases and plant growth promotion.

Abstract

Tomato Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (Fol), is a destructive disease that threatens the agricultural production of tomatoes. In the present study, the biocontrol potential of strain KR2-7 against Fol was investigated through integrated genome mining and chemical analysis. Strain KR2-7 was identified as B. inaquosorum based on phylogenetic analysis. Through the genome mining of strain KR2-7, we identified nine antifungal and antibacterial compound biosynthetic gene clusters (BGCs) including fengycin, surfactin and Bacillomycin F, bacillaene, macrolactin, sporulation killing factor (skf), subtilosin A, bacilysin, and bacillibactin. The corresponding compounds were confirmed through MALDI-TOF-MS chemical analysis. The gene/gene clusters involved in plant colonization, plant growth promotion, and induced systemic resistance were also identified in the KR2-7 genome, and their related secondary metabolites were detected. In light of these results, the biocontrol potential of strain KR2-7 against tomato Fusarium wilt was identified. This study highlights the potential to use strain KR2-7 as a plant-growth promotion agent.

In Silico and In Vitro Evaluation of the Antimicrobial Potential of Bacillus cereus Isolated from Apis dorsata Gut against Neisseria gonorrhoeae

Antimicrobial resistance is a major public health and development concern on a global scale. The increasing resistance of the pathogenic bacteria Neisseria gonorrhoeae to antibiotics necessitates efforts to identify potential alternative antibiotics from nature, including insects, which are already recognized as a source of natural antibiotics by the scientific community. This study aimed to determine the potential of components of gut-associated bacteria isolated from Apis dorsata, an Asian giant honeybee, as an antibacterial against N. gonorrhoeae by in vitro and in silico methods as an initial process in the stage of new drug discovery. The identified gut-associated bacteria of A. dorsata included Acinetobacter indicus and Bacillus cereus with 100% identity to referenced bacteria from GenBank. Cell-free culture supernatants (CFCS) of B. cereus had a very strong antibacterial activity against N. gonorrhoeae in an in vitro antibacterial testing. Meanwhile, molecular docking revealed that antimicrobial lipopeptides from B. cereus (surfactin, fengycin, and iturin A) had a comparable value of binding-free energy (BFE) with the target protein receptor for N. gonorrhoeae, namely penicillin-binding protein (PBP) 1 and PBP2 when compared with the ceftriaxone, cefixime, and doxycycline. The molecular dynamics simulation (MDS) study revealed that the surfactin remains stable at the active site of PBP2 despite the alteration of the H-bond and hydrophobic interactions. According to this finding, surfactin has the greatest antibacterial potential against PBP2 of N. gonorrhoeae.

Genomic insights into biocontrol potential of Bacillus stercoris LJBS06

Bacillus spp. have been widely reported with the ability to control plant diseases. In this work, we analyzed the whole genome of LJBS06, which was isolated from grapevine rhizosphere soil. In view of physiological and biochemical characteristics, genome data, and phylogenetic analysis of 16S rRNA, LJBS06 was affiliated with Bacillus stercoris. LJBS06 showed antagonistic activities against a variety of plant pathogens. The inhibition rate of Magnaporthe oryzae was up to 75.05% and the inhibition rates of Colletotrichum gloeosporioides, Coniothyrium diplodiella, and Botrytis cinerea were all above 50% in the plate assays. The genome of LJBS06 had a 4,154,362-bp circular chromosome, with an average GC content of 43.96%, containing an 82,935-bp plasmid with a GC content of 35.18%. The circular chromosome of LJBS06 contained 4231 protein-coding genes, 30 rRNA genes, and 87 tRNA genes, including genes related to the synthesis of plant defense-related enzymes and the promotion of plant growth. Meanwhile, 11 gene clusters involved in biosynthesis of secondary metabolites were present in the genome of LJBS06. In conclusion, our findings indicated that LJBS06 strain had the necessary genetic machinery to control plant pathogens and provided insights for future studies of the biocontrol mechanisms of B. stercoris LJBS06.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03000-6.

Biological Control of Plant Diseases: An Evolutionary and Eco-Economic Consideration

Biological control is considered as a promising alternative to pesticide and plant resistance to manage plant diseases, but a better understanding of the interaction of its natural and societal functions is necessary for its endorsement. The introduction of biological control agents (BCAs) alters the interaction among plants, pathogens, and environments, leading to biological and physical cascades that influence pathogen fitness, plant health, and ecological function. These interrelationships generate a landscape of tradeoffs among natural and social functions of biological control, and a comprehensive evaluation of its benefits and costs across social and farmer perspectives is required to ensure the sustainable development and deployment of the approach. Consequently, there should be a shift of disease control philosophy from a single concept that only concerns crop productivity to a multifaceted concept concerning crop productivity, ecological function, social acceptability, and economical accessibility. To achieve these goals, attempts should make to develop “green” BCAs used dynamically and synthetically with other disease control approaches in an integrated disease management scheme, and evolutionary biologists should play an increasing role in formulating the strategies. Governments and the public should also play a role in the development and implementation of biological control strategies supporting positive externality.

Biocontrol Ability and Mechanism of a Broad-Spectrum Antifungal Strain Bacillus safensis sp. QN1NO-4 Against Strawberry Anthracnose Caused by Colletotrichum fragariae

Strawberry is a very popular fruit with a special taste, color, and nutritional value. Anthracnose caused by Colletotrichum fragariae severely limits fruit shelf life during post-harvest storage. Use of traditional chemical fungicides leads to serious environment pollution and threatens food safety. Biocontrol is considered as a promising strategy to manage the post-harvest fruit diseases. Here, strain QN1NO-4 isolated from noni (Morinda citrifolia L.) fruit exhibited a high antifungal activity against C. fragariae. Based on its physicochemical profiles and phylogenetic tree of the 16S rRNA sequence, strain QN1NO-4 belonged to the genus Bacillus. The average nucleotide identity (ANI) calculated by comparing two standard strain genomes was below 95-96%, suggesting that the strain might be a novel species of the genus Bacillus and named as Bacillus safensis sp. QN1NO-4. Its extract effectively reduced the incidence of strawberry anthracnose of harvested fruit. Fruit weight and TSS contents were also maintained significantly. The antifungal mechanism assays indicated that the extract of the test antagonist inhibited mycelial growth and spore germination of C. fragariae in vitro. Cells of strain QN1NO-4 demonstrated the cytoplasmic heterogeneity, disappeared organelles, and ruptured ultrastructure. Notably, the strain extract also had a broad-spectrum antifungal activity. Compared with the whole genome of strain QN1NO-4, several functional gene clusters involved in the biosynthesis of active secondary metabolites were observed. Fifteen compounds were identified by gas chromatography-mass spectrometry (GC-MS). Hence, the fruit endophyte B. safensis sp. QN1NO-4 is a potential bio-agent identified for the management of post-harvest disease of strawberry fruit.

Comprehensive genomic analysis of Bacillus velezensis AL7 reveals its biocontrol potential against Verticillium wilt of cotton

Verticilllium wilt of cotton is a devastating soil-borne disease, which is caused by Verticillium dahliae Kleb. Bacillus velezensis strain AL7 was isolated from cotton soil. This strain efficiently inhibited the growth of V. dahliae. But the mechanism of the biocontrol strain AL7 remains poorly understood. To understand the possible genetic determinants for biocontrol traits of this strain, we conducted phenotypic, phylogenetic and comparative genomics analysis. Phenotypic analysis showed that strain AL7 exhibited broad-spectrum antifungal activities. We determined that the whole genome sequence of B. velezensis AL7 is a single circular chromosome that is 3.89 Mb in size. The distribution of putative gene clusters that could benefit to biocontrol activities was found in the genome. Phylogenetic analysis of Bacillus strains by using single core-genome clearly placed strain AL7 into the B. velezensis. Meantime, we performed comparative analyses on four Bacillus strains and observed subtle differences in their genome sequences. In addition, comparative genomics analysis showed that the core genomes of B. velezensis are more abundant in genes relevant to secondary metabolism compared with B. subtilis strains. Single mutant in the biosynthetic genes of fengycin demonstrated the function of fengycin in the antagonistic activity of B. velezensis AL7. Here, we report a new biocontrol bacterium B. velezensis AL7 and fengycin contribute to the biocontrol efficacy of the strain. The results showed in the research further sustain the potential of B. velezensis AL7 for application in agriculture production and may be a worthy biocontrol strain for further studies.

Isolation and Characterization of Endophyte Bacillus velezensis KOF112 from Grapevine Shoot Xylem as Biological Control Agent for Fungal Diseases

As the use of chemical fungicides has raised environmental concerns, biological control agents have attracted interest as an alternative to chemical fungicides for plant-disease control. In this study, we attempted to explore biological control agents for three fungal phytopathogens causing downy mildew, gray mold, and ripe rot in grapevines, which are derived from shoot xylem of grapevines. KOF112, which was isolated from the Japanese indigenous wine grape Vitis sp. cv. Koshu, inhibited mycelial growth of Botrytis cinerea, Colletotrichum gloeosporioides, and Phytophthora infestans. The KOF112-inhibited mycelial tips were swollen or ruptured, suggesting that KOF112 produces antifungal substances. Analysis of the 16S rDNA sequence revealed that KOF112 is a strain of Bacillus velezensis. Comparative genome analysis indicated significant differences in the synthesis of non-ribosomal synthesized antimicrobial peptides and polyketides between KOF112 and the antagonistic B. velezensis FZB42. KOF112 showed biocontrol activities against gray mold caused by B. cinerea, anthracnose by C. gloeosporioides, and downy mildew by Plasmopara viticola. In the KOF112–P. viticola interaction, KOF112 inhibited zoospore release from P. viticola zoosporangia but not zoospore germination. In addition, KOF112 drastically upregulated the expression of genes encoding class IV chitinase and β-1,3-glucanase in grape leaves, suggesting that KOF112 also works as a biotic elicitor in grapevine. Because it is considered that endophytic KOF112 can colonize well in and/or on grapevine, KOF112 may contribute to pest-management strategies in viticulture and potentially reduce the frequency of chemical fungicide application.

Genomic Analysis and Secondary Metabolites Production of the Endophytic Bacillus velezensis Bvel1: A Biocontrol Agent against Botrytis cinerea Causing Bunch Rot in Post-Harvest Table Grapes

Botrytis bunch rot caused by Botrytis cinerea is one of the most economically significant post-harvest diseases of grapes. In the present study, we showed that the bacterial strain Bvel1 is phylogenetically affiliated to Bacillus velezensis species. The strain Bvel1 and its secreted metabolites exerted an antifungal activity, under in vitro conditions, against B. cinerea. UHPLC-HRMS chemical analysis revealed that iturin A2, surfactin-C13 and -C15, oxydifficidin, bacillibactin, L-dihydroanticapsin, and azelaic acid were among the metabolites secreted by Bvel1. Treatment of wounded grape berries with Bacillus sp. Bvel1 cell culture was effective for controlling grey mold ingress and expansion in vivo. The effectiveness of this biological control agent was a function of the cell culture concentration of the antagonist applied, while preventive treatment proved to be more effective compared to curative. The strain Bvel1 exhibited an adequate colonization efficiency in wounded grapes. The whole-genome phylogeny, combined with ANI and dDDH analyses, provided compelling evidence that the strain Bvel1 should be taxonomically classified as Bacillus velezensis. Genome mining approaches showed that the strain Bvel1 harbors 13 antimicrobial biosynthetic gene clusters, including iturin A, fengycin, surfactin, bacilysin, difficidin, bacillaene, and bacillibactin. The results provide new insights into the understanding of the endophytic Bacillus velezensis Bvel1 biocontrol mechanism against post-harvest fungal pathogens, including bunch rot disease in grape berries.

Exploiting RNA thermometer-driven molecular bioprocess control as a concept for heterologous rhamnolipid production

A key challenge to advance the efficiency of bioprocesses is the uncoupling of biomass from product formation, as biomass represents a by-product that is in most cases difficult to recycle efficiently. Using the example of rhamnolipid biosurfactants, a temperature-sensitive heterologous production system under translation control of a fourU RNA thermometer from Salmonella was established to allow separating phases of preferred growth from product formation. Rhamnolipids as bulk chemicals represent a model system for future processes of industrial biotechnology and are therefore tied to the efficiency requirements in competition with the chemical industry. Experimental data confirms function of the RNA thermometer and suggests a major effect of temperature on specific rhamnolipid production rates with an increase of the average production rate by a factor of 11 between 25 and 38 °C, while the major part of this increase is attributable to the regulatory effect of the RNA thermometer rather than an unspecific overall increase in bacterial metabolism. The production capacity of the developed temperature sensitive-system was evaluated in a simple batch process driven by a temperature switch. Product formation was evaluated by efficiency parameters and yields, confirming increased product formation rates and product-per-biomass yields compared to a high titer heterologous rhamnolipid production process from literature.

Killing Effect of Bacillus Velezensis FZB42 on a Xanthomonas Campestris pv. Campestris (Xcc) Strain Newly Isolated from Cabbage Brassica Oleracea Convar. Capitata (L.): A Metabolomic Study

The potential use of Bacillus velezensis FZB42 for biological control of various phytopathogens has been documented over the past few years, but its antagonistic interactions with xanthomonads has not been studied in detail. Novel aspects in this study consist of close observation of the death of Xanthomonas campestris pv. campestris cells in a co-culture with B. velezensis FZB42, and quantification of lipopeptides and a siderophore, bacillibactin, involved in the killing process. A new robust Xcc-SU isolate tolerating high concentrations of ferric ions was used. In a co-culture with the antagonist, the population of Xcc-SU was entirely destroyed within 24–48 h, depending on the number of antagonist cells used for inoculation. No inhibitory effect of Xcc-SU on B. velezensis was observed. Bacillibactin and lipopeptides (surfactin, fengycin, and bacillomycin) were present in the co-culture and the monoculture of B. velezensis. Except for bacillibactin, the maximum contents of lipopeptides were higher in the antagonist monoculture compared with the co-culture. Scanning electron microscopy showed that the death of Xcc-SU bacteria in co-culture was caused by cell lysis, leading to an enhanced occurrence of distorted cells and cell ghosts. Analysis by mass spectrometry showed four significant compounds, bacillibactin, surfactin, fengycin, and bacillomycin D amongst a total of 24 different forms detected in the co-culture supernatant: Different forms of surfactin and fengycin with variations in their side-chain length were also detected. These results demonstrate the ability of B. velezensis FZB42 to act as a potent antagonistic strain against Xcc.

Bacillus amyloliquefaciens YN201732 Produces Lipopeptides With Promising Biocontrol Activity Against Fungal Pathogen Erysiphe cichoracearum

Bacillus amyloliquefaciens YN201732 is an endophytic bacteria with high biocontrol efficiency and broad-spectrum antimicrobial activities. In order to clarify the main active ingredients and their antifungal mechanisms against powdery mildew of tobacco, this study is focused on lipopeptide obtained through acid precipitation and organic solvent extraction. HPLC and LCMS-IT-TOF were used to separate and identify antimicrobial lipopeptides. Findings revealed that bacillomycin D plays an important role against surrogate fungal pathogen Fusarium solani. Synthetic pathways of sfp, bacillomycin D, and fengycin were separately disrupted. The sfp gene knockout mutant B. amyloliquefaciens YN201732M1 only showed minor antagonistic activity against F. solani. While Erysiphe cichoracearum spore germination was inhibited and pot experiments displayed a significant decrease in tobacco powdery mildew. The spore inhibition rate of YN201732M1 was only 30.29%, and the pot experiment control effect was less than 37.39%, which was significantly lower than that of the wild type. The inhibitory effect of mutant YN201732M2 (deficient in the production of bacillomycin D) and mutant YN201732M3 (deficient in the production of fengycin) on the spore germination of E. cichoracearum were 50.22% and 53.06%, respectively, suggesting that both fengycin and bacillomycin D had potential effects on spore germination of powdery mildew. Interestingly, in a greenhouse assay, both B. amyloliquefaciens YN201732M2 and YN201732M3 mutants displayed less of a control effect on tobacco powdery mildew than wild type. The results from in vitro, spore germination, and greenhouse-pot studies demonstrated that antimicrobial lipopeptides especially bacillomycin D and fengycin may contribute to the prevention and control of tobacco powdery mildew. In addition, gene mutation related to lipopeptide synthesis can also affect the biofilm formation of strains.

Bacillus subtilis High Cell Density Fermentation Using a Sporulation-Deficient Strain for the Production of Surfactin

Abstract

Bacillus subtilis 3NA is a strain capable of reaching high cell densities. A surfactin producing sfp⁺ variant of this strain, named JABs32, was utilized in fed-batch cultivation processes. Both a glucose and an ammonia solution were fed to set a steady growth rate μ of 0.1 h^-1. In this process, a cell dry weight of up to 88 g L^-1 was reached after 38 h of cultivation, and surfactin titers of up to 26.5 g L^-1 were detected in this high cell density fermentation process, achieving a Y_P/X value of 0.23 g g^-1 as well as a q_P/X of 0.007 g g^-1 h^-1. In sum, a 21-fold increase in surfactin titer was obtained compared with cultivations in shake flasks. In contrast to fed-batch operations using Bacillus subtilis JABs24, an sfp⁺ variant derived from B. subtilis 168, JABs32, reached an up to fourfold increase in surfactin titers using the same fed-batch protocol. Additionally, a two-stage feed process was established utilizing strain JABs32. Using an optimized mineral salt medium in this high cell density fermentation approach, after 31 h of cultivation, surfactin titers of 23.7 g L^-1 were reached with a biomass concentration of 41.3 g L^-1, thus achieving an enhanced Y_P/X value of 0.57 g g^-1 as well as a q_P/X of 0.018 g g^-1 h^-1. The mutation of spo0A locus and an elongation of AbrB in the strain utilized in combination with a high cell density fed-batch process represents a promising new route for future enhancements on surfactin production.

Key points

• Utilization of a sporulation deficient strain for fed-batch operations

• High cell density process with Bacillus subtilis for lipopeptide production was established

• High titer surfactin production capabilities confirm highly promising future platform strain

Evaluation of an oxygen-dependent self-inducible surfactin synthesis in B. subtilis by substitution of native promoter PsrfA by anaerobically active PnarG and PnasD

A novel approach targeting self-inducible surfactin synthesis under oxygen-limited conditions is presented. Because both the nitrate (NarGHI) and nitrite (NasDE) reductase are highly expressed during anaerobic growth of B. subtilis, the native promoter PsrfA of the surfactin operon in strain B. subtilis JABs24 was replaced by promoters PnarG and PnasD to induce surfactin synthesis anaerobically. Shake flask cultivations with varying oxygen availabilities indicated no significant differences in native PsrfA expression. As hypothesized, activity of PnarG and PnasD increased with lower oxygen levels and surfactin was not produced by PsrfA::PnarG as well as PsrfA::PnasD mutant strains under conditions with highest oxygen availability. PnarG showed expressions similar to PsrfA at lowest oxygen availability, while maximum value of PnasD was more than 5.5-fold higher. Although the promoter exchange PsrfA::PnarG resulted in a decreased surfactin titer at lowest oxygen availability, the strain carrying PsrfA::PnasD reached a 1.4-fold increased surfactin concentration with 696 mg/L and revealed an exceptional high overall YP/X of 1.007 g/g. This value also surpassed the YP/X of the reference strain JABs24 at highest and moderate oxygen availability. Bioreactor cultivations illustrated that significant cell lysis occurred when the process of "anaerobization" was performed too fast. However, processes with a constantly low agitation and aeration rate showed promising potential for process improvement, especially by employing the strain carrying PsrfA::PnasD promoter exchange. Additionally, replacement of other native promoters by nitrite reductase promoter PnasD represents a promising tool for anaerobic-inducible bioprocesses in Bacillus.

Cell-Free Supernatants of Plant Growth-Promoting Bacteria: A Review of Their Use as Biostimulant and Microbial Biocontrol Agents in Sustainable Agriculture

Plant growth-promoting bacteria (PGPB) afford plants several advantages (i.e., improvement of nutrient acquisition, growth, and development; induction of abiotic and biotic stress tolerance). Numerous PGPB strains have been isolated and studied over the years. However, only a few of them are available on the market, mainly due to the failed bacterial survival within the formulations and after application inside agroecosystems. PGPB strains with these challenging limitations can be used for the formulation of cell-free supernatants (CFSs), broth cultures processed through several mechanical and physical processes for cell removal. In the scientific literature there are diverse reviews and updates on PGPB in agriculture. However, no review deals with CFSs and the CFS metabolites obtainable by PGPB. The main objective of this review is to provide useful information for future research on CFSs as biostimulant and biocontrol agents in sustainable agriculture. Studies on CFS agricultural applications, both for biostimulant and biocontrol applications, have been reviewed, presenting limitations and advantages. Among the 109 articles selected and examined, the Bacillus genus seems to be the most promising due to the numerous articles that support its biostimulant and biocontrol potentialities. The present review underlines that research about this topic needs to be encouraged; evidence so far obtained has demonstrated that PGPB could be a valid source of secondary metabolites useful in sustainable agriculture.

Towards the Anaerobic Production of Surfactin Using Bacillus subtilis

The anaerobic growth of B. subtilis to synthesize surfactin poses an alternative strategy to conventional aerobic cultivations. In general, the strong foam formation observed during aerobic processes represents a major obstacle. Anaerobic processes have, amongst others, the distinct advantage that the total bioreactor volume can be exploited as foaming does not occur. Recent studies also reported on promising product per biomass yields. However, anaerobic growth in comparison to aerobic processes has several disadvantages. For example, the overall titers are comparably low and cultivations are time-consuming due to low growth rates. B. subtilis JABs24, a derivate of strain 168 with the ability to synthesize surfactin, was used as model strain in this study. Ammonium and nitrite were hypothesized to negatively influence anaerobic growth. Ammonium with initial concentrations up to 0.2 mol/L was shown to have no significant impact on growth, but increasing concentrations resulted in decreased surfactin titers and reduced nitrate reductase expression. Anaerobic cultivations spiked with increasing nitrite concentrations resulted in prolonged lag-phases. Indeed, growth rates were in a similar range after the lag-phase indicating that nitrite has a neglectable effect on the observed decreasing growth rates. In bioreactor cultivations, the specific growth rate decreased with increasing glucose concentrations during the time course of both batch and fed-batch processes to less than 0.05 1/h. In addition, surfactin titers, overall Y _P/X and Y _P/S were 53%, ∼42%, and ∼57% lower than in serum flask with 0.190 g/L, 0.344 g/g and 0.015 g/g. The Y _X/S, on the contrary, was 30% lower in the serum flask with 0.044 g/g. The productivities q were similar with ∼0.005 g/(g⋅h). However, acetate strongly accumulated during cultivation and was posed as further metabolite that might negatively influence anaerobic growth. Acetate added to anaerobic cultivations in a range from 0 g/L up to 10 g/L resulted in a reduced maximum and overall growth rate μ by 44% and 30%, respectively. To conclude, acetate was identified as a promising target for future process enhancement and strain engineering. Though, the current study demonstrates that the anaerobic cultivation to synthesize surfactin represents a reasonable perspective and feasible alternative to conventional processes.

Development of a Bioprocess for the Production of Cyclic Lipopeptides Pseudofactins With Efficient Purification From Collected Foam

Microbial surfactants (biosurfactants) have gained interest as promising substitutes of synthetic surface-active compounds. However, their production and purification are still challenging, with significant room for efficiency and costs optimization. In this work, we introduce a method for the enhanced production and purification of cyclic lipopeptides pseudofactins (PFs) from Pseudomonas fluorescens BD5 cultures. The method is directly applicable in a technical scale with the possibility of further upscaling. Comparing to the original protocol for production of PFs (cultures in mineral salt medium in shaken flasks followed by solvent-solvent extraction of PFs), our process offers not only ∼24-fold increased productivity, but also easier and more efficient purification. The new process combines high yield of PFs (∼7.2 grams of PFs per 30 L of working volume), with recovery levels of 80–90% and purity of raw PFs up to 60–70%. These were achieved with an innovative, single-step thermal co-precipitation and extraction of PFs directly from collected foam, as a large amount of PF-enriched foam was produced during the bioprocess. Besides we present a protocol for the selective production of PF structural analogs and their separation with high-performance liquid chromatography. Our approach can be potentially utilized in the efficient production and purification of other lipopeptides of Pseudomonas and Bacillus origin.

Biosurfactants in Plant Protection Against Diseases: Rhamnolipids and Lipopeptides Case Study

Biosurfactants are amphiphilic surface-active molecules that are produced by a variety of microorganisms including fungi and bacteria. Pseudomonas, Burkholderia, and Bacillus species are known to secrete rhamnolipids and lipopeptides that are used in a wide range of industrial applications. Recently, these compounds have been studied in a context of plant-microbe interactions. This mini-review describes the direct antimicrobial activities of these compounds against plant pathogens. We also provide the current knowledge on how rhamnolipids and lipopeptides stimulate the plant immune system leading to plant resistance to phytopathogens. Given their low toxicity, high biodegradability and ecological acceptance, we discuss the possible role of these biosurfactants as alternative strategies to reduce or even replace pesticide use in agriculture.

A New Active Substance Derived from Lyzed Willaertia magna C2c Maky Cells to Fight Grapevine Downy Mildew

Downy mildew of grapevine is one of the most destructive grapevine diseases worldwide. Nowadays, downy mildew control relies almost exclusively on the use of chemical pesticides, including copper products, which are efficient but controversial due to their environmental toxicity. Natural plant protection products have become important solutions in the quest for the sustainable production of food and pest management. However, most biocontrol agents currently on the market, such as biofungicides or elicitors, have a limited efficacy; thus, they cannot replace chemical compounds in full. Our innovation is a natural active substance, which is a lysate of the amoeba Willaertia magna C2c Maky. This active substance is not only able to elicit grapevine defenses, but it also demonstrates direct fungicidal activity against Plasmopara viticola. The efficacy of this new natural substance was demonstrated both in a greenhouse and in a field. The amoeba lysate provided up to 77% protection to grapevine bunches in the field in a natural and safe way.

Optimization of laboratory cultivation conditions for the synthesis of antifungal metabolites by bacillus subtilis strains

In order to achieve the optimal number of colony forming units and a high level of antifungal metabolites synthesis, we carried out the periodic cultivation of the Bacillus subtilis BZR 336 g and Bacillus subtilis BZR 517 strains at various pH and temperature levels. In the experiment for determining the optimal temperature, the maximum titer of B. subtilis BZR 336 g bacterium (1.6–1.7 × 10⁹ CFU/ml) was recorded at a cultivation temperature of 20–25 °C. For B. subtilis BZR 517 strain, the temperature turned out to be optimal at 30 °C: the titer was 8.9 × 10⁸ CFU/ml. The maximum antifungal activity of B. subtilis BZR 336 g strain against the test culture of Fusarium oxysporum var. orthoceras was observed at a cultivation temperature of 20–25 °C; for B. subtilis BZR 517 strain, 25–30 °C. When determining the optimal pH level, it was found that a high titer of B. subtilis BZR 336 g strain cells was determined at pH 8.0 (2.7 × 10⁹ CFU/ml), for B. subtilis BZR 517 strain it was at pH 6.0–8.0 (1.0 × 10⁹ CFU/ml). The maximum antifungal activity was noted with the same indicators. Chromatographic and bioautographic analyses suggest that the synthesized antifungal metabolites belong to surfactin and iturin A. The data obtained in this research can be used in the development of the technology for the production of effective biofungicides to protect crops against Fusarium pathogens.

Lesson from Ecotoxicity: Revisiting the Microbial Lipopeptides for the Management of Emerging Diseases for Crop Protection

Microorganisms area treasure in terms of theproduction of various bioactive compounds which are being explored in different arenas of applied sciences. In agriculture, microbes and their bioactive compounds are being utilized in growth promotion and health promotion withnutrient fortification and its acquisition. Exhaustive explorations are unraveling the vast diversity of microbialcompounds with their potential usage in solving multiferous problems incrop production. Lipopeptides are one of such microbial compounds which havestrong antimicrobial properties against different plant pathogens. These compounds are reported to be produced by bacteria, cyanobacteria, fungi, and few other microorganisms; however, genus Bacillus alone produces a majority of diverse lipopeptides. Lipopeptides are low molecular weight compounds which havemultiple industrial roles apart from being usedas biosurfactants and antimicrobials. In plant protection, lipopeptides have wide prospects owing totheirpore-forming ability in pathogens, siderophore activity, biofilm inhibition, and dislodging activity, preventing colonization bypathogens, antiviral activity, etc. Microbes with lipopeptides that haveall these actions are good biocontrol agents. Exploring these antimicrobial compounds could widen the vistasof biological pest control for existing and emerging plant pathogens. The broader diversity and strong antimicrobial behavior of lipopeptides could be a boon for dealing withcomplex pathosystems and controlling diseases of greater economic importance. Understanding which and how these compounds modulate the synthesis and production of defense-related biomolecules in the plants is a key question—the answer of whichneeds in-depth investigation. The present reviewprovides a comprehensive picture of important lipopeptides produced by plant microbiome, their isolation, characterization, mechanisms of disease control, behavior against phytopathogens to understand different aspects of antagonism, and potential prospects for future explorations as antimicrobial agents. Understanding and exploring the antimicrobial lipopeptides from bacteria and fungi could also open upan entire new arena of biopesticides for effective control of devastating plant diseases.

Elicitors of Plant Immunity Triggered by Beneficial Bacteria

The molecular basis of plant immunity triggered by microbial pathogens is being well-characterized as a complex sequential process leading to the activation of defense responses at the infection site, but which may also be systemically expressed in all organs, a phenomenon also known as systemic acquired resistance (SAR). Some plant-associated and beneficial bacteria are also able to stimulate their host to mount defenses against pathogen ingress via the phenotypically similar, induced systemic resistance phenomenon. Induced systemic resistance resembles SAR considering its mechanistic principle as it successively involves recognition at the plant cell surface, stimulation of early cellular immune-related events, systemic signaling via a fine-tuned hormonal cross-talk and activation of defense mechanisms. It thus represents an indirect but efficient mechanism by which beneficial bacteria with biocontrol potential improve the capacity of plants to restrict pathogen invasion. However, according to our current vision, induced systemic resistance is specific considering some molecular aspects underpinning these different steps. Here we overview the chemical diversity of compounds that have been identified as induced systemic resistance elicitors and thereby illustrating the diversity of plants species that are responsive as well as the range of pathogens that can be controlled via this phenomenon. We also point out the need for further investigations allowing better understanding how these elicitors are sensed by the host and the diversity and nature of the stimulated defense mechanisms.

Suppression of Sclerotinia sclerotiorum by the Induction of Systemic Resistance and Regulation of Antioxidant Pathways in Tomato Using Fengycin Produced by Bacillus amyloliquefaciens FZB42

Lipopeptides from Bacillus species exhibit promising biological control activity against plant pathogens. This study aimed to explore the potential of purified fengycin to induce systemic resistance in tomato against Sclerotinia sclerotiorum. Bacillus amyloliquefaciens FZB42, its mutant AK1S, and their corresponding metabolites showed in vitro inhibition of S. sclerotiorum mycelium. Fengycin derived from an AK1S mutant was purified and identified through HPLC and MALDI-TOF-MS, respectively. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) revealed structural deformities in the fungal mycelium. Moreover, fengycin induced the accumulation of reactive oxygen species (ROS) in S. sclerotiorum mycelium and downregulated the expression of ROS-scavenging genes viz., superoxide dismutase (SsSOD1), peroxidase (SsPO), and catalase (SsCAT1) compared to the untreated control. Furthermore, the lesion size was dramatically reduced in fengycin-treated tomato plants compared to plants infected with S. sclerotiorum only in a greenhouse experiment. Additionally, the transcriptional regulation of defense-related genes GST, SOD, PAL, HMGR, and MPK3 showed the highest upsurge in expression at 48 h post-inoculation (hpi). However, their expression was subsequently decreased at 96 hpi in fengycin + S. sclerotiorum treatment compared to the plants treated with fengycin only. Conversely, the expression of PPO increased in a linear manner up to 96 hpi.