Identification of antifungal antibiotics of Bacillus species isolated from different microhabitats using polymerase chain reaction and MALDI-TOF mass spectrometry

Genomic Insights into the Bactericidal and Fungicidal Potential of Bacillus mycoides b12.3 Isolated in the Soil of Olkhon Island in Lake Baikal, Russia

The dispersal of plant pathogens is a threat to the global economy and food industry which necessitates the need to discover efficient biocontrol agents such as bacteria, fungi, etc., inhibiting them. Here, we describe the Bacillus mycoides strain b12.3 isolated from the soil of Olkhon Island in Lake Baikal, Russia. By applying the co-cultivation technique, we found that the strain inhibits the growth of plant pathogens, such as the bacteria Xanthomonas campestris, Clavibacter michiganensis, and Pectobacterium atrospecticum, as well as the fungus Alternaria solani. To elucidate the genomic fundament explaining these activities, we leveraged next-generation whole-genome sequencing and obtained a high-quality assembly based on short reads. The isolate bore seven known BGCs (biosynthetic gene clusters), including those responsible for producing bacillibactin, fengycin, and petrobactin. Moreover, the genome contained insecticidal genes encoding for App4Aa1, Tpp78Ba1, and Spp1Aa1 toxins, thus implicating possible pesticidal potential. We compared the genome with the 50 closest assemblies and found that b12.3 is enriched with BGCs. The genomic analysis also revealed that genomic architecture corresponds to the experimentally observed activity spectrum implying that the combination of produced secondary metabolites delineates the range of inhibited phytopathogens Therefore, this study deepens our knowledge of the biology and ecology of B. mycoides residing in the Lake Baikal region.

Bacillus cereus sensu lato antimicrobial arsenal: An overview

The Bacillus cereus group contains genetically closed bacteria displaying a variety of phenotypic features and lifestyles. The group is mainly known through the properties of three major species: the entomopathogen Bacillus thuringiensis, the animal and human pathogen Bacillus anthracis and the foodborne opportunistic strains of B. cereus sensu stricto. Yet, the actual diversity of the group is far broader and includes multiple lifestyles. Another less-appreciated aspect of B. cereus members lies within their antimicrobial potential which deserves consideration in the context of growing emergence of resistance to antibiotics and pesticides, and makes it crucial to find new sources of antimicrobial molecules. This review presents the state of knowledge on the known antimicrobial compounds of the B. cereus group members, which are grouped according to their chemical features and biosynthetic pathways. The objective is to provide a comprehensive review of the antimicrobial range exhibited by this group of bacteria, underscoring the interest in its potent biocontrol arsenal and encouraging further research in this regard.

Synthesis of silver nanoparticles using Bacillus velezensis M3-7 lipopeptides: Enhanced antifungal activity and potential use as a biocontrol agent against Fusarium crown rot disease of wheat seedlings

Bacillus velezensis M3-7 is a hyperactive mutant, 12-fold improved in its antifungal activity, obtained during a previous study from the wild strain BLB371 after a combination of random mutagenesis and medium component optimization. This study explores the use of this mutant in synthesizing silver nanoparticles (Ag-NPs) for the control of Fusarium crown rot disease (FCR) in wheat seedlings. LC-MS/MS analysis proved that both strains co-produced different families of lipopeptides and that mutagenesis caused the hyper-production of iturin A C14 and C15, the liberation of iturin A C10 and C12, and the inhibition of fengycin release. Our aim was a further improvement in the antifungal activity of the wild strain and the mutant M3-7 in order to control Fusarium crown rot disease (FCR) in wheat seedlings. Therefore, a nanotechnology approach was adopted, and different lipopeptide concentrations produced by the wild strain and the mutant M3-7 were used as capping agents to synthesize silver nanoparticles (Ag-NPs) with enhanced antifungal activity. Ag-NPs formed using 3 mg·mL-1 of the mutant lipopeptides were found to exhibit a good distribution, improved antifungal activity, a promising potential to be used as a biofortified agent for seed germination, and an effective compound to control FCR in wheat seedlings.

Lipopeptides development in cosmetics and pharmaceutical applications: A comprehensive review

Lipopeptides are surface active, natural products of bacteria, fungi and green-blue algae origin, having diverse structures and functionalities. In analogy, a number of chemical synthesis techniques generated new designer lipopeptides with desirable features and functions. Lipopetides are self-assembly guided, supramolecular compounds which have the capacity of high-density presentation of the functional epitopes at the surface of the nanostructures. This feature contributes to their successful application in several industry sectors, including food, feed, personal care, and pharmaceutics. In this comprehensive review, the novel class of ribosomally synthesized lipopeptides is introduced alongside the more commonly occuring non-ribosomal lipopeptides. We highlight key representatives of the most researched as well as recently described lipopeptide families, with emphasis on structural features, self-assembly and associated functions. The common biological, chemical and hybrid production routes of lipopeptides, including prominent analogues and derivatives are also discussed. Furthermore, genetic engineering strategies aimed at increasing lipopeptide yields, diversity and biological activity are summarized and exemplified. With respect to application, this work mainly details the potential of lipopeptides in personal care and cosmetics industry as cleansing agents, moisturizer, anti-aging/anti-wrinkling, skin whitening and preservative agents as well as the pharmaceutical industry as anitimicrobial agents, vaccines, immunotherapy, and cancer drugs. Given that this review addresses human applications, we conclude on the topic of safety of lipopeptide formulations and their sustainable production.

Detection and evaluation of volatile and non-volatile antifungal compounds produced by Bacillus spp. strains

The identification of antifungal compounds produced by microorganisms is crucial in the context of sustainable agriculture. Bacteria of the genus Bacillus have a broad spectrum of action that can influence plant growth and control pests, vectors of public health relevance and phytopathogens. Lipopeptides are the main compounds related to the biological control of several pathogen species. Strains with biotechnological potential are identified by means of in vitro bioassays and molecular tests. In this study, strains from the Bacillus Bank of Brazilian Agricultural Research Corporation (EMBRAPA/DF/Brazil) were selected to control the fungal pathogens Sclerotinia sclerotiorum and Fusarium oxysporum by pairing assays. The detection of genes for biosynthesis of antifungal compounds from strains with high pathogen-inhibition capacity was correlated with peptide synthesis, such as bacillomycin D, fengycin d, bacilysin and surfactin. Their gene expression in contact with the pathogen was analyzed by Real-Time PCR. The volatile organic compounds produced by selected Bacillus strains were identified and quantified. In co-culture assays, the inhibition zone between Bacillus strains and Sclerotinia sclerotiorum was evaluated by scanning electron microscopy. Thirteen potentially anti-pathogenic strains were selected. Genes related to the synthesis of antifungal peptides were detected in 11 of them. In five strains, all tested genes were detected. Bacillomycin was the most frequently found lipopeptide gene. The fungus-bacteria interaction potentiated the production of volatiles. Several ketones and other volatile compounds with antifungal activity were identified. Relevant morphological changes in the fungus were observed when paired with bacteria. The study demonstrated the efficacy of the selected strains with regard to the biological control of phytopathogens and their biotechnological potential.

Production of antibacterial compounds using Bacillus spp. isolated from thermal springs in Saudi Arabia

Seventeen water samples were collected from four different thermal springs in Saudi Arabia. Microbiological assays were used to assess the antibacterial activities of bacterial colonies against antibiotic-resistant and susceptible-bacterial strains, and 16S rRNA gene sequencing was used to identify the genus and species of these antibiotic-producing bacteria. Chromatography and spectroscopy were used to separate the active compounds and help figuring out what their structures were. Four compounds were isolated using bacteria: N-acetyltryptamine (1), isovaleric acid (2), ethyl-4-ethoxybenzoate (3) and phenylacetic acid (4). Compounds 1, 2 and 4 were produced from Bacillus pumilus and 3 was from Bacillus licheniformis (AH-E1). The outcomes of the minimum inhibitory concentrations (MICs) showed that all pure compounds produced in this work had antibacterial activities against Gram-positive pathogens (between 128 mg/L and 512 mg/L compared to the control) and compound 2 had activity against E. coli.

Purification of lipopeptide biosurfactant extracts obtained from a complex residual food stream using Tricine-SDS-PAGE electrophoresis

Protocols to identify lipopeptide biosurfactant extracts contained in complex residual streams are very important, as fermented agri-food matrices are potential sources of these valuable compounds. For instance, corn steep liquor (CSL), a secondary stream of the corn wet-milling industry, is composed of a mixture of microbial metabolites, produced during the corn steeping process, and other natural metabolites released from corn, that can interfere with the purification and analysis of lipopeptides. Electrophoresis could be an interesting technique for the purification and further characterization of lipopeptide biosurfactant extracts contained in secondary residual streams like CSL, but there is little existing literature about it. It is necessary to consider that lipopeptide biosurfactants, like Surfactin, usually are substances that are poorly soluble in water at acidic or neutral pH, forming micelles what can inhibit their separation by electrophoresis. In this work, two lipopeptide biosurfactant extracts obtained directly from CSL, after liquid-liquid extraction with chloroform or ethyl acetate, were purified by applying a second liquid extraction with ethanol. Following that, ethanolic biosurfactant extracts were subjected to electrophoresis under different conditions. Lipopeptides on Tricine-SDS-PAGE (polyacrylamide gels) were better visualized and identified by fluorescence using SYPRO Ruby dye than using Coomassie blue dye. The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of lipopeptide isoforms separated by electrophoresis revealed the presence of masses at 1,044, 1,058, and 1,074 m/z, concluding that Tricine-SDS-PAGE electrophoresis combined with MALDI-TOF-MS could be a useful tool for purifying and identifying lipopeptides in complex matrices.

Cold plasma treatment advancements in food processing and impact on the physiochemical characteristics of food products

Cold plasma processing is a nonthermal approach that maintains food quality while minimizing the effects of heat on its nutritious qualities. Utilizing activated, highly reactive gaseous molecules, cold plasma processing technique inactivates contaminating microorganisms in food and packaging materials. Pesticides and enzymes that are linked to quality degradation are currently the most critical issues in the fresh produce industry. Using cold plasma causes pesticides and enzymes to degrade, which is associated with quality deterioration. The product surface characteristics and processing variables, such as environmental factors, processing parameters, and intrinsic factors, need to be optimized to obtain higher cold plasma efficiency. The purpose of this review is to analyse the impact of cold plasma processing on qualitative characteristics of food products and to demonstrate the effect of cold plasma on preventing microbiological concerns while also improving the quality of minimally processed products.

Characteristic Analysis of Soil-Isolated Bacillus velezensis HY-3479 and Its Antifungal Activity Against Phytopathogens

During the investigation of beneficial agricultural microorganisms, a novel Bacillus strain was isolated. To isolate an effective microorganism that has antifungal activity, soil samples were collected from an agricultural field in the southern area of Pohang, Korea. One strain that had specificity on plant pathogens was analyzed. According to 16S rRNA sequencing, the isolated bacterium was identified as Bacillus velezensis and was designated as HY-3479. Few assays were taken to analyze the characteristics of the HY-3479 strain. In agar plate assay, HY-3479 showed antifungal effects on Colletotrichum acutatum, Cylindrocarpon destructans, Rhizoctonia solani, and Sclerotinia sclerotiorum. The strain also had various enzymatic activities including protease, amylase, and β-1,3-glucanase, which were relatively higher than control strains. Metabolites study of strain HY-3479 was conducted by GC-MS analysis and the bacterium contained many plant growth promoters like 3-methyl-1-butanol, (R, R)-2,3-butanediol, acetoin, and benzoic acid which were not found in untreated TSB medium. In gene expression analysis, antifungal lipopeptide genes like srfc (surfactin) and ituD (iturin A) were highly produced in the HY-3479 strain compared to the control strain KCTC 13417. B. velezensis strain HY-3479 may be the candidate to be an effective microorganism in agriculture and become a beneficial biocontrol agent with plant growth-promoting activities.

Recent trends and technological development in plasma as an emerging and promising technology for food biosystems

The rising need for wholesome, fresh, safe and “minimally-processed” foods has led to pioneering research activities in the emerging non-thermal technology of food processing. Cold plasma is such an innovative and promising technology that offers several potential applications in the food industry. It uses the highly reactive, energetic and charged gas molecules and species to decontaminate the food and package surfaces and preserve the foods without causing thermal damage to the nutritional and quality attributes of food. Cold plasma technology showed promising results about the inactivation of pathogens in the food industry without affecting the food quality. It is highly effective for surface decontamination of fruits and vegetables, but extensive research is required before its commercial utilization. Recent patents are focused on the applications of cold plasma in food processing and preservation. However, further studies are strongly needed to scale up this technology for future commercialization and understand plasma physics for getting better results and expand the applications and benefits. This review summarizes the emerging trends of cold plasma along with its recent applications in the food industry to extend shelf life and improve the quality of food. It also gives an overview of plasma generation and principles including mechanism of action. Further, the patents based on cold plasma technology have also been highlighted comprehensively for the first time.

The combination of two Bacillus strains suppresses Meloidogyne incognita and fungal pathogens, but does not enhance plant growth

BACKGROUND

The combination of biocontrol agents is a desirable strategy to improve control efficacy against the root-knot nematode (RKN) Meloidogyne incognita under field conditions. However, strains compatibility is generally tested in vitro and incompatible combinations are normally not further examined in experiments in planta. Therefore, there is virtually no information on the performance of incompatible strains. In this study, we evaluated two Bacillus strains previously described as incompatible in vitro for effects on plant growth and suppression of M. incognita, pathogenic fungi and nematophagous fungi.

RESULTS

Strains BMH and INV were shown to be closely related to Bacillus velezensis. These strains, when applied individually, reduced the number of galls and eggs of M. incognita by more than 90% in tomato roots. When BMH and INV were combined (BMH + INV), RKN suppression and tomato shoot weight were lower compared to single-strain applications. Additionally, metabolites in cell-free supernatants and volatile organic compounds (VOCs) from strains BMH and INV had strong effects against the plant pathogens M. incognita, Fusarium oxysporum, Rhizoctonia solani and Sclerotium rolfsiii, but not against three species of nematophagous fungi. Although strain INV and the combination BMH + INV emitted fewer VOCs than strain BMH, they were still capable of killing second-stage juveniles of M. incognita.

CONCLUSIONS

Bacillus strains BMH and INV inhibited M. incognita and fungal pathogens, and promoted tomato growth. However, strain INV emitted fewer VOCs and the combination BMH + INV did not enhance the activity of the biocontrol strains against the RKN or their capacity to promote plant growth. © 2021 Society of Chemical Industry.

Isolation and Characterization of Bacillus velezensis Strain P2-1 for Biocontrol of Apple Postharvest Decay Caused by Botryosphaeria dothidea

Botryosphaeria dothidea causes apple ring rot, which is among the most prevalent postharvest diseases of apples and causes significant economic loss during storage. In this study, we investigated the biocontrol activity and possible mechanism of Bacillus velezensis strain P2-1 isolated from apple branches against B. dothidea in postharvest apple fruit. The results showed strain P2-1, one of the 80 different endophytic bacterial strains from apple branches, exhibited strong inhibitory effects against B. dothidea growth and resulted in hyphal deformity. B. velezensis P2-1 treatment significantly reduced the ring rot caused by B. dothidea. Additionally, the supernatant of strain P2-1 exhibited antifungal activity against B. dothidea. Re-isolation assay indicated the capability of strain P2-1 to colonize and survive in apple fruit. PCR and qRT-PCR assays revealed that strain P2-1 harbored the gene clusters required for biosynthesis of antifungal lipopeptides and polyketides. Strain P2-1 treatment significantly enhanced the expression levels of pathogenesis-related genes (MdPR1 and MdPR5) but did not significantly affect apple fruit qualities (measured in fruit firmness, titratable acid, ascorbic acid, and soluble sugar). Thus, our results suggest that B. velezensis strain P2-1 is a biocontrol agent against B. dothidea-induced apple postharvest decay. It acts partially by inhibiting mycelial growth of B. dothidea, secreting antifungal substances, and inducing apple defense responses.

Antimicrobial Bacillus: Metabolites and Their Mode of Action

The agricultural industry utilizes antibiotic growth promoters to promote livestock growth and health. However, the World Health Organization has raised concerns over the ongoing spread of antibiotic resistance transmission in the populace, leading to its subsequent ban in several countries, especially in the European Union. These restrictions have translated into an increase in pathogenic outbreaks in the agricultural industry, highlighting the need for an economically viable, non-toxic, and renewable alternative to antibiotics in livestock. Probiotics inhibit pathogen growth, promote a beneficial microbiota, regulate the immune response of its host, enhance feed conversion to nutrients, and form biofilms that block further infection. Commonly used lactic acid bacteria probiotics are vulnerable to the harsh conditions of the upper gastrointestinal system, leading to novel research using spore-forming bacteria from the genus Bacillus. However, the exact mechanisms behind Bacillus probiotics remain unexplored. This review tackles this issue, by reporting antimicrobial compounds produced from Bacillus strains, their proposed mechanisms of action, and any gaps in the mechanism studies of these compounds. Lastly, this paper explores omics approaches to clarify the mechanisms behind Bacillus probiotics.

Acid tolerant bacterium Bacillus amyloliquefaciens MBNC retains biocontrol efficiency against fungal phytopathogens in low pH

Soil pH conditions have important consequences for microbial community structure, their dynamics, ecosystem processes, and interactions with plants. Low soil pH affects the growth and functional activity of bacterial biocontrol agents which may experience a paradigm shift in their ability to act antagonistically against fungal phytopathogens. In this study, the antifungal activity of an acid-tolerant soil bacterium Bacillus amyloliquefaciens MBNC was evaluated under low pH and compared to its activity in neutral pH conditions. Bacterial supernatant from 3-day-old culture (approximately 11.2 × 10⁸ cells/mL) grown in low pH conditions was found more effective against fungal pathogens. B. amyloliquefaciens MBNC harboured genes involved in the synthesis of secondary metabolites of which surfactin homologues, with varying chain length (C11-C15), were identified through High-Resolution Mass Spectroscopy. The pH of the medium influenced the production of these metabolites. Surfactin C15 was exclusive to the extract of pH 4.5; production of iturinA and surfactin C11 was detected only in pH 7.0, while surfactin C12, C13 and C14 were detected in extracts of both the pH conditions. The secretion of phytohormones viz. indole acetic acid and gibberellic acid by B. amyloliquefaciens MBNC was detected in higher amounts in neutral condition compared to acidic condition. Although, secretion of metabolites and phytohormones in B. amyloliquefaciens MBNC was influenced by the pH condition of the medium, the isolate retained its antagonistic efficiency against several fungal phyto-pathogens under acidic condition.

Control Efficacy of Bacillus velezensis AFB2-2 against Potato Late Blight Caused by Phytophthora infestans in Organic Potato Cultivation

Although late blight is an important disease in eco-friendly potato cultivation in Korea, it is highly dependent on the use of eco-friendly agricultural materials and the development of biological control technology is low. It is a necessary to develop an effective biocontrol agent to inactivate late blight in the field. AFB2-2 strain is a gram-positive with peritrichous flagella. It can utilize 20 types of carbon sources, like L-arabinose, and D-trehalose at 35°C. The optimal growth temperature of the strain is 37°C. It can survive at 20-50°C in tryptic soy broth. The maximum salt concentration tolerated by AFB2-2 strain is 7.5% NaCl. AFB2-2 strain inhibited the mycelial growth of seven plant pathogens by an average inhibitory zone of 10.2 mm or more. Among the concentrations of AFB2-2, 107 cfu/ml showed the highest control value of 85.7% in the greenhouse. Among the three concentrations of AFB2-2, the disease incidence and severity of potato late blight at 107 cfu/ml was lowest at 0.07 and 6.7, respectively. The nucleotide sequences of AFB2-2 strain were searched in the NCBI GenBank; Bacillus siamensis strain KCTC 13613, Bacillus velezensis strain CR-502, and Bacillus amyloliquefaciens strain DSM7 were found to have a genetic similarity of 99.7%, 99.7%, and 99.5%, respectively. The AFB2-2 strain was found to harbor the biosynthetic genes for bacillomycin D, iturin, and surfactin. Obtained data recommended that the B. velezensis AFB2-2 strain could be considered as a promising biocontrol agent for P. infestans in the field.

Antagonistic Strain Bacillus amyloliquefaciens XZ34-1 for Controlling Bipolaris sorokiniana and Promoting Growth in Wheat

Common root rot, caused by Bipolaris sorokiniana, is one of the most prevalent diseases of wheat and has led to major declines in wheat yield and quality worldwide. Here, strain XZ34-1 was isolated from soil and identified as Bacillus amyloliquefaciens based on the morphological, physiological, biochemical characteristics and 16S rDNA sequence. Culture filtrate (CF) of strain XZ34-1 showed a high inhibition rate against B.sorokiniana and had a broad antifungal spectrum. It also remarkably inhibited the mycelial growth and spore germination of B. sorokiniana. In pot control experiments, the incidence and disease index of common root rot in wheat seedlings were decreased after treatment with CF, and the biological control efficacy was significant, up to 78.24%. Further studies showed XZ34-1 could produce antifungal bioactive substances and had the potential of promoting plant growth. Lipopeptide genes detection with PCR indicated that strain XZ34-1 may produce lipopeptides. Furthermore, activities of defense-related enzymes were enhanced in wheat seedlings after inoculation with B.sorokiniana and treatment with CF, which showed induced resistance could be produced in wheat to resist pathogens. These results reveal that strain XZ34-1 is a promising candidate for application as a biological control agent against B.sorokiniana.

Possible impacts of the predominant Bacillus bacteria on the Ophiocordyceps unilateralis s. l. in its infected ant cadavers

Animal hosts infected and killed by parasitoid fungi become nutrient-rich cadavers for saprophytes. Bacteria adapted to colonization of parasitoid fungi can be selected and can predominate in the cadavers, actions that consequently impact the fitness of the parasitoid fungi. In Taiwan, the zombie fungus, Ophiocordyceps unilateralis sensu lato (Clavicipitaceae: Hypocreales), was found to parasitize eight ant species, with preference for a principal host, Polyrhachis moesta. In this study, ant cadavers grew a fungal stroma that was predominated by Bacillus cereus/thuringiensis. The bacterial diversity in the principal ant host was found to be lower than the bacterial diversity in alternative hosts, a situation that might enhance the impact of B. cereus/thuringiensis on the sympatric fungus. The B. cereus/thuringiensis isolates from fungal stroma displayed higher resistance to a specific naphthoquinone (plumbagin) than sympatric bacteria from the environment. Naphthoquinones are known to be produced by O. unilateralis s. l., and hence the resistance displayed by B. cereus/thuringiensis isolates to these compounds suggests an advantage to B. cereus/thuringiensis to grow in the ant cadaver. Bacteria proliferating in the ant cadaver inevitably compete for resources with the fungus. However, the B. cereus/thuringiensis isolates displayed in vitro capabilities of hemolysis, production of hydrolytic enzymes, and antagonistic effects to co-cultured nematodes and entomopathogenic fungi. Thus, co-infection with B. cereus/thuringiensis offers potential benefits to the zombie fungus in killing the host under favorable conditions for reproduction, digesting the host tissue, and protecting the cadaver from being taken over by other consumers. With these potential benefits, the synergistic effect of B. cereus/thuringiensis on O. unilateralis infection is noteworthy given the competitive relationship of these two organisms sharing the same resource.

A Review of the Effects and Production of Spore-Forming Probiotics for Poultry

Simple Summary

Spore-forming probiotics are widely used in the poultry industry for their beneficial impact on host health. The main feature that separates spore-forming probiotics from the more common lactic acid probiotics is their high resistance to external and internal factors, resulting in higher viability in the host and correspondingly, greater efficiency. Their most important effect is the ability to confront pathogens, which makes them a perfect substitute for antibiotics. In this review, we cover and discuss the interactions of spore-forming probiotic bacteria with poultry as the host, their health promotion effects and mechanisms of action, impact on poultry productivity parameters, and ways to manufacture the probiotic formulation. The key focus of this review is the lack of reproducibility in poultry research studies on the evaluation of probiotics’ effects, which should be solved by developing and publishing a set of standard protocols in the professional community for conducting probiotic trials in poultry.

Abstract

One of the main problems in the poultry industry is the search for a viable replacement for antibiotic growth promoters. This issue requires a “one health” approach because the uncontrolled use of antibiotics in poultry can lead to the development of antimicrobial resistance, which is a concern not only in animals, but for humans as well. One of the promising ways to overcome this challenge is found in probiotics due to their wide range of features and mechanisms of action for health promotion. Moreover, spore-forming probiotics are suitable for use in the poultry industry because of their unique ability, encapsulation, granting them protection from the harshest conditions and resulting in improved availability for hosts’ organisms. This review summarizes the information on gastrointestinal tract microbiota of poultry and their interaction with commensal and probiotic spore-forming bacteria. One of the most important topics of this review is the absence of uniformity in spore-forming probiotic trials in poultry. In our opinion, this problem can be solved by the creation of standards and checklists for these kinds of trials such as those used for pre-clinical and clinical trials in human medicine. Last but not least, this review covers problems and challenges related to spore-forming probiotic manufacturing.

Understanding the molecular basis on the biological suppression of bacterial leaf blight of anthurium exerted by Bacillus subtilis (BIO3) through proteomic approach

We attempted to study the antibacterial activity of rhizospheric Bacillus spp., to curb the bacterial blight of anthurium caused by Xanthomonas axonopodis pv. dieffenbachiae (Xad). Twenty-eight bacterial isolates from rhizospheric regions were identified as different Bacillus spp. and Ochrobactrum sp. using 16S rRNA gene sequencing. B. subtilis BIO3 effectively inhibited the growth of Xad up to 1450.7 mm², and extracted volatile organic metabolites from the isolate BIO3 inhibited the growth of Xad up to 1024 mm². Tritrophic interaction of anthurium leaves bacterized with B. subtilis BIO3 and challenged with Xad resulted in the expression of 12 unique proteins compared to untreated control. Mascot Peptide Mass Fingerprint-based identification indicated that one was glutathione peroxidase, involved in defence mechanism, other six proteins were identified as leghemoglobin II, CTP synthase-like, predicted protein (Physcomitrella patens), centromere-associated protein E, grain size protein, and five proteins were hypothetical proteins. Foliar application with 1% liquid formulations (10⁸ CFU/ml) of B. subtilis BIO3 significantly suppressed the bacterial leaf blight of anthurium up to 78% over untreated control and also increased the stem length and flower yield.

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.

Transcriptional Profiling of Diffusible Lipopeptides and Fungal Virulence Genes During Bacillus amyloliquefaciens EZ1509-Mediated Suppression of Sclerotinia sclerotiorum

Sclerotinia sclerotiorum is a devastating necrotrophic pathogen that infects multiple crops, and its control is an unremitting challenge. In this work, we attempted to gain insights into the pivotal role of lipopeptides (LPs) in the antifungal activity of Bacillus amyloliquefaciens EZ1509. In a comparative study involving five Bacillus strains, B. amyloliquefaciens EZ1509 harboring four LPs biosynthetic genes (viz. surfactin, iturin, fengycin, and bacilysin) exhibited promising antifungal activity against S. sclerotiorum in a dual-culture assay. Our data demonstrated a remarkable upsurge in LPs biosynthetic gene expression through quantitative reverse transcription PCR during in vitro interaction assay with S. sclerotiorum. Maximum upregulation in LPs biosynthetic genes was observed on the second and third days of in vitro interaction, with iturin and fengycin being the highly expressed genes. Subsequently, Matrix-assisted laser desorption/ionization-time of flight-mass spectrometry analysis confirmed the presence of LPs in the inhibition zone. Scanning electron microscope analysis showed disintegration, shrinkage, plasmolysis, and breakdown of fungal hyphae. During in planta evaluation, S. sclerotiorum previously challenged with EZ1509 showed significant suppression in pathogenicity on detached leaves of tobacco and rapeseed. The oxalic acid synthesis was also significantly reduced in S. sclerotiorum previously confronted with antagonistic bacterium. The expression of major virulence genes of S. sclerotiorum, including endopolygalacturonase-3, oxalic acid hydrolase, and endopolygalacturonase-6, was significantly downregulated during in vitro confrontation with EZ1509.

Probiotic Properties of Bacillus Strains Isolated from Stingless Bee (Heterotrigona itama) Honey Collected across Malaysia

This study aimed to isolate, identify, and evaluate the probiotic properties of Bacillus species from honey of the stingless bee Heterotrigona itama. Bacillus spp. were isolated from five different H. itama meliponicultures, and the isolates were characterized through Gram-staining and a catalase test. Tolerance to acidic conditions and bile salt (0.3%), hydrophobicity, and autoaggregation tests were performed to assess the probiotic properties of the selected isolates, B. amyloliquefaciens HTI-19 and B. subtilis HTI-23. Both Bacillus isolates exhibited excellent antimicrobial activity against both Gram-positive and Gram-negative bacteria and possessed significantly high survival rates in 0.3% bile solution for 3 h. Their survival rates in acidic conditions were also comparable to a commercial probiotic strain, Lactobacillus rhamnosus GG. Interestingly, the hydrophobicity and autoaggregation percentage showed no significant difference from L. rhamnosus GG, a commercial probiotic strain. The results from this study suggest that B. amyloliquefaciens HTI-19 and B. subtilis HTI-23 isolated from stingless bee honey have considerably good probiotic properties. Therefore, more studies should be done to investigate the effects of these bacteria cultures on gastrointestinal health.

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.

Bacterial communities of plum phyllosphere and characterization of indigenous antagonistic Bacillus thuringiensis R3/3 isolate

AIMS

The characterization of bacterial communities diversity on four local plum cultivars in two phenological stages using culture-dependent and culture-independent methods and screening among culturable plum community for indigenous bacteria active against phytopathogens.

METHODS AND RESULTS

The bacterial communities associated with leaves and fruits of four local Serbian plum cultivars (Požegača, Ranka, Čačanska Lepotica and Čačanska Rodna) were investigated in two phenological stages during early (May) and late (July) fruit maturation. Metagenomic approach revealed Methylobacterium, Sphingomonas and Hymenobacter as dominant genera. The most frequently isolated representatives with cultivable approach were pseudomonads with Pseudomonas syringae and Pseudomonas graminis, the most likely resident species of plum community. Antagonistic Bacillus thuringiensis R3/3 isolate from plum phyllosphere had ability to produce exoenzymes, reduce the growth of phytopathogenic bacteria in co-culture environment and show quorum quenching activity.

CONCLUSIONS

Plum cultivar and growth season contribute to the structure of the bacterial community associated with plum. Plum phyllosphere is good source of antagonists effective against phytopathogens.

SIGNIFICANCE AND IMPACT OF STUDY

Knowledge of bacterial communities on plum will have an impact on studies related to phyllosphere ecology and biocontrol. The indigenous antagonistic isolate, B. thuringiensis R3/3, from plum could be further investigated for its potential use in biological control of plum diseases.

Halotolerant bacteria belonging to operational group Bacillus amyloliquefaciens in biocontrol of the rice brown stripe pathogen Acidovorax oryzae

AIMS

The aim of this study was to evaluate the antagonistic activity of halotolerant bacteria against rice brown stripe pathogen Acidovorax oryzae.

METHODS AND RESULTS

Fifteen of 136 isolates of halotolerant bacteria exhibited strong in vitro and in vivo antagonistic activity against both strains of A. oryzae. The 15 antagonistic isolates were identified as 'operational group Bacillus amyloliquefaciens' based on physiological and biochemical features, fatty acid profiles as well as sequence analysis of 16S rRNA, gyrA and rpoB genes. Furthermore, this result indicated that the most effective antagonistic isolates K5-3 and PPB6 could produce siderophore in iron-limiting medium, and four kinds of secondary metabolites based on MALDI-TOF analysis. In addition, the culture filtrates of isolates K5-3 and PPB6 caused the damage of cell membrane evidenced by the TEM images, and resulted in 73-80% reduction in cell numbers, 55-65% reduction in biofilm formation, and 42-50% reduction in swimming ability of both strains of A. oryzae.

CONCLUSIONS

These isolates in particular K5-3 and PPB6 of halotolerant bacteria markedly inhibited the growth of A. oryzae.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, this is the first report on biological control of halotolerant bacteria against bacterial brown stripe of rice.

Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity

Bacillus spp. produce a broad spectrum of lipopeptide biosurfactants, among which surfactin, iturin and fengycin are widely studied families. The goals of this study were to characterize the biosurfactant activity of Bacillus spp. and to investigate their motility and biofilm formation capabilities. In addition, we extracted lipopeptides from these bacteria to assess their antifungal activities and analyzed these products by mass spectrometry (MS). B. amyloliquefaciens FZB42, Bacillus sp. NH 217 and B. subtilis NH-100 exhibited excellent biosurfactant and surface spreading activities, whereas B. atrophaeus 176s and Paenibacillus polymyxa C1225 showed moderate activity, and B. subtilis 168 showed no activity. Strains FZB42, NH-100, NH-217, 176s and CC125 exhibited excellent biofilm formation capabilities. Lipopeptide extracts displayed good antifungal activity against various phytopathogens and their associated diseases, such as Fusarium moniliforme (rice bakanae disease), Fusarium oxysporum (root rot), Fusarium solani (root rot) and Trichoderma atroviride (ear rot and root rot). Lipopeptide extracts of these strains also showed hemolytic activity, demonstrating their strong potential to produce surfactants. LCMS-ESI analyses identified the presence of surfactin, iturin and fengycin in the extracts of Bacillus strains. Thus, the strains assayed in this study show potential as biocontrol agents against various Fusarium and Trichoderma species.

Rapid identification of Streptomyces tetracycline producers by MALDI-TOF mass spectrometry

The main objective of this study was using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for assembling of DSM (German Collection of Microorganisms) Streptomyces spectral database and identification of wild Streptomyces cultures, which were clustered by MALDI-TOF Biotyper OC software as well as for teracycline detection by observing of obtained spectra using flexAnalysis software. Production of tetracycline was confirmed by thin-layer chromatography. Presence of tetracycline mass spectrum was verified by several tetracycline producers (Streptomyces aureofaciens LMG 5968, S. aureofaciens 84/25, and S. aureofaciens BMK) and by pure tetracycline mass. Our results showed that it is possible to use MALDI-TOF MS for identification of tetracycline producers within Streptomyces genera by several easy steps. The purpose of this study was to establish cheap and quick detection of tetracycline producers.

Optimized fluorescent proteins for the rhizosphere-associated bacterium Bacillus mycoides with endophytic and biocontrol agent potential

Tracking of fluorescent protein (FP)-labelled rhizobacteria is a key prerequisite to gain insights into plant-bacteria interaction mechanisms. However, the performance of FPs mostly has to be optimized for the bacterial host and for the environment of intended application. We report on the construction of mutational libraries of the superfolder green fluorescent protein sfGFP and the red fluorescent protein mKate2 in the bacterium B. mycoides, which next to its potential as plant-biocontrol agent occasionally enters an endophytic lifestyle. By fluorescence-activated cell sorting and comparison of signal intensities at the colony and single-cell level, the variants sfGFP(SPS6) and mKate (KPS12) with significantly increased brightness were isolated. Their high applicability for plant-bacteria interaction studies was shown by confocal laser scanning microscopy tracking of FP-tagged B. mycoides strains after inoculation to Chinese cabbage plants in a hydroponic system. During the process of colonization, strain EC18 rapidly attached to plant roots and formed a multicellular matrix, especially at the branching regions of the root hair, which probably constitute entrance sites to establish an endophytic lifestyle. The universal applicability of the novels FPs was proven by expression from a weak promoter, dual-labelling of B. mycoides, and by excellent expression and detectability in additional soil- and rhizosphere-associated Bacillus species.

The Profile and Antimicrobial Activity of Bacillus Lipopeptide Extracts of Five Potential Biocontrol Strains

In this study the efficacy of two different methods for extracting lipopeptides produced by five Bacillus strains-ethyl acetate extraction, and acid precipitation followed by methanol extraction—was investigated using mass spectrometry. High performance thin layer chromatography (HPTLC) was also used for the simultaneous separation of complex mixtures of lipopeptide extracts and for the determination of antimicrobial activity of their components. The mass spectra clearly showed well-resolved groups of peaks corresponding to different lipopeptide families (kurstakins, iturins, surfactins, and fengycins). The ethyl acetate extracts produced the most favorable results. The extracts of SS-12.6, SS-13.1, and SS-38.4 showed the highest inhibition zones. An iturin analog is responsible for the inhibition of Xanthomonas arboricola and Pseudomonas syringae phytopathogenic strains. HPTLC bioautography effectively identified the active compounds from a mixture of lipopeptide extracts, proving in situ its potential for use in direct detection and determination of antimicrobials. In the test of potential synergism among individual extracts used in different mixtures, stronger antimicrobial effects were not observed. Biochemical and phylogenetic analysis clustered isolates SS-12.6, SS-13.1, SS-27.2, and SS-38.4 together with Bacillus amyloliquefaciens, while SS-10.7 was more closely related to Bacillus pumilus.

Identification and Characterization of Lipopeptides from Bacillus subtilis B1 Against Sapstain Fungus of Rubberwood Through MALDI-TOF-MS and RT-PCR

Bacillus subtilis is a potent biocontrol agent producing a wide array of antifungal lipopeptides for the inhibition of fungal growth. B. subtilis B1 isolated from market-available compost provided an efficient control of rubberwood sapstain fungus, Lasiodiplodia theobromae. The current study is aimed to identify and characterize the lipopeptides responsible for the biocontrol of rubberwood sapstain fungus by Bacillus subtilis B1. The bacterial whole-cell surface extract from the dual culture of B. subtilis B1 and sapstain fungus (L. theobromae) was analysed using MALDI-TOF-MS. The protonated as well as sodium, potassium adducts of homologues of iturin C, surfactin, bacillomycin D and fengycin A and B were identified and expression of the lipopeptide biosynthetic genes could be confirmed through RT-PCR. This is the first report of mycobacillin and trimethylsilyl derivative of bacilysin during antagonism through MALDI-TOF-MS. MALDI-TOF-MS with RT-PCR offered easy platforms to characterize the antifungal lipopeptides. The identification of antifungal lipopeptides can lead to the formulation of prospective biocontrol by-products which have wide-scale utility.

Synergistic Effects of [Ile⁷]Surfactin Homologues with Bacillomycin D in Suppression of Gray Mold Disease by Bacillus amyloliquefaciens Biocontrol Strain SD-32

We previously reported that Bacillus amyloliquefaciens biocontrol strain SD-32 produces powerful antifungal lipopeptides, C17 bacillomycin D homologues. In the course of the investigation we found that the antifungal activity of the culture supernatant of this bacterium was not ascribed exclusively to bacillomycin D. We attempted to identify metabolites other than bacillomycin D to gain insight into the mechanism for the biocontrol by this bacterium. After purifying the fractions of the culture supernatant exhibiting synergistic activity with bacillomycin D, we isolated two new cyclic lipodepsipeptides, anteiso-C13 and iso-C13 [Ile(7)]surfactins, together with three known [Ile(7)]surfactins. Interestingly, [Ile(7)]surfactins showed synergistic activities with bacillomycin D to gray mold disease on cucumber leaves but not to Botrytis cinerea itself in vitro, suggesting that the synergistic effects might be on infection processes of the fungus. Actually, we observed that they did not show synergistic actions on conidial germination or mycelial growth of B. cinerea on the leaves.

Cyclic Lipopeptide Biosynthetic Genes and Products, and Inhibitory Activity of Plant-Associated Bacillus against Phytopathogenic Bacteria

The antibacterial activity against bacterial plant pathogens and its relationships with the presence of the cyclic lipopeptide (cLP) biosynthetic genes ituC (iturin), bmyB (bacillomycin), fenD (fengycin) and srfAA (surfactin), and their corresponding antimicrobial peptide products have been studied in a collection of 64 strains of Bacillus spp. isolated from plant environments. The most frequent antimicrobial peptide (AMP) genes were bmyB, srfAA and fenD (34-50% of isolates). Most isolates (98.4%) produced surfactin isoforms, 90.6% iturins and 79.7% fengycins. The antibacterial activity was very frequent and generally intense among the collection of strains because 75% of the isolates were active against at least 6 of the 8 bacterial plant pathogens tested. Hierarchical and correspondence analysis confirmed the presence of two clearly differentiated groups. One group consisted of Bacillus strains that showed a strong antibacterial activity, presented several cLPs genes and produced several isoforms of cLPs simultaneously, mainly composed of B. subtilis and B. amyloliquefaciens, although the last one was exclusive to this group. Another group was characterized by strains with very low or none antibacterial activity, that showed one or none of the cLP genes and produced a few or none of the corresponding cLPs, and was the most heterogenous group including B. subtilis, B. licheniformis, B. megaterium, B. pumilus, B. cereus and B. thuringiensis, although the last two were exclusive to this group. This work demonstrated that the antagonistic capacity of plant-associated Bacillus against plant pathogenic bacteria is related to the presence of cLP genes and to the production of the corresponding cLPs, and it is mainly associated to the species B. subtilis and B. amyloliquefaciens. Our findings would help to increase the yield and efficiency of screening methods to obtain candidate strains to biocontrol agents with a mechanism of action relaying on the production of antimicrobial cLPs.

Bacillus amyloliquefaciens strain 32a as a source of lipopeptides for biocontrol of Agrobacterium tumefaciens strains

AIMS

A Bacillus amyloliquefaciens strain, designated 32a, was used to identify new compounds active against Agrobacterium tumefaciens and to evaluate their efficiency to control crown gall on carrot discs.

METHODS AND RESULTS

Based on PCR-assays, four gene clusters were shown to direct the synthesis of the cyclic lipopeptides surfactin, iturin A, bacillomycin D and fengycin. Mass spectrometry analysis of culture supernatant led to the identification of these secondary metabolites, except bacillomycin, with heterogeneous mixture of homologues. Antimicrobial assays using lipopeptides-enriched extract showed a strong inhibitory activity against several bacterial and fungal strains, including Ag. tumefaciens. Biological control assays on carrot discs using both 32a spores and extract resulted in significant protection against crown gall disease, similar to that provided by the reference antagonistic strain Agrobacterium rhizogenes K1026.

CONCLUSIONS

In contrast to all active compounds against Ag. tumefaciens that are of proteinaceous nature, this work enables for the first time to correlate the strong protective effect of B. amyloliquefaciens strain 32a towards crown gall disease with the production of a mixture of lipopeptides.

SIGNIFICANCE AND IMPACT OF THE STUDY

The findings could be useful for growers and nursery men who are particularly interested in the biocontrol of the crown gall disease.

Chemical structure, property and potential applications of biosurfactants produced by Bacillus subtilis in petroleum recovery and spill mitigation

Lipopeptides produced by microorganisms are one of the five major classes of biosurfactants known and they have received much attention from scientific and industrial communities due to their powerful interfacial and biological activities as well as environmentally friendly characteristics. Microbially produced lipopeptides are a series of chemical structural analogues of different families and, among them, 26 families covering about 90 lipopeptide compounds have been reported in the last two decades. This paper reviews the chemical structural characteristics and molecular behaviors of surfactin, one of the representative lipopeptides of the 26 families. In particular, two novel surfactin molecules isolated from cell-free cultures of Bacillus subtilis HSO121 are presented. Surfactins exhibit strong self-assembly ability to form sphere-like micelles and larger aggregates at very low concentrations. The amphipathic and surface properties of surfactins are related to the existence of the minor polar and major hydrophobic domains in the three 3-D conformations. In addition, the application potential of surfactin in bioremediation of oil spills and oil contaminants, and microbial enhanced oil recovery are discussed.

In-vitro antibacterial, antifungal, antioxidant and functional properties of Bacillus amyloliquefaciens

BACKGROUND

Food born pathogenic bacteria and filamentous fungi are able to grow on most foods, including natural foods, processed foods, and fermented foods and create considerable economic loss. The aim of this study was to determine the antibacterial, antifungal, antioxidant and functional properties of Bacillus amyloliquefaciens recovered from silage.

METHODS

Minimum Inhibitory Concentration (MIC) of the compounds was assessed by using broth micro dilution method. The 1,1-diphenyl-2-picrylhydrazyl (DPPH)-radical scavenging and hydroxyl radical-scavenging abilities were measured to evaluate antioxidant activity of the strain.

RESULTS

Primary antimicrobial compound production screening revealed that B. amyloliquefaciens exhibited significant activity against all the tested bacteria and fungi compared to other strains. The 16S rRNA and gyrase A gene sequence analysis determined using molecular biological tools confirmed that the strain was 99% similarity towards B. amyloliquefaciens. The Minimum Inhibitory Concentration (MIC) of ethyl acetate extract against Bacillus subtilis, Enterococcus cloacae and Staphylococcus aureus were 25.0 μg ml-1, and S, epidermidis were 12.5 μg ml-1, respectively. Filamentous fungi Aspergillus clavatus, A. fumigates, A. niger and Gibberella moniliformis showed 25 μg ml-1. VJ-1 was able to survive the gastrointestinal conditions simulating the stomach and duodenum passage with the highest percentage of hydrophobicity. In addition, its resistance to hydrogen peroxide and highest hydroxyl radical and 2, 2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activities, with inhibition rates of 56.84% and 67.12% respectively, were its advantage. An antimicrobial susceptibility pattern was an intrinsic feature of this strain, and thus, consumption does not represent a health risk to humans.

CONCLUSION

Bacillus amyloliquefaciens might be a promising candidate for new pharmaceutical agents and probiotics.

Detection and characterization of broad-spectrum antipathogen activity of novel rhizobacterial isolates and suppression of Fusarium crown and root rot disease of tomato

AIMS

To detect and characterize broad-spectrum antipathogen activity of indigenous bacterial isolates obtained from potato soil and soya bean leaves for their potential to be developed as biofungicides to control soilborne diseases such as Fusarium crown and root rot of tomato (FCRR) caused by Fusarium oxysporum f. sp. radicis-lycopersici (Forl).

METHODS AND RESULTS

Thirteen bacterial isolates (Bacillus amyloliquefaciens (four isolates), Paenibacillus polymyxa (three isolates), Pseudomonas chlororaphis (two isolates), Pseudomonas fluorescens (two isolates), Bacillus subtilis (one isolate) and Pseudomonas sp. (one isolate)) or their volatiles showed antagonistic activity against most of the 10 plant pathogens in plate assays. Cell-free culture filtrates (CF) of five isolates or 1-butanol extracts of CFs also inhibited the growth of most pathogen mycelia in plate assays. PCR analysis confirmed the presence of most antibiotic biosynthetic genes such as phlD, phzFA, prnD and pltC in most Pseudomonas isolates and bmyB, bacA, ituD, srfAA and fenD in most Bacillus isolates. These bacterial isolates varied in the production of hydrogen cyanide (HCN), siderophores, β-1,3-glucanases, chitinases, proteases, indole-3-acetic acid, salicylic acid, and for nitrogen fixation and phosphate solubilization. Gas chromatography-mass spectrometry analysis identified 10 volatile compounds from 10 isolates and 18 compounds from 1-butanol extracts of CFs of five isolates. Application of irradiated peat formulation of six isolates to tomato roots prior to transplanting in a Forl-infested potting mix and field soil provided protection of tomato plants from FCRR disease and enhanced plant growth under greenhouse conditions.

CONCLUSIONS

Five of the 13 indigenous bacterial isolates were antagonistic to eight plant pathogens, both in vitro and in vivo. Antagonistic and plant-growth promotion activities of these isolates might be related to the production of several types of antibiotics, lytic enzymes, phytohormones, secondary metabolites, siderophores and volatile compounds; however, any specific role of each needs to be determined.

SIGNIFICANCE AND IMPACT OF THE STUDY

Indigenous antagonistic bacterial isolates have the potential to be developed as biofungicides for minimizing early crop losses due to soilborne diseases caused by Fusarium and other soilborne pathogens.

Genetic, physiological and biochemical characterization of Bacillus sp. strain RMB7 exhibiting plant growth promoting and broad spectrum antifungal activities

Background

Plant growth promoting rhizobacteria (PGPR) are functionally diverse group of bacteria having immense potential as biofertilizers and biopesticides. Depending upon their function, they may serve as partial replacements for chemical fertilizer or pesticides as an eco-friendly and cost-effective alternatives as compared to their synthetic counterparts. Therefore, isolation, characterization and practical evaluation of PGPRs having the aforementioned multifaceted beneficial characteristics, are essentially required. This study describes the detailed polyphasic characterization of Bacillus sp. strain RMB7 having profound broad spectrum antifungal activity and plant growth promoting potential.

Results

Based on 16S rRNA gene sequencing, strain RMB7 was identified as Bacillus specie. This strain exhibited the production of 8 mg. L⁻¹of indole-3-acetic acid (IAA) in tryptophan-supplemented medium. It was able to solubilize 50.6 mg. L⁻¹ tri-calcium phosphate, reduced 601ηmol acetylene h⁻¹/vial and inhibited >70% growth of nine fungal phytopathogens tested in vitro. Under natural pathogen pressure, inoculation with strain RMB7 and RMB7-supernatant conferred resistance by arugula plant against Pythium irregulare with a concurrent growth improvement over non-inoculated plants. The T-RFLP analysis based on 16S rRNA gene showed that inoculation with RMB7 or its supernatant have a major impact on the indigenous rhizosphere bacterial population. Mass spectrometric analysis revealed the production of lipopeptide surfactins as well as iturin A presence in crude extract of RMB7. PCR-amplification further confirmed the presence of genes involved in the biosynthesis of these two bioactive lipopeptide compounds.

Conclusions

The data show that Bacillus sp. strain RMB7 has multifaceted beneficial characteristics. It may be an ideal plant growth promoting as well as biocontrol agent, for its integrated use in disease and nutrient management strategies.

Isolation and characterization of putative endophytic bacteria antagonistic to Phoma tracheiphila and Verticillium albo-atrum

A collection of 200 bacterial isolates recovered from citrus plants (Citrus limon, Citrus sinensis, and Citrus reticulata), Medicago truncatula and Laurus nobilis, was established. In vitro screening indicated that 28 isolates exhibited an inhibitory activity against the vascular pathogens Phoma tracheiphila and Verticillium albo-atrum. Isolates were screened according to their hydrolytic activities, plant growth-promoting bacteria (PGPB) abilities, as well as for the presence of nonribosomal peptide synthetase (NRPS) genes responsible of the lipopeptide biosynthesis. The results were positive for 16 isolates which exhibited at least two PGPB activities and a single NRPS gene. Genetic diversity of the selected isolates was studied using random amplified polymorphic DNA (RAPD) and repetitive element PCR (REP) tools that showed clustering of strains into three major groups (I, II, and III) (i, ii, and iii), respectively. Clustering was further confirmed by the 16S rDNA sequencing that assigned nine isolates to Bacillus velezensis, four isolates to Bacillus methyltrophicus, one isolate to Bacillus amyloliquefaciens, and two isolates to Bacillus mojavensis. Organ-bacterial genotype interaction as well as positive correlation with NRPS genes are discussed.

Enhancement of Biocontrol Activities and Cyclic Lipopeptides Production by Chemical Mutagenesis of Bacillus subtilis XF-1, a Biocontrol Agent of Plasmodiophora brassicae and Fusarium solani

Bacillus subtilis XF-1 has been used as a biocontrol agent of clubroot disease of crucifers infected by Plasmodiophora brassicae, an obligate pathogen. In order to maximize the growth inhibition of the pathogen, random mutagenesis using N-methyl-N'-nitro-N-nitrosoguanidine was applied to strain XF-1. The efficacy of 226 selected mutants was assessed against the growth of an indicator fungal pathogen: Fusarium solani using agar plate assay and the disruptive effects on the resting spores of P. brassicae. Four mutants exhibited inhibition activity significantly higher than the wild type. The cell extracts of these mutants and the XF-1 were subjected to matrix-assisted laser desorption ionization-time of flight mass spectra analysis, and three families of cyclic lipopeptides (CLPs) fengycin, surfactin and iturin were identified from the parental strain and the screened mutants. However, the relative contents and compound diversity changed after mutagenesis, and there was slight variation in the surfactin and fengycin. Notably, only 5 iturin components were discovered from the wild strain XF-1, but 13 were obtained from the mutant strains, and the relative CLPs contents of all mutant strains increased substantially. The results suggested that CLPs might be one of main biocontrol mechanisms of the clubroot disease by XF-1. The 4 mutants are far more effective than the parental strain, and they would be promising biocontrol candidates not only against P. brassicae but probably other plant diseases caused by fungi.

Isolation of anteiso-C17, iso-C17, iso-C16, and iso-C15 bacillomycin D from Bacillus amyloliquefaciens SD-32 and their antifungal activities against plant pathogens

Two new cyclic lipopeptides (3 and 4) were isolated from the culture filtrate of Bacillus amyloliquefaciens strain SD-32, together with two known metabolites, iso-C15 and iso-C16 bacillomycin D (1 and 2). Spectroscopic and chemical analyses identified the structures of the new compounds 3 and 4 as anteiso-C17 bacillomycin D, cyclic (l-Asn-d-Tyr-d-Asn-l-Pro-l-Glu-d-Ser-l-Thr-3-amino-14-methylhexadecanoic acid) and iso-C17 bacillomycin D, cyclic (l-Asn-d-Tyr-d-Asn-l-Pro-l-Glu-d-Ser-l-Thr-3-amino-15-methylhexadecanoic acid), respectively. The absolute configuration of C-3 in the β-amino fatty acid was determined to be R on the basis of the CD spectrum of its dinitrophenyl-p-methoxyaniline derivative. The activities of compounds 1-4 were evaluated against 13 plant pathogens: the activities of anteiso- and iso-C17 bacillomycin D (3 and 4) were almost the same and stronger than those of iso-C15 and iso-C16 bacillomycin D (1 and 2); iso-C15 bacillomycin D (1) was weakest. Compounds 2-4 inhibited the growth of all fungi tested; however, Pythium aphanidermatum was not inhibited at all by any of the compounds. Furthermore, compounds 1-4 at concentrations of 80, 40, 30, and 30 μM, respectively, inhibited completely the Botrytis cinerea infection in cucumber leaf.

Characterization of antagonistic-potential of two Bacillus strains and their biocontrol activity against Rhizoctonia solani in tomato

To investigate the biocontrol mechanism of two antagonistic Bacillus strains (Bacillus subtilis MB14 and Bacillus amyloliquefaciens MB101), three in vitro antagonism assays were screened and the results were concluded that both strains inhibited Rhizoctonia solani growth in a similar manner by dual culture assay, but the maximum percent of inhibition only resulted with MB101 by volatile and diffusible metabolite assays. Moreover, cell free supernatant (CFS) of MB101 also showed significant (p > 0.05) growth inhibition as compared to MB14, when 10 and 20% CFS mix with the growth medium of R. solani. After in vitro-validation, both strains were evaluated under greenhouse and the results concluded that strain MB101 had significant biocontrol potential as compared to MB14. Strain MB101 was enhanced the plant height, biomass and chlorophyll content of tomato plant through a higher degree of root colonization. In field trials, strain MB101 showed higher lessening in root rot symptoms with significant fruit yield as compare to strain MB14 and infected control. Next to the field study, the presence of four antibiotic genes (srfAA, fenD, ituC, and bmyB) also concluded the antifungal nature of both Bacillus strains. Phylogenetic analysis of protein sequences revealed a close relatedness of three genes (srfAA, fenD, and ituC) with earlier reported sequences of B. subtilis and B. amyloliquefaciens. However, bmyB showed heterogeneity in among both strains (MB14 and MB101) and it may be concluded that higher degree of antagonism, root colonization and different antibiotic producing genes may play an important role in biocontrol mechanism of strain MB101.