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

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.

The Role of Aspergillus niger in Regulating Internal Browning Involves Flavonoid Biosynthesis and the Endophytic Fungal Community of Pineapple

Endophytic fungi are commonly used to control plant diseases, overcoming the drawbacks of chemical agents. The internal browning (IB) of postharvest pineapple fruit, a physiological disease, leads to quality losses and limits industrial development. This work investigated the relationship among the effects of Aspergillus niger (An) on IB controlling, flavonoid metabolism and the endophytic fungal community of pineapple through metabolomics, transcriptomics, microbiomics and microorganism mutagenesis technology. We obtained an endophyte An that can control the IB of pineapple and screened its mutant strain AnM, through chemical mutagenesis, that cannot control IB. The transcriptome of fungi showed that An and AnM were different in oxidative metabolism. Transcriptome and metabolome analyses of pineapple showed that An upregulated genes of flavonoid synthesis, including dihydroflavonol 4-reductase and flavonoid 3'-monooxygenase and increased the flavonoid content in pineapple fruit, i.e., Hispidulin, Hispidulin-7-O-Glucoside, and Diosmetin, while AnM could not. Microbiomics analysis identified an increase in the abundance of eight endophytic fungi in An-inoculated fruit, among which the abundance of six endophytic fungi (Filobasidium magnum, Naganishia albida, A. niger, Aureobasidium melanogenum, Kwoniella heveanensis and Lysurus cruciatus) was positively correlated with the content of three flavonoids mentioned above but not in AnM-inoculated fruit. Overall, this suggested, for the first time, that A. niger alleviated IB mainly by enhancing flavonoid synthesis and content and the abundance of endophytic fungi and by regulating the interaction between flavonoid content and endophytic fungi abundance in pineapple. This work adds to the understanding of the IB mechanism in postharvest pineapple and provides a new green approach for reducing postharvest losses and controlling physiological diseases.

Bacillus subtilis YZ-1 surfactins are involved in effective toxicity against agricultural pests

BACKGROUND

Insect pests negatively affect crop quality and yield. The excessive use of chemical pesticides has serious impacts on the environment and food safety. Therefore, development of effective management strategies in the form of bio-agents have important agricultural applications. Tenebrio molitor, a storage pest, causes losses of grains, medicinal materials, and various agricultural and related products in the warehouse. Bacillus subtilis YZ-1 isolated from naturally deceased Pieris rapae has been found to exhibit significant toxicity against T. molitor.

RESULTS

Treatment with B. subtilis YZ-1 fermentation broth resulted in a 90-95% mortality rate of T. molitor within 36 h post-treatment, indicating some active substances may have insecticidal activity in the bacterial supernatant. A bioactivity-guided fractionation method was used to isolate the insecticidal compounds from YZ-1, which led to the identification of surfactins. Additionally, a surfactin deletion mutant YZ-1△srfAA was constructed and the surfactin production by the mutant YZ-1△srfAA was verified through liquid chromatography-mass spectrometry (LC-MS). Further, YZ-1△srfAA exhibited loss of insecticidal activity against T. molitor, Plutella xylostella and Achelura yunnanensis. The insecticidal activity and surfactins contents of several strains of Bacillus sp. were also tested and correlation was found between varying surfactins yield and insecticidal activity exhibited by different strains.

CONCLUSION

Conclusively, our results suggest that B. subtilis YZ-1 may provide a novel approach for plant protection against agricultural pests. © 2023 Society of Chemical Industry.

Protein-protein Interaction and Molecular Dynamics of Iturin A Gene on Effector Proteins of Phytophthora infestans

AIM AND OBJECTIVES

Phytophthora infestans (Mont.) de Bary, the fungal pathogen causes late blight, which results in devastating economic loss among the Solanaceae. The bacillus lipopeptides show the antagonistic activity against the many plant pathogens, among bacillus lipopeptides reported as the antifungal gene. Hence, to understand the in silico antifungal activity, we have selected gene iturin A (AXN89987) produced by Bacillus spp to check the molecular dynamics study with the effector proteins of the P. infestanse. In this concern, known effector proteins of P. infestans were subjected to the protein-protein interaction followed by simulation.

MATERIALS AND METHODS

Iturin A gene was amplified using the soil bacterium Bacillus subtilis with gene-specific primers, cloned into pTZ 57R/T vector and confirmed by sequencing. To get better insights, the protein model was developed for Iturin A using Modeller 9.17, using PDB structure of ID 4MRT (Phosphopantetheine transferase Sfp) and 1QR0 (4'-phosphopantetheinyl moiety of coenzyme A) as a template, it shared the identity 72% and expected P-value: 3e-121, respectively. The model quality was assessed using ProSA and PROCHECK programs.

RESULTS

The potency of modelled protein against effector proteins of P. infestans were evaluated in silico using the HADDOCK server and the results showed the high affinity of towards the effector protein Host ATG8 (PDB-5L83). Finally, the simulation was performed to the docked conformation of with Host ATG8 to further understand the stability of the complex using the Desmond program.

CONCLUSION

Altogether, the protein-protein interaction and simulation study propose a new methodology and to uncover possible antifungal activity of iturin A against effector proteins of P. infestans.

The Mode of Action of Bacillus Species against Fusarium graminearum, Tools for Investigation, and Future Prospects

Fusarium graminearum is a pervasive plant pathogenic fungal species. Biological control agents employ various strategies to weaken their targets, as shown by Bacillus species, which adopt various mechanisms, including the production of bioactive compounds, to inhibit the growth of F. graminearum. Various efforts to uncover the antagonistic mechanisms of Bacillus against F. graminearum have been undertaken and have yielded a plethora of data available in the current literature. This perspective article attempts to provide a unified record of these interesting findings. The authors provide background knowledge on the use of Bacillus as a biocontrol agent as well as details on techniques and tools for studying the antagonistic mechanism of Bacillus against F. graminearum. Emphasizing its potential as a future biological control agent with extensive use, the authors encourage future studies on Bacillus as a useful antagonist of F. graminearum and other plant pathogens. It is also recommended to take advantage of the newly invented analytical platforms for studying biochemical processes to understand the mechanism of action of Bacillus against plant pathogens in general.

Antagonistic Activity and the Mechanism of Bacillus amyloliquefaciens DH-4 Against Citrus Green Mold

Citrus fruit usually suffer significant losses during the storage and transportation stages. Green mold, a postharvest rot of citrus fruit caused by Penicillium digitatum, is one of the most serious fungal diseases. In this study, the antagonist strain DH-4 was identified as Bacillus amyloliquefaciens according to morphological observation and 16S ribosomal DNA analysis. In addition, it showed broad antifungal activity, especially the suppression of Penicillium spp. The culture filtrate of strain DH-4 exhibited apparent activity against P. digitatum in vitro and in vivo. In storage, the culture filtrate with DH-4 in it showed a better antiseptic effect. The antifungal substances in the culture filtrate, produced by strain DH-4, displayed stable activity in various extreme conditions. In addition, the antifungal substances in the culture filtrate were identified as macrolactin, bacillaene, iturins, fengycin, and surfactin by ultraperformance liquid chromatography (UPLC) electrospray ionization mass spectrometry analysis. The UPLC fractions containing these antifungal compounds were basically heat tolerant and all responsible for the antagonistic activity against P. digitatum. Transmission electron microscope observation indicated that the antifungal substances might cause abnormalities in the P. digitatum cellular ultrastructure, which could be the possible mode of action of B. amyloliquefaciens against P. digitatum. In addition, it was confirmed via scanning electron microscope analysis that the main way it inhibited P. digitatum was by secreting antimicrobial compounds without direct interaction. This study contributes to the understanding of the mechanism of B. amyloliquefaciens against citrus green mold as well as providing a potential application for the biocontrol of postharvest rot diseases in citrus fruit.

Control of Multidrug-Resistant Gene Flow in the Environment Through Bacteriophage Intervention

The spread of multidrug-resistant (MDR) bacteria is an emerging threat to the environment and public wellness. Inappropriate use and indiscriminate release of antibiotics in the environment through un-metabolized form create a scenario for the emergence of virulent pathogens and MDR bugs in the surroundings. Mechanisms underlying the spread of resistance include horizontal and vertical gene transfers causing the transmittance of MDR genes packed in different host, which pass across different food webs. Several controlling agents have been used for combating pathogens; however, the use of lytic bacteriophages proves to be one of the most eco-friendly due to their specificity, killing only target bacteria without damaging the indigenous beneficial flora of the habitat. Phages are part of the natural microflora present in different environmental niches and are remarkably stable in the environment. Diverse range of phage products, such as phage enzymes, phage peptides having antimicrobial properties, and phage cocktails also have been used to eradicate pathogens along with whole phages. Recently, the ability of phages to control pathogens has extended from the different areas of medicine, agriculture, aquaculture, food industry, and into the environment. To avoid the arrival of pre-antibiotic epoch, phage intervention proves to be a potential option to eradicate harmful pathogens generated by the MDR gene flow which are uneasy to cure by conventional treatments.

Purification and identification of Bacillus subtilis SPB1 lipopeptide biosurfactant exhibiting antifungal activity against Rhizoctonia bataticola and Rhizoctonia solani

This study reports the potential of a soil bacterium, Bacillus subtilis strain SPB1, to produce lipopeptide biosurfactants. Firstly, the crude lipopeptide mixture was tested for its inhibitory activity against phytopathogenic fungi. A minimal inhibitory concentration (MIC), an inhibitory concentration at 50% (IC50%), and an inhibitory concentration at 90% (IC90%) values were determined to be 0.04, 0.012, and 0.02 mg/ml, respectively, for Rhizoctonia bataticola with a fungistatic mode of action. For Rhizoctonia solani, a MIC, an IC50%, and IC90% values were determined to be 4, 0.25, and 3.3 mg/ml, respectively, with a fungicidal mode of action. For both of the fungi, a loss of sclerotial integrity, granulation and fragmentation of hyphal mycelia, followed by hyphal shriveling and cell lysis were observed with the treatment with SPB1 biosurfactant fraction. After extraction, separation, and purification, different lipopeptide compounds were identified in the culture filtrate of strain SPB1. Mass spectroscopic analysis confirmed the presence of different lipopeptide compounds consisting of surfactin isoforms with molecular weights of 1007, 1021, and 1035 Da; iturin isoforms with molecular weights of 1028, 1042, and 1056 Da; and fengycin isoforms with molecular weights of 1432 and 1446 Da. Two new clusters of lipopeptide isoforms with molecular weights of 1410 and 1424 Da and 973 and 987 Da, respectively, were also detected. This study reported the ability of a B. subtilis strain to co-produce lipopeptide isoforms with potential use as antifungal compounds.