Isolation and partial characterization of an antifungal protein produced by Bacillus licheniformis BS-3

Establishment of the CRISPR-Cpf1 gene editing system in Bacillus licheniformis and multiplexed gene knockout

Bacillus licheniformis is a significant industrial microorganism. Traditional gene editing techniques relying on homologous recombination often exhibit low efficiency due to their reliance on resistance genes. Additionally, the established CRISPR gene editing technology, utilizing Cas9 endonuclease, faces challenges in achieving simultaneous knockout of multiple genes. To address this limitation, the CRISPR-Cpf1 system has been developed, enabling multiplexed gene editing across various microorganisms. Key to the efficient gene editing capability of this system is the rigorous screening of highly effective expression elements to achieve conditional expression of protein Cpf1. In this study, we employed mCherry as a reporter gene and harnessed P mal for regulating the expression of Cpf1 to establish the CRISPR-Cpf1 gene editing system in Bacillus licheniformis. Our system achieved a 100 % knockout efficiency for the single gene vpr and up to 80 % for simultaneous knockout of the double genes epr and mpr. Furthermore, the culture of a series of protease-deficient strains revealed that the protease encoded by aprE contributed significantly to extracellular enzyme activity (approximately 80 %), whereas proteases encoded by vpr, epr, and mpr genes contributed to a smaller proportion of extracellular enzyme activity. These findings provide support for effective molecular modification and metabolic regulation in industrial organisms.

The Prospect of Hydrolytic Enzymes from Bacillus Species in the Biological Control of Pests and Diseases in Forest and Fruit Tree Production

Plant diseases and insect pest damage cause tremendous losses in forestry and fruit tree production. Even though chemical pesticides have been effective in the control of plant diseases and insect pests for several decades, they are increasingly becoming undesirable due to their toxic residues that affect human life, animals, and the environment, as well as the growing challenge of pesticide resistance. In this study, we review the potential of hydrolytic enzymes from Bacillus species such as chitinases, β-1,3-glucanases, proteases, lipases, amylases, and cellulases in the biological control of phytopathogens and insect pests, which could be a more sustainable alternative to chemical pesticides. This study highlights the application potential of the hydrolytic enzymes from different Bacillus sp. as effective biocontrol alternatives against phytopathogens/insect pests through the degradation of cell wall/insect cuticles, which are mainly composed of structural polysaccharides like chitins, β-glucans, glycoproteins, and lipids. This study demonstrates the prospects for applying hydrolytic enzymes from Bacillus sp. as effective biopesticides in forest and fruit tree production, their mode of biocidal activity and dual antimicrobial/insecticidal potential, which indicates a great prospect for the simultaneous biocontrol of pests/diseases. Further research should focus on optimizing the production of hydrolytic enzymes, and the antimicrobial/insecticidal synergism of different Bacillus sp. which could facilitate the simultaneous biocontrol of pests and diseases in forest and fruit tree production.

Bacillus licheniformis reduces mortality, improves symptoms, and controls residual pathogenicity in juvenile sea cucumbers Apostichopus japonicus infected with skin ulceration syndrome

Mass mortality caused by skin ulceration syndrome (SUS) is the bottle-neck for the sustainable aquaculture of the sea cucumber Apostichopus japonicus. In the present study, probiotic Bacillus licheniformis (0.25 × 109 CFU/g) was used as the treatment for A. japonicus infected with the SUS that caused by Vibrio harveyi. We found that B. licheniformis significantly reduced the number of infected sea cucumbers 5 days and 7 days after the treatment (group B), compared to those without B. licheniformis treatment (group C) (P < 0.001; P < 0.001). Further, the sea cucumbers fed B. licheniformis had significantly lower mortality at the end of the experiment (<10%) than that of those without the B. licheniformis treatment (>60%) (P < 0.001). These results suggest that the treatment of B. licheniformis is an effective method to reduce the mass mortality resulted from SUS in sea cucumber aquaculture. Further, 3-5 days of treatment significantly improved the adverse symptoms of SUS on the physiology and behavior of sea cucumbers, including the righting behavior, adhesion behavior, food consumption, fecal output and mobility. This indicates B. licheniformis treatment has the advantage in the recovery of sea cucumbers after SUS. Moreover, there was no significant difference observed in the physiology and behavior of sea cucumbers between the SUS infected sea cucumbers after the 7-day treatment of B. licheniformis and the healthy individuals. SUS infected sea cucumbers effectively returned to a stage of normalcy. Further, we found a significantly lower infected rate in sea cucumbers exposed to the culture water of group B (∼5%) than that of those in exposure to the culture water of group C (∼60%). This indicates that the treatment of B. licheniformis efficiently controls the residual pathogenicity of SUS in culture water. The present study demonstrated the effectiveness of B. licheniformis treatment as an environmentally friendly approach to reducing mortality, improving symptoms, and controlling residual pathogenicity in sea cucumber aquaculture.

Bacillus licheniformis: A Producer of Antimicrobial Substances, including Antimycobacterials, Which Are Feasible for Medical Applications

Bacillus licheniformis produces several classes of antimicrobial substances, including bacteriocins, which are peptides or proteins with different structural composition and molecular mass: ribosomally synthesized by bacteria (1.4-20 kDa), non-ribosomally synthesized peptides and cyclic lipopeptides (0.8-42 kDa) and exopolysaccharides (>1000 kDa). Different bacteriocins act against Gram-positive or Gram-negative bacteria, fungal pathogens and amoeba cells. The main mechanisms of bacteriocin lytic activity include interaction of peptides with membranes of target cells resulting in structural alterations, pore-forming, and inhibition of cell wall biosynthesis. DNase and RNase activity for some bacteriocines are also postulated. Non-ribosomal peptides are synthesized by special non-ribosomal multimodular peptide synthetases and contain unnatural amino acids or fatty acids. Their harmful effect is due to their ability to form pores in biological membranes, destabilize lipid packaging, and disrupt the peptidoglycan layer. Lipopeptides, as biosurfactants, are able to destroy bacterial biofilms. Secreted polysaccharides are high molecular weight compounds, composed of repeated units of sugar moieties attached to a carrier lipid. Their antagonistic action was revealed in relation to bacteria, viruses, and fungi. Exopolysaccharides also inhibit the formation of biofilms by pathogenic bacteria and prevent their colonization on various surfaces. However, mechanism of the harmful effect for many secreted antibacterial substances remains unknown. The antimicrobial activity for most substances has been studied in vitro only, but some substances have been characterized in vivo and they have found practical applications in medicine and veterinary. The cyclic lipopeptides that have surfactant properties are used in some industries. In this review, special attention is paid to the antimycobacterials produced by B. licheniformis as a possible approach to combat multidrug-resistant and latent tuberculosis. In particular, licheniformins and bacitracins have shown strong antimycobacterial activity. However, the medical application of some antibacterials with promising in vitro antimycobacterial activity has been limited by their toxicity to animals and humans. As such, similar to the enhancement in the antimycobacterial activity of natural bacteriocins achieved using genetic engineering, the reduction in toxicity using the same approach appears feasible. The unique capability of B. licheniformis to synthesize and produce a range of different antibacterial compounds means that this organism can act as a natural universal vehicle for antibiotic substances in the form of probiotic cultures and strains to combat various types of pathogens, including mycobacteria.

Antifungal Activity and Possible Mechanism of Bacillus amyloliquefaciens FX2 Against the Postharvest Apple Ring Rot Pathogen

Botryosphaeria dothidea-induced apple ring rot is one of the most serious postharvest diseases in apple production. In our preliminary work, we isolated a bacterial strain (FX2) from an infested apple orchard. Here, we confirmed the strong antifungal activity of FX2 on B. dothidea. Through phylogenetic analysis and morphological observations, we identified FX2 as a Bacillus amyloliquefaciens strain. We also found that 10% cell-free supernatant (CFS) of FX2 significantly affected mycelial growth and morphology and almost completely inhibited spore germination and germ tube elongation in B. dothidea. Furthermore, 10% CFS damaged the cell ultrastructure, resulting in a remarkable increase in cellular leakage in B. dothidea mycelia. Thus, CFS has the potential to effectively reduce in vivo B. dothidea infection, reduced lesion diameters to 64.7% compared with the control group, and reduced disease incidence by 15%. Finally, ultrafiltration, desalting chromatography, and anion exchange chromatography showed that the antifungal constituents in CFS are composed mainly of antifungal proteins. We further characterized these potential antifungal proteins via liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Herein, we provide novel insights into the antifungal mechanisms of B. amyloliquefaciens FX2, and we highlight its potential as a novel biocontrol agent for controlling postharvest apple ring rot.

Broad-spectrum resistance mechanism of serine protease Sp1 in Bacillus licheniformis W10 via dual comparative transcriptome analysis

Antagonistic microorganisms are considered to be the most promising biological controls for plant disease. However, they are still not as popular as chemical pesticides due to complex environmental factors in the field. It is urgent to exploit their potential genetic characteristics and excellent properties to develop biopesticides with antimicrobial substances as the main components. Here, the serine protease Sp1 isolated from the Bacillus licheniformis W10 strain was confirmed to have a broad antifungal and antibacterial spectrum. Sp1 treatment significantly inhibited fungal vegetative growth and damaged the structure of hyphae, in accordance with that caused by W10 strain. Furthermore, Sp1 could activate the systemic resistance of peach twigs, fruits and tobacco. Dual comparative transcriptome analysis uncovered how Sp1 resisted the plant pathogenic fungus Phomopsis amygdali and the potential molecular resistance mechanisms of tobacco. In PSp1 vs. P. amygdali, RNA-seq identified 150 differentially expressed genes (DEGs) that were upregulated and 209 DEGs that were downregulated. Further analysis found that Sp1 might act on the energy supply and cell wall structure to inhibit the development of P. amygdali. In TSp1 vs. Xanthi tobacco, RNA-seq identified that 5937 DEGs were upregulated and 2929 DEGs were downregulated. DEGs were enriched in the metabolic biosynthesis pathways of secondary metabolites, plant hormone signal transduction, plant–pathogen interactions, and MAPK signaling pathway–plant and further found that the genes of salicylic acid (SA) and jasmonic acid (JA) signaling pathways were highly expressed and the contents of SA and JA increased significantly, suggesting that systemic resistance induced by Sp1 shares features of SAR and ISR. In addition, Sp1 might induce the plant defense responses of tobacco. This study provides insights into the broad-spectrum resistance molecular mechanism of Sp1, which could be used as a potential biocontrol product.

Biotechnological applications of Bacillus licheniformis

Bacillus licheniformis is a Gram positive spore-forming bacterial species of high biotechnological interest with numerous present and potential uses, including the production of bioactive compounds that are applied in a wide range of fields, such as aquaculture, agriculture, food, biomedicine, and pharmaceutical industries. Its use as an expression vector for the production of enzymes and other bioproducts is also gaining interest due to the availability of novel genetic manipulation tools. Furthermore, besides its widespread use as a probiotic, other biotechnological applications of B. licheniformis strains include: bioflocculation, biomineralization, biofuel production, bioremediation, and anti-biofilm activity. Although authorities have approved the use of B. licheniformis as a feed additive worldwide due to the absence of toxigenic potential, some probiotics containing this bacterium are considered unsafe due to the possible transference of antibiotic resistance genes. The wide variability in biological activities and genetic characteristics of this species makes it necessary to establish an exact protocol for describing the novel strains, in order to evaluate its biotechnological potential.

Isolation, purification, gene cloning and expression of antifungal protein from Bacillus amyloliquefaciens MG-3

The antifungal protein MG-3A was isolated from Bacillus amyloliquefaciens MG-3, and was purified and identified. The results showed that antifungal protein MG-3A was likely a serine protease with a molecular weight of ~48 kDa. The serine protease exhibited a broad antifungal spectrum and effectively extended the shelf-life of loquat fruit up to 25 d. The antifungal protein MG-3A showed good stabilities to temperature, pH and protease K. Primers were designed according to the mass spectrum of antifungal protein and the comparison with proteins in the NCBI database. The serine protease gene MG-3A from B. amyloliquefaciens genome was isolated and cloned using PCR. The prokaryotic expression plasmid pET28a-MG-3A was constructed and used to express the antimicrobial protein in vitro. The SDS-PAGE results showed that the recombinant protein expressed in Escherichia coli BL21 (DE3) was highly soluble. Affinity chromatography was used to purify the recombinant protein and its antifungal activity was evaluated.

Biocontrol and Action Mechanism of Bacillus amyloliquefaciens and Bacillus subtilis in Soybean Phytophthora Blight

With the improper application of fungicides, Phytophthora sojae begins to develop resistance to fungicides, and biological control is one of the potential ways to control it. We screened two strains of Bacillus; Bacillus amyloliquefaciens JDF3 and Bacillus subtilis RSS-1, which had an efficient inhibitory effect on P. sojae. They could inhibit mycelial growth, the germination of the cysts, and the swimming of the motile zoospores. To elucidate the response of P. sojae under the stress of B. amyloliquefaciens and B. subtilis, and the molecular mechanism of biological control, comparative transcriptome analysis was applied. Transcriptome analysis revealed that the expression gene of P. sojae showed significant changes, and a total of 1616 differentially expressed genes (DEGs) were detected. They participated in two major types of regulation, namely "specificity" regulation and "common" regulation. They might inhibit the growth of P. sojae mainly by inhibiting the activity of ribosome. A pot experiment indicated that B. amyloliquefaciens and B. subtilis enhanced the resistance of soybean to P. sojae, and their control effects of them were 70.7% and 65.5%, respectively. In addition, B. amyloliquefaciens fermentation broth could induce an active oxygen burst, NO production, callose deposition, and lignification. B. subtilis could also stimulate the systemic to develop the resistance of soybean by lignification, and phytoalexin.

Immunomodulatory activities of proteins from Astragalus membranaceus waste

BACKGROUND

Astragalus membranaceus is a traditional Chinese medicine that has a long history of medical applications. It is of interest to investigate the functional components of A. membranaceus waste with regard to its development and utilization and increasing resource utilization.

RESULTS

The protein AMWP was isolated from the A. membranaceus waste. This protein was further purified by DEAE-cellulose-52 chromatography and Sephadex G-200 size-exclusion chromatography to obtain three fractions, named AMWPDG2, AMWPDG4 and AMWPDG6. Then, their immunomodulatory activities were evaluated by using cell model experiments. The results indicated that the protein fractions could significantly increase the proliferation of splenic lymphocytes, peritoneal macrophages and bone-marrow-derived cells (BMDCs). AMWPDG2 showed the highest immunocompetence. AMWPDG2, AMWPDG4 and AMWPDG6 not only significantly improved the phagocytosis and immunomodulatory factors (interleukin (IL)-6, tumor necrosis factor-α, nitric oxide, hydrogen peroxide) secretion of peritoneal macrophages, but also promoted the expression of inflammatory cytokines (IL-6, IL-12 p40, IL-1β, IL-1α) and chemokines (CXCL1, CCL3) in BMDCs.

CONCLUSION

Taken together, these results indicated that three protein fractions from the A. membranaceus waste might be a potential natural immunomodulator. Moreover, it also provided the theoretical basis for further researching the mechanism of AMWPDG2, AMWPDG4 and AMWPDG6 on improving the immune response. © 2019 Society of Chemical Industry.

Biosynthesis of Low Molecular Weight Antifungal Protein from Aspergillus giganteus in Batch Fermentation and In-Vitro Assay

　In present study, Taguchi's design of experiment L₉ orthogonal array was created using Qualitek-4 software with four most critical factors namely, K₂HPO₄, MgSO₄, CaCl₂ and culture pH. Production of a new intracellular antifungal protein in submerged fermentation was optimized with yield of 0.98±0.1 mg/gram dry cell weight mycelia from Aspergillus giganteus MTCC 8408. The average molecular mass of the purified protein was figured as 5.122 kDa using Electro Spray Ionization-Mass Spectrometry. Scanning electron microscopy was used to correlate the effect of selected factors on fungal cell morphology and its metabolite production. In vitro antifungal susceptibility assay was profiled against Aspergillus niger and minimum inhibitory concentrations were in the range 0.3±0.06 µg/ml. The stronger influencing factors on afp production and mycelial biomass were noted with CaCl₂ and K₂HPO₄ respectively. The validation experiments using optimized conditions confirmed an improvement in afp by 3.86 times with mycelial biomass by 1.52 times, compared to the basal medium. The present statistical optimization study revealed an opportunity to promote economical design at the industrial level for future scale up of effective antifungal agent against systemic aspergillosis as well as possible post harvest loss.

Plipastatin A1 produced by a marine sediment-derived Bacillus amyloliquefaciens SH-B74 contributes to the control of gray mold disease in tomato

Certain Bacillus species have the capacity to produce cyclic lipopeptides and these lipopeptides are promising determinants contributing to the biocontrol of plant diseases. In the current study, a cyclic lipopeptide plipastatin A1 was isolated from the fermentation broth of a marine sediment-derived Bacillus amyloliquefaciens SH-B74 by the combination of solid-phase extraction and reversed-phase high-performance liquid chromatography, and its structure was identified by tandem mass spectrometry, high-resolution electro-spray ionization mass spectrometry, and gas chromatography-mass spectrometry together with nuclear magnetic resonance analysis. Moreover, data from activity evaluation revealed that plipastatin A1 has excellent in vitro activity on the suppression of the conidia germination of B. cinerea, the causal agent of gray mold disease in tomato. Furthermore, plipastatin A1 can successfully decrease the incidence of gray mold disease on tomato leaves at 50 µM concentration. This study indicates that B. amyloliquefaciens SH-B74 appears to be a potentially sustainable pesticide to control gray mold disease in tomato plants, and its cyclic lipopeptide plipastatin A1 plays an important role in the in vitro and in planta biocontrol of B. cinerea.

Exploration, antifungal and antiaflatoxigenic activity of halophilic bacteria communities from saline soils of Howze-Soltan playa in Iran

In the present study, halophilic bacteria communities were explored in saline soils of Howze-Soltan playa in Iran with special attention to their biological activity against an aflatoxigenic Aspergillus parasiticus NRRL 2999. Halophilic bacteria were isolated from a total of 20 saline soils using specific culture media and identified by 16S rRNA sequencing in neighbor-joining tree analysis. Antifungal and antiaflatoxigenic activities of the bacteria were screened by a nor-mutant A. parasiticus NRRL 2999 using visual agar plate assay and confirmed by high-performance liquid chromatography. Among a total of 177 halophilic bacteria belonging to 11 genera, 121 isolates (68.3%) inhibited A. parasiticus growth and/or aflatoxin production. The most potent inhibitory bacteria of the genera Bacillus, Paenibacillus and Staphylococcus were distributed in three main phylogenetic clusters as evidenced by 16S rRNA sequence analysis. A. parasiticus growth was inhibited by 0.7-92.7%, while AFB₁ and AFG₁ productions were suppressed by 15.1-98.9 and 57.0-99.6%, respectively. Taken together, halophilic bacteria identified in this study may be considered as potential sources of novel bioactive metabolites as well as promising candidates to develop new biocontrol agents for managing toxigenic fungi growth and subsequent aflatoxin contamination of food and feed in practice.

Isolation and identification of antifungal peptides from Bacillus amyloliquefaciens W10

Antifungal metabolites produced by Bacillus sp. W10, which was previously isolated from the tomato rhizosphere, were investigated. Strain W10 was identified as Bacillus amyloliquefaciens by analysis of its 16S rDNA and gyrB gene partial sequences. PCR analysis showed the presence of fenB, sfp, and ituD genes, coding for fengycin, surfactin, and iturin, respectively. A novel small antifungal peptide, designated 5240, produced by this strain was isolated by ammonium sulfate precipitation and Superdex 200 gel filtration chromatography. The 5240 peptide was stable at 100 °C for 20 min and remained active throughout a wide pH range (4-10). The antagonistic activity was not affected by protease K and trypsin. The purified 5240 peptide exhibited a broad inhibitory spectrum against various plant pathogenic fungi and was identified as iturin A (C₁₄-C₁₆). Moreover, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry indicated the presence of fengycin A (C₁₄-C₁₅), fengycin B (C₁₆-C₁₇), and surfactin (C₁₃-C₁₆) isoforms in supernatants from strain W10. These results suggest that B. amyloliquefaciens W10 has significant potential as a biocontrol agent.

Isolation and characterization of an antifungal protein from Bacillus licheniformis HS10

Bacillus licheniformis HS10 is a good biocontrol agent against Pseudoperonospora cubensis which caused cucumber downy disease. To identify and characterize the antifungal proteins produced by B.licheniformis HS10, the proteins from HS10 were isolated by using 30-60% ammonium sulfate precipitation, and purified with column chromatography on DEAE Sepharose Fast Flow, RESOURCE Q and Sephadex G-75. And the SDS-PAGE and MALDI-TOF/TOF-MS analysis results demonstrated that the antifungal protein was a monomer with molecular weight of about 55 kDa, identified as carboxypeptidase. Our experiments also showed that the antifungal protein from B. licheniformis HS10 had significantly inhibition on eight different kinds of plant pathogenic fungi, and it was stable with good biological activity at as high as 100°C for 30 min and in pH value ranged from 6 to 10. The biological activity was negatively affected by protease K and 10mM metal cations except Ca(2+).