Probiotic Potential of Bacillus amyloliquefaciens Isolated from Tibetan Yaks

The Tibetan livestock sector is now ailing from many infectious ailments brought on by harmful microorganisms. Therefore, this research aimed to assess the probiotic potential and safety of Bacillus amyloliquefaciens isolated from yaks in the Tibet area to provide upper-edge strain resources for probiotics development. The four strains isolated from the intestine of yaks had been identified as Bacillus amyloliquefaciens after the 16S rRNA sequence. The ethanol, bile salt, and acid tolerance revealed that the isolates had significant tolerance levels. The antibiotics susceptibility assay showed that the strains were sensitive to commonly used antibiotics, while the antibacterial assay prevented the isolates from outperforming five harmful bacteria in terms of antibacterial potency. Moreover, it was evident that strain BA5 had the strongest activity to scavenge hydroxyl radical and reduce power. According to the animal experiment, no apparent pathological change was observed in intestinal tissue sections. Furthermore, the strain had a positive effect on promoting the development of jejunal villi referred to its safety. Therefore, more research is required into the bacteriostatic and antioxidant capabilities of isolates in animal production.

An oxalate decarboxylase-like cupin domain containing protein is involved in imparting acid stress tolerance in Bacillus amyloliquefaciens MBNC

We report here the structural and functional properties of an oxalate decarboxylase (OxDC)-like cupin domain-containing protein of Bacillus amyloliquefaciens MBNC and its role in imparting tolerance to acid stress conditions. Quantitative real-time PCR (qPCR) analysis revealed 32-fold and 20-fold upregulation of the target gene [(OxDC')cupin] under acetic acid stress and hydrochloric acid stress, respectively, indicating its association with the acid stress response. Bacterial cells with targeted inactivation of the (OxDC')cupin gene using the pMUTIN4 vector system showed decreased growth and survival rate in acidic pH, with drastically reduced exopolysaccharide production. In Silico protein-protein interaction studies revealed seven genes (viz. glmS, nagA, nagB, tuaF, tuaF, gcvT, and ykgA) related to cell wall biosynthesis and biofilm production to interact with OxDC-like cupin domain containing protein. While all these seven genes were upregulated in B. amyloliquefaciens MBNC after 6 h of exposure to pH 4.5, the mutant cells containing the inactivated (OxDC')cupin gene displayed significantly lower expression (RQ: 0.001-0.02) (compared to the wild-type cells) in both neutral and acidic pH. Our results indicate that the OxDC-like cupin domain containing protein is necessary for cell wall biosynthesis and biofilm production in Bacillus amyloliquefaciens MBNC for survival in acid-stress conditions.

Bioactivity and genome analysis of Bacillus amyloliquefaciens GL18 isolated from the rhizosphere of Kobresia myosuroides in an alpine meadow

The unique eco-environment of the Qinghai-Tibet Plateau breeds abundant microbial resources. In this research, Bacillus amyloliquefaciens GL18, isolated from the rhizosphere of Kobresia myosuroides from an alpine meadow, and the antagonistic activity, bacteriostatic hydrolase activity, and low temperature, salt, and drought resistance of it were determined and analysed. The seedlings of Avena sativa were root-irrigated using bacteria suspensions (cell concentration 1 × 107 cfu/mL) of GL18, and the growth-promoting effect of GL18 on it was determined under cold, salt and drought stress, respectively. The whole genome of GL18 was sequenced, and its functional genes were analysed. GL18 presented significant antagonistic activity to Fusarium graminearum, Fusarium acuminatum, Fusarium oxysporum and Aspergillus niger (inhibition zone diameter > 17 mm). Transparent zones formed on four hydrolase detection media, indicating that GL18 secreted cellulase, protease, pectinase and β-1,3-glucanase. GL18 tolerated conditions of 10 °C, 11% NaCl and 15% PEG-6000, presenting cold, salt and drought resistance. GL18 improved the cold, salt and drought tolerance of A. sativa and it showed significant growth effects under different stress. The total length of the GL18 genome was 3,915,550 bp, and the number of coding DNA sequence was 3726. Compared with the clusters of orthologous groups of proteins, gene ontology and kyoto encyclopedia of genes and genomes databases, 3088, 2869 and 2357 functional genes were annotated, respectively. GL18 contained gene clusters related to antibacterial substances, functional genes related to the synthesis of plant growth-promoting substances, and encoding genes related to stress resistance. This study identified an excellent Bacillus strain and provided a theoretical basis for improving stress resistance and promoting the growth of herbages under abiotic stress.

Bacillus amyloliquefaciens A-1 inhibiting fungal spoilage in agricultural products is improved by metabolic engineering of enhancing surfactin yield

Fungi and subsequent mycotoxins contamination in agricultural products have caused enormous losses and great harm to human and animal health. Biological control has attracted the attention of researchers due to its advantages, including mild conditions, low cost, high efficiency and low nutrient loss. In this study, a newly isolated strain Bacillus amyloliquefaciens A-1 (A-1), was screened for its ability to inhibit the growth and Aflatoxin B1 (AFB1) production of Aspergillus flavus NRRL 3357. Electron microscopy results revealed that mycelium and conidia of A. flavus were destroyed by A-1, affecting hyphae, cell walls, cell membranes and organelles. RNA-seq analysis indicated disturbance in gene expression profiles of A. flavus, including amino acid degradation and starch and sucrose metabolism pathways. Importantly, the biosynthesis of AFB1 was significantly inhibited by the down-regulation of key regulatory genes, aflR and aflS, and the simultaneous down-regulation of most structural genes. Genome analysis predicted six secondary metabolites biosynthetic gene clusters. Then, four surfactin synthesized by cluster C were identified as the main active substance of A-1 using HPLC-Q-TOF-MS. The addition of alanine, threonine, Fe2+ increased surfactin production. Notably, the overexpression of comX also improved surfactin production. The vivo test results indicated that A-1 could significantly inhibit the decay of pear by Aspergillus westerdijkiae, and the mildew of maize and peanuts. Especially, the overexpression of comX in A-1 could enhance the inhibitory activity. In conclusion, the inhibition mechanism of A-1 was revealed, and comX was found can improve the production of surfactin and subsequent activities, which provides the scientific basis for the development of biocontrol agents to reduce spoilage in agricultural products.

Identification and investigation of the effects of N-acetylmuramoyl-L-alanine amidase in Bacillus amyloliquefaciens for the cell lysis and heterologous protein production

Bacillus amyloliquefaciens (BA) is considered as an important industrial strain for heterologous proteins production. However, its severe autolytic behavior leads to reduce the industrial production capacity of the chassis cells. In this study, we aimed to evaluate the autolysis of N-acetylmuranyl-L-alanine amidase in BA TCCC11018, and further slowed down the cell lysis for improved the heterologous protein production by a series of modifications. Firstly, we identified six N-acetylmuramic acid-L-alanines by bioinformatics, and analyzed the transcriptional levels at different culture time points by transcriptome and quantitative real-time PCR. Then, by establishing an efficient CRISPR-nCas9 gene editing method, N-acetylmuramic acid-L-alanine genes were knocked out or overexpressed to verify its effect on cell lysis. Then, by single or tandem knockout N-acetylmuramic acid-L-alanines, it was determined that the reasonable modification of LytH and CwlC1 can slow down cell lysis. After 48 h of culture, the autolysis rate of the mutant strain BA ΔlytH-cwlC1 decreased by 4.83 %, and the amylase activity reached 176 U/mL, which was 76.04 % higher than that of the control strain BA Δupp. The results provide a reference for mining the functional characteristics of autolysin in Bacillus spp., and provide from this study reveal valuable insights delaying the cell lysis and increasing heterologous proteins production.

CRISPR-dCpf1 mediated whole genome crRNA inhibition library for high-throughput screening of growth characteristic genes in Bacillus amyloliquefaciens LB1ba02

Bacillus amyloliquefaciens LB1ba02 is generally recognized as food safe (GRAS) microbial host and important enzyme-producing strain in the industry. However, autolysis affects the growth of bacteria, further affecting the yield of target products. Besides, the restriction-modification system, existed in B. amyloliquefaciens LB1ba02, results in a low transformation efficiency, which further leads to a lack of high-throughput screening tools. Here, we constructed a genome-wide crRNA inhibition library based on the CRISPR/dCpf1 system and high-throughput screening of related genes affecting the cell growth and autolysis using flow cytometry in B. amyloliquefaciens LB1ba02. The whole genome crRNA library was first validated for resistance to the toxic chemical 5-fluorouracil, and then used for validation of essential genes. In addition, seven gene loci (oppD, flil, tuaA, prmA, sigO, hslU, and GE03231) that affect the growth characteristics of LB1ba02 were screened. Among them, the Opp system had the greatest impact on growth. When the expression of operon oppA-oppB-oppC-oppD-oppF was inhibited, the cell growth difference was most significant. Inhibition of other sites could also promote rapid growth of bacteria to varying degrees; however, inhibition of GE03231 site accelerated cell autolysis. Therefore, the whole genome crRNA inhibition library is well suited for B. amyloliquefaciens LB1ba02 and can be further applied to high-throughput mining of other functional genes.

Siderophore-producing Bacillus amyloliquefaciens BM3 mitigate arsenic contamination and suppress Fusarium wilt in brinjal plants

AIM

Arsenic contamination in agricultural soils poses a serious health risk for humans. Bacteria that produce siderophores, primarily for iron acquisition, can be relevant in combating arsenic toxicity in agricultural soils and simultaneously act as biocontrol agents against plant diseases. We evaluated the arsenic bioremediation and biocontrol potential of the rhizosphere isolate Bacillus amyloliquefaciens BM3 and studied the interaction between the purified siderophore bacillibactin and arsenic.

METHODS AND RESULTS

BM3 showed high arsenic resistance [MIC value 475 and 24 mM against As(V) and As(III), respectively] and broad spectrum in-vitro antagonism against several phytopathogenic fungi. BM3 was identified by biochemical characterization and 16S rRNA gene sequencing. Scanning electron microscopy (SEM) analysis revealed increased cell size of BM3 when grown in presence of sub-lethal arsenic concentrations. Bioremediation assays showed a 74% and 88.1% reduction in As(V) and As(III) concentrations, respectively. Genetic determinants for arsenic resistance (arsC and aoxB) and antifungal traits (bacAB and chiA) were detected by PCR. Arsenic chelating ability of bacillibactin, the siderophore purified from culture filtrate of BM3 and identified through spectroscopic data analysis, was observed in CAS assay and fluorescence spectrometry. In-vivo application of talc-based formulation of BM3 in brinjal seedlings showed significant reduction in Fusarium wilt disease.

CONCLUSION

Strain B. amyloliquefaciens BM3 may be useful in arsenic bioremediation and may be considered for large field trials as an alternative to chemical fungicides by inhibiting soil borne pathogens.

Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants

While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.

Whole genome analysis of Bacillus amyloliquefaciens TA-1, a promising biocontrol agent against Cercospora arachidicola pathogen of early leaf spot in Arachis hypogaea L

BACKGROUND

Early leaf spot disease, caused by Cercospora arachidicola, is a devastating peanut disease that has severely impacted peanut production and quality. Chemical fungicides pollute the environment; however, Bacillus bacteria can be used as an environmentally friendly alternative to chemical fungicides. To understand the novel bacterial strain and unravel its molecular mechanism, De novo whole-genome sequencing emerges as a rapid and efficient omics approach.

RESULTS

In the current study, we identified an antagonistic strain, Bacillus amyloliquefaciens TA-1. In-vitro assay showed that the TA-1 strain was a strong antagonist against C. arachidicola, with an inhibition zone of 88.9 mm. In a greenhouse assay, results showed that the TA-1 strain had a significant biocontrol effect of 95% on peanut early leaf spot disease. De novo whole-genome sequencing analysis, shows that strain TA-1 has a single circular chromosome with 4172 protein-coding genes and a 45.91% guanine and cytosine (GC) content. Gene function was annotated using non-redundant proteins from the National Center for Biotechnology Information (NCBI), Swiss-Prot, the Kyoto Encyclopedia of Genes and Genomes (KEGG), clusters of orthologous groups of proteins, gene ontology, pathogen-host interactions, and carbohydrate-active enZYmes. antiSMASH analysis predicted that strain TA-1 can produce the secondary metabolites siderophore, tailcyclized peptide, myxochelin, bacillibactin, paenibactin, myxochelin, griseobactin, benarthin, tailcyclized, and samylocyclicin.

CONCLUSION

The strain TA-1 had a significant biological control effect against peanut early leaf spot disease in-vitro and in greenhouse assays. Whole genome analysis revealed that, TA-1 strain belongs to B. amyloliquefaciens and could produce the antifungal secondary metabolites.

Identifying, Characterizing, and Engineering a Phenolic Acid-Responsive Transcriptional Factor from Bacillus amyloliquefaciens

Transcriptional factors-based biosensors are commonly used in metabolic engineering for inducible control of gene expression and related applications such as high-throughput screening and dynamic pathway regulations. Mining for novel transcriptional factors is essential for expanding the usability of these toolsets. Here, we report the identification, characterization, and engineering of a phenolic acid responsive regulator PadR from Bacillus amyloliquefaciens (BaPadR). This BaPadR-based biosensor system showed a unique ligand preference and exhibited a high output strength comparable to that of commonly used inducible expression systems. Through engineering the DNA binding region of BaPadR, we further enhanced the dynamic range of the biosensor system. The DNA sequences that are responsible for BaPadR recognition were located by promoter truncation and hybrid promoter building. To further explore the tunability of the sensor system, base substitutions were performed on the BaPadR binding region of the phenolic acid decarboxylase promoter (PpadC) and the hybrid promoter. This novel biosensor system can serve as a valuable tool in future synthetic biology applications.

Transcription Factor Spo0A Regulates the Biosynthesis of Difficidin in Bacillus amyloliquefaciens

Bacillus amyloliquefaciens WH1 produces multiple antibiotics with antimicrobial activity and can control bacterial wilt disease caused by Ralstonia solanacearum. Antibacterial substances produced by WH1 and the regulation mechanism are unknown. In this study, it was found that difficidin, and to a minor extent bacillibactin, exhibited antibacterial activity against R. solanacearum. Lipopeptides, macrolactin, bacillaene, and bacilysin had no antibacterial activity. Ferric iron uptake transcriptional regulator Fur bound the promoter region of the dhb gene cluster of bacillibactin biosynthesis. Mutant Δfur showed a higher bacillibactin production and its antibacterial activity increased by 27% than wild-type WH1. Difficidin inhibited R. solanacearum growth and disrupted the integrity of the cells. Lack of transcription factor Spo0A abolished difficidin biosynthesis. Spo0A bound the promoter region of the dfn gene cluster of difficidin biosynthesis. Changing phosphorylation levels of Spo0A via deletion of phosphatase gene spo0E and histidine kinases genes kinA and kinD affected the biosynthesis of difficidin. Deletion of spo0E increased the phosphorylation level of Spo0A and consequently improved the difficidin production. The antibacterial activity of mutant Δspo0E and ΔkinA increased by 12% and 19%. The antibacterial activity of mutant ΔkinD decreased by 28%. Collectively, WH1 produced difficidin to disrupt the cell of R. solanacearum and secreted siderophore bacillibactin to compete for ferric iron. Spo0A regulated difficidin biosynthesis. Spo0A regulates quorum-sensing responses and controls the biosynthesis of secondary metabolites in B. amyloliquefaciens. This study has important findings in the regulation mechanism of antibiotic synthesis and helps to improve antibiotic yield in Bacillus. IMPORTANCE Pathogen R. solanacearum causes bacterial wilt disease in many crops. There is no chemical bactericide that can control bacterial wilt disease. It is vital to find antagonistic microorganisms and antibacterial substances that can efficiently control bacterial wilt disease. B. amyloliquefaciens WH1 could inhibit the growth of R. solanacearum. Via genetic mutation, it was found that difficidin and to a minor extent bacillibactin produced by WH1 acted efficiently against R. solanacearum. The transcription factor Spo0A regulated the synthesis of difficidin. Phosphorylation of Spo0A affected the production of difficidin. Increasing the phosphorylation level of Spo0A improved the difficidin production and antibacterial activity. In-depth analysis of the regulation mechanism of antibiotic difficidin is meaningful for enhancing the control efficiency of WH1. B. amyloliquefaciens WH1 and the antibacterial substances have vast application potential in controlling bacterial wilt disease.

Improving thermostability of Bacillus amyloliquefaciens alpha-amylase by multipoint mutations

The medium-temperature alpha-amylase of Bacillus amyloliquefaciens is widely used in the food and washing process. Enhancing the thermostability of alpha-amylases and investigating the mechanism of stability are important for enzyme industry development. The optimal temperature and pH of the wild-type BAA and mutant MuBAA (D28E/V118A/S187D/K370 N) were all 60 °C and 6.0, respectively. The mutant MuBAA showed better thermostability at 50 °C and 60 °C, with a specific activity of 206.61 U/mg, which was 99.1% greater than that of the wild-type. By analyzing predicted structures, the improving thermostability of the mutant MuBAA was mainly related to enhanced stabilization of a loop region in domain B via more calcium-binding sites and intramolecular interactions around Asp187. Furthermore, additional intramolecular interactions around sites 28 and 370 in domain A were also beneficial for improving thermostability. Additionally, the decrease of steric hindrance at the active cavity increased the specific activity of the mutant MuBAA. Improving the thermostability of BAA has theoretical reference values for the modification of alpha-amylases.

Mutualistic microbial community of Bacillus amyloliquefaciens and recombinant Yarrowia lipolytica co-produced lipopeptides and fatty acids from food waste

Bioconversion is an important method for transforming food waste (FW) into high value-added products, rendering it harmless, and recycling resources. An artificial microbial consortium (AMC) was constructed to produce FW-based lipopeptides in order to investigate the strategy of FW bioconversion into value-added products. Exogenous fatty acids as a precursor significantly improved the lipopeptide production of Bacillus amyloliquefaciens HM618. To enhance fatty acid synthesis and efflux in AMC, the recombinant Yarrowia lipolytica YL21 (strain YL21) was constructed by screening 12 target genes related to fatty acids to replace exogenous fatty acids in order to improve lipopeptide production. The levels of fengycin, surfactin, and iturin A in the AMC of strains HM618 and YL21 reached 76.19, 192.80, and 31.32 mg L^-1, increasing 7.24-, 12.13-, and 3.23-fold compared to the results from the pure culture of strain HM618 in flask with Landy medium, respectively. Furthermore, free fatty acids were almost undetectable in the co-culture of strains HM618 and YL21, although its level was around 1.25 g L^-1 in the pure culture of strain YL21 with Landy medium. Interestingly, 470.24 mg L^-1 of lipopeptides and 18.11 g L^-1 of fatty acids were co-produced in this AMC in a bioreactor with FW medium. To our knowledge, it is the first report of FW biotransformation into co-produce of lipopeptides and fatty acids in the AMC of B. amyloliquefaciens and Y. lipolytica. These results provide new insights into the biotransformation potential of FW for value-added co-products by AMC.

Bacillus amyloliquefaciens PMB05 Increases Resistance to Bacterial Wilt by Activating Mitogen-Activated Protein Kinase and Reactive Oxygen Species Pathway Crosstalk in Arabidopsis thaliana

Bacterial wilt caused by Ralstonia solanacearum can infect many crops, causing significant losses worldwide. The use of beneficial microorganisms is considered a feasible method for controlling this disease. Our previous study showed that Bacillus amyloliquefaciens PMB05 can control bacterial wilt through intensifying immune signals triggered by a pathogen-associated molecular pattern (PAMP) from R. solanacearum. It is still uncertain whether induction of the mitogen-activated protein kinase (MAPK) pathway during PAMP-triggered immunity (PTI) is responsible for enhancing disease resistance. To gain more insights on how the presence of PMB05 regulates PTI signaling, its association with the MAPK pathway was assayed. Our results showed that the activation of MPK3/6 and expression of wrky22 upon treatment with the PAMP, PopW, was increased during co-treatment with PMB05. Moreover, the disease resistance conferred by PMB05 to bacterial wilt was abolished in mekk1, mkk5, and mpk6 mutants. To determine the relationship between the MAPK pathway and plant immune signals, the assay on reactive oxygen species (ROS) generation and callose deposition showed that only the ROS generation was strongly reduced in these mutants. Because ROS generation is highly correlated with RbohD, the results revealed that the effects of PMB05 on both PopW-induced ROS generation and disease resistance to bacterial wilt were eliminated in the rbohD mutant, suggesting that the generation of ROS is also required for PMB05-enhanced disease resistance. Taken together, we concluded that the crosstalk between the initiation of ROS generation and further activation of the MAPK pathway is necessary when PMB05 is used to improve disease resistance to bacterial wilt. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Remodeling Bacillus amyloliquefaciens Cell Wall Rigidity to Reduce Cell Lysis and Increase the Yield of Heterologous Proteins

Bacillus amyloliquefaciens has great potential as a host for heterologous protein production, but its severe autolytic behavior has precluded its industrial application to date. Because d,l-endopeptidase activity-guided cell wall rigidity is considered essential for autolysis resistance, we investigated the effects of d,l-endopeptidase genes lytE, lytF, cwlO, and cwlS play on the growth, lysis, and morphology remodeling of B. amyloliquefaciens strain TCCC11018. Individual and combinatorial deletion of lytE, lytF, and cwlS enhanced the cell growth and delayed cell lysis. For the best mutant with the lytF and cwlS double deletion, the viable cell number at 24 h increased by 11.90% and the cell wall thickness at 6 h increased by 25.87%. Transcriptomic and proteomic analyses indicated that the improvement was caused by enhanced peptidoglycan synthesis. With the lytF and cwlS double deletion, the extracellular green fluorescent protein and phospholipase D expression levels increased by 113 and 55.89%, respectively. This work broadens our understanding of the relationship between d,l-endopeptidases and B. amyloliquefaciens cell characteristics, which provides an effective strategy to improve the heterologous protein expression in B. amyloliquefaciens-based cell factories.

Induction of Systemic Resistance to Tobacco mosaic virus in Tomato through Foliar Application of Bacillus amyloliquefaciens Strain TBorg1 Culture Filtrate

The application of microbe-derived products as natural biocontrol agents to boost systemic disease resistance to virus infections in plants is a prospective strategy to make agriculture more sustainable and environmentally friendly. In the current study, the rhizobacterium Bacillus amyloliquefaciens strain TBorg1 was identified based on 16S rRNA, rpoB, and gyrA gene sequences, and evaluated for its efficiency in conferring protection of tomato from infection by Tobacco mosaic virus (TMV). Under greenhouse circumstances, foliar sprays of TBorg1 culture filtrate (TBorg1-CF) promoted tomato growth, lowered disease severity, and significantly decreased TMV accumulation in systemically infected leaves of treated plants relative to untreated controls. TMV accumulation was reduced by 90% following the dual treatment, applied 24 h before and after TMV infection. Significant increases in levels of total soluble carbohydrates, proteins, and ascorbic acid were also found. In addition, a significant rise in activities of enzymes capable of scavenging reactive oxygen species (PPO and POX), as well as decreased levels of non-enzymatic oxidative stress markers (H₂O₂ and MDA) were observed, compared to untreated plants. Enhanced systemic resistance to TMV was indicated by significantly increased transcript accumulation of polyphenolic pathway (C4H, HCT, and CHI) and pathogenesis-related (PR-1 and PR-5) genes. Out of the 15 compounds identified in the GC-MS analysis, 1,2-benzenedicarboxylic acid mono(2-ethylhexyl) ester and phenol, 2,4-bis(1,1-dimethylethyl), as well as L-proline, N-valeryl-, and heptadecyl ester were present in the highest concentrations in the ethyl acetate extract of TBorg1-CF. In addition, significant amounts of n-hexadecanoic acid, pyrrolo [1,2-a] pyrazine-1,4-dione hexahydro-3-(2-methylpropyl)-, nonane, 5-butyl-, and eicosane were also detected. These compounds may act as inducers of systemic resistance to viral infection. Our findings indicate that the newly isolated B. amyloliquefaciens strain TBorg1 could be a potentially useful rhizobacterium for promoting plant growth and a possible source of biocontrol agents for combating plant virus infections.

Integrative analysis of transcriptome and metabolome reveals the mechanism of foliar application of Bacillus amyloliquefaciens to improve summer tea quality (Camellia sinensis)

Bacillus amyloliquefaciens is a promising microbial agent for quality improvement in crops; however, the effects of B. amyloliquefaciens biofertilizers on tea leaf metabolites are relatively unknown. Herein, a combination of metabolome profiling and transcriptome analysis was employed to investigate the effects of foliar spraying with B. amyloliquefaciens biofertilizers on tea leaf quality. The tea polyphenol to amino acid ratio (TP/AA), catechin, and caffeine levels decreased, but theanine level increased in tea leaves after foliar spraying with B. amyloliquefaciens. The differentially accumulated metabolites included flavonoids, phenolic acids, organic acids, amino acids, and carbohydrates. The decrease in catechin was correlated with the catechin/flavonoid biosynthesis pathway. The AMPD gene was highly associated with caffeine content, while the GOGAT gene was associated with theanine accumulation. Foliar spraying with B. amyloliquefaciens biofertilizers may improve summer tea quality. Our findings provide a basis for the application of B. amyloliquefaciens biofertilizers in tea plants and new insights on summer tea leaf resource utilization.

Synergistic Effects of Bacillus amyloliquefaciens SDTB009 and Difenoconazole on Fusarium Wilt of Tomato

Fusarium wilt is a destructive and widespread disease of tomatoes in China, and currently, there are no effective and environmentally friendly control measures. Combining biological control agents with fungicides has become an executable method for disease control. Here, Bacillus amyloliquefaciens SDTB009 showed excellent in vitro antagonistic activity against Fusarium oxysporum and tolerance to high concentrations of difenoconazole (200 mg/liter) in vitro. The combination of SDTB009 and difenoconazole exhibited more effectiveness in mycelial growth inhibition than either treatment alone. Compared with that in the SDTB009 bulk solution in vitro (5.22 g/liter), surfactin titer reached 7.15 g/liter in the 100 mg/liter of difenoconazole-containing medium. Interestingly, the upregulation of 20 genes in the surfactin biosynthesis pathway from 2-fold to 4-fold was observed, explaining the synergistic effect. The SDTB009 combined with varying concentrations of difenoconazole (60, 120, and 150 g a.i./ha) showed a synergistic effect in two consecutive years of field trials. These results show that the integration of difenoconazole with the biocontrol agent B. amyloliquefaciens SDTB009 synergistically increases the control efficacy of the fungicide against tomato Fusarium wilt.

Transcriptome Analysis of Bacillus amyloliquefaciens Reveals Fructose Addition Effects on Fengycin Synthesis

Fengycin is a lipopeptide produced by Bacillus that has a strong inhibitory effect on filamentous fungi; however, its use is restricted due to poor production and low yield. Previous studies have shown that fengycin biosynthesis in B. amyloliquefaciens was found to be significantly increased after fructose addition. This study investigated the effect of fructose on fengycin production and its regulation mechanism in B. amyloliquefaciens by transcriptome sequencing. According to the RNA sequencing data, 458 genes were upregulated and 879 genes were downregulated. Transcriptome analysis results showed that fructose changed the transcription of amino acid synthesis, fatty acid metabolism, and energy metabolism; alterations in these metabolic pathways contribute to the synthesis of fengycin. In an MLF medium (modified Landy medium with fructose), the expression level of the fengycin operon was two-times higher than in an ML medium (modified Landy medium). After fructose was added to B. amyloliquefaciens, the fengycin-synthesis-associated genes were activated in the process of fengycin synthesis.

[Effects of deleting peptidoglycan hydrolase genes on the viable cell counts of Bacillus amyloliquefaciens and the yield of alkaline protease]

In order to explore the effect of peptidoglycan hydrolase on the viable cell counts of Bacillus amyloliquefaciens and the yield of alkaline protease, five peptidoglycan hydrolase genes (lytC, lytD, lytE, lytF and lytG) of B. amyloliquefaciens TCCC111018 were knocked out individually. The viable cell counts of the bacteria and their alkaline protease activities before and after gene deletion were determined. The viable cell counts of the knockout mutants BA ΔlytC and BA ΔlytE achieved 1.67×10⁶ CFU/mL and 1.44×10⁶ CFU/mL respectively after cultivation for 60 h, which were 32.5% and 14.3% higher than that of the control strain BA Δupp. Their alkaline protease activities reached 20 264 U/mL and 17 265 U/mL, respectively, which were 43.1% and 27.3% higher than that of the control strain. The results showed that deleting some of the peptidoglycan hydrolase genes effectively maintained the viable cell counts of bacteria and increased the activity of extracellular enzymes, which may provide a new idea for optimization of the microbial host for production of industrial enzymes.

Improved the lipopeptide production of Bacillus amyloliquefaciens HM618 under co-culture with the recombinant Corynebacterium glutamicum producing high-level proline

The application of antibacterial lipopeptides is limited by high cost and low yield. Herein, the exogenous L-proline significantly improved lipopeptide production by Bacillus amyloliquefaciens HM618. A recombinant Corynebacterium glutamicum producing high levels of proline using genetically modifying proB and putA was used to establish consortium, to improve lipopeptide production of strain HM618. Compared to a pure culture, the levels of iturin A, fengycin, and surfactin in consortium reached 67.75, 39.32, and 37.25 mg L^-1, respectively, an increase of 3.19-, 2.05-, and 1.63-fold over that produced by co-cultures of B. amyloliquefaciens and recombinant C. glutamicum with normal medium. Commercial amylase and recombinant Pichia pastoris with a heterologous amylase gene were used to hydrolyze kitchen waste. A three-strain consortium with recombinant P. pastoris and C. glutamicum increased the lipopeptide production of strain HM618 in medium containing KW. This work provides new strategies to improve lipopeptide production by B. amyloliquefaciens.

Isolation, Purification, and Characterization of a Laccase-Degrading Aflatoxin B1 from Bacillus amyloliquefaciens B10

Aflatoxins, widely found in feed and foodstuffs, are potentially harmful to human and animal health because of their high toxicity. In this study, a strain of Bacillus amyloliquefaciens B10 with a strong ability to degrade aflatoxin B1 (AFB1) was screened; it could degrade 2.5 μg/mL of AFB1 within 96 h. The active substances of Bacillus amyloliquefaciens B10 for the degradation of AFB1 mainly existed in the culture supernatant. A new laccase with AFB1-degrading activity was separated by ammonium sulfate precipitation, diethylaminoethyl (DEAE) and gel filtration chromatography. The results of molecular docking showed that B10 laccase and aflatoxin had a high docking score. The coding sequence of the laccase was successfully amplified from cDNA by PCR and cloned into E. coli. The purified laccase could degrade 79.3% of AFB1 within 36 h. The optimum temperature for AFB1 degradation was 40 °C, and the optimum pH was 6.0–8.0. Notably, Mg²⁺ and dimethyl sulfoxide (DMSO) could enhance the AFB1-degrading activity of B10 laccase. Mutation of the three key metal combined sites of B10 laccase resulted in the loss of AFB1-degrading activity, indicating that these three metal combined sites of B10 laccase play an essential role in the catalytic degradation of AFB1.

Comparative Study of Bacillus amyloliquefaciens X030 on the Intestinal Flora and Antibacterial Activity Against Aeromonas of Grass Carp

Beneficial microorganisms to control bacterial diseases has been widely used in aquaculture, Bacillus amyloliquefaciens (BaX030) as a probiotic feed additive was a commonly biological control method. Added sucrose promoted the growth of BaX030, and the yield of its antibacterial substance macrolactin A was enhanced by 1.46-fold. A total of 2055 proteins were screened through proteomics, with 143 upregulated and 307 downregulated. Differential protein expression analysis and qRT-PCR verification showed that the pentose phosphate pathway and the fatty acid synthesis pathway were upregulated, thereby providing sufficient energy and precursors for the synthesis of macrolactin A. The influence of some potential regulatory factors (SecG, LiaI, MecG and ComG) on macrolactin A was discovered. After grass carp were fed with BaX030, the abundance of probiotics (Fusobacterium, Proteobacteria, Gemmobacter) were higher than the control group, and the abundance of potential pathogenic bacteria (Planctomycetes, Aeromonas) were significantly lower than the control group. The cell and challenge experiments showed that BaX030 can significantly increase the expression of C3 and IL8 in the liver and kidney, which decreases the risk of immune organ disease. Moreover, BaX030 effectively reduced the mortality of grass carp. The results revealed that BaX030 can significantly improve the structure of the intestinal flora, enhance immunity and it is beneficial to the control of grass carp Aeromonas.

Biofilm-overproducing Bacillus amyloliquefaciens P29ΔsinR decreases Pb availability and uptake in lettuce in Pb-polluted soil

In this study, one mutant strain P29ΔsinR with increased biofilm production was constructed from a biofilm-producing Bacillus amyloliquefaciens strain P29. Then, the effect of strain P29 and its biofilm-overproducing mutant strain P29ΔsinR on Pb availability and accumulation in lettuce and the associated mechanisms were characterized in the Pb-contaminated soil. The live strains P29 and P29ΔsinR increased the dry masses of roots and edible tissues by 31-74% compared to the controls. The live strains P29 and P29ΔsinR reduced the Pb uptake in the roots by 36-52% and edible tissues by 24-43%, Pb bioconcentration factor by 36-52%, and rhizosphere soil available Pb content by 12-25%, respectively, compared to the controls. The live strains P29 and P29ΔsinR increased the pH, proportion of biofilm-producing bacteria by 46-154%, contents of polysaccharides by 99-139% and proteins by 32-57%, and gene relative abundances of epsC by 7.1-10.2-fold, tasA by 10.3-10.8-fold, and sipW by 6.5-26.1-fold, which were associated with biofilm formation and Pb adsorption in the rhizosphere soils, respectively, compared to the controls. Furthermore, the mutant strain P29ΔsinR showed higher ability to reduce Pb availability and uptake in lettuce and increase the pH, proportion of biofilm-producing bacteria, polysaccharide and protein contents, and relative abundances of these genes. These results showed that the biofilm-overproducing strain P29ΔsinR induced lower Pb availability and accumulation in the vegetable and more biofilm-producing bacteria, polysaccharide and protein production, and Pb-immobilizing related gene abundances in the Pb-contaminated soil.

Bacillus amyloliquefaciens 35 M can exclusively produce and secrete proteases when cultured in soybean-meal-based medium

Some microbial strains are ideal producers of extracellular enzymes that can be used in various industries. However, in many fields, especially in the pharmaceutical field, these enzymes need to be recovered and purified through multistep processes and tedious procedures before they can be used. The recovery process is difficult and increases the cost of enzyme production. Therefore, reducing purification steps will greatly benefit the utilization of microbial enzymes. The 35 M strain of Bacillus amyloliquefaciens, which has high extracellular protease production, was isolated from a phosphate mine. When cultured in a medium with soybean meal as the main component, the maximum activity of extracellular protease reached 16,992 U/mL. SDS-PAGE showed that there were two main proteins in the fermentation supernatant, with a paucity of other defined protein bands. Mass spectrometry and zymogram analysis showed that the two main bands were two proteases, corresponding to alkaline protease (AprM) and neutral protease (NprM), respectively. Gene cloning, sequencing, and further comparisons were used to confirm AprM and NprM correspond to these proteases from B. amyloliquefaciens. Notably, SDS-PAGE and zymogram analysis showed that NprM had obviously higher catalytic efficiency toward casein than did AprM. Strain 35 M is a promising protease producer with great potential for applications in industrial protease production. Additionally, this study demonstrates strain 35 M may be particularly well suited to use in degrading anti-nutritional factors in soybean meal, so as to improve the nutritional value of soybean meal.

Novel amylomacins from seaweed-associated Bacillus amyloliquefaciens as prospective antimicrobial leads attenuating resistant bacteria

The rise in antibiotic-resistant bacterial strains prompting nosocomial infections drives the search for new bioactive substances of promising antibacterial properties. The surfaces of seaweeds are rich in heterotrophic bacteria with prospective antimicrobial substances. This study aimed to isolate antibacterial leads from a seaweed-associated bacterium. Heterotrophic Bacillus amyloliquefaciens MTCC 12716 associated with the seaweed Hypnea valentiae, was isolated and screened for antimicrobial properties against drug-resistant pathogens. The bacterial crude extract was purified and three novel amicoumacin-class of isocoumarin analogues, 11'-butyl acetate amicoumacin C (amylomacin A), 4'-hydroxy-11'-methoxyethyl carboxylate amicoumacin C (amylomacin B) and 11'-butyl amicoumacin C (amylomacin C) were isolated to homogeneity. The studied amylomacins possessed potential activities against Pseudomonas aeruginosa, vancomycin-resistant Enterococcus faecalis, Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus, and Shigella flexneri with a range of minimum inhibitory concentration values from 0.78 to 3.12 µg/mL, although standard antibiotics ampicillin and chloramphenicol were active at 6.25-25 µg/mL. Noticeably, the amylomacin compound encompassing 4'-hydroxy-11'-methoxyethyl carboxylate amicoumacin C functionality (amylomacin B), displayed considerably greater antagonistic activities against methicillin-resistant S. aureus, vancomycin-resistant E. faecalis, Vibrio parahaemolyticus, Escherichia coli, and K. pneumoniae (minimum inhibitory concentration 0.78 μg/mL) compared to the positive controls and other amylomacin analogues. Antimicrobial properties of the amylomacins, coupled with the presence of polyketide synthase-I/non-ribosomal peptide synthetase hybrid gene attributed the bacterium as a promising source of antimicrobial compounds with pharmaceutical and biotechnological applications.

Overexpression of uracil permease and nucleoside transporter from Bacillus amyloliquefaciens improves cytidine production in Escherichia coli

Cytidine is an important raw material for nucleic acid health food and genetic engineering research. In recent years, it has shown irreplaceable effects in anti-virus, anti-tumor, and AIDS drugs. Its biosynthetic pathway is complex and highly regulated. In this study, overexpression of uracil permease and a nucleoside transporter from Bacillus amyloliquefaciens related to cell membrane transport in Escherichia coli strain BG-08 was found to increase cytidine production in shake flask cultivation by 1.3-fold (0.91 ± 0.03 g/L) and 1.8-fold (1.26 ± 0.03 g/L) relative to that of the original strain (0.70 ± 0.03 g/L), respectively. Co-overexpression of uracil permease and a nucleoside transporter further increased cytidine yield by 2.7-fold (1.59 ± 0.05 g/L) compared with that of the original strain. These results indicate that the overexpressed uracil permease and nucleoside transporter can promote the accumulation of cytidine, and the two proteins play a synergistic role in the secretion of cytidine in Escherichia coli.

Bacillus amyloliquefaciens strain QST713 may contribute to the management of SDHI resistance in Botrytis cinerea

BACKGROUND

Resistance of Botrytis cinerea to SDHI fungicides is widely distributed throughout the world and is associated with mutations in sdhB, differentially affecting mutant sensitivity to several succinate dehydrogenase inhibitors (SDHI) and the fitness of the strains. This study was initiated to test the hypothesis that Bacillus amyloliquefaciens QST713 (Ba QST713) can be utilized in Integrated Pest Management (IPM) programs aiming to control grey mould and eliminate sdhB mutants (H272R/Y, N230I and P225F/H/L).

RESULTS

Protective and curative applications of Ba QST713 on artificially inoculated bean plants resulted in a significant reduction of disease incidence and severity. Competition experiments between sdhB mutants and wild-type isolates conducted either in the absence of any treatment or in the presence of Ba QST713 or fluopyram showed a dominance of sensitive strains over the mutated strains on untreated and Ba QST713-treated plants. Additionally, the efficacy of Ba QST713 in controlling grey mould and its effects on the selection of sdhB mutants was assessed in a greenhouse experiment. The applications of Ba QST713 in alternation schemes with fluopyram provided high control efficacy and reduced SDHI resistance frequency.

CONCLUSIONS

The results of the study showed that Ba QST713 can contribute both to moderate/high levels of grey mould suppression and to a reduction in SDHI resistance frequency. Thus, Ba QST713 can be an efficient tool for SDHI resistance management of B. cinerea in the field. © 2020 Society of Chemical Industry.

Triaging of Culture Conditions for Enhanced Secondary Metabolite Diversity from Different Bacteria

Over the past decade, the one strain many compounds (OSMAC) approach has been established for the activation of biosynthetic gene clusters (BGCs), which mainly encode the enzymes of secondary metabolite (SM) biosynthesis pathways. These BGCs were successfully activated by altering various culture conditions, such as aeration rate, temperature, and nutrient composition. Here, we determined the biosynthetic potential of 43 bacteria using the genome mining tool antiSMASH. Based on the number of BGCs, biological safety, availability of deposited cultures, and literature coverage, we selected five promising candidates: Bacillus amyloliquefaciens DSM7, Corallococcus coralloides DSM2259, Pyxidicoccus fallax HKI727, Rhodococcus jostii DSM44719, and Streptomyces griseochromogenes DSM40499. The bacteria were cultivated under a broad range of OSMAC conditions (nutrient-rich media, minimal media, nutrient-limited media, addition of organic solvents, addition of biotic additives, and type of culture vessel) to fully assess the biosynthetic potential. In particular, we investigated so far scarcely applied OSMAC conditions to enhance the diversity of SMs. We detected the four predicted compounds bacillibactin, desferrioxamine B, myxochelin A, and surfactin. In total, 590 novel mass features were detected in a broad range of investigated OSMAC conditions, which outnumber the predicted gene clusters for all investigated bacteria by far. Interestingly, we detected mass features of the bioactive compounds cyclo-(Tyr-Pro) and nocardamin in extracts of DSM7 and DSM2259. Both compounds were so far not reported for these strains, indicating that our broad OSMAC screening approach was successful. Remarkably, the infrequently applied OSMAC conditions in defined medium with and without nutrient limitation were demonstrated to be very effective for BGC activation and for SM discovery.

Biosynthesis of a Novel Bioactive Metabolite of Spermidine from Bacillus amyloliquefaciens: Gene Mining, Sequence Analysis, and Combined Expression

Spermidine is a biologically active polyamine with extensive application potential in functional foods. However, previously reported spermidine titers by biosynthesis methods are relatively low, which hinders its industrial application. To improve the spermidine titer, key genes affecting the spermidine production were mined to modify Bacillus amyloliquefaciens. Genes of S-adenosylmethionine decarboxylase (speD) and spermidine synthase (speE) from different microorganisms were expressed and compared in B. amyloliquefaciens. Therein, the speD from Escherichia coli and speE from Saccharomyces cerevisiae were confirmed to be optimal for spermidine synthesis, respectively. Gene and amino acid sequence analysis further confirmed the function of speD and speE. Then, these two genes were co-expressed to generate a recombinant strain B. amyloliquefaciens HSAM2(PDspeD-SspeE) with a spermidine titer of 105.2 mg/L, improving by 11.0-fold compared with the control (HSAM2). Through optimization of the fermentation medium, the spermidine titer was increased to 227.4 mg/L, which was the highest titer among present reports. Moreover, the consumption of the substrate S-adenosylmethionine was consistent with the accumulation of spermidine, which contributed to understanding its synthesis pattern. In conclusion, two critical genes for spermidine synthesis were obtained, and an engineering B. amyloliquefaciens strain was constructed for enhanced spermidine production.

New Class of Chitosanase from Bacillus amyloliquefaciens for the Generation of Chitooligosaccharides

Chitooligosaccharides (COS) generated from either chitin (chitin oligosaccharides) or chitosan (chitosan oligosaccharides) have a wide range of applications in agriculture, medicine, and other fields. Here, we report the characterization of a chitosanase from Bacillus amyloliquefaciens (BamCsn) and the importance of a tryptophan (Trp), W204, for BamCsn activity. BamCsn hydrolyzed the chitosan polymer by an endo mode. It also hydrolyzed chitin oligosaccharides and interestingly exhibited transglycosylation activity on chitotetraose and chitopentaose. Mutation of W204, a nonconserved amino acid in chitosanases, to W204A abolished the hydrolytic activity of BamCsn, with a change in the structure that resulted in a decreased affinity for the substrate and impaired the catalytic ability. Phylogenetic analysis revealed that BamCsn could belong to a new class of chitosanases that showed unique properties like transglycosylation, cleavage of chitin oligosaccharides, and the presence of W204 residues, which is important for activity. Chitosanases belonging to the BamCsn class showed a high potential to generate COS from chitinous substrates.

Development of a Strain-Specific Quantification Method for Monitoring Bacillus amyloliquefaciens TF28 in the Rhizospheric Soil of Soybean

Bacillus amyloliquefaciens TF28 can be used to control soybean root disease. To assess its commercial potential as a biocontrol agent, it is necessary to develop a strain-specific quantification method to monitor its colonization dynamics in the rhizospheric soil of soybean under field conditions. Based on genomic comparison with the same species in NCBI databases, a strain-unique gene ukfpg was used as molecular marker to develop strain-specific PCR assay. Among three primer pairs, only primer pairs (F2/R2) could specifically differentiate TF28 from other strains of B. amyloliquefaciens with the detection limit of 10 fg and 100 CFU/g for DNA extracted from pure culture and dry soil, respectively. Then, a colony count coupled with PCR assay was used to monitor the population of TF28 in the rhizospheric soil of soybean in the field. The results indicated that TF28 successfully colonized in the rhizospheric soil of soybean. The colonization population of TF28 changed dynamically within the 120-day growth period with high population at the branching (V6) and flowering stages (R2). This study provides an efficient method to quantitatively monitor the colonization dynamics of TF28 in the rhizospheric soil of soybean in the field and demonstrates the potential of TF28 as a biocontrol agent for commercial development.

Identification of a Bacillus amyloliquefaciens H6 Thioesterase Involved in Zearalenone Detoxification by Transcriptomic Analysis

Zearalenone (ZEA), a nonsteroidal estrogenic mycotoxin produced by Fusarium graminearum, induces hyperestrogenic responses in mammals and can cause reproductive disorders in farm animals. In this study, a transcriptome analysis of Bacillus amyloliquefaciens H6, which was previously identified as a ZEA-degrading bacterium, was conducted with high-throughput sequencing technology, and the differentially expressed genes were subjected to gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses. Among the 16 upregulated genes, BAMF_RS30125 was predicted to be the key gene responsible for ZEA degradation. The protein encoded by BAMF_RS30125 was then expressed in Escherichia coli, and this recombinant protein (named ZTE138) significantly reduced the ZEA content, as determined by the enzyme-linked immunosorbent assay (ELISA) and high-performance liquid chromatography (HPLC), and decreased the proliferating activity of ZEA in MCF-7 cells. What is more, the liquid chromatography-tandem mass spectrometry (LC-MS/MS) results showed that the relative molecular mass and the structure of ZEA also changed. Sequence alignment of the ZTE138 protein showed that it is a protease that belongs to the YBGC/FADM family of coenzyme A thioesterases, and thus, the protein can presumably cleave the ZEA lactone bond and break down its macrolide ring.

Genome sequencing, purification, and biochemical characterization of a strongly fibrinolytic enzyme from Bacillus amyloliquefaciens Jxnuwx-1 isolated from Chinese traditional douchi

A strongly fibrinolytic enzyme was purified from Bacillus amyloliquefaciens Jxnuwx-1, found in Chinese traditional fermented black soya bean (douchi). The molecular mass of the enzyme, estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), was 29 kDa. The optimal pH and temperature for the enzyme were 7.6 and 41°C, respectively. The enzyme was inhibited by phenylmethylsulfonyl fluoride, soybean trypsin inhibitor, ethylenediaminetetraacetic acid, Fe3+, and Fe2+. The highest affinity exhibited by the enzyme was towards N-Succinyl-Ala-Ala-Pro-Phe-pNA. These results indicated that it is a subtilisin-like serine metalloprotease. The enzyme degraded both fibrinogen and fibrin, displaying its highest degrading activity towards the Aα-chains followed by Bβ chains and Cγ chains. The enzyme was also activated by plasminogen, indicating its ability to degrade fibrinogen and fibrin in two ways: (a) by activating plasminogen conversion into plasmin, or (b) by direct hydrolysis. It degraded thrombin, suggesting that it may act as an anticoagulant to prevent thrombosis. Taken together, our results indicate the potential of this enzyme in controlling cardiovascular disease.

Overexpression of an endogenous raw starch digesting mesophilic α-amylase gene in Bacillus amyloliquefaciens Z3 by in vitro methylation protocol

BACKGROUND

Mesophilic α-amylases function effectively at low temperatures with high rates of catalysis and require less energy for starch hydrolysis. Bacillus amyloliquefaciens is an essential producer of mesophilic α-amylases. However, because of the existence of the restriction-modification system, introducing exogenous DNAs into wild-type B. amyloliquefaciens is especially tricky.

RESULTS

α-Amylase producer B. amyloliquefaciens strain Z3 was screened and used as host for endogenous α-amylase gene expression. In vitro methylation was performed in recombinant plasmid pWB980-amyZ3. With the in vitro methylation, the transformation efficiency was increased to 0.96 × 10² colony-forming units μg^-1 plasmid DNA. A positive transformant BAZ3-16 with the highest α-amylase secreting capacity was chosen for further experiments. The α-amylase activity of strain BAZ3-16 reached 288.70 ± 16.15 U mL^-1 in the flask and 386.03 ± 16.25 U mL^-1 in the 5-L stirred-tank fermenter, respectively. The Bacillus amyloliquefaciens Z3 expression system shows excellent genetic stability and high-level extracellular production of the target protein. Moreover, the synergistic interaction of AmyZ3 with amyloglucosidase was determined during the hydrolysis of raw starch. The hydrolysis degree reached 92.34 ± 3.41% for 100 g L^-1 raw corn starch and 81.30 ± 2.92% for 100 g L^-1 raw cassava starch after 24 h, respectively.

CONCLUSION

Methylation of the plasmid DNA removes a substantial barrier for transformation of B. amyloliquefaciens strain Z3. Furthermore, the exceptional ability to hydrolyze starch makes α-amylase AmyZ3 and strain BAZ3-16 valuable in the starch industry. © 2020 Society of Chemical Industry.

Identification of a Spermidine Synthase Gene from Soybean by Recombinant Expression, Transcriptional Verification, and Sequence Analysis

Spermidine possesses multiple healthy functions, and soybeans contain the most abundant spermidine. In this study, spermidine contents of soybeans from different varieties and production regions in China were evaluated, and a spermidine synthase gene (speE) was identified by recombinant expression, transcriptional verification, and sequence analysis. Spermidine contents of soybean samples from 18 varieties ranged 72.38-228.82 mg/kg, and those from 19 production regions ranged 134.64-242.32 mg/kg. The highest-spermidine sample GZ was used to clone four predicted speE genes. Expressing the gene speE5 improved the spermidine titer by 54% in Bacillus amyloliquefaciens, confirming that speE5 was involved in spermidine synthesis. Transcriptional verification was performed through a soybean germination model. Germination for 48 h led to a onefold increase of spermidine in samples SHX and HB, and corresponding speE5 transcriptional levels were improved by 26-fold and 18-fold, respectively, further verifying the function of speE5. Finally, the sequences of the speE5 gene and deduced amino acids were analyzed, and the conserved sites and catalysis mechanisms were presented. This study identified an active spermidine synthase gene from soybean for the first time, which provided an important gene resource for genetic breeding of spermidine-rich soybean or microbial cell factory.

Evaluation of the Strain Bacillus amyloliquefaciens YP6 in Phoxim Degradation via Transcriptomic Data and Product Analysis

Phoxim, a type of organophosphorus pesticide (OP), is widely used in both agriculture and fisheries. The persistence of phoxim has caused serious environmental pollution problems. In this study, Bacillus amyloliquefaciens YP6 (YP6), which is capable of promoting plant growth and degrading broad-spectrum OPs, was used to study phoxim degradation. Different culture media were applied to evaluate the growth and phoxim degradation of YP6. YP6 can grow rapidly and degrade phoxim efficiently in Luria-Bertani broth (LB broth) medium. Furthermore, it can also utilize phoxim as the sole phosphorus source in a mineral salt medium. Response surface methodology was performed to optimize the degradation conditions of phoxim by YP6 in LB broth medium. The optimum biodegradation conditions were 40 °C, pH 7.20, and an inoculum size of 4.17% (v/v). The phoxim metabolites, O,O-diethylthiophosphoric ester, phoxom, and α-cyanobenzylideneaminooxy phosphonic acid, were confirmed by liquid chromatography-mass spectrometry. Meanwhile, transcriptome analysis and qRT-PCR were performed to give insight into the phoxim-stress response at the transcriptome level. The hydrolase-, oxidase-, and NADPH-cytochrome P450 reductase-encoding genes were significantly upregulated for phoxim hydrolysis, sulfoxidation, and o-dealkylation. Furthermore, the phoxim biodegradation pathways by YP6 were proposed, for the first time, based on transcriptomic data and product analysis.

Plant growth promoting and antifungal activity in endophytic Bacillus strains from pearl millet (Pennisetum glaucum)

Bacterial endophytes are well known inhabitants of living plant system and perform important assignments in maintaining plant growth and health. Currently, limited reports are available on the endophytes of pearl millet (Pennisetum glaucum) reflecting antagonistic and plant growth promoting (PGP) attributes. Therefore, the major objectives of current investigation were to identify antagonistic strains of endophytic Bacillus from pearl millet and further illustrate their PGP capabilities. In this study, 19 endophytic Bacillus strains (EPP5, EPP21, EPP30, EPP32, EPP35, EPP42, EPP49, EPP55, EPP62, EPP65, EPP70, EPP71, EPP74, EPP78, EPP83, EPP86, EPP93, EPP100, and EPP102) displaying antagonistic activity towards Rhizoctonia solani (RS), Sclerotium rolfsii (SR), and Fusarium solani (FS) were isolated from different sections (root, leaf, stem, and root) of pearl millet. Phenotypic (shape, colony, gram staining reaction, endospore formation, and motility) and biochemical features (catalase, oxidase, citrate, gelatinase, urease, Voges Proskauer's, methyl red, indole, and nitrate reduction), along with the similarly comparison of 16S rRNA gene sequence with type strains identified eight antagonistic endophyhtes as B. amyloliquefaciens (EPP35, EPP 42, EPP62, and EPP 102), Bacillus subtilis subsp. subtilis (EPP65), and Bacillus cereus (EPP5, EPP71, and EPP74). The production of indole acetic acid and siderophores was varied among the isolated endophytes. Besides displaying enzymatic activities, these isolates varied in solubilizing capabilities of phosphate, potassium, and zinc. The presence of three antimicrobial peptide genes (ituD, bmyC, and srfA) also confirmed their antifungal nature. Further, single treatment of three promising strains (EPP5, EPP62, and EPP65) offered protection ranging from 35.68 to 45.74% under greenhouse conditions. However, microbial consortium (EPP5+ EPP62 + EPP65) provided the highest protection (71.96%) against root rot and wilt infection with significant increase in plant biomass. Overall, the current study indicated that pearl millet plant harbors various species of endophytic Bacillus that possess excellent biocontrol and growth promotion activities.

Metabolic engineering of Bacillus amyloliquefaciens LL3 for enhanced poly-γ-glutamic acid synthesis

Poly-γ-glutamic acid (γ-PGA) is a biocompatible and biodegradable polypeptide with wide-ranging applications in foods, cosmetics, medicine, agriculture and wastewater treatment. Bacillus amyloliquefaciens LL3 can produce γ-PGA from sucrose that can be obtained easily from sugarcane and sugar beet. In our previous work, it was found that low intracellular glutamate concentration was the limiting factor for γ-PGA production by LL3. In this study, the γ-PGA synthesis by strain LL3 was enhanced by chromosomally engineering its glutamate metabolism-relevant networks. First, the downstream metabolic pathways were partly blocked by deleting fadR, lysC, aspB, pckA, proAB, rocG and gudB. The resulting strain NK-A6 synthesized 4.84 g l-1 γ-PGA, with a 31.5% increase compared with strain LL3. Second, a strong promoter PC 2up was inserted into the upstream of icd gene, to generate strain NK-A7, which further led to a 33.5% improvement in the γ-PGA titre, achieving 6.46 g l-1 . The NADPH level was improved by regulating the expression of pgi and gndA. Third, metabolic evolution was carried out to generate strain NK-A9E, which showed a comparable γ-PGA titre with strain NK-A7. Finally, the srf and itu operons were deleted respectively, from the original strains NK-A7 and NK-A9E. The resulting strain NK-A11 exhibited the highest γ-PGA titre (7.53 g l-1 ), with a 2.05-fold improvement compared with LL3. The results demonstrated that the approaches described here efficiently enhanced γ-PGA production in B. amyloliquefaciens fermentation.

Di-n-butyl phthalate degrading endophytic bacterium Bacillus amyloliquefaciens subsp. strain JR20 isolated from garlic chive and its colonization in a leafy vegetable

Di-n-butyl phthalate (DBP) is one of the primary PAEs (phthalate acid esters) pollutants. DBP can be absorbed by plants and threaten human health via the food chain. Some DBP-degrading bacteria have been successfully isolated from the environment (water, soil, etc.). However, only a few DBP-degrading plant endophytes have been isolated. In this study, an endophytic bacterium, Bacillus amyloliquefaciens subsp. strain JR20, which was found capable of degrading DBP, was isolated from garlic chive. We found that strain JR20 metabolized 89.74% of DBP at a 5 mg/L concentration within 4 d in liquid mineral salts medium (MSM). The optimized conditions for maximum removal of DBP were as follows: DBP concentration, 5 mg/L; pH, 7-8; temperature, 30-40 °C. The colonization of strain JR20 significantly improved the degradation rate of DBP in the roots, stems and leaves of leafy vegetables.

Fengycin Produced by Bacillus amyloliquefaciens FZB42 Inhibits Fusarium graminearum Growth and Mycotoxins Biosynthesis

Fusarium graminearum is a notorious pathogen that causes Fusarium head blight (FHB) in cereal crops. It produces secondary metabolites, such as deoxynivalenol, diminishing grain quality and leading to lesser crop yield. Many strategies have been developed to combat this pathogenic fungus; however, considering the lack of resistant cultivars and likelihood of environmental hazards upon using chemical pesticides, efforts have shifted toward the biocontrol of plant diseases, which is a sustainable and eco-friendly approach. Fengycin, derived from Bacillus amyloliquefaciens FZB42, was purified from the crude extract by HPLC and further analyzed by MALDI-TOF-MS. Its application resulted in structural deformations in fungal hyphae, as observed via scanning electron microscopy. In planta experiment revealed the ability of fengycin to suppress F. graminearum growth and highlighted its capacity to combat disease incidence. Fengycin significantly suppressed F. graminearum, and also reduced the deoxynivalenol (DON), 3-acetyldeoxynivalenol (3-ADON), 15-acetyldeoxynivalenol (15-ADON), and zearalenone (ZEN) production in infected grains. To conclude, we report that fengycin produced by B. amyloliquefaciens FZB42 has potential as a biocontrol agent against F. graminearum and can also inhibit the mycotoxins produced by this fungus.

Characterization of a Regulator pgsR on Endogenous Plasmid p2Sip and Its Complementation for Poly(γ-glutamic acid) Accumulation in Bacillus amyloliquefaciens

Bacillus amyloliquefaciens NX-2S154 is a promising poly(γ-glutamic acid) (γ-PGA) producing strain discovered in previous studies. However, the wild-type strain contains an unknown endogenous plasmid, p2Sip, which causes low transformation efficiency and instability of exogenous plasmids. In our study, p2Sip is 5622 bp with 41% G+C content and contains four putative open reading frames (ORFs), including genes repB, hsp, and mobB and γ-PGA-synthesis regulator, pgsR. Elimination of p2Sip from strain NX-2S154 delayed γ-PGA secretion and decreased production of γ-PGA by 18.1%. Integration of a pgsR expression element into the genomic BamHI locus using marker-free manipulation based on pheS* increased the γ-PGA titer by 8%. pgsR overexpression upregulated the expression of γ-PGA synthase pgsB, regulator degQ, and glutamic acid synthase gltA, thus increasing the γ-PGA production in B. amyloliquefaciens NB. Our results indicated that pgsR from p2Sip plays an important regulatory role in γ-PGA synthesis in B. amyloliquefaciens.

Antimicrobial activity and spectroscopic characterization of surfactin class of lipopeptides from Bacillus amyloliquefaciens SR1

A bacterial isolate screened from wet land soil sample, found to posses antimicrobial activity against an array of fungal plant pathogens viz., Rhizoctonia solani, Sclerotium rolfsii, Alternaria solani, Fusarium oxysporum under in vitro dual culture plate assay. Further the isolate was identified into Bacillus amyloliquefaciens based on 16S rRNA sequencing. The antimicrobial fraction from the extracellular supernatant of the isolate comprises chiefly of surfactin molecules and also iturin and fengycin group of compounds. The surfactins were partially purified by tangential flow ultra-filtration and quantified with liquid chromatography yielding 316.1 mg L^-1. Further the surfactin molecules were characterized by HPLC separation, FT-IR, LC-MS spectroscopy and PCR amplification of antibiotic genes. The surfactin molecule with m/z 1022 performed for MS-MS fragmentation and produced two different patterns of ion dissociation.

Efficient Biosynthesis of Low-Molecular-Weight Poly-γ-glutamic Acid by Stable Overexpression of PgdS Hydrolase in Bacillus amyloliquefaciens NB

Low-molecular-weight poly-γ-glutamic acid (LMW-γ-PGA) has attracted much attention owing to its great potential in food, agriculture, medicine, and cosmetics. Current methods of LMW-γ-PGA production, including enzymatic hydrolysis, are associated with low operational stability. Here, an efficient method for stable biosynthesis of LMW-γ-PGA was conceived by overexpression of γ-PGA hydrolase in Bacillus amyloliquefaciens NB. To establish stable expression of γ-PGA hydrolase (PgdS) during fermentation, a novel plasmid pNX01 was constructed with a native replicon from endogenous plasmid p2Sip, showing a loss rate of 4% after 100 consecutive passages. Subsequently, this plasmid was applied in a screen of high activity PgdS hydrolase, leading to substantial improvements to γ-PGA titer with concomitant decrease in the molecular weight. Finally, a satisfactory yield of 17.62 ± 0.38 g/L LMW-γ-PGA with a weight-average molecular weight of 20-30 kDa was achieved by direct fermentation of Jerusalem artichoke tuber extract. Our study presents a potential method for commercial production of LMW-γ-PGA.

C-di-GMP turnover influences motility and biofilm formation in Bacillus amyloliquefaciens PG12

Bis-(3'→5') cyclic dimeric guanosine monophosphate (c-di-GMP) is defined as a highly versatile secondary messenger in bacteria, coordinating diverse aspects of bacterial growth and behavior, including motility and biofilm formation. Bacillus amyloliquefaciens PG12 is an effective biocontrol agent against apple ring rot caused by Botryosphaeria dothidea. In this study, we characterized the core regulators of c-di-GMP turnover in B. amyloliquefaciens PG12. Using bioinformatic analysis, heterologous expression and biochemical characterization of knockout and overexpression derivatives, we identified and characterized two active diguanylate cyclases (which catalyze c-di-GMP biosynthesis), YhcK and YtrP and one active c-di-GMP phosphodiesterase (which degrades c-di-GMP), YuxH. Furthermore, we showed that elevating c-di-GMP levels up to a certain threshold inhibited the swimming motility of B. amyloliquefaciens PG12. Although yhcK, ytrP and yuxH knockout mutants did not display defects in biofilm formation, significant increases in c-di-GMP levels induced by YtrP or YuxH overexpression stimulated biofilm formation in B. amyloliquefaciens PG12. Our results indicate that B. amyloliquefaciens possesses a functional c-di-GMP signaling system that influences the bacterium's motility and ability to form biofilms. Since motility and biofilm formation influence the efficacy of biological control agent, our work provides a basis for engineering a more effective strain of B. amyloliquefaciens PG12.

Knockout of rapC Improves the Bacillomycin D Yield Based on De Novo Genome Sequencing of Bacillus amyloliquefaciens fmbJ

Bacillus amyloliquefaciens, a Gram-positive and soil-dwelling bacterium, could produce secondary metabolites that suppress plant pathogens. In this study, we provided the whole genome sequence results of B. amyloliquefaciens fmbJ, which had one circular chromosome of 4 193 344 bp with 4249 genes, 87 tRNA genes, and 27 rRNA genes. In addition, fmbJ was found to contain several gene clusters of antimicrobial lipopeptides (bacillomycin D, surfactin, and fengycin), and bacillomycin D homologues were further comprehensively identified. To clarify the influence of rapC regulating the synthesis of lipopeptide on the yield of bacillomycin D, rapC gene in fmbJ was successfully deleted by the marker-free method. Finally, it was found that the deletion of rapC gene in fmbJ significantly improved bacillomycin D production from 240.7 ± 18.9 to 360.8 ± 30.7 mg/L, attributed to the increased the expression of bacillomycin D synthesis-related genes through enhancing the transcriptional level of comA, comP, and phrC. These results showed that the production of bacillomycin D in B. amyloliquefaciens fmbJ might be regulated by the RapC-PhrC system. The findings are expected to advance further agricultural application of Bacillus spp. as a promising source of natural bioactive compounds.

Biological control of potato common scab by Bacillus amyloliquefaciens Ba01

Potato common scab, which is caused by soil-borne Streptomyces species, is a severe plant disease that results in a significant reduction in the economic value of potatoes worldwide. Due to the lack of efficacious pesticides, crop rotations, and resistant potato cultivars against the disease, we investigated whether biological control can serve as an alternative approach. In this study, multiple Bacillus species were isolated from healthy potato tubers, and Bacillus amyloliquefaciens Ba01 was chosen for further analyses based on its potency against the potato common scab pathogen Streptomyces scabies. Ba01 inhibited the growth and sporulation of S. scabies and secreted secondary metabolites such as surfactin, iturin A, and fengycin with potential activity against S. scabies as determined by imaging mass spectrometry. In pot assays, the disease severity of potato common scab decreased from 55.6 ± 11.1% (inoculated with S. scabies only) to 4.2 ± 1.4% (inoculated with S. scabies and Ba01). In the field trial, the disease severity of potato common scab was reduced from 14.4 ± 2.9% (naturally occurring) to 5.6 ± 1.1% after Ba01 treatment, representing evidence that Bacillus species control potato common scab in nature.

Effects of substrate binding site residue substitutions of xynA from Bacillus amyloliquefaciens on substrate specificity

BACKGROUND

The aromatic residues of xylanase enzyme, W187, Y124, W144, Y128 and W63 of substrate binding pocket from Bacillus amyloliquefaciens were investigated for their role in substrate binding by homology modelling and sequence analysis. These residues are highly conserved and play an important role in substrate binding through steric hindrance. The substitution of these residues with alanine allows the enzyme to accommodate nonspecific substrates.

RESULTS

Wild type and mutated genes were cloned and overexpressed in BL21. Optimum pH and temperature of rBAxn exhibited pH 9.0 and 50 °C respectively and it was stable up to 215 h. Along with the physical properties of rBAxn, kinetic parameters (Km 19.34 ± 0.72 mg/ml; kcat 6449.12 ± 155.37 min- 1 and kcat/Km 333.83 ± 6.78 ml min- 1 mg- 1) were also compared with engineered enzymes. Out of five mutations, W63A, Y128A and W144A lost almost 90% activity and Y124A and W187A retained almost 40-45% xylanase activity.

CONCLUSIONS

The site-specific single mutation, led to alteration in substrate specificity from xylan to CMC while in case of double mutant the substrate specificity was altered from xylan to CMC, FP and avicel, indicating the role of aromatic residues on substrate binding, catalytic process and overall catalytic efficiency.

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 a Bacillus amyloliquefaciens strain with zearalenone removal ability and its probiotic potential

Zearalenone (ZEN) is a non-steroidal estrogenic mycotoxin produced by Fusarium species, which has been shown to be associated with reproductive disorders in livestock, and to a lesser extent with hyperoestrogenic syndromes in humans. The aim of this study was to characterize a Bacillus amyloliquefaciens strain with ZEN removal ability. A pure culture of a strain designated LN isolated from moldy corn samples showed a high ZEN removal capability. Based on microscopic observations, biochemical characteristics, and phylogenetic analysis of the 16S rRNA gene sequence, LN was identified as B. amyloliquefaciens. After incubation of B. amyloliquefaciens LN in Luria-Bertani (LB) medium containing 3.5 ppm of ZEN, the ZEN concentration fell below the detection limit within 24 h. In ZEN-contaminated corn meal medium, B. amyloliquefaciens LN decreased ZEN concentration by 92% after 36 h of incubation. In phosphate-buffered saline (PBS) containing 5 ppm of ZEN, B. amyloliquefaciens LN reduced the ZEN concentration from 5 ppm to 3.28 ppm immediately after coming into contact with ZEN, and further reduced the ZEN concentration to 0.36 ppm after 4 h of incubation. The amounts of ZEN adsorbed by the cells of B. amyloliquefaciens LN did not increase with the extension of incubation time, indicating that B. amyloliquefaciens LN not only possessed ZEN adsorption ability, but also exhibited the ability to degrade ZEN. In addition, B. amyloliquefaciens LN was non-hemolytic, non-enterotoxin producing, and displayed probiotic characteristics including acidic tolerance, bile salt tolerance, and anti-pathogenic activities. These findings suggest that B. amyloliquefaciens LN has a potential to be used as a feed additive to reduce the concentrations of ZEN in feedstuffs.