Enhancing fengycin production in the co-culture of Bacillus subtilis and Corynebacterium glutamicum by engineering proline transporter

ComQXPA Quorum Sensing Dynamic Regulation Enhanced Fengycin Production of Bacillus subtilis

Fengycin is an antifungal drug that could be used as a biocontrol agent if it could be produced in high amounts. The ComQXPA quorum sensing (QS) system is a natural mechanism, regulating cell density-dependent behaviors in Bacillus subtilis. This study employed the QS-targeted promoter PsrfA to express the pps gene cluster in B. subtilis, coupling the ComQXPA system to produce fengycin. Mutations in the ComA regulatory protein-binding site RE3 exhibited a 2.45-fold increase in promoter expression intensity and resulted in an elevation of fengycin production from 489 to 1832 mg/L, a 2.74-fold enhancement. Transcriptomic analysis revealed the upregulation of genes associated with carbon source uptake and utilization and metabolic pathways related to amino acids and fatty acids, which are precursors for fengycin synthesis. Additionally, knockout of rapJ and rapE increased fengycin production to 3190 mg/L. In a coculture system constructed with Corynebacterium glutamicum, fengycin production reached 4005 mg/L. This work provides a strategy for dynamically regulating fengycin synthesis.

Complete genome analysis and antimicrobial mechanism of Bacillus velezensis GX0002980 reveals its biocontrol potential against mango anthracnose disease

Post-harvest anthracnose significantly affects the yield and quality of mangoes. In this study, an antagonist bacterium, GX0002980, with strong inhibitory effect against Colletotrichum gloesporioides, the pathogen of mango anthracnose, was isolated from the rhizosphere soil of plants. Based on morphological characteristics, physiological and biochemical tests, and 16S rRNA gene and gyrB gene sequencing analysis, the strain was identified as Bacillus velezensis. Strain GX0002980 exhibits broad-spectrum antibacterial capabilities, and its volatile substances and sterile fermentation filtrate also demonstrate antagonistic effects against C. gloesporioides. This strain can produce antimicrobial substances that inhibit pathogen growth, such as amylase, cellulase, protease, pectinase, and siderophores, and has plant-growth-promoting characteristics, such as nitrogen fixation, NH3 production, and phosphate solubilization. Whole-genome sequencing results show that the genome size of GX0002980 is 3,907,381 bp with a guanine and cytosine content of 47.44%. The antiSMASH analysis predicts 14 antimicrobial biosynthesis gene clusters within the GX0002980 genome, including surfactin, fengycin, bacilysin, macrolactin H, bacillaene, difficidin, and bacillibactin. Liquid chromatography-mass spectrometry analysis revealed that the antimicrobial active substances secreted by GX0002980 include surfactin, bacilysin, butirosin A, and more. Strain GX0002980 has an in vitro control efficiency of 52% against mango anthracnose, and it can effectively suppress the occurrence of post-harvest diseases in mangoes, extending their storage time. In conclusion, B. velezensis GX0002980 possesses multiple biocontrol mechanisms and has potential for application in the biological control of mango anthracnose.IMPORTANCEBacillus velezensis GX0002980 showed biocontrol potential against Colletotrichum gloesporioides, a causative agent of mango anthracnose. B. velezensis GX0002980 produces a variety of secondary metabolites with antibacterial properties. Whole-genome sequencing revealed potential active metabolite synthesis gene clusters of B. velezensis GX0002980. B. velezensis GX0002980 has a significant effect on the control of post-harvest disease in mango fruits.

Biosynthesis and yield improvement strategies of fengycin

Fengycin is a cyclic lipopeptide antibiotic predominantly synthesized by Bacillus species. It exhibits remarkable antifungal, antitumor, and antiadhesion activities. It also possesses advantageous properties such as low toxicity, effective antibacterial activity, and biodegradability, making it a promising candidate for applications in biocontrol, medicine, and industry. However, challenges including low yield, complex purification processes, and high production costs currently restrict its large-scale commercialization. To promote the research and development of fengycin and facilitate its practical applications, this review summarizes fengycin's structural characteristics, subclasses, and producing bacteria. Additionally, it delves into the biosynthesis process, known regulatory factors and mechanism, as well as strategies for enhancing yield through strain improvement and fermentation condition optimization. Furthermore, it addresses the limitations and future directions for fengycin research. This review provides a valuable insights and guidance for future researchers aiming to expand fengycin's applications in medical and agricultural fields. This work also establishes a theoretical foundation for realizing its significant commercial potential.

Strategies and tools to construct stable and efficient artificial coculture systems as biosynthetic platforms for biomass conversion

Inspired by the natural symbiotic relationships between diverse microbial members, researchers recently focused on modifying microbial chassis to create artificial coculture systems using synthetic biology tools. An increasing number of scientists are now exploring these systems as innovative biosynthetic platforms for biomass conversion. While significant advancements have been achieved, challenges remain in maintaining the stability and productivity of these systems. Sustaining an optimal population ratio over a long time period and balancing anabolism and catabolism during cultivation have proven difficult. Key issues, such as competitive or antagonistic relationships between microbial members, as well as metabolic imbalances and maladaptation, are critical factors affecting the stability and productivity of artificial coculture systems. In this article, we critically review current strategies and methods for improving the stability and productivity of these systems, with a focus on recent progress in biomass conversion. We also provide insights into future research directions, laying the groundwork for further development of artificial coculture biosynthetic platforms.

Improved engineered fungal-bacterial commensal consortia simultaneously degrade multiantibiotics and biotransform food waste into lipopeptides

Resource utilization of food waste is necessary to reduce environmental pollution. However, antibiotics can enter the environment through food waste, resulting in antibiotic residues, which pose potential risks to human health. In this study, commensal artificial consortia were constructed through intercellular adaptation to simultaneously degrade antibiotics and bioconvert food waste into lipopeptides. The biodegradation efficiency of oxytetracycline in the three-strain consortium, which contained lipopeptide-producing Bacillus amyloliquefaciens HM618, high-level proline-producing Corynebacterium glutamate, and laccase-producing Pichia pastoris, was around 100% in the food waste medium at 72 h; this was higher than that in the pure culture of P. pastoris-Lac. Sulfamethoxazole could be removed at 48 h. However, the lipopeptide level in the three-strain consortium was only 77 mg/L. The four-strain consortium containing free fatty acid-producing Yarrowia lipolytica improved the lipopeptide level to around 218 mg/L. The degradation efficiency of oxytetracycline in the four-strain consortium was 100% at 48 h; however, only 56% of the sulfamethoxazole was removed over 96 h. Three five-strain consortia were formed by introducing recombinant manganese peroxidase-producing P. pastoris, recombinant HM618 with high-level amylase, and serine-producing C. glutamicum. In low starch food waste, the highest degradation efficiency of sulfamethoxazole was 71%, while oxytetracycline could be completely removed at 48 h. However, oxytetracycline inhibited starch degradation and lipopeptide production. The high level of starch improved lipopeptide synthesis to 1280 mg/L. The results of this study provide a feasible strategy for the resource utilization of inferior biomass food waste.

Production-optimized fermentation of antifungal compounds by bacillus velezensis LZN01 and transcriptome analysis

Fusarium wilt is one of the major constraints on global watermelon production, and Fusarium oxysporum f. sp. niveum (Fon) is the causative agent of Fusarium wilt in watermelon and results in severe yield and quality losses worldwide. The enhancement of antifungal activity from antagonistic bacteria against Fon is highly practical for managing Fusarium wilt in watermelon. The aim of this study was to maximize the antifungal activity of Bacillus velezensis LZN01 by optimizing fermentation conditions and analysing its regulatory mechanism via transcriptome sequencing. The culture and fermentation conditions for strain LZN01 were optimized by single-factor and response surface experiments. The optimum culture conditions for this strain were as follows: the addition of D-fructose at 35 g/L and NH4Cl at 5 g/L in LB medium, pH 7, and incubation at 30°C for 72 h. The fungal inhibition rate for strain LZN01 reached 71.1%. The improvement of inhibition rate for strain LZN01 in optimization fermentation was supported by transcriptomic analysis; a total of 491 genes were upregulated, while 736 genes were downregulated. Transcriptome analysis revealed that some differentially expressed genes involved in carbon and nitrogen metabolism, oxidation-reduction, fatty acid and secondary metabolism; This optimization process could potentially lead to significant alterations in the production levels and types of antimicrobial compounds by the strain. Metabolomics and UPLC/Q-Exactive Orbitrap MS analysis revealed that the production yields of antimicrobial compounds, such as surfactin, fengycin, shikimic acid, and myriocin, increased or were detected in the cell-free supernatant (CFS) after the fermentation optimization process. Our results indicate that fermentation optimization enhances the antifungal activity of the LZN01 strain by influencing the expression of genes responsible for the synthesis of antimicrobial compounds.

An Integrated Pipeline and Overexpression of a Novel Efflux Transporter, YoeA, Significantly Increases Plipastatin Production in Bacillus subtilis

Plipastatin, an antimicrobial peptide produced by Bacillus subtilis, exhibits remarkable antimicrobial activity against a diverse range of pathogenic bacteria and fungi. However, the practical application of plipastatin has been significantly hampered by its low yield in wild Bacillus species. Here, the native promoters of both the plipastatin operon and the sfp gene in the mono-producing strain M-24 were replaced by the constitutive promoter P43, resulting in plipastatin titers being increased by 27% (607 mg/mL) and 50% (717 mg/mL), respectively. Overexpression of long chain fatty acid coenzyme A ligase (LCFA) increased the yield of plipastatin by 105% (980 mg/mL). A new efflux transporter, YoeA, was identified as a MATE (multidrug and toxic compound extrusion) family member, overexpression of yoeA enhanced plipastatin production to 1233 mg/mL, an increase of 157%, and knockout of yoeA decreased plipastatin production by 70%; in contrast, overexpression or knockout of yoeA in mono-producing surfactin and iturin engineered strains only slightly affected their production, demonstrating that YoeA acts as the major exporter for plipastatin. Co-overexpression of lcfA and yoeA improved plipastatin production to 1890 mg/mL, which was further elevated to 2060 mg/mL after abrB gene deletion. Lastly, the use of optimized culture medium achieved 2514 mg/mL plipastatin production, which was 5.26-fold higher than that of the initial strain. These results suggest that multiple strain engineering is an effective strategy for increasing lipopeptide production, and identification of the novel transport efflux protein YoeA provides new insights into the regulation and industrial application of plipastatin.

Improving salt-tolerant artificial consortium of Bacillus amyloliquefaciens for bioconverting food waste to lipopeptides

High-salt content in food waste (FW) affects its resource utilization during biotransformation. In this study, adaptive laboratory evolution (ALE), gene editing, and artificial consortia were performed out to improve the salt-tolerance of Bacillus amyloliquefaciens for producing lipopeptide under FW and seawater. High-salt stress significantly decreased lipopeptide production in the B. amyloliquefaciens HM618 and ALE strains. The total lipopeptide production in the recombinant B. amyloliquefaciens HM-4KSMSO after overexpressing the ion transportor gene ktrA and proline transporter gene opuE and replacing the promoter of gene mrp was 1.34 times higher than that in the strain HM618 in medium containing 30 g/L NaCl. Lipopeptide production under salt-tolerant consortia containing two strains (HM-4KSMSO and Corynebacterium glutamicum) and three-strains (HM-4KSMSO, salt-tolerant C. glutamicum, and Yarrowia lipolytica) was 1.81- and 2.28-fold higher than that under pure culture in a medium containing FW or both FW and seawater, respectively. These findings provide a new strategy for using high-salt FW and seawater to produce value-added chemicals.

Strategies for improving fengycin production: a review

Fengycin is an important member of the lipopeptide family with a wide range of applications in the agricultural, food, medical and cosmetic industries. However, its commercial application is severely hindered by low productivity and high cost. Therefore, numerous studies have been devoted to improving the production of fengycin. We summarize these studies in this review with the aim of providing a reference and guidance for future researchers. This review begins with an overview of the synthesis mechanism of fengycin via the non-ribosomal peptide synthetases (NRPS), and then delves into the strategies for improving the fengycin production in recent years. These strategies mainly include fermentation optimization and metabolic engineering, and the metabolic engineering encompasses enhancement of precursor supply, application of regulatory factors, promoter engineering, and application of genome-engineering (genome shuffling and genome-scale metabolic network model). Finally, we conclude this review with a prospect of fengycin production.

Comparative Genomics Unveils Functional Diversity, Pangenome Openness, and Underlying Biological Drivers among Bacillus subtilis Group

The Bacillus subtilis group (Bs group), with Bacillus subtilis as its core species, holds significant research and economic value in various fields, including science, industrial production, food, and pharmaceuticals. However, most studies have been confined to comparative genomics analyses and exploration within individual genomes at the level of species, with few conducted within groups across different species. This study focused on Bacillus subtilis, the model of Gram-positive bacteria, and 14 other species with significant research value, employing comparative pangenomics as well as population enrichment analysis to ascertain the functional enrichment and diversity. Through the quantification of pangenome openness, this work revealed the underlying biological drivers and significant correlation between pangenome openness and various factors, including the distribution of toxin-antitoxin- and integrase-related genes, as well as the number of endonucleases, recombinases, repair system-related genes, prophages, integrases, and transfer mobile elements. Furthermore, the functional enrichment results indicated the potential for secondary metabolite, probiotic, and antibiotic exploration in Bacillus licheniformis, Bacillus paralicheniformis, and Bacillus spizizenii, respectively. In general, this work systematically exposed the quantification of pangenome openness, biological drivers, the pivotal role of genomic instability factors, and mobile elements, providing targeted exploration guidance for the Bs group.

Combinatorial metabolic engineering of Bacillus subtilis for de novo production of polymyxin B

Polymyxin is a lipopeptide antibiotic that is effective against multidrug-resistant Gram-negative bacteria. However, its clinical development is limited due to low titer and the presence of homologs. To address this, the polymyxin gene cluster was integrated into Bacillus subtilis, and sfp from Paenibacillus polymyxa was expressed heterologously, enabling recombinant B. subtilis to synthesize polymyxin B. Regulating NRPS domain inhibited formation of polymyxin B2 and B3. The production of polymyxin B increased to 329.7 mg/L by replacing the native promoters of pmxA, pmxB, and pmxE with PfusA, C2up, and PfusA, respectively. Further enhancement in this production, up to 616.1 mg/L, was achieved by improving the synthesis ability of 6-methyloctanoic acid compared to the original strain expressing polymyxin heterologously. Additionally, incorporating an anikasin-derived domain into the hybrid nonribosomal peptide synthase of polymyxin increased the B1 ratio in polymyxin B from 57.5% to 62.2%. Through optimization of peptone supply in the fermentation medium and fermentation in a 5.0-L bioreactor, the final polymyxin B titer reached 962.1 mg/L, with a yield of 19.24 mg/g maltodextrin and a productivity of 10.02 mg/(L·h). This study demonstrates a successful approach for enhancing polymyxin B production and increasing the B1 ratio through combinatorial metabolic engineering.

Enhancement of polymyxin B1 production by an artificial microbial consortium of Paenibacillus polymyxa and recombinant Corynebacterium glutamicum producing precursor amino acids

Polymyxin B, produced by Paenibacillus polymyxa, is used as the last line of defense clinically. In this study, exogenous mixture of precursor amino acids increased the level and proportion of polymyxin B1 in the total of polymyxin B analogs of P. polymyxa CJX518-AC (PPAC) from 0.15 g/L and 61.8 % to 0.33 g/L and 79.9 %, respectively. The co-culture of strain PPAC and recombinant Corynebacterium glutamicum-leu01, which produces high levels of threonine, leucine, and isoleucine, increased polymyxin B1 production to 0.64 g/L. When strains PPAC and C. glu-leu01 simultaneously inoculated into an optimized medium with 20 g/L peptone, polymyxin B1 production was increased to 0.97 g/L. Furthermore, the polymyxin B1 production in the co-culture of strains PPAC and C. glu-leu01 increased to 2.21 g/L after optimized inoculation ratios and fermentation medium with 60 g/L peptone. This study provides a new strategy to improve polymyxin B1 production.

An Engineered Microbial Consortium Provides Precursors for Fengycin Production by Bacillus subtilis

Fengycin has great potential for applications in biological control because of its biosafety and degradability. In this study, the addition of exogenous precursors increased fengycin production by Bacillus subtilis. Corynebacterium glutamicum was engineered to produce high levels of precursors (Thr, Pro, Val, and Ile) to promote the biosynthesis of fengycin. Furthermore, recombinant C. glutamicum and Yarrowia lipolytica providing amino acid and fatty acid precursors were co-cultured to improve fengycin production by B. subtilis in a three-strain artificial consortium, in which fengycin production was 2100 mg·L-1. In addition, fengycin production by the consortium in a 5 L bioreactor reached 3290 mg·L-1. Fengycin had a significant antifungal effect on Rhizoctonia solani, which illustrates its potential as a food preservative. Taken together, this work provides a new strategy for improving fengycin production by a microbial consortium and metabolic engineering.