Effects of mixed culture fermentation of Bacillus amyloliquefaciens and Trichoderma longibrachiatum on its constituent strains and the biocontrol of tomato Fusarium wilt.

AIMS: To study the effects of mixed culture fermentation (MCF) of Bacillus amyloliquefaciens and Trichoderma longibrachiatum on its constituent strains and the application values for agricultural production, with the intention of developing efficient and environmentally friendly biocontrol agents. METHODS AND RESULTS: In this study, an in vitro antifungal growth experiment showed that the inhibitory rate of the MCF broth on pathogenic fungi (Fusarium oxysporum f. sp. lycopersici, Botrytis cinerea, Trichothecium roseum and Colletotrichum gloeosporioides) was less than that of B. amyloliquefaciens culture fermentation (BCF). Moreover, the content and gene expression of lipopeptide antibiotics were also lower than that in the BCF group. However, the pot experiments based on irrigation with appropriately diluted fermentation broth showed that the biocontrol effect of MCF on tomato Fusarium wilt was significantly higher than that of TCF (T. longibrachiatum culture fermentation) and BCF, and was approximately 15.79% higher than that of the BTF group which made by mixing equivalent amounts of BCF and TCF. In MCF broth, two micro-organisms antagonized and coexisted, and the growth of T. longibrachiatum was inhibited. Using transcriptomic analysis, we speculated that MCF can upregulate the expression of genes related to carbon and nitrogen metabolism, oxidation-reduction activity, sporulation, environmental information response and chemotaxis, and biosynthesis of secondary metabolites of B. amyloliquefaciens, which might enhance the nutrient substances metabolism and competitiveness, survival ability, colonization and adaptability to the environment to increase its biocontrol potential. CONCLUSIONS: Mixed culture fermentation could promote the more reasonable and effective utilization of biocontrol micro-organisms though improving biocontrol effect, enhancing strains survival and competitiveness, increasing beneficial metabolites, combined with resistance induction or synergistic control. SIGNIFICANCE AND IMPACT OF THE STUDY: Using MCF agronomically utilizes biocontrol agents in an efficient way, which has a good potential for commercial implementation and could reduce production costs.

The action mechanism of daptomycin.

Daptomycin is a lipopeptide antibiotic produced by the soil bacterium Streptomyces roseosporus that is clinically used to treat severe infections with Gram-positive bacteria. In this review, we discuss the mode of action of this important antibiotic. Although daptomycin is structurally related to amphomycin and similar lipopeptides that inhibit peptidoglycan biosynthesis, experimental studies have not produced clear evidence that daptomycin shares their action mechanism. Instead, the best characterized effect of daptomycin is the permeabilization and depolarization of the bacterial cell membrane. This activity, which can account for daptomycin's bactericidal effect, correlates with the level of phosphatidylglycerol (PG) in the membrane. Accordingly, reduced synthesis of PG or its increased conversion to lysyl-PG promotes bacterial resistance to daptomycin. While other resistance mechanisms suggest that daptomycin may indeed directly interfere with cell wall synthesis or cell division, such effects still await direct experimental confirmation. Daptomycin's complex structure and biosynthesis have hampered the analysis of its structure activity relationships. Novel methods of total synthesis, including a recent one that is carried out entirely on a solid phase, will enable a more thorough and systematic exploration of the sequence space.

Design, synthesis, and bioactivity investigation of novel cyclic lipopeptide antibiotics targeting top-priority multidrug-resistant gram-negative bacteria.

OBJECTIVES: Polymyxins are the last-line therapy for top-priority multidrug-resistant (MDR) gram-negative bacteria. However, polymyxin nephrotoxicity impedes its clinical application. This study aimed to design, synthesize, and identify a novel and promising polymyxin derivative with high efficacy and low toxicity. METHODS: To design polymyxin derivatives, we reduced the hydrophobicity of the two hydrophobic domains (fatty acyl chain and D-Phe6-L-Leu7) and modified the positive charged L-2,4-diaminobutyric acid (Dab) residues. Twenty-five derivatives were synthesized, and their antibacterial activities in vitro and renal cytotoxicities were determined. The nephrotoxicity and pharmacokinetic parameters of compound 12 were examined in rats. Antibacterial efficacy in vivo was evaluated using a mouse systemic infection model. Surface plasmon resonance analysis, compound 12-rifampicin combination therapy, and scanning electron microscopy were used to study the mechanism of action of compound 12. RESULTS: This research found a new compound, identified as compound 12, which showed similar or increased antibacterial activity against all tested sensitive and carbapenem-resistant gram-negative bacteria. It exhibited reduced renal cytotoxicity and nephrotoxicity, a favorable pharmacokinetic profile, and maintained or improved antibacterial efficacy in vivo. Importantly, its anti-Pseudomonas aeruginosa activity significantly improved. Compound 12, when combined with rifampicin, enhanced the activity of rifampin against gram-negative bacteria. Compound 12 also showed a high affinity for lipopolysaccharide and disrupted cell membrane integrity. CONCLUSION: Reducing the hydrophobicity of the two domains reduced renal cytotoxicity and nephrotoxicity. Shortening the side chain of Dab3 by one carbon maintained or increased its antibacterial activity both in vitro and in vivo. Furthermore, only the length of the side chain of Dab9 could be shortened by one carbon among the Dab1,5 and Dab8,9 residues. The bactericidal effects of compound 12 were related to the disruption of cell membrane integrity. Compound 12 may be a promising candidate for combating sensitive and carbapenem-resistant gram-negative bacterial infections, especially Pseudomonas aeruginosa.

Graphene oxide-based a network porous poly (trially isocyanurate-co-methacrylate) monolithic column for HPLC separation of aromatic molecular and lipopeptide antibiotics.

Graphene oxide (GO) was introduced into a monolithic column and a network porous poly (GO-co-TAIC-co-MMA) monolith was prepared by redox polymerization. The internal morphology and pore size distribution of the polymer were observed by scanning electron microscopy, and the nitrogen adsorption-desorption and mercury intrusion methods. After optimization, 8 kinds of aromatic compounds were effectively separated in 5 min, and the theoretical plates number of the monolithic column exceeded 33, 070 plates m-1. Five kinds of main ingredients were separated from the traditional Chinese medicine (Schisandra) ingredients and 26 peaks were successfully separated from the fermentation broth containing natural lipopeptide antibiotics. The addition of GO material enhanced the interaction between the compound and the monolithic column, increased the binding sites, improved the uniformity of the internal pore structure of the monolithic column, and improved the separation performance of the monolith. Methodologic validation of five ingredients in Schisandra showed that the correlation coefficients of the linear regressions were in the range of 0.9987-0.9997. The intra- and inter-day values of the relative standard deviation for precision were in the range of 0.6-4.1% and 1.1-4.8%, respectively. The values of accuracy (expressed as recovery) were in the range of 97.7-103.2%, 100.5-105.0%, 98.2-101.8%, 101.3-104.1%, and 101.2-103.3% for the 5 ingredients in order. In terms of the relative standard deviation of the retention time, the reproducibility of the monolithic column M1 was <3.7%. The monolithic column based on GO has great potential in chromatographic separation.

Binding Studies Reveal Phospholipid Specificity and Its Role in the Calcium-Dependent Mechanism of Action of Daptomycin.

Multidrug-resistant bacteria pose a serious global health threat as antibiotics are increasingly losing their clinical efficacy. A molecular level understanding of the mechanism of action of antimicrobials plays a key role in developing new agents to combat the threat of antimicrobial resistance. Daptomycin, the only clinically used calcium-dependent lipopeptide antibiotic, selectively disrupts Gram-positive bacterial membranes to illicit its bactericidal effect. In this study, we use isothermal titration calorimetry to further characterize the structural features of the target bacterial phospholipids that drive daptomycin binding. Our studies reveal that daptomycin shows a clear preference for the phosphoglycerol headgroup. Furthermore, unlike other calcium-dependent lipopeptide antibiotics, calcium binding by daptomycin is strongly dependent on the presence of phosphatidylglycerol. These investigations provide new insights into daptomycin's phospholipid specificity and calcium binding behavior.

Characterization of multimeric daptomycin bound to lipid nanodiscs formed by calcium-tolerant styrene-maleic acid copolymer.

Daptomycin is a lipopeptide antibiotic that is important in the treatment of infections with Gram-positive bacteria. In the presence of calcium, daptomycin binds to phosphatidylglycerol in the bacterial cytoplasmic membrane and then forms oligomers that mediate its bactericidal effect. The structure of these bactericidal oligomers has not been elucidated. We here explore the feasibility of structural studies on the oligomer by solution-state NMR. To this end, we use nanodiscs that contain DMPC and DMPG, stabilized with a styrene-maleic acid copolymer that has been modified to minimize calcium chelation. We show that these nanodiscs bind daptomycin and induce the formation of stable oligomers under physiologically relevant conditions. The findings suggest that this membrane model is suitable for structural and functional characterization of oligomeric daptomycin, and possibly of other calcium-dependent lipopeptide antibiotics. We show that these nanodiscs bind daptomycin and induce the formation of stable oligomers, under conditions that are suitable for biomolecular NMR. The findings suggest that this membrane model is suitable for structural elucidation of oligomeric daptomycin, and possibly of other calcium-dependent lipopeptide antibiotics.

Plant Growth Enhancement, Disease Resistance, and Elemental Modulatory Effects of Plant Probiotic Endophytic Bacillus sp. Fcl1.

Endophytic bacteria have already been studied for their beneficial support to plants to manage both biotic and abiotic stress through an array of well-established mechanisms. They have either direct or indirect impact on mobilizing diverse nutrients and elements from soil to plants. However, detailed insight into the fine-tuning of plant elemental composition by associated microorganism is very limited. In this study, endophytic Bacillus Fcl1 characterized from the rhizome of Curcuma longa was found to have broad range of plant growth-promoting and biocontrol mechanisms. The organism was found to have indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase production properties along with nitrogen fixation. The Bacillus Fcl1 could also inhibit diverse phytopathogens as confirmed by dual culture and well diffusion. By LC-MS/MS analysis, chemical basis of its antifungal activity has been proved to be due to the production of iturin A and a blend of surfactin compounds. Moreover, the organism was found to induce both plant growth and disease resistance in vivo in model plant system. Because of these experimentally demonstrated multiple plant probiotic features, Bacillus Fcl1 was selected as a candidate organism to study its role in modulation of plant elemental composition. ICP-MS analysis of Bacillus Fcl1-treated plants provided insight into relation of bacterial interaction with elemental composition of plants.

Mechanistic studies on the effect of membrane lipid acyl chain composition on daptomycin pore formation.

Daptomycin is a lipopeptide antibiotic that binds and permeabilizes the cell membranes of Gram-positive bacteria. Membrane permeabilization requires both calcium and phosphatidylglycerol (PG) in the target membrane, and it correlates with the formation of an oligomer that likely comprises eight subunits, which are evenly distributed between the two membrane leaflets. In both bacterial cells and model membranes, changes in the fatty acyl composition of the membrane phospholipids can prevent permeabilization. We here used liposomes to study the effect of phospholipids containing oleoyl and other fatty acyl residues on daptomycin activity, and made the following observations: (1) Oleic acid residues inhibited permeabilization when part not only of PG, but also of other phospholipids (PC or cardiolipin). (2) When included in an otherwise daptomycin-susceptible lipid mixture, even 10% of dioleoyl lipid (DOPC) can strongly inhibit permeabilization. (3) The inhibitory effect of fatty acyl residues appears to correlate more with their chain length than with unsaturation. (4) Under all conditions tested, permeabilization coincided with octamer formation, whereas tetramers were observed on membranes that were not permeabilized. Overall, our findings further support the notion that the octamer is indeed the functional transmembrane pore, and that fatty acyl residues may prevent pore formation by preventing the alignment of tetramers across the two membrane leaflets.

Daptomycin Pore Formation Is Restricted by Lipid Acyl Chain Composition.

Daptomycin is a calcium-dependent lipopeptide antibiotic that is used clinically against various Gram-positive pathogens. It acts on bacterial cell membranes, whose susceptibility varies with the content of phosphatidylglycerol (PG). Some studies have reported that daptomycin permeabilizes and depolarizes bacterial cell membranes, while others have found no evidence of membrane permeabilization and thus proposed different mechanisms of antibacterial action. Divergent observations have also been reported regarding the effect of daptomycin on model membranes, which were found to be permeabilized nonselectively, selectively for small cations, or not at all. While these diverging model studies did consider the functional roles of different lipid head groups, they assumed that the acyl chains were interchangeable. We here show this assumption to be erroneous. In equimolar mixtures of PG and phosphatidylcholine (PC), dimyristoyl lipids support membrane permeabilization, whereas dioleyl and palmitoleyl lipids do not, even though daptomycin does bind to and form oligomers on all of these membranes. These observations help reconcile some of the discrepant findings in the literature.

An Acyl-Linked Dimer of Daptomycin Is Strongly Inhibited by the Bacterial Cell Wall.

The lipopeptide antibiotic daptomycin is active against Gram-positive pathogens. It permeabilizes bacterial cell membranes, which involves the formation of membrane-associated oligomers. We here studied a dimer of daptomycin whose two subunits were linked through a bivalent aliphatic acyl chain. Unexpectedly, the dimer had very low activity on vegetative Staphylococcus aureus and Bacillus subtilis cells. However, activity resembled that of monomeric daptomycin on liposomes and on B. subtilis L-forms. These findings underscore the importance of the bacterial cell wall in daptomycin resistance.

Identification of endophytic Bacillus mojavensis with highly specialized broad spectrum antibacterial activity.

Biosynthetic adaptation of endophytic bacteria to chemically support host plant is very remarkable. Hence these organisms from medicinal plants are considered as highly valuable sources for natural products with diverse bioactivity. Their metabolite diversity and biosynthetic versatility have been increasingly explored for drug discovery. In this study, an endophytic Bacillus mojavensis with broad spectrum antibacterial properties has been analyzed for the chemical basis of its activity. By LC-MS/MS the organism was identified to have the biosynthetic ability to produce lipopeptides surfactin and fengycin. The impressive antibacterial activity of B. mojavensis as reported in the study indicates its broad antimicrobial applications.

Paenibacillus polymyxa A26 Sfp-type PPTase inactivation limits bacterial antagonism against Fusarium graminearum but not of F. culmorum in kernel assay.

Fusarium graminearum and F. culmorum are the causing agents of a destructive disease known as Fusarium head blight (FHB). FHB is a re-emerging disease in small grain cereals which impairs both the grain yield and the quality. Most serious consequence is the contamination of grain with Fusarium mycotoxins that are severe threat to humans and animals. Biological control has been suggested as one of the integrated management strategies to control FHB. Paenibacillus polymyxa is considered as a promising biocontrol agent due to its unique antibiotic spectrum. P. polymyxa A26 is an efficient antagonistic agent against Fusarium spp. In order to optimize strain A26 production, formulation and application strategies traits important for its compatibility need to be revealed. Here we developed a toolbox, comprising of dual culture plate assays and wheat kernel assays, including simultaneous monitoring of FHB causing pathogens, A26, and mycotoxin production. Using this system we show that, besides generally known lipopeptide antibiotic production by P. polymyxa, biofilm formation ability may play a crucial role in the case of stain A26 F. culmorum antagonism. Application of the system for effective strain selection and maintenance is discussed.

Two novel amphomycin analogues from Streptomyces canus strain FIM-0916.

Three lipopeptides, the known compound amphomycin, together with two novel compounds named aspartocin D (1) and aspartocin E (2) were obtained from the fermentation broth extraction of Streptomyces canus strain FIM0916 by using various column chromatography techniques. Their structures were elucidated by using spectroscopic methods, mainly by an extensive NMR analysis. It was demonstrated that compounds 1 and 2 are novel analogues of amphomycin, whose structures are similar to aspartocins. Compounds 1 and 2 share the same cyclic decapeptide core of cyclo (Dab2-Pip3-MeAsp4-Asp5-Gly6-Asp7-Gly8-Dab9-Val10-Pro11-), differing only in the side-chain moiety corresponding to Asp1-△3-isohendecenoic acid and Asp1-△3-isododecenoic acid, for aspartocin D and aspartocin E. In bioassays, compounds 1 and 2 exhibited antimicrobial activities against Gram-positive bacteria in the presence of Ca(2+) (1.25 mM); particularly, the activities were enhanced with higher concentrations of calcium.

Responses of beneficial Bacillus amyloliquefaciens SQR9 to different soilborne fungal pathogens through the alteration of antifungal compounds production.

Bacillus amyloliquefaciens SQR9 exhibited predominantly antagonistic activities against a broad range of soilborne pathogens. The fungi-induced SQR9 extracts possess stronger antifungal activities compared with SQR9 monoculture extracts. To investigate how SQR9 fine-tunes lipopeptides (LPs) and a siderophore bacillibactin production to control different fungal pathogens, LPs and bacillibactin production and transcription of the respective encoding genes in SQR9 were measured and compared with six different soilborne fungal pathogens. SQR9 altered its spectrum of antifungal compounds production responding to different fungal pathogen. Bacillomycin D was the major LP produced when SQR9 was confronted with Fusarium oxysporum. Fengycin contributed to the antagonistic activity against Verticillium dahliae kleb, Fusarium oxysporum, Fusarium solani, and Phytophthora parasitica. Surfactin participated in the antagonistic process against Sclerotinia sclerotiorum, Rhizoctonia solani, and Fusarium solani. Bacillibactin was up-regulated when SQR9 was confronted with all tested fungi. The reduction in antagonistic activities of three LP and bacillibactin deficient mutants of SQR9 when confronted with the six soilborne fungal pathogens provided further evidence of the contribution of LPs and bacillibactin in controlling fungal pathogens. These results provide a new understanding of specific cues in bacteria-fungi interactions and provide insights for agricultural applications.