Enhanced heat stable antifungal factor production by Lysobacter enzymogenes OH11 with cheap feedstocks: medium optimization and quantitative determination

Old role with new feature: T2SS ATPase as a cyclic-di-GMP receptor to regulate antibiotic production

Cyclic di-GMP (c-di-GMP) is a crucial signaling molecule found extensively in bacteria, involved in the regulation of various physiological and biochemical processes such as biofilm formation, motility, and pathogenicity through binding to downstream receptors. However, the structural dissimilarity of c-di-GMP receptor proteins has hindered the discovery of many such proteins. In this study, we identified LspE, a homologous protein of the type II secretion system (T2SS) ATPase GspE in Lysobacter enzymogenes, as a receptor protein for c-di-GMP. We identified the more conservative c-di-GMP binding amino acid residues as K358 and T359, which differ from the previous reports, indicating that GspE proteins may represent a class of c-di-GMP receptor proteins. Additionally, we found that LspE in L. enzymogenes also possesses a novel role in regulating the production of the antifungal antibiotic HSAF. Further investigations revealed the critical involvement of both ATPase activity and c-di-GMP binding in LspE-mediated regulation of HSAF (Heat-Stable Antifungal Factor) production, with c-di-GMP binding having no impact on LspE's ATPase activity. This suggests that the control of HSAF production by LspE encompasses two distinct processes: c-di-GMP binding and the inherent ATPase activity of LspE. Overall, our study unraveled a new function for the conventional protein GspE of the T2SS as a c-di-GMP receptor protein and shed light on its role in regulating antibiotic production.IMPORTANCEThe c-di-GMP signaling pathway in bacteria is highly intricate. The identification and functional characterization of novel receptor proteins have posed a significant challenge in c-di-GMP research. The type II secretion system (T2SS) is a well-studied secretion system in bacteria. In this study, our findings revealed the ATPase GspE protein of the T2SS as a class of c-di-GMP receptor protein. Notably, we discovered its novel function in regulating the production of antifungal antibiotic HSAF in Lysobacter enzymogenes. Given that GspE may be a conserved c-di-GMP receptor protein, it is worthwhile for researchers to reevaluate its functional roles and mechanisms across diverse bacterial species.

Iron ions regulate antifungal HSAF biosynthesis in Lysobacter enzymogenes by manipulating the DNA-binding affinity of the ferric uptake regulator (Fur)

Heat-stable antifungal factor (HSAF), produced by Lysobacter enzymogenes OH11, is regarded as a potential biological pesticide due to its broad-spectrum antifungal activity and novel mode of action. However, the current production of HSAF is low and cannot meet the requirements for large-scale production. Herein, we discovered that iron ions greatly promoted HSAF production, and the ferric uptake regulator (Fur) was involved in this regulatory process. Fur was also found to participate in the regulation of iron homeostasis in OH11 via the classic inhibition mechanism of Holo-Fur. Furthermore, Fur was collectively observed to directly bind to the promoter of the HSAF biosynthesis gene, and its DNA-binding affinity was attenuated by the addition of iron ions in vitro and in vivo. Its regulatory mechanism followed the uncommon inhibition mechanism of Apo-Fur. In summary, Fur exhibited a bidirectional regulatory mechanism in OH11. This study reveals a novel regulatory mechanism whereby Fur upregulates the biosynthesis of secondary metabolites. These findings contribute to the improvement of HSAF production and may guide its development into biological pesticides. IMPORTANCE HSAF possesses potent and broad antifungal activity with a novel mode of action. The HSAF yield is critical for fermentation production. In this study, iron ions were found to increase HSAF production, and the specific mechanism was elaborated. These results provide theoretical support for genetic transformation to improve HSAF yield, supporting its development into biological pesticides.

A novel and high-efficient method for the preparation of heat-stable antifungal factor from Lysobacter enzymogenes by high-speed counter-current chromatography

Heat-stable antifungal factor (HSAF) produced by the biocontrol bacterium Lysobacter enzymogenes shows considerable antifungal activity and has broad application potential in the agricultural and medical fields. There is a great demand for pure HSAF compounds in academic or industrial studies. However, an efficient preparation method that produces a high yield and high purity of HSAF is lacking, limiting the development of HSAF as a new drug. In the present study, high-speed counter-current chromatography (HSCCC) combined with column chromatography was successfully developed for the separation and preparation of HSAF from the crude extract of L. enzymogenes OH11. The crude extract was obtained by macroporous resin adsorption and desorption, and the main impurities were partly removed by ultraviolet light (254 nm) and gel filtration (Sephadex LH-20). In the HSCCC procedure, the selected suitable two-phase solvent system (n-hexane/ethyl acetate/methanol/water = 3:5:4:5, v/v, the lower phase added with 0.1% TFA) with a flow rate of 2.0 mL/min and a sample loading size of 100 mg was optimized for the separation. As a result, a total of 42 mg HSAF with a purity of 97.6% and recovery of 91.7% was yielded in one separation. The structure elucidation based on HR-TOF-MS, 1H and 13C NMR, and antifungal activities revealed that the isolated compound was unambiguously identified as HSAF. These results are helpful for separating and producing HSAF at an industrial scale, and they further demonstrate that HSCCC is a useful tool for isolating bioactive constituents from beneficial microorganisms.

Characterization of a Disease-Suppressive Isolate of Lysobacter enzymogenes with Broad Antagonistic Activity against Bacterial, Oomycetal and Fungal Pathogens in Different Crops

Although synthetic pesticides play a major role in plant protection, their application needs to be reduced because of their negative impact on the environment. This applies also to copper preparations, which are used in organic farming. For this reason, alternatives with less impact on the environment are urgently needed. In this context, we evaluated eight isolates of the genus Lysobacter (mainly Lysobacter enzymogenes) for their activity against plant pathogens. In vitro, the investigated Lysobacter isolates showed broad antagonistic activity against several phytopathogenic fungi, oomycetes and bacteria. Enzyme assays revealed diverse activities for the tested isolates. The most promising L. enzymogenes isolate (LEC) was used for further detailed analyses of its efficacy and effective working concentrations. The experiments included in vitro spore and sporangia germination tests and leaf disc assays as well as ad planta growth chamber trials against Alternaria solani and Phytophthora infestans on tomato plants, Pseudoperonospora cubensis on cucumbers and Venturia inaequalis on young potted apple trees. When applied on leaves, dilutions of a culture suspension of LEC had a concentration-dependent, protective effect against the tested pathogens. In all pathosystems tested, the effective concentrations were in the range of 2.5-5% and similarly efficacious to common plant protection agents containing copper hydroxide, wettable sulphur or fenhexamid. Thus, the isolate of L. enzymogenes identified in this study exhibits a broad activity against common plant pathogens and is therefore a promising candidate for the development of a microbial biocontrol agent.

Developing a new treatment for superficial fungal infection using antifungal Collagen-HSAF dressing

Fungal pathogens are common causes of superficial clinical infection. Their increasing drug resistance gradually makes existing antifungal drugs ineffective. Heat stable antifungal factor (HSAF) is a novel antifungal natural product with a unique structure. However, the application of HSAF has been hampered by very low yield in the current microbial producers and from extremely poor solubility in water and common solvents. In this study, we developed an effective mode of treatment applying HSAF to superficial fungal infections. The marine-derived Lysobacter enzymogenes YC36 contains the HSAF biosynthetic gene cluster, which we activated by the interspecific signaling molecule indole. An efficient extraction strategy was used to significantly improve the purity to 95.3%. Scanning electron microscopy images revealed that the Type I collagen-based HSAF (Col-HSAF) has a transparent appearance and good physical properties, and the in vitro sustained-release effect of HSAF was maintained for more than 2 weeks. The effective therapeutic concentration of Col-HSAF against superficial fungal infection was explored, and Col-HSAF showed good biocompatibility, lower clinical scores, mild histological changes, and antifungal capabilities in animals with Aspergillus fumigatus keratitis and cutaneous candidiasis. In conclusion, Col-HSAF is an antifungal reagent with significant clinical value in the treatment of superficial fungal infections.

Antifungal weapons of Lysobacter, a mighty biocontrol agent

Bacteria interact with fungi in a variety of ways to inhibit fungal growth, while the underlying mechanisms remain only partially characterized. The plant-beneficial Bacillus and Pseudomonas species are well-known antifungal biocontrol agents, whereas Lysobacter are far less studied. Members of Lysobacter are easy to grow in fermenters and are safe to humans, animals and plants. These environmentally ubiquitous bacteria use a diverse arsenal of weapons to prey on other microorganisms, including fungi and oomycetes. The small molecular toxins secreted by Lysobacter represent long-range weapons effective against filamentous fungi. The secreted hydrolytic enzymes act as intermediate-range weapons against non-filamentous fungi. The contact-dependent killing devices are proposed to work as short-range weapons. We describe here the structure, biosynthetic pathway, action mode and applications of one of the best-characterized long-range weapons, the heat-stable antifungal factor (HSAF) produced by Lysobacter enzymogenes. We discuss how the flagellar type III secretion system has evolved into an enzyme secretion machine for the intermediate-range antifungal weapons. We highlight an intricate mechanism coordinating the production of the long-range weapon, HSAF and the proposed contact-dependent killing device, type VI secretion system. We also overview the regulatory mechanisms of HSAF production involving specific transcription factors and the bacterial second messenger c-di-GMP.

Separation of Heat-Stable Antifungal Factor From Lysobacter enzymogenes Fermentation Broth via Photodegradation and Macroporous Resin Adsorption

Heat-stable antifungal factor (HSAF) is produced by the fermentation of Lysobacter enzymogenes, which is known for its broad-spectrum antifungal activity and novel mode of action. However, studies on the separation of HSAF have rarely been reported. Herein, alteramide B (the main byproduct) was removed firstly from the fermentation broth by photodegradation to improve the purity of HSAF. Then, the separation of HSAF via adsorption by macroporous adsorption resins (MARs) was evaluated and NKA resin showed highest static adsorption and desorption performances. After optimizing the static and dynamic adsorption characteristics, the content of HSAF in the purified product increased from 8.67 ± 0.32% (ethyl acetate extraction) to 31.07 ± 1.12% by 3.58-fold. These results suggest that the developed strategy via photodegradation and macroporous resin adsorption is an effective process for the separation of HSAF, and it is also a promising method for the large-scale preparation of HSAF for agricultural applications.

Biocontrol ability and action mechanism of dihydromaltophilin against Colletotrichum fructicola causing anthracnose of pear fruit

BACKGROUND

Anthracnose caused by Colletotrichum fructicola is one of the most important diseases in pear fruit, resulting in huge economic losses. Public awareness of protecting the environment and food safety, together with pathogen resistance to many key fungicides have led to an urgent need to develop alternative strategies for controlling fruit diseases. Here, the antifungal activity of a natural product, dihydromaltophilin [heat-stable antifungal factor (HSAF)], against C. fructicola in vitro and in vivo was investigated to determine its efficacy for anthracnose management.

RESULTS

HSAF exhibited pronounced antifungal activity against in vitro mycelial growth of C. fructicola, with a half-inhibition concentration of 0.43 mg L^-1 . Hyphae treated with HSAF showed defects such as hyperbranching, swelling and depolarized growth. Conidia germination in the pathogen was inhibited by HSAF in a dose-dependent manner. In the presence of 4 mg L^-1 HSAF, conidia germination was significantly delayed, and germ tube growth was inhibited. HSAF at 8 mg L^-1 completely blocked conidia germination in C. fructicola. In addition, HSAF disrupted coordination of cytokinesis with growth and nuclear division, induced reactive oxygen species production in conidia, and damaged the integrity of the conidia cell wall. Moreover, an in vivo test confirmed that 50 mg L^-1 HSAF significantly reduced the development of anthracnose decay in pear fruit caused by C. fructicola.

CONCLUSION

HSAF was highly effective in reducing pear anthracnose caused by C. fructicola and has great potential to become a new type of fruit preservative.

Efficient direct preparation of antifungal Alteramide B from Lysobacter enzymogenes fermentation broth by macroporous resin adsorption

Alteramide B (ATB) is an antifungal metabolite produced by Lysobacter enzymogenes. However, its separation method has not been explored. This study attempted to directly adsorb ATB from fermentation broth using macroporous adsorption resins (MARs) NKA resin exhibited better adsorption as well as desorption capacities. The static and dynamic adsorption characteristics were assessed to determine the following optimal separation conditions: initial fermentation broth with a pH of 12.0, 2 BV/h flow rate, 8 BV loading volume, and 6 BV 80% aqueous ethanol for elution. After a single treatment, ATB content in the final product was higher by 4.51-fold (i.e, from 12.72 ± 1.21% to 57.35 ± 3.46%), resulting in a recovery yield of 86.20 ± 4.47%. In addition, NKA resin showed superior reusability within eight cycles of adsorption/desorption. The developed method is thus a simple, efficient, and economical process for ATB separation.

Knockout of Diguanylate Cyclase Genes in Lysobacter enzymogenes to Improve Production of Antifungal Factor and Increase Its Application in Seed Coating

Heat-stable antifungal factor (HSAF) is a broad-spectrum antifungal antibiotic produced by the biological control agent, Lysobacter enzymogenes. In our earlier works, we have applied HSAF to effectively control wheat and pear fungal disease. However, a major bottleneck in its practical application is the low HSAF production level; therefore, boosting its production is essential for its wide application. In the past, we find that c-di-GMP, a universal bacterial second messenger, is inhibitory to HSAF production. In this work, we further identified eight active diguanylate cyclases (DGCs) responsible for c-di-GMP synthesis in Lysobacter enzymogenes via both bioinformatics and genetic analyses. We generated a strain lacking seven active DGC genes and found that this DGC-modified strain, OH11LC, produced a higher HSAF amount in a c-di-GMP concentration-dependent manner. Subsequently, by employing OH11LC as the host fermentation strain, we could even produce a much higher HSAF amount (> 200-fold). After improving the HSAF production, we further developed a technique of seed coating method with HSAF, which turned out to be effective in fighting against the maize seed-borne filamentous pathogen, Pythium gramineacola. Overall, via combining strain modification and fermentation optimization, we demonstrated a good example of translating fundamental knowledge of bacterial c-di-GMP signaling into biological control application in which we relieved the inhibitory effect of c-di-GMP on HSAF biosynthesis by deleting a bunch of potentially active L. enzymogenes DGC genes to improve HSAF yield and to expand its usage in antifungal seed coating.

Biocontrol of Root Diseases and Growth Promotion of the Tuberous Plant Aconitum carmichaelii Induced by Actinomycetes Are Related to Shifts in the Rhizosphere Microbiota

Soil Actinomycetes have been used as biocontrol agents against soil-borne plant diseases, yet little is known about their effects on the structure of the rhizosphere microbiota and the long-term effects on crop yield and disease intensity after the application of Actinomycetes is stopped. Here, we conducted 3-year plot experiments to investigate the roles of two Actinomycetes strains (Streptomyces pactum Act12 and Streptomyces rochei D74) in the biocontrol of soil-borne root diseases and growth promotion of monkhood (Aconitum carmichaelii). We also examined their long-term effects after soil application of a mixed Actinomycetes preparation (spore powder) was completed. High-throughput sequencing was used to analyze shifts in the rhizosphere microbiota. The antifungal activity and root colonization ability of the two Actinomycetes were also tested. Disease severity of southern blight and root rot decreased following application of the Actinomycetes preparation, whereas biomass yield of tubers increased compared with the control group. Significant effects of disease control and plant growth promotion were also observed after application was stopped. The Actinomycetes preparation induced marked increases in the abundance of beneficial microbes and decreases in the abundance of harmful microbes in rhizosphere soil. Adding cell-free culture filtrates of both strains Act12 and D74 inhibited the growth of fungal pathogens capable of causing southern blight (Sclerotium rolfsii) and root rot (Fusarium oxysporum) in A. carmichaelii. A GFP-labeled strain was used to show that D74 can colonize roots of A. carmichaelii. In conclusion, a preparation of two Actinomycetes plays a role in the biocontrol of root diseases and growth promotion of A. carmichaelii by inhibiting pathogen growth and shaping the rhizosphere microbiota.

The AHL Quorum-Sensing System Negatively Regulates Growth and Autolysis in Lysobacter brunescens

Lysobacter species are emerging as novel sources of antibiotics, but the regulation of their physiological metabolism is still poorly understood. In this work, we extracted AHL (acyl-homoserine lactone) autoinducers, identified the structures of AHLs and described the AHL quorum-sensing system in Lysobacter brunescens OH23. AHLs were isolated from the supernatant of L. brunescens OH23, and ESI-MS/MS (electrospray ionization mass spectrometry) analysis revealed biosynthesis of three different AHL chemical structures by L. brunescens OH23: N-(3-oxohexanoyl)- homoserine lactone (HSL), 3-OH-C₁₀-HSL and C₈-HSL. The growth rate of AHL quorum-sensing knockout mutants was dramatically increased compared to that of wildtype. Sucrose consumptions were also twice as high in AHL quorum-sensing knockout mutants than that in wildtype in early-log phase. Additionally, expression of key genes related to sucrose metabolism α-glucosidase was enhanced in AHL quorum-sensing knockout mutants, which indicated that AHL quorum sensing negatively regulates sucrose uptake and metabolism which further affects the growth rate of L. brunescens. Furthermore, autolysis was strongly induced in AHL quorum-sensing knockout mutants compared to wildtype, suggesting that AHL quorum sensing plays a negative regulatory role in cell autolysis. Moreover, compared to wildtype, XSAC (Xanthomonas-specific antibiotic compound) production was significantly increased in AHL knockout mutants in the early-log and late-log phases, and surface motility capabilities are also enhanced also in AHL knockout mutants; the normalized data of XSAC production and surface motility and expressions of key genes related to these two phenotypes reveal that growth rare and autolysis strongly affects XSAC biosynthesis and surface motility rather than AHL quorum-sensing system. Our results show that the AHL quorum-sensing system negatively regulates cell growth and autolysis, and further maintain nutrition homeostasis and population stability in L. brunescens.

Efficient β-poly(l-malic acid) production from Jerusalem artichoke by Aureobasidium pullulans ipe-1 immobilized in luffa sponge matrices

β-poly(l-malic acid) (PMLA) production by Aureobasidium pullulans ipe-1 using Jerusalem artichoke tuber (JA) hydrolysate as a low cost carbon source was developed. The PMLA production was favored by JA pretreated with 0.06 M nitric acid without adding exogenous nitrogen sources into fermentation medium. With an initial 130 g/L total sugar of the JA hydrolysate, the highest PMLA productivity 0.52 g/L·h was achieved, which was increased by 2.0 folds compared to that with sole glucose case. To further enhance PMLA productivity, the cells were immobilized in luffa sponge matrices, and repeated batch culture was carried out for 4 cycles. The resulting PMLA productivity was further enhanced by 50% compared with the batch culture. The cost of PMLA production in the JA case was only 5.4% of that in the glucose case. The outcomes of this work provided a strategy of PMLA production on a commercial scale.

Protecting books from mould damage by decreasing paper bioreceptivity to fungal attack using decoloured cell-free supernatant of Lysobacter enzymogenes C3

AIMS

To evaluate whether decoloured cell-free supernatant of Lysobacter enzymogenes C3 can decrease paper bioreceptivity to fungal attack.

METHODS AND RESULTS

To prepare colourless C3 supernatant, single-factor design and uniform design were applied. The optimum conditions with high decolouration degree and low antifungal activity loss were achieved as follows: carbon granule content 1·6% (M/V), temperature 27°C, decolouring time 1·2 h and pH 8·0. An agar plate bioassay was used to assess the antifungal activity of the decoloured supernatant against the fungal isolates obtained from contaminated books, and strong suppression was observed. Small-sacle laboratory test was further introduced, in which common book papers were artificially inoculated with the fungal isolates, and then sprayed uniformly with decoloured supernatant or water. The results showed that, after treatment, the paper showed a significantly low extent of fungal colonization and high tensile strength, and maintained the same colour before and after treatment.

CONCLUSION

These results suggest that the decoloured C3 supernatant inhibits fungal growth on types of paper commonly used in books.

SIGNIFICANCE AND IMPACT OF THE STUDY

Decoloured C3 supernatant could be used as a preventive agent to protect books and other paper-based items against fungal growth.

Improving the production of a novel antifungal alteramide B in Lysobacter enzymogenes OH11 by strengthening metabolic flux and precursor supply

Lysobacter enzymogenes OH11 is currently considered to be a novel biocontrol agent for various plant fungi diseases. At present, only heat-stable antifungal factor (HSAF) has been isolated and identified in culture, although other active compounds also showed antifungal activity. In the present study, a novel active compound, alteramide B (ATB), which exhibits broad-spectrum antagonistic activity against phytopathogenic fungi and oomycetes, was isolated. The genes responsible for ATB biosynthesis were also determined. In addition, a strain producing ATB with minimal HSAF production was successfully generated by redirecting metabolic flux, namely L. enzymogenes OH57. Furthermore, ATB production increased to 893.32 ± 15.57 mg/L through medium optimization and precursor supply strategy, which was 24.36-fold higher than that of 10% tryptic soy broth (36.67 ± 1.63 mg/L). Taken together, this study indicates ATB has great development value as a biopesticide because of its bioactivity and high production.

Optimization of culture conditions for promoting heat-stable antifungal factor production level in Lysobacter enzymogenes

Heat-stable antifungal factor (HSAF), which was first isolated from Lysobacter enzymogenes, exhibits inhibitory activities against a wide range of pathogens; however, a low level of HSAF was obtained from L. enzymogenes cultured in 0.1 × tryptic soy broth (TSB), an amount that does not satisfy HSAF application in disease control. In this study, the optimization of media components and environmental conditions were examined for improving the production of HSAF from L. enzymogenes OH11. The one factor at a time method was used to screen optimal nitrogen and carbon sources and inorganic salt. Then the orthogonal matrix method was used to determine the optimal concentration of the media components and environmental factors. The results showed that the maximum level of HSAF (23361 mAU·s) was achieved when OH11 cultured in the media of 0.7% (w/v) soybean powder, 0.5% (w/v) glucose and 0.08% CaCl2 at 200 rpm at 30°C for 60 h, which is much higher than that cultured in 0.1 × TSB. This opens up the possibility of HSAF or L. enzymogenes utilization for biological control of plant disease.

Efficient production of heat-stable antifungal factor through integrating statistical optimization with a two-stage temperature control strategy in Lysobacter enzymogenes OH11

Background

Heat-stable antifungal factor (HSAF) is a newly identified broad-spectrum antifungal antibiotic from the biocontrol agent Lysobacter enzymogenes and is regarded as a potential biological pesticide, due to its novel mode of action. However, the production level of HSAF is quite low, and little research has reported on the fermentation process involved, representing huge obstacles for large-scale industrial production.

Results

Medium capacity, culture temperature, and fermentation time were identified as the most significant factors affecting the production of HSAF and employed for further optimization through statistical methods. Based on the analysis of kinetic parameters at different temperatures, a novel two-stage temperature control strategy was developed to improve HSAF production, in which the temperature was increased to 32 °C during the first 12 h and then switched to 26 °C until the end of fermentation. Using this strategy, the maximum HSAF production reached 440.26 ± 16.14 mg L^− 1, increased by 9.93% than that of the best results from single-temperature fermentation. Moreover, the fermentation time was shortened from 58 h to 54 h, resulting in the enhancement of HSAF productivity (17.95%) and yield (9.93%).

Conclusions

This study provides a simple and efficient method for producing HSAF that could be feasibly applied to the industrial-scale production of HSAF.

Electronic supplementary material

The online version of this article (10.1186/s12896-018-0478-2) contains supplementary material, which is available to authorized users.