Synergic chitin degradation by Streptomyces sp. SCUT-3 chitinases and their applications in chitinous waste recycling and pathogenic fungi biocontrol

Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation

Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.IMPORTANCESoil moisture and porosity are critical in shaping microbial metabolism. However, accurately representing the soil environment in tractable laboratory experiments remains a challenging frontier. Through our reduced complexity microbial consortium experiment in porous media, we reveal that predicting microbial metabolism from gene-based pathways alone often falls short of capturing the intricate phenotypes driven by cellular interactions. Our findings highlight that porosity and moisture significantly affect chitin decomposition, with environmental matrix (i.e., glass beads) shifting community metabolism towards stress tolerance, reduced resource acquisition, and increased carbon conservation, ultimately invoking unique microbial strategies not evident in liquid cultures. Moreover, we find evidence that changes in moisture relate to community shifts regarding motility, transporters, and biofilm formation, which likely influence chitin degradation. Ultimately, our incubations showcase how reduced complexity communities can be informative of microbial metabolism and present a useful alternative to liquid cultures for studying soil microbial phenotypes.

Identification of chitinase from Bacillus velezensis strain S161 and its antifungal activity against Penicillium digitatum

Previous studies have demonstrated the presence of chitinase in Bacillus velezensis through extensive genomic sequencing and experimental analyses. However, the detailed structure, functional roles, and antifungal activity of these chitinases remain poorly characterized. In this study, genomic screening identified three genes-chiA, chiB, and lpmo10-associated with chitinase degradation in B. velezensis S161. These genes encode chitinases ChiA and ChiB, and lytic polysaccharide monooxygenase LPMO10. Both ChiA and ChiB contain two CBM50 binding domains and one catalytic domain, whereas LPMO10 includes a signal peptide and a single catalytic domain. The chitinases ChiA, its truncated variant ChiA2, and ChiB were heterologously expressed in Escherichia coli. The purified enzymes efficiently degraded colloidal chitin and inhibited the spore germination of Penicillium digitatum. Notably, even after losing one CBM50 domain, the resultant enzyme, consisting of the remaining CBM50 domain and the catalytic domain, maintained its colloidal chitin hydrolysis and antifungal activity, indicating commendable stability. These results underscore the role of B. velezensis chitinases in suppressing plant pathogenic fungi and provide a solid foundation for developing and applying chitinase-based biocontrol strategies.

Biochemical Properties of a Novel Cold-Adapted GH19 Chitinase with Three Chitin-Binding Domains from Chitinilyticum aquatile CSC-1 and Its Potential in Biocontrol of Plant Pathogenic Fungi

GH19 (glycoside hydrolase 19) chitinases play crucial roles in the enzymatic conversion of chitin and biocontrol of phytopathogenic fungi. Herein, a novel multifunctional chitinase of GH19 (CaChi19A), which contains three chitin-binding domains (ChBDs), was successfully cloned from Chitinilyticum aquatile CSC-1 and heterologously expressed in Escherichia coli. We also generated truncated mutants of CaChi19A_ΔI, CaChi19A_ΔIΔII, and CaChi19A_CatD consisting of two ChBDs and a catalytic domain, one ChBD and a catalytic domain, and only a catalytic domain, respectively. CaChi19A, CaChi19A_ΔI, CaChi19A_ΔIΔII, and CaChi19A_CatD exhibited cold adaptation, as their relative enzyme activities at 5 °C were 40.7, 51.6, 66.2, and 82.6%, respectively. Compared with CaChi19A and other variants, CaChi19A_ΔIΔII demonstrated a higher level of stability below 50 °C and retained relatively high activity over a wide pH range of 5-12. Analysis of the hydrolysis products revealed that CaChi19A and CaChi19A_ΔIΔII exhibit exoacting, endoacting, and N-acetyl-β-d-glucosaminidase activities toward colloidal chitin. Furthermore, CaChi19A and CaChi19A_ΔIΔII exhibited inhibitory effects on the hyphal growth of Fusarium oxysporum, Fusarium redolens, Fusarium fujikuroi, Fusarium solani, and Coniothyrium diplodiella, thereby illustrating effective biocontrol activity. These results indicated that CaChi19A and CaChi19A_ΔIΔII show advantages in some applications where low temperatures were demanded in industries as well as the biocontrol of fungal diseases in agriculture.

Identification, expression, and characterization of a marine-derived chitinase Ce0303 from Chitiniphilus eburneus YS-30 with exo- and endo-hydrolytic properties

N-acetyl-oligosaccharides exhibit antioxidant and antibacterial activities. However, the low catalytic efficiency of chitinase on crystalline chitin hinders the eco-friendly production of N-acetyl-oligosaccharides. A marine-derived chitinase-producing strain Chitiniphilus eburneus YS-30 was screened in this study. The genome of C. eburneus YS-30 spans 4,522,240 bp, with a G + C content of 63.96 % and 4244 coding genes. Among the chitinases secreted by C. eburneus YS-30, Ce0303 showed the highest content at 19.10 %, with a molecular weight of 73.5 kDa. Recombinant Ce0303 exhibited optimal activity at 50 °C and pH 5.0, maintaining stability across pH 4.0-10.0. Ce0303 demonstrated strict substrate specificity, with a specific activity toward colloidal chitin of 6.41 U mg-1, Km of 2.34 mg mL-1, and kcat of 3.27 s-1. The specific activity of Ce0303 toward α-chitin was 18.87 % of its activity on colloidal chitin. Ce0303 displayed both exo- and endo-hydrolytic properties, primarily producing (GlcNAc)1-3 from colloidal chitin. The structure of Ce0303 includes one catalytic domain and two chitin-binding domains. Docking results revealed that the GlcNAc at -1 subsite formed two hydrogen bonds with conserved Trp380. The hydrolytic properties of Ce0303 will provide technical support for the comprehensive utilization of crustacean raw materials.

Production of a new chitinase from Nocardiopsis halophila TN-X8 utilizing bio-waste from the blue swimming crab: enzyme characterization and immobilization

In accordance with the framework of the Circular Blue Bioeconomy in the Mediterranean region, the objective of this study was to evaluate the biotransformation of blue swimming crab (Portunus segnis) residues obtained from the port of Sfax by an extracellular chitinase produced by Nocardiopsis halophila strain TN-X8 isolated from Chott El Jerid (Tozeur, Tunisia). From the analysis of multiple extremophilic Actinomycetota, it was determined that strain TN-X8 exclusively utilized 60 g/L of raw blue swimming crab as its carbon and energy source, achieving a chitinase activity of approximately 950 U/mL following a 6-day incubation period at 40 °C. Pure chitinase, designated as ChiA-Nh30, was obtained after heat treatment, followed by ammonium sulfate fractionation and Sephacryl® S-200 column chromatography. The maximum ChiA-Nh30 activity was observed at pH 3 and 75 °C. Interestingly, compared with cyclohexamidine, ChiA-Nh30 showed a good antifungal effect against four pathogenic fungi. Furthermore, when using colloidal chitin as substrate, ChiA-Nh30 demonstrated a higher degree of catalytic efficiency than the commercially available Chitodextrinase®. In addition, ChiA-Nh30 could be immobilized by applying encapsulation and encapsulation-adsorption techniques. The kaolin and charcoal used acted as excellent binders, resulting in improved ChiA-Nh30 stability. For the immobilized ChiA-Nh30, the yield of N-acetyl-D-glucosamine monomers released from 20% (w/v) blue swimming crab residues increased by 3.1 (kaolin) and 2.65 (charcoal) times, respectively.

Chitinases: expanding the boundaries of knowledge beyond routinized chitin degradation

Chitinases, enzymes that degrade chitin, have long been studied for their role in various biological processes. They play crucial roles in the moulting process of invertebrates, the digestion of chitinous food, and defense against chitin-bearing pathogens. Additionally, chitinases are involved in physiological functions in crustaceans, such as chitinous food digestion, moulting, and stress response. Moreover, chitinases are universally distributed in organisms from viruses to mammals and have diverse functions including tissue degradation and remodeling, nutrition uptake, pathogen invasion, and immune response regulation. The discovery of these diverse functions expands our understanding of the biological significance and potential applications of chitinases. However, recent research has shown that chitinases possess several other functions beyond just chitin degradation. Their potential as biopesticides, therapeutic agents, and tools for bioremediation underscores their significance in addressing global challenges. More importantly, we noted that they may be applied as bioweapons if ethical regulations regarding production, engineering and application are overlooked.

Sustainable valorizing high-protein feather waste utilization through solid-state fermentation by keratinase-enhanced Streptomyces sp. SCUT-3 using a novel promoter

Feather waste, a rich source of proteins, has traditionally been processed through high-temperature puffing and acid-base hydrolysis, contributing to generation of greenhouse gases and H2S. To address this issue, we employed circular economy techniques to recover the nutritional value of feather waste. Streptomyces sp. SCUT-3, an efficient proteolytic and chitinolytic bacterium, was isolated for feather degradation previously. This study aimed to valorize feather waste for feed purposes by enhancing its feather transformation ability through promoter optimization. Seven promoters were identified through omics analysis and compared to a common Streptomyces promoter ermE*p. The strongest promoter, p24880, effectively enhanced the expression of three candidate keratinases (Sep39, Sep40, and Sep53). The expression efficiency of double-, triple-p24880 and sandwich p24880-sep39-p24880 promoters were further verified. The co-overexpression strain SCUT-3-p24880-sep39-p24880-sep40 exhibited a 16.21-fold increase in keratinase activity compared to the wild-type. Using this strain, a solid-state fermentation process was established that increased the feather/water ratio (w/w) to 1:1.5, shortened the fermentation time to 2.5 days, and increased soluble peptide and free amino acid yields to 0.41 g/g and 0.14 g/g, respectively. The resulting has high protein content (90.49 %), with high in vitro digestibility (94.20 %). This method has the potential to revolutionize the feather waste processing industry.

Biocontrol Potential of Serratia Marcescens (B8) and Bacillus sp. (B13) Isolated from Urban Mangroves in Raposa, Brazil

This study analyzed the antifungal potential of 16 bacterial strains isolated from mangrove sediment. Bacterial selection was conducted in a solid medium. This was followed by the production and extraction of metabolites using ethyl acetate to evaluate chitinase production, antifungal activity, and toxicity toward Allium cepa and Tenebrio molitor. Bacterial strains B8, B11, and B13 produced the largest inhibition halos (>30 mm) toward Fusarium solani, Fusarium oxysporum, and Rhizoctonia solani fungi. Strains B1, B3, B6, B8, B11, B13, B14, and B16 produced chitinases. In assays using liquid media, B8 and B13 produced the largest inhibition halos. Exposing the fungal inocula to metabolic extracts of strains B6, B8, B11, B13, B14, B15, and B16 caused micromorphological alterations in the inocula, culminating in the inhibition of R. solani sporulation and spore germination. Toxicity tests using Allium cepa and Tenebrio molitor revealed that the metabolites showed low toxicity. Six of the bacterial strains were molecularly identified to species levels, and a further two to genus level. These included Serratia marcescens (B8), which exhibited activity in all tests. Mangroves provide a useful resource for the isolation of microorganisms for biocontrol. Among the isolates, Serratia marcescens and Bacillus spp. showed the greatest potential to produce metabolites for use as biocontrol agents in agriculture.

Ascochyta Blight in Chickpea: An Update

Chickpea (Cicer arietinum L.), one of the most cultivated legumes worldwide, is crucial for the economy of several countries and a valuable source of nutrients. Yields may be severely affected by Ascochyta blight, a disease caused by the fungus Ascochyta rabiei. Molecular and pathological studies have not yet managed to establish its pathogenesis, since it is highly variable. Similarly, much remains to be elucidated about plant defense mechanisms against the pathogen. Further knowledge of these two aspects is fundamental for the development of tools and strategies to protect the crop. This review summarizes up-to-date information on the disease's pathogenesis, symptomatology, and geographical distribution, as well as on the environmental factors that favor infection, host defense mechanisms, and resistant chickpea genotypes. It also outlines existing practices for integrated blight management.