Biocontrol potential of chitinases produced by newly isolated Chitinophaga sp. S167

Identification and characterization of chitinase producing marine microorganism: Unleashing the potential of chitooligosaccharides for bioethanol synthesis

The dwindling supply of the petroleum product and its carbon footprint has initiated search for a sustainable fuel and alternate feed-stocks. One such underexplored feedstock is chitin, a waste derived from sea food processing. The limitation of insolubility and crystallinity inherent in chitin is addressed with the chitin hydrolysates. In the present study, a chitinases producing marine isolate was isolated from the sediments of Arabian Sea from a depth of 20 m. In order to increase the expression of the chitinases, sequential optimisation using one factor at a time and Taguchi experimental designs were employed which resulted in a yield of 13.46 U/mL which was 2.62 fold higher than the initial bioprocess condition values. In a two-step refinery protocol, Candida albicans was evolved towards chitooligosaccharides using chemically synthesized hydrolysates. In a fed -batch fermentation design the Candida yielded a 12.8 % conversion of these commercial chitin oligosaccharides into bioethanol in a run time of 48 h. This is the first report demonstrating the potential of Candida to utilise chitin oligosaccharides for the production of bioethanol.

Next Generation Neuropeptide Y Receptor Small Molecule Agonists Inhibit Mosquito Biting Behavior

Female Aedes aegypti mosquitoes can spread disease-causing pathogens when they bite humans to obtain blood nutrients required for egg production. Following a complete blood meal, host-seeking is suppressed until eggs are laid. Neuropeptide Y-like Receptor 7 (NPYLR7) plays a role in endogenous host-seeking suppression and previous work identified small molecule NPYLR7 agonists that suppress host-seeking and blood feeding when fed to mosquitoes at high micromolar doses. Using structure activity relationship analysis and structure-guided design we synthesized 128 compounds with similarity to known NPYLR7 agonists. Although in vitro potency (EC50) was not strictly predictive of in vivo effect, we identified 3 compounds that suppressed blood feeding from a live host when fed to mosquitoes at a 1 μM dose, a 100-fold improvement over the original reference compound. Exogenous activation of NPYLR7 represents an innovative vector control strategy to block mosquito biting behavior and prevent mosquito/human host interactions that lead to pathogen transmission.

Pharmamedia and pectinase production by Bacillus subtilis Mz-12P

Bacterial isolates collected from the environment were screened for pectinolytic activity, and a strain with the highest activity was selected and identified as Bacillus subtilis Mz-12. The presence of pectin hydrolase, lyase, and esterase activities was confirmed. Pectinase was purified and characterized. Enzyme production was optimized with respect to temperature, pH, and growth medium. Enzyme stability and activity were characterized under different temperatures and pH values. The results showed that this strain was capable of producing high yields of pectinase in commercial medium (Pharmamedia) 24.6 U/mL compared to other media. The purified pectinase of 22.3 kDa produced was constitutive in nature. The isolated enzyme from this strain displayed a wide range of temperature and pH stability, with the optimal activity observed at pH 9.0 and 50°C. These results indicate that the B. subtilis Mz-12 strain is a favorable candidate for industrial enzyme production. The use of Pharmamedia is reported for first time for pectinase production.

A study of microbial diversity in a biofertilizer consortium

Biofertilizers supply living microorganisms to help plants grow and keep their health. This study examines the microbiome composition of a commercial biofertilizer known for its plant growth-promoting activity. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of a biofertilizer, with 163 fungal species and 485 bacterial genera found. The biofertilizer contains a variety of microorganisms previously reported to enhance nutrient uptake, phytohormone production, stress tolerance, and pathogen resistance in plants. Plant roots created a microenvironment that boosted bacterial diversity but filtered fungal communities. Notably, preserving the fungal-inoculated substrate proves critical for keeping fungal diversity in the root fraction. We described that bacteria were more diverse in the rhizosphere than in the substrate. In contrast, root-associated fungi were less diverse than the substrate ones. We propose using plant roots as bioreactors to sustain dynamic environments that promote the proliferation of microorganisms with biofertilizer potential. The study suggests that bacteria grow close to plant roots, while root-associated fungi may be a subset of the substrate fungi. These findings show that the composition of the biofertilizer may be influenced by the selection of microorganisms associated with plant roots, which could have implications for the effectiveness of the biofertilizer in promoting plant growth. In conclusion, our study sheds light on the intricate interplay between plant roots and the biofertilizer's microbial communities. Understanding this relationship can aid in optimizing biofertilizer production and application, contributing to sustainable agricultural practices and improved crop yields.

Effective combination of arugula vermicompost, chitin and inhibitory bacteria for suppression of the root-knot nematode Meloidogyne javanica and explanation of their beneficial properties based on microbial analysis

Root-knot nematodes (Meloidogyne spp.) are dangerous parasites of many crops worldwide. The threat of chemical nematicides has led to increasing interest in studying the inhibitory effects of organic amendments and bacteria on plant-parasitic nematodes, but their combination has been less studied. One laboratory and four glasshouse experiments were conducted to study the effect on M. javanica of animal manure, common vermicompost, shrimp shells, chitosan, compost and vermicompost from castor bean, chinaberry and arugula, and the combination of arugula vermicompost with some bacteria, isolated from vermicompost or earthworms. The extract of arugula compost and vermicompost, common vermicompost and composts from castor bean and chinaberry reduced nematode egg hatch by 12-32% and caused 13-40% mortality of second-stage juveniles in vitro. Soil amendments with the combination vermicompost of arugula + Pseudomonas. resinovorans + Sphingobacterium daejeonense + chitosan significantly increased the yield of infected tomato plants and reduced nematode reproduction factor by 63.1-76.6%. Comparison of chemical properties showed that arugula vermicompost had lower pH, EC, and C/N ratio than arugula compost. Metagenomics analysis showed that Bacillus, Geodermatophilus, Thermomonas, Lewinella, Pseudolabrys and Erythrobacter were the major bacterial genera in the vermicompost of arugula. Metagenomics analysis confirmed the presence of chitinolytic, detoxifying and PGPR bacteria in the vermicompost of arugula. The combination of arugula vermicompost + chitosan + P. resinovorans + S. daejeonense could be an environmentally friendly approach to control M. javanica.

Biocontrol potential of Chitinophaga flava HK235 producing antifungal-related peptide chitinocin

Botrytis cinerea is a necrotrophic fungal pathogen with an extremely broad host range, causing significant economic losses in agricultural production. In this study, we discovered a culture filtrate of bacterial strain HK235, which was identified as Chitinophaga flava, exhibiting high levels of antifungal activity against B. cinerea. From the HK235 culture filtrate, we isolated a new antimicrobial peptide molecule designated as chitinocin based on activity-guided fractionation followed by characterization of the amino acid composition and spectroscopic analyses. The HK235 culture filtrate and chitinocin completely inhibited both conidial germination and mycelial growth of B. cinerea at a concentration of 20% and 200 μg/mL, respectively. In addition to antibiosis against B. cinerea, the active compound chitinocin had a broad antifungal and antibacterial activity in vitro. When tomato plants were treated with the culture filtrate and chitinocin, the treatment strongly reduced the development of gray mold disease in a concentration-dependent manner compared to the untreated control. Here, considering the potent antifungal property in vitro and in vivo, we present the biocontrol potential of C. flava HK235 for the first time.

The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers

Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.

Microbial chitinases and their relevance in various industries

Chitin, the second most abundant biopolymer on earth after cellulose, is composed of β-1,4-N-acetylglucosamine (GlcNAc) units. It is widely distributed in nature, especially as a structural polysaccharide in the cell walls of fungi, the exoskeletons of crustaceans, insects, and nematodes. However, the principal commercial source of chitin is the shells of marine or freshwater invertebrates. Microbial chitinases are largely responsible for chitin breakdown in nature, and they play an important role in the ecosystem's carbon and nitrogen balance. Several microbial chitinases have been characterized and are gaining prominence for their applications in various sectors. The current review focuses on chitinases of microbial origin, their diversity, and their characteristics. The applications of chitinases in several industries such as agriculture, food, the environment, and pharmaceutical sectors are also highlighted.

Multiple enzymatic approaches to hydrolysis of fungal β-glucans by the soil bacterium Chitinophaga pinensis

The genome of the soil Bacteroidota Chitinophaga pinensis encodes a large number of glycoside hydrolases (GHs) with noteworthy features and potentially novel functions. Several are predicted to be active on polysaccharide components of fungal and oomycete cell walls, such as chitin, β-1,3-glucan and β-1,6-glucan. While several fungal β-1,6-glucanase enzymes are known, relatively few bacterial examples have been characterised to date. We have previously demonstrated that C. pinensis shows strong growth using β-1,6-glucan as the sole carbon source, with the efficient release of oligosaccharides from the polymer. We here characterise the capacity of the C. pinensis secretome to hydrolyse the β-1,6-glucan pustulan and describe three distinct enzymes encoded by its genome, all of which show different levels of β-1,6-glucanase activity and which are classified into different GH families. Our data show that C. pinensis has multiple tools to deconstruct pustulan, allowing the species' broad utility of this substrate, with potential implications for bacterial biocontrol of pathogens via cell wall disruption. Oligosaccharides derived from fungal β-1,6-glucans are valuable in biomedical research and drug synthesis, and these enzymes could be useful tools for releasing such molecules from microbial biomass, an underexploited source of complex carbohydrates.

Isolation, Identification and Characterization of Growth Parameters of Pseudomonas putida HSM-C2 with Coumarin-Degrading Bacteria

Natural coumarins contribute to the aroma of licorice, and they are often used as a flavoring and stabilizing agents. However, coumarins usage in food has been banned by various countries due to its toxic effect. In this study, a strain of HSM-C2 that can biodegrade coumarin with high efficiency was isolated from soil and identified as Pseudomonas putida through performing 16S rDNA sequence analysis. The HSM-C2 catalyzed the biodegradation up to 99.83% of 1 mg/mL coumarin within 24 h under optimal culture conditions, such as 30 °C and pH 7, which highlights the strong coumarin biodegrading potential of this strain. The product, such as dihydrocoumarin, generated after the biodegradation of coumarin was identified by performing GC-MS analysis. The present study provides a theoretical basis and microbial resource for further research on coumarin biodegradation.

Degradation of Decabromodiphenyl Ether in an Aerobic Clay Slurry Microcosm Using a Novel Immobilization Technique

A novel chitosan immobilization technique that entraps photocatalyst and microbes was developed and applied to decompose decabromodiphenyl ether (BDE-209) in a clay slurry microcosm. The optimized conditions for immobilization were obtained by mixing 1.2% (w/v) chitosan dissolved in 1% (v/v) acetic acid with nano-TiO2 particles and the BDE-209-degrading bacterial mixed culture. This aqueous mixture was injected into 1% (w/v) water solution containing sodium tripolyphosphate to form spherical immobilized beads. The surface of the immobilized beads was reinforced by 0.25% (v/v) glutaraldehyde cross-linking. These beads had enough mechanical strength during BDE-209 degradation to maintain their shape in the system at a stirring rate of 200-rpm, while undergoing continuous 365 nm UVA irradiation. This novel TiO2-Yi-Li immobilized chitosan beads system allowed a successful simultaneous integration of photolysis, photocatalysis and biodegradation to remove BDE-209. The remaining percentage of BDE-209 was 41% after 70 days of degradation using this system. The dominant bacteria in the BDE-209-degrading bacterial mixed culture during remediation were Chitinophaga spp., Methyloversatilis spp., Terrimonas spp. and Pseudomonas spp. These bacteria tolerated the long-term UVA irradiation and high-level free radicals present, while utilizing BDE-209 as their primary carbon resource. This new method has great potential for the treatment of a range of pollutants.

Analysis of Internal and External Microorganism Community of Wild Cicada Flowers and Identification of the Predominant Cordyceps cicadae Fungus

The parasitoid fungus Cordyceps cicadae, whose fruiting bodies are known in China as “chan hua,” literally “cicada flower,” has been used as a traditional Chinese medicinal ingredient for centuries. However, systematic disclosure of the vital factors responsible for the formation of wild cicada flower is limited. Here, we determined the physicochemical properties of soil and simultaneously analyzed the diversities and the structures of microbial community inhabiting the coremia, sclerotia, and soil around wild cicada flowers through high-throughput sequencing. Our results indicated that cicada flower more preferentially occurred in acidic soil (pH 5.9) with abundant moisture content (MC), total nitrogen (TN), and organic matter (OM). The dominant fungal genera in soil mainly included Isaria, f__Clavariaceae_Unclassified, Umbelopsis, f__Chaetomiaceae_Unclassified, Mortierella, f__Sordariaceae_Unclassified, and Arcopilus. Among them, C. cicadae was the only fungus that was massively detected in both the coremia and sclerotia with abundance of 83.5 and 53.6%, respectively. Based on this, a C. cicadae strain named AH10-4 with excellent adenosine- and N⁶-(2-hydroxyethyl)-adenosine (HEA)-producing capability was successfully isolated. However, to the aspect of bacteria, Burkholderia–Caballeronia–Paraburkholderia, Bacillus, Acidibacter, f__Xanthobacteraceae_Unclassified, and Candidatus_Solibacter were the dominant genera in soil. Pedobacter, f__Enterobacteriaceae_Unclassified, Pandoraea, Achromobacter, Stenotrophomonas, Burkholderia–Caballeronia–Paraburkholderia, and Chitinophaga were the dominant genera in the coremia and sclerotia. Notably, Burkholderia–Caballeronia–Paraburkholderia was the shared bacteria among them with high abundance of 3.1, 11.4, and 5.2% in the sclerotia, coremia, and soil, respectively. However, the possible role of these bacteria to the occurrence of cicada flower has been unclear to our knowledge. By analyzing the correlation between physicochemical properties and microbial community of soil, we found that MC, Fe, and Zn were significantly negatively correlated with soil Isaria and that Cu was significantly negatively correlated with most dominant soil bacterial genera. But Mg was significantly positively correlated with most dominant taxa. This study provides new insight into the formation mechanisms of cicada flower and may contribute to the large-scale cultivation of cicada flowers.

Current Perspectives on Chitinolytic Enzymes and Their Agro-Industrial Applications

Chitinases are a large and diversified category of enzymes that break down chitin, the world's second most prevalent polymer after cellulose. GH18 is the most studied family of chitinases, even though chitinolytic enzymes come from a variety of glycosyl hydrolase (GH) families. Most of the distinct GH families, as well as the unique structural and catalytic features of various chitinolytic enzymes, have been thoroughly explored to demonstrate their use in the development of tailor-made chitinases by protein engineering. Although chitin-degrading enzymes may be found in plants and other organisms, such as arthropods, mollusks, protozoans, and nematodes, microbial chitinases are a promising and sustainable option for industrial production. Despite this, the inducible nature, low titer, high production expenses, and susceptibility to severe environments are barriers to upscaling microbial chitinase production. The goal of this study is to address all of the elements that influence microbial fermentation for chitinase production, as well as the purifying procedures for attaining high-quality yield and purity.

Pathway for biodegrading coumarin by a newly isolated Pseudomonas sp. USTB-Z

Coumarin is widely used in personal care products and pharmaceutical industry, which leads to the release of this compound into environment as an emerging contaminant. Here, a promising strain USTB-Z for biodegrading coumarin was successfully isolated from botanical soil and characterized as a potential novel Pseudomonas sp. based on 16S rDNA sequence analysis and orthologous average nucleotide identity tool. Initial coumarin up to 800 mg/L could be completely removed by USTB-Z within 48 h at the optimal culture conditions of pH 7.3 and 30 °C, which indicates that USTB-Z has a strong capacity in coumarin biodegradation. The biodegradation products of coumarin were further investigated using HPLC and Q-TOF LC/MS, and melilotic acid and 2,3-dihydroxyphenylpropionic acid were identified. The draft genome of strain USTB-Z was sequenced by Illumina NovaSeq, and 21 CDSs for NAD (P)-dependent oxidoreductase, 43 CDSs for hydrolase, 1 CDS for FAD-depend monooxygenase, 1 CDS for 3-hydroxycinnamic acid hydroxylase, 21 CDSs for dioxygenase, and 5 CDSs for fumarylacetoacetate (FAA) hydrolase were annotated and correlated to coumarin biodegradation. The present study provides a theoretical basis and microbial resource for further research on the coumarin biodegradation.

Drought Exposed Burkholderia seminalis JRBHU6 Exhibits Antimicrobial Potential Through Pyrazine-1,4-Dione Derivatives Targeting Multiple Bacterial and Fungal Proteins

The present study aimed to explore the antimicrobial potentials of soil bacteria and identify the bioactive compounds and their likely targets through in silico studies. A total 53 bacterial isolates were screened for their antimicrobial potential of which the strain JRBHU6 showing highest antimicrobial activity was identified as Burkholderia seminalis (GenBank accession no. MK500868) based on 16S ribosomal RNA (rRNA) gene sequencing and phylogenetic analysis. B. seminalis JRBHU6 also produced hydrolytic enzymes chitinases and cellulase of significance in accrediting its antimicrobial nature. The bioactive metabolites produced by the isolate were extracted in different organic solvents among which methanolic extract showed best growth-suppressing activities toward multidrug resistant Staphylococcus aureus and fungal strains, viz Fusarium oxysporum, Aspergillus niger, Microsporum gypseum, Trichophyton mentagrophytes, and Trichoderma harzianum. The antimicrobial compounds were purified using silica gel thin layer chromatography and high-performance liquid chromatography (HPLC). On the basis of spectroscopic analysis, the bioactive metabolites were identified as pyrrolo(1,2-a)pyrazine-1,4-dione,hexahydro (PPDH) and pyrrolo(1,2-a)pyrazine-1,4-dione, hexahydro-3(2-methylpropyl) (PPDHMP). In silico molecular docking studies showed the bioactive compounds targeting fungal and bacterial proteins, among which PPDHMP was multitargeting in nature as reported for the first time through this study.

Identification and Characterization of a Newly Isolated Chitinase-Producing Strain Bacillus licheniformis SSCL-10 for Chitin Degradation

Chitinases or chitinolytic enzymes have different applications in the field of medicine, agriculture, and industry. The present study is aimed at developing an effective hyperchitinase-producing mutant strain of novel Bacillus licheniformis. A simple and rapid methodology was used for screening potential chitinolytic microbiota by chemical mutagenesis with ethylmethane sulfonate and irradiation with UV. There were 16 mutant strains exhibiting chitinase activity. Out of the chitinase-producing strains, the strain with maximum chitinase activity was selected, the protein was partially purified by SDS-PAGE, and the strain was identified as Bacillus licheniformis (SSCL-10) with the highest specific activity of 3.4 U/mL. The induced mutation model has been successfully implemented in the mutant EMS-13 (20.2 U/mL) that produces 5-6-fold higher yield of chitinase, whereas the mutant UV-11 (13.3 U/mL) has 3-4-fold greater chitinase activity compared to the wild strain. The partially purified chitinase has a molecular weight of 66 kDa. The wild strain (SSCL-10) was identified as Bacillus licheniformis using 16S rRNA sequence analysis. This study explores the potential applications of hyperchitinase-producing bacteria in recycling and processing chitin wastes from crustaceans and shrimp, thereby adding value to the crustacean industry.

The Use of Plant Growth-Promoting Bacteria to Prevent Nematode Damage to Plants

Simple Summary

It has been estimated that 100 g of bulk soil can host about 2000–4000 nematodes and this amount is increased 5-fold in the rhizosphere. A certain number of these nematodes are pathogenic for plants and cause yield and economic losses. Application of chemical nematicides is the most common method used to reduce nematode populations, but these chemicals can have a negative impact on both the environment and human health. Therefore, other more environmentally friendly methods of suppression of plant-parasitic nematodes have been proposed. Among them, the use of plant beneficial soil bacteria, behaving as biocontrol agents against nematodes, represent a potential alternative to chemicals.

Abstract

Plant-parasitic nematodes have been estimated to annually cause around US $173 billion in damage to plant crops worldwide. Moreover, with global climate change, it has been suggested that the damage to crops from nematodes is likely to increase in the future. Currently, a variety of potentially dangerous and toxic chemical agents are used to limit the damage to crops by plant-parasitic nematodes. As an alternative to chemicals and a more environmentally friendly means of decreasing nematode damage to plants, researchers have begun to examine the possible use of various soil bacteria, including plant growth-promoting bacteria (PGPB). Here, the current literature on some of the major mechanisms employed by these soil bacteria is examined. It is expected that within the next 5–10 years, as scientists continue to elaborate the mechanisms used by these bacteria, biocontrol soil bacteria will gradually replace the use of chemicals as nematicides.