Biocontrol potential of Halotolerant bacterial chitinase from high yielding novel Bacillus Pumilus MCB-7 autochthonous to mangrove ecosystem

Comparative metagenomic analysis from Sundarbans ecosystems advances our understanding of microbial communities and their functional roles

The Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world's largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz., Alphaproteobacteria, Actinomycetota, Bacilli, Clostridia, Desulfobacterota, Gammaproteobacteria, and Nitrospira, from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like Alkalibacillus haloalkaliphilus, Halomonas anticariensis, and Salinivibrio socompensis. We found some probiotic species, viz., Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei and Vibrio fluvialis, from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were Nitrococcus mobilis, Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii, and others. Methanogenic archaea, viz., Methanoculleus marisnigri, Methanobrevibacter gottschalkii, and Methanolacinia petrolearia, were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz., Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans, and Methylosarcina lacus are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified, Pseudomonas alcaligenes, Pseudomonas mendocina, Paracoccus denitrificans, and Shewanella putrefaciens play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria.

Polysaccharide degradation in Cellvibrionaceae: Genomic insights of the novel chitin-degrading marine bacterium, strain KSP-S5-2, and its chitinolytic activity

In this study, we present the genome characterization of a novel chitin-degrading strain, KSP-S5-2, and comparative genomics of 33 strains of Cellvibrionaceae. Strain KSP-S5-2 was isolated from mangrove sediment collected in Balik Pulau, Penang, Malaysia, and its 16S rRNA gene sequence showed the highest similarity (95.09%) to Teredinibacter franksiae. Genome-wide analyses including 16S rRNA gene sequence similarity, average nucleotide identity, digital DNA-DNA hybridization, and phylogenomics, suggested that KSP-S5-2 represents a novel species in the family Cellvibrionaceae. The Cellvibrionaceae pan-genome exhibited high genomic variability, with only 1.7% representing the core genome, while the flexible genome showed a notable enrichment of genes related to carbohydrate metabolism and transport pathway. This observation sheds light on the genetic plasticity of the Cellvibrionaceae family and the gene pools that form the basis for the evolution of polysaccharide-degrading capabilities. Comparative analysis of the carbohydrate-active enzymes across Cellvibrionaceae strains revealed that the chitinolytic system is not universally present within the family, as only 18 of the 33 genomes encoded chitinases. Strain KSP-S5-2 displayed an expanded repertoire of chitinolytic enzymes (25 GH18, two GH19 chitinases, and five GH20 β-N-acetylhexosaminidases) but lacked genes for agar, xylan, and pectin degradation, indicating specialized enzymatic machinery focused primarily on chitin degradation. Further, the strain degraded 90% of chitin after 10 days of incubation. In summary, our findings provided insights into strain KSP-S5-2's genomic potential, the genetics of its chitinolytic system, genomic diversity within the Cellvibrionaceae family in terms of polysaccharide degradation, and its application for chitin degradation.

Novel Endophytic Pseudescherichia sp. GSE25 Strain Significantly Controls Fusarium graminearum and Reduces Deoxynivalenol in Wheat

Fusarium heading blight (FHB) is a devastating disease in wheat, primarily caused by field invasion of Fusarium graminearum. Due to the scarcity of resistant wheat varieties, the agricultural sector resorts to chemical fungicides to control FHB incidence. On the other hand, biocontrol represents a promising, eco-friendly approach aligned with sustainable and green agriculture concepts. In the present study, a bacterial endophyte, Pseudescherichia sp. (GSE25), was isolated from wheat seeds and identified through complete genome sequencing and phylogenetic analysis. In vitro testing of this endophytic strain demonstrated strong antifungal activity against F. graminearum PH-1 by inhibiting spore germination, suppressing germ tube growth, and causing cell membrane damage. Under field conditions, the strain GSE25 significantly reduced the FHB incidence and the associated deoxynivalenol mycotoxin accumulation by over 60% and 80%, respectively. These findings highlight the potential of the isolated bacterial endophyte Pseudescherichia sp. GSE25 strain as a biocontrol agent in protecting wheat from FHB-caused F. graminearum. This is the first report showing a biocontrol effect of Pseudescherichia sp. a strain against phytopathogens.

Biocontrol of fungal phytopathogens by Bacillus pumilus

Plant growth-promoting bacteria are one of the most interesting methods of controlling fungal phytopathogens. These bacteria can participate in biocontrol via a variety of mechanisms including lipopeptide production, hydrolytic enzymes (e.g., chitinase, cellulases, glucanase) production, microbial volatile organic compounds (mVOCs) production, and induced systemic resistance (ISR) triggering. Among the bacterial genera most frequently studied in this aspect are Bacillus spp. including Bacillus pumilus. Due to the range of biocontrol traits, B. pumilus is one of the most interesting members of Bacillus spp. that can be used in the biocontrol of fungal phytopathogens. So far, a number of B. pumilus strains that exhibit biocontrol properties against fungal phytopathogens have been described, e.g., B. pumilus HR10, PTB180, B. pumilus SS-10.7, B. pumilus MCB-7, B. pumilus INR7, B. pumilus SE52, SE34, SE49, B. pumilus RST25, B. pumilus JK-SX001, and B. pumilus KUDC1732. B. pumilus strains are capable of suppressing phytopathogens such as Arthrobotrys conoides, Fusarium solani, Fusarium oxysporum, Sclerotinia sclerotiorum, Rhizoctonia solani, and Fagopyrum esculentum. Importantly, B. pumilus can promote plant growth regardless of whether it alters the native microbiota or not. However, in order to increase its efficacy, research is still needed to clarify the relationship between the native microbiota and B. pumilus. Despite that, it can already be concluded that B. pumilus strains are good candidates to be environmentally friendly and commercially effective biocontrol agents.

Bioengineered microbial strains for detoxification of toxic environmental pollutants

Industrialization and other anthropogenic human activities pose significant environmental risks. As a result of the hazardous pollution, numerous living organisms may suffer from undesirable diseases in their separate habitats. Bioremediation, which removes hazardous compounds from the environment using microbes or their biologically active metabolites, is one of the most successful remediation approaches. According to the United Nations Environment Program (UNEP), deteriorating soil health negatively impacts food security and human health over time. Soil health restoration is critical right now. Microbes are widely known for their importance in cleaning up toxins present in the soil, such as heavy metals, pesticides, and hydrocarbons. However, the capacity of local bacteria to digest these pollutants is limited, and the process takes an extended time. Genetically modified organisms (GMOs), whose altered metabolic pathways promote the over-secretion of a variety of proteins favorable to the bioremediation process, can speed up the breakdown process. The need for remediation procedures, degrees of soil contamination, site circumstances, broad adoptions, and numerous possibilities occurring at various cleaning stages are all studied in detail. Massive efforts to restore contaminated soils have also resulted in severe issues. This review focuses on the enzymatic removal of hazardous pollutants from the environment, such as pesticides, heavy metals, dyes, and plastics. There are also in-depth assessments of present discoveries and future plans for efficient enzymatic degradation of hazardous pollutants.

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.

Antagonistic Activity and Mechanism of Bacillus subtilis XZ16-1 Suppression of Wheat Powdery Mildew and Growth Promotion of Wheat

Wheat powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is one of the most serious wheat diseases in the world. Biological control is considered an environmentally safe approach to control plant diseases. Here, to develop effective biocontrol agents for controlling wheat powdery mildew, antagonistic strain XZ16-1 was isolated and identified as Bacillus subtilis based on the morphological, biochemical, and physiological characteristics and 16S rDNA sequence. The culture filtrate of B. subtilis XZ16-1 and its extracts had a significant inhibitory effect on the spore germination of Bgt. Moreover, the therapeutic and prevention efficacy of the 100% culture filtrate on wheat powdery mildew reached 81.18 and 83.72%, respectively, which was better than that of chemical fungicide triadimefon. Further antimicrobial mechanism analysis showed that the XZ16-1 culture filtrate could inhibit the development of powdery mildew spores by disrupting the cell membrane integrity, causing reductions in the mitochondrial membrane potential, and inducing the accumulation of reactive oxygen species in the spores. Biochemical detection indicated that XZ16-1 could solubilize phosphate, fix nitrogen, and produce hydrolases, lipopeptides, siderophores, and indole-3-acetic acid. Defense-related enzymes activated in wheat seedlings treated with the culture filtrate indicated that disease resistance was induced in wheat to resist pathogens. Furthermore, a 10⁶ CFU/ml suspension of XZ16-1 increased the height, root length, fresh weight, and dry weight of wheat seedlings by 77.13, 63.46, 76.73, and 19.16%, respectively, and showed good growth-promotion properties. This study investigates the antagonistic activity and reveals the action mechanism of XZ16-1, which can provide an effective microbial agent for controlling wheat powdery mildew.

A Contemporary Appraisal on Impending Industrial and Agricultural Applications of Thermophilic-Recombinant Chitinolytic Enzymes from Microbial Sources

The ability of chitinases to degrade the second most abundant polymer, chitin, into potentially useful chitooligomers and chitin derivatives has not only rendered them fit for chitinous waste management but has also made them important from industrial point of view. At the same time, they have also been recognized to have an imperative role as promising biocontrol agents for controlling plant diseases. As thermostability is an important property for an industrially important enzyme, various bacterial and fungal sources are being exploited to obtain such stable enzymes. These stable enzymes can also play a role in agriculture by maintaining their stability under adverse environmental conditions for longer time duration when used as biocontrol agent. Biotechnology has also played its role in the development of recombinant chitinases with enhanced activity, thermostability, fungicidal and insecticidal activity via recombinant DNA techniques. Furthermore, a relatively new approach of generating pathogen-resistant transgenic plants has opened new ways for sustainable agriculture by minimizing the yield loss of valuable crops and plants. This review focuses on the potential applications of thermostable and recombinant microbial chitinases in industry and agriculture.

Bioengineered Microbes for Soil Health Restoration - Present Status and Future

According to the United Nations Environment Programme (UNEP), soil health is declining over the decades and it has an adverse impact on human health and food security. Hence, soil health restoration is a need of the hour. It is known that microorganisms play a vital role in remediation of soil pollutants like heavy metals, pesticides, hydrocarbons, etc. However, the indigenous microbes have a limited capacity to degrade these pollutants and it will be a slow process. Genetically modified organisms (GMOs) can catalyze the degradation process as their altered metabolic pathways lead to hypersecretions of various biomolecules that favor the bioremediation process. This review provides an overview on the application of bioengineered microorganisms for the restoration of soil health by degradation of various pollutants. It also sheds light on the challenges of using GMOs in environmental application as their introduction may affect the normal microbial community in soil. Since soil health also refers to the potential of native organisms to survive, the possible changes in the native microbial community with the introduction of GMOs are also discussed. Finally, the future prospects of using bioengineered microorganisms in environmental engineering applications to make the soil fertile and healthy have been deciphered. With the alarming rates of soil health loss, the treatment of soil and soil health restoration need to be fastened to a greater pace and the combinatorial efforts unifying GMOs, plant growth-promoting rhizobacteria, and other soil amendments will provide an effective solution to soil heath restoration ten years ahead.

Purification, characterization, and antifungal activity of Bacillus cereus strain NK91 chitinase from rhizospheric soil samples of Himachal Pradesh, India

Newly isolated Bacillus cereus strain NK91 was characterized for extracellular chitinase production. Partially purified chitinase showed a molecular weight of 43.7 kDa in SDS-PAGE analysis. The optimum pH and temperature for the partially purified enzyme were 7.0 and 40°C, respectively. The addition of Mn²⁺ resulted in a 21% increase in enzyme activity as compared to the control. The V_max and K_m of the enzyme were determined as 76.9 μmol/min and 0.07 mg/mL, respectively. This enzyme exhibited stronger antifungal activity towards Fusarium oxysporum (66.7%), Rhizoctonia solani (64.6%), and Colletotrichum gloeosporioides (63%), and transmission electron microscopy and scanning transmission electron microscopy analysis showed considerable changes in cell wall structure with the treatment of purified chitinase as compared to control. Therefore, this enzyme reveals its biocontrol potential against potent phytopathogens in agriculture that can be helpful in swapping harmful as well as expensive fungicides.

A Broad-Specificity Chitinase from Penicillium oxalicum k10 Exhibits Antifungal Activity and Biodegradation Properties of Chitin

Penicillium oxalicum k10 isolated from soil revealed the hydrolyzing ability of shrimp chitin and antifungal activity against Sclerotinia sclerotiorum. The k10 chitinase was produced from a powder chitin-containing medium and purified by ammonium sulfate precipitation and column chromatography. The purified chitinase showed maximal activity toward colloidal chitin at pH 5 and 40 °C. The enzymatic activity was enhanced by potassium and zinc, and it was inhibited by silver, iron, and copper. The chitinase could convert colloidal chitin to N-acetylglucosamine (GlcNAc), (GlcNAc)2, and (GlcNAc)3, showing that this enzyme had endocleavage and exocleavage activities. In addition, the chitinase prevented the mycelial growth of the phytopathogenic fungi S. sclerotiorum and Mucor circinelloides. These results indicate that k10 is a potential candidate for producing chitinase that could be useful for generating chitooligosaccharides from chitinous waste and functions as a fungicide.

Extracellular Antifungal Activity of Chitinase-Producing Bacteria Isolated From Guano of Insectivorous Bats

A reduction in the use of agrochemicals requires the development of either alternatives or complementary control methods in order to limit their dangerousness. An alternative is the biological control of fungi by bacteria. The fungal cell wall is a unique structure of the fungi, composed of glucan, chitin, and glycoproteins. Therefore, bacteria producing mycolytic enzymes, like chitinases, are of great interest to degrade fungal cell-wall components. The objectives of this work were to isolate chitinolytic bacteria from the guano of insectivorous bats (Tadarida brasiliensis) and to verify the presence of antifungal activities against phytopathogenic fungi. From the guano samples, 28 bacterial isolates were obtained, 70% of which presented chitinolytic activity. Four isolates were selected since they showed the highest values of chitinase activity, and they were characterized as belonging to Bacillus genus, by analyzing the 16S ribosomal RNA gene sequence. Cell-free supernatants of bacterial cultures were used in inhibition tests on 16 fungi: Alternaria and Colletotrichum acutatum were the most affected. Chitinase and antifungal activities were observed in the cell-free supernatant regardless of the culture medium used. Both activities were stable to heat and proteinase K treatments. Finally, when the culture medium was supplemented with 1 ml of cell-free supernatants (0.33%) and incubated for 120 h, the inhibition of hyphae formation and germination spores of reporter fungus were observed under light microscopy. These results suggest the feasibility of using cell-free supernatants as eco-friendly fungicides. The use of them may contribute to reducing the dose of toxic chemicals.

Exploring the properties of chitinolytic Bacillus isolates for the pathogens biological control

Plant fungal diseases generate serious losses in the agriculture. The bacteria producing biologically active substances that inhibit the growth of fungal pathogens can be an alternative to the chemicals. The chitinolytic bacteria were isolated from the rhizosphere of wheat (Triticum aestivum L.) and their physiological properties which may be useful in the promotion of plant growth have been investigated. Their chitinases and antifungal activity were studied. The isolates were also tested for indirect growth-promoting traits such as ammonia production, siderophore production, hydrogen cyanide production, and salicylic acid production. Two chitinolytic strains B3 and B5 were identified as Bacillus subtilis and Bacillus sp., respectively. They produced active chitinases on a medium containing shrimp shell powder. The purified chitinases having the molecular weight of 35-45 kDa inhibited the growth of important plant pathogens such as Alternaria alternata, and Fusarium oxysporum. Additionally, the isolates showed the ability to produce a broad range of biological substances promoting the growth of plants.

Expression and biochemical characterization of a novel chitinase ChiT-7 from the metagenome in the soil of a mangrove tidal flat in China

Chitinases play an important role in the process of chitin bioavailability. In this study, we cloned a new chitinase gene and characterized its recombinant protein. The new 1251 bp gene of chitinase (ChiT-7) was cloned from the metagenome of the mangrove tidal flat soil in the city of Zhangzhou in Fujian Province (China) by genome walking. The gene encoded a mature protein with 381 amino acids, which manifested certain sequence similarity (59% identity) to characterized GH18 chitinases. The mature protein of ChiT-7 was successfully expressed in E. coli BL21 (DE3). After purification, the specific activity of the recombinant enzyme was 0.63 U/mg at the optimal pH of 6.0 and the optimal temperature of 45 °C. The rChiT-7 was active over a wide pH range, and the residual enzyme activity reached 80% or higher at 30 °C-50 °C. rChiT-7 hydrolyzed colloidal chitin with (GlcNAc)2 and GlcNAc as the main final products. Structural analysis of ChiT-7 indicated that ChiT-7 could be a processive chitinase. rChiT-7 manifested characteristics analogous to those of fungi and actinomycetes and exhibited sequence homology.

Progress in research and application development of surface display technology using Bacillus subtilis spores

Bacillus subtilis is a widely distributed aerobic Gram-positive species of bacteria. As a tool in the lab, it has the advantages of nonpathogenicity and limited likelihood of becoming drug resistant. It is a probiotic strain that can be directly used in humans and animals. It can be induced to produce spores under nutrient deficiency or other adverse conditions. B. subtilis spores have unique physical, chemical, and biochemical characteristics. Expression of heterologous antigens or proteins on the surface of B. subtilis spores has been successfully performed for over a decade. As an update and supplement to previously published research, this paper reviews the latest research on spore surface display technology using B. subtilis. We have mainly focused on the regulation of spore coat protein expression, display and application of exogenous proteins, and identification of developing research areas of spore surface display technology.

Comparative biocontrol ability of chitinases from bacteria and recombinant chitinases from the thermophilic fungus Thermomyces lanuginosus

Microbial chitinases (EC 3.2.1.14) are known to hydrolyse the chitinous gut epithelium of insects and cell walls of many fungi. In this study, seven chitinases from different bacteria and fungi were produced, characterized and their biocontrol abilities against graminaceous stem borers Eldana saccharina, Chilo partellus and Sesamia calamistis were assessed. All chitinases were stable over broad ranges of pH and temperature, however, recombinant fungal chitinases were more acid-stable than the bacterial counterparts. Chitinases from the thermophilic filamentous fungi Thermomyces lanuginosus SSBP (Chit1) and from Bacillus licheniformis (Chit lic) caused 70% and 80% mortality, respectively, in second instar larvae of E. saccharina. Six of the seven partially-purified microbial chitinases inhibited Aspergillus niger, A. flavus, A. alliaceus, A. ochraceus, Fusarium verticillioides and Mucor sp. Overall, microbial chitinases show promise as biocontrol agents of fungi and stalk-boring lepidopterans.

Sugarcane growth and nutrition levels are differentially affected by the application of PGPR and cane waste

Mineral and organic fertilization can be optimized by using rhizobacteria which increases dry matter, yield, and nutrients in the soil and plant, among the other biological inputs. However, the discovery of single microbes or a consortium that can benefit plants has been a challenge. In this context, this study aimed to evaluate the effects of Bacillus subtilis and Bacillus pumilus combined with mineral fertilization and sugar and alcohol industry by‐products in presprouted and the initial growth phase of sugar cane seedlings. The study was carried out in two phases. Phase 1 included presprouted seedlings with T1 =  untreated control, T2 =  B. subtilis, T3 =  B. pumilus, and T4 =  B. subtilis + B. pumilus treatments. Phase 2 included the same treatments with four types of fertilization: F1 =  mineral fertilization, F2 =  mineral fertilization + vinasse, F3 =  mineral fertilization + filter cake, and F4 =  mineral fertilization + filter cake compost. Of the phase 1 treatments, T2 (B. subtilis) was the best promoter of root growth and the total dry matter compared to the control with an increase of 23.0% compared to the control. In phase 2, B. pumilus application, increased the total dry matter by 13%, the number of tillers by 37%, and the diameter of the tillers by 48% when combined with mineral fertilization. The combined application of B. subtilis and B. pumilus increased the phosphorus content by 13% in soil treated with mineral fertilization and filter cake compost. The results of the this study strongly suggest that the use of B. subtilis and B. pumilus together with these by‐products can improve soil fertility parameters and decrease adverse effects associated with vinasse fertilization, in addition to providing shoot and root growth and providing collective synergy for a high yield of sugarcane production with environmental benefits.

Two novel cationic antifungal peptides isolated from Bacillus pumilus HN-10 and their inhibitory activity against Trichothecium roseum

Public concern for food safety and environmental issues and the increase in fungicide-resistant pathogen have enhanced the interest in developing alternative methods to fungicides to control postharvest fruit decay. In this study, a bacterial strain isolated from stale potato vermicelli was identified as Bacillus pumilus HN-10 based on morphological characteristics and 16S rRNA gene sequence analysis. Furthermore, two novel cationic antifungal peptides named P-1 and P-2 were purified from B. pumilus HN-10 using macroporous adsorbent resin AB-8, Sephadex G-100 chromatography, and reversed-phase high-performance liquid chromatography. The primary structure of P-1 and P-2, which were proved to be novel antifungal peptides by BLAST search in NCBI database, was PLSSPATLNSR and GGSGGGSSGGSIGGR with a molecular weight of 1142.28 and 1149.14 Da, respectively, as indicated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Both P-1 and P-2 exhibited strong antifungal activity against Trichothecium roseum with minimum inhibitory concentrations starting from 1 μg/mL. The two novel antifungal peptides were stable below 80 °C for 2 h, but lost their activity in 15 min at 121 °C. In addition, they were resistant to the proteolytic action of pepsin, trypsin, and papain, and stable within a wide range of pH (2.0-12.0). These results showed that P-1 and P-2 are novel cationic antifungal peptides with specific activity against T. roseum.

Chitinase-producing bacteria and their role in biocontrol

Chitin is an important component of the exteriors of insects and fungi. Upon degradation of chitin by a number of organisms, severe damage and even death may occur in pathogens and pests whose external surfaces contain this polymer. Currently, chemical fungicides and insecticides are the major means of controlling these disease-causing agents. However, due to the potential harm that these chemicals cause to the environment and to human and animal health, new strategies are being developed to replace or reduce the use of fungal- and pest-killing compounds in agriculture. In this context, chitinolytic microorganisms are likely to play an important role as biocontrol agents and pathogen antagonists and may also function in the control of postharvest rot. In this review, we discuss the literature concerning chitin and the basic knowledge of chitin-degrading enzymes, and also describe the biocontrol effects of chitinolytic microorganisms and their potential use as more sustainable pesticides and fungicides in the field.