Chitinase-producing bacteria and their role in biocontrol

Chitinase-functionalized UiO-66 framework nanoparticles active against multidrug-resistant Candida Auris

Candida auris (C. auris) is a yeast that has caused several outbreaks in the last decade. Cell wall chitin plays a primary role in the antifungal resistance of C. auris. Herein, we investigated the potential of chitinase immobilized with UiO-66 to act as a potent antifungal agent against C. auris. Chitinase was produced from Talaromyces varians SSW3 in a yield of 8.97 U/g dry substrate (ds). The yield was statistically enhanced to 120.41 U/g ds by using Plackett-Burman and Box-Behnken design. We synthesized a UiO-66 framework that was characterized by SEM, TEM, XRD, FTIR, a particle size analyzer, and a zeta sizer. The produced framework had a size of 70.42 ± 8.43 nm with a uniform cubic shape and smooth surface. The produced chitinase was immobilized on UiO-66 with an immobilization yield of 65% achieved after a 6 h loading period. The immobilization of UiO-66 increased the enzyme activity and stability, as indicated by the obtained Kd and T1/2 values. Furthermore, the hydrolytic activity of chitinase was enhanced after immobilization on UiO-66, with an increase in the Vmax and a decrease in the Km of 2- and 38-fold, respectively. Interestingly, the antifungal activity of the produced chitinase was boosted against C. auris by loading the enzyme on UiO-66, with an MIC50 of 0.89 ± 0.056 U/mL, compared to 5.582 ± 0.57 U/mL for the free enzyme. This study offers a novel promising alternative approach to combat the new emerging pathogen C. auris.

Diversity and functional characteristics of culturable bacterial endosymbionts from cassava whitefly biotype Asia II-5, Bemisia tabaci

Whitefly Bemisia tabaci, a carrier of cassava mosaic disease (CMD), poses a significant threat to cassava crops. Investigating culturable bacteria and their impact on whiteflies is crucial due to their vital role in whitefly fitness and survival. The whitefly biotype associated with cassava and transmitting CMD in India has been identified as Asia II 5 through partial mitochondrial cytochrome oxidase I gene sequencing. In this study, bacteria associated with adult B. tabaci feeding on cassava were extracted using seven different media. Nutrient Agar (NA), Soyabean Casein Digest Medium (SCDM), Luria Bertani agar (LBA), and Reasoner's 2A agar (R2A) media resulted in 19, 6, 4, and 4 isolates, respectively, producing a total of 33 distinct bacterial isolates. Species identification through 16SrRNA gene sequencing revealed that all isolates belonged to the Bacillota and Pseudomonadota phyla, encompassing 11 genera: Bacillus, Cytobacillus, Exiguobacterium, Terribacillus, Brevibacillus, Enterococcus, Staphylococcus, Brucella, Novosphingobium, Lysobacter, and Pseudomonas. All bacterial isolates were tested for chitinase, protease, siderophore activity, and antibiotic sensitivity. Nine isolates exhibited chitinase activity, 28 showed protease activity, and 23 displayed siderophore activity. Most isolates were sensitive to antibiotics such as Vancomycin, Streptomycin, Erythromycin, Kanamycin, Doxycycline, Tetracycline, and Ciprofloxacin, while they demonstrated resistance to Bacitracin and Colistin. Understanding the culturable bacteria associated with cassava whitefly and their functional significance could contribute to developing effective cassava whitefly and CMD control in agriculture.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03949-0.

Gene Cloning, Heterologous Expression, and In Silico Analysis of Chitinase B from Serratia marcescens for Biocontrol of Spodoptera frugiperda Larvae Infesting Maize Crops

Spodoptera frugiperda, the fall armyworm (FAW), is a highly invasive polyphagous insect pest that is considered a source of severe economic losses to agricultural production. Currently, the majority of chemical insecticides pose tremendous threats to humans and animals besides insect resistance. Thus, there is an urgent need to develop new pest management strategies with more specificity, efficiency, and sustainability. Chitin-degrading enzymes, including chitinases, are promising agents which may contribute to FAW control. Chitinase-producing microorganisms are reported normally in bacteria and fungi. In the present study, Serratia marcescens was successfully isolated and identified from the larvae of Spodoptera frugiperda. The bacterial strain NRC408 displayed the highest chitinase enzyme activity of 250 units per milligram of protein. Subsequently, the chitinase gene was cloned and heterologously expressed in E. coli BL21 (DE3). Recombinant chitinase B was overproduced to 2.5-fold, driven by the T7 expression system. Recombinant chitinase B was evaluated for its efficacy as an insecticidal bioagent against S. frugiperda larvae, which induced significant alteration in subsequent developmental stages and conspicuous malformations. Additionally, our study highlights that in silico analyses of the anticipated protein encoded by the chitinase gene (ChiB) offered improved predictions for enzyme binding and catalytic activity. The effectiveness of (ChiB) against S. frugiperda was evaluated in laboratory and controlled field conditions. The results indicated significant mortality, disturbed development, different induced malformations, and a reduction in larval populations. Thus, the current study consequently recommends chitinase B for the first time to control FAW.

Genome analysis and hyphal movement characterization of the hitchhiker endohyphal Enterobacter sp. from Rhizoctonia solani

Bacterial-fungal interactions are pervasive in the rhizosphere. While an increasing number of endohyphal bacteria have been identified, little is known about their ecology and impact on the associated fungal hosts and the surrounding environment. In this study, we characterized the genome of an Enterobacter sp. Crenshaw (En-Cren), which was isolated from the generalist fungal pathogen Rhizoctonia solani, and examined the genetic potential of the bacterium with regard to the phenotypic traits associated with the fungus. Overall, the En-Cren genome size was typical for members of the genus and was capable of free-living growth. The genome was 4.6 MB in size, and no plasmids were detected. Several prophage regions and genomic islands were identified that harbor unique genes in comparison with phylogenetically closely related Enterobacter spp. Type VI secretion system and cyanate assimilation genes were identified from the bacterium, while some common heavy metal resistance genes were absent. En-Cren contains the key genes for indole-3-acetic acid (IAA) and phenylacetic acid (PAA) biosynthesis, and produces IAA and PAA in vitro, which may impact the ecology or pathogenicity of the fungal pathogen in vivo. En-Cren was observed to move along hyphae of R. solani and on other basidiomycetes and ascomycetes in culture. The bacterial flagellum is essential for hyphal movement, while other pathways and genes may also be involved.IMPORTANCEThe genome characterization and comparative genomics analysis of Enterobacter sp. Crenshaw provided the foundation and resources for a better understanding of the ecology and evolution of this endohyphal bacteria in the rhizosphere. The ability to produce indole-3-acetic acid and phenylacetic acid may provide new angles to study the impact of phytohormones during the plant-pathogen interactions. The hitchhiking behavior of the bacterium on a diverse group of fungi, while inhibiting the growth of some others, revealed new areas of bacterial-fungal signaling and interaction, which have yet to be explored.

Improved Expression of a Thermostable GH18 Bacterial Chitinase in Two Different Escherichia coli Strains and Its Potential Use in Plant Protection and Biocontrol of Phytopathogenic Fungi

Chitinases are enzymes that can break down chitin, a major component of the exoskeleton of insects and fungi. This feature makes them potential biopesticides in agriculture since they are considered a safe and environmentally friendly alternative to synthetic pesticides. In this work, we performed a comparative study between two different bacterial expression strains to produce a recombinant chitinase with improved stability. Escherichia coli strains Origami B and BL21 (DE3) were selected for their distinct cytosolic environment to express BhChitA chitinase of Bacillus halodurans C-125 and to investigate the role of disulfide bond formation and proper folding on its stability and activity. Expression of the recombinant BhChitA in bacterial strain containing oxidative cytosol (Origami B) improved its activity and stability. Although both expression systems have comparable biochemical properties (temperature range 20-80 °C and pH spectrum 3-10), BhChitA expressed in Origami strain seems more stable than expressed in BL21. Furthermore, the optimal expression conditions of the recombinant BhChitA has been carried out at 30 °C during 6 h for the Origami strain, against 20 °C during 2 h for BL21. On the other hand, no significant differences were detected between the two enzymes when the effect of metal ions was tested. These findings correlate with the analysis of the overall structure of BhChitA. The model structure permitted to localize disulfide bond, which form a stable connection between the substrate-binding residues and the hydrophobic core. This link is required for efficient binding of the chitin insertion domain to the substrate. BhChitA exhibited in vitro antifungal effect against phytopathogenic fungi and suppressed necrosis of Botrytis cinerea on detached tomato leaves. In vitro assays showed the influence of BhChitA on growth suppression of Botrytis cinerea (53%) Aspergillus niger (65%), Fusarium graminearum (25%), and Fusarium oxysporum (34%). Our results highlight the importance of the bacterial expression system with oxidative cytosol in producing promising biopesticides that can be applied for post-harvest processing and crop protection.

Draft genome analysis for Enterobacter kobei, a promising lead bioremediation bacterium

Lead pollution of the environment poses a major global threat to the ecosystem. Bacterial bioremediation offers a promising alternative to traditional methods for removing these pollutants, that are often hindered by various limitations. Our research focused on isolating lead-resistant bacteria from industrial wastewater generated by heavily lead-containing industries. Eight lead-resistant strains were successfully isolated, and subsequently identified through molecular analysis. Among these, Enterobacter kobei FACU6 emerged as a particularly promising candidate, demonstrating an efficient lead removal rate of 83.4% and a remarkable lead absorption capacity of 571.9 mg/g dry weight. Furthermore, E. kobei FACU6 displayed a remarkable a maximum tolerance concentration (MTC) for lead reaching 3,000 mg/L. To further investigate the morphological changes in E. kobei FACU6 in response to lead exposure, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were employed. These analyses revealed significant lead adsorption and intracellular accumulation in treated bacteria in contrast to the control bacterium. Whole-genome sequencing was performed to gain deeper insights into E. kobei's lead resistance mechanisms. Structural annotation revealed a genome size of 4,856,454 bp, with a G + C content of 55.06%. The genome encodes 4,655 coding sequences (CDS), 75 tRNA genes, and 4 rRNA genes. Notably, genes associated with heavy metal resistance and their corresponding regulatory elements were identified within the genome. Furthermore, the expression levels of four specific heavy metal resistance genes were evaluated. Our findings revealed a statistically significant upregulation in gene expression under specific environmental conditions, including pH 7, temperature of 30°C, and high concentrations of heavy metals. The outstanding potential of E. kobei FACU6 as a source of diverse genes related to heavy metal resistance and plant growth promotion makes it a valuable candidate for developing safe and effective strategies for heavy metal disposal.

Genome-Wide Identification and Expression Analysis of Chitinase Genes in Watermelon under Abiotic Stimuli and Fusarium oxysporum Infection

Chitinases, which catalyze the hydrolysis of chitin, the primary components of fungal cell walls, play key roles in defense responses, symbiotic associations, plant growth, and stress tolerance. In this study, 23 chitinase genes were identified in watermelon (Citrullus lanatus [Thunb.]) and classified into five classes through homology search and phylogenetic analysis. The genes with similar exon-intron structures and conserved domains were clustered into the same class. The putative cis-elements involved in the responses to phytohormone, stress, and plant development were identified in their promoter regions. A tissue-specific expression analysis showed that the ClChi genes were primarily expressed in the roots (52.17%), leaves (26.09%), and flowers (34.78%). Moreover, qRT-PCR results indicate that ClChis play multifaceted roles in the interaction between plant/environment. More ClChi members were induced by Race 2 of Fusarium oxysporum f. sp. niveum, and eight genes were expressed at higher levels on the seventh day after inoculation with Races 1 and 2, suggesting that these genes play a key role in the resistance of watermelon to Fusarium wilt. Collectively, these results improve knowledge of the chitinase gene family in watermelon species and help to elucidate the roles played by chitinases in the responses of watermelon to various stresses.

Microbial diversity in soils suppressive to Fusarium diseases

Fusarium species are cosmopolitan soil phytopathogens from the division Ascomycota, which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to Fusarium diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to Fusarium diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic Fusarium and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to Fusarium diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the Bacillus, Pseudomonas, Paenibacillus and Streptomyces species are involved in plant protection from Fusarium diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to Fusarium diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the Fusarium pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to Fusarium diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for Fusarium disease management in sustainable agriculture.

Mechanistic insights into the role of actinobacteria as potential biocontrol candidates against fungal phytopathogens

Worldwide mounting demand for better food production to nurture exasperating population emphasizes on reduced crop losses. The incidence of pathogens into the agricultural fields has tend to dwindle plethora of cereal, vegetable, and other fodder crops. This, in turn, has seriously impacted the economic losses on global scale. Apart from this, it is quite challenging to feed the posterity in the coming decades. To counteract this problem, various agrochemicals have been commercialized in the market that no doubt shows positive results but along with adversely affecting the ecosystem. Therefore, the excessive ill-fated use of agrochemicals to combat the plant pests and diseases highlights that alternatives to chemical pesticides are need of the hour. In recent days, management of plant diseases using plant-beneficial microbes is gaining interest as safer and potent alternatives to replace chemically based pesticides. Among these beneficial microbes, actinobacteria especially streptomycetes play considerable role in combating plant diseases along with promoting the plant growth and development along with their productivity and yield. The mechanisms exhibited by actinobacteria include antibiosis (antimicrobial compounds and hydrolytic enzymes), mycoparasitism, nutrient competition, and induction of resistance in plants. Thus, in cognizance with potential of actinobacteria as potent biocontrol agents, this review summarizes role of actinobacteria and the multifarious mechanisms exhibited by actinobacteria for commercial applications.

An overview of viral chitinases: General properties and biotechnological potential

Chitin is a biopolymer profusely present in nature and of pivotal importance as a structural component in cells. It is degraded by chitinases, enzymes naturally produced by different organisms. Chitinases are proteins enrolled in many cellular mechanisms, including the remodeling process of the fungal cell wall, the cell growth process, the autolysis of filamentous fungi, and cell separation of yeasts, among others. These enzymes also have properties with different biotechnological applications. They are used to produce polymers, for biological control, biofilm formation, and as antitumor and anti-inflammatory target molecules. Chitinases are classified into different glycoside hydrolase (GH) families and are widespread in microorganisms, including viruses. Among them, the GH18 family is highly predominant in the viral genomes, being present and active enzymes in baculoviruses and nucleocytoplasmic large DNA viruses (NCLDV), especially chloroviruses from the Phycodnaviridae family. These viral enzymes contain one or more GH domains and seem to be involved during the viral replication cycle. Curiously, only a few DNA viruses have these enzymes, and studying their properties could be a key feature for biological and biotechnological novelties. Here, we provide an overview of viral chitinases and their probable function in viral infection, showing evidence of at least two distinct origins for these enzymes. Finally, we discuss how these enzymes can be applied as biotechnological tools and what one can expect for the coming years on these GHs.

Chitinases as key virulence factors in microbial pathogens: Understanding their role and potential as therapeutic targets

Chitinases are crucial for the survival of bacterial and fungal pathogens both during host infection and outside the host in the environment. Chitinases facilitate adhesion onto host cells, act as virulence factors during infection, and provide protection from the host immune system, making them crucial factors in the survival of microbial pathogens. Understanding the mechanisms behind chitinase action is beneficial to design novel therapeutics to control microbial infections. This review explores the role of chitinases in the pathogenesis of bacterial, fungal, and viral infections. The mechanisms underlying the action of chitinases of bacterial, fungal, and viral pathogens in host cells are thoroughly reviewed. The evolutionary relationships between chitinases of various bacterial, fungal, and viral pathogens are discussed to determine their involvement in processes, such as adhesion and host immune system modulation. Gaining a better understanding of the distribution and activity of chitinases in these microbial pathogens can help elucidate their role in the invasion and infection of host cells.

Characterization of chitinolytic bacteria newly isolated from the termite Microcerotermes sp. and their biocontrol potential against plant pathogenic fungi

Chitinolytic bacteria were isolated from guts and shells of the termite Microcerotermes sp. Among the nineteen morphologically different chitinolytic isolates, three isolates with highest extracellular chitinase production ratio (≥2.26) were selected. Based on molecular identification of 16S rRNA gene sequences and biochemical characterizations using API test kits and MALDI-TOF MS, these isolates were closely related to Bacillus thuringiensis (Mc_E02) and Paenibacillus species (Mc_E07 and Mc_G06). Isolate Mc_E02 exhibited the highest chitinase-specific activity (2.45 U/mg protein) at 96 h of cultivation, and the enzyme activity was optimized at pH 7.0 and 45 °C. The isolate showed highest and broad-spectrum inhibitory effect against three phytopathogenic fungi (Curvularia lunata, Colletotrichum capsici, and Fusarium oxysporum). Its 36-kDa chitinase exhibited the biomass reduction and mycelium inhibition against all fungi, with highest effects to Curvularia lunata. This research provides novel information about termite chitinolytic bacteria and their effective chitinase, with potential use as biocontrol tool.

Phyto-microbiome to mitigate abiotic stress in crop plants

Plant-associated microbes include taxonomically diverse communities of bacteria, archaebacteria, fungi, and viruses, which establish integral ecological relationships with the host plant and constitute the phyto-microbiome. The phyto-microbiome not only contributes in normal growth and development of plants but also plays a vital role in the maintenance of plant homeostasis during abiotic stress conditions. Owing to its immense metabolic potential, the phyto-microbiome provides the host plant with the capability to mitigate the abiotic stress through various mechanisms like production of antioxidants, plant growth hormones, bioactive compounds, detoxification of harmful chemicals and toxins, sequestration of reactive oxygen species and other free radicals. A deeper understanding of the structure and functions of the phyto-microbiome and the complex mechanisms of phyto-microbiome mediated abiotic stress mitigation would enable its utilization for abiotic stress alleviation of crop plants and development of stress-resistant crops. This review aims at exploring the potential of phyto-microbiome to alleviate drought, heat, salinity and heavy metal stress in crop plants and finding sustainable solutions to enhance the agricultural productivity. The mechanistic insights into the role of phytomicrobiome in imparting abiotic stress tolerance to plants have been summarized, that would be helpful in the development of novel bioinoculants. The high-throughput modern approaches involving candidate gene identification and target gene modification such as genomics, metagenomics, transcriptomics, metabolomics, and phyto-microbiome based genetic engineering have been discussed in wake of the ever-increasing demand of climate resilient crop plants.

Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species

Chitin is the second most abundant polysaccharide worldwide as part of arthropods' exoskeletons and fungal cell walls. Low concentrations in soils and sediments indicate rapid decomposition through chitinolytic organisms in terrestrial and aquatic ecosystems. The enacting enzymes, so-called chitinases, and their products, chitooligosaccharides, exhibit promising characteristics with applications ranging from crop protection to cosmetics, medical, textile, and wastewater industries. Exploring novel chitinolytic organisms is crucial to expand the enzymatical toolkit for biotechnological chitin utilization and to deepen our understanding of diverse catalytic mechanisms. In this study, we present two long-read sequencing-based genomes of highly similar Jeongeupia species, which have been screened, isolated, and biochemically characterized from chitin-amended soil samples. Through metabolic characterization, whole-genome alignments, and phylogenetic analysis, we could demonstrate how the investigated strains differ from the taxonomically closest strain Jeongeupia naejangsanensis BIO-TAS4-2T (DSM 24253). In silico analysis and sequence alignment revealed a multitude of highly conserved chitinolytic enzymes in the investigated Jeongeupia genomes. Based on these results, we suggest that the two strains represent a novel species within the genus of Jeongeupia, which may be useful for environmentally friendly N-acetylglucosamine production from crustacean shell or fungal biomass waste or as a crop protection agent.

Screening for chitin degrading bacteria in the environment of Saudi Arabia and characterization of the most potent chitinase from Streptomyces variabilis Am1

Forty-six promising chitinolytic isolates were recovered during a screening for chitinolytic bacteria in the environment of Saudi Arabia. The top three isolates belonged to the genus Streptomyces. Streptomyces variabilis Am1 was able to excrete the highest amount of chitinases, reaching the maximum at 84 h with 0.5% yeast extract and nitrogen source and 2% galactose as a carbon source. Purification of chitinase by DEAE-Cellulose and Sephadex G75 improved the specific activity to 18.6-fold and the recovery to 23.8% and showed a mass at 56 kDa. The optimal catalysis of the purified chitinase was at 40 °C and pH 8 with high thermostability and pH stability as reflected by a midpoint temperature value of 66.6 °C and stability at pH 4-9. The protein reagents SDS, EDTA, and EGTA significantly inhibited the enzyme and the EDTA-chelated chitinase restored its activity after the addition of Fe2+ ions suggesting a metallo-chitinase type with ferric ions as cofactors. Chitinase exerted high antifungal activity against some phytopathogenic fungi. Interestingly, the tested Streptomyces were able to produce chitosan nanocubes along with chitosan from chitin degradation which may be an additional power in their antifungal activity in nature. This work also reveals the importance of unexplored environments as a pool of promising microorganisms with biotechnological applications.

Bacterial Chitinases and Their Role in Human Infection

It has been widely appreciated that numerous bacterial species express chitinases for the purpose of degrading environmental chitin. However, chitinases and chitin-binding proteins are also expressed by pathogenic bacterial species during infection even though mammals do not produce chitin. Alternative molecular targets are therefore likely present within the host. Here, we will describe our current understanding of chitinase/chitin-binding proteins as virulence factors that promote bacterial colonization and infection. The targets of these chitinases in the host have been shown to include immune system components, mucins, and surface glycans. Bacterial chitinases have also been shown to interact with other microorganisms, targeting the peptidoglycan or chitin in the bacterial and fungal cell wall, respectively. This review highlights that even though the name "chitinase" implies activity toward chitin, chitinases can have a wide diversity of targets, including ones relevant to host infection. Chitinases may therefore be useful as a target of future anti-infective therapeutics.

In Vitro Evaluation of Some Endophytic Bacillus to Potentially Inhibit Grape and Grapevine Fungal Pathogens

Romania has a long history of grapevine culturing and winemaking. However, like any agricultural sector, viticulture faces devastating biological threats. Fungi responsible for grapevine trunk diseases (GTDs) and grape spoilage lead to considerable yield losses and a decline in grapevine quality. In the actual context, many countries, including Romania, have reoriented their approaches to minimize chemical inputs, which have been proven to be toxic and to have negative impacts on the environment, and to replace them with sustainable biocontrol strategies for the wine-growing sector. Within biocontrol strategies, Bacillus spp. is a well-known plant-protective bacteria with antifungal properties. Within this paper, six endophytic bacteria from various plant sources were studied. The bacterial strains were identified as B. pumilus, B. subtilis, and B. velezensis by sequencing their 16S rDNA region. Regardless of the in vitro test methods (using living bacterial cells, bacterial-cell-free supernatant (CFS), and volatile active compounds (VOCs)), B. velezensis strains revealed strong and broad antifungal activity against grape and grapevine fungal pathogens such as Aspergillus spp., Botrytis cinerea, Penicillium expansum, Diplodia seriata, Eutypa lata, Fusarium spp., Clonostachys rosea, Neofusicoccum parvum, and Stereum hirsutum. The functional antifungal genes encoding for difficidin, fengycin, iturins, macrolactin, and mycosubtilin were molecularly detected, which could support the proven antifungal activity of the endophytic strains. Lytic enzymes involved in fungal growth inhibition, such as chitinase, cellulase, and proteases, were also revealed to be produced by some of these bacterial strains. Various other in vitro tests, such as phosphate and phytate solubilization, phytohormone synthesis, the production of enzymes involved in the polyamine biosynthetic pathway, and pH as well as temperature tolerance tests were carried out to reveal the plant-beneficial potential of these bacterial strains. These results revealed that the B. velezensis strains, especially BAHs1, are the most suitable endophytes for grapevine biologic control, which could lead to the future development of sustainable management strategies.

Cyanobacteria: A Promising Source of Antifungal Metabolites

Cyanobacteria are a rich source of secondary metabolites, and they have received a great deal of attention due to their applicability in different industrial sectors. Some of these substances are known for their notorious ability to inhibit fungal growth. Such metabolites are very chemically and biologically diverse. They can belong to different chemical classes, including peptides, fatty acids, alkaloids, polyketides, and macrolides. Moreover, they can also target different cell components. Filamentous cyanobacteria have been the main source of these compounds. This review aims to identify the key features of these antifungal agents, as well as the sources from which they are obtained, their major targets, and the environmental factors involved when they are being produced. For the preparation of this work, a total of 642 documents dating from 1980 to 2022 were consulted, including patents, original research, review articles, and theses.

Exploring the Biologically Active Metabolites Produced by Bacillus cereus for Plant Growth Promotion, Heat Stress Tolerance, and Resistance to Bacterial Soft Rot in Arabidopsis

Eight gene clusters responsible for synthesizing bioactive metabolites associated with plant growth promotion were identified in the Bacillus cereus strain D1 (BcD1) genome using the de novo whole-genome assembly method. The two largest gene clusters were responsible for synthesizing volatile organic compounds (VOCs) and encoding extracellular serine proteases. The treatment with BcD1 resulted in an increase in leaf chlorophyll content, plant size, and fresh weight in Arabidopsis seedlings. The BcD1-treated seedlings also accumulated higher levels of lignin and secondary metabolites including glucosinolates, triterpenoids, flavonoids, and phenolic compounds. Antioxidant enzyme activity and DPPH radical scavenging activity were also found to be higher in the treated seedlings as compared with the control. Seedlings pretreated with BcD1 exhibited increased tolerance to heat stress and reduced disease incidence of bacterial soft rot. RNA-seq analysis showed that BcD1 treatment activated Arabidopsis genes for diverse metabolite synthesis, including lignin and glucosinolates, and pathogenesis-related proteins such as serine protease inhibitors and defensin/PDF family proteins. The genes responsible for synthesizing indole acetic acid (IAA), abscisic acid (ABA), and jasmonic acid (JA) were expressed at higher levels, along with WRKY transcription factors involved in stress regulation and MYB54 for secondary cell wall synthesis. This study found that BcD1, a rhizobacterium producing VOCs and serine proteases, is capable of triggering the synthesis of diverse secondary metabolites and antioxidant enzymes in plants as a defense strategy against heat stress and pathogen attack.

Optimization of Osthole in the Lactone Ring as an Agrochemical Candidate: Synthesis, Characterization, and Pesticidal Activities of Osthole Amide/Ester Derivatives and Their Effects on Morphological Changes of Mite Epidermis

Structural modification of natural products is one of the important ways in the discovery of novel pesticides. Based on a diversity-oriented synthesis strategy, herein, two series of amide/ester derivatives (52 compounds) were obtained by opening the lactone of osthole. Interestingly, the effect of different concentrations of aq. sodium hydroxide on the ratio of two isomers (cis- and trans-2) was investigated, and a magical phenomenon of ultraviolet (UV) light irradiation on intertransformation of two isomers (cis- and trans-2) was observed. Against Mythimna separata, when compared with the precursor osthole, compounds 4b, 4l, 5l, 5m, 7h, 7l, and 7m displayed more pronounced growth inhibitory activity with the final mortality rates of 62.0-68.9%. Compounds 4b, 4i, and 5m showed 5.7-6.6 times stronger acaricidal activity against Tetranychus cinnabarinus than osthole, and notably, control effects of compounds 4i and 5m were 2.4- and 2.7-fold that of osthole in the management of T. cinnabarinus in the greenhouse. Scanning electron microscopy (SEM) images of the epidermis of 5m-treated T. cinnabarinus indicated that compound 5m can destroy the mite cuticle layer. Compounds 4b and 5m can be used as leads to further explore more promising pesticidal agents.

Recombinant production, characterization and industrial application testing of a novel acidic exo/endo-chitinase from Rasamsonia emersonii

An acid-active exo/endo-chitinase; comprising a GH18 catalytic domain and substrate insertion domain; originating from the thermophilic filamentous fungus Rasamsonia emersonii, was expressed in Pichia pastoris. In silico analysis including phylogenetic analysis, and recombinant production, purification, biochemical characterisation, and industrial application testing, was carried out. The expressed protein was identified by SDS-PAGE as a smear from 56.3 to 125.1 kDa, which sharpens into bands at 46.0 kDa, 48.4 kDa and a smear above 60 kDa when treated with PNGase F. The acid-active chitinase was primarily a chitobiosidase but displayed some endo-chitinase and acetyl-glucosamidase activity. The enzyme was optimally active at 50 °C, and markedly low pH of 2.8. As far as the authors are aware, this is the lowest pH optima reported for any fungal chitinase. The acid-active chitinase likely plays a role in chitin degradation for cell uptake in its native environment, perhaps in conjunction with a chitin deacetylase. Comparative studies with other R. emersonii chitinases indicate that they may play a synergistic role in this. The acid-active chitinase displayed some efficacy against non-treated substrates; fungal chitin and chitin from shrimp. Thus, it may be suited to industrial chitin hydrolysis reactions for extraction of glucosamine and chitobiose at low pH.

Prospects of chitinase in sustainable farming and modern biotechnology: an update on recent progress and challenges

Chitinases are multifunctional biocatalysts for the pest control and useful in modern biotechnology and pharmaceutical industries. Chemical-based fungicides and insecticides have caused more severe effects on environment and human health. Many pathogenic fungal species and insects became resistant to the chemical pesticides. The resistant fungi emerged as a multidrug resistant also and less susceptible insects are not possible to control adequately. Chitinases have an immense potential to be exploited as a biopesticide against fungi and insects. The direct use of chitinase in liquid formulation or whole microbial enzyme producing cells, both act as antagonistically against the pests. Chitinase can disintegrate the fungal cell wall and insect integument that holds the chitin as a vital structural component. Moreover, chitinase is applied for the synthesis of pharmaceutically important chitooligosaccharides. Chitinase producing microbes have the huge potential to utilize against the waste management of sea food remains like shells of crustaceans. Chitinase is valuable for the synthesis of protoplasts from industrially important fungi, further it act as the biocontrol agent of malaria and dengue fever causing larvae of mosquitoes. Chitinases also have been successfully used in wine and single cell protein producing industries. Present review is illustrating the updated information on the state of the art of different applications of chitinases in agriculture and biotechnology industry. It also bestows the understanding to the readers about the areas of extensively studied and the field where there is still much left to be done.

Comparative genomics of Bacillus cereus sensu lato spp. biocontrol strains in correlation to in-vitro phenotypes and plant pathogen antagonistic capacity

Bacillus cereus sensu lato (Bcsl) strains are widely explored due to their capacity to antagonize a broad range of plant pathogens. These include B. cereus sp. UW85, whose antagonistic capacity is attributed to the secondary metabolite Zwittermicin A (ZwA). We recently isolated four soil and root-associated Bcsl strains (MO2, S-10, S-25, LSTW-24) that displayed different growth profiles and in-vitro antagonistic effects against three soilborne plant pathogens models: Pythium aphanidermatum (oomycete) Rhizoctonia solani (basidiomycete), and Fusarium oxysporum (ascomycete). To identify genetic mechanisms potentially responsible for the differences in growth and antagonistic phenotypes of these Bcsl strains, we sequenced and compared their genomes, and that of strain UW85 using a hybrid sequencing pipeline. Despite similarities, specific Bcsl strains had unique secondary metabolite and chitinase-encoding genes that could potentially explain observed differences in in-vitro chitinolytic potential and anti-fungal activity. Strains UW85, S-10 and S-25 contained a (~500 Kbp) mega-plasmid that harbored the ZwA biosynthetic gene cluster. The UW85 mega-plasmid contained more ABC transporters than the other two strains, whereas the S-25 mega-plasmid carried a unique cluster containing cellulose and chitin degrading genes. Collectively, comparative genomics revealed several mechanisms that can potentially explain differences in in-vitro antagonism of Bcsl strains toward fungal plant pathogens.

Exploring the Potentiality of Native Actinobacteria to Combat the Chilli Fruit Rot Pathogens under Post-Harvest Pathosystem

Chilli is an universal spice cum solanaceous vegetable crop rich in vitamin A, vitamin C, capsaicin and capsanthin. Its cultivation is highly threatened by fruit rot disease which cause yield loss as high as 80-100% under congenial environment conditions. Currently actinobacteria are considered as eco-friendly alternatives to synthetic fungicides at pre and post-harvest pathosystems. Hence, this research work focuses on the exploitation of rhizospheric, phyllospheric and endophytic actinobacteria associated with chilli plants for their antagonistic activity against fruit rot pathogens viz., Colletotrichum scovillei, Colletotrichum truncatum and Fusarium oxysporum. In vitro bioassays revealed that the actinobacterial isolate AR26 was found to be the most potent antagonist with multifarious biocontrol mechanisms such as production of volatile, non-volatile, thermostable compounds, siderophores, extracellular lytic enzymes. 16S rRNA gene sequence confirmed that the isolate AR26 belongs to Streptomyces tuirus. The results of detached fruit assay revealed that application of liquid bio-formulation of Stretomyces tuirus @ 10 mL/L concentration completely inhibited the development of fruit rot symptoms in pepper fruits compared to methanol extracts. Hence, the present research work have a great scope for evaluating the biocontrol potential of native S. tuirus AR26 against chilli fruit rot disease under field condition as well against a broad spectrum of post-harvest plant pathogens.

Neighbours in nodules: the interactions between Frankia sp. ACN10a and non-Frankia nodular endophytes of alder

In the present study, we report the in vitro interactions between Frankia sp. ACN10a and non-Frankia nodular endophytes (NFNE) isolated from alder. The supernatant of NFNE grown in nitrogen-replete medium had neutral or negative effects on Frankia growth; none had a stimulatory effect. Inhibitory effects were observed for supernatants of some NFNE, notably Micromonospora, Pseudomonas, Serratia and Stenotrophomonas isolates. However, some NFNE-Frankia coculture supernatants could stimulate Frankia growth when used as a culture medium supplement. This was observed for supernatants of Frankia cocultured with Microvirga and Streptomyces isolates. In nitrogen-limited conditions, cocultures of Frankia with some NFNE, including some rhizobia and Cytobacillus, resulted in higher total biomass than Frankia-only cultures, suggesting cooperation, while other NFNE were strongly antagonistic. Microscopic observation of cocultures also revealed compromised Frankia membrane integrity, and some differentiation into stress resistance-associated morphotypes such as sporangia and reproductive torulose hyphae (RTH). Furthermore, the coculture of Frankia with Serratia sp. isolates resulted in higher concentrations of the auxinic plant hormone indole-3-acetic acid and related indolic compounds in the culture supernatant. This study sheds new light on the breadth of microbial interactions that occur amongst bacteria that inhabit the understudied ecological niche of the alder nodule.

Deciphering the role of non-Frankia nodular endophytes in alder through in vitro and genomic characterization

Endophytic bacterial populations are well-positioned to provide benefits to their host plants such as nutrient acquisition and plant hormone level manipulation. Actinorhizal plants such as alders are well known for their microbial symbioses that allow them to colonize harsh environments whether natural or anthropized. Although the nitrogen-fixing actinobacterium Frankia sp. is the main endophyte found in alder root nodules, other bacterial genera, whose roles remain poorly defined, inhabit this niche. In this study, we isolated a diverse panel of non-Frankia nodular endophytes (NFNE). Some NFNE were isolated from alders grown from surface-sterilized seeds and maintained in sterile conditions, suggesting these may have been seed-borne. In vitro testing of 24 NFNE revealed some possessed putative plant growth promotion traits. Their genomes were also sequenced to identify genes related to plant growth promotion traits. This study highlights the complexity of the alder nodular microbial community. It paves the way for further understanding of the biology of nodules and could help improve land reclamation practices that involve alders.

Draft genome of Raoultella planticola, a high lead resistance bacterium from industrial wastewater

Isolation of heavy metals-resistant bacteria from their original habitat is a crucial step in bioremediation. Six lead (Pb) resistant bacterial strains were isolated and identified utilizing 16S rRNA to be Enterobacter ludwigii FACU 4, Shigella flexneri FACU, Microbacterium paraoxydans FACU, Klebsiella pneumoniae subsp. pneumonia FACU, Raoultella planticola FACU 3 and Staphylococcus xylosus FACU. It was determined that all these strains had their Minimum inhibitory concentration (MIC) to be 2500 ppm except R. planticola FACU 3 has a higher maximum tolerance concentration (MTC) up to 2700 ppm. We evaluated the survival of all six strains on lead stress, the efficiency of biosorption and lead uptake. It was found that R. planticola FACU 3 is the highest MTC and S. xylosus FACU was the lowest MTC in this evaluation. Therefore, transmission electron microscopy (TEM) confirmed the difference between the morphological responses of these two strains to lead stress. These findings led to explore more about the genome of R. planticola FACU 3 using illumine Miseq technology. Draft genome sequence analysis revealed the genome size of 5,648,460 bp and G + C content 55.8% and identified 5526 CDS, 75 tRNA and 4 rRNA. Sequencing technology facilitated the identification of about 47 genes related to resistance to many heavy metals including lead, arsenic, zinc, mercury, nickel, silver and chromium of R. planticola FACU 3 strain. Moreover, genome sequencing identified plant growth-promoting genes (PGPGs) including indole acetic acid (IAA) production, phosphate solubilization, phenazine production, trehalose metabolism and 4-hydroxybenzoate production genes and a lot of antibiotic-resistant genes.

Comparative studies of two AA10 family lytic polysaccharide monooxygenases from Bacillus thuringiensis

Bacillus thuringiensis, known to be one of the most important biocontrol microorganisms, contains three AA10 family lytic polysaccharide monooxygenases (LPMOs) in its genome. In previous reports, two of them, BtLPMO10A and BtLPMO10B, have been preliminarily characterized. However, some important biochemical features and substrate preference, as well as their potential applications in chitin degradation, still deserve further investigation. Results from present study showed that both BtLPMO10A and BtLPMO10B exhibit similar catalytic domains as well as highly conserved substrate-binding planes. However, unlike BtLPMO10A, which has comparable binding ability to both crystalline and amorphous form of chitins, BtLPMO10B exhibited much stronger binding ability to colloidal chitin, which mainly attribute to its carbohydrate-binding module-5 (CBM5). Interestingly, the relative high binding ability of BtLPMO10B to colloidal chitin does not lead to high catalytic activity of the enzyme. In contrast, the enzyme exhibited higher activity on β-chitin. Further experiments showed that the binding of BtLPMO10B to colloidal chitin was mainly non-productive, indicating a complicated role for CBM5 in LPMO activity. Furthermore, synergistic experiments demonstrated that both LPMOs boosted the activity of the chitinase, and the higher efficiency of BtLPMO10A can be overridden by BtLPMO10B.

Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease

The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.

Genome profiling of an indigenous Bacillus thuringiensis isolate, T405 toxic against the fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae)

In this study, we present the molecular and insecticidal characteristics of an indigenous Bt isolate T405 toxic against the maize fall armyworm (FAW), Spodoptera frugiperda. The presence of cry1, cry2 (cry2Aa & cry2Ab) and vip3A1 genes in T405 was confirmed. The SDS-PAGE gel analysis confirmed the occurrence of Cry and Vip proteins with molecular masses of 130, ∼88 and 65 kDa in T405. LC₅₀ estimates of T405 and HD1 were 161.37 and 910.73 μg ml^-1 for neonates whereas, 412.29 and 1014.95 μg ml^-1 correspondingly for 2^nd instar FAW larvae. Scanning Electron Microscopy depicted the existence of bipyramidal, spherical and cubic crystals in T405 spore suspension. The whole genome sequencing and assembly of T405 produced a total of 563 scaffolds with a genome size of 6,673,691 bp. The BLAST similarity search showed that 12 plasmids were distributed in this genome. Genome annotation revealed the presence of 6174 protein coding genes, 13 rRNA and 98 tRNA, in which 6126 genes were completely annotated for their functions through sequence similarity search, domains/motifs identification and gene ontology studies. Further analysis of these genes identified the presence of many insecticidal toxin protein coding genes viz., cry1Ac32, cry1Ab9, cry1Aa6, cry1Ac5, cry1Aa18, cry1Ab8, cry1Ab11, cry2Aa9, cry1Ia40, cry2Aa9, cry1Ia40, cry2Ab35, cyt, vip3Aa7 and tpp80Aa and several additional virulence assisted factors viz., immune inhibitor A, phospholipase C, sphingomyelinase, cell wall hydrolases, chitinase, hemolysin XhlA and seven urease subunit coding genes (ureA, ureB, ureC, ureD, ureE, ureF, ureG) in the annotated genome.

Bioinoculants as mitigators of multiple stresses: A ray of hope for agriculture in the darkness of climate change

Plant encounters various biotic and abiotic stresses, that affect agricultural productivity and reduce farmer's income especially under changing global climate. These environmental stresses can advance plant senescence by inducing osmotic stress, nutrient stress, hormonal imbalance, production of oxygen radicals, and ion toxicity, etc. Additionally, these stresses are not limited to plant health but also deteriorate soil health by affecting the microbial diversity of soil. To tackle this global delinquent of agriculture, several methods are suggested to ameliorate the negative effect of different types of stresses, the application of beneficial microorganisms or bioinoculants is one of them. Beneficial microorganisms that are used as bioinoculants not only facilitate plant growth by fulfilling the nutrient requirements but also assist the plant to withstand these stresses. These microorganisms produce certain chemicals such as 1-aminocyclopropane-1-carboxylate (ACC) deaminase, phytohormones, antioxidants, extracellular polysaccharide (EPS), siderophores, antibiotics, and volatile organic compounds (VOCs), etc. which help the plants to mitigate various stresses. Besides, these microbes also activate plant defence responses. Thus, these bioinoculants can effectively replace chemical inputs to supplement nutrient requirements and mitigation of multiple stresses in plants.

An overview of bats microbiota and its implication in transmissible diseases

Recent pandemic events have raised the attention of the public on the interactions between human and environment, with particular regard to the more and more feasible transmission to humans of micro-organisms hosted by wild-type species, due to the increasing interspecies contacts originating from human’s activities. Bats, due to their being flying mammals and their increasing promiscuity with humans, have been recognized as hosts frequently capable of transmitting disease-causing microorganisms. Therefore, it is of considerable interest and importance to have a picture as clear as possible of the microorganisms that are hosted by bats. Here we focus on our current knowledge on bats microbiota. We review the most recent literature on this subject, also in view of the bat’s body compartments, their dietary preferences and their habitat. Several pathogenic bacteria, including many carrying multidrug resistance, are indeed common guests of these small mammals, underlining the importance of preserving their habitat, not only to protect them from anthropogenic activities, but also to minimize the spreading of infectious diseases.

Antifungal Chitinase Production by Bacillus paramycoides B26 using Squid Pen Powder as a Carbon Source

This study aimed to optimize the medium compositions and cultural conditions for improved chitinase production by a potential strain of Bacillus isolated from the marine environment and determine the antifungal activity of its chitinase against plant pathogenic fungi. Five potential isolates were cultured for chitinase production by submerged fermentation using colloidal chitin in a liquid medium. In this study, chitinase activity was determined by measuring reducing sugars, which were determined by the 3,5-dinitrosalicylic acid (DNS) assay. The most potential isolate, B26, showed similarity to Bacillus paramycoides based on the 16S rRNA gene sequence. The maximum chitinase production was achieved at 6.52±0.02 U/mL after 72 h of incubation in a medium containing 2% squid pen powder, supplemented with 0.5% sodium nitrate and 2% NaCl, with an initial pH of 7. It was observed that the optimization of cultural conditions resulted in 2.83 times higher chitinase production than an unoptimized medium. The antifungal activity of crude chitinase against phytopathogenic fungi was evaluated by a well-diffusion method. The chitinase of B. paramycoides B26 effectively inhibited the growth of Fusarium solani TISTR 3436 (83.4%) and Penicillium chrysogenum TISTR 3554 (80.12%).

Development of curcumin incorporated composite films based on chitin and glucan complexes extracted from Agaricus bisporus for active packaging of chicken breast meat

Composite films were prepared by combining different concentrations of curcumin with chitin and glucan complexes (CGCs) extracted from Agaricus bisporus via a solution casting method. The developed curcumin doped CGC (CGC/Cu) films were characterized in terms of surface, optical, structural, barrier, mechanical, antioxidant, and antimicrobial properties. The biodegradability of CGC/Cu films was determined in soil for 14 days. The incorporation of curcumin significantly affected the surface morphology and improved light barrier properties, radical scavenging activity, and total phenolic content of the films. The CGC/Cu films containing different concentrations of curcumin showed antibacterial activity against Escherichia coli, while antibacterial activity against Staphylococcus aureus was not observed with the developed films. Afterward, the microbial properties of the fresh chicken breast were examined during refrigerated storage for 10 days. The shelf-life of chicken samples wrapped in the developed film was extended at least 40 % compared to the control sample. In conclusion, curcumin incorporated CGC based films can serve as a promising biodegradable active packaging material to improve the shelf-life of meat products.

Isolation and Molecular Identification of Serratia Strains Producing Chitinases, Glucanases, Cellulases, and Prodigiosin and Determination of Their Antifungal Effect against Colletotrichum siamense and Alternaria alternata In Vitro and on Mango Fruit

Microorganisms represent a viable option for the control of phytopathogens. From the surface of healthy mangoes, different bacteria were isolated. For all isolated bacterial strains, we determined their antimicrobial activity against a fungal strain that caused anthracnose in mangoes and against Alternaria alternata, both in the culture medium and directly on mangoes. The bacterial strains with the highest antifungal activity were identified by sequencing the 16s rRNA gene. Two species of Serratia were identified: marcescens and nematodiphila. Finally, the chitinolytic, glucanolytic, and cellulolytic activity and prodigiosin production of bacteria with antifungal activity was determined. Five fungal strains were isolated from mangoes with anthracnose. Only one strain was responsible for anthracnose in mangoes. This fungal strain was identified as Colletotrichum siamense. Against C. siamense and A. alternata in vitro and in mango selected strains of Serratia showed antifungal activity. Finally, the Serratia strains produced chitinases, glucanases, cellulases and prodigiosin, and the two S. marcescens strains did not produce hemolysins. The three Serratia strains isolated in this study can potentially be used in the biological control of anthracnose caused by C. siamense and A. alternata on mango.

Potentiality of actinobacteria to combat against biotic and abiotic stresses in tea [Camellia sinensis (L) O. Kuntze]

Tea (Camellia sinensis (L) O. Kuntze) is a long-duration monoculture crop prone to several biotic (fungal diseases and insect pest) and abiotic (nutrient deficiency, drought, and salinity) stress that eventually result in extensive annual crop loss. The specific climatic conditions and the perennial nature of the tea crop favor growth limiting abiotic factors, numerous plant pathogenic fungi (PPF), and insect pests. The review focuses on the susceptibility of tea crops to PPF/pests, drought, salinity, and nutrient constraints and the potential role of beneficial actinobacteria in promoting tea crop health. The review also focuses on some of the major PPF associated with tea, such as Exobasidium vexans, Pestalotiopsis theae, Colletotrichum acutatum, and pests (Helopeltis theivora). The phylum actinobacteria own a remarkable place in agriculture due to the biosynthesis of bioactive metabolites that assist plant growth by direct nutrient assimilation, phytohormone production, and by indirect aid in plant defense against PPF and pests. The chemical diversity and bioactive significance of actinobacterial metabolites (antibiotics, siderophore, volatile organic compounds, phytohormones) are valuable in the agro-economy. This review explores the recent history of investigations in the role of actinobacteria and its secondary metabolites as a biocontrol agent and proposes a commercial application in tea cultivation.

Insect frass and exuviae to promote plant growth and health

Beneficial soil microorganisms can contribute to biocontrol of plant pests and diseases, induce systemic resistance (ISR) against attackers, and enhance crop yield. Using organic soil amendments has been suggested to stimulate the abundance and/or activity of beneficial indigenous microbes in the soil. Residual streams from insect farming (frass and exuviae) contain chitin and other compounds that may stimulate beneficial soil microbes that have ISR and biocontrol activity. Additionally, changes in plant phenotype that are induced by beneficial microorganisms may directly influence plant-pollinator interactions, thus affecting plant reproduction. We explore the potential of insect residual streams derived from the production of insects as food and feed to promote plant growth and health, as well as their potential benefits for sustainable agriculture.

Assessing the potentials of bacterial antagonists for plant growth promotion, nutrient acquisition, and biological control of Southern blight disease in tomato

Southern blight of tomato caused by Sclerotium rolfsii can cause severe plant mortality and yield losses. The use of rhizobacteria for the biological control of Southern blight disease is a potent alternative to chemical fungicides. Although rhizobacteria are prolific candidates, comprehensive reports regarding their use in tomato disease management are limited. The present study screened six rhizobacterial strains for antagonism against S. rolfsii in dual culture and culture filtrate assays. The selected promising strains were tested further for plant-growth-promoting and biocontrol potentials under in vitro, greenhouse, and field conditions. Of the six strains screened, Stenotrophomonas maltophilia PPB3 and Bacillus subtilis PPB9 showed the superior performance displaying the highest antagonism against S. rolfsii in dual culture (PPB3 88% and PPB9 71% inhibition), and culture filtrate assays (PPB3 53–100% and PPB9 54–100% inhibition at various concentrations). Oxalic acid produced by S. rolfsii was significantly inhibited by both rhizobacteria and supported their growth as a carbon source. The strains produced hydrogen cyanide, chitinases, siderophores, biofilm, and indole acetic acid. They showed the potential to solubilize phosphate and fix nitrogen. Seed treatment with S. maltophilia PPB3 and B. subtilis PPB9 improved seed germination and tomato seedling vigour. Significant increases in plant growth, chlorophyll contents, and N, P, and K concentrations were attained in bacterized plants compared to non-treated controls. The application of antagonists on container-grown seedlings in a greenhouse environment and field-grown tomato plants reduced symptoms of damping-off and Southern blight. The sclerotial counts decreased significantly in these soils. Bacteria-inoculated plants had a higher yield than those in the non-treated control. Bacteria colonized the entire roots, and their populations increased significantly in the protected plants. The results show the potential capabilities of S. maltophilia PPB3 and B. subtilis PPB9 for growth promotion, nutrient acquisition, and biocontrol of southern blight disease in tomatoes.

Kinetic, Thermodynamic and Bio-applicable Studies on Aspergillus niger Mk981235 Chitinase

Chitinases have many applications in food, agricultural, medical, and pharmaceutical fields. This study succeeded in investigating Aspergillus niger MK981235 chitinase in the spot of its physiochemical, kinetic, thermodynamic, and application. The optimum temperature, pH and p-nitrophenyl-β-d-N-acetyl glucosaminide (PNP-β-GlcNAc) concentration to obtain the highest chitinase activity of 2334.79 U ml−1 were at 60 °C, 5 and 0.25%, respectively. The kinetic parameters, including Km and Vmax were determined to be 0.78 mg ml−1 and 2222.22 µmol ml−1 min−1, respectively. Furthermore, the thermodynamic parameters T1/2, D-values, ΔH, ΔG and ΔS at 40, 50 and 60 °C were determined to be (864.10, 349.45, 222.34 min), (2870.99, 1161.07, 738.74 min), (126.40, 126.36, 126.32 kJ mol−1), (101.59, 100.62, 100.86 kJ mol−1), (74.50, 76.17, 47.24 J mol−1 K−1), respectively. A. niger chitinase showed, insecticidal activity on Galleria mellonella by feeding and spraying treatments (72 and 52%, respectively), anti-lytic activity against Candida albicans, and effectiveness in improving the dye removal in the presence of crab shell powder as bio-absorbant. A. niger chitinase can be used in the pharmaceutical field for the bio-control of diseases caused by C. albicans and for the pretreatment of wastewater from the textile industry.

Graphical Abstract

A mixed blessing of viruses in wastewater treatment plants

Activated sludge of wastewater treatment plants harbors a very high diversity of both microorganisms and viruses, wherein the latter control microbial dynamics and metabolisms by infection and lysis of cells. However, it remains poorly understood how viruses impact the biochemical processes of activated sludge, for example in terms of treatment efficiency and pollutant removal. Using metagenomic and metatranscriptomic deep sequencing, the present study recovered thousands of viral sequences from activated sludge samples of three conventional wastewater treatment plants. Gene-sharing network indicated that most of viruses could not be assigned to known viral genera, implying activated sludge as an underexplored reservoir for new viruses and viral diversity. In silico predictions of virus-host linkages demonstrated that infected microbial hosts, mostly belonging to bacteria, were transcriptionally active and able to hydrolyze polymers including starches, celluloses, and proteins. Some viruses encode auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and sulfur cycling, and antibiotic resistance genes (ARGs) for resistance to multiple drugs. The virus-encoded AMGs may enhance the biodegradation of contaminants like starches and celluloses, suggesting a positive role for viruses in strengthening the performance of activated sludge. However, ARGs would be disseminated to different microorganisms using viruses as gene shuttles, demonstrating the possibility for viruses to facilitate the spread of antibiotic resistance in the environment. Collectively, this study highlights the mixed blessing of viruses in wastewater treatment plants, and deciphers how they manipulate the biochemical processes in the activated sludge, with implications for both environmental protection and ecosystem security.

Draft Genome Sequences of Two Streptomyces Isolates Obtained from Volcanic Soils in the Philippines

We report here the draft genome sequences of two Streptomyces isolates, namely, UNOB3_S3 and UNOC14_S4, obtained from volcanic soils in Albay, Philippines. The genome assemblies comprised 7.63 Mb and 8.24 Mb, respectively. Genome mining revealed genes and biosynthetic gene clusters that encode putative insecticidal products.

Paenibacillus sp. Strain UY79, Isolated from a Root Nodule of Arachis villosa, Displays a Broad Spectrum of Antifungal Activity

A nodule-inhabiting Paenibacillus sp. strain (UY79) isolated from wild peanut (Arachis villosa) was screened for its antagonistic activity against diverse fungi and oomycetes (Botrytis cinerea, Fusarium verticillioides, Fusarium oxysporum, Fusarium graminearum, Fusarium semitectum, Macrophomina phaseolina, Phomopsis longicolla, Pythium ultimum, Phytophthora sojae, Rhizoctonia solani, Sclerotium rolfsii, and Trichoderma atroviride). The results obtained show that Paenibacillus sp. UY79 was able to antagonize these fungi/oomycetes and that agar-diffusible compounds and volatile compounds (different from HCN) participate in the antagonism exerted. Acetoin, 2,3-butanediol, and 2-methyl-1-butanol were identified among the volatile compounds produced by strain UY79 with possible antagonistic activity against fungi/oomycetes. Paenibacillus sp. strain UY79 did not affect symbiotic association or growth promotion of alfalfa plants when coinoculated with rhizobia. By whole-genome sequence analysis, we determined that strain UY79 is a new species of Paenibacillus within the Paenibacillus polymyxa complex. Diverse genes putatively involved in biocontrol activity were identified in the UY79 genome. Furthermore, according to genome mining and antibiosis assays, strain UY79 would have the capability to modulate the growth of bacteria commonly found in soil/plant communities. IMPORTANCE Phytopathogenic fungi and oomycetes are responsible for causing devastating losses in agricultural crops. Therefore, there is enormous interest in the development of effective and complementary strategies that allow the control of the phytopathogens, reducing the input of agrochemicals in croplands. The discovery of new strains with expanded antifungal activities and with a broad spectrum of action is challenging and of great future impact. Diverse strains belonging to the P. polymyxa complex have been reported to be effective biocontrol agents. Results presented here show that the novel discovered strain of Paenibacillus sp. presents diverse traits involved in antagonistic activity against a broad spectrum of pathogens and is a potential and valuable strain to be further assessed for the development of biofungicides.

Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy

The microbial biogeochemical processes occurring in marine sediment in Antarctica remain underexplored due to limited access. Further, these polar habitats are unique, as they are being exposed to significant changes in their climate. To explore how microbes drive biogeochemistry in these sediments, we performed a shotgun metagenomic survey of marine surficial sediment (0 to 3 cm of the seafloor) collected from 13 locations in western Antarctica and assembled 16 high-quality metagenome assembled genomes for focused interrogation of the lifestyles of some abundant lineages. We observe an abundance of genes from pathways for the utilization of reduced carbon, sulfur, and nitrogen sources. Although organotrophy is pervasive, nitrification and sulfide oxidation are the dominant lithotrophic pathways and likely fuel carbon fixation via the reverse tricarboxylic acid and Calvin cycles. Oxygen-dependent terminal oxidases are common, and genes for reduction of oxidized nitrogen are sporadically present in our samples. Our results suggest that the underlying benthic communities are well primed for the utilization of settling organic matter, which is consistent with findings from highly productive surface water. Despite the genetic potential for nitrate reduction, the net catabolic pathway in our samples remains aerobic respiration, likely coupled to the oxidation of sulfur and nitrogen imported from the highly productive Antarctic water column above. IMPORTANCE The impacts of climate change in polar regions, like Antarctica, have the potential to alter numerous ecosystems and biogeochemical cycles. Increasing temperature and freshwater runoff from melting ice can have profound impacts on the cycling of organic and inorganic nutrients between the pelagic and benthic ecosystems. Within the benthos, sediment microbial communities play a critical role in carbon mineralization and the cycles of essential nutrients like nitrogen and sulfur. Metagenomic data collected from sediment samples from the continental shelf of western Antarctica help to examine this unique system and document the metagenomic potential for lithotrophic metabolisms and the cycles of both nitrogen and sulfur, which support not only benthic microbes but also life in the pelagic zone.

Performance of halotolerant bacteria associated with Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L. ameliorate tomato plant growth and tolerance to saline stress: from selective isolation to genomic analysis of potential determinants

The use of halotolerant beneficial plant-growth-promoting (PGP) bacteria is considered as a promising eco-friendly approach to improve the salt tolerance of cash crops. One strategy to enhance the possibility of obtaining stress-alleviating bacteria is to screen salt impacted soils. In this study, amongst the 40 endophytic bacteria isolated from the roots of Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L., 8 showed interesting NaCl tolerance in vitro. Their evaluation, through different tomato plant trials, permitted the isolate IS26 to be distinguished as the most effective seed inoculum for both plant growth promotion and mitigation of salt stress. On the basis of 16S rRNA gene sequence, the isolate was closely related to Stenotrophomonas rhizophila. It was then screened in vitro for multiple PGP traits and the strain-complete genome was sequenced and analysed to further decipher the genomic basis of the putative mechanisms underlying its osmoprotective and plant growth abilities. A remarkable number of genes putatively involved in mechanisms responsible for rhizosphere colonization, plant association, strong competition for nutrients, and the production of important plant growth regulator compounds, such as AIA and spermidine, were highlighted, as were substances protecting against stress, including different osmolytes like trehalose, glucosylglycerol, proline, and glycine betaine. By having genes related to complementary mechanisms of osmosensing, osmoregulation and osmoprotection, the strain confirmed its great capacity to adapt to highly saline environments. Moreover, the presence of various genes potentially related to multiple enzymatic antioxidant processes, able to reduce salt-induced overproduction of ROS, was also detected.

Biosafe Management of Botrytis Grey Mold of Strawberry Fruit by Novel Bioagents

Recently, there have been urgent economic and scientific demands to decrease the use of chemical fungicides during the treatment of phytopathogens, due to their human health and environmental impacts. This study explored the biocontrol efficacy of novel and eco-friendly preen (uropygial) oil and endophytic Bacillus safensis in managing postharvest Botrytis grey mold in strawberry fruit. The preen oil (25 μL/mL) showed high antifungal activity against B. cinerea Str5 in terms of the reduction in the fungal radial growth (41.3%) and the fungal colony-forming units (28.6%) compared to the control. A new strain of Bacillus safensis B3 had a good potential to produce chitinase enzymes (3.69 ± 0.31 U/mL), hydrolytic lipase (10.65 ± 0.51 U/mL), and protease enzymes (13.28 ± 0.65 U/mL), which are responsible for the hydrolysis of the B. cinerea Str5 cell wall and, consequently, restrict fungal growth. The in vivo experiment on strawberry fruit showed that preen (uropygial) oil reduced the disease severity by 87.25%, while the endophytic bacteria B. safensis B3 reduced it by 86.52%. This study reports the efficiency of individually applied bioagents in the control of phytopathogenic fungi for the first time and, consequently, encourages their application as a new and innovative strategy for prospective agricultural technology and food safety.

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.

Heterologous Expression of a Thermostable Chitinase from Myxococcus xanthus and Its Application for High Yield Production of Glucosamine from Shrimp Shell

Glucosamine (GlcN) is a widely used food supplement. Hence, enormous attention has been concerned with enzymatic production of GlcN owing to its advantage over a chemical approach. In this study, a previously unstudied chitinase gene (MxChi) in the genome of Myxococcus xanthus was cloned, expressed in recombinant soluble form and purified to homogeneity. TLC-, UPLC-, and microplate-reader- based activity tests confirmed MxChi hydrolyzes colloidal chitin to chitobiose as sole product. The optimal catalytic pH and temperature of MxChi was identified as 7.0 and 55 °C, respectively. MxChi exhibited 80% activity after 72 h incubation at 37 °C. The site-directed mutagenesis revealed that the amino acids D323A, D325A, and E327A of MxChi were in the DXDXE catalytic motif of GH18. When coupled with β-N-acetylhexosaminidase (SnHex) and deacetylase (CmCBDA), the enzyme allowed one-pot extraction of GlcN from colloidal chitin and shrimp shell. The optimal condition was 37 °C, pH 8.0, and 1/3/16.5 (MxChi/SnHex/CmCBDA), conducted by orthogonal design for the enzymatic cascades. Under this condition, the yield of GlcN was 26.33 mg from 400 mg shrimp shell. Facile recombinant in E. coli, robust thermostability and pure product herein makes newly discovered chitinase a valuable candidate for the green recycling of chitin rich waste.

Evaluation of Bacillus velezensis for Biological Control of Rhizoctonia solani in Bean by Alginate/Gelatin Encapsulation Supplemented with Nanoparticles

Plant growth promoting rhizobacteria (PGPR) are a group of bacteria that can increase plant growth; but due to unfavorable environmental conditions, PGPR are biologically unstable and their survival rates in soil are limited. Therefore, the suitable application of PGPR as a plant growth stimulation is one of the significant challenges in agriculture. This study presents an intelligent formulation based on Bacillus velezensis VRU1 encapsulation enriched with nanoparticles that was able to control Rhizoctonia solani on the bean. The spherical structure of the capsule was observed based on the Scanning Electron Microscope image. Results indicated that with increasing gelatin concentration, the swelling ratio and moisture content were increased; and since the highest encapsulation efficiency and bacterial release were observed at a gelatin concentration of 1.5%, this concentration was considered in mixture with alginate for encapsulation. The application of this formulation which is based on encapsulation and nanotechnology appears to be a promising technique to deliver PGPR in soil and is more effective for plants.