Enhanced nematicidal potential of the chitinase pachi from Pseudomonas aeruginosa in association with Cry21Aa

Rational Design of a Potential New Nematicide Targeting Chitin Deacetylase

In a previously published study, the authors devised a molecular topology QSAR (quantitative structure-activity relationship) approach to detect novel fungicides acting as inhibitors of chitin deacetylase (CDA). Several of the chosen compounds exhibited noteworthy activity. Due to the close relationship between chitin-related proteins present in fungi and other chitin-containing plant-parasitic species, the authors decided to test these molecules against nematodes, based on their negative impact on agriculture. From an overall of 20 fungal CDA inhibitors, six showed to be active against Caenorhabditis elegans. These experimental results made it possible to develop two new molecular topology-based QSAR algorithms for the rational design of potential nematicides with CDA inhibitor activity for crop protection. Linear discriminant analysis was employed to create the two algorithms, one for identifying the chemo-mathematical pattern of commercial nematicides and the other for identifying nematicides with activity on CDA. After creating and validating the QSAR models, the authors screened several natural and synthetic compound databases, searching for alternatives to current nematicides. Finally one compound, the N2-(dimethylsulfamoyl)-N-{2-[(2-methyl-2-propanyl)sulfanyl]ethyl}-N2-phenylglycinamide or nematode chitin deacetylase inhibitor, was selected as the best candidate and was further investigated both in silico, through molecular docking and molecular dynamic simulations, and in vitro, through specific experimental assays. The molecule shows favorable binding behavior on the catalytic pocket of C. elegans CDA and the experimental assays confirm potential nematicide activity.

Enterobacter Strain IPPBiotE33 Displays a Synergistic Effect with Bacillus thuringiensis Bt185

The discovery and isolation of new non-Bt insecticidal bacteria and genes are significant for the development of new biopesticides against coleopteran pests. In this study, we evaluated the insecticidal activity of non-Bt insecticidal bacteria, PPBiotE33, IPPBiotC41, IPPBiotA42 and IPPBiotC43, isolated from the peanut rhizosphere. All these strains showed insecticidal activity against first- and third-instar larvae of Holotrichia parallela, Holotrichia oblita, Anomala corpulenta and Potosia brevitarsis. IPPBiotE33 showed the highest toxicity among the four strains and exhibited virulence against Colaphellus bowringi. The genome of IPPBiotE33 was sequenced, and a new protein, 03673, with growth inhibition effects on C. bowringi was obtained. In addition, IPPBiotE33 had a synergistic effect with Bacillus thuringiensis Bt185 against H. parallela in bioassays and back-inoculation experiments with peanut seedlings. IPPBiotE33 induced a decrease in hemocytes and an increase in phenol oxidase activity in H. parallela hemolymph, known as the immunosuppressive effect, which mediated synergistic activity with Bt185. This study increased our knowledge of the new insecticidal strain IPPBiotE33 and shed new light on the research on new insecticidal coaction mechanisms and new blended pesticides.

Diversity of bioprotective microbial organisms in Upper Region of Assam and its efficacy against Meloidogyne graminicola

Meloidogyne graminicola has a well-established negative impact on rice yield in transplanted and direct-seeded rice, resulting in yield losses of up to 20 to 90 percent. Studies were undertaken to isolate potential native strains of bio-control agents to manage the devastating Rice Root Knot Nematode (M. graminicola). Eighteen bacterial strains and eleven fungal strains were isolated from the rhizosphere of crops like rice, okra, ash gourd, chili, beans and cucumber, enveloping diverse soil types from the Upper Brahmaputra Valley region of Assam. Six bacterial strains were gram-positive according to morphological results, while twelve others stained negatively. Fifteen bacteria were rod-shaped, two were coccus and one was diplococcus, and all the bacterial isolates showed signs of movement. All the bacterial strains exhibited positivity for gelatin hydrolysis and catalase test. Seven bacteria showed positive, while eleven showed negative reactions to possess the ability to deduce carbon and energy from citrate. The study of the in vitro efficacy of the twenty-nine bacterial and fungal isolates tested against second-stage juveniles (J₂) of Meloidogyne graminicola revealed that all the bacterial and fungal isolates potentially inhibited the test organism and caused significant mortality over sterile water treatment. The promising bacterial and fungal isolates that exhibited mortality above 50% were identified as BSH8, BTS4, BTS5, BJA15, FJB 11 and FSH5. The strain BSH8 exhibited the best result of mortality, with 80.79% mortality against J₂ of M. graminicola. The strain BTS4 and BTS5 expressed mortality of 71.29% and 68.75% under in-vitro conditions and were significant. The effective and promising bioagents were identified using the 16 S rRNA sequencing as Bacillis subtilis (BSH8), Bacillus velezensis (BTS4), Alcaligenes faecalis (BTS5), Rhizobium pusense (BJA15), Talaromyces allahabadensis (FSH5) and Trichoderma asperellum (FJB11). These results indicated the microorganism's potential against M. graminicola and its potential for successful biological implementation. Further, the native strains could be tested against various nematode pests of rice in field conditions. Its compatibility with various pesticides and the implication of the potential strains in integrated pest management can be assessed.

Nematicidal effects of a peptidase (NlpC/P60) from the phytopathogen Pseudomonas syringae MB03 on the model nematode Caenorhabditis elegans and plant-parasitic Meloidogyne incognita

BACKGROUND

Plant-parasitic nematodes (PPNs) are severe threats to agricultural yields and continue to be challenging to treat in several crops worldwide. Microbial-based control has been suggested as a better alternative to chemical control. In this study, we aimed to identify and characterize nematicidal virulence factors of a common phytopathogenic bacterium, Pseudomonas syringae, mainly focusing on the nematicidal and suppressive activities of an NlpC/P60 family peptidase, namely, Peptidase03, against the model nematode Caenorhabditis elegans and an agriculturally important PPN, Meloidogyne incognita.

METHODS AND RESULTS

Genome-wide virulence factor prediction of the P. syringae wild-type strain MB03 revealed numerous nematode pathogenic determinants. We selected 11 predicted nematicidal genes for cloning and induced expression in an Escherichia coli expression system and then performed comparative nematicidal bioassays on the model nematode C. elegans. The recombinant strain expressing Peptidase03 showed the highest level of toxicity against C. elegans, with 75.9% mortality, compared to the other tested strains. Purified Peptidase03 showed significant toxicity against C. elegans and M. incognita, with half lethal concentration (LC50) values of 147.9 µg/mL and 211.50 µg/mL, respectively. We also demonstrated that Peptidase03 could damage the intestinal tissues of C. elegans and exhibit detrimental effects on its growth, brood size, and locomotion.

CONCLUSIONS

The Peptidase03 protein from P. syringae MB03 had significant nematicidal and suppressive activities against C. elegans and M. incognita, thereby showing potential for the development of an effective PPN-controlling agent for use in agricultural practice.

Characterization of Nematicidal Activity and Nematode-Toxic Metabolites of a Soilborne Brevundimonas bullata Isolate

The increasing prevalence of crop-threatening root-knot nematodes (RKNs) has stimulated extensive research to discover effective nematicides. A highly focused strategy for accomplishing this is the development of biocontrol agents by a variety of soilborne microorganisms, as different bacterial metabolites have demonstrated promising nematicidal activities. In this study, we characterized the nematicidal and suppressive activity of a bacterial isolate against the agriculturally important RKN Meloidogyne incognita and the model nematode Caenorhabditis elegans, and the main M. incognita-toxic metabolite of the strain. After a preliminary screening of 22 bacterial isolates with a corrected mortality (CM) of whole-cell culture greater than 50% against C. elegans from different RKN-incident soils in China, a total of 14 isolates with CM of the supernatant of culture suspension (SCS) higher than 50% against both M. incognita and C. elegans were rescreened. An isolate with the highest CM of 86.1% and 95.0% for M. incognita and C. elegans, respectively, was further identified as the species Brevundimonas bullata via morphological examination, physiological and biochemical assays and alignment analysis of 16S rRNA gene sequences. The SCS of this strain, namely, B. bullata MB756, exhibited synchronous M. incognita killing activity along with significant detrimental effects on the growth, brood size, and locomotion of C. elegans. The effects of heat treatment, pH, inoculations, and protease K proteolysis on the CM of MB756 SCS were evaluated. A major M. incognita-toxic substance in the MB756 SCS was assayed and identified using thin-layer chromatography, column chromatography and high-performance liquid chromatography with a mass spectrometer, and it was preliminarily identified as 2-ethylhexan-1-ol, with a molecular formula of C₈H₁₈O and a molecular weight of 130.3 Da.

Plants-nematodes-microbes crosstalk within soil: A trade-off among friends or foes

Plants interact with enormous biotic and abiotic components within ecosystem. For instance, microbes, insects, herbivores, animals, nematodes etc. In general, these interactions are studied independently with plants, that condenses only specific information about the interaction. However, the limitation to study the cross-interactions masks the collaborative role of organisms within ecosystem. Beneficial microbes are most prominent organisms that are needed to be studied due to their bidirectional nature towards plants. Fascinatingly, Plant-Parasitic Nematodes (PPNs) have been profoundly observed to cause mass destruction of agricultural crops worldwide. The huge demand for agriculture for present-day population requires optimization of production potential by curbing the damage caused by PPNs. Chemical nematicides combats their proliferation, but their extended usage has abruptly affected flora, fauna and human populations. Because of consistent pressing issues in regard to environment, the use of biocontrol agents are most favourable alternatives for managing agriculture. However, this association is somehow, tug of war, and understanding of plant-nematode-microbial relation would enable the agriculturists to monitor the overall development of plants along with limiting the use of agrochemicals. Soil microbes are contemporary bio-nematicides emerging in the market, that stimulates the plant growth and impedes PPNs populations. They form natural enemies and trap nematodes, henceforth, it is crucial to understand these interactions for ecological and biotechnological perspectives for commercial use. Moreover, acquiring the diversity of their relationship and molecular-based mechanisms, outlines their cascade of signaling events to serve as biotechnological ecosystem engineers. The omics based mechanisms encompassing hormone gene regulatory pathways and elicitors released by microbes are able to modulate pathogenesis-related (PR) genes within plants. This is achieved via Induced Systemic Resistance (ISR) or acquired systemic channels. Taking into account all these validations, the present review mainly advocates the relationship among microbes and nematodes in plants. It is believed that this review will boost zest and zeal within researchers to effectively understand the plant-nematodes-microbes relations and their ecological perspectives.

Selection and characterization of two Bacillus thuringiensis strains showing nematicidal activity against Caenorhabditis elegans and Meloidogyne incognita

Bacillus thuringiensis has been widely used as a biological control agent against insect pests. Additionally, nematicidal strains have been under investigation. In this report, 310 native strains of B. thuringiensis against Caenorhabditis elegans were tested. Only the LBIT-596 and LBIT-107 strains showed significant mortality. LC50s of spore-crystal complexes were estimated at 37.18 and 31.89 μg/mL for LBIT-596 and LBIT-107 strains, respectively, while LC50s of partially purified crystals was estimated at 23.76 and 20.25 μg/mL for LBIT-596 and LBIT-107, respectively. The flagellin gene sequence and plasmid patterns indicated that LBIT-596 and LBIT-107 are not related to each other. Sequences from internal regions of a cry5B and a cyt1A genes were found in the LBIT-596 strain, while a cry21A, a cry14A and a cyt1A genes were found in the LBIT-107 strain. Genome sequence of the LBIT-107 strain showed new cry genes, along with other virulence factors, hence, total nematicidal activity of the LBIT-107 strain may be the result of a multifactorial effect. The highlight of this contribution is that translocation of spore-crystal suspensions of LBIT-107 into tomato plants inoculated at their rhizosphere decreased up to 90% the number of galls of Meloidogyne incognita, perhaps the most important nematode pest in the world.

Combating Parasitic Nematode Infections, Newly Discovered Antinematode Compounds from Marine Epiphytic Bacteria

Parasitic nematode infections cause debilitating diseases and impede economic productivity. Antinematode chemotherapies are fundamental to modern medicine and are also important for industries including agriculture, aquaculture and animal health. However, the lack of suitable treatments for some diseases and the rise of nematode resistance to many available therapies necessitates the discovery and development of new drugs. Here, marine epiphytic bacteria represent a promising repository of newly discovered antinematode compounds. Epiphytic bacteria are ubiquitous on marine surfaces where they are under constant pressure of grazing by bacterivorous predators (e.g., protozoans and nematodes). Studies have shown that these bacteria have developed defense strategies to prevent grazers by producing toxic bioactive compounds. Although several active metabolites against nematodes have been identified from marine bacteria, drug discovery from marine microorganisms remains underexplored. In this review, we aim to provide further insight into the need and potential for marine epiphytic bacteria to become a new source of antinematode drugs. We discuss current and emerging strategies, including culture-independent high throughput screening and the utilization of Caenorhabditis elegans as a model target organism, which will be required to advance antinematode drug discovery and development from marine microbial sources.

TOXiTAXi: a web resource for toxicity of Bacillus thuringiensis protein compositions towards species of various taxonomic groups

Bioinsecticides consisting of different sets of Bacillus thuringiensis (Bt) Cry, Cyt and Vip toxins are broadly used in pest control. Possible interactions (synergistic, additive or antagonistic) between these proteins can not only influence the overall efficacy of certain Bt-based bioinsecticide, but also raise questions regarding environmental safety. Here, we assemble, summarize and analyze the outcomes of experiments published over 30 years, investigating combinatorial effects among Bt Cry, Cyt and Vip toxins. We collected the results on 118 various two-to-five-component combinations that have been bioassayed against 38 invertebrate species. Synergism, additive effect and antagonism was indicated in 54%, 32% and 14% of experiments, respectively. Synergism was noted most frequently for Cry/Cyt combinations, followed by Cyt/Vip and Cry/Cry. In Cry/Vip combinations, antagonism is more frequent and higher in magnitude compared to other categories. Despite a significant number of tested Bt toxin combinations, most of them have been bioassayed only against one pest species. To aid the research on Bt pesticidal protein activity, we present TOXiTAXi ( http://www.combio.pl/toxitaxi/ ), a universal database and a dedicated web tool to conveniently gather and analyze the existing and future bioassay results on biocidal activity of toxins against various taxonomic groups.

Serratia sp., an endophyte of Mimosa pudica nodules with nematicidal, antifungal activity and growth-promoting characteristics

In the present study, the nematicidal activity of an isolated strain of Mimosa pudica nodules was evaluated against the Nacobbus aberrans (J2) phytonymatodes with a mortality of 88.8%, while against the gastrointestinal nematode Haemonchus contortus (L3) and free-living Panagrellus redivivus was 100%. The ability to inhibit the growth of phytopathogenic fungi Fusarium sp., and Alternaria solani, as well as the oomycete Phytophthora capsici, this antifungal activity may be related to the ability to produce cellulases, siderophores and chitinases by this bacterial strain. Another important finding was the detection of plant growth promoter characteristics, such as auxin production and phosphate solubilization. The strain identified by sequences of the 16S and rpoB genes as Serratia sp. is genetically related to Serratia marcescens and Serratia nematodiphila. The promoter activity of plant growth, antifungal and nematicide of the Serratia sp. strain makes it an alternative for the biocontrol of fungi and nematodes that affect both the livestock and agricultural sectors, likewise, candidate as a growth-promoting bacterium.

Thermophilic Chitinases: Structural, Functional and Engineering Attributes for Industrial Applications

Chitin is the second most widely found natural polymer next to cellulose. Chitinases degrade the insoluble chitin to bioactive chitooligomers and monomers for various industrial applications. Based on their function, these enzymes act as biocontrol agents against pathogenic fungi and invasive pests compared with conventional chemical fungicides and insecticides. They have other functional roles in shellfish waste management, fungal protoplast generation, and Single-Cell Protein production. Among the chitinases, thermophilic and thermostable chitinases are gaining popularity in recent years, as they can withstand high temperatures and maintain the enzyme stability for longer periods. Not all chitinases are thermostable; hence, tailor-made thermophilic chitinases are designed to enhance their thermostability by direct evolution, genetic engineering involving mutagenesis, and proteomics approach. Although research has been done extensively on cloning and expression of thermophilic chitinase genes, there are only few papers discussing on the mechanism of chitin degradation using thermophiles. The current review discusses the sources of thermophilic chitinases, improvement of protein stability by gene manipulation, metagenomics approaches, chitin degradation mechanism in thermophiles, and their prospective applications for industrial, agricultural, and pharmaceutical purposes.

Chitinase production by Trichoderma koningiopsis UFSMQ40 using solid state fermentation

The chitinases have extensive biotechnological potential but have been little exploited commercially due to the low number of good chitinolytic microorganisms. The purpose of this study was to identify a chitinolytic fungal and optimize its production using solid state fermentation (SSF) and agroindustry substrate, to evaluate different chitin sources for chitinase production, to evaluate different solvents for the extraction of enzymes produced during fermentation process, and to determine the nematicide effect of enzymatic extract and biological control of Meloidogyne javanica and Meloidogyne incognita nematodes. The fungus was previously isolated from bedbugs of Tibraca limbativentris Stal (Hemiptera: Pentatomidae) and selected among 51 isolated fungal as the largest producer of chitinolytic enzymes in SSF. The isolate UFSMQ40 has been identified as Trichoderma koningiopsis by the amplification of tef1 gene fragments. The greatest chitinase production (10.76 U gds^-1) occurred with wheat bran substrate at 55% moisture, 15% colloidal chitin, 100% of corn steep liquor, and two discs of inoculum at 30 °C for 72 h. Considering the enzymatic inducers, the best chitinase production by the isolated fungus was achieved using chitin in colloidal, powder, and flakes. The usage of 1:15 g/mL of sodium citrate-phosphate buffer was the best ratio for chitinase extraction of SSF. The Trichoderma koningiopsis UFSMQ40 showed high mortality of M. javanica and M. incognita when applied to treatments with enzymatic filtrated and the suspension of conidia.

Identification and Nematicidal Characterization of Proteases Secreted by Endophytic Bacteria Bacillus cereus BCM2

The endophytic bacterium Bacillus cereus BCM2 has shown great potential as a biocontrol organism against Meloidogyne incognita, which causes severe root-knot diseases in crops. In our previous study, the metabolite of BCM2 showed high nematicidal activity against the M. incognita second-stage juveniles. However, the mechanism employed by endophytic bacteria to infect and kill nematodes is still unclear. Here, we investigate both the endophytic bacterial extracellular proteins with nematicidal activity and their mechanism of killing nematodes. The first step was detecting the nematicidal activities of crude proteins. The results show that the nematode mortality rate reached 100% within 72 h, and the crude proteins damaged both the cuticle and eggshell, before finally destroying the targets. This suggests possible proteinaceous pathogeny in BCM2. Throughout the process, the fine-detail changes in the nematode cuticle and the intestinal structure were observed using scanning electron microscopy and transmission electron microscopy. These images show that BCM2 extracellular proteins did not damage the internal organization of the nematode but did severely damage its cuticle, which led to content leakage. From the crude proteins, chitosanase, alkaline serine protease, and neutral protease were purified and identified. The M. incognita-B. cereus BCM2 microenvironment simulation demonstrates that BCM2 adheres to the surface of nematodes and helps the metabolites that were produced by BCM2 to rapidly recognize and kill M. incognita. This relationship between plants, endophytic bacteria, and nematodes offers insight into the biological mechanisms that can be utilized for of nematode management.

Molecular characterization of lepidopteran-specific toxin genes in Bacillus thuringiensis strains from Thailand

A total of 511 local isolates of Bacillus thuringiensis from different geographical regions of Thailand were analyzed for the presence of the cry1A, cry1B, cry2A, cry9, and vip3A genes encoding for lepidopteran-specific toxins. PCR results revealed that 94.32% (482/511) of B. thuringiensis isolates harbored at least one of the detected genes, of which the cry1A, cry1B, cry2A, cry9, and vip3A genes were detected at frequencies of 90.61%, 89.63%, 76.32%, 40.70%, and 48.18%, respectively. Nineteen gene-combination profiles were discovered among 482 B. thuringiensis isolates, of which the most frequently detected profile contained the cry1A, cry1B, cry2A, and vip3A genes. Sixty-one isolates (12.66%), which harbored all of the detected insecticidal toxin genes, were further detected for the exochitinase (chi36) gene and chitinase activity. The results revealed that all 61 isolates contained the chi36 gene and exhibited chitinase activity. Insect bioassays showed that five isolates were highly toxic (more than 80% mortality) against second instar larvae of Spodoptera litura, of which the highest insect mortality (93%) was obtained from the B. thuringiensis isolates 225-15 and 417-1. Scanning electron microscopy revealed that the crystal morphologies of the five effective isolates were bipyramidal and cuboidal shapes. SDS-PAGE analysis of the spore-crystal mixture showed major bands of approximately 65 and 130 kDa. These five effective strains are alternative candidates for use as a microbial insecticide for the control of the S. litura pest.

The Nif3-Family Protein YqfO03 from Pseudomonas syringae MB03 Has Multiple Nematicidal Activities against Caenorhabditis elegans and Meloidogyne incognita

The nematicidal activity of the common plant-pathogenic bacterium Pseudomonas syringae against certain nematodes has been recently identified, but little is known about its virulence factors. In the current study, predictive analysis of nematode-virulent factors in the genome of a P. syringae wild-type strain MB03 revealed a variety of factors with the potential to be pathogenic against nematodes. One of these virulence factors that was predicted with a high score, namely, YqfO03, was a protein with structural domains that are similar to the Nif3 superfamily. This protein was expressed and purified in Escherichia coli, and was investigated for nematicidal properties against the model nematode Caenorhabditis elegans and an agriculturally important pest Meloidogyne incognita. Our results showed that YqfO03 exhibits lethal activity toward C. elegans and M. incognita worms, and it also caused detrimental effects on the growth, brood size, and motility of C. elegans worms. However, C. elegans worms were able to defend themselves against YqfO03 via a physical defense response by avoiding contact with the protein. Discovery of the diverse nematicidal activities of YqfO03 provides new knowledge on the biological function of a bacterial Nif3-family protein and insight into the potential of this protein as a specific means of controlling agricultural nematode pests.

Improvement of chitinase Pachi with nematicidal activities by random mutagenesis

Chitinase, an enzyme that can degrade the main compositions of insect intestine and cuticle, has been used in the bio-control field. Our previous work has reported the chitinase Pachi with nematicidal activity (Caenorhabditis elegans). In the present study, to improve the chitinolytic and nematicidal activities of Pachi, a random mutant library was constructed by error-prone PCR and screened by bacteriophage T7-based high-throughput screening system. One mutant, Pachi_N35D was obtained from about 10, 000 clones. The kinetics analysis revealed that Pachi_N35D exhibited a 63% decrease in K_m value against chitosan, a 2.1-fold enhancement in k_cat/K_m value and a 1.2-fold increase in specific activity over the wild-type Pachi. Moreover, the mortality analysis against Caenorhabditis elegans showed that the 50% lethal concentration (LC₅₀) of Pachi_N35D is 309.6±1.1μg/ml and a 20% increase in nematicidal activity over the wild-type Pachi (with a LC₅₀ value of 387.3±31.7μg/ml). The structure modeling and superimposition indicated that the substitution N35D reduced the distance between substrate and substrate-binding site Asp141, finally resulting in an increase in substrate affinity, catalytic efficiency and specific activity. These results provide useful information for the study of structure-function relationship of Pachi and lay a foundation for its potential applications in agro-biotechnology.

Rhizobacteria with nematicide aptitude: enzymes and compounds associated

The use of rhizobacteria to control plant parasitic nematodes has been widely studied. Currently, the research focuses on bacteria-nematode interactions that can mitigate this complex microbiome in agriculture. Various enzymes, toxins and metabolic by-products from rhizobacteria antagonize plant parasitic nematodes, and many different modes of action have been proposed. Hydrolytic enzymes, primarily proteases, collagenases and chitinases, have been related to the nematicide effect in rhizobacteria, proving to be an important factor involved in the degradation of different chemical constituents of nematodes at distinct developmental stages. Exuded metabolites may also alter the nematode-plant recognition process or create a hostile environment for nematodes in the rhizosphere. Specific bacteria strains responsible for the production of toxins, such as Cry proteins, are one of the strategies used by rhizobacteria. Characterization of the rhizobacteria mode of action could strengthen the development of commercial products to control populations of plant parasitic nematodes. This review aims to provide an overview of different enzymes and compounds produced by rhizobacteria related to the process of antagonism to plant-parasitic nematodes.