Nematicidal Volatiles from Bacillus atrophaeus GBSC56 Promote Growth and Stimulate Induced Systemic Resistance in Tomato against Meloidogyne incognita

Ascorbate, plant hormones and their interactions during plant responses to biotic stress

Plants can experience a variety of environmental stresses that significantly impact their fitness and survival. Additionally, biotic stress can harm agriculture, leading to reduced crop yields and economic losses worldwide. As a result, plants have developed defense strategies to combat potential invaders. These strategies involve regulating redox homeostasis. Several studies have documented the positive role of plant antioxidants, including Ascorbate (Asc), under biotic stress conditions. Asc is a multifaceted antioxidant that scavenges ROS, acts as a co-factor for different enzymes, regulates gene expression, and facilitates iron transport. However, little attention has been given to Asc and its transport, regulatory effects, interplay with phytohormones, and involvement in defense processes under biotic stress. Asc interacts with other components of the redox system and phytohormones to activate various defense responses that reduce the growth of plant pathogens and promote plant growth and development under biotic stress conditions. Scientific reports indicate that Asc can significantly contribute to plant resistance against biotic stress through mutual interactions with components of the redox and hormonal systems. This review focuses on the role of Asc in enhancing plant resistance against pathogens. Further research is necessary to gain a more comprehensive understanding of the molecular and cellular regulatory processes involved.

Molecular Characterization Reveals Biodiversity and Biopotential of Rhizobacterial Isolates of Bacillus Spp

Bacillus species appearas the most attractive plant growth-promoting rhizobacteria (PGPR) and alternative to synthetic chemical pesticides. The present study examined the antagonistic potential of spore forming-Bacilli isolated from organic farm soil samples of Allahabad, India. Eighty-seven Bacillus strains were isolated and characterized based on their morphological, plant growth promoting traits and molecular characteristics. The diversity analysis used 16S-rDNA, BOX-element, and enterobacterial repetitive intergenic consensus. Two strains, PR30 and PR32, later identified as Bacillus sp., exhibited potent in vitro antagonistic activity against Ralstonia solanaceorum. These isolates produced copious amounts of multiple PGP traits, such as indole-3-acetic acid (40.0 and 54.5 μg/mL), phosphate solubilization index (PSI) (4.4 and 5.3), ammonia, siderophore (3 and 4 cm), and 1-aminocyclopropane-1-carboxylate deaminase (8.1and 9.2 μM/mg//h) and hydrogen cyanide. These isolates were subjected to the antibiotic sensitivity test. The two potent isolates based on the higher antagonistic and the best plant growth-promoting ability were selected for plant growth-promoting response studies in tomatoe, broccoli, and chickpea. In the pot study, Bacillus subtilis (PR30 and PR31) showed significant improvement in seed germination (27-34%), root length (20-50%), shoot length (20-40%), vigor index (50-75%), carotenoid content (0.543-1.733), and lycopene content (2.333-2.646 mg/100 g) in tomato, broccoli, and chickpea. The present study demonstrated the production of multiple plant growth-promoting traits by the isolates and their potential as effective bioinoculants for plant growth promotion and biocontrol of phytopathogens.

Volatile organic compounds of the soil bacterium Bacillus halotolerans suppress pathogens and elicit defense-responsive genes in plants

Volatile organic compounds (VOCs) produced by bacteria play an important, yet relatively unexplored role in interactions between plants and phytopathogens. In this study, the soil bacterium Bacillus halotolerans NYG5 was identified as a potent biocontrol agent against several phytopathogenic fungi (Macrophomina phaseolina, Rhizoctonia solani, Pythium aphanidermatum, and Sclerotinia sclerotiorum) through the production of VOCs. NYG5-emitted VOCs also inhibited the growth of bacterial pathogens (Agrobacterium tumefaciens, Xanthomonas campestris, Clavibacter michiganensis, and Pseudomonas syringae). When cultured in various growth media, NYG5 produced a variety of VOCs. Five distinct VOCs (2-methylbutanoic acid, 5-methyl-2-hexanone, 2,3-hexanedione, 2-ethyl-1-hexanol, and 6-methyl-2-heptanone) were identified using headspace GC-MS. 2,3-Hexanedione exhibited potent lethal effects on the tested phytopathogens and nematicidal activity against Meloidogyne javanica at a concentration of 50 ppm. In addition, 0.05 ppm 2,3-hexanedione stimulated the expression of pathogenesis-related genes 1 and 2 in Arabidopsis thaliana. Interestingly, 2,3-hexanedione is used as a food additive at higher concentrations than those tested in this study. Hence, 2,3-hexanedione is a promising biologically active compound that might serve as a sustainable alternative to common chemical pesticides and an elicitor of plant defense.

Genomic and phenotypic analyses reveal Paenibacillus polymyxa PJH16 is a potential biocontrol agent against cucumber fusarium wilt

In recent years, bacterial-based biocontrol agents (BCA) have become a new trend for the control of fungal diseases such as fusarium wilt that seriously threaten the yield and quality of cucumber, which are transmitted through infested soil and water. This study was set out with the aim of figuring the mechanism of the isolated rhizobacterial strain Paenibacillus polymyxa PJH16 in preventing Fusarium oxysporum f. sp. cucumerinum (Foc). Biocontrol and growth-promoting experiments revealed that bacterial strain causes effective inhibition of the fungal disease through a significant growth-promoting ability of plants, and had activities of β-1,3-glucanase, cellulase, amylase and protease. It could produce siderophore and indole-3-acetic acid, too. Using the high-throughput sequencing tool PacBio Sequel II system and the database annotation, the bacterial strain was identified as P. polymyxa PJH16 and contained genes encoding for presence of biofilm formation, antimicrobial peptides, siderophores and hydrolyases. From comparing data between the whole genome of P. polymyxa PJH16 with four closely related P. polymyxa strains, findings revealed markedly the subtle differences in their genome sequences and proposed new antifungal substances present in P. polymyxa PJH16. Therefore, P. polymyxa PJH16 could be utilized in bioengineering a microbial formulation for application as biocontrol agent and bio-stimulant, in the future.

Biocontrol Efficacy and Induced Resistance of Paenibacillus polymyxa J2-4 Against Meloidogyne incognita Infection in Cucumber

Meloidogyne incognita is one of the most destructive agricultural pathogens around the world, resulting in severe damage to yield and quality in agricultural production. Biological control promises to be a great potential alternative to chemical agents against M. incognita. Paenibacillus polymyxa J2-4, isolated from ginger plants injured by M. incognita, has shown excellent biocontrol efficacy against M. incognita in cucumber. In vitro experiments with the strain J2-4 resulted in a correct mortality rate of 88.79% (24 h) and 98.57% (48 h) for second-stage juveniles (J2s) of M. incognita. Strain J2-4 significantly suppressed nematode infection on potted plants, with a 65.94% reduction in galls and a 51.64% reduction in eggs compared with the control. The split-root assay demonstrated that strain J2-4 not only reduced J2s' invasion but also inhibited nematode development through the dependence on salicylic acid and jasmonic acid signaling of strain J2-4 induction of plant resistance in local and systemic roots of cucumbers. Genomic analysis of strain J2-4 indicated biosynthetic gene clusters encoding polymyxin, fusaricidin B, paenilan, and tridecaptin. In addition, genetic analysis showed that none of the genes encoding virulence factors were detected in the genome of J2-4 compared with the pathogenic Bacillus species. Taking all the data together, we conclude that P. polymyxa J2-4 has potential as a biological control agent against M. incognita on cucumbers and can be considered biologically safe when used in agriculture.

Volatile organic compounds produced by Paenibacillus polymyxa J2-4 exhibit toxic activity against Meloidogyne incognita

BACKGROUND

Root knot nematodes cause great damage to crops worldwide. Due to the negative effects of the application of fumigant and old chemical nematicides, biological nematicides have drawn increasing attention in recent years. Here we tested the fumigant activity of the volatile organic compounds (VOCs) blends emitted from Paenibacillus polymyxa and pure commercial VOCs against M. incognita.

RESULTS

In this study, we investigated whether P. polymyxa strain J2-4 could produce VOCs that exhibit nematicidal activity. In vitro assays indicated that J2-4 VOCs were highly toxic to second stage juveniles (J2s) and could inhibit egg hatching. Three-layered pot experiments showed that the number of nematodes that penetrating in cucumber roots was reduced by 69.27% after the application of J2-4 VOCs under greenhouse conditions. We identified 14 volatiles using solid-phase micro-extraction gas chromatography-mass spectrometry. The efficacy of six commercially available VOCs, namely 2-isobutyl-3-methylpyrazine, 2,4-dimethoxybenzaldoxime, 2-dodecanone, 2-tridecanol, 2-tridecanone, and 2-tetradecanol, against M. incognita were examined. Except for 2,4-dimethoxybenzaldoxime, the remaining five VOCs showed strong direct-contact nematicidal activity against J2s of M. incognita, and only 2-isobutyl-3-methylpyrazine showed strong fumigant activity against J2s of M. incognita. In pot experiments, 2-isobutyl-3-methylpyrazine and 2-dodecanone reduced the number of root galls by about 70%, and 2-tridecanone reduced the number of root galls and egg masses by about 63% compared with controls.

CONCLUSION

Paenibacillus polymyxa strain J2-4 exhibited high fumigant activity against M. incognita. Our results provide evidence for the use of J2-4 and its VOCs as biocontrol agents in the management of root-knot nematodes. © 2023 Society of Chemical Industry.

3-(Methylthio)Propionic Acid from Bacillus thuringiensis Berliner Exhibits High Nematicidal Activity against the Root Knot Nematode Meloidogyne incognita (Kofoid and White) Chitwood

Root knot nematodes cause serious damage to global agricultural production annually. Given that traditional chemical fumigant nematicides are harmful to non-target organisms and the environment, the development of biocontrol strategies has attracted significant attention in recent years. In this study, it was found that the Bacillus thuringiensis Berliner strain NBIN-863 exhibits strong fumigant nematicidal activity and has a high attraction effect on Meloidogyne incognita (Kofoid and White) Chitwood. Four volatile organic compounds (VOCs) produced by NBIN-863 were identified using solid-phase microextraction and gas chromatography-mass spectrometry. The nematicidal activity of four VOCs, namely, N-methylformamide, propenamide, 3-(methylthio)propionic acid, and phenylmalonic acid, was detected. Among these compounds, 3-(methylthio)propionic acid exhibited the highest direct contact nematicidal activity against M. incognita, with an LC50 value of 6.27 μg/mL at 24 h. In the fumigant bioassay, the mortality rate of M. incognita treated with 1 mg/mL of 3-(methylthio)propionic acid for 24 h increased to 69.93%. Furthermore, 3-(methylthio)propionic acid also exhibited an inhibitory effect on the egg-hatching of M. incognita. Using chemotaxis assays, it was determined that 3-(methylthio)propionic acid was highly attractive to M. incognita. In pot experiments, the application of 3-(methylthio)propionic acid resulted in a reduction in gall numbers, decreasing the number of galls per gram of tomato root from 97.58 to 6.97. Additionally, the root length and plant height of the treated plants showed significant increases in comparison with the control group. The current study suggests that 3-(methylthio)propionic acid is a novel nematicidal virulence factor of B. thuringiensis. Our research provides evidence for the potential use of NBIN-863 or its VOCs in biocontrol against root knot nematodes.

Bioactivity and genome analysis of Bacillus amyloliquefaciens GL18 isolated from the rhizosphere of Kobresia myosuroides in an alpine meadow

The unique eco-environment of the Qinghai-Tibet Plateau breeds abundant microbial resources. In this research, Bacillus amyloliquefaciens GL18, isolated from the rhizosphere of Kobresia myosuroides from an alpine meadow, and the antagonistic activity, bacteriostatic hydrolase activity, and low temperature, salt, and drought resistance of it were determined and analysed. The seedlings of Avena sativa were root-irrigated using bacteria suspensions (cell concentration 1 × 107 cfu/mL) of GL18, and the growth-promoting effect of GL18 on it was determined under cold, salt and drought stress, respectively. The whole genome of GL18 was sequenced, and its functional genes were analysed. GL18 presented significant antagonistic activity to Fusarium graminearum, Fusarium acuminatum, Fusarium oxysporum and Aspergillus niger (inhibition zone diameter > 17 mm). Transparent zones formed on four hydrolase detection media, indicating that GL18 secreted cellulase, protease, pectinase and β-1,3-glucanase. GL18 tolerated conditions of 10 °C, 11% NaCl and 15% PEG-6000, presenting cold, salt and drought resistance. GL18 improved the cold, salt and drought tolerance of A. sativa and it showed significant growth effects under different stress. The total length of the GL18 genome was 3,915,550 bp, and the number of coding DNA sequence was 3726. Compared with the clusters of orthologous groups of proteins, gene ontology and kyoto encyclopedia of genes and genomes databases, 3088, 2869 and 2357 functional genes were annotated, respectively. GL18 contained gene clusters related to antibacterial substances, functional genes related to the synthesis of plant growth-promoting substances, and encoding genes related to stress resistance. This study identified an excellent Bacillus strain and provided a theoretical basis for improving stress resistance and promoting the growth of herbages under abiotic stress.

Metagenomic profiling of tomato rhizosphere delineates the diverse nature of uncultured microbes as influenced by Bacillus velezensis VB7 and Trichoderma koningiopsis TK towards the suppression of root-knot nematode under field conditions

The plant-parasitic Root Knot Nematodes (Meloidogyne spp.,) play a pivotal role to devastate vegetable crops across the globe. Considering the significance of plant-microbe interaction in the suppression of Root Knot Nematode, we investigated the diversity of microbiome associated with bioagents-treated and nematode-infected rhizosphere soil samples through metagenomics approach. The wide variety of organisms spread across different ecosystems showed the highest average abundance within each taxonomic level. In the rhizosphere, Proteobacteria, Firmicutes, and Actinobacteria were the dominant bacterial taxa, while Ascomycota, Basidiomycota, and Mucoromycota were prevalent among the fungal taxa. Regardless of the specific treatments, bacterial genera like Bacillus, Sphingomonas, and Pseudomonas were consistently found in high abundance. Shannon diversity index vividly ensured that, bacterial communities were maximum in B. velezensis VB7-treated soil (1.4-2.4), followed by Root Knot Nematode-associated soils (1.3-2.2), whereas richness was higher with Trichoderma konigiopsis TK drenched soils (1.3-2.0). The predominant occurrence of fungal genera such as Aspergillus Epicoccum, Choanephora, Alternaria and Thanatephorus habituate rhizosphere soils. Shannon index expressed the abundant richness of fungal species in treated samples (1.04-0.90). Further, refraction and species diversity curve also depicted a significant increase with maximum diversity of fungal species in B. velezensis VB7-treated soil than T. koningiopsis and nematode-infested soil. In field trial, bioagents-treated tomato plant (60% reduction of Meloidogyne incognita infection) had reduced gall index along with enhanced plant growth and increased fruit yield in comparison with the untreated plant. Hence, B. velezensis VB7 and T. koingiopsis can be well explored as an antinemic bioagents against RKN.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03851-1.

Broad-spectrum antagonistic potential of Bacillus spp. volatiles against Rhizoctonia solani and Xanthomonas oryzae pv. oryzae

Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (Xoo) are the two major diseases affecting the quality and quantity of rice production. In the current study, volatile organic compounds (VOCs) of Bacillus spp. were used as green biocontrol agents for plant diseases. In in vitro experiments, Bacillus spp. FZB42, NMTD17, and LLTC93-VOCs displayed strong antimicrobial volatile activity with inhibition rates of 76, 66, and 78% for R. solani and 78, 81, and 76% for Xoo, respectively, compared to control. The synthetic VOCs, namely Pentadecane (PDC), Benzaldehyde (BDH), 1,2-Benz isothiazol-3(2H)-one (1,2-BIT), and mixture (MIX) of VOCs showed high volatile activity with inhibition rates of 86, 86, 89, and 92% against R. solani and 81, 81, 82, and 86%, respectively, against Xoo as compared to control. In addition, the scanning and transmission electron microscopes (SEM and TEM) analyses were performed to examine the effect of Bacillus and synthetic VOC treatments on R. solani and Xoo morphology. The analysis revealed the deformed and irregularized morphology of R. solani mycelia and Xoo cells after VOC treatments. The microscopic analysis showed that the rapid inhibition was due to severe oxidative productions inside the R. solani mycelia and Xoo cells. By using molecular docking, it was determined that the synthetic VOCs entered the active binding site of trehalase and NADH dehydrogenase proteins, causing R. solani and Xoo cells to die prematurely and an accumulation of ROS. In the greenhouse experiment, FZB42, NMTD17, and LLTC93-VOCs significantly reduced the lesions of R. solani 8, 7, and 6 cm, and Xoo 7, 6, and 6 cm, respectively, then control. The synthetic VOCs demonstrated that the PDC, BDH, 1,2-BIT, and MIX-VOCs significantly reduced R. solani lesions on leaves 6, 6, 6, and 5 cm and Xoo 6, 5, 5, and 4 cm, respectively, as compared to control. Furthermore, plant defence-related genes and antioxidant enzymes were upregulated in rice plants. These findings provide novel mechanisms by which Bacillus antimicrobial VOCs control plant diseases.

Plant growth promoting Bacillus species elicit defense against Meloidogyne incognita infecting tomato in polyhouse

The effects of four nematicidal rhizobacterial isolates; Bacillus subtilis, Bacillus pumilus, Bacillus megaterium, and Bacillus cereus on infection and multiplication of root-knot nematode, Meloidogyne incognita on tomato were compared with the application of a chemical nematicide, fluopyram 34.48% SC (Velum Prime). The bio-efficacy trial conducted in pots preinoculated with the above isolates followed by M. incognita inoculation resulted in a significant reduction in percent root galling viz. 91.95 in B. subtilis, 84.21 in B. pumilus, 83.70 in B. megaterium, and 81.8 in B. cereus, at 75 days after inoculation (DAI). The reproduction factor of the nematode was the lowest (15.83) in B. subtilis, followed by B. pumilus (21.00), compared with 48.16 in control, with enhanced photosynthetic and transpiration rates. The mechanism of induced resistance was assessed using quantitative reverse-transcription polymerase chain reaction (qRT-PCR) for quantification of three key defense genes (PR-1b, JERF3, and CAT) at 0,2,4,8 and16 days DAI. The defence genes, PR-1b, JERF3, and CAT were expressed at 2.5-7.5-folds in rhizobacterialtreated plants, but not in nematicide treatment. The defense enzymes viz., super oxide dismutase (SOD), polyphenol oxidase (PPO), peroxidase (PO), and phenylalanine ammonia lyase (PAL) when quantified (μmol/mg protein) showed an increase from 1.5 to 17.5 for SOD, 2.1 to 7.8 in PPO, 1.8 to 10.2 in PO, and 1.8 to 8.7 in PAL during 0 to 16 DAI, in rhizobacteria-treated plants.

Volatile Organic Compounds of Bacillus pumilus Strain S1-10 Exhibit Fumigant Activity Against Meloidogyne incognita

Root-knot nematodes (RKNs) are highly specialized parasites that cause significant yield losses worldwide. In this study, we isolated Bacillus pumilus strain S1-10 from the rhizosphere soil of Zingiber officinale Rosc. plants and evaluated its fumigant activity against Meloidogyne incognita. S1-10 exhibited a strong repellent effect on second-stage juveniles (J2s) of M. incognita, and in vitro assays indicated that S1-10 volatile organic compounds (VOCs) suppressed J2 activity and egg hatching. Under greenhouse conditions, 71 and 79% reductions of nematodes and eggs were detected on plants treated with S-10 VOCs compared with controls. Ten VOCs were identified through gas chromatography and mass spectrometry (GC-MS), of which 2-(methylamino)-ethanol (2-ME) had strong fumigant activity against J2s of M. incognita, with an LC50 value of 1.5 mM at 12 h. These results indicate that S1-10 represents a potential novel biocontrol agent for RKNs.

Exploring the potential of halotolerant bacteria from coastal regions to mitigate salinity stress in wheat: physiological, molecular, and biochemical insights

Salinity stress, a significant global abiotic stress, is caused by various factors such as irrigation with saline water, fertilizer overuse, and drought conditions, resulting in reduced agricultural production and sustainability. In this study, we investigated the use of halotolerant bacteria from coastal regions characterized by high salinity as a solution to address the major environmental challenge of salinity stress. To identify effective microbial strains, we isolated and characterized 81 halophilic bacteria from various sources, such as plants, rhizosphere, algae, lichen, sea sediments, and sea water. We screened these bacterial strains for their plant growth-promoting activities, such as indole acetic acid (IAA), phosphate solubilization, and siderophore production. Similarly, the evaluation of bacterial isolates through bioassay revealed that approximately 22% of the endophytic isolates and 14% of rhizospheric isolates exhibited a favorable influence on seed germination and seedling growth. Among the tested isolates, GREB3, GRRB3, and SPSB2 displayed a significant improvement in all growth parameters compared to the control. As a result, these three isolates were utilized to evaluate their efficacy in alleviating the negative impacts of salt stress (150 mM, 300 mM, and seawater (SW)) on the growth of wheat plants. The result showed that shoot length significantly increased in plants inoculated with bacterial isolates up to 15% (GREB3), 16% (GRRB3), and 24% (SPSB2), respectively, compared to the control. The SPSB2 strain was particularly effective in promoting plant growth and alleviating salt stress. All the isolates exhibited a more promotory effect on root length than shoot length. Under salt stress conditions, the GRRB3 strain significantly impacted root length, leading to a boost of up to 6%, 5%, and 3.8% at 150 mM, 300 mM, and seawater stress levels, respectively. The bacterial isolates also positively impacted the plant's secondary metabolites and antioxidant enzymes. The study also identified the WDREB2 gene as highly upregulated under salt stress, whereas DREB6 was downregulated. These findings demonstrate the potential of beneficial microbes as a sustainable approach to mitigate salinity stress in agriculture.

Bacterial and Fungal Biocontrol Agents for Plant Disease Protection: Journey from Lab to Field, Current Status, Challenges, and Global Perspectives

Plants are constantly exposed to various phytopathogens such as fungi, Oomycetes, nematodes, bacteria, and viruses. These pathogens can significantly reduce the productivity of important crops worldwide, with annual crop yield losses ranging from 20% to 40% caused by various pathogenic diseases. While the use of chemical pesticides has been effective at controlling multiple diseases in major crops, excessive use of synthetic chemicals has detrimental effects on the environment and human health, which discourages pesticide application in the agriculture sector. As a result, researchers worldwide have shifted their focus towards alternative eco-friendly strategies to prevent plant diseases. Biocontrol of phytopathogens is a less toxic and safer method that reduces the severity of various crop diseases. A variety of biological control agents (BCAs) are available for use, but further research is needed to identify potential microbes and their natural products with a broad-spectrum antagonistic activity to control crop diseases. This review aims to highlight the importance of biocontrol strategies for managing crop diseases. Furthermore, the role of beneficial microbes in controlling plant diseases and the current status of their biocontrol mechanisms will be summarized. The review will also cover the challenges and the need for the future development of biocontrol methods to ensure efficient crop disease management for sustainable agriculture.

Biocontrol of fungal phytopathogens by Bacillus pumilus

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

Assessment of nematicidal and plant growth-promoting effects of Burkholderia sp. JB-2 in root-knot nematode-infested soil

Root-knot nematodes (RKN), Meloidogyne spp., are plant-parasitic nematodes that are responsible for considerable economic losses worldwide, because of the damage they cause to numerous plant species and the inadequate biological agents available to combat them. Therefore, developing novel and eco-friendly nematicides is necessary. In the present study, Burkholderia sp. JB-2, isolated from RKN-infested rhizosphere soil in South Korea, was evaluated to determine its nematicidal and plant growth-promoting effects under in vitro and in vivo conditions. Cell-free filtrates of the JB-2 strain showed high levels of nematicidal activity against second-stage juveniles (J2) of M. incognita, with 87.5% mortality following two days of treatment. In addition, the assessment of the activity against other six plant parasitic nematodes (M. javanica, M. hapla, M. arenaria, Ditylenchus destructor, Aphelenchoides subtenuis, and Heterodera trifolii) showed that the cell-free filtrates have a broad nematicidal spectrum. The three defense-responsive (MiMIF-2, MiDaf16-like1, and MiSkn1-like1) genes were activated, while Mi-cm-3 was downregulated when treated with cell-free filtrates of JB-2 cultures on J2. The greenhouse experiments suggested that the cell-free filtrates of the JB-2 strain efficiently controlled the nematode population in soil and egg mass formations of M. incognita in tomato (Solanum lycopersicum L., cv. Rutgers). An improvement in the host plant growth was observed, in which the shoot length and fresh weights of shoots and roots increased. The treatment with 10% of JB-2 cell-free filtrates significantly upregulated the expression levels of plant defenses (SlPR1, SlPR5, and SlPAL) and growth-promoting (ACO1, Exp18, and SlIAA1) genes compared with the corresponding parameters of the control group. Therefore, JB-2 could be a promising candidate for the sustainable management of RKN.

Plant-Microbes Interaction: Exploring the Impact of Cold-Tolerant Bacillus Strains RJGP41 and GBAC46 Volatiles on Tomato Growth Promotion through Different Mechanisms

The interaction between plant and bacterial VOCs has been extensively studied, but the role of VOCs in growth promotion still needs to be explored. In the current study, we aim to explore the growth promotion mechanisms of cold-tolerant Bacillus strains GBAC46 and RJGP41 and the well-known PGPR strain FZB42 and their VOCs on tomato plants. The result showed that the activity of phytohormone (IAA) production was greatly improved in GBAC46 and RJGP41 as compared to FZB42 strains. The in vitro and in-pot experiment results showed that the Bacillus VOCs improved plant growth traits in terms of physiological parameters as compared to the CK. The VOCs identified through gas chromatography-mass spectrometry (GC-MS) analysis, namely 2 pentanone, 3-ethyl (2P3E) from GBAC46, 1,3-cyclobutanediol,2,2,4,4-tetramethyl (CBDO) from RJGP41, and benzaldehyde (BDH) from FZB42, were used for plant growth promotion. The results of the partition plate (I-plate) and in-pot experiments showed that all the selected VOCs (2P3E, CBDO, and BDH) promoted plant growth parameters as compared to CK. Furthermore, the root morphological factors also revealed that the selected VOCs improved the root physiological traits in tomato plants. The plant defense enzymes (POD, APX, SOD, and CAT) and total protein contents were studied, and the results showed that the antioxidant enzymes and protein contents significantly increased as compared to CK. Similarly, plant growth promotion expression genes (IAA4, ARF10A, GA2OX2, CKX2, and EXP1) were significantly upregulated and the ERF gene was downregulated as compared to CK. The overall findings suggest that both Bacillus isolates and their pure VOCs positively improved plant growth promotion activities by triggering the antioxidant enzyme activity, protein contents, and relative gene expressions in tomato plants.

Antagonistic Bacteria Bacillus velezensis VB7 Possess Nematicidal Action and Induce an Immune Response to Suppress the Infection of Root-Knot Nematode (RKN) in Tomato

Meloidogyne incognita, the root-knot nematode (RKN), a devastating plant parasitic nematode, causes considerable damage to agricultural crops worldwide. As a sedentary root parasite, it alters the root's physiology and influences the host's phytohormonal signaling to evade defense. The sustainable management of RKN remains a challenging task. Hence, we made an attempt to investigate the nematicide activity of Bacillus velezensis VB7 to trigger the innate immune response against the infection of RKN. In vitro assay, B. velezensis VB7 inhibited the hatchability of root-knot nematode eggs and juvenile mortality of M. incognita by 87.95% and 96.66%, respectively at 96 hrs. The application of B. velezensis VB7 challenged against RKN induced MAMP-triggered immunity via the expression of transcription factors/defense genes by several folds pertaining to WRKY, LOX, PAL, MYB, and PR in comparison to those RKN-inoculated and healthy control through RT-PCR. Additionally, Cytoscape analysis of defense genes indicated the coordinated expression of various other genes linked to immune response. Thus, the current study clearly demonstrated the effectiveness of B. velezensis VB7 as a potential nematicide and inducer of immune responses against RKN infestation in tomato.

Two plant-associated Bacillus velezensis strains selected after genome analysis, metabolite profiling, and with proved biocontrol potential, were enhancing harvest yield of coffee and black pepper in large field trials

Elimination of chemically synthesized pesticides, such as fungicides and nematicides, in agricultural products is a key to successful practice of the Vietnamese agriculture. We describe here the route for developing successful biostimulants based on members of the Bacillus subtilis species complex. A number of endospore-forming Gram-positive bacterial strains with antagonistic action against plant pathogens were isolated from Vietnamese crop plants. Based on their draft genome sequence, thirty of them were assigned to the Bacillus subtilis species complex. Most of them were assigned to the species Bacillus velezensis. Whole genome sequencing of strains BT2.4 and BP1.2A corroborated their close relatedness to B. velezensis FZB42, the model strain for Gram-positive plant growth-promoting bacteria. Genome mining revealed that at least 15 natural product biosynthesis gene clusters (BGCs) are well conserved in all B. velezensis strains. In total, 36 different BGCs were identified in the genomes of the strains representing B. velezensis, B. subtilis, Bacillus tequilensis, and Bacillus. altitudinis. In vitro and in vivo assays demonstrated the potential of the B. velezensis strains to enhance plant growth and to suppress phytopathogenic fungi and nematodes. Due to their promising potential to stimulate plant growth and to support plant health, the B. velezensis strains TL7 and S1 were selected as starting material for the development of novel biostimulants, and biocontrol agents efficient in protecting the important Vietnamese crop plants black pepper and coffee against phytopathogens. The results of the large-scale field trials performed in the Central Highlands in Vietnam corroborated that TL7 and S1 are efficient in stimulating plant growth and protecting plant health in large-scale applications. It was shown that treatment with both bioformulations resulted in prevention of the pathogenic pressure exerted by nematodes, fungi, and oomycetes, and increased harvest yield in coffee, and pepper.

Bacillus velezensis Strain HN-Q-8 Induced Resistance to Alternaria solani and Stimulated Growth of Potato Plant

Bacillus velezensis HN-Q-8, isolated in our previous study, has an antagonistic effect on Alternaria solani. After being pretreated with a fermentation liquid with HN-Q-8 bacterial cell suspensions, the potato leaves inoculated with A. solani displayed smaller lesion areas and less yellowing than the controls. Interestingly, the activity levels of superoxide dismutase, peroxidase, and catalase in potato seedlings were enhanced by the addition of the fermentation liquid with bacterial cells. Additionally, the overexpression of key genes related to induced resistance in the Jasmonate/Ethylene pathway was activated by the addition of the fermentation liquid, suggesting that the HN-Q-8 strain induced resistance to potato early blight. In addition, our laboratory and field experiments showed that the HN-Q-8 strain can promote potato seedling growth and significantly increase tuber yield. The root activity and chlorophyll content of potato seedlings were significantly increased along with the levels of indole acetic acid, gibberellic acid 3, and abscisic acid upon addition of the HN-Q-8 strain. The fermentation liquid with bacterial cells was more efficient in inducing disease resistance and promoting growth than bacterial cell suspensions alone or the fermentation liquid without bacterial cells. Thus, the B. velezensis HN-Q-8 strain is an effective bacterial biocontrol agent, augmenting the options available for potato cultivation.

Microbial landscapes of the rhizosphere soils and roots of Luffa cylindrica plant associated with Meloidogyne incognita

Introduction

The root-knot nematodes (RKN), especially Meloidogyne spp., are globally emerging harmful animals for many agricultural crops.

Methods

To explore microbial agents for biological control of these nematodes, the microbial communities of the rhizosphere soils and roots of sponge gourd (Luffa cylindrica) infected and non-infected by M. incognita nematodes, were investigated using culture-dependent and -independent methods.

Results

Thirty-two culturable bacterial and eight fungal species, along with 10,561 bacterial and 2,427 fungal operational taxonomic units (OTUs), were identified. Nine culturable bacterial species, 955 bacterial and 701 fungal OTUs were shared in both four groups. More culturable bacterial and fungal isolates were detected from the uninfected soils and roots than from the infected soils and roots (except no fungi detected from the uninfected roots), and among all samples, nine bacterial species (Arthrobacter sp., Bacillus sp., Burkholderia ambifaria, Enterobacteriaceae sp., Fictibacillus barbaricus, Microbacterium sp., Micrococcaceae sp., Rhizobiaceae sp., and Serratia sp.) were shared, with Arthrobacter sp. and Bacillus sp. being dominant. Pseudomonas nitroreducens was exclusively present in the infested soils, while Mammaliicoccus sciuri, Microbacterium azadirachtae, and Priestia sp., together with Mucor irregularis, Penicillium sp., P. commune, and Sordariomycetes sp. were found only in the uninfected soils. Cupriavidus metallidurans, Gordonia sp., Streptomyces viridobrunneus, and Terribacillus sp. were only in the uninfected roots while Aspergillus sp. only in infected roots. After M. incognita infestation, 319 bacterial OTUs (such as Chryseobacterium) and 171 fungal OTUs (such as Spizellomyces) were increased in rhizosphere soils, while 181 bacterial OTUs (such as Pasteuria) and 166 fungal OTUs (such as Exophiala) rose their abundance in plant roots. Meanwhile, much more decreased bacterial or fungal OTUs were identified from rhizosphere soils rather than from plant roots, exhibiting the protective effects of host plant on endophytes. Among the detected bacterial isolates, Streptomyces sp. TR27 was discovered to exhibit nematocidal activity, and B. amyloliquefaciens, Bacillus sp. P35, and M. azadirachtae to show repellent potentials for the second stage M. incognita juveniles, which can be used to develop RKN bio-control agents.

Discussion

These findings provided insights into the interactions among root-knot nematodes, host plants, and microorganisms, which will inspire explorations of novel nematicides.

Evaluation of Fungal Volatile Organic Compounds for Control the Plant Parasitic Nematode Meloidogyne incognita

Plant parasitic nematodes are a serious threat to crop production worldwide and their control is extremely challenging. Fungal volatile organic compounds (VOCs) provide an ecofriendly alternative to synthetic nematicides, many of which have been withdrawn due to the risks they pose to humans and the environment. This study investigated the biocidal properties of two fungal VOCs, 1-Octen-3-ol and 3-Octanone, against the widespread root-knot nematode Meloidogyne incognita. Both VOCs proved to be highly toxic to the infective second-stage juveniles (J2) and inhibited hatching. Toxicity was dependent on the dose and period of exposure. The LD50 of 1-Octen-3-ol and 3-Octanone was 3.2 and 4.6 µL, respectively. The LT50 of 1-Octen-3-ol and 3-Octanone was 71.2 and 147.1 min, respectively. Both VOCs were highly toxic but 1-Octen-3-ol was more effective than 3-Octanone. Exposure of M. incognita egg-masses for 48 h at two doses (0.8 and 3.2 µL) of these VOCs showed that 1-Octen-3-ol had significantly greater nematicidal activity (100%) than 3-Octanone (14.7%) and the nematicide metham sodium (6.1%). High levels of reactive oxygen species detected in J2 exposed to 1-Octen-3-ol and 3-Octanone suggest oxidative stress was one factor contributing to mortality and needs to be investigated further.

Volatile Metabolites from Brevundimonas diminuta and Nematicidal Esters Inhibit Meloidogyne javanica

Brevundimonas diminuta is broadly distributed in terrestrial and aquatic environments and has various biological activities. In this study, we found that B. diminuta exhibited nematicidal activity against the plant root-knot nematode, Meloidogyne javanica. A total of 42 volatile organic compounds (VOCs) from B. diminuta were identified using gas chromatography-mass spectrometry (GC-MS). The nematicidal activity of the 10 main VOCs was tested against M. javanica. Butyl butanoate (4 µL) caused the mortality of 80.13% of M. javanica after 4 h. The nematicidal activity of an additional 38 butyl-butyrate-like volatile esters was also investigated. Of these, seven had strong nematicidal activity against M. javanica, five of which showed egg-hatching inhibitory activity. This study is the first to report that butyl butanoate, ethyl 2-methylbutanoate, ethyl 4-methylpentanoate, ethyl pent-4-enoate, and methyl undecanoate have nematicidal activity against M. javanica. The results indicated that B. diminuta could serve as a candidate microorganism for the biocontrol of plant root-knot nematodes, showing that volatile esters have great potential as nematicides.

Volatile Organic Compounds of Bacillus velezensis GJ-7 against Meloidogyne hapla through Multiple Prevention and Control Modes

The Bacillus velezensis GJ-7 strain isolated from the rhizosphere soil of Panax notoginseng showed high nematicidal activity and therefore has been considered a biological control agent that could act against the root-knot nematode Meloidogyne hapla. However, little was known about whether the GJ-7 strain could produce volatile organic compounds (VOCs) that were effective in biocontrol against M. hapla. In this study, we evaluated the nematicidal activity of VOCs produced by the fermentation of GJ-7 in three-compartment Petri dishes. The results revealed that the mortality rates of M. hapla J2s were 85% at 24 h and 97.1% at 48 h after treatment with the VOCs produced during GJ-7 fermentation. Subsequently, the VOCs produced by the GJ-7 strain were identified through solid-phase micro-extraction gas chromatography mass spectrometry (SPME-GC/MS). Six characteristic VOCs from the GJ-7 strain fermentation broth were identified, including 3-methyl-1-butanol, 3-methyl-2-pentanone, 5-methyl-2-hexanone, 2-heptanone, 2,5-dimethylpyrazine, and 6-methyl-2-heptanone. The in vitro experimental results from 24-well culture plates showed that the six volatiles had direct-contact nematicidal activity against M. hapla J2s and inhibition activity against egg hatching. In addition, 3-methyl-1-butanol and 2-heptanone showed significant fumigation effects on M. hapla J2s and eggs. Furthermore, all six of the VOCs repelled M. hapla J2 juveniles in 2% water agar Petri plates. The above data suggested that the VOCs of B. velezensis GJ-7 acted against M. hapla through multiple prevention and control modes (including direct-contact nematicidal activity, fumigant activity, and repellent activity), and therefore could be considered as potential biocontrol agents against root-knot nematodes.

Bacillus VOCs in the Context of Biological Control

A contemporary agricultural production system relying on heavy usage of agrochemicals represents a questionable outlook for sustainable food supply in the future. The visible negative environmental impacts and unforeseen consequences to human and animal health have been requiring a shift towards the novel eco-friendly alternatives for chemical pesticides for a while now. Microbial-based biocontrol agents have shown a promising potential for plant disease management. The bacteria of the genus Bacillus have been among the most exploited microbial active components due to several highly efficient mechanisms of action against plant pathogens, as well as a palette of additional plant-beneficial mechanisms, together with their suitable properties for microbial biopesticide formulations. Among other bioactive metabolites, volatile organic compounds (VOCs) have been investigated for their biocontrol applications, exhibiting the main advantage of long-distance effect without the necessity for direct contact with plants or pathogens. The aim of this study is to give an overview of the state-of-the-art in the field of Bacillus-based VOCs, especially in terms of their antibacterial, antifungal, and nematicidal action as the main segments determining their potential for biocontrol applications in sustainable agriculture.

Bacterial volatile organic compounds as biopesticides, growth promoters and plant-defense elicitors: Current understanding and future scope

Bacteria emit a large number of volatile organic compounds (VOCs) into the environment. VOCs are species-specific and their emission depends on environmental conditions, such as growth medium, pH, temperature, incubation time and interaction with other microorganisms. These VOCs can enhance plant growth, suppress pathogens and act as signaling molecules during plant-microorganism interactions. Some bacterial VOCs have been reported to show strong antimicrobial, nematicidal, pesticidal, plant defense, induced tolerance and plant-growth-promoting activities under controlled conditions. Commonly produced antifungal VOCs include dimethyl trisulfide, dimethyl disulfide, benzothiazole, nonane, decanone and 1-butanol. Species of Bacillus, Pseudomonas, Arthrobacter, Enterobacter and Burkholderia produce plant growth promoting VOCs, such as acetoin and 2,3-butenediol. These VOCs affect expression of genes involved in defense and development in plant species (i.e., Arabidopsis, tobacco, tomato, potato, millet and maize). VOCs are also implicated in altering pathogenesis-related genes, inducing systemic resistance, modulating plant metabolic pathways and acquiring nutrients. However, detailed mechanisms of action of VOCs need to be further explored. This review summarizes the bioactive VOCs produced by diverse bacterial species as an alternative to agrochemicals, their mechanism of action and challenges for employment of bacterial VOCs for sustainable agricultural practices. Future studies on technological improvements for bacterial VOCs application under greenhouse and open field conditions are warranted.

Differential effects of rhizobacteria from uninfected and infected tomato on Meloidogyne incognita under protected cultivation

Intermingled uninfected and root-knot nematode-infected tomato plants are commonly observed under protected cultivation. To understand the role of rhizobacteria underlying the susceptibility to nematode infectivity in these tomato plants, 36 rhizobacteria (18 from each type) with morphologically distinct colony characteristics were isolated from the rhizosphere of uninfected and root-knot nematode-infected tomato plants. The in vitro nematicidal potential of rhizobacteria from the uninfected rhizosphere was significantly higher than that from the infested rhizosphere. The three most effective antagonists were identified as Microbacterium laevaniformans, Staphylococcus kloosii, Priestia aryabhattai from root-knot-nematode-infected tomato rhizosphere and Staphylococcus sciuri, Bacillus pumilus, and Priestia megaterium from the rhizosphere of uninfected tomato. Volatile organic compounds from these rhizobacteria were characterized. Except for S. kloosi, the soil drenching with other rhizobacteria significantly reduced juvenile penetration (>60%) in tomato roots. Furthermore, the application of a single or consortium of these rhizobacteria affected nematode reproduction in tomato. Four consortia of rhizobacteria (S. sciuri + B. pumilus + P. megaterium), (B. pumilus + P. megaterium), (S. sciuri + B. pumilus), and (S. sciuri + P. megaterium) from uninfested rhizosphere and two consortia (M. laevaniformans + P. aryabhattai), (M. laevaniformans + S. kloosii + P. aryabhattai) from infested rhizosphere (IRh) effectively reduced M. incognita reproduction and considerably enhanced plant growth and yield in tomato. The nematicidal efficacy, however, decreased when S. kloosii was applied in the consortium. These distinctive effects illustrate how the plant susceptibility to nematode infectivity is modulated under natural conditions.

Plant growth-promoting rhizobacteria: Salt stress alleviators to improve crop productivity for sustainable agriculture development

Soil salinity, a growing issue worldwide, is a detrimental consequence of the ever-changing climate, which has highlighted and worsened the conditions associated with damaged soil quality, reduced agricultural production, and decreasing land areas, thus resulting in an unsteady national economy. In this review, halo-tolerant plant growth-promoting rhizo-microbiomes (PGPRs) are evaluated in the salinity-affected agriculture as they serve as excellent agents in controlling various biotic-abiotic stresses and help in the augmentation of crop productivity. Integrated efforts of these effective microbes lighten the load of agro-chemicals on the environment while managing nutrient availability. PGPR-assisted modern agriculture practices have emerged as a green strategy to benefit sustainable farming without compromising the crop yield under salinity as well as salinity-affected supplementary stresses including increased temperature, drought, salinity, and potential invasive plant pathogenicity. PGPRs as bio-inoculants impart induced systemic tolerance (IST) to plants by the production of volatile organic compounds (VOCs), antioxidants, osmolytes, extracellular polymeric substances (EPS), phytohormones, and ACC-deaminase and recuperation of nutritional status and ionic homeostasis. Regulation of PGPR-induced signaling pathways such as MAPK and CDPK assists in salinity stress alleviation. The "Next Gen Agriculture" consists of the application of designer crop microbiomes through gene editing tools, for instance, CRISPR, and engineering of the metabolic pathways of the microbes so as to gain maximum plant resistance. The utilization of omics technologies over the traditional approaches can fulfill the criteria required to increase crop yields in a sustainable manner for feeding the burgeoning population and augment plant adaptability under climate change conditions, ultimately leading to improved vitality. Furthermore, constraints such as the crop specificity issue of PGPR, lack of acceptance by farmers, and legal regulatory aspects have been acknowledged while also discussing the future trends for product commercialization with the view of the changing climate.

High killing rate of nematode and promotion of rice growth by synthetic volatiles from Bacillus strains due to enhanced oxidative stress response

The plant parasitic nematode Aphelenchoides besseyi is a major pest that poses serious threats to different vegetables and crop plants. In the present study, volatiles isolated from Bacillus spp. were utilized as green biocontrol agents to overcome nematodes. In in vitro experiment, Bacillus spp. GBSC56, SYST2, and FZB42 showed the strongest nematicidal activity with killing rates of 80.78%, 75.69%, and 60.45%, respectively, as compared with control. The selected synthetic volatile organic compounds (VOCs), namely albuterol, benzaldehyde (BDH), 1,2-benzisothiazol-3(2H)-one (1,2-HIT), dimethyl disulfide (DMDS), 2-undecanone (2-UD), and 1,3-propanediole (1,3-PD), exhibited strong nematicidal activity, with A. besseyi killing rate of 85.58%, 82.65%, 81.75%, 80.36%, 84.45%, and 82.36%, respectively, at 400 μg/mL. Microscopic analysis proved that the rapid mortality was due to the production of reactive oxygen species (ROS). Molecular docking attributed this ROS production to the nematicidal effect of synthetic VOCs on NADH DEHYDROGENASE SUBUNIT 2, which is known to play a critical role in the suppression of ROS in nematode models. In a greenhouse experiment, the Bacillus strains GBSC56, SYST2, and FZB42 and their synthetic VOCs significantly improved the physiological parameters in terms of growth promotion traits. In addition, selected genes related to growth promotion and defense genes showed a significant upregulation of their expression in rice seedlings treated with those synthetic VOCs. Overall, these findings revealed that the selected Bacillus strains and their synthetic VOCs possess high potential against A. besseyi. Moreover, this study also sheds new light on the mechanisms by which specific Bacillus nematicidal VOCs influence important genes involved in rice plant growth promotion and could effectively be used to suppress plant parasitic nematodes.

Deciphering the Biomolecules from Bacillus atrophaeus NMB01 Untangles the Anti-Oomycetes Action of Trioxsalen and Corynan-17-ol, Against Phytophthora infestans Inciting Late Blight of Potato

The antagonistic Bacillus spp. is known well for the production of versatile antimicrobial biomolecules with broad spectrum of action against different types of plant pathogens. Considering the significance of metabolically active biomolecules, attempts were made to decipher the anti-oomycete nature of biomolecules produced by Bacillus atrophaeus NMB01 during di-trophic interaction with Phytophthora infestans. Ten biomolecules produced by B. atrophaeus NMB01 during di-trophic interaction with P. infestans were docked against the twelve target proteins of P. infestans. Molecular docking of biomolecules reported trioxsalen and corynan-17-ol,18,19-didehydro-10-methoxy-acetate(ester) as best hits with highest binding energy in the range of - 7.5 to - 5 kcal/mol against target proteins of P. infestans. Comparatively less binding energy was observed for commercially available fungicides mandipropamid and metalaxyl on docking against the target proteins of P. infestans. We also confirmed the direct impact of trioxsalen andcorynan-17-ol, on P. infestans under in vitro with 66% and 50% inhibition of mycelial growth of P. infestans, respectively. This is the first study attempted to untangle the role of bioactive anti-oomycete compounds produced by B. atrophaeus strain NMB01 during di-trophic interaction with P. infestans against late blight pathogen P. infestans infecting potato. From the present study, we conclude that the biomolecules, trioxsalen and corynan-17-ol, can be explored for the management of P. infestans, the incitant of late blight of potato.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-022-01044-7.

Biocontrol efficacy of Bacillus velezensis strain YS-AT-DS1 against the root-knot nematode Meloidogyne incognita in tomato plants

Root-knot nematodes (RKNs; Meloidogyne spp.), one of the most economically important plant-parasitic nematodes (PPNs), cause severe yield and quality losses in agriculture annually. The application of biological control agents is an environmentally safe and effective approach to control RKNs. Here, we report the genomic characteristics of a Bacillus velezensis strain YS-AT-DS1 (Bv-DS1) isolated from the tidal soil, revealing that it has a 4.73 Mb circular chromosome with an average GC-content of 46.43%, 3,977 genes, 86 tRNAs, and 27 rRNAs, and contains secondary metabolite clusters for producing antimicrobial compounds. In vitro assays indicated that Bv-DS1 has not only antagonistic activities against fungal pathogens, but also shows nematicidal activity, with a mortality rate of 71.62% mortality rates in second-stage juvenile (J2s) Meloidogyne incognita. We then focused on the biocontrol efficiency of Bv-DS1 against M. incognita in pot assays. Preinoculation with Bv-DS1 enhanced tomato growth, and significantly reduced the infection rate of J2s, and the number of galls and egg masses on tomato roots. The underlying mechanism in Bv-DS1-induced resistance to M. incognita was further investigated through split-root experiments, and analysing the expression of the genes related to jasmonic acid (JA), salicylic acid (SA), and the tonoplast intrinsic protein (TIP). The results indicated that Bv-DS1 could not activate host systemic-induced resistance (ISR) in the split-root system of tomatoes. Additionally, the expression of JA- (LOX D and MC) and SA- (PAL2 and PR) responsive genes did not change in Bv-DS1-pretreated plants at 3 and 14 days after nematode inoculation. The presented data showed that JA-and SA-dependent pathways were not required for the biocontrol action of the Bv-DS1 against RKN. The TIP genes, responsible for transport of water and small substrates in plants, have previously been shown to negatively regulate the parasitism of PPNs. Surprisingly, Bv-DS1 compromised the downregulation of TIP1.1 and TIP1.3 by M. incognita. Together, our data suggest that Bv-DS1 exhibits a dual effect on plant growth promotion and protection against RKN, possibly related to the regulation of water and solute transport via TIPs. Thus, the Bv-DS1 strain could be used as a biocontrol agent for RKN control in sustainable agriculture.

Bacillus spp.-Mediated Growth Promotion of Rice Seedlings and Suppression of Bacterial Blight Disease under Greenhouse Conditions

Rice (Oryza sativa L.) is a major cereal and staple food crop worldwide, and its growth and production are affected by several fungal and bacterial phytopathogens. Bacterial blight (BB) is one of the world's most devastating rice diseases, caused by Xanthomonas oryzae pv. oryzae (Xoo). In the current study, Bacillus atrophaeus FA12 and B. cabrialesii FA26 were isolated from the rice rhizosphere and characterized as having broad-range antifungal and antibacterial activities against various phytopathogens, including Xoo. In addition, the selected strains were further evaluated for their potent rice growth promotion and suppression efficacy against BB under greenhouse conditions. The result shows that FA12 and FA26, applied as seed inoculants, significantly enhanced the vigor index of rice seedlings by 78.89% and 108.70%, respectively. Suppression efficacy against BB disease by FA12 and FA26 reached up to 59.74% and 54.70%, respectively, in pot experiments. Furthermore, MALDI-TOF MS analysis of selected strains revealed the masses ranged from m/z 1040 to 1540, representing that iturins and fengycin are the major antimicrobial compounds in the crude extracts, which might have beneficial roles in rice defence responses against BB. In conclusion, FA12 and FA26 possess broad-range antagonistic activity and have the capability to promote plant growth traits. More importantly, applying these strains has a high potential for implementing eco-friendly, cost-effective, and sustainable management practices for BB disease.

Salt Tolerant Bacillus Strains Improve Plant Growth Traits and Regulation of Phytohormones in Wheat under Salinity Stress

Soil salinity is a major constraint adversely affecting agricultural crops including wheat worldwide. The use of plant growth promoting rhizobacteria (PGPR) to alleviate salt stress in crops has attracted the focus of many researchers due to its safe and eco-friendly nature. The current study aimed to study the genetic potential of high halophilic Bacillus strains, isolated from the rhizosphere in the extreme environment of the Qinghai-Tibetan plateau region of China, to reduce salt stress in wheat plants. The genetic analysis of high halophilic strains, NMCN1, LLCG23, and moderate halophilic stain, FZB42, revealed their key genetic features that play an important role in salt stress, osmotic regulation, signal transduction and membrane transport. Consequently, the expression of predicted salt stress-related genes were upregulated in the halophilic strains upon NaCl treatments 10, 16 and 18%, as compared with control. The halophilic strains also induced a stress response in wheat plants through the regulation of lipid peroxidation, abscisic acid and proline in a very efficient manner. Furthermore, NMCN1 and LLCG23 significantly enhanced wheat growth parameters in terms of physiological traits, i.e., fresh weight 31.2% and 29.7%, dry weight 28.6% and 27.3%, shoot length 34.2% and 31.3% and root length 32.4% and 30.2%, respectively, as compared to control plants under high NaCl concentration (200 mmol). The Bacillus strains NMCN1 and LLCG23 efficiently modulated phytohormones, leading to the substantial enhancement of plant tolerance towards salt stress. Therefore, we concluded that NMCN1 and LLCG23 contain a plethora of genetic features enabling them to combat with salt stress, which could be widely used in different bio-formulations to obtain high crop production in saline conditions.

Enhancement of nitrogen use efficiency through agronomic and molecular based approaches in cotton

Cotton is a major fiber crop grown worldwide. Nitrogen (N) is an essential nutrient for cotton production and supports efficient crop production. It is a crucial nutrient that is required more than any other. Nitrogen management is a daunting task for plants; thus, various strategies, individually and collectively, have been adopted to improve its efficacy. The negative environmental impacts of excessive N application on cotton production have become harmful to consumers and growers. The 4R's of nutrient stewardship (right product, right rate, right time, and right place) is a newly developed agronomic practice that provides a solid foundation for achieving nitrogen use efficiency (NUE) in cotton production. Cropping systems are equally crucial for increasing production, profitability, environmental growth protection, and sustainability. This concept incorporates the right fertilizer source at the right rate, time, and place. In addition to agronomic practices, molecular approaches are equally important for improving cotton NUE. This could be achieved by increasing the efficacy of metabolic pathways at the cellular, organ, and structural levels and NUE-regulating enzymes and genes. This is a potential method to improve the role of N transporters in plants, resulting in better utilization and remobilization of N in cotton plants. Therefore, we suggest effective methods for accelerating NUE in cotton. This review aims to provide a detailed overview of agronomic and molecular approaches for improving NUE in cotton production, which benefits both the environment and growers.

Cadmium tolerant microbial strains possess different mechanisms for cadmium biosorption and immobilization in rice seedlings

Heavy metal remediation, such as cadmium (Cd²⁺) by microbial strains is efficient and environment-friendly. In this current study, we exploited the potential of Bacillus strains (Cd²⁺-tolerant; NMTD17, GBSW22, and LLTC96) to regulate Cd²⁺ biosorption mechanisms and improve rice seedling growth. The results showed that initial concentration and contact time affected Cd²⁺ biosorption, and the kinetic models of pseudo orders were effective in the elaborate biosorption process. Mainly, the bacterial cell wall had the potential for Cd²⁺ biosorption, and we found non-significant biosorption alterations among bacterial strains' inner and outer surfaces of cell membranes. Furthermore, the Fourier transform infrared (FTIR) spectroscopy analysis identified the differences in functional groups, such as C-N, PO₂, -SO₃, CO, COOH, C-O, C-N, -OH, and -NH that interact in biosorption by Bacillus strains. The scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) examination revealed that the binding of Cd²⁺ to microbes was mostly based on ion exchange pathways. Moreover, the Bacillus strains responded to Cd²⁺ stress in rice under pot experiment at various concentrations (0, 0.25, and 0.50 mg kg^-1), and they also influenced the chlorophyll contents and antioxidants activities were studied. The analysis of physio-morphological parameters was observed to be increased, which indicated that all Bacillus strains showed significant effects on rice growth under Cd²⁺ stress. These results revealed that the selected strains had the capability for additional use in the development of Cd²⁺ bioremediation methods. These strains also provided plant growth-promoting (PGP) traits that can alleviate the harmful effects of Cd²⁺ in rice plants.

Inhibitory Effects of Phenazine Compounds and Volatile Organic Compounds Produced by Pseudomonas aurantiaca ST-TJ4 Against Phytophthora cinnamomi

Phytophthora cinnamomi is an important plant pathogen that is widely distributed worldwide and has caused serious ecological damage and significant economic losses in forests and plantations in many countries. The use of plant growth-promoting rhizobacteria is an effective and environmentally friendly strategy for controlling diseases caused by P. cinnamomi. In this study, we investigated the antagonistic mechanism of Pseudomonas aurantiaca ST-TJ4 against P. cinnamomi through different antagonistic approaches, observations of mycelial morphology, study of mycelial metabolism, and identification of antagonistic substances. The results showed that Pseudomonas aurantiaca ST-TJ4 was able to significantly inhibit mycelial growth, causing mycelial deformation and disrupting internal cell structures. Additionally, pathogen cell membranes were damaged by ST-TJ4, and mycelial cell content synthesis was disrupted. Ultraperformance liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry analyses showed that phenazine compounds and 2-undecanone were the main antagonistic components. The ammonia produced by the ST-TJ4 strain also contributed to the inhibition of the growth of P. cinnamomi. In conclusion, our results confirm that Pseudomonas aurantiaca ST-TJ4 can inhibit P. cinnamomi through multiple mechanisms and can be used as a biological control agent for various plant diseases caused by P. cinnamomi.

Overview of biofertilizers in crop production and stress management for sustainable agriculture

With the increase in world population, the demography of humans is estimated to be exceeded and it has become a major challenge to provide an adequate amount of food, feed, and agricultural products majorly in developing countries. The use of chemical fertilizers causes the plant to grow efficiently and rapidly to meet the food demand. The drawbacks of using a higher quantity of chemical or synthetic fertilizers are environmental pollution, persistent changes in the soil ecology, physiochemical composition, decreasing agricultural productivity and cause several health hazards. Climatic factors are responsible for enhancing abiotic stress on crops, resulting in reduced agricultural productivity. There are various types of abiotic and biotic stress factors like soil salinity, drought, wind, improper temperature, heavy metals, waterlogging, and different weeds and phytopathogens like bacteria, viruses, fungi, and nematodes which attack plants, reducing crop productivity and quality. There is a shift toward the use of biofertilizers due to all these facts, which provide nutrition through natural processes like zinc, potassium and phosphorus solubilization, nitrogen fixation, production of hormones, siderophore, various hydrolytic enzymes and protect the plant from different plant pathogens and stress conditions. They provide the nutrition in adequate amount that is sufficient for healthy crop development to fulfill the demand of the increasing population worldwide, eco-friendly and economically convenient. This review will focus on biofertilizers and their mechanisms of action, role in crop productivity and in biotic/abiotic stress tolerance.

Toxicity of Bacillus thuringiensis Strains Derived from the Novel Crystal Protein Cry31Aa with High Nematicidal Activity against Rice Parasitic Nematode Aphelenchoides besseyi

The plant parasitic nematode, Aphelenchoides besseyi, is a serious pest causing severe damage to various crop plants and vegetables. The Bacillus thuringiensis (Bt) strains, GBAC46 and NMTD81, and the biological strain, FZB42, showed higher nematicidal activity against A. besseyi, by up to 88.80, 82.65, and 75.87%, respectively, in a 96-well plate experiment. We screened the whole genomes of the selected strains by protein-nucleic acid alignment. It was found that the Bt strain GBAC46 showed three novel crystal proteins, namely, Cry31Aa, Cry73Aa, and Cry40ORF, which likely provide for the safe control of nematodes. The Cry31Aa protein was composed of 802 amino acids with a molecular weight of 90.257 kDa and contained a conserved delta-endotoxin insecticidal domain. The Cry31Aa exhibited significant nematicidal activity against A. besseyi with a lethal concentration (LC₅₀) value of 131.80 μg/mL. Furthermore, the results of in vitro experiments (i.e., rhodamine and propidium iodide (PI) experiments) revealed that the Cry31Aa protein was taken up by A. besseyi, which caused damage to the nematode's intestinal cell membrane, indicating that the Cry31Aa produced a pore-formation toxin. In pot experiments, the selected strains GBAC46, NMTD81, and FZB42 significantly reduced the lesions on leaves by up to 33.56%, 45.66, and 30.34% and also enhanced physiological growth parameters such as root length (65.10, 50.65, and 55.60%), shoot length (68.10, 55.60, and 59.45%), and plant fresh weight (60.71, 56.45, and 55.65%), respectively. The number of nematodes obtained from the plants treated with the selected strains (i.e., GBAC46, NMTD81, and FZB42) and A. besseyi was significantly reduced, with 0.56, 0.83., 1.11, and 5.04 seedling mL^-1 nematodes were achieved, respectively. Moreover, the qRT-PCR analysis showed that the defense-related genes were upregulated, and the activity of hydrogen peroxide (H₂O₂) increased while malondialdehyde (MDA) decreased in rice leaves compared to the control. Therefore, it was concluded that the Bt strains GBAC46 and NMTD81 can promote rice growth, induce high expression of rice defense-related genes, and activate systemic resistance in rice. More importantly, the application of the novel Cry31Aa protein has high potential for the efficient and safe prevention and green control of plant parasitic nematodes.

Application Potential of Bacterial Volatile Organic Compounds in the Control of Root-Knot Nematodes

Plant-parasitic nematodes (PPNs) constitute the most damaging group of plant pathogens. Plant infections by root-knot nematodes (RKNs) alone could cause approximately 5% of global crop loss. Conventionally, chemical-based methods are used to control PPNs at the expense of the environment and human health. Accordingly, the development of eco-friendly and safer methods has been urged to supplement or replace chemical-based methods for the control of RKNs. Using microorganisms or their metabolites as biological control agents (BCAs) is a promising approach to controlling RKNs. Among the metabolites, volatile organic compounds (VOCs) have gained increasing attention because of their potential in the control of not only RKNs but also other plant pathogens, such as insects, fungi, and bacteria. This review discusses the biology of RKNs as well as the status of various control strategies. The discovery of VOCs emitted by bacteria from various environmental sources and their application potential as BCAs in controlling RKNs are specifically addressed.

Nematicidal Effects of Volatile Organic Compounds from Microorganisms and Plants on Plant-Parasitic Nematodes

Plant-parasitic nematodes (PPNs) are one of the most destructive plant pathogens worldwide, and controlling them is extremely challenging. Volatile organic compounds (VOCs), which naturally exist in plants and microorganisms, play an important role in the biological control of PPNs and are considered potential substances for the development of commercial nematicides. This paper summarizes the VOCs produced by microorganisms and plants as well as their toxic effects on PPNs. VOCs from 26 microbial strains and 51 plants that are active against nematodes from over the last decade were reviewed. Furthermore, the mechanisms of toxicity of some VOCs against PPNs are also illustrated.

Ambiguities of PGPR-Induced Plant Signaling and Stress Management

The growth and stress responses developed by the plant in virtue of the action of PGPR are dictated by the changes in hormone levels and related signaling pathways. Each plant possesses its specific type of microbiota that is shaped by the composition of root exudates and the signal molecules produced by the plant and microbes. Plants convey signals through diverse and complex signaling pathways. The signaling pathways are also controlled by phytohormones wherein they regulate and coordinate various defense responses and developmental stages. On account of improved growth and stress tolerance provided by the PGPR to plants, there exist crosstalk of signaling events between phytohormones and other signaling molecules secreted by the plants and the PGPR. This review discusses some of the important aspects related to the ambiguities of signaling events occurring in plants, allowing the interaction of PGPR with plants and providing stress tolerance to the plant.

Fluoroalkenyl-Grafted Chitosan Oligosaccharide Derivative: An Exploration for Control Nematode Meloidogyne Incognita

The exploration of novel, environmentally friendly, and efficient nematicides is essential, and modifying natural biomacromolecules is one feasible approach. In this study, 6-O-(trifluorobutenyl-oxadiazol)-chitosan oligosaccharide derivative was synthesized and characterized by FTIR, NMR, and TG/DTG. Its bioactivity and action mode against root-knot nematode M. incognita were estimated. The results show that the derivative shows high nematicidal activity against J2s, and egg hatching inhibitory activity at 1 mg/mL. The derivative may affect nematode ROS metabolism and further damage intestinal tissue to kill nematode. Meanwhile, by synergism with improving crop resistance, the derivative performed a high control effect on the nematode with low phytotoxicity. These findings suggested that chitosan oligosaccharide derivatives bearing fluoroalkenyl groups are promising green nematicides.

Induced Systemic Resistance for Improving Plant Immunity by Beneficial Microbes

Plant beneficial microorganisms improve the health and growth of the associated plants. Application of beneficial microbes triggers an enhanced resistance state, also termed as induced systemic resistance (ISR), in the host, against a broad range of pathogens. Upon the activation of ISR, plants employ long-distance systemic signaling to provide protection for distal tissue, inducing rapid and strong immune responses against pathogens invasions. The transmission of ISR signaling was commonly regarded to be a jasmonic acid- and ethylene-dependent, but salicylic acid-independent, transmission. However, in the last decade, the involvement of both salicylic acid and jasmonic acid/ethylene signaling pathways and the regulatory roles of small RNA in ISR has been updated. In this review, the plant early recognition, responsive reactions, and the related signaling transduction during the process of the plant-beneficial microbe interaction was discussed, with reflection on the crucial regulatory role of small RNAs in the beneficial microbe-mediated ISR.

Foliar melatonin stimulates cotton boll distribution characteristics by modifying leaf sugar metabolism and antioxidant activities during drought conditions

Drought is a severe abiotic stress affecting the plant's antioxidant system and interrupting compatible solute translocation processes, which leads to low productivity. Melatonin acts as a common growth regulator enhancing the plants defense system and regulates sugar metabolism in challenging environments. Melatonin treatments enable plants to be tolerant to abiotic stresses via enhancing their recovery potential, but its impact using various concentrations has not yet been studied in leaf physiological aspects when applied to cotton foliage during their peak flowering and boll loading stage. The overall objective of this research was to facilitate cotton boll distribution characteristics by modifying cotton leaf sugar metabolism and antioxidant activity by applying foliar melatonin (0, 25, 50, and 100 μmol l^-1 ) under drought levels with a relative soil water content of 75%, 60%, and 45% ± 5 (FC1, FC2, and FC3, respectively). Higher rates of melatonin application (100 μmol l^-1 ) enhanced boll distribution characteristics and controlled the boll shedding rate during drought conditions. An increase in melatonin rates proved to be more helpful in stimulating cotton sympodial leaf physiological attributes, including leaf gas exchange parameters, sugar metabolism, proline content, and antioxidants defense system as compared with less or no melatonin application during all FC conditions and showed the most significant effect at a higher melatonin concentration (M100) at 7-21 DAF. The total proline content and antioxidant activity were enhanced in the M100 treatment during all FC levels, which caused a reduction in the total malondialdehyde (MDA) contents and hydrogen peroxide (H₂ O₂ ) concentrations in cotton leaves. Moreover, sugar metabolism responsible genes GhSusA and SPS2 showed an upsurge in expression levels and enhanced sucrose degradation in M100 treatments during all FC levels. Furthermore, cotton boll attributes showed also a positive relation with leaf physiological and gas exchange attributes. The results suggested that foliar melatonin application during the flowering initiation stage improved the overall performance and is helpful for cotton crops productivity against drought stress.

Revealing plant growth-promoting mechanisms of Bacillus strains in elevating rice growth and its interaction with salt stress

Soil salinity is a major environmental stress that has been negatively affecting the growth and productivity of rice. However, various salt-resistant plant growth-promoting rhizobacteria (PGPR) have been known to promote plant growth and alleviate the damaging effects of salt stress via mitigating physio-biochemical and molecular characteristics. This study was conducted to examine the salt stress potential of Bacillus strains identified from harsh environments of the Qinghai-Tibetan plateau region of China. The Bacillus strains NMTD17, GBSW22, and FZB42 were screened for their response under different salt stress conditions (1, 4, 7, 9, 11, 13, and 16%). The screening analysis revealed strains NMTD17, GBSW22, and FZB42 to be high-salt tolerant, moderate-salt tolerant, and salt-sensitive, respectively. The NMTD17 strain produced a strong biofilm, followed by GBSW22 and FZB42. The expression of salt stress-related genes in selected strains was also analyzed through qPCR in various salt concentrations. Further, the Bacillus strains were used in pot experiments to study their growth-promoting ability and antioxidant activities at various concentrations (0, 100, 150, and 200 mmol). The analysis of growth-promoting traits in rice exhibited that NMTD17 had a highly significant effect and GSBW22 had a moderately significant effect in comparison with FZB42. The highly resistant strain NMTD17 that stably promoted rice plant growth was further examined for its function in the composition of rhizobacterial communities. The inoculation of NMTD17 increased the relative abundance and richness of rhizobacterial species. These outcomes propose that NMTD17 possesses the potential of PGPR traits, antioxidants enzyme activities, and reshaping the rhizobacterial community that together mitigate the harmful effects of salinity in rice plants.

5-Methoxyindole, a Chemical Homolog of Melatonin, Adversely Affects the Phytopathogenic Fungus Fusarium graminearum

Fusarium graminearum is a destructive fungal pathogen that threatens the production and quality of wheat, and controlling this pathogen is a significant challenge. As the cost-effective homolog of melatonin, 5-methoxyindole showed strong activity against F. graminearum. In the present study, our results showed the strong adverse activity of 5-methoxyindole against F. graminearum by inhibiting its growth, formation, and conidia germination. In addition, 5-methoxyindole could induce malformation, reactive oxygen species (ROS) accumulation, and cell death in F. graminearum hyphae and conidia. In response to 5-methoxyindole, F. graminearum genes involved in scavenging reactive oxygen species were significantly downregulated. Overall, these findings reveal the mechanism of antifungal action of melatonin-homolog 5-methoxyindole. To the best of our knowledge, this is the first report that a novel melatonin homolog confers strong antifungal activity against F. graminearum, and 5-methoxyindole is a potential compound for protecting wheat plants from F. graminearum infection.