Volatile organic compounds from Paenibacillus polymyxa KM2501-1 control Meloidogyne incognita by multiple strategies

Sulfonamide modified chitosan oligosaccharide with high nematicidal activity against Meloidogyne incognita

Chitosan oligosaccharide (COS) modification is a feasible way to develop novel green nematicides. This study involved the synthesis of various COS sulfonamide derivatives via hydroxylated protection and deprotection, which were then characterized using NMR, FTIR, MS, elemental analysis, XRD, and TG/DTG. In vitro experiments found that COS-alkyl sulfonamide derivatives (S6 and S11-S13) exhibited high mortality (>98 % at 1 mg/mL) against Meloidogyne incognita second-instar larvaes (J2s) among the derivatives. S6 can cause vacuole-like structures in the middle and tail regions of the nematode body and effectively inhibit egg hatching. In vivo tests have found that S6 has well control effects and low plant toxicity. Additionally, the structure-activity studies revealed that S6 with a high degree of substitution, a low molecular weight, and a sulfonyl bond on the amino group of the COS backbone exhibited increased nematicidal activity. The sulfonamide group is a potential active group for developing COS-based nematicides.

Exopolysaccharides of Paenibacillus polymyxa: A review

Paenibacillus polymyxa (P. polymyxa) is a member of the genus Paenibacillus, which is a rod-shaped, spore-forming gram-positive bacterium. P. polymyxa is a source of many metabolically active substances, including polypeptides, volatile organic compounds, phytohormone, hydrolytic enzymes, exopolysaccharide (EPS), etc. Due to the wide range of compounds that it produces, P. polymyxa has been extensively studied as a plant growth promoting bacterium which provides a direct benefit to plants through the improvement of N fixation from the atmosphere and enhancement of the solubilization of phosphorus and the uptake of iron in the soil, and phytohormones production. Among the metabolites from P. polymyxa, EPS exhibits many activities, for example, antioxidant, immunomodulating, anti-tumor and many others. EPS has various applications in food, agriculture, environmental protection. Particularly, in the field of sustainable agriculture, P. polymyxa EPS can be served as a biofilm to colonize microbes, and also can act as a nutrient sink on the roots of plants in the rhizosphere. Therefore, this paper would provide a comprehensive review of the advancements of diverse aspects of EPS from P. polymyxa, including the production, extraction, structure, biosynthesis, bioactivity and applications, etc. It would provide a direction for future research on P. polymyxa EPS.

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.

Isolation and Characterization of Paenibacillus polymyxa B7 and Inhibition of Aspergillus tubingensis A1 by Its Antifungal Substances

Screening of Bacillus with antagonistic effects on paddy mold pathogens to provide strain resources for biological control of mold in Oryza sativa L. screening of Bacillus isolates antagonistic towards Aspergillus tubingensis from rhizosphere soil of healthy paddy; classification and identification of antagonistic strains by biological characteristics and 16S rDNA sequence analysis; transcriptome sequencing after RNA extraction from Bacillus-treated Aspergillus tubingensis; and extraction of inhibitory crude proteins of Bacillus by ammonium sulfate precipitation; inhibitory crude protein and Bacillus spp. were treated separately for A. tubingensis and observed by scanning electron microscopy (SEM). An antagonistic strain of Bacillus, named B7, was identified as Paenibacillus polymyxa by 16S rDNA identification and phylogenetic evolutionary tree comparison analysis. Analysis of the transcriptome results showed that genes related to secondary metabolite biosynthesis such as antifungal protein were significantly downregulated. SEM results showed that the mycelium of A. tubingensis underwent severe rupture after treatment with P. polymyxa and antifungal proteins, respectively. In addition, the sporocarp changed less after treatment with P. polymyxa, and the sporangium stalks had obvious folds. P. polymyxa B7 has a good antagonistic effect against A. tubingensis and has potential for biocontrol applications of paddy mold pathogens.

Christensenella strain resources, genomic/metabolomic profiling, and association with host at species level

The gut commensal bacteria Christensenellaceae species are negatively associated with many metabolic diseases, and have been seen as promising next-generation probiotics. However, the cultured Christensenellaceae strain resources were limited, and their beneficial mechanisms for improving metabolic diseases have yet to be explored. In this study, we developed a method that enabled the enrichment and cultivation of Christensenellaceae strains from fecal samples. Using this method, a collection of Christensenellaceae Gut Microbial Biobank (ChrisGMB) was established, composed of 87 strains and genomes that represent 14 species of 8 genera. Seven species were first described and the cultured Christensenellaceae resources have been significantly expanded at species and strain levels. Christensenella strains exerted different abilities in utilization of various complex polysaccharides and other carbon sources, exhibited host-adaptation capabilities such as acid tolerance and bile tolerance, produced a wide range of volatile probiotic metabolites and secondary bile acids. Cohort analyses demonstrated that Christensenellaceae and Christensenella were prevalent in various cohorts and the abundances were significantly reduced in T2D and OB cohorts. At species level, Christensenellaceae showed different changes among healthy and disease cohorts. C. faecalis, F. tenuis, L. tenuis, and Guo. tenuis significantly reduced in all the metabolic disease cohorts. The relative abundances of C. minuta, C. hongkongensis and C. massiliensis showed no significant change in NAFLD and ACVD. and C. tenuis and C. acetigenes showed no significant change in ACVD, and Q. tenuis and Geh. tenuis showed no significant change in NAFLD, when compared with the HC cohort. So far as we know, this is the largest collection of cultured resource and first exploration of Christensenellaceae prevalences and abundances at species level.

Toxicity of fungal-derived volatile organic compounds against root-knot nematodes

BACKGROUND

Root-knot nematodes (RKNs), including Meloidogyne species, are among the most destructive plant-parasites worldwide. Recent evidence suggests that entomopathogenic fungi (EPF) can antagonize RKNs. Such antagonistic effects are likely mediated by toxic metabolites, including volatile organic compounds (VOCs), produced by the fungi. However, how widespread these effects are across EPF species, and which VOCs mediate negative interactions between EPF and RKNs needs to be further elucidated.

RESULTS

First, we evaluated the nematicidal effect of VOCs emitted by 46 EPF isolates against Meloidogyne incognita and found variable toxicity depending on the isolate. Second, we measured the nematicidal effect of highly toxic isolates, including species in the genus Talaromyces, Aspergillus, Clonostachys, and Purpureocillium and, third, we analyzed the nematicidal effect of major VOCs, including 2-methyl-1-propanol, 3-methyl-1-butanol, isopropyl alcohol and 2-methyl-3-pentanone. The mortality of M. incognita juveniles (J2s) was generally high (50%) either via airborne or in-solution contact with VOCs. Moreover, the tested VOCs significantly inhibited egg hatching, and repelled J2s away from the VOCs.

CONCLUSION

This study not only provides insights into the ecological function of VOCs in the rhizosphere, but also provides new approaches for developing environmentally friendly control methods of RKNs in agroecosystems. © 2023 Society of Chemical Industry.

Unveiling the Potential of Bacillus safensis Y246 for Enhanced Suppression of Rhizoctonia solani

Rhizoctonia solani is a significant pathogen affecting various crops, including tobacco. In this study, a bacterial strain, namely Y246, was isolated from the soil of healthy plants and exhibited high antifungal activity. Based on morphological identification and DNA sequencing, this bacterial strain was identified as Bacillus safensis. The aim of this investigation was to explore the antifungal potential of strain Y246, to test the antifungal stability of Y246 by adjusting different cultivation conditions, and to utilize gas chromatography-mass spectrometry (GC-MS) to predict the volatile compounds related to antifungal activity in Y246. In vitro assays demonstrated that strain Y246 exhibited a high fungal inhibition rate of 76.3%. The fermentation broth and suspension of strain Y246 inhibited the mycelial growth of R. solani by 66.59% and 63.75%, respectively. Interestingly, treatment with volatile compounds derived from the fermentation broth of strain Y246 resulted in abnormal mycelial growth of R. solani. Scanning electron microscopy analysis revealed bent and deformed mycelium structures with a rough surface. Furthermore, the stability of antifungal activity of the fermentation broth of strain Y246 was assessed. Changes in temperature, pH value, and UV irradiation time had minimal impact on the antifungal activity, indicating the stability of the antifungal activity of strain Y246. A GC-MS analysis of the volatile organic compounds (VOCs) produced by strain Y246 identified a total of 34 compounds with inhibitory effects against different fungi. Notably, the strain demonstrated broad-spectrum activity, exhibiting varying degrees of inhibition against seven pathogens (Alternaria alternata, Phomopsis. sp., Gloeosporium musarum, Dwiroopa punicae, Colletotrichum karstii, Botryosphaeria auasmontanum, and Botrytis cinerea). In our extensive experiments, strain Y246 not only exhibited strong inhibition against R. solani but also demonstrated remarkable inhibitory effects on A. alternata-induced tobacco brown spot and kiwifruit black spot, with impressive inhibition rates of 62.96% and 46.23%, respectively. Overall, these findings highlight the significant antifungal activity of B. safensis Y246 against R. solani. In addition, Y246 has an excellent antifungal stability, with an inhibition rate > 30% under different treatments (temperature, pH, UV). The results showed that the VOCs of strain Y246 had a strong inhibitory effect on the colony growth of R. solani, and the volatile substances produced by strain Y246 had an inhibitory effect on R. solani at rate of 70.19%. Based on these results, we can conclude that Y246 inhibits the normal growth of R. solani. These findings can provide valuable insights for developing sustainable agricultural strategies.

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.

Chemotaxis of Meloidogyne incognita Response to Rhizosphere Bacteria

Rhizosphere microorganisms and the volatile organic compounds (VOCs) produced by them take part in the regulation of the chemotaxis of nematodes. A total of 150 strains of rhizosphere bacteria were screened via a chemotaxis experiment with Meloidogyne incognita. Some isolates affected the behavior of the nematodes, including attraction, randomness, and repulsion. Volatile metabolites produced via the selected bacteria were associated with the chemotaxis of nematodes. M. incognita was highly attracted to decanal. In addition, dimethyl disulfide, 2,5-dimethylpyrazine, pentadecanoic acid, and palmitic acid were found to attract weakly M. incognita. Furthermore, the chemotaxis of M. incognita was tested in a pot experiment. The bacteria Bacillus sp. 1-50, Brevibacillus brevis 2-35, B. cereus 5-14, Chryseobacterium indologens 6-4, and VOC decanal could regulate the movement of M. incognita in the pot with or without plants. The results provide insights into rhizosphere microorganisms and their VOCs and how they regulate the chemotaxis of the nematodes.

Effect of 4-Ethylbenzaldehyde from the Volatilome of Annona muricata on Meloidogyne incognita

The demand for new soil fumigants has increased as a result of more restrictive legislation regarding the use of pesticides. In the present study, the potent nematicidal activity of volatile organic compounds released by the Annona muricata leaf macerate was demonstrated. In addition, we searched in the A. muricata volatilome for a molecule with potential to be developed as a new fumigant nematicide. In the greenhouse, even the lowest concentration of soursop leaf macerate tested (1.0%) as a biofumigant caused a significant (P < 0.05) reduction in Meloidogyne incognita infectivity and reproduction when compared with the nontreated control (0%). Forty-one compounds were identified through gas chromatography-mass spectrometry analysis, of which three (sabinene, caryophyllene oxide, and 4-ethylbenzaldehyde) were selected for studies against the nematode. Among these compounds, in in vitro trails, only 4-ethylbenzaldehyde showed nematicidal activity at 250 µg ml-1. The effective doses of 4-ethylbenzaldehyde predicted to kill 50 and 95% of the M. incognita second-stage juvenile population after 48 h of exposure were 35 and 88 µg ml-1, respectively. In in vitro tests, 4-ethylbenzaldehyde at 150 µg ml-1 reduced M. incognita egg hatching to values similar (P > 0.05) to those of the commercial nematicide fluensulfone at a concentration of 200 µg ml-1. In plant experiments, as a soil fumigant, 4-ethylbenzaldehyde at a dose of 1 ml/liter of substrate had an effect similar (P > 0.05) to that of the commercial fumigant Dazomet (250 µg ml-1). Therefore, 4-ethylbenzaldehyde shows potential for development as a new nematicide.

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.

Identification and Surveys of Promoting Plant Growth VOCs from Biocontrol Bacteria Paenibacillus peoriae GXUN15128

The role of microbial volatile organic compounds (MVOCs) in promoting plant growth has received much attention. We isolated Paenibacillus peoriae from mangrove rhizosphere soil, which can produce VOCs to promote the growth of Arabidopsis thaliana seedlings, increase the aboveground biomass of A. thaliana, and increase the number of lateral roots of A. thaliana. The effects of different inoculation amounts and different media on the composition of MVOCs were studied by solid-phase microextraction/gas chromatography-mass spectrometry (SPME/GC-MS) and headspace sampler/GC-MS. We found that the growth medium influences the function and composition of MVOCs. To survey the growth-promoting functions, the transcriptome of the receptor A. thaliana was then determined. We also verified the inhibitory effect of the soluble compounds produced by P. peoriae on the growth of 10 pathogenic fungi. The ability of P. peoriae to produce volatile and soluble compounds to promote plant growth and disease resistance has shown great potential for application in the sustainability of agricultural production. IMPORTANCE Microbial volatile organic compounds (MVOCs) have great potential as "gas fertilizers" for agricultural applications, and it is a promising research direction for the utilization of microbial resources. This study is part of the field of interactions between microorganisms and plants. To study the function and application of microorganisms from the perspective of VOCs is helpful to break the bottleneck of traditional microbial application. At present, the study of MVOCs is lacking; there is a lack of functional strains, especially with plant-protective functions and nonpathogenic application value. The significance of this study is that it provides Paenibacillus peoriae, which produces VOCs with plant growth-promoting effects and broad-spectrum antifungal activity against plant-pathogenic fungi. Our study provides a more comprehensive, new VOC component analysis method and explains how MVOCs promote plant growth through transcriptome analysis. This will greatly increase our understanding of MVOC applications as a model for other MVOC research.

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.

An agroecological structure model of compost-soil-plant interactions for sustainable organic farming

Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that amino acids, antioxidant activity, flavonoids and/or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus and nitrogen compounds were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by the compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.

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.

Multiple Receptors Contribute to the Attractive Response of Caenorhabditis elegans to Pathogenic Bacteria

Nematodes feed mainly on bacteria and sense volatile signals through their chemosensory system to distinguish food from pathogens. Although nematodes recognizing bacteria by volatile metabolites are ubiquitous, little is known of the associated molecular mechanism. Here, we show that the antinematode bacterium Paenibacillus polymyxa KM2501-1 exhibits an attractive effect on Caenorhabditis elegans via volatile metabolites, of which furfural acetone (FAc) acts as a broad-spectrum nematode attractant. We show that the attractive response toward FAc requires both the G-protein-coupled receptors STR-2 in AWC neurons and SRA-13 in AWA and AWC neurons. In the downstream olfactory signaling cascades, both the transient receptor potential vanilloid channel and the cyclic nucleotide-gated channel are necessary for FAc sensation. These results indicate that multiple receptors and subsequent signaling cascades contribute to the attractive response of C. elegans to FAc, and FAc is the first reported ligand of SRA-13. Our current work discovers that P. polymyxa KM2501-1 exhibits an attractive effect on nematodes by secreting volatile metabolites, especially FAc and 2-heptanone, broadening our understanding of the interactions between bacterial pathogens and nematodes. IMPORTANCE Nematodes feed on nontoxic bacteria as a food resource and avoid toxic bacteria; they distinguish them through their volatile metabolites. However, the mechanism of how nematodes recognize bacteria by volatile metabolites is not fully understood. Here, the antinematode bacterium Paenibacillus polymyxa KM2501-1 is found to exhibit an attractive effect on Caenorhabditis elegans via volatile metabolites, including FAc. We further reveal that the attractive response of C. elegans toward FAc requires multiple G-protein-coupled receptors and downstream olfactory signaling cascades in AWA and AWC neurons. This study highlights the important role of volatile metabolites in the interaction between nematodes and bacteria and confirms that multiple G-protein-coupled receptors on different olfactory neurons of C. elegans can jointly sense bacterial volatile signals.

Volatile Organic Compounds from a Lichen-Associated Bacterium, Paenibacillus etheri, Interact with Plant-Parasitic Cyst Nematodes

Healthy food is one of the major challenges to develop in this century. Plant-parasitic nematodes cause significant damage to many crops worldwide and till now, the use of chemical nematicides is the main means to control their populations. These chemical products must be replaced by more environmental-friendly control methods. Biocontrol methods seem to be one promising option, and the number of biopesticides derived from living organisms has increased in the last decades. To develop new plant protection products, we have decided to combine our skills in natural products chemistry and nematology and to focus on the lichen microecosystem as underexploited ecological niches of microorganisms. We present herein the potential of lichen-associated bacterial suspensions from Paenibacillus etheri as nematicides against the beet cyst nematode Heterodera schachtii and the potato cyst nematode Globodera pallida, in particular the effects of volatile organic compounds (VOCs) produced by the bacteria. A solid phase micro-extraction method associated to gas chromatography-mass spectrometry analysis of 14 day cultures was used to analyze these VOCs in order to identify the main produced compounds (isoamyl acetate and 2-phenylethyl acetate) and to evaluate them on the nematodes.

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.

Endophytic Paenibacillus polymyxa LMG27872 inhibits Meloidogyne incognita parasitism, promoting tomato growth through a dose-dependent effect

The root-knot nematode, Meloidogyne incognita, is a major pest in tomato production. Paenibacillus polymyxa, which is primarily found in soil and colonizing roots, is considered a successful biocontrol organism against many pathogens. To evaluate the biocontrol capacity of P. polymyxa LMG27872 against M. incognita in tomato, experiments were conducted both in vitro and in vivo. A dose-response effect [30, 50, and 100% (108 CFU/mL)] of bacterial suspensions (BSs) on growth and tomato susceptibility to M. incognita with soil drenching as a mode of application was first evaluated. The results show that the biological efficacy of P. polymyxa LMG27872 against M. incognita parasitism in tomato was dose-dependent. A significantly reduced number of galls, egg-laying females (ELF), and second-stage juveniles (J2) were observed in BS-treated plants, in a dose-dependent manner. The effect of P. polymyxa on tomato growth was also dose-dependent. A high dose of BSs had a negative effect on growth; however, this negative effect was not observed when the BS-treated plants were challenged with M. incognita, indicating tolerance or a defense priming mechanism. In subsequent in vivo experiments, the direct effect of BSs was evaluated on J2 mortality and egg hatching of M. incognita. The effect of BS on J2 mortality was observed from 12 to 24 h, whereby M. incognita J2 was significantly inhibited by the BS treatment. The effect of P. polymyxa on M. incognita egg hatching was also dependent on the BS dose. The results show a potential of P. polymyxa LMG27872 to protect plants from nematode parasitism and its implementation in integrated nematode management suitable for organic productions.

Identification and combinatorial engineering of indole-3-acetic acid synthetic pathways in Paenibacillus polymyxa

Background

Paenibacillus polymyxa is a typical plant growth-promoting rhizobacterium (PGPR), and synthesis of indole-3-acetic acid (IAA) is one of the reasons for its growth-promoting capacity. The synthetic pathways of IAA in P. polymyxa must be identified and modified.

Results

P. polymyxa SC2 and its spontaneous mutant SC2-M1 could promote plant growth by directly secreting IAA. Through metabonomic and genomic analysis, the genes patA, ilvB3, and fusE in the native IPyA pathway of IAA synthesis in strain SC2-M1 were predicted. A novel strong promoter P₀₄₄₂₀ was rationally selected, synthetically analyzed, and then evaluated on its ability to express IAA synthetic genes. Co-expression of three genes, patA, ilvB3, and fusE, increased IAA yield by 60% in strain SC2-M1. Furthermore, the heterogeneous gene iaam of the IAM pathway and two heterogeneous IPyA pathways of IAA synthesis were selected to improve the IAA yield of strain SC2-M1. The genes ELJP6_14505, ipdC, and ELJP6_00725 of the entire IPyA pathway from Enterobacter ludwigii JP6 were expressed well by promoter P₀₄₄₂₀ in strain SC2-M1 and increased IAA yield in the engineered strain SC2-M1 from 13 to 31 μg/mL, which was an increase of 138%.

Conclusions

The results of our study help reveal and enhance the IAA synthesis pathways of P. polymyxa and its future application.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02181-3.

Verifying an entire native IPyA pathway of IAA synthesis in P. polymyxa.

Introducing heterologous IAM and IPyA pathways of IAA synthesis to P. polymyxa.

Selecting and analyzing a novel strong promoter P₀₄₄₂₀ to express IAA synthesis genes.

Comparative Genomics Insights into a Novel Biocontrol Agent Paenibacillus peoriae Strain ZF390 against Bacterial Soft Rot

Simple Summary

Bacterial soft rot, attributed to Pectobacterium brasiliense infection, has caused destructive impacts and colossal economic losses to China’s agricultural industry. Chemical control, which was ubiquitously used, cannot manage this disease as expected, so biocontrol has been followed with interest to date. In this study, we found a Paenibacillus peoriae strain ZF390 that had a potent control efficiency over cucumber plants against Pectobacterium brasiliense, and the comparative genomic analysis revealed biocontrol mechanisms might be involved in the strain ZF390.

Abstract

Bacterial soft rot, caused by Pectobacterium brasiliense, can infect several economically important horticultural crops. However, the management strategies available to control this disease are limited. Plant-growth-promoting rhizobacteria (PGPR) have been considered to be promising biocontrol agents. With the aim of obtaining a strain suitable for agricultural applications, 161 strains were isolated from the rhizosphere soil of healthy cucumber plants and screened through plate bioassays and greenhouse tests. Paenibacillus peoriae ZF390 exhibited an eminent control effect against soft rot disease and a broad antagonistic activity spectrum in vitro. Moreover, ZF390 showed good activities of cellulase, protease, and phosphatase and a tolerance of heavy metal. Whole-genome sequencing was performed and annotated to explore the underlying biocontrol mechanisms. Strain ZF390 consists of one 6,193,667 bp circular chromosome and three plasmids. Comparative genome analysis revealed that ZF390 involves ten gene clusters responsible for secondary metabolite antibiotic synthesis, matching its excellent biocontrol activity. Plenty of genes related to plant growth promotion, biofilm formation, and induced systemic resistance were mined to reveal the biocontrol mechanisms that might consist in strain ZF390. Overall, these findings suggest that strain ZF390 could be a potential biocontrol agent in bacterial-soft-rot management, as well as a source of antimicrobial mechanisms for further exploitation.

Nematicidal activity of volatile organic compounds produced by Bacillus altitudinis AMCC 1040 against Meloidogyne incognita

The application of nematicidal microorganisms and their virulence factors provides more opportunities to control root-knot nematodes. Bacillus altitudinis AMCC 1040, previously isolated from suppressive soils, showed significant nematicidal activity, and in this study, nematicidal substances produced by Bacillus altitudinis AMCC 1040 were investigated. The results of the basic properties of active substances showed that these compounds have good thermal stability and passage, are resistant to acidic environment and sensitive to alkaline conditions. Further analysis showed that it is a volatile component. Using HS-SPME-GC/MS, the volatile compounds produced by Bacillus altitudinis AMCC 1040 were identified and grouped into four major categories: ethers, alcohols, ketone, and organic acids, comprising a total of eight molecules. Six of them possess nematicidal activities, including 2,3-butanedione, acetic acid, 2-isopropoxy ethylamine, 3-methylbutyric acid, 2-methylbutyric acid and octanoic acid. Our results further our understanding of the effects of Bacillus altitudinis and its nematicidal metabolites on the management of Meloidogyne incognita and may help in finding less toxic nematicides to control root knot nematodes.

Fumigant Activity of Bacterial Volatile Organic Compounds against the Nematodes Caenorhabditis elegans and Meloidogyne incognita

Plant-parasitic nematodes infect a diversity of crops, resulting in severe economic losses in agriculture. Microbial volatile organic compounds (VOCs) are potential agents to control plant-parasitic nematodes and other pests. In this study, VOCs emitted by a dozen bacterial strains were analyzed using solid-phase microextraction followed by gas chromatography-mass spectrometry. Fumigant toxicity of selected VOCs, including dimethyl disulfide (DMDS), 2-butanone, 2-pentanone, 2-nonanone, 2-undecanone, anisole, 2,5-dimethylfuran, glyoxylic acid, and S-methyl thioacetate (MTA) was then tested against Caenorhabditis elegans. DMDS and MTA exhibited much stronger fumigant toxicity than the others. Probit analysis suggested that the values of LC₅₀ were 8.57 and 1.43 μg/cm³ air for DMDS and MTA, respectively. MTA also showed stronger fumigant toxicity than DMDS against the root-knot nematode Meloidogyne incognita, suggesting the application potential of MTA.

Endophytic Bacteria and Essential Oil from Origanum vulgare ssp. vulgare Share Some VOCs with an Antibacterial Activity

Medicinal aromatic plants’ essential oils (EOs) are mixtures of volatile compounds showing antimicrobial activity, which could be exploited to face the emerging problem of multi-drug resistance. Their chemical composition can depend on the interactions between the plant and its endophytic microbiota, which is known to synthesize volatile organic compounds (VOCs). However, it is still not clear whether those volatile metabolites can contribute to the composition of the aroma profile of plants’ EOs. The aims of this study were to characterize medicinal plant O. vulgare ssp. vulgare bacterial endophyte VOCs, evaluating their ability to antagonize the growth of opportunistic human pathogens belonging to the Burkholderia cepacia complex (Bcc) and compare them with O. vulgare EO composition. Many of the tested endophytic strains showed (i) a bactericidal and/or bacteriostatic activity against most of Bcc strains and (ii) the production of VOCs with widely recognized antimicrobial properties, such as dimethyl disulfide, dimethyl trisulfide, and monoterpenes. Moreover, these monoterpenes were also detected in the EOs extracted from the same O. vulgare plants from which endophytes were isolated. Obtained results suggest that endophytes could also play a role in the antibacterial properties of O. vulgare ssp. vulgare and, potentially, in determining its aromatic composition.

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.

Potential of rhizobacteria native to Argentina for the control of Meloidogyne javanica

Biocontrol of the nematode Meloidogyne javanica was studied using the Argentinean strains Pseudomonas fluorescens MME3, TAE4, TAR5 and ZME4 and Bacillus sp. B7S, B9T and B19S. Pseudomonas protegens CHA0 was used as a positive control. Egg hatching and juvenile mortality were evaluated in vitro by exposure of nematodes to bacterial suspensions or their cell-free supernatants (CFS). The effect of bacteria on nematode infestation of lettuce was also studied. results showed that most of the tested strains and CFS reduced egg hatching and juvenile survival in vitro. The bacterial suspension of Bacillus sp. B9T produced the lowest hatching of eggs. Juvenile mortality was higher when M. javanica was exposed to Bacillus sp. than to Pseudomonas spp. suspensions. Except for CFS of B9T, all filtrates inhibited hatching at levels similar to or higher than the biocontrol strain P. protegens CHA0. The CFS of CHA0 showed the highest level of juvenile mortality followed by Bacillus sp. strains and P. fluorescens TAE4. None of the inoculated rhizobacteria reverted the negative effect of infestation on the aerial dry weight of lettuce plants. However, inoculation impacted on reproduction of M. javanica by reducing the development of galls and egg masses on roots and diminishing the number of individuals both on roots and in the substrate, as well as the reproduction factor. These results show that most of the analyzed native strains can control the nematode M. javanica. Among them, P. fluorescens TAE4 and Bacillus sp. B9T showed the most promising performances for the biocontrol of this pathogen and have a potential use in the formulation of commercial products.

Nematicidal Activity of Burkholderia arboris J211 Against Meloidogyne incognita on Tobacco

Root-knot nematode (Meloidogyne incognita) is the most widespread nematode affecting Solanaceae crops. Due to the lack of effective measures to control this nematode, its management can be achieved, using biocontrol agents. This study investigated in vitro efficacy of the antagonistic bacterial strain J211 isolated from tobacco rhizosphere soil against M. incognita, and further assessed its role in controlling nematodes, both in pot and field trials. Phylogenetic analysis of the 16S rRNA gene sequence of strain J211 assigned to Burkholderia arboris. Culture filtrates B. arboris J211 exhibited anematicidal activity against the second-stage juveniles (J2s) of M. incognita, with a 96.6% mortality after 24 h exposure. Inoculation of J211 in tobacco roots significantly reduced the root galling caused by M. incognita, both in pot and field trials. Meanwhile, plant growth-promoting (PGP) traits results showed that J211 had outstanding IAA-producing activity, and the IAA production reached 66.60 mg L⁻¹. In the field study, B. arboris J211 also promoted tobacco growth and increase flue-cured tobacco yield by 8.7–24.3%. Overall, B. arboris J211 as a high-yielding IAA nematicidal strain effectively controlled M. incognita and improved tobacco yield making it a promising alternative bionematocide.

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.

Root-Associated Bacteria Are Biocontrol Agents for Multiple Plant Pests

Biological control is an important process for sustainable plant production, and this trait is found in many plant-associated microbes. This study reviews microbes that could be formulated into pesticides active against various microbial plant pathogens as well as damaging insects or nematodes. The focus is on the beneficial microbes that colonize the rhizosphere where, through various mechanisms, they promote healthy plant growth. Although these microbes have adapted to cohabit root tissues without causing disease, they are pathogenic to plant pathogens, including microbes, insects, and nematodes. The cocktail of metabolites released from the beneficial strains inhibits the growth of certain bacterial and fungal plant pathogens and participates in insect and nematode toxicity. There is a reinforcement of plant health through the systemic induction of defenses against pathogen attack and abiotic stress in the plant; metabolites in the beneficial microbial cocktail function in triggering the plant defenses. The review discusses a wide range of metabolites involved in plant protection through biocontrol in the rhizosphere. The focus is on the beneficial firmicutes and pseudomonads, because of the extensive studies with these isolates. The review evaluates how culture conditions can be optimized to provide formulations containing the preformed active metabolites for rapid control, with or without viable microbial cells as plant inocula, to boost plant productivity in field situations.

Reproductive Toxicity of Furfural Acetone in Meloidogyne incognita and Caenorhabditis elegans

Furfural acetone (FAc) is a promising alternative to currently available nematicides, and it exhibits equivalent control efficiency on root-knot nematodes with avermectin in fields. However, its effect on the reproduction of root-knot nematode is poorly understood. In this study, the natural metabolite FAc was found to exhibit reproductive toxicity on Meloidogyne incognita and Caenorhabditis elegans. The number of germ cells of C. elegans was observed to decrease after exposure to FAc, with a reduction of 59.9% at a dose of 200 mg/L. FAc in various concentrations induced the germ-cell apoptosis of C. elegans, with an increase over six-fold in the number of apoptotic germ cells at 200 mg/L. These findings suggested that FAc decreased the brood size of nematode by inducing germ-cell apoptosis. Moreover, FAc-induced germ-cell apoptosis was suppressed by the mutation of gene hus-1, clk-2, cep-1, egl-1, ced-3, ced-4, or ced-9. The expression of genes spo-11, cep-1, and egl-1 in C. elegans was increased significantly after FAc treatment. Taken together, these results indicate that nematode exposure to FAc might inflict DNA damage through protein SPO-11, activate CEP-1 and EGL-1, and induce the core apoptosis pathway to cause germ-cell apoptosis, resulting in decreased brood size of C. elegans.

Identification of Volatile Organic Compounds Emitted by Two Beneficial Endophytic Pseudomonas Strains from Olive Roots

The production of volatile organic compounds (VOCs) represents a promising strategy of plant-beneficial bacteria to control soil-borne phytopathogens. Pseudomonas sp. PICF6 and Pseudomonas simiae PICF7 are two indigenous inhabitants of olive roots displaying effective biological control against Verticillium dahliae. Additionally, strain PICF7 is able to promote the growth of barley and Arabidopsis thaliana, VOCs being involved in the growth of the latter species. In this study, the antagonistic capacity of these endophytic bacteria against relevant phytopathogens (Verticillium spp., Rhizoctonia solani, Sclerotinia sclerotiorum and Fusarium oxysporum f.sp. lycopersici) was assessed. Under in vitro conditions, PICF6 and PICF7 were only able to antagonize representative isolates of V. dahliae and V. longisporum. Remarkably, both strains produced an impressive portfolio of up to twenty VOCs, that included compounds with reported antifungal (e.g., 1-undecene, (methyldisulfanyl) methane and 1-decene) or plant growth promoting (e.g., tridecane, 1-decene) activities. Moreover, their volatilomes differed strongly in the absence and presence of V. dahliae. For example, when co incubated with the defoliating pathotype of V. dahliae, the antifungal compound 4-methyl-2,6-bis(2-methyl-2-propanyl)phenol was produced. Results suggest that volatiles emitted by these endophytes may differ in their modes of action, and that potential benefits for the host needs further investigation in planta.

Bacterial volatile organic compounds induce adverse ultrastructural changes and DNA damage to the sugarcane pathogenic fungus Thielaviopsis ethacetica

Due to an increasing demand for sustainable agricultural practices, the adoption of microbial volatile organic compounds (VOCs) as antagonists against phytopathogens has emerged as an eco-friendly alternative to the use of agrochemicals. Here, we identified three Pseudomonas strains that were able to inhibit, in vitro, up to 80% of mycelial growth of the phytopathogenic fungus Thielaviopsis ethacetica, the causal agent of pineapple sett rot disease in sugarcane. Using GC/MS, we found that these bacteria produced 62 different VOCs, and further functional validation revealed compounds with high antagonistic activity to T. ethacetica. Transcriptomic analysis of the fungal response to VOCs indicated that these metabolites downregulated genes related to fungal central metabolism, such as those involved in carbohydrate metabolism. Interestingly, genes related to the DNA damage response were upregulated, and micro-FTIR analysis corroborated our hypothesis that VOCs triggered DNA damage. Electron microscopy analysis showed critical morphological changes in mycelia treated with VOCs. Altogether, these results indicated that VOCs hampered fungal growth and could lead to cell death. This study represents the first demonstration of the molecular mechanisms involved in the antagonism of sugarcane phytopathogens by VOCs and reinforces that VOCs can be a sustainable alternative for use in phytopathogen biocontrol.

Volatile Organic Compounds from Bacillus aryabhattai MCCC 1K02966 with Multiple Modes against Meloidogyne incognita

Plant-parasitic nematodes cause severe losses to crop production and economies all over the world. Bacillus aryabhattai MCCC 1K02966, a deep-sea bacterium, was obtained from the Southwest Indian Ocean and showed nematicidal and fumigant activities against Meloidogyne incognita in vitro. The nematicidal volatile organic compounds (VOCs) from the fermentation broth of B. aryabhattai MCCC 1K02966 were investigated further using solid-phase microextraction gas chromatography-mass spectrometry. Four VOCs, namely, pentane, 1-butanol, methyl thioacetate, and dimethyl disulfide, were identified in the fermentation broth. Among these VOCs, methyl thioacetate exhibited multiple nematicidal activities, including contact nematicidal, fumigant, and repellent activities against M. incognita. Methyl thioacetate showed a significant contact nematicidal activity with 87.90% mortality at 0.01 mg/mL by 72 h, fumigant activity in mortality 91.10% at 1 mg/mL by 48 h, and repellent activity at 0.01-10 mg/mL. In addition, methyl thioacetate exhibited 80-100% egg-hatching inhibition on the 7th day over the range of 0.5 mg/mL to 5 mg/mL. These results showed that methyl thioacetate from MCCC 1K02966 control M. incognita with multiple nematicidal modes and can be used as a potential biological control agent.

Attraction and toxicity: Ways volatile organic compounds released by Pochonia chlamydosporia affect Meloidogyne incognita

The production of volatile organic compounds (VOCs) acting against plant-parasitic nematodes has been characterized in different fungi; however, the role of VOCs emitted by Pochonia chlamydosporia in its trophic interaction with Meloidogyne incognita is still unknown. The aim of this study was to determine the effects of VOCs emitted by P. chlamydosporia strain Pc-10 on different stages (eggs, juveniles and female) of the M. incognita life cycle. Exposure of M. incognita eggs to VOCs released by Pc-10 resulted in a reduction up to 88 % in the nematode egg hatching, when compared to the control treatments. The VOCs emitted by Pc-10 also attracted M. incognita second-stage juveniles (J2). Through gas chromatography-mass spectrometry (GC-MS), three molecules were identified from the volatiles of the strain Pc-10, with 1,4-dimethoxybenzene being the major compound. In tests performed in vitro, 1,4-dimethoxybenzene at a concentration of 1050 μg mL-1 inhibited M. incognita egg hatching by up to 78.7 % compared to the control (0 μg mL-1) and attracted M. incognita J2 in all concentrations evaluated (1, 10, 100, 1000, and 10000 μg mL-1). The 1,4-dimethoxybenzene also showed fumigant and non-fumigant nematicidal activity against M. incognita. This compound presented lethal concentration for 50 % (LC50) of M. incognita J2 ranged from 132 to 136 μg mL-1. Fumigation with 1,4-dimethoxybenzene (100 mg) reduced egg hatching by up to 89 % and killed up to 86 % of M. incognita J2 compared to the control (0 μg mL-1). In vivo, the VOCs produced by Pc-10, 1,4-dimethoxybenzene, and the combination of both (Pc-10 + 1,4-dimethoxybenzene) attracted the M. incognita J2, compared to the respective controls. To the best of our knowledge, this is the first report on the attraction of M. incognita J2 and the toxicity to eggs and J2 by VOCs from P. chlamydosporia in which 1,4-dimethoxybenzene is the main toxin and attractant.

Fusaricidins, Polymyxins and Volatiles Produced by Paenibacillus polymyxa Strains DSM 32871 and M1

Paenibacilli are efficient producers of potent agents against bacterial and fungal pathogens, which are of great interest both for therapeutic applications in medicine as well as in agrobiotechnology. Lipopeptides produced by such organisms play a major role in their potential to inactivate pathogens. In this work we investigated two lipopeptide complexes, the fusaricidins and the polymyxins, produced by Paenibacillus polymyxa strains DSM 32871 and M1 by MALDI-TOF mass spectrometry. The fusaricidins show potent antifungal activities and are distinguished by an unusual variability. For strain DSM 32871 we identified numerous yet unknown variants mass spectrometrically. DSM 32871 produces polymyxins of type E (colistins), while M1 forms polymyxins P. For both strains, novel but not yet completely characterized polymyxin species were detected, which possibly are glycosylated. These compounds may be of interest therapeutically, because polymyxins have gained increasing attention as last-resort antibiotics against multiresistant pathogenic Gram-negative bacteria. In addition, the volatilomes of DSM 32781 and M1 were investigated with a GC–MS approach using different cultivation media. Production of volatile organic compounds (VOCs) was strain and medium dependent. In particular, strain M1 manifested as an efficient VOC-producer that exhibited formation of 25 volatiles in total. A characteristic feature of Paenibacilli is the formation of volatile pyrazine derivatives.

Development of Portable E-Nose System for Fast Diagnosis of Whitefly Infestation in Tomato Plant in Greenhouse

An electronic nose (E-nose) system equipped with a gas sensor array and real-time control panel was developed for a fast diagnosis of whitefly infestation in tomato plants. Profile changes of volatile organic compounds (VOCs) released from tomato plants under different treatments (i.e., whitefly infestation, mechanical damage, and no treatment) were successfully determined by the developed E-nose system. A rapid sensor response with high sensitivity towards whitefly-infested tomato plants was observed in the E-nose system. Results of principal component analysis (PCA) and hierarchical clustering analysis (HCA) indicated that the E-nose system was able to provide accurate distinguishment between whitefly-infested plants and healthy plants, with the first three principal components (PCs) accounting for 87.4% of the classification. To reveal the mechanism of whitefly infestation in tomato plants, VOC profiles of whitefly-infested plants and mechanically damaged plants were investigated by using the E-nose system and GC-MS. VOCs of 2-nonanol, oxime-, methoxy-phenyl, and n-hexadecanoic acid were only detected in whitefly-infested plants, while compounds of dodecane and 4,6-dimethyl were only found in mechanically damaged plant samples. Those unique VOC profiles of different tomato plant groups could be considered as bio-markers for diagnosing different damages. Moreover, the E-nose system was demonstrated to have the capability to differentiate whitefly-infested plants and mechanically damaged plants. The relationship between sensor performance and VOC profiles confirmed that the developed E-nose system could be used as a fast and smart device to detect whitefly infestation in greenhouse cultivation.

Phenazine 1-carboxylic acid Producing Seed Harbored Endophytic Bacteria from Cultivated Rice Variety of Kerala and Its Broad Range Antagonism to Diverse Plant Pathogens

Endophytic microorganisms residing within the diverse parts of plants play a significant role in the plant growth and defense response. In the case of the vertically transmitted seed-borne endophytes, they form the promising initiator of the juvenile plant microbiome by supporting the growth and establishment of the seedlings. Hence, the current study emphasizes the isolation and screening of plant beneficial traits of seed endophytes from the cultivated rice variety Jyothi of Kerala, India. Among the 14 bacterial endophytes obtained in the study, the isolate S3 was found to have promising activity against the phytopathogens such as Fusarium oxysporum, Pythium aphanidermatum, Pythium myriotylum, Phytophthora infestans, Rhizoctonia solani, Colletotrichum acutatum, and Sclerotium rolfsii. The isolate S3 was further identified as Paenibacillus polymyxa by the 16S rRNA-based sequence analysis. Furthermore, the isolate was confirmed for its capability for hydrogen cyanide (HCN) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, biofilm formation, and nitrogen fixation. The P. polymyxa S3 was also found to have the potential to provide post-harvest protection to the rice kernels from Sclerotium rolfsii. By the LC-MS/MS analysis, the organism was confirmed for the production of phenazine 1-carboxylic acid which could be the prime chemical basis of its antifungal activity. The in vivo plant growth evaluation has also demonstrated the root length enhancement effect of P. polymyxa S3 in Vigna unguiculata. Here, the root length of P. polymyxa S3-treated plant was enhanced to 12.44 ± 0.58223 cm when compared with distilled water control (10.261 ± 0.38151 cm) and the observed change was statistically significant as per the analysis of variance at P value less than 0.05. Based on all these properties, the isolated P. polymyxa S3 could be considered as a promising agent to be used for the development of competent plant probiotic formulations.

Nematicidal Activity of Grammicin Biosynthesis Pathway Intermediates in Xylaria grammica KCTC 13121BP against Meloidogyne incognita

Grammicin, a polyketide metabolite produced by the endolichenic fungus Xylaria grammica KCTC 13121BP, shows strong nematicidal activity against Meloidogyne incognita. This study was performed to elucidate the grammicin biosynthesis pathway of X. grammica KCTC 13121BP and to examine the nematicidal activity of the biosynthesis intermediates and derivatives against M. incognita. Two grammicin biosynthesis intermediates were isolated from a T-DNA insertion transformant (strain TR-74) of X. grammica KCTC 13121BP and identified as 2-(hydroxymethyl)cyclohexa-2,5-diene-1,4-dione (compound 1) and 2,5-dihydroxybenzaldehyde (compound 2), which were also reported to be intermediates in the biosynthesis pathway of patulin, an isomer of grammicin. This indicates that the grammicin biosynthesis pathway overlaps almost with that of patulin, except for the last few steps. Among 13 grammicin biosynthesis intermediates and their derivatives (except grammicin), toluquinol caused the highest M. incognita J2 mortality, with an LC_{50/72 h} value of 11.13 µg/mL, which is similar to grammicin with an LC_{50/72 h} value of 15.95 µg/mL. In tomato pot experiments, the wettable powder type formulations (WP) of toluquinol (17.78 µg/mL) and grammicin (17.78 µg/mL) also effectively reduced gall formation on the roots of tomato plants with control values of 72.22% and 77.76%, respectively, which are much higher than abamectin (16.67%), but lower than fosthiazate (100%). The results suggest that toluquinol can be used directly as a biochemical nematicide or as a lead molecule for the development of new synthetic nematicides for the control of root-knot nematode diseases.

Control of Meloidogyne incognita in Three-Dimensional Model Systems and Pot Experiments by the Attract-and-Kill Effect of Furfural Acetone

Meloidogyne incognita causes large-scale losses of agricultural crops worldwide. The natural metabolite furfural acetone has been reported to attract and kill M. incognita, but whether the attractant and nematicidal activities of furfural acetone on M. incognita function simultaneously in the same system, especially in three-dimensional spaces or in soil, is still unknown. Here, we used 23% Pluronic F-127 gel and a soil simulation device to demonstrate that furfural acetone has a significant attract-and-kill effect on M. incognita in both three-dimensional model systems. At 24 h, the chemotaxis index and the corrected mortality of nematodes exposed to 60 mg/ml of furfural acetone in 23% Pluronic F-127 gel were as high as 0.82 and 74.44%, respectively. Soil simulation experiments in moist sand showed that at 48 h, the chemotaxis index and the corrected mortality of the nematode toward furfural acetone reached 0.63 and 82.12%, respectively, and the effect persisted in the presence of tomato plants. In choice experiments, nematodes selected furfural acetone over plant roots and were subsequently killed. In pot studies, furfural acetone had a control rate of 82.80% against M. incognita. Collectively, these results provide compelling evidence for further investigation of furfural acetone as a novel nematode control agent.

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

Bacillus volatiles to control plant nematodes is a topic of great interest among researchers due to its safe and environmentally friendly nature. Bacillus strain GBSC56 isolated from the Tibet region of China showed high nematicidal activity against M. incognita, with 90% mortality as compared with control in a partition plate experiment. Pure volatiles produced by GBSC56 were identified through gas chromatography and mass spectrometry (GC-MS). Among 10 volatile organic compounds (VOCs), 3 volatiles, i.e., dimethyl disulfide (DMDS), methyl isovalerate (MIV), and 2-undecanone (2-UD) showed strong nematicidal activity with a mortality rate of 87%, 83%, and 80%, respectively, against M. incognita. The VOCs induced severe oxidative stress in nematodes, which caused rapid death. Moreover, in the presence of volatiles, the activity of antioxidant enzymes, i.e., SOD, CAT, POD, and APX, was observed to be enhanced in M. incognita-infested roots, which might reduce the adverse effect of oxidative stress-induced after infection. Moreover, genes responsible for plant growth promotion SlCKX1, SlIAA1, and Exp18 showed an upsurge in expression, while AC01 was downregulated in infested plants. Furthermore, the defense-related genes (PR1, PR5, and SlLOX1) in infested tomato plants were upregulated after treatment with MIV and 2-UD. These findings suggest that GBSC56 possesses excellent biocontrol potential against M. incognita. Furthermore, the study provides new insight into the mechanism by which GBSC56 nematicidal volatiles regulate antioxidant enzymes, the key genes involved in plant growth promotion, and the defense mechanism M. incognita-infested tomato plants use to efficiently manage root-knot disease.

Volatile organic compounds of Metarhizium brunneum influence the efficacy of entomopathogenic nematodes in insect control

The entomopathogenic fungus (EPF) Metarhizium brunneum occupies the same ecological niche as entomopathogenic nematodes (EPN), with both competing for insects as a food source in the rhizosphere. Interactions between these biocontrol agents can be antagonistic or synergistic. To better understand these interactions, this study focussed on investigating the effect of M. brunneum volatile organic compounds (VOCs), 1-octen-3-ol and 3-octanone, on EPN survival and behaviour. These VOCs proved to be highly toxic to the infective juveniles (IJs) of the EPN Steinernema carpocapsae, Steinernema feltiae and Heterorhabditis bacteriophora with mortality being dose dependent. Chemotaxis studies of H. bacteriophora IJs in Pluronic F127 gel revealed significant preference for the VOCs compared with controls for all tested concentrations. The VOCs also impacted on the test insects in a dose-dependent manner with 3-octanone being more toxic to Galleria mellonella, Cydia splendana and Curculio elephas larvae than 1-octen-3-ol. Mortality of C. splendana and G. mellonella larvae was significantly higher when exposed to relatively high doses (>25%) of 3-octanone. Lower doses of 3-octanone and 1-octen-3-ol immobilised test insects, which recovered after exposure to fresh air for 2 hrs. In depth studies on H. bacteriophora showed that exposure of IJs to > 10% concentration of 3-octanone or 1-octen-3-ol negatively affected infectivity whereas exposure to lower doses (0.1%, 0.01%) had no effect. The VOCs affected IJs, reducing penetration efficacy and the number of generations inside G. mellonella but they failed to inhibit the bacterial symbiont, Photorhabdus kayaii. The ecological significance of VOCs and how they could influence EPF-EPN insect interactions is discussed.

Volatile Organic Compounds of Bacillus cereus Strain Bc-cm103 Exhibit Fumigation Activity against Meloidogyne incognita

Bacillus cereus strain Bc-cm103 shows nematicidal activity and, therefore, has been used as a biological control agent to control the root-knot nematode Meloidogyne incognita. However, it remains unknown whether volatile organic compounds (VOCs) produced by B. cereus strain Bc-cm103 are effective in biocontrol against M. incognita. Therefore, in this study, we investigated the activity of Bc-cm103 VOCs against M. incognita. The B. cereus strain Bc-cm103 significantly repelled the second-stage juveniles (J2s) of M. incognita. In vitro evaluation of VOCs produced by the fermentation of Bc-cm103 in a three-compartment Petri dish revealed the mortality rates of M. incognita J2s as 90.8% at 24 h and 97.2% at 48 h. Additionally, evaluation of the ability of Bc-cm103 VOCs to suppress M. incognita infection in a double-layered pot test showed that root galls on cucumber roots decreased by 46.1%. Furthermore, 21 VOCs were identified from strain Bc-cm103 by solid-phase microextraction gas chromatography-mass spectrometry, including alkanes, alkenes, esters, and sulfides. Among them, dimethyl disulfide (30.63%) and S-methyl ester butanethioic acid (30.29%) were reported to have strong nematicidal activity. Together, these results suggest that B. cereus strain Bc-cm103 exhibits fumigation activity against M. incognita.

Paenibacillus polymyxa, a Jack of all trades

The bacterium Paenibacillus polymyxa is found naturally in diverse niches. Microbiome analyses have revealed enrichment in the genus Paenibacillus in soils under different adverse conditions, which is often accompanied by improved growth conditions for residing plants. Furthermore, Paenibacillus is a member of the core microbiome of several agriculturally important crops, making its close association with plants an interesting research topic. This review covers the versatile interaction possibilities of P. polymyxa with plants and its applicability in industry and agriculture. Thanks to its array of produced compounds and traits, P. polymyxa is likely an efficient plant growth-promoting bacterium, with the potential of biofertilization, biocontrol and protection against abiotic stresses. By contrast, cases of phytotoxicity of P. polymyxa have been described as well, in which growth conditions seem to play a key role. Because of its adjustable character, we propose this bacterial species as an outstanding model for future studies on host-microbe communications and on the manner how the environment can influence these interactions.

Isolation and characterization of antagonistic Paenibacillus polymyxa HX-140 and its biocontrol potential against Fusarium wilt of cucumber seedlings

Objective

The aim of this study is to evaluate the efficacy of the strain Paenibacillus polymyxa HX-140, isolated from the rhizosphere soil of rape, to control Fusarium wilt of cucumber seedlings caused by Fusarium oxysporum f. sp. cucumerinum.

Results

Strain HX-140 was able to produce protease, cellulase, β-1,3-glucanase and antifungal volatile organic compounds. An in vitro dual culture test showed that strain HX-140 exhibited broad spectrum antifungal activity against soil-borne plant pathogenic fungi. Strain HX-140 also reduced the infection of Fusarium wilt of cucumber seedlings by 55.6% in a greenhouse pot experiment. A field plot experiment confirmed the biocontrol effects and further revealed that antifungal activity was positively correlated with inoculum size by the root-irrigation method. Here, inoculums at 10⁶ 10⁷ and 10⁸ cfu/mL of HX-140 bacterial suspension reduced the incidence of Fusarium wilt of cucumber seedling by 19.5, 41.1, and 50.9%, respectively.

Conclusions

Taken together, our results suggest that P. polymyxa HX-140 has significant potential in the control of Fusarium wilt and possibly other fungal diseases of cucumber.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02131-3.

Volatile compounds as potential bio-fumigants against plant-parasitic nematodes - a mini review

Soil fumigation remains the standard practice to manage soilborne pathogens such as plant-parasitic nematodes, bacteria, and fungi, especially in high-value crops. However, increasing regulatory pressure due to the inherent and broad-spectrum toxicity and negative environmental impact of chemical soil fumigants, its negative effect on overall soil health, and increasing demand for organic produce, has created a growing interest in biological fumigants. Many plants and microorganisms emit volatile compounds, which can potentially be used as bio-fumigants. In this mini-review, we summarize the current status of nematology studies focused on the development of volatile compounds emitted from plants and microorganisms as fumigants to control plant-parasitic nematodes. The gap of knowledge and challenges of studying volatile compounds are also addressed.