Cyclo(l-Pro⁻l-Leu) of Pseudomonas putida MCCC 1A00316 Isolated from Antarctic Soil: Identification and Characterization of Activity against Meloidogyne incognita

Arbuscular mycorrhizal fungus and Pseudomonas bacteria affect tomato response to Tuta absoluta (Lepidoptera: Gelechiidae) herbivory

Tuta absoluta (Lepidoptera: Gelechiidae) is one of the most significant invasive and destructive pests worldwide, causing serious economic losses to the tomato industry. Rhizosphere microorganism, such as arbuscular mycorrhizal fungi (AMF) and Pseudomonas bacteria, can interact with plants individually or collectively to improve plant growth and resistance to pests and disease. However, the effects of AMF, Pseudomonas, and their interactions on plant responses to insect herbivores remain unclear. A pot experiment was conducted to investigate the effects of single/dual inoculation with AMF (Funneliformis mosseae, M) and Pseudomonas putida (P) on the growth and defense of tomato variety Dafen (Solanum lycopersicum L.) in response to infestation by T. absoluta, as well as the growth, development, and enzyme activity of insect. The results showed that M, P, and MP promoted tomato growth by increasing nutrient concentrations, with the growth-promoting effect of dual-inoculation significantly surpassing that of single inoculation. M, P, and MP still improved tomato growth in T. absoluta infestation, with biomass increases of 57.34%, 54.46%, and 255.49%. M, P, and MP significantly increased the defense ability of tomato, with jasmonic acid concentrations increasing by 42.15%, 60.87% and 90.02%, and phenylalanine ammonia-lyase activity increasing by 47.40%, 47.68%, and 59.97%. The inoculation treatments inhibited the growth and development of T. absoluta, reduced its feeding, prolonged its growth and development, decreased egg weight, and increased the activity of protective and detoxifying enzymes. Overall, our results indicated that AMF and bacteria can stimulate each other, positively influence tomato growth and enhance resistance to T. absoluta. These findings indicate the feasibility of AMF and bacteria in combinations as potential biocontrol agents for the management of T. absoluta.

Profiling Metabolites with Antifungal Activities from Endophytic Plant-Beneficial Strains of Pseudomonas chlororaphis Isolated from Chamaecytisus albus (Hack.) Rothm

Fungal phytopathogens represent a large and economically significant challenge to food production worldwide. Thus, the application of biocontrol agents can be an alternative. In the present study, we carried out biological, metabolomic, and genetic analyses of three endophytic isolates from nodules of Chamaecytisus albus, classified as Pseudomonas chlororaphis acting as antifungal agents. The efficiency of production of their diffusible and volatile antifungal compounds (VOCs) was verified in antagonistic assays with the use of soil-borne phytopathogens: B. cinerea, F. oxysporum, and S. sclerotiorum. Diffusible metabolites were identified using chromatographic and spectrometric analyses (HPTLC, GC-MS, and LC-MS/MS). The phzF, phzO, and prnC genes in the genomes of bacterial strains were confirmed by PCR. In turn, the plant growth promotion (PGP) properties (production of HCN, auxins, siderophores, and hydrolytic enzymes, phosphate solubilization) of pseudomonads were bioassayed. The data analysis showed that all tested strains have broad-range antifungal activity with varying degrees of antagonism. The most abundant bioactive compounds were phenazine derivatives: phenazine-1-carboxylic acid (PCA), 2-hydroxy-phenazine, and diketopiperazine derivatives as well as ortho-dialkyl-aromatic acids, pyrrolnitrin, siderophores, and HCN. The results indicate that the tested P. chlororaphis isolates exhibit characteristics of biocontrol organisms; therefore, they have potential to be used in sustainable agriculture and as commercial postharvest fungicides to be used in fruits and vegetables.

Penisimplicins A and B: Novel Polyketide-Peptide Hybrid Alkaloids from the Fungus Penicillium simplicissimum JXCC5

In this study, two previously undescribed nitrogen-containing compounds, penisimplicins A (1) and B (2), were isolated from Penicillium simplicissimum JXCC5. The structures of 1 and 2 were elucidated on the basis of comprehensive spectroscopic data analysis, including 1D and 2D NMR and HRESIMS data. The absolute configuration of 2 was determined by Marfey's method, ECD calculation, and DP4+ analysis. Both structures of 1 and 2 feature an unprecedented manner of amino acid-derivatives attaching to a polyketide moiety by C-C bond. The postulated biosynthetic pathways for 1 and 2 were discussed. Additionally, compound 1 exhibited significant acetylcholinesterase inhibitory activity, with IC50 values of 6.35 μM.

Identification of isomeric cyclo(leu-pro) produced by Pseudomonas sesami BC42 and its differential antifungal activities against Colletotrichum orbiculare

Pseudomonas spp. produce various antimicrobial substances, including cyclic peptides, which have been shown to suppress fungal pathogens. In a previous study, Pseudomonas sesami BC42 was selected to control anthracnose caused by Colletotrichum orbiculare in cucumber plants, and the bioactive extract of strain BC42 inhibited fungal growth and development. In this work, preparative thin-layer chromatography was conducted to identify the antifungal compounds in the extract of strain BC42, and the portion of the extract that exhibited antifungal activity was further analyzed by gas chromatography-mass spectrometry. Three different isomers of the cyclic dipeptide, cyclo(Leu-Pro), were identified: cyclo(l-Leu-l-Pro), cyclo(d-Leu-d-Pro), and cyclo(d-Leu-l-Pro). Among these, 100 μg/mL of cyclo(l-Leu-l-Pro) significantly and more effectively inhibited the germination of conidia and appressorium formation and reduced leaf lesion size caused by C. orbiculare, relative to the control; cyclo(d-Leu-d-Pro) significantly reduced conidia germination and lesion occurrence, however, cyclo(d-Leu-l-Pro) did not exhibit antifungal activity. Therefore, the cyclo(l-Leu-l-Pro) and cyclo(d-Leu-d-Pro) derived from P. sesami BC42 may be a promising candidate for biocontrol applications in agriculture.

Implications of Below-Ground Allelopathic Interactions of Camelina sativa and Microorganisms for Phosphate Availability and Habitat Maintenance

Toxic breakdown products of young Camelina sativa (L.) Crantz, glucosinolates can eliminate microorganisms in the soil. Since microorganisms are essential for phosphate cycling, only insensitive microorganisms with phosphate-solubilizing activity can improve C. sativa's phosphate supply. In this study, 33P-labeled phosphate, inductively coupled plasma mass spectrometry and pot experiments unveiled that not only Trichoderma viride and Pseudomonas laurentiana used as phosphate-solubilizing inoculants, but also intrinsic soil microorganisms, including Penicillium aurantiogriseum, and the assemblies of root-colonizing microorganisms solubilized as well phosphate from apatite, trigger off competitive behavior between the organisms. Driving factors in the competitiveness are plant and microbial secondary metabolites, while glucosinolates of Camelina and their breakdown products are regarded as key compounds that inhibit the pathogen P. aurantiogriseum, but also seem to impede root colonization of T. viride. On the other hand, fungal diketopiperazine combined with glucosinolates is fatal to Camelina. The results may contribute to explain the contradictory effects of phosphate-solubilizing microorganisms when used as biofertilizers. Further studies will elucidate impacts of released secondary metabolites on coexisting microorganisms and plants under different environmental conditions.

Multiplatform Metabolomics Characterization Reveals Novel Metabolites and Phospholipid Compositional Rules of Haemophilus influenzae Rd KW20

Haemophilus influenzae is a gram-negative bacterium of relevant clinical interest. H. influenzae Rd KW20 was the first organism to be sequenced and for which a genome-scale metabolic model (GEM) was developed. However, current H. influenzae GEMs are unable to capture several aspects of metabolome nature related to metabolite pools. To directly and comprehensively characterize the endometabolome of H. influenzae Rd KW20, we performed a multiplatform MS-based metabolomics approach combining LC-MS, GC-MS and CE-MS. We obtained direct evidence of 15-20% of the endometabolome present in current H. influenzae GEMs and showed that polar metabolite pools are interconnected through correlating metabolite islands. Notably, we obtained high-quality evidence of 18 metabolites not previously included in H. influenzae GEMs, including the antimicrobial metabolite cyclo(Leu-Pro). Additionally, we comprehensively characterized and evaluated the quantitative composition of the phospholipidome of H. influenzae, revealing that the fatty acyl chain composition is largely independent of the lipid class, as well as that the probability distribution of phospholipids is mostly related to the conditional probability distribution of individual acyl chains. This finding enabled us to provide a rationale for the observed phospholipid profiles and estimate the abundance of low-level species, permitting the expansion of the phospholipidome characterization through predictive probabilistic modelling.

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.

Natural nematicidal metabolites and advances in their biocontrol capacity on plant parasitic nematodes

Covering: 2010 to 2021Natural nematicidal metabolites are important sources of nematode control. This review covers the isolation and structural determination of nematicidal metabolites from 2010 to 2021. We summarise chemical structures, bioactivity, metabolic regulation and biosynthesis of potential nematocides, and structure-activity relationship and application potentiality of natural metabolites in plant parasitic nematodes' biocontrol. In doing so, we aim to provide a comprehensive overview of the potential roles that natural metabolites can play in anti-nematode strategies.

In silico analysis of koranimine, a cyclic imine compound from Peribacillus frigoritolerans reveals potential nematicidal activity

Pine wilt disease (PWD) is a destructive vector-borne forest disease caused by the nematode Bursaphelenchus xylophilus. To date, several options are available for the management of pine wilt disease; however constant development and search for natural products with potential nematicidal activity are imperative to diversify management options and to cope with the possible future emergence of resistance in parasitic nematodes. Here, a combined metabolomics and genomics approach was employed to investigate the chemical repertoire and biosynthetic potential of the bacterial endophyte Peribacillus frigoritolerans BE93, previously characterized to exhibit nematicidal activity against B. xylophilus. Feature-based molecular networking revealed the presence of diverse secondary metabolites. A cyclic imine heptapeptide, koranimine, was found to be among the most abundant secondary metabolites produced. Genome mining displayed the presence of several putative biosynthetic gene clusters (BGCs), including a dedicated non-ribosomal peptide synthase (NRPS) BGC for koranimine. Given the non-ribosomal peptide nature of koranimine, in silico molecular docking analysis was conducted to investigate its potential nematicidal activity against the target receptor ivermectin-sensitive invertebrate α glutamate-gated chloride channel (GluCl). Results revealed the binding of koranimine at the allosteric site of the channel-the ivermectin binding site. Moreover, the ligand-receptor interactions observed were mostly shared between koranimine and ivermectin when bound to the α GluCl receptor thus, suggesting a possibly shared mechanism of potential nematicidal activity. This study highlights the efficiency of combined metabolomics and genomics approach in the identification of candidate compounds.

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.

Pharmacological Properties, Volatile Organic Compounds, and Genome Sequences of Bacterial Endophytes from the Mangrove Plant Rhizophora apiculata Blume

Mangrove plant endophytic bacteria are prolific sources of bioactive secondary metabolites. In the present study, twenty-three endophytic bacteria were isolated from the fresh roots of the mangrove plant Rhizophora apiculata. The identification of isolates by 16S rRNA gene sequences revealed that the isolated endophytic bacteria belonged to nine genera, including Streptomyces, Bacillus, Pseudovibrio, Microbacterium, Brevibacterium, Microbulbifer, Micrococcus, Rossellomorea, and Paracoccus. The ethyl acetate extracts of the endophytic bacteria’s pharmacological properties were evaluated in vitro, including antimicrobial, antioxidant, α-amylase and α-glucosidase inhibitory, xanthine oxidase inhibitory, and cytotoxic activities. Gas chromatography–mass spectrometry (GC-MS) analyses of three high bioactive strains Bacillus sp. RAR_GA_16, Rossellomorea vietnamensis RAR_WA_32, and Bacillus sp. RAR_M1_44 identified major volatile organic compounds (VOCs) in their ethyl acetate extracts. Genome analyses identified biosynthesis gene clusters (BGCs) of secondary metabolites of the bacterial endophytes. The obtained results reveal that the endophytic bacteria from R. apiculata may be a potential source of pharmacological secondary metabolites, and further investigations of the high bioactive strains—such as fermentation and isolation of pure bioactive compounds, and heterologous expression of novel BGCs in appropriate expression hosts—may allow exploring and exploiting the promising bioactive compounds for future drug development.

Biocontrol of the root-knot nematode Meloidogyne incognita by a nematicidal bacterium Pseudomonas simiae MB751 with cyclic dipeptide

BACKGROUND

Root-knot nematodes (RKNs) are harmful plant-parasitic nematodes that cause serious damage to plant hosts. In the long-term practice of RKN management, bacterial nematicides have attracted increasing attention as an effective biocontrol means. Here we determined the active substances against Meloidogyne incognita from a nematicidal bacterium, developed a biocontrol agent (BCA) based on optimized culture processes. The effects of the BCA on RKN control and plant growth-promotion were evaluated in tomato pot trials.

RESULTS

Pseudomonas simiae strain MB751 exhibiting significant nematicidal activity against M. incognita second-stage juveniles (J2) with approximately 80% mortality (with culture supernatant, 96% volume percentage) was isolated from a vineyard. A set of purification and identification experiments was performed to determine the main nematicidal component in MB751. A cyclic dipeptide Cyclo(L-Pro-L-Leu) was identified with a lethal concentration necessary to kill 50% of the population (LC₅₀ ) of 65.3 μg mL^-1 against M. incognita J2. Following optimization trials on culture medium/fermentation conditions, such as the single factor test, Plackett-Burman test, steepest ascent, and response surface methodology experiments, the MB751 fermentation broth was then prepared as a BCA via a cold-air drying process. The BCA and was evaluated in tomato pot experiments for effectiveness in suppressing M. incognita. Significant effects on M. incognita suppression and plant-growth promotion as well as induced systemic resistance to M. incognita of tomato, were observed.

CONCLUSION

The cyclic dipeptide-producing bacterium P. simiae MB751 exhibited high nematicidal activity and performance. Further development of this BCA should be pursued for the management of M. incognita in agriculture. © 2021 Society of Chemical Industry.

Optimizing Safe Approaches to Manage Plant-Parasitic Nematodes

Plant-parasitic nematodes (PPNs) infect and cause substantial yield losses of many foods, feed, and fiber crops. Increasing concern over chemical nematicides has increased interest in safe alternative methods to minimize these losses. This review focuses on the use and potential of current methods such as biologicals, botanicals, non-host crops, and related rotations, as well as modern techniques against PPNs in sustainable agroecosystems. To evaluate their potential for control, this review offers overviews of their interactions with other biotic and abiotic factors from the standpoint of PPN management. The positive or negative roles of specific production practices are assessed in the context of integrated pest management. Examples are given to reinforce PPN control and increase crop yields via dual-purpose, sequential, and co-application of agricultural inputs. The involved PPN control mechanisms were reviewed with suggestions to optimize their gains. Using the biologicals would preferably be backed by agricultural conservation practices to face issues related to their reliability, inconsistency, and slow activity against PPNs. These practices may comprise offering supplementary resources, such as adequate organic matter, enhancing their habitat quality via specific soil amendments, and reducing or avoiding negative influences of pesticides. Soil microbiome and planted genotypes should be manipulated in specific nematode-suppressive soils to conserve native biologicals that serve to control PPNs. Culture-dependent techniques may be expanded to use promising microbial groups of the suppressive soils to recycle in their host populations. Other modern techniques for PPN control are discussed to maximize their efficient use.

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.

Taxonomic and Metabolomics Profiling of Actinobacteria Strains from Himalayan Collection Sites in Pakistan

Actinobacteria have proven themselves as the major producers of bioactive compounds with wide applications. In this study, 35 actinobacteria strains were isolated from soil samples collected from the Himalayan mountains region in Pakistan. The isolated strains were identified by polyphasic taxonomy and were prioritized based on biological and chemical screening to identify the strains with ability to produce inimitable metabolites. The biological screening included antimicrobial activity against Staphylococcus aureus, Micrococcus luteus, Salmonella enterica, Escherichia coli, Mycobacterium aurum, and Bacillus subtilis and anticancer activity using human cancer cell lines PC3 and A549. For chemical screening, methanolic extracts were investigated using TLC, HPLC-UV/MS. The actinobacteria strain PU-MM93 was selected for scale-up fermentation based on its unique chemical profile and cytotoxicity (50-60% growth inhibition) against PC3 and A549 cell lines. The scale-up fermentation of PU-MM93, followed by purification and structure elucidation of compounds revealed this strain as a promising producer of the cytotoxic anthracycline aranciamycin and aglycone SM-173-B along with the potent neuroprotective carboxamide oxachelin C. Other interesting metabolites produced include taurocholic acid as first report herein from microbial origin, pactamycate and cyclo(L-Pro-L-Leu). The study suggested exploring more bioactive microorganisms from the untapped Himalayan region in Pakistan, which can produce commercially significant compounds.

Evaluation of Multiple Impacts of Furfural Acetone on Nematodes In Vitro and Control Efficiency against Root-Knot Nematodes in Pots and Fields

Root-knot nematodes (RKNs) seriously endanger agricultural development and cause great economic losses worldwide. Natural product furfural acetone (FAc) is a promising nematicide with strong attractant and nematicidal activities, but baseline information about the impact of FAc on the reproduction, egg hatching, feeding, and growth of nematodes and its pest control efficiency in field are lacking. Here, the inhibition effects of FAc on nematodes in vitro and its RKN control efficiency in pot and field were investigated. FAc inhibited the egg hatching of Meloidogyne incognita by 91.7% at 200 mg/L after 2 days and suppressed the reproduction, feeding, and growth of Caenorhabditis elegans in vitro. In pot experiments, FAc in various dosages reduced the disease index of plant root significantly. In field experiments, FAc exhibited control effect on RKNs equivalent to commercial nematicides avermectin and metam sodium, with a reduction in disease index by 36.9% at a dose of 50 mg/plant. FAc also reduced the population density of RKNs in soil, with a reduction rate of 75.3% at the dose of 750 mg/m². No adverse effect was detected on plant growth after FAc application. These results provide compelling evidence for development of FAc as an appropriate alternative for current nematicides.

Identification and Characterization of Nematicidal Volatile Organic Compounds from Deep-Sea Virgibacillus dokdonensis MCCC 1A00493

Root-knot nematode diseases cause severe yield and economic losses each year in global agricultural production. Virgibacillus dokdonensis MCCC 1A00493, a deep-sea bacterium, shows a significant nematicidal activity against Meloidogyne incognita in vitro. However, information about the active substances of V. dokdonensis MCCC 1A00493 is limited. In this study, volatile organic compounds (VOCs) from V. dokdonensis MCCC 1A00493 were isolated and analyzed through solid-phase microextraction and gas chromatography-mass spectrometry. Four VOCs, namely, acetaldehyde, dimethyl disulfide, ethylbenzene, and 2-butanone, were identified, and their nematicidal activities were evaluated. The four VOCs had a variety of active modes on M. incognita juveniles. Acetaldehyde had direct contact killing, fumigation, and attraction activities; dimethyl disulfide had direct contact killing and attraction activities; ethylbenzene had an attraction activity; and 2-butanone had a repellent activity. Only acetaldehyde had a fumigant activity to inhibit egg hatching. Combining this fumigant activity against eggs and juveniles could be an effective strategy to control the different developmental stages of M. incognita. The combination of direct contact and attraction activities could also establish trapping and killing strategies against root-knot nematodes. Considering all nematicidal modes or strategies, we could use V. dokdonensis MCCC 1A00493 to set up an integrated strategy to control root-knot nematodes.