Wheat Production Alters Soil Microbial Profiles and Enhances Beneficial Microbes in Double-Cropping Soybean

Plant-parasitic nematodes represent a substantial constraint on global food security by reducing the yield potential of all major crops. The soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is widely distributed across important soybean production areas of the U.S., being the major soybean yield-limiting factor, especially in the Midwestern U.S. Double cropped (DC) soybean is commonly planted following winter wheat. We previously reported double-cropping soybean fields with reduced SCN counts compared to fallow at both R1 growth stage (beginning of flowering) (−31.8%) and after soybean harvest (−32.7%). To test if higher counts of beneficial and SCN antagonistic microorganisms could be correlated with the suppression of SCN in fields previously planted with wheat, three field locations with noted SCN suppression were selected for a metagenomics study. Ten subplots were selected (5 wheat and 5 fallow pre-soybean) from each location. A total of 90 soil samples were selected: 3 fields ×2 treatments × 3 timepoints × 5 replications. Three DNA markers targeted distinct microbial groups: bacteria (16S V4-V5), fungi (ITS2), and Fusarium (tef1). Amplicons were sequenced using an Illumina MiSeq platform (300 bp paired-end). Sequencing datasets were processed in R using the DADA2 pipeline. Fungal populations were affected by location in all sampling periods and differed significantly between DC and fallow plots at soybean planting and after harvest (P < 0.001). Several enriched fungal and bacterial taxa in wheat plots, including Mortierella, Exophiala, Conocybe, Rhizobacter spp., and others, were previously reported to parasitize SCN and other plant-parasitic nematodes, suggesting a potential role of beneficial microbes in suppression of SCN in soybean fields double-cropped with wheat.

Biosolid-Amended Soil Enhances Defense Responses in Tomato Based on Metagenomic Profile and Expression of Pathogenesis-Related Genes

Biosolid application is an effective strategy, alternative to synthetic chemicals, for enhancing plant growth and performance and improving soil properties. In previous research, biosolid application has shown promising results with respect to tomato resistance against Fusarium oxysporum f. sp. radicis-lycopersici (Forl). Herein, we aimed at elucidating the effect of biosolid application on the plant–microbiome response mechanisms for tomato resistance against Forl at a molecular level. More specifically, plant–microbiome interactions in the presence of biosolid application and the biocontrol mechanism against Forl in tomato were investigated. We examined whether biosolids application in vitro could act as an inhibitor of growth and sporulation of Forl. The effect of biosolid application on the biocontrol of Forl was investigated based on the enhanced plant resistance, measured as expression of pathogen-response genes, and pathogen suppression in the context of soil microbiome diversity, abundance, and predicted functions. The expression of the pathogen-response genes was variably induced in tomato plants in different time points between 12 and 72 h post inoculation in the biosolid-enriched treatments, in the presence or absence of pathogens, indicating activation of defense responses in the plant. This further suggests that biosolid application resulted in a successful priming of tomato plants inducing resistance mechanisms against Forl. Our results have also demonstrated that biosolid application alters microbial diversity and the predicted soil functioning, along with the relative abundance of specific phyla and classes, as a proxy for disease suppression. Overall, the use of biosolid as a sustainable soil amendment had positive effects not only on plant health and protection, but also on growth of non-pathogenic antagonistic microorganisms against Forl in the tomato rhizosphere and thus, on plant–soil microbiome interactions, toward biocontrol of Forl.

Effect of cultivation media and temperature on metabolite profiles of three nematicidal Bacillus species

Summary Globally, root-knot nematode (RKN) infestations cause great financial losses. Although agrochemicals are used to manage these pests, there is increased interest in using biocontrol agents based on natural antagonistic microorganisms, such as Bacillus. These nematicidal bacteria demonstrate antagonism towards RKN through different modes of action, including specialised metabolite production. The aim of this study was to compare metabolite profiles of nematicidal Bacillus species and assess the influence of cultivation conditions on these profiles. Two hyphenated metabolomics platforms, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QTOF-MS), were employed to profile and compare metabolite features produced during the cultivation of three nematicidal Bacillus species (Bacillus firmus, B. cereus and B. soli) in complex Luria-Bertani broth (LB) and a simpler minimal broth (MB), at three different temperatures (25, 30 and 37°C). Cultivation in complex LB as opposed to simpler MB resulted in the production of more statistically significant metabolite features. Selected temperatures in this study did not have a significant influence on metabolite profiles. Moreover, media-specific influences outweighed temperature-specific influences on metabolite profiles. Results from this study are a valuable first step in establishing suitable cultivation conditions for the production of Bacillus metabolites of interest.

Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition

The rhizosphere microbiome forms a first line of defense against soilborne pathogens. To date, most microbiome enhancement strategies have relied on bioaugmentation with antagonistic microorganisms that directly inhibit pathogens. Previous studies have shown that some root-associated bacteria are able to facilitate pathogen growth. We therefore hypothesized that inhibiting such pathogen helpers may help reduce pathogen densities. We examined tripartite interactions between a model pathogen, Ralstonia solanacearum, two model helper strains and a collection of 46 bacterial isolates recovered from the tomato rhizosphere. This system allowed us to examine the importance of direct (effects of rhizobacteria on pathogen growth) and indirect (effects of rhizobacteria on helper growth) pathways affecting pathogen growth. We found that the interaction between rhizosphere isolates and the helper strains was the major determinant of pathogen suppression both in vitro and in vivo. We therefore propose that controlling microbiome composition to prevent the growth of pathogen helpers may become part of sustainable strategies for pathogen control.

Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes—A Review

The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a “soil environment” that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs.

Proposal for Integrated Management of Verticillium Wilt Disease in Avocado Cultivar Hass Crops

The area planted with avocado crops in Colombia has been growing rapidly in recent years, especially for export varieties such as Hass. The increase in planted area coincided with increased phytosanitary problems, where pathogens such as fungi of the genus Verticillium spp. are becoming of economic importance. The objective of this study was to evaluate different control strategies for avocado wilt disease caused by Verticillium spp., under in vitro, net house, and field conditions. Strategies tested included fungicides (benomyl, azoxystrobin, captan, and carbendazim), beneficial and antagonistic microorganisms (Trichoderma sp., and Rhizoglomus fasciculatum), and physical and cultural practices such as solarization, drainage and removal of diseased tissues. Treatments T7fi (pruning-solarization-Trichoderma-mycorrhiza-sucrose-organic matter-drainage) and T8fi (fungicide-pruning-solarization-Trichoderma-mycorrhiza-sucrose-organic matter-drainage), showed the greatest reduction in the area under disease progress curve and Verticillium dahliae inoculum in soil and plant tissues under field conditions. Fruit with extra quality increased 120.8% with T7fi and 108% with T8fi, compared to the control with diseased trees. The highest costs were identified for T7fi and T8fi; however, these treatments also showed the best cost/benefit relationship. Integrated approaches as in T7fi and T8fi showed the best results for Verticillium wilt control. As no fungicides of chemical synthesis are included in T7fi (pruning-solarisation-Trichoderma-mycorrhiza-sucrose-organic matter-drainage), it should be preferred to T8fi, which does include them, to avoid their negative impacts on avocado production.

Analysis of Stored Wheat Grain-Associated Microbiota Reveals Biocontrol Activity among Microorganisms against Mycotoxigenic Fungi

Wheat grains are colonized by complex microbial communities that have the potential to affect seed quality and susceptibility to disease. Some of the beneficial microbes in these communities have been shown to protect plants against pathogens through antagonism. We evaluated the role of the microbiome in seed health: in particular, against mycotoxin-producing fungi. Amplicon sequencing was used to characterize the seed microbiome and determine if epiphytes and endophytes differ in their fungal and bacterial diversity and community composition. We then isolated culturable fungal and bacterial species and evaluated their antagonistic activity against mycotoxigenic fungi. The most prevalent taxa were found to be shared between the epiphytic and endophytic microbiota of stored wheat seeds. Among the isolated bacteria, Bacillus strains exhibited strong antagonistic properties against fungal pathogens with noteworthy fungal load reduction in wheat grain samples of up to a 3.59 log10 CFU/g compared to untreated controls. We also found that a strain of the yeast, Rhodotorula glutinis, isolated from wheat grains, degrades and/or metabolizes aflatoxin B1, one of the most dangerous mycotoxins that negatively affects physiological processes in animals and humans. The mycotoxin level in grain samples was significantly reduced up to 65% in the presence of the yeast strain, compared to the untreated control. Our study demonstrates that stored wheat grains are a rich source of bacterial and yeast antagonists with strong inhibitory and biodegradation potential against mycotoxigenic fungi and the mycotoxins they produce, respectively. Utilization of these antagonistic microorganisms may help reduce fungal and mycotoxin contamination, and potentially replace traditionally used synthetic chemicals.

Antagonism of Bacillus thuringiensis to phytopathogenic micromicetes as pathogens of apple trees

Antagonistic microorganisms, producing bactericidal and fungicidal substances, spread in space and occupy various ecological niches. Antagonistic action of microorganisms can be combined with a number of other properties that can be used by humans for their own purposes. Microorganisms — agents of biological products often have a multifunctional effect on the components of the agroecosystem, which under the influence of various environmental factors could have positive and negative consequences. The aim of the study was to study the effect of new highly active entomopathogenic strains of Bacillus thuringiensis on non-target objects — components of the biocenosis of the apple orchard. When developing technologies for biocontrol of the number of apple trees pests using B. thuringiensis revealed an additional positive protective effect — reducing the number of pathogens of fungal diseases on the leaf surface. Treatment of apple leaves with a liquid culture of strain B. thuringiensis 0376 after 72 hours of application reduced the number of scab of Fusicladium dendriticum by 7 times, and the pathogen of monolisis of Monilia fructigena — 9 times. Strain B. thuringiensis 0371 showed the highest level of antagonism, because in vitro completely inhibited the growth and development of micromycetes on the surface of the nutrient medium. On the leaf surface, the application of culture strain 0371 reduced the number of Fusicladium dendriticum by 92%, and Monilia fructigena — by 86% after 72 hours of treatment. In a field experiment when treating apple trees with a culture of this strain, scab development decreased by 7.1%. Strain B. thuringiensis 787 did not show antagonism against phytopathogenicmicromycetes during co-cultivation on nutrient medium, which may be explained by its inability to produce water-soluble exotoxin, in contrast to strains of B. thuringiensis, which are antagonists of scab and apple monolisis. Strain B. thuringiensis 0371 requires further research and development of its formulations, because it is promising for the creation of a complex biological product with insect-fungicidal properties for use in ecological and agriculture friendly technologies.

Effect of Aureobasidium Pullulans S-2 on the Postharvest Microbiome of Tomato During Storage

Background: Biological control of fruit postharvest diseases by antagonistic microorganisms has been considered an effective alternative to chemical fungicides. The influence of microbial antagonists on fruit-associated microbiome will provide a new perspective for in-depth study of the antagonistic mechanism. In this study, the biocontrol efficacy of A. pullulans S-2 against postharvest diseases of tomatoes was investigated. Meanwhile, the fungal and bacterial microbiota on tomato surfaces were examined by high-throughput sequencing. Results: A. pullulans S-2 can significantly inhibit the decay rate, maintain fruit firmness and reduce weight loss of tomatoes. In addition, the treatment group can maintain higher titratable acid, ascorbic acid and lycopene than the control group. After using A. pullulans S-2, more dramatic changes were observed in fungal diversity than bacterial in the microbiota. Aureobasidium was significantly enriched in the treatment group, while Cladosporium, Mycosphaerella, Alternaria and Penicillium were deficient compared with the control group. Pantoea, Brevibacterium, Brachybacterium, Serratia, Glutamicibacter and Pseudomonas also had significant differences between the two groups.Conclusions: This study demonstrated that the application of A. pullulans S-2 resulted in alterations in the bacterial and fungal community and that could inhibit pathogens and decrease fruit disease incidence. It provides new insights into the dynamics of the tomato's surface microbiome after microbial antagonist treatment.