Ecological Dynamics and Microbial Treatments against Oomycete Plant Pathogens

In this review, we explore how ecological concepts may help assist with applying microbial biocontrol agents to oomycete pathogens. Oomycetes cause a variety of agricultural diseases, including potato late blight, apple replant diseases, and downy mildew of grapevine, which also can lead to significant economic damage in their respective crops. The use of microbial biocontrol agents is increasingly gaining interest due to pressure from governments and society to reduce chemical plant protection products. The success of a biocontrol agent is dependent on many ecological processes, including the establishment on the host, persistence in the environment, and expression of traits that may be dependent on the microbiome. This review examines recent literature and trends in research that incorporate ecological aspects, especially microbiome, host, and environmental interactions, into biological control development and applications. We explore ecological factors that may influence microbial biocontrol agents’ efficacy and discuss key research avenues forward.

Mechanisms of Action of Microbial Biocontrol Agents against Botrytis cinerea

Botrytis cinerea is a phytopathogenic fungus responsible for economic losses from USD 10 to 100 billion worldwide. It affects more than 1400 plant species, thus becoming one of the main threats to the agriculture systems. The application of fungicides has for years been an efficient way to control this disease. However, fungicides have negative environmental consequences that have changed popular opinion and clarified the need for more sustainable solutions. Biopesticides are products formulated based on microorganisms (bacteria or fungi) with antifungal activity through various mechanisms. This review gathers the most important mechanisms of antifungal activities and the microorganisms that possess them. Among the different modes of action, there are included the production of diffusible molecules, both antimicrobial molecules and siderophores; production of volatile organic compounds; production of hydrolytic enzymes; and other mechanisms, such as the competition and induction of systemic resistance, triggering an interaction at different levels and inhibition based on complex systems for the production of molecules and regulation of crop biology. Such a variety of mechanisms results in a powerful weapon against B. cinerea; some of them have been tested and are already used in the agricultural production with satisfactory results.

Winter rye cover cropping changes squash (Cucurbita pepo) phyllosphere microbiota and reduces Pseudomonas syringae symptoms

Cover cropping is a soil conservation practice that may reduce the impacts of the economically important pathogen Pseudomonas syringae on crops including squash (Cucurbita pepo). To date, no studies have directly quantified the effect of rye cover crops on P. syringae populations, nor on the bacterial community of squash leaves. In this work, we tested the hypothesis that the protective effects of cover cropping on squash may be mediated by cover cropping effects on the plant’s microbiota that in turn protects against P. syringae. Using combined 16S sequencing and culture-based approaches, we showed that rye cover cropping protects squash against P. syringae, by decreasing pathogen population size on squash leaves and increasing fruit health and marketability at harvest. We also found evidence of a strong effect of rye cover crops on bacterial communities of the squash phyllosphere. Those findings were more striking early in the growing season. Finally, we identified numerous phyllosphere bacteria belonging to the genera Sphingomonas, Methylobacterium and Pseudomonas that were promoted by rye cover crops. Overall, our findings suggest cover cropping is effective for the sustainable management of P. syringae on squash and may provide a reservoir of potential microbial biocontrol agents colonizing the phyllosphere.

Bacillus-based nano-bioformulations for phytopathogens and insect–pest management

Background Recent concerns linked with the application of chemical pesticides and the increasing necessity of low inputs sustainable agriculture have put the use of microbial biocontrol agents and bio-pesticides to the forefront for their application against plant pathogens and insect–pest management. Results This review tended to scrutinize the prospects of microbial biocontrol agents and microbes-based nano-formulations against plant diseases and for pest management with emphasis on bacteria-based nanoparticles, especially derived from Bacillus species. It also tended to discuss the probable mechanism of action and effect on plant growth along with its prospects in a brief manner. Conclusion The use of microbial biocontrol agents offers effective, eco-friendly, and long-lasting management of plant diseases. The employment of nanotechnology in the field of biopesticides has emerged as a promising solution. Nano-biopesticides in the form of biologically derived active pesticides or compounds integrated as nanoparticles and integrated into a suitable polymer have application in insect–pest management.

Winter rye cover cropping changes squash (Cucurbita pepo) phyllosphere microbiota and reduces Pseudomonas syringae symptoms

Cover cropping is a soil conservation practice that may reduce the impacts of the economically important pathogen Pseudomonas syringae on crops including squash (Cucurbita pepo). To date, no studies have directly quantified the effect of rye cover crops on P. syringae populations, nor on the bacterial community of squash leaves. In this work, we tested the hypothesis that the protective effects of cover cropping on squash may be mediated by cover cropping effects on the plant’s microbiota that in turn protects against P. syringae. Using combined 16S sequencing and culture-based approaches, we showed that rye cover cropping protects squash against P. syringae, by decreasing pathogen population size on squash leaves and increasing fruit health and marketability at harvest. We also found evidence of a strong effect of rye cover crops on bacterial communities of the squash phyllosphere. Those findings were more striking early in the growing season. Finally, we identified numerous phyllosphere bacteria belonging to the genera Sphingomonas, Methylobacterium and Pseudomonas that were promoted by rye cover crops. Overall, our findings suggest cover cropping is effective for the sustainable management of P. syringae on squash and may provide a reservoir of potential microbial biocontrol agents colonizing the phyllosphere.

Production of Candicidin Isomers Is Essential for Biocontrol of Cucumber Rhizoctonia rot By Streptomyces albidoflavus W68

Diseases caused by soil-borne fungal pathogens result in significant crop yield losses and quality reduction. Streptomyces albidoflavus strain W68 is effective in controlling several soil-borne fungal diseases. To identify antifungal substances critical for biocontrol activity of W68, the genome of W68 was sequenced and a linear chromosome of 6.80 Mb was assembled. A total of 21 secondary metabolite biosynthesis gene clusters (BGCs), accounting for 12.27% of the genome, were identified. Core gene deletion mutants for each of all 8 BGCs for non-ribosomal peptide synthetases and polyketide synthases, were created. Among them, only the mutant lacking gene ctg1-5755 (the gene was renamed as fscDW68) in BGC 19, which shares 100% sequence similarity to the BGC for candicidin synthesis, showed obvious reduction in antifungal activity. A pot experiment revealed that biocontrol effects of the ΔfscDW68 mutant in Rhizoctonia rot of cucumber were also significantly compromised relative to W68. LC-MS analysis revealed that W68 but not ΔfscDW68 can produce candicidin isomers, indicating that the production of candicidin isomers is key for antifungal activity and biocontrol activity of S. albidoflavus W68. Importance This study provides the first report that candicidin-like secondary metabolites produced by microbial cells in natural soil environment can effectively control soil-borne fungal diseases, revealing a novel mechanism of microbial biocontrol agents. We demonstrated that the main antifungal activity and biocontrol activity of Streptomyces albidoflavus strain W68 is attributed to the production of candicidin isomers, suggesting gene clusters for candicidin-like compound biosynthesis might be used as molecular markers to screen and breed microbial strains for biocontrol agent development.

Construction and Selection of an Entomopathogenic Fungal Library From Soil Samples for Controlling Spodoptera litura

Chemical pesticides have been used for pest control for many decades, but they cause serious problems, including insecticide resistance, secondary pest resurgence, and negative environmental impacts. Therefore, sustainable alternatives to chemical pesticides are necessary for pest control. Entomopathogenic fungi (EPF) are natural epizootic pathogens of insects, and some of them have been used as microbial biocontrol agents. Herein, we attempted to construct an entomopathogenic fungal library (EFLib) via the “Tenebrio molitor pathogenicity-based fungal collection method (TmPC)” to select EPF for control of the serious agricultural pest Spodoptera litura. A total of 172 soil samples were collected in northern and central Taiwan for the EFLib construction. The isolation efficiency of TmPC was 64.02%. The EFLib consisted of 101 isolates and was designated as the National Chung Hsing University (NCHU) EFLib. Among these isolates, 26 showed high virulence (mortality = 100%) to T. molitor larvae. Based on the results of molecular identification, the highly virulent isolates belonged to seven genera, including Beauveria, Clonostachys, Fusarium, Cordyceps, Penicillium, Purpureocillium, and Metarhizium. To evaluate the potential of these isolates for Spodoptera litura control, 12 isolates were selected for pathogenicity screening against S. litura larvae. A total of six EPF isolates belonging to the genera Beauveria and Metarhizium showed rapid eradication of the S. litura larvae. To rank the potential of these fungal strains for pest management, the six isolates were subjected to thermotolerance and conidial production assays, and a novel effective conidia number (ECN) formula was applied. The results indicated that the ECN index of Beauveria australis (NCHU-113) was much higher than that of Metarhizium isolates. However, among the Metarhizium isolates, NCHU-95 showed the highest ECN index. Altogether, NCHU-69 and NCHU-113 should be further tested in field trials. To our knowledge, this is the first attempt to integrate pathogenicity or virulence and ECN data into EPF screening and ranking, providing a baseline for mass selection of potential EPF strains for further applications.