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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.

Fusarium head blight (FHB) is a devastating disease of wheat. Worldwide, Fusarium graminearum is the most dominant FHB-causing species. Its most common toxin, deoxynivalenol (DON), impairs food and feed safety and has an enormous economic impact. Agronomic factors such as crop rotation, soil management and host genotype strongly influence the occurrence of F. graminearum. Infected plant debris from previous crops, on which perithecia and ascospores develop, represent the main source for FHB, and hence, improved cropping systems aim to reduce this inoculum to decrease the infection risk. The best measure to evaluate the disease pressure is spore traps that detect deposited airborne ascospores. Commercial spore traps are expensive and require power sources, thus, they are not suitable for investigations in field experiments with different treatments. In consequence, we developed spore traps containing a Petri dish with Fusarium-selective agar, protected by aluminum dishes and attached on a wooden board. We compared the data of our low-cost trap with those of a commercial high-throughput jet sampler and obtained equivalent results. In field experiments to compare cropping systems, we observed a high correlation between the DON content in wheat grains and the number of colonies from deposited spores. Our spore trap proved to be a highly valuable tool to not only study FHB epidemiology but also to identify innovative cropping systems with a lower risk for FHB and DON contamination.

Suspensions or solutions with 1% of Chinese galls (Galla chinensis, GC) or 1% of tannic acid (TA), inhibited germination of conidia or mycelium growth of Fusarium graminearum (FG) by 98%–100% or by 75%–80%, respectively, whereas dried bark from buckthorn (Frangula alnus, FA) showed no effect at this concentration. In climate chamber experiments where the wheat variety “Apogee” was artificially inoculated with FG and F. crookwellense (FCr) and treated with 5% suspensions of TA, GC and FA, the deoxynivalenol (DON) content in grains was reduced by 81%, 67% and 33%, respectively. In field experiments with two commercial wheat varieties and artificial or semi-natural inoculations, mean DON reductions of 66% (TA) and 58% (FA), respectively, were obtained. Antifungal toxicity can explain the high efficacies of TA and GC but not those of FA. The Fusarium head blight (FHB) and mycotoxin reducing effect of FA is probably due to elicitation of resistance in wheat plants. With semi-natural inoculation, a single FA application in the first half of the flowering period performed best. However, we assume that applications of FA at the end of ear emergence and a treatment, triggered by an infection period, with TA or GC during flowering, might perform better than synthetic fungicides.

Potato late blight (PLB) caused by Phytophthora infestans (Pi) is the most harmful disease in potato production worldwide. In organic farming, copper is used despite its persistence in soil and toxicity to soil organisms. To replace copper, suspensions of powders from three promising botanicals, including bark of buckthorn (Frangula alnus, FA), roots of medicinal rhubarb (Rheum palmatum) and galls of the nutgall tree (Galla chinensis), were tested in multi-year field experiments. The current study shows for the first time that botanicals could replace copper under field conditions and best PLB reduction on leaves was achieved with FA, reaching a level close to that of 2 to 3 kg copper per hectare and year. Better results than with copper were achieved with Phosfik® (Ph), a phosphonate-based product. For both FA and Ph, the mode of action is based on induced resistance, for Ph also on direct fungicidal effects. A disadvantage of Ph is the accumulation of residues in potato tubers. Nevertheless, two to three applications with 2 to 3 L/ha of Ph would be feasible to not exceed a minimal risk level (MLR) of 20 mg/kg of phosphorous acid as proposed by the European Food Safety Authority. Due to an excellent environmental profile and a complex mode of action counteracting Pi resistance, phosphonate-based products would be most suitable for sustainable PLB management in integrated pest management (IPM) programmes.

The authors wish to correct Figures 3–5 in this paper [1]. In all three figures, the y axis stated as a unit “milligram/kg” (mg/kg) instead of “microgram/kg” (µg/kg).

To assess the occurrence of Fusarium toxins in wheat in Switzerland, an eight-year survey was conducted by analysing a total of 686 harvest samples from growers using LC-MS/MS. Between 2007 and 2010, 527 samples were obtained from 17 cantons. Between 2011 and 2014, 159 samples were collected from the canton Berne. The most frequent toxins detected were deoxynivalenol (DON), zearalenone (ZEA) and nivalenol (NIV). The overall mean DON content in all samples was 607 µg/kg, and 11% exceeded the European limit for unprocessed cereals for foodstuffs (1250 µg/kg). For ZEA (mean 39 µg/kg), 7% exceeded the respective limit (100 µg/kg), and the mean content of NIV (no limit established) was 15 µg/kg. Between the years, the ratio of mycotoxin-contaminated samples ranged between 52% and 98% for DON, 9% and 43% for ZEA and 0% and 49% for NIV. The yearly mean contents varied substantially between 68 and 1310 µg/kg for DON, 5 and 56 µg/kg for ZEA and 6 and 29 µg/kg for NIV. The geographic origin showed a significant effect on DON and ZEA contamination, but was inconsistent between the years. This study has shown that the majority of Swiss-produced wheat is, in terms of Fusarium toxins, fit for human consumption and feed purposes. Nevertheless, depending on the year, high toxin contents can be expected, an issue that growers, cereal collection centres and the food industry have to deal with to ensure food and feed safety.

Abstract  In order to replace copper fungicides in organic potato production, 53 copper-free preparations (CFPs) based on natural compounds, including plant extracts and microorganisms, and five copper preparations were evaluated for their potential to control Phytophthora infestans, the pathogen that causes late blight of potatoes. In in vitro assays, 30% of the CFPs inhibited indirect germination of sporangia, 26% mycelial growth and in growth chamber experiments, 21% efficiently reduced foliar blight of tomato plants. In micro-plot field trials with applications twice a week, the copper preparations were the most effective and reduced foliar blight by 99%. Of the CFPs tested, Oekofluid P, Mycosin and other sulphuric clays, and C-2000 reduced late blight the most, from 63% to 37%. In small-plot trials in 2001, 2002 and 2004, 27 CFPs with different formulations and four copper preparations were examined. In 2004, copper preparations at full and reduced rates and sulphuric clays were applied either weekly or according to the decision support system Bio-PhytoPRE. With Bio-PhytoPRE, copper preparations reduced foliar blight of potatoes by 23–77% and increased tuber yield by 2–28%, depending on the copper rate applied and year. With CFPs, maximal efficacy was 17% and no effect on tuber yield was observed. In vitro and in vivo trials showed that the rainfastness and the persistence of CFPs was low compared with copper preparations. This indicates that the failure of CFPs under field conditions is probably due to a lack of stability under prevailing environmental conditions and not to a lack of efficacy. Until stable formulations for CFPs are developed, an optimised and restricted use of copper fungicides using a decision support system could help to control late blight in organic potato production and to reduce copper input into the environment. [ABSTRACT FROM AUTHOR]