A High-Throughput Microtiter-Based Fungicide Sensitivity Assay for Oomycetes Using Z'-Factor Statistic

Methods for Fungicide Efficacy Screenings: Multiwell Testing Procedures for the Oomycetes Phytophthora infestans and Pythium ultimum

Oomycetes-borne diseases represent a serious problem for agriculture sustainability due to the high use of chemical products employed for their control. In recent years, increasing concerns on side effects associated with fungicide utilization have led to the reduction of the permissible modes of action, with the remaining ones continuously threatened by the increase of resistant strains in the pathogen populations. In this context, it is mandatory to develop new generation fungicides characterized by high specificity towards the target species and low environmental impact to guarantee the sustainability, productivity, and quality of food production. Fungicide discovery is a lengthy and costly process, and despite these urgent needs, poor description and formalization of high-throughput methodologies for screening the efficacy of active compounds are commonly reported for these kinds of organisms. In this study, a comprehensive picture of two high-throughput practices for efficient fungicide screening against plant-pathogenic oomycetes has been provided. Different protocols using multiwell plates were validated on approved crop protection products using Phytophthora infestans and Pythium ultimum as the model species. In addition, detailed statistical inputs useful for the analysis of data related to the efficacy of screenings are included.

Development of a microplate absorbance assay for assessing fungicide sensitivity of filamentous fungi and comparison to an amended agar assay

Assessment of the sensitivity of non-sporulating fungi to fungicides through amended-media assays is labor intensive. As an alternative, we developed an absorbance assay using 96-well microplates to assess the sensitivity of Clarireedia jacksonii, a non-sporulating fungus, to the fungicide propiconazole based on the change in absorbance corresponding to fungal growth. This microplate assay can allow for the assessment of multiple isolates of C. jacksonii at different concentrations of a fungicide with many technical replications in a single plate. Three methods for inoculating microplate wells were compared. The "microplug" method was the simplest to perform, requiring only a micropipette with 1 ml tips. EC₅₀ values from this microplate assay were compared to those of a traditional amended agar assay using 30 isolates of C. jacksonii with varying sensitivity to propiconazole. The non-transformed relationship between the two assays was low but weakly significant (R² = 0.137, p = 0.037). However, correlation of log₁₀ transformed EC₅₀ values from both assays revealed a stronger and highly significant relationship (R² = 0.56, p < 0.001). Additionally, the microplate assay appears to be more sensitive in detecting resistance (EC₅₀ > 0.1 μg/ml), and revealed five of the assessed isolates to be resistant to propiconazole that were not found as such with the amended agar assay. These results imply that EC₅₀ results from the microplate assay were not exactly equivalent to the amended agar assay for estimating EC₅₀ values, but it may be useful in assigning or confirming general sensitivity classifications.

Phytophthora sojae Pathotype Distribution and Fungicide Sensitivity in Michigan

Identifying the pathotype structure of a Phytophthora sojae population is crucial for the effective management of Phytophthora stem and root rot of soybean (PRR). P. sojae has been successfully managed with major resistance genes, partial resistance, and fungicide seed treatments. However, prolonged use of resistance genes or fungicides can cause pathogen populations to adapt over time, rendering resistance genes or fungicides ineffective. A statewide survey was conducted to characterize this pathotype structure and fungicide sensitivity of P. sojae within Michigan. Soil samples were collected from 69 fields with a history of PRR and fields having consistent plant stand establishment issues. Eighty-three isolates of P. sojae were obtained, and hypocotyl inoculations were performed on 14 differential soybean cultivars, all of which carry a single Rps gene or no resistance gene. The survey identified a loss of effectiveness of Rps genes 1b, 1k, 3b, and 6, compared with a previous survey conducted in Michigan from 1993 to 1997. Three effective resistance genes were identified for P. sojae management in Michigan; Rps 3a, 3c, and 4. Additionally, the effective concentration of common seed treatment fungicides to inhibit mycelial growth by 50% (EC50) was determined. No P. sojae isolates were insensitive to the tested chemistries with mean EC50 values of 2.60 × 10-2 μg/ml for ethaboxam, 3.03 × 10-2 μg/ml for mefenoxam, 2.88 × 10-4 μg/ml for oxathiapiprolin, and 5.08 × 10-2 μg/ml for pyraclostrobin. Results suggest that while there has been a significant shift in Rps gene effectiveness, seed treatments are still effective for early season management of this disease.

Influence of Soybean Tissue and Oomicide Seed Treatments on Oomycete Isolation

Soybean seedlings are vulnerable to different oomycete pathogens. Seed treatments containing the two antioomycete (oomicide) chemicals, metalaxyl-M (mefenoxam) and ethaboxam, are used for protection against oomycete pathogens. This study aimed to evaluate the influence of these two oomicides on isolation probability of oomycetes from soybean taproot or lateral root sections. Soybean plants were collected between the first and third trifoliate growth stages from five Midwest field locations in 2016 and four of the same fields in 2017. Oomycetes were isolated from taproot and lateral root. In 2016, 369 isolation attempts were completed, resulting in 121 isolates from the taproot and 154 isolates from the lateral root. In 2017, 468 isolation attempts were completed, with 44 isolates from the taproot and 120 isolates from the lateral roots. In three of nine site-years, the probability of isolating an oomycete from a taproot or lateral root section was significantly different. Seed treatments containing a mixture of ethaboxam and metalaxyl significantly reduced the probability of oomycete isolation from lateral roots in Illinois in 2016 and 2017, but not in other locations, which may have been related to the heavy soil type (clay loam). Among the 439 isolates collected from the two years sampled, 24 oomycete species were identified, and community compositions differed depending on location and year. The five most abundant species were Pythium sylvaticum (28.9%), P. heterothallicum (14.3%), P. ultimum var. ultimum (11.8%), P. attrantheridium (7.9%), and P. irregulare (6.6%), which accounted for 61.7% of the isolates collected. Oomicide sensitivity to ethaboxam and mefenoxam was assessed for >300 isolates. There were large differences in ethaboxam sensitivity among oomycete species, with effective concentrations to reduce optical density at 600 nm by 50% compared with the nonamended control (EC50 values) ranging from <0.01 to >100 μg/ml and a median of 0.65 μg/ml. Isolates with insensitivity to ethaboxam (>12 μg/ml) belonged to the species P. torulosum and P. rostratifingens but were sensitive to mefenoxam. Oomicide sensitivity to mefenoxam ranged from <0.01 to 0.62 μg/ml with a median of 0.03 μg/ml. The mean EC50 value of the five most abundant species to ethaboxam ranged from 0.35 to 0.97 μg/ml of ethaboxam and from 0.02 to 0.04 μg/ml of mefenoxam. No shift in sensitivity to mefenoxam or ethaboxam was observed as a result of soybean seed treatment or year relative to the nontreated seed controls. In summary, this study contributed to the understanding of the composition of oomycete populations from different soybean root tissues, locations, years, and seed treatments. Finally, seed treatments containing mefenoxam or metalaxyl plus ethaboxam can be effective in reducing the probability of oomycete isolation from soybean roots.

Convergent Evolution of C239S Mutation in Pythium spp. β-Tubulin Coincides with Inherent Insensitivity to Ethaboxam and Implications for Other Peronosporalean Oomycetes

Ethaboxam is a benzamide antioomycete chemical (oomicide) used in corn and soybean seed treatments. Benzamides are hypothesized to bind to β-tubulin, thus disrupting microtubule assembly. Recently, there have been reports of corn- and soybean-associated oomycetes that are insensitive to ethaboxam despite never having been exposed. Here, we investigate the evolutionary history and molecular mechanism of ethaboxam insensitivity. We tested the sensitivity of 194 isolates representing 83 species across four oomycete genera in the Peronosporalean lineage that were never exposed to ethaboxam. In all, 84% of isolates were sensitive to ethaboxam (effective concentration to reduce optical density at 600 nm by 50% when compared with the nonamended control [EC₅₀] < 5 μg ml^-1), whereas 16% were insensitive (EC₅₀ > 11 μg ml^-1). Of the insensitive isolates, two different transversion mutations were present in the 239th codon in β-tubulin within three monophyletic groups of Pythium spp. The transversion mutations lead to the same amino acid change from an ancestral cysteine to serine (C239S), which coincides with ethaboxam insensitivity. In a treated soybean seed virulence assay, disease severity was not reduced on ethaboxam-treated seed for an isolate of Pythium aphanidermatum containing a S239 but was reduced for an isolate of P. irregulare containing a C239. We queried publicly available β-tubulin sequences from other oomycetes in the Peronosporalean lineage to search for C239S mutations from other species not represented in our collection. This search resulted in other taxa that were either homozygous or heterozygous for C239S, including all available species within the genus Peronospora. Evidence presented herein supports the hypothesis that the convergent evolution of C239S within Peronosporalean oomycetes occurred without selection from ethaboxam yet confers insensitivity. We propose several evolutionary hypotheses for the repeated evolution of the C239S mutation.