Oomycete Species Associated with Soybean Seedlings in North America-Part II: Diversity and Ecology in Relation to Environmental and Edaphic Factors

Characterizing the Diversity of Oomycetes Associated with Diseased Cotton Seedlings in Alabama

Many oomycete species are associated with the seedlings of crops, including upland cotton (Gossypium hirsutum L.), which leads to annual threats. The diversity of oomycete species in Alabama needs to be better understood since the last survey of oomycetes associated with cotton in Alabama was 20 years ago-before significant updates to taxonomy and improvements in identification of oomycetes using molecular tools. Our current study aimed to identify oomycetes associated with Alabama cotton seedlings, correlate diversity with soil edaphic factors, and assess virulence toward cotton seed. Thirty symptomatic cotton seedlings were collected independently from 25 fields in 2021 and 2022 2 to 4 weeks after planting. Oomycetes were isolated by plating root sections onto a semiselective medium. The internal transcribed spacer (ITS) region was sequenced to identify the resulting isolates. A seed virulence assay was conducted in vitro to verify pathogenicity, and 347 oomycete isolates were obtained representing 36 species. Northern Alabama soils had the richest oomycete communities and a greater silt and clay concentration than sandier soils in the central and southern coastal plains. Globisporangium irregulare and Phytophthora nicotianae were consistently recovered from cotton roots in both years. Globisporangium irregulare was pathogenic and recovered from all Alabama regions, whereas P. nicotianae was pathogenic but recovered primarily in areas with lower sand content in northern Alabama. Many oomycete species have not been previously reported in Alabama or the southeastern United States. Altogether, this knowledge will help facilitate effective management strategies for cotton seedling diseases caused by oomycetes in Alabama and the United States.

Dilution of specialist pathogens drives productivity benefits from diversity in plant mixtures

Productivity benefits from diversity can arise when compatible pathogen hosts are buffered by unrelated neighbors, diluting pathogen impacts. However, the generality of pathogen dilution has been controversial and rarely tested within biodiversity manipulations. Here, we test whether soil pathogen dilution generates diversity- productivity relationships using a field biodiversity-manipulation experiment, greenhouse assays, and feedback modeling. We find that the accumulation of specialist pathogens in monocultures decreases host plant yields and that pathogen dilution predicts plant productivity gains derived from diversity. Pathogen specialization predicts the strength of the negative feedback between plant species in greenhouse assays. These feedbacks significantly predict the overyielding measured in the field the following year. This relationship strengthens when accounting for the expected dilution of pathogens in mixtures. Using a feedback model, we corroborate that pathogen dilution drives overyielding. Combined empirical and theoretical evidence indicate that specialist pathogen dilution generates overyielding and suggests that the risk of losing productivity benefits from diversity may be highest where environmental change decouples plant-microbe interactions.

Effect of Infection Timing by Four Pythium spp. on Soybean Damping-Off Symptoms with and Without Cold Stress

Pythium spp. cause damping-off of soybean, especially when soil conditions at or shortly after planting are cool and wet. Soybean planting dates continue to shift to earlier dates, so germinating seed and seedlings are exposed to periods of cold stress at a time which favors infection by Pythium, and seedling disease occurs. The objective of this study was to assess infection timing and cold stress on soybean seedling disease severity caused by four Pythium spp. prevalent in Iowa, namely P. lutarium, P. oopapillum, P. sylvaticum, and P. torulosum. Each species was used individually to inoculate soybean cultivar 'Sloan' using a rolled towel assay. Two temperature treatments (continuous 18°C [C18]; a 48-h cold stress period at 10°C [CS]) were applied. Soybean seedling age was divided into five growth stages (GS1 to GS5). Root rot severity and root length were assessed at 2, 4, 7, and 10 days after inoculation (DAI). At C18, root rot was greatest when soybean was inoculated with P. lutarium or P. sylvaticum at GS1 (seed imbibes water) and with P. oopapillum or P. torulosum at GS1, GS2 (radicle elongation), and GS3 (hypocotyl emergence). After CS, soybean susceptibility to P. lutarium and P. sylvaticum was reduced compared to C18 for inoculation at all GSs except GS5 (unifoliate leaf emergence). Conversely, root rot by P. oopapillum and P. torulosum was greater after CS compared to C18. Data from this study demonstrate that greater root rot, and consequently more damping-off, is likely if infection occurs at early germination stages before seedling emergence.

Oomycete Soil Diversity Associated with Betula and Alnus in Forests and Urban Settings in the Nordic-Baltic Region

This study aimed to determine the differences and drivers of oomycete diversity and community composition in alder- and birch-dominated park and natural forest soils of the Fennoscandian and Baltic countries of Estonia, Finland, Lithuania, Norway, and Sweden. For this, we sequenced libraries of PCR products generated from the DNA of 111 soil samples collected across a climate gradient using oomycete-specific primers on a PacBio high-throughput sequencing platform. We found that oomycete communities are most affected by temperature seasonality, annual mean temperature, and mean temperature of the warmest quarter. Differences in composition were partly explained by the higher diversity of Saprolegniales in Sweden and Norway, as both total oomycete and Saprolegniales richness decreased significantly at higher longitudes, potentially indicating the preference of this group of oomycetes for a more temperate maritime climate. None of the evaluated climatic variables significantly affected the richness of Pythiales or Peronosporales. Interestingly, the relative abundance and richness of Pythiales was higher at urban sites compared to forest sites, whereas the opposite was true for Saprolegniales. Additionally, this is the first report of Phytophthora gallica and P. plurivora in Estonia. Our results indicate that the composition of oomycetes in soils is strongly influenced by climatic factors, and, therefore, changes in climate conditions associated with global warming may have the potential to significantly alter the distribution range of these microbes, which comprise many important pathogens of plants.

Long-Term Tillage and Crop Rotation Regimes Reshape Soil-Borne Oomycete Communities in Soybean, Corn, and Wheat Production Systems

Soil-borne oomycetes include devastating plant pathogens that cause substantial losses in the agricultural sector. To better manage this important group of pathogens, it is critical to understand how they respond to common agricultural practices, such as tillage and crop rotation. Here, a long-term field experiment was established using a split-plot design with tillage as the main plot factor (conventional tillage (CT) vs. no till (NT), two levels) and rotation as the subplot factor (monocultures of soybean, corn, or wheat, and corn-soybean-wheat rotation, four levels). Post-harvest soil oomycete communities were characterized over three consecutive years (2016-2018) by metabarcoding the Internal Transcribed Spacer 1 (ITS1) region. The community contained 292 amplicon sequence variants (ASVs) and was dominated by Globisporangium spp. (85.1% in abundance, 203 ASV) and Pythium spp. (10.4%, 51 ASV). NT decreased diversity and community compositional structure heterogeneity, while crop rotation only affected the community structure under CT. The interaction effects of tillage and rotation on most oomycetes species accentuated the complexity of managing these pathogens. Soil and crop health represented by soybean seedling vitality was lowest in soils under CT cultivating soybean or corn, while the grain yield of the three crops responded differently to tillage and crop rotation regimes.

Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia

Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate.

Evidence of a Natural Hybrid Oomycete Isolated from Ornamental Nursery Stock

The oomycete genus Phytophthora includes many plant pathogens important in agricultural and environmental systems. Natural interspecific hybridization has been reported several times in Phytophthora, and although the fundamental processes of interspecific hybridization and the consequences of subsequent ecological distribution are poorly understood, reports suggest some hybrids can infect a broader host range and display enhanced virulence compared to the putative parental species. During a survey carried out at the University of Aberdeen in 2014-2015, of oomycetes present in ornamental plants purchased via the internet, a batch of oomycete isolates remained unidentified, showing, in some isolates, features generally related to hybridization. The aim of this study was to determine whether hybridization events had occurred between endemic and introduced oomycetes, probably/possibly facilitated through the international plant trade. The list of isolates examined included a putative hybrid closely related to Phytophthora cryptogea. The putative hybrid isolate was further characterized, and pathogenicity were tests carried out on Eucalyptus globulus, using an isolate of P. cryptogea as a positive control. Cloning of ITS, COXI and β-tubulin genes resulted in different sequence versions of the putative hybrid isolate; after mapping and a polymorphism position comparison, it was concluded that the studied isolate contained genetic information from P. cryptogea, P. erythroseptica, P. kelmanii, P. sansomeana and Phytopythium chamaehyphon. A PCR-RFLP assay, a NEBcutter analysis and flow cytometry analysis (genomes ranged between 0.168 to 0.269 pg/2C) added further evidence of the hybrid nature of this isolate. The putative hybrid presented complex growing patterns ranging from rosaceous to chrysanthemum-like and had an optimum growth temperature of 25 °C. Although the putative hybrid produced visible symptoms of disease on E. globulus seedlings, assessment of the relative susceptibility of E. globulus to P. cryptogea and the putative hybrid indicated that P. cryptogea was significantly more virulent than the putative hybrid, based on mortality, disease severity and foliar symptoms.

Soil Chemistry and Soil History Significantly Structure Oomycete Communities in Brassicaceae Crop Rotations

Oomycetes are critically important in soil microbial communities, especially for agriculture, where they are responsible for major declines in yields. Unfortunately, oomycetes are vastly understudied compared to bacteria and fungi. As such, our understanding of how oomycete biodiversity and community structure vary through time in the soil remains poor. Soil history established by previous crops is one factor known to structure other soil microbes, but this has not been investigated for its influence on oomycetes. In this study, we established three different soil histories in field trials; the following year, these plots were planted with five different Brassicaceae crops. We hypothesized that the previously established soil histories would structure different oomycete communities, regardless of their current Brassicaceae crop host, in both the roots and rhizosphere. We used a nested internal transcribed spacer amplicon strategy incorporated with MiSeq metabarcoding, where the sequencing data was used to infer amplicon sequence variants of the oomycetes present in each sample. This allowed us to determine the impact of different soil histories on the structure and biodiversity of the oomycete root and rhizosphere communities from the five different Brassicaceae crops. We found that each soil history structured distinct oomycete rhizosphere communities, regardless of different Brassicaceae crop hosts, while soil chemistry structured the oomycete communities more during a dry year. Interestingly, soil history appeared specific to oomycetes but was less influential for bacterial communities previously identified from the same samples. These results advance our understanding of how different agricultural practices and inputs can alter edaphic factors to impact future oomycete communities. Examining how different soil histories endure and impact oomycete biodiversity will help clarify how these important communities may be assembled in agricultural soils. IMPORTANCE Oomycetes cause global plant diseases that result in substantial losses, yet they are highly understudied compared to other microbes, like fungi and bacteria. We wanted to investigate how past soil events, like changing crops in rotation, would impact subsequent oomycete communities. We planted different oilseed crops in three different soil histories and found that each soil history structured a distinct oomycete community regardless of which new oilseed crop was planted, e.g., oomycete communities from last year's lentil plots were still detected the following year regardless of which new oilseed crops we planted. This study demonstrated how different agricultural practices can impact future microbial communities differently. Our results also highlight the need for continued monitoring of oomycete biodiversity and quantification.

Reduction of Pythium Damping-Off in Soybean by Biocontrol Seed Treatment

Pythium spp. is one of the major groups of pathogens that cause seedling diseases on soybean, leading to both preemergence and postemergence damping-off and root rot. More than 100 species have been identified within this genus, with Pythium irregulare, P. sylvaticum, P. ultimum var ultimum, and P. torulosum being particularly important for soybean production given their aggressiveness, prevalence, and abundance in production fields. This study investigated the antagonistic activity of potential biological control agents (BCAs) native to the U.S. Midwest against Pythium spp. First, in vitro screening identified BCAs that inhibit P. ultimum var. ultimum growth. Scanning electron microscopy demonstrated evidence of mycoparasitism of all potential biocontrol isolates against P. ultimum var. ultimum and P. torulosum, with the formation of appressorium-like structures, short hyphal branches around host hyphae, hook-shaped structures, coiling, and parallel growth of the mycoparasite along the host hyphae. Based on these promising results, selected BCAs were tested under field conditions against six different Pythium spp. Trichoderma afroharzianum 26 used alone and a mix of T. hamatum 16 + T. afroharzianum 19 used as seed treatments protected soybean seedlings from Pythium spp. infection, as BCA-treated plots had on average 15 to 20% greater plant stand and vigor than control plots. Our results also indicate that some of these potential BCAs could be added with a fungicide seed treatment with minimum inhibition occurring, depending on the fungicide active ingredient. This research highlights the need to develop tools incorporating biological control as a facet of soybean seedling disease management programs. The harnessing of native BCAs could be integrated with other management strategies to provide efficient control of seedling diseases.

Oxathiapiprolin Alone or Mixed with Metalaxyl Seed Treatment for Management of Soybean Seedling Diseases Caused by Species of Phytophthora, Phytopythium, and Pythium

Species of Phytophthora, Phytopythium, and Pythium affect soybean seed and seedlings each year, primarily through reduced plant populations and yield. Oxathiapiprolin is effective at managing several foliar diseases caused by some oomycetes. The objectives of these studies were to evaluate oxathiapiprolin in a discriminatory dose assay in vitro; evaluate oxathiapiprolin as a soybean seed treatment on a moderately susceptible cultivar in 10 environments; compare the impact of seed treatment on plant populations and yields in environments with low and high precipitation; and compare a seed treatment mixture on cultivars with different levels of resistance in four environments. There was no reduction in growth in vitro among 13 species of Pythium at 0.1 µg ml-1. Soybean seed treated with the base fungicide plus oxathiapiprolin (12 and 24 µg a.i. seed-1) alone, oxathiapiprolin (12 µg a.i. seed-1) plus mefenoxam (6 µg a.i. seed-1), or oxathiapiprolin (24 µg a.i. seed-1) plus ethaboxam (12.1 µg a.i. seed-1) had greater yields in environments that received ≥50 mm of precipitation within 14 days after planting compared with those that received less. Early plant population and yield were significantly higher for seed treated with oxathiapiprolin (24 µg a.i. seed-1) + metalaxyl (13.2 µg a.i. seed-1) compared with nontreated for six of seven cultivars in at least one of four environments. Oxathiapiprolin combined with another Oomycota fungicide applied to seed has the potential to be used to protect soybean plant establishment and yield in regions prone to poor drainage after high levels of precipitation.

Microbial community shifts association with physicochemical parameters: Visualizing enset bacterial wilt from different states of enset health

Bacterial wilt of enset caused by Xanthomonas campestris is a devastating disease in Ethiopia, where enset is domesticated and served as a staple food for about 20 million people in the country. While enset is infected by bacteria, it shows different wilting stages. However, the microbial community shifts at the different stages of enset infection and associated physicochemical parameter changes remain poorly understood. This study was aimed to visualize the proportion of enset wilt bacterium from other microbial community and its association with physicochemical parameter at different states of enset health. Soil and enset (zero, first, second and third stages) samples were collected from three districts in Gamo Highlands for physicochemical and biological (culture dependent and16S rRNA gene sequence) analysis. The results of culture dependent analysis which has been complemented by 16S rRNA gene sequence confirmed that increasing trends were observed for Xanthomonadaceae, Pseudomonadaceae, Lactobacillaceae and Flavobacteriaceae, while Bacillaceae and Enterobacteriaceae showed progressive decrease from zero to the third stage. Particularly, the 16S rRNA data showed that Xanthomonadaceae increased significantly from zero to different (2.5 × 10² times at the onset of disease and 1.0-2.0 × 10⁴ times at the second and third) stages of enset infection. Most physicochemical results showed that a decreasing trends from zero to third stage, while few parameters are showing an increasing trend. Moisture content (R² ≥ 0.951, P ≤ 0.049) of the soil and plant samples positively influenced Xanthomonas abundance, while this bacterium showed a strongly negative significant correlation with pH (R² ≥ -0.962, P ≤ 0.038), temperature (R² ≥ -0.958, P ≤ 0.042), OM (R² ≥ -0.952, P ≤ 0.048), and TN (R² ≥ -0.951, P ≤ 0.049). A strongly negative significant correlation (R² ≥ -0.948, P ≤ 0.050) was also observed between Xanthomonas and nutrients (K, Mg, Ca, and Cu). Overall, this study implies that different environmental factors found a key driving force of Xanthomonas proportional increment from low abundance at zero stage to higher abundance at the last stage of enset infection suggesting that considering these factors help to design an effective enset disease management strategy, for which further studies will be needed.

Characterization of soils conducive and non-conducive to Prunus replant disease

Successive orchard plantings of almond and other Prunus species exhibit reduced growth and yield in many California soils. This phenomenon, known as Prunus replant disease (PRD), can be prevented by preplant soil fumigation or anaerobic soil disinfestation, but its etiology is poorly understood and its incidence and severity are hard to predict. We report here on relationships among physicochemical variables, microbial community structure, and PRD induction in 25 diverse replant soils from California. In a greenhouse bioassay, soil was considered to be "PRD-inducing" when growth of peach seedlings in it was significantly increased by preplant fumigation and pasteurization, compared to an untreated control. PRD was induced in 18 of the 25 soils, and PRD severity correlated positively with soil exchangeable-K, pH, %clay, total %N, and electrical conductivity. The structure of bacterial, fungal, and oomycete communities differed significantly between the PRD-inducing and non-inducing soils, based on PERMANOVA of Bray Curtis dissimilarities. Bacterial class MB-A2-108 of phylum Actinobacteria had high relative abundances among PRD-inducing soils, while Bacteroidia were relatively abundant among non-inducing soils. Among fungi, many ASVs classified only to kingdom level were relatively abundant among PRD-inducing soils whereas ASVs of Trichoderma were relatively abundant among non-inducing soils. Random forest classification effectively discriminated between PRD-inducing and non-inducing soils, revealing many bacterial ASVs with high explanatory values. Random forest regression effectively accounted for PRD severity, with soil exchangeable-K and pH having high predictive value. Our work revealed several biotic and abiotic variables worthy of further examination in PRD etiology.

Pathogenicity and Host Range of Pythium kashmirense-A Soil-Borne Oomycete Recently Discovered in the UK

During a survey of oomycetes in ornamental plants carried out at the University of Aberdeen in 2014–2015, Pythium kashmirense was isolated from a specimen of Viburnum plicatum ‘Lanarth’, the first report of this oomycete in the UK (and in Europe). Pathogenicity of a Py. kashmirense isolate was examined using a range of plant species. Inoculations were carried out under controlled conditions in the absence of other Pythium and Phytophthora species, on Glycine max (soya bean), Phaseolus vulgaris (common bean), Lupinus angustifolius (blue lupin), Cucumis sativa (cucumber) and Viburnum opulus. The majority of inoculations caused pre-emergence damping-off, as well as seed rot and root rot. In the in vitro assays, germination rates (%) of soya bean and blue lupin seeds were less than 50%; in the in vivo inoculations on plants, over 50% of soya bean, blue lupin and common bean plants died; in contrast, cucumber plants showed lower susceptibility in pathogenicity tests, with an approximately 80% germination rate in in vitro tests, and 25% dead plants in the in planta inoculations. Inoculations carried out on root systems of Viburnum opulus caused severe necrosis and root rot. Little research was previously conducted on pathogenicity of Py. kashmirense and its relationship with losses in crop yield and quality. The present study showed varying virulence on the different plant species tested after inoculation with Py. kashmirense. Despite the lack of clear host specialization, infection by Py. kashmirense decreased seedling survival and health of plants in a range of important agricultural and ornamental plant species.

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.

Characterization of Pythium Species Collected from a Multiple Time-Point Sampling of Cucurbits in South Carolina

Species of Pythium cause root and stem rot in cucurbits, but no formal surveys have been conducted in the United States to identify which species are responsible. The cucurbit hosts bottle gourd, cucumber, Hubbard squash, and watermelon were transplanted in May, July, September, and November into sentinel plots in four and five different fields in 2017 and 2018, respectively, in South Carolina. Eight of the nine fields were replanted in March 2019. Isolates (600) were collected and identified by sequencing DNA of the mitochondrial cytochrome oxidase I region. The four most common species were P. spinosum (45.6% of all isolates), P. myriotylum (20.0%), P. irregulare (15.3%), and P. aphanidermatum (12.8%). P. myriotylum and P. aphanidermatum were predominantly isolated in May, July, and September, whereas P. spinosum and P. irregulare were predominantly isolated in November and March. Isolates of P. ultimum, P. irregulare, and P. spinosum were more virulent than isolates of P. myriotylum and P. aphanidermatum at 25°C. Representative isolates were screened in vitro for sensitivity to three fungicides: mefenoxam, propamocarb, and oxathiapiprolin. All isolates were sensitive to mefenoxam and propamocarb, but these same isolates were insensitive to oxathiapiprolin, except those classified taxonomically in Pythium clade I.

Root pathogen diversity and composition varies with climate in undisturbed grasslands, but less so in anthropogenically disturbed grasslands

Soil-borne pathogens structure plant communities, shaping their diversity, and through these effects may mediate plant responses to climate change and disturbance. Little is known, however, about the environmental determinants of plant pathogen communities. Therefore, we explored the impact of climate gradients and anthropogenic disturbance on root-associated pathogens in grasslands. We examined the community structure of two pathogenic groups-fungal pathogens and oomycetes-in undisturbed and anthropogenically disturbed grasslands across a natural precipitation and temperature gradient in the Midwestern USA. In undisturbed grasslands, precipitation and temperature gradients were important predictors of pathogen community richness and composition. Oomycete richness increased with precipitation, while fungal pathogen richness depended on an interaction of precipitation and temperature, with precipitation increasing richness most with higher temperatures. Disturbance altered plant pathogen composition and precipitation and temperature had a reduced effect on pathogen richness and composition in disturbed grasslands. Because pathogens can mediate plant community diversity and structure, the sensitivity of pathogens to disturbance and climate suggests that degradation of the pathogen community may mediate loss, or limit restoration of, native plant diversity in disturbed grasslands, and may modify plant community response to climate change.

Resistance of the SoyNAM Parents to Seed and Root Rot Caused by Four Pythium Species

Some Pythium spp. cause damping off and root rot in soybeans and other crop species. One of the most effective management tools to reduce disease is host resistance; however, little is known about resistance in soybean to Pythium spp. The soybean nested associated mapping (SoyNAM) parent lines are a set of germplasms that were crossed to a single hub parent to create recombinant inbred line populations for the purpose of mapping agronomic traits. The SoyNAM parents were screened for resistance to Pythium lutarium, Pythium oopapillum, Pythium sylvaticum, and Pythium torulosum in separate assays to evaluate seed and root rot severity. Of the 40 SoyNAM parents, only 'Maverick' was resistant to the four species tested; however, 13 were resistant to three species. Other lines were resistant to two, one, or none of the species tested. Correlations between seed and root rot severity for the lines assessed were weak or insignificant. Results indicate that mechanisms of resistance to seed and root rot caused by Pythium spp. may not necessarily be the same.

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.

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

Current methods to quantitatively assess fungicide sensitivity for a diverse range of oomycetes are slow and labor intensive. Microtiter-based assays can be used to increase throughput. However, many factors can affect their quality and reproducibility. Therefore, efficient and reliable methods for detection of assay quality are desirable. The objective of this study was to develop and validate a robust high-throughput fungicide phenotyping assay based on spectrophotometric quantification of mycelial growth in liquid culture and implementation of quality control with Z' factor and growth curves. Z' factor was used to ensure that each isolate grew enough in the absence of fungicides compared with the negative control, and growth curves were used to ensure active growth at the time of concentration of a fungicide that reduces growth by 50% (EC₅₀) estimation. EC₅₀ and relative growth values were correlated in a side-by-side comparison with values obtained using the amended medium (gold standard) assay. Concordance correlation indicated that the high-throughput assay is accurate but may not be as precise as the amended medium assay. To demonstrate the utility of the high-throughput assay, the sensitivity of 216 oomycete isolates representing four genera and 81 species to mefenoxam and ethaboxam was tested. The assay developed herein will enable high-throughput fungicide phenotyping at a population or community level.

Molecular characterization of genomic regions for resistance to Pythium ultimum var. ultimum in the soybean cultivar Magellan

KEY MESSAGE

Two novel QTL for resistance to Pythium ultimum var. ultimum were identified in soybean using an Illumina SNP Chip and whole genome re-sequencing. Pythium ultimum var. ultimum is one of numerous Pythium spp. that causes severe pre- and post-emergence damping-off of seedlings and root rot of soybean [Glycine max (L.) Merr.]. The objective of this research was to identify quantitative trait loci (QTL) for resistance to P. ultimum var. ultimum in a recombinant inbred line population derived from a cross of 'Magellan' (moderately resistant) and PI 438489B (susceptible). Two different mapping approaches were utilized: the universal soybean linkage panel (USLP 1.0) and the bin map constructed from whole genome re-sequencing (WGRS) technology. Two genomic regions associated with variation in three disease-related parameters were detected using both approaches, with the bin map providing higher resolution. Using WGRS, the first QTL were mapped within a 350-kbp region on Chr. 6 and explained 7.5-13.5% of the phenotypic variance. The second QTL were positioned in a 260-kbp confidence interval on Chr. 8 and explained 6.3-16.8% of the phenotypic variation. Candidate genes potentially associated with disease resistance were proposed. High-resolution genetic linkage maps with a number of significant SNP markers could benefit marker-assisted breeding and dissection of the molecular mechanisms underlying soybean resistance to Pythium damping-off in 'Magellan.' Additionally, the outputs of this study may encourage more screening of diverse soybean germplasm and utilization of genome-wide association studies to understand the genetic basis of quantitative disease resistance.

Evaluation of Major Ancestors of North American Soybean Cultivars for Resistance to Three Pythium Species that Cause Seedling Blight

Pythium seedling blight, which can be caused by a number of Pythium spp., is a disease that affects soybean (Glycine max) in the United States and Canada. Pythium ultimum var. ultimum, one of the most common pathogenic species, is favored by cool, wet conditions in early spring and causes seed decay, root rot, and seedling damping-off. In all, 102 major ancestors of modern North American cultivars and "first progeny" cultivars developed directly from ancestral lines were evaluated for resistance to P. ultimum var. ultimum and two other species of Pythium in greenhouse assays. Several ancestors and first progeny cultivars, as well as the resistant check Archer, had varying levels of partial resistance to an Illinois isolate of P. ultimum var. ultimum. In a subsequent experiment, four of the most resistant lines (PI 84637, Maple Isle, Fiskeby III, and Fiskeby 840-7-3) and the susceptible cultivar Kanro were screened for resistance against isolates of P. irregulare and P. sylvaticum, and resistance to P. ultimum var. ultimum was confirmed. The lines that were partially resistant to P. ultimum var. ultimum in the first experiment were also partially resistant to P. irregulare and P. sylvaticum. The P. ultimum var. ultimum isolate was the most aggressive of the three isolates, followed by the P. irregulare and P. sylvaticum isolates. Modern cultivars descended from the soybean lines with partial resistance to these pathogens could be useful sources of resistance to Pythium seedling blight if they are found to have similar levels of resistance.

Mapping Quantitative Trait Loci for Tolerance to Pythium irregulare in Soybean (Glycine max L.)

Pythium root rot is one of the significant diseases of soybean (Glycine max (L.) Merr.) in the United States. The causal agent of the disease is a soil-borne oomycete pathogen Pythium irregulare, the most prevalent and aggressive species of Pythium in North Central United States. However, few studies have been conducted in soybean for the identification of quantitative trait loci (QTL) for tolerance to P. irregulare In this study, two recombinant inbred line (RIL) populations (designated as POP1 and POP2) were challenged with P. irregulare (isolate CMISO2-5-14) in a greenhouse assay. POP1 and POP2 were derived from 'E09014' × 'E05226-T' and 'E05226-T' × 'E09088', and contained 113 and 79 lines, respectively. Parental tests indicated that 'E05226-T' and 'E09014' were more tolerant than 'E09088', while 'E09088' was highly susceptible to the pathogen. The disease indices, root weight of inoculation (RWI) and ratio of root weight (RRW) of both populations showed near normal distributions, with transgressive segregation, suggesting the involvement of multiple QTL from both parents contributed to the tolerance. All the lines were genotyped using Illumina Infinium BARCSoySNP6K iSelect BeadChip and yielded 1373 and 1384 polymorphic markers for POP1 and POP2, respectively. Notably, despite high density, polymorphic markers coverage was incomplete in some genomic regions. As such, 28 and 37 linkage groups were obtained in POP1 and POP2, respectively corresponding to the 20 soybean chromosomes. Using RRW, one QTL was identified in POP1 on Chromosome 20 that explained 12.7-13.3% of phenotypic variation. The desirable allele of this QTL was from 'E05226-T'. Another QTL was found in POP2 on Chromosome 11. It explained 15.4% of the phenotypic variation and the desirable allele was from 'E09088'. However, no QTL were identified using RWI in either population. These results supported that RRW was more suitable to be used to evaluate P. irregulare tolerance in soybean.

Profile distribution of CO2 in an arid saline-alkali soil with gypsum and wheat straw amendments: a two-year incubation experiment

Adding gypsum and/or straw is a common practice for ameliorating saline-alkali soils. However, the effect of amendment on soil CO₂ is poorly known. An incubation experiment was conducted for over two years in a saline-alkali soil of Yanqi Basin, which included four treatments: control, gypsum addition (Ca), wheat straw addition (S) and gypsum-wheat straw combination (Ca+S). We continuously monitored soil CO₂ concentration, temperature and moisture at 15, 30, 45 and 60 cm. There was a clear seasonality in soil CO₂ under all four treatments, which was generally similar to those in soil temperature and moisture. Straw addition led to a significant increase in soil CO₂ over 0-60 cm in summer. While there was a significant increase of soil CO₂ with gypsum addition only, soil CO₂ significantly decreased with the addition of gypsum and straw (relative to straw addition only) during autumn and winter in 2014. Interestingly, integrated soil CO₂ was lowest in soil profile under the Ca+S treatment during winter and spring. Our study implies that different amendments of organic matter and gypsum may result in various responses and interactions of biological, chemical and physical processes, with implications for the carbon cycle in saline-alkaline soils of arid region.

Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean (Phaseolus vulgaris L.)

Climate change models predict temporal and spatial shifts in precipitation resulting in more frequent incidents of flooding, particularly in regions with poor soil drainage. In these flooding conditions, crop losses are inevitable due to exposure of plants to hypoxia and the spread of root rot diseases. Improving the tolerance of bean cultivars to flooding is crucial to minimize crop losses. In this experiment, we evaluated the phenotypic responses of 277 genotypes from the Andean Diversity Panel to flooding at germination and seedling stages. A randomized complete block design, with a split plot arrangement, was employed for phenotyping germination rate, total weight, shoot weight, root weight, hypocotyl length, SPAD index, adventitious root rate, and survival score. A subset of genotypes (n = 20) were further evaluated under field conditions to assess correlations between field and greenhouse data and to identify the most tolerant genotypes. A genome-wide association study (GWAS) was performed using ~203 K SNP markers to understand the genetic architecture of flooding tolerance in this panel. Survival scores between field and greenhouse data were significantly correlated (r = 0.55, P = 0.01). Subsequently, a subset of the most tolerant and susceptible genotypes were evaluated under pathogenic Pythium spp. pressure. This experiment revealed a potential link between flooding tolerance and Pythium spp. resistance. Several tolerant genotypes were identified that could be used as donor parents in breeding pipelines, especially ADP-429 and ADP-604. Based on the population structure analysis, a subpopulation consisting of 20 genotypes from the Middle American gene pool was detected that also possessed the highest root weight, hypocotyl length, and adventitious root development under flooding conditions. Genomic regions associated with flooding tolerance were identified including a region on Pv08/3.2 Mb, which is associated with germination rate and resides in vicinity of SnRK1.1, a central gene involved in response of plants to hypoxia. Furthermore, a QTL at Pv07/4.7 Mb was detected that controls survival score of seedlings under flooding conditions. The association of these QTL with the survivability traits including germination rate and survival score, indicates that these loci can be used in marker-assisted selection breeding to improve flooding tolerance in the Andean germplasm.

Effect of potassium and manganese phosphites in the control of Pythium damping-off in soybean: a feasible alternative to fungicide seed treatments

BACKGROUND

Use of fungicide seed treatments for control of soybean soilborne diseases such as Pythium damping-off has increased worldwide. However, emergence of Pythium strains resistant to metalaxyl-M has prompted the need for alternative technologies to fungicides for damping-off control. The use of phosphites (Phis) has been proposed as a method to control oomycetes, but their use as seed treatments in soybean is limited by the lack of information on their efficacy. The effect of potassium (K) and manganese (Mn) Phis (as seed treatments) in the control of Pythium damping-off in soybean was evaluated in vitro and in vivo. In vitro, treated seeds and a control were placed on potato dextrose agar and the damping-off severity caused by Pythium aphanidermatum (Edson) Fitzpatrick, Pythium irregulare Buisman, and Pythium ultimum Trow was assessed 5 days after incubation using an ordinal scale. In vivo, treated seeds and a control were planted in polystyrene pots and emergence was evaluated 21 days after planting.

RESULTS

Analysis of the in vitro data using a multinomial generalized linear model showed that the probabilities of non-germinated, dead seeds ranged from 0.64 to 1.00 in the control and from 0 to 0.13 in the Phi treatments in each of the Pythium species. Probabilities of seed germination without or with damping-off symptoms were significantly higher for seeds treated with the Phi products than for the control. In the in vivo experiment, the Phi-based products increased seedling emergence by up to 29% on average compared with the untreated control.

CONCLUSION

Mn and K Phis are feasible alternatives as seed treatments to control Pythium damping-off in soybean. This study is the first, worldwide, to document the efficacy of K and Mn Phis in the control of soybean Pythium damping-off. © 2017 Society of Chemical Industry.

Probability Models Based on Soil Properties for Predicting Presence-Absence of Pythium in Soybean Roots

Associations between soil properties and Pythium groups on soybean roots were investigated in 83 commercial soybean fields in North Dakota. A data set containing 2877 isolates of Pythium which included 26 known spp. and 1 unknown spp. and 13 soil properties from each field were analyzed. A Pearson correlation analysis was performed with all soil properties to observe any significant correlation between properties. Hierarchical clustering, indicator spp., and multi-response permutation procedures were used to identify groups of Pythium. Logistic regression analysis using stepwise selection was employed to calculate probability models for presence of groups based on soil properties. Three major Pythium groups were identified and three soil properties were associated with these groups. Group 1, characterized by P. ultimum, was associated with zinc levels; as zinc increased, the probability of group 1 being present increased (α = 0.05). Pythium group 2, characterized by Pythium kashmirense and an unknown Pythium sp., was associated with cation exchange capacity (CEC) (α < 0.05); as CEC increased, these spp. increased. Group 3, characterized by Pythium heterothallicum and Pythium irregulare, were associated with CEC and calcium carbonate exchange (CCE); as CCE increased and CEC decreased, these spp. increased (α = 0.05). The regression models may have value in predicting pathogenic Pythium spp. in soybean fields in North Dakota and adjacent states.

Development and Application of qPCR and RPA Genus- and Species-Specific Detection of Phytophthora sojae and P. sansomeana Root Rot Pathogens of Soybean

Phytophthora root rot of soybean, caused by Phytophthora sojae, is one of the most important diseases in the Midwestern United States, and is estimated to cause losses of up to 1.2 million metric tons per year. Disease may also be caused by P. sansomeana; however, the prevalence and damage caused by this species is not well known, partly due to limitations of current diagnostic tools. Efficient, accurate, and sensitive detection of pathogens is crucial for management. Thus, multiplex qPCR and isothermal RPA (recombinase polymerase amplification) assays were developed using a hierarchical approach to detect these Phytophthora spp. The assays consist of a genus-specific probe and two species-specific probes that target the atp9-nad9 region of the mitochondrial genome that is highly specific for the genus Phytophthora. The qPCR approach multiplexes the three probes and a plant internal control. The RPA assays run each probe independently with a plant internal control multiplexed in one amplification, obtaining a result in as little as 20 mins. The multicopy mitochondrial genome provides sensitivity with sufficient variability to discern among different Phytophthora spp. The assays were highly specific when tested against a panel of 100 Phytophthora taxa and range of Pythium spp. The consistent detection level of the assay was 100 fg for the qPCR assay and 10 pg for the RPA assay. The assays were validated on symptomatic plants collected from Michigan (U.S.) and Ontario (Canada) during the 2013 field season, showing correlation with isolation. In 2014, the assays were validated with samples from nine soybean producing states in the U.S. The assays are valuable diagnostic tools for detection of Phytophthora spp. affecting soybean.

Oomycete Species Associated with Soybean Seedlings in North America-Part I: Identification and Pathogenicity Characterization

Oomycete pathogens are commonly associated with soybean root rot and have been estimated to reduce soybean yields in the United States by 1.5 million tons on an annual basis. Limited information exists regarding the frequency and diversity of oomycete species across the major soybean-producing regions in North America. A survey was conducted across 11 major soybean-producing states in the United States and the province of Ontario, Canada. In 2011, 2,378 oomycete cultures were isolated from soybean seedling roots on a semiselective medium (CMA-PARPB) and were identified by sequencing of the internal transcribed spacer region of rDNA. Sequence results distinguished a total of 51 Pythium spp., three Phytophthora spp., three Phytopythium spp., and one Aphanomyces sp. in 2011, with Pythium sylvaticum (16%) and P. oopapillum (13%) being the most prevalent. In 2012, the survey was repeated, but, due to drought conditions across the sampling area, fewer total isolates (n = 1,038) were collected. Additionally, in 2012, a second semiselective medium (V8-RPBH) was included, which increased the Phytophthora spp. isolated from 0.7 to 7% of the total isolates. In 2012, 54 Pythium spp., seven Phytophthora spp., six Phytopythium spp., and one Pythiogeton sp. were recovered, with P. sylvaticum (14%) and P. heterothallicum (12%) being recovered most frequently. Pathogenicity and virulence were evaluated with representative isolates of each of the 84 species on soybean cv. Sloan. A seed-rot assay identified 13 and 11 pathogenic species, respectively, at 13 and 20°C. A seedling-root assay conducted at 20°C identified 43 species as pathogenic, having a significantly detrimental effect on the seedling roots as compared with the noninoculated control. A total of 15 species were pathogenic in both the seed and seedling assays. This study provides a comprehensive characterization of oomycete species present in soybean seedling roots in the major production areas in the United States and Ontario, Canada and provides a basis for disease management and breeding programs.