Brief Summary of Minutes of Annual Meeting

The annual Multistate W5147 meeting was held on December 1, 2023, at the Multidisciplinary Research Building, University of California, Riverside, CA. It was the first in-person get-together after the Covid pandemic. Tim Paulitz and James Borneman organized the meeting. Antoon Ploeg arranged a one-hour guided tour of the UCR Botanical Garden in the early afternoon. In addition to 10 attendees at UCR, 10 participated via Zoom.

Tim Paulitz opened the meeting at 8:30 AM. He thanked those members who participated in the renewal proposal writing that was approved for another 5 years as W5147.

After the attendees introduced themselves, each presenter had about 15 minutes to talk about their project, followed by questions and often lively discussion by the audience.

• Jennifer McBeath reported disease observations on Rhodiola rosea (Arctic Root), a medicinal succulent plant, and Paeonia (Peony), perennials with showy blossoms and use in traditional Chinese medicine.
• Jim Farrar presented a "roadmap for sustainable pest management" developed by a workgroup of California's DPR, CalEPA, and CDFA.
• Johan Leveau reported that combinations of Collimonas strains with Bacillus biocontrol products resulted in a booster protection effect against Fusarium wilt.
• James Borneman proposed research identifying critical factors for Hyalorbilia to parasitize sugarbeet cyst nematodes in different soils.
• Antoon Ploeg showed that the peach root-knot nematode (Meloidogyne floridensis) can infest and multiply on several crops resistant to incognita.
• Harsh Bais discussed whether plants recruit beneficial microbes by baiting them to roots and which regions are colonized.
• James White talked about the ability of plants to attract, internalize, and utilize beneficial microbes as a nutrient source (Rhizophagy Cycle).
• Chris Little reported about charcoal rot (Macrophomina phaseolina) in soybean production and attempts to mitigate the fungal disease with different crop management systems.
• Maren Friesen described her peaola investigations (intercropping of peas and canola) that significantly increased productivity.
• Tessie Wilkerson evaluated commercial and new USDA cotton cultivars for resistance against reniform and root-knot nematodes.
• Pratibha Sharma talked about crop residue management on Cercospora leaf spot (C. beticola) on table beets.
• Bode Olukolu presented his comparisons of sequencing methods.
• Mike Kolomiets showed Trichoderma virens secretes a highly effective elicitor that induces systemic disease resistance in cotton.
• Jiue-in Yang discussed the importance of IPM in Taiwan after a regulatory-initiated 50% pesticide cut. Her lab found several entomopathogenic fungi that effectively parasitize nematode eggs.
• Emma Gachomo found in carrot greenhouse trials temporary indirect effects of mefenoxam on non-target fungal diversity.
• Jay Hao talked about attempts to optimize potato production in the presence of Verticillium and nematodes with lobster meal, metam sodium soil fumigation, and crop rotation.
• Tika Adhikari reported trials with molasses and mustard meal as carbon sources for anaerobic soil disinfection (ASD) in strawberries.
• Tim Paulitz talked about the effects of rotation crops on soil communities of the following crops, the microbiome of camelina, and the use of artificial intelligence for nematode identification.

The meeting was concluded at about 5 PM.

The group met at the festive-decorated downtown Riverside to enjoy dinner and camaraderie.

Submitted by Ole Becker

Objective 1 To identify and characterize new biological agents, microbial community structure and function, naturally suppressive soils, cultural practices, and organic amendments that provide management of diseases caused by soilborne plant pathogens.

CA- Several sugarbeet cyst nematode-suppressive soils were discovered and analyzed in sugarbeet and broccoli fields in southern and coastal California, respectively. The lab and greenhouse studies suggest that members of the clade Hyalorbilia oviparasitica (syn. Brachyphoris oviparasitica, Dactylella oviparasitica) were the causal organisms. Several Hyalorbilia strains were obtained from young Heterodera schachtii females using enrichment and double-baiting cultivation techniques. Both strains suppressed H. schachtii populations by more than 80% in soil-based assays. They are genetically different from our standard strain, Hyalorbilia DoUCR50. We demonstrated that detecting indigenous populations of members of the H. oviparasitica clade can be used to predict cyst nematode suppression in Imperial Valley sugarbeet field soils.

CA- The goal of this research is to create more effective and sustainable strategies to manage cyst nematodes. Towards this goal, we have identified a group of fungi that dramatically reduces the population densities of cyst nematodes. This group is called the Hyalorbilia oviparasitica Clade, which was formerly called Dactylella oviparasitica. In this reported period, we demonstrated that we could predict which fields would suppress cyst nematode populations by quantifying the amount of these fungi in soil before a crop was planted. We expect that this will lead to the development of new cropping decision models that will enable growers to create and maintain soils that suppress H. schachtii, which we anticipate will lead to higher crop yields and profitability for the growers. This work was published in this reporting period.

CA-  The goal of this research is to create more effective and sustainable strategies to manage citrus Huanglongbing (HLB) disease, which is a citrus disease causing enormous damage in the US and across the planet. We have examined Huanglongbing (HLB) Survivor and Non-Survivor trees in Florida over the last seven years. Survivor trees are those that have a very slow rate of disease. In this reporting period, we have identified one key root-associated bacterium that correlates with this phenotype, along with the RNA transcripts from this bacterium that correlates with this phenotype. We expect that this will lead to the development of effective treatments for citrus HLB disease, which we anticipate will lead to higher crop yields and profitability for the growers.

CA- An endophyte KRS015, isolated from the seed of Verticillium wilt-resistant Gossypium hirsutum cultivar, was identified as Bacillus subtilis by morphological, phylogenetic, physiological and biochemical analyses. The volatile organic compounds (VOCs) produced by KRS015 or its cell-free fermentation extract had significant antagonistic effects on various pathogenic fungi including V. dahliae. KRS015 reduced Verticillium wilt and colonization of V. dahliae in treated cotton seedlings significantly, and the disease reduction rate was ~62%. KRS015 also promoted plant growth. These results suggest that KRS015 is a potential agent for controlling Verticillium wilt and promoting growth of cotton.

MT- Across the United States northern Great Plains (USNGP), Fusarium pseudograminearum, a fungus causing root crown rot, and Bromus tectorum (L), also known as cheatgrass or downy brome, are significant burdens threatening the economic and environmental sustainability of small grain production systems. These two species form a multi-trophic pest complex and few studies have systematically assessed the interconnected relationships and joint management of these agricultural pests. Our work seeks to unravel the complex multitrophic interactions associated with this disease complex. Current efforts are focused on characterizing the rhizosphere microbiome of wheat grown in competition of B. tectorum, with and without Fusarium infection.

MT- A new project is underway to elucidate the effects of Fusarium infection on the rhizosphere microbiome and competitive ability of Canada thistle. Understanding how this pathogen interacts with Canada thistle and the rhizosphere microbial community is important for assessing the effect of fusarium on the competitive ability of Canada thistle.

NY- Characterizing the microbiome associated with table beet. Bacteria and fungi in plant-associated microbiomes are involved in many aspects of plant health. Host-microbiome interactions have been shown to moderate tolerance to multiple biotic and abiotic stressors, prompting interest in utilizing beneficial bacteria and fungi to manage plant diseases and improve crop production. To achieve these goals, an in-depth knowledge of the identity and distribution of plant-associated microbial communities is essential. Table beet is an important crop in New York, where it is grown on large broadacre fields and small diversified farms. Increasing demand for organically grown table beet and additional options to conventional fungicides for disease control has motivated interest in the microbiomes associated with table beet. The purpose of this project was to evaluate the bacteria and fungi in the rhizosphere and phyllosphere microbiome and identify core taxa. In 2021 and 2022, microbiome samples from nine table beet fields were collected from the rhizosphere and phyllosphere. Twice during each growing season, five adjacent plants were sampled at each of five locations within each field. Bulk soil samples were also collected at each location. Shoot tissue from five seedlings was collected for each early-season sample. Late-season foliar samples were separated into the epiphytic and endophytic microbiome. Fungal and bacterial DNA was amplified separately, sequenced, and the DADA2 pipeline was used to filter reads and assign taxonomy. Most of the differences in the bacterial and fungal communities were associated with sample type, with additional variation explained by field. Ordination of Bray-Curtis distances showed that rhizosphere soil communities were similar to bulk soil communities, and both separated from the phyllosphere microbiomes. Bulk soil and rhizosphere microbiomes also had higher alpha diversity than phyllosphere microbiomes. Only bacteria and fungi in the leaf epiphyte community were present in over 90% of samples and had higher relative abundance compared to the bulk soil community, and therefore considered within the core microbiome. The core microbiome included members of the bacterial genera Sphingomonas, Methylobacterium, Pseudomonas, and Massilia, and members of the fungal genera Alternaria, Epicoccum, and Cladosporium. Overall, this study identified a small number of core bacteria and fungi that were consistently present in the table beet microbiome despite geographic and temporal variation.

NY- Impact of azoxystrobin and Rhizoctonia solani on soil and rhizosphere microbiomes of table beet. In-furrow fungicides are broadly used in agriculture to control soilborne diseases, but the effect of this practice on the soil and rhizosphere microbiome is largely unknown. Both fungicides and pathogen growth in the soil present a disturbance to microbial communities and may affect crop health and resilience by altering important microbial interactions within the rhizosphere and soil environment. Table beet production in New York relies on azoxystrobin applied in-furrow to control the fungal pathogen, Rhizoctonia solani, which causes damping off and root rot. Field trials were conducted in each of two years (2021 and 2022) to evaluate the effect of both in-furrow azoxystrobin application and post-emergent R. solani inoculation on microbial communities in bulk soil and the table beet rhizosphere. Soil samples were collected during the 2 to 4 leaf stage and at root maturity from plots receiving one of four treatments: in-furrow azoxystrobin, post-emergent inoculum, in-furrow azoxystrobin plus post-emergent inoculum, or nontreated. Rhizoctonia disease incidence and severity was collected during the growing season and at harvest. Illumina sequencing of the 16S rRNA gene and the internal transcribed spacer region from rhizosphere and bulk soil samples and community diversity and composition analysis revealed that treatments had no effect on alpha or beta diversity of the microbial communities. Sample type (rhizosphere and bulk soil) was the main driver of community composition. The most abundant bacterial and fungal phyla were Proteobacteria and Ascomycota. While relative abundance in the bacterial community was unaffected by either treatment, sample type, or sampling time, relative abundance of the fungal class Saccharomycetes was increased in the table beet rhizosphere. Alpha diversity was negatively correlated with disease incidence and severity in 2021, but not in 2022. Overall, there were few consistent relationships in both 2021 and 2022 between disease incidence and severity and abundance of microbial taxa. The abundance of Acidobacteria and Bacteroidota was negatively correlated with R. solani abundance, and both phyla were enriched in the table beet rhizosphere. The identification of these and other microbial taxa associated with plots that had low disease incidence and severity may lead to further investigations for microbiome-mediated management of R. solani and other soilborne plant pathogens.

NY- Effects of table beet residue management on the microbiome associated with table beet. A small plot replicated trial was conducted to evaluate the effectiveness of selected residue management strategies, including plowing, flaming, urea, and lime application, for Cercospora leaf spot control in table beet. Treatments were applied to infested residue in fall and disease intensity was evaluated throughout summer. Samples to evaluate the microbiome in the phyllosphere, rhizosphere and bulk soil were also taken from each treatment. The second year of this trial was conducted in 2023. Results from this trial are being combined across years and data analysis is pending.

OR – Soil microbiome variation in potato cropping systems. We described regional variability in a dataset consisting of over 1300 potato soil microbiomes from nine U.S. field sites. We found that soil microbial communities tend to cluster based on their geographic origin. Field site alone accounted for more than 54% and 60% of the variance in bacterial and eukaryotic community structure, respectively. We also found that pH, organic matter, percent total and organic carbon, cation exchange capacity, and nitrate, phosphate and potassium concentrations explained much of the variation observed in bacterial and eukaryotic communities at the continental scale. The results indicate that biological soil health indicators vary at smaller scales (e.g., regional-, local-, field-scales). Identification of and recommendations for use of specific biological indicators of soil health will likely need to occur at regional or local levels.

TN- Using an inexpensive quantitative reduced representation sequencing of metagenomes, we aim to characterize host-associated metagenome of crops at the population level. The cost-efficient approach allows for investigation multipartite and multitrophic interactions in order to identify the core metagenomic community that has co-evolved with the crop. We aim to identify known and novel disease-suppressing microbes under low and high pathogen pressure under field conditions.

VA • Collected boxwood and soil samples from four cultivars with different levels of resistance to boxwood blight at two nurseries - one in Virginia and the other in Oregon and extracted their DNA for metagenomic analyses.

• Surveyed 17 nurseries across the country to document boxwood production shift to less susceptible cultivars since the first report of boxwood blight in North Carolina and Connecticut in 2011.
• Reviewed and summarized the studies on boxwood cultivar resistance breeding to date, and published it in Plant Health Progress to further promote the adoption of more resistant cultivars and build health into boxwood crops and plantings.
• Researched and published one paper on the blight pathogen adaption to different hosts - boxwood, pachysandra and sweet box.
• Sequenced and analyzed 16S and ITS amplicon data, wrote and published three papers on boxwood bacterial and fungal communities and identified beneficial groups and species.

WA- Nematode communities can reveal soil health. Nematodes are the most numerous soil invertebrate and occupy all trophic levels in the food web, from fungal and bacterial feeders to herbivores to predators. Potato and wheat field soils were sampled across eastern Washington and Oregon, including soils that have never been cropped. Over 30 genera and trophic levels were identified based on nematode morphology and mouth parts. Analysis showed that cropped soils, which are more disturbed, are dominated by bacterial and fungal feeders, as compared to native non-cropped soils. These results show that nematode analysis may be used as another indication of soil health for growers.

WA- Previous crops of canola may shift the microbiome of the following wheat crop. Rotation crops often give a yield increase to the following wheat crop, due to breaking of diseases cycles, nitrogen fixation and other benefits. However, a yield decrease in spring wheat after winter canola has been observed in intermediate and low precipitation areas, and water and nutrients were ruled out as factors. The microbiome of spring wheat was sampled following winter canola, winter triticale, winter wheat and spring barley. Spring wheat after canola had significantly less arbuscular mycorrhizal fungi and higher levels of the pathogen Waitea circinata. Canola is one of the few non-mycorrhizal plant families, and may deplete these beneficial, symbiotic fungi. This information is important for growers to consider in their cropping systems plans.

WA- Bacteria isolated from the rhizosphere of camelina can promote growth. Camelina, a member of the Brassicaceae family, is a potential low-input bioenergy crop that can be grown in rotation with wheat in dryland areas. However, nothing is known about the microbial communities on the roots, and how this may influence crop performance and nutrient uptake. A collection of over 3000 bacterial strains was made from the roots of camelina grown in 33 different locations in eastern Washington and Montana. The strains were tested for growth promotion in the lab and greenhouse, and several promising growth-promoting strains were identified, including isolates of Pseudomonas. In conjunction with a microbiome analysis, key components of the camelina bacterial community that may play a role in increasing nutrient uptake, pathogen resistance and drought tolerance in this biofuel crop were identified.

WA- Streptomyces are key members of the microbiome of wheat roots. Streptomyces are abundant in association with plants and are known for their ability to promote drought tolerance and produce antibiotics that inhibit a wide range of pathogens. To assess the role of these bacteria in the protection of cereal crops, a large collection of Streptomyces isolates was made including over 115 from the rhizosphere and 201 from the endosphere of wheat collected from irrigated and dryland plots at various stages of maturity in Lind, Washington from 2021 to 2023. The isolates are being characterized phenotypically and phylogenetically by multilocus sequence analysis for their ability to suppress fungal root pathogens and to ameliorate drought stress in crops grown under a variety of soil moisture conditions. The results of these analyses are expected to provide new tools to maintain crop productivity under conditions of increasing biotic and abiotic stress mediated by climate change.

WA- We characterized the nitrogenase diversity at Cook farm LTAR and found diverse nitrogen-fixing bacteria present on both the no-till and business as usual sides of the site, with some distinct taxa in each. We sampled neighboring prairie and agricultural sites for nifH characterization to determine how cultivation impacts these communities. We also conducted a microbiome manipulation experiment with prairie and ag soils across a N gradient and are characterizing N-fixing communities. This knowledge will give insight into the nitrogen-fixing bacteria present in agroecosystems as well as how management impacts these microbes.

WA- We characterized the peaola microbiome and found no differences in bulk soil under monocrops and intercrop. The rhizosphere microbiome was distinct for pea and canola, and many but not all of these differences persisted when intercropped. Intercropping also had some distinct taxa not consistently found under either monocrop. This information will be used to help understand how microbes impact intercropping success.

WA We conducted a microbiome manipulation of wild vs domesticated chickpea in the field, and found surprisingly that domesticated plants were more responsive to microbes. We are currently sequencing these microbes to give insight into whether this effect is due to known mutualists.

WA- We completed a multiyear data collection effort in switchgrass and found complex ecological drivers of the root associated microbiome. We also characterized root exudates and found that neighboring plants altered exudate chemistry, which could be important for plant-microbe interactions in diversified cropping systems.

WA- We continued mining antimicrobial NCR peptide genes in wild North American clover genomes, and refined our gene calls. We are finding hundreds of distinct and novel NCR sequences, which could be useful as sources of resistance to diverse pathogens.

WA- We conducted mesocosm experiments investigating the electrochemical signatures of soil microbial communities and found that polarization and carbon source both play a role. This will be important for developing novel soil sensors for microbial function.

Objective 2  To understand how microbial populations and microbial gene expression are regulated by the biological (plants and microbes) and physical environment and how they influence disease.

DE- Research has focused on lytic and lysogenic viruses (phages) that infect soybean bradyrhizobia (Bradyrhizobium spp.), a group of symbiotic nitrogen-fixing bacteria that nodulate soybean roots and circumvent both the need for fossil fuel-derived nitrogen fertilizers and associated ground and surface water pollution and greenhouse gas emissions.  The overall arching goal is to understand how these phages shape the host bacterium’s symbiotic effectiveness (evolution) and ultimately soybean yields.  Specific goals include:

1. elucidate phage replication parameters when infecting various bradyrhizobial hosts,
2. genomic DNA sequencing of host bradyrhizobia and associated phages and subsequent bioinformatic and pangenome analyses,
3. identify genome-to-phenome connections within/between host bacteria and phages, and
4. develop strategies to sustainably enhance soybean yields.

MT- Ongoing work is focused on understanding genetic mechanisms in barley and environmental factors that are involved in recruitment of the rhizosphere microbiome. Current efforts are focused on evaluating the rhizosphere microbiome composition to gain insight into key microorganisms and specific genes responsible for enabling plants to resist abiotic stress.

NY Differentiating inoculum sources for Cercospora leaf spot epidemics in table beet. Cercospora beticola (cause of Cercospora leaf spot of table beet) is the most important disease affecting foliar health in table beet. Despite the importance of this disease, little is known of the dominant inoculum sources for CLS epidemics. Potential inoculum sources include infested seed, alternative weed and crop hosts, infested residue, and soil. However, despite C. beticola populations being heterothallic and that sexual recombination is likely (through population genetic analyses), the sexual morph and hence a potential source of long-distance dispersal is unknown.  This knowledge will improve the design of effective disease management strategies. To address this question, a table beet field was established in an isolated location without a history of table beet (or alternative crop hosts). Specific genotypes of C. beticola were inoculated (MAT 1-1, and MAT1-2) in a transect perpendicular to the crop rows, and compared to a noninoculated area. CLS severity was quantified at regular intervals at specific distances from the inoculum source and samples were taken at the end of the season for isolation and genotype characterization. Data from two years is being compiled and analyzed.

OR – Powdery scab suppressive activity of field soils. We developed a greenhouse bioassay to classify soils as suppressive or conducive to powdery scab. To date, two greenhouse bioassays have been conducted and ten field soils have been evaluated for powder scab suppressive activity. Based on Spongospora subterranea f. sp. subterranea (Sss) root infection, there was variation in powdery scab suppressive activity among the field soils that were assayed. While some of that disease suppressive activity appeared to be due to soil physical properties (i.e., disease suppressive activity was eliminated when raw soils were “diluted” with potting media), three soils were identified with suppressive activity that appeared to be associated with microbial activity (i.e., disease suppressive activity remained after raw soils were “diluted” with potting media and were eliminated by autoclaving). Future research is planned to characterize the microbial taxa linked to the suppression of powdery scab and identify indicator species associated with powdery scab suppression. We also plan to identify the soil physical and chemical properties that correlate with shifts in microbial communities associated with disease suppression and examine if salinity affects the soil microbial community and powdery scab incidence or severity.

TN- We aim to understand the modulation of plant traits, disease resistance in particular, by members of the host-associated metagenomic community. This information can be applied to breeding resistance to complex disease while accounting for microbes that modulate host the host defense response pathway and that positively and negatively interact with pathogens. We are also identifying potential biocontrols and underlying multipartite interactions that might explain the often-observed variability in efficacy. By understanding these interactions at a systems level, we hope to predict biocontrol efficacy and identify a blend of microbes to maintain stable efficacy. On the long-term, breeding strategies can select alleles/genetic backgrounds that actively recruit and enrich for beneficial/disease-suppressing microbes from the environment.

WA- Phenazines play a key role in the health and sustainability of dryland wheat. Wheat grown without irrigation in the low-precipitation zone of the Columbia Plateau of the Pacific Northwest (PNW) selects for phenazine-1-carboxylic acid (PCA)-producing Pseudomonas spp. that comprise 1 to 10% of the culturable bacteria on wheat roots. Analysis of the microbiome of dryland wheat and continue to show that PCA-producing Pseudomonas spp. suppress a wide range of soilborne fungal pathogens, including Gaeumannomyces, Fusarium, and Rhizoctonia. They produce biofilms, which help soil particles stick together, thus preventing erosion; they enhance the reactivity and mobility of Fe derived from soil minerals, thus increasing the quantities of bioavailable iron to the plants; and they strongly induce resistance to foliar pathogens. These findings show that PCA producing pseudomonads are one of the most important groups of bacteria in soil microbiome contributing to the health and sustainability of dryland wheat.

WA- Phenotyping to detect early effects of pathogen infection on tomato before symptom development. Tomato seedlings were used as a model plant to determine the early impact of infection by the pathogen Pseudomonas syringae pv. tomato (Pst) on growth. In less than 24 hours after application of Pst to leaves at a dose of log 7 CFU per mL, phenotyping via 3D laser scanning triangulation and RGB, fluorescence, and VNIR hyperspectral imaging detected significant changes in the physiology and morphology of the leaves, even though no symptoms were visible. Within hours of Pst inoculation, the leaf area and density of leaves and stems decreased significantly because leaves were unable to fully expand, and the photosynthetic activity of the leaves significantly declined. Phenotyping tools are playing an increasing role in identifying how biotic and abiotic stresses affect plant growth prior to the appearance of any visible damage or symptoms, facilitating early intervention to alleviate the stress.

Objective 3 Implement sustainable management strategies for soilborne pathogens that are biologically based and are compatible with soil health management practices.

CA- A metagenomics study demonstrated that land-use practices differentially affect the composition of the soil microbiomes. This study included native undisturbed soil, soil from a field in transition from pasture to organic agriculture and soil from an intense agricultural production system. The work also demonstrated that disease suppression is tied to the presence of specific groups of bacterial and fungal communities. This work is an important step toward the understanding of how natural soil succession patterns and associated factors affect the soil microbial structures and how these key ecological drivers lead to the development of sustainable farming systems in coastal California by enriching specific microbiomes to limit plant disease and increase crop production.

NY- Efficacy of fungicides for Cercospora leaf spot control in table beet, 2023. The experiment was conducted at Cornell AgriTech in Geneva, New York. The crop was planted on 31 May using a Monosem planter at the rate of 17 seeds/ft with 30-in. row spacing. Fertilizer (300 lb/A 10-5-10 + 2 lb/A Boron) was banded at planting following incorporation of 300 lb/A of the same fertilizer one day earlier. For weed management, the herbicides Dual Magnum (0.67 pt/A) + Nortron (30 fl oz/A) were applied directly after planting. Treatments (n = 12) were arranged in a randomized complete block design with four replications, including a nontreated control. The trial was irrigated using solid set sprinklers for optimal plant growth and disease development. Plots consisted of 10-ft sections of two adjacent rows, with a nontreated buffer of 5-ft between plots within rows. Two nontreated rows separated adjacent plots. Fungicides were applied using a CO₂-pressurized backpack sprayer (26.4 gal/A; psi = 30), with three TeeJet 8002VS flat fan nozzles spaced 19 in. apart along a 38-in. boom. Fungicides were applied at 62, 68, 78, and 83 DAP. A backpack sprayer was used to apply an inoculum suspension (8.5 × 10³ viable cfu/ml) at 63 DAP, containing a mixture of four Cercospora beticola isolates representative of the New York genotypes. Plant density was assessed at 49 DAP by counting the number of plants in a 3.2-ft section within each row. Cercospora leaf spot (CLS) severity (%) was quantified by estimating the area of the leaf covered by disease compared to the entire leaf area on 20 arbitrarily selected leaves within each plot (10/row) at 63, 74, 81, 89, 96, 102, and 109 DAP, and used to calculate epidemic progress (area under the disease progress curve; AUDPC). At 109 DAP, the normalized difference vegetative index (NDVI) was measured using a GreenSeeker hand-held radiometer by scanning the entire length of one row, 3.2-ft above the canopy. At 110 DAP, the effect of treatment on foliar biomass and root yield components was evaluated by removing foliage from plants within a 3.2-ft section of each plot and recording weight after drying at 140ºF for 48 h. The effect of fungicides on final CLS severity, AUDPC, NDVI, root number and weight, and dry weight of foliage was analyzed using a generalized linear model.

Final CLS severity in nontreated plots was high with an average of 90.1%. Plant density was not significantly different across the trial at 49 DAP (P = 0.593) and varied between an average of 21.6 and 31.6 plants per 3.2-ft section. Root number at 110 DAP was not significantly affected by treatment (P = 0.195). Treatment also had no significant effect on root weight (P = 0.765). All treatments significantly reduced CLS severity at 109 DAP and AUDPC. The conventional fungicide standard program (Miravis Prime and Tilt) was highly efficacious and reduced final CLS severity and AUDPC compared to the nontreated control by 64.3% and 87.4%, respectively. Champ 2F was also highly efficacious and significantly decreased final CLS severity and AUDPS by 75.1% and 89.4%, compared to the nontreated control, respectively, and was not significantly different from the Miravis Prime and Tilt rotation. Four applications of Theia or Howler provided moderate CLS control and final CLS severity was reduced by an average of 41.5% compared to the nontreated control plots. AUDPC in plots receiving rotations of Miravis Prime and Theia or Howler was not significantly different from the Miravis Prime and Tilt rotation, and Champ. AUDPC in plots receiving BF009-03 was moderately reduced and not significantly different from Curezin and SeCurezin. Reductions in disease intensity led to significant increases in NDVI and dry weight of foliage.

2023. Efficacy of OMRI-listed fungicides for white mold control in black bean in New York, 2023. The experiment was conducted at the Gates West Organic Farm of Cornell AgriTech in Geneva, New York. The crop was planted on 6 Jun using a Monosem planter at the rate of 9 seeds/ft with 30-in. row spacing and managed using organic practices. Poultry manure (500 lb/A 5-4-3) was broadcast applied and incorporated on the same day of planting. For Japanese beetle control, Entrust (6 fl oz/A) was applied at 50 days after planting (DAP). Treatments (n=8) were arranged in a randomized complete block design with four replications including a non-treated control. The entire trial area was irrigated as necessary for optimal plant growth and disease development using solid set sprinklers. Individual plots consisted of 10 ft sections of two adjacent rows, with a non-treated buffer of 5 ft between plots within rows. Two non-treated rows separated adjacent plots. Fungicides (+ 0.25% v/v NuFilm) were applied using a CO₂-pressurized backpack sprayer (26.4 gal/A), with three TJ 8002VS flat fan nozzles spaced 19 in. apart along a 38 in. boom. Fungicides were applied at 55 and 62 DAP. Plants were inoculated with Sclerotinia sclerotiorum ascospores within 24 h of the first fungicide applications at a concentration of 1.28× 10³ ascospores/ml using a backpack sprayer. The average germination efficiency of ascospores was 68%. Plant density (number of plants/ft) was assessed in each of the two inner rows prior to the application of fungicides at 16 DAP. Canopy health was evaluated by scanning the entire length of each plot with a hand-held GreenSeeker radiometer to measure the Normalized Difference Vegetative Index (NDVI) at 1 m above the bean canopy at 72 DAP. The effect of treatment on the incidence of white mold on plants and pods, and yield was quantified at 76 DAP. Entire plants were removed from an arbitrarily selected 3.2-ft section within each plot and pods were manually removed. Individual pods and plants were classified as either healthy or diseased. Diseased plants and pods had either white mold symptoms and/or signs of S. sclerotiorum (mycelia and/or sclerotia). The incidence of white mold on pods and plants was then calculated as a function of the total number of pods or plants per plot × 100. Healthy pods from each plot were weighed and the number of pods counted to calculate the average weight for an individual healthy pod. The efficacy of fungicides on white mold incidence (%) on pod and plants, NDVI, and pod yield components was quantified by analysis of variance. Means of each variable were separated by a Fisher’s protected least significant difference test (P = 0.05) (Genstat Version 22).

The incidence of white mold was high in non-treated plots with an average of 51.1% and 7.2% on plants and pods, respectively. Plant density was not significantly different across the trial area according to treatment allocation (P = 0.653) and varied between 68.1 and 73.9 plants per 10 feet. All treatments significantly (P < 0.001) reduced the incidence of white mold on plants and pods, and increased the NDVI, compared to the nontreated plots. All treatments significantly reduced disease incidence and were not significantly different between each other. The average reduction in white mold incidence in plants and pods from the treatments was 68.2% and 77%, respectively. All treatments also significantly increased NDVI compared to the nontreated plots and were not significantly different between each other. Treatment had no significant effect on pod number (P = 0.838) and the average weight of one pod (P = 0.706).

NY- Survival of Sclerotinia sclerotiorum sclerotia in NY. White mold caused by Sclerotinia sclerotiorum is a serious disease affecting many field and specialty crops in New York (NY). The primary inoculum for white mold is sclerotia that are hardened masses of mycelia that survive adverse environmental conditions and periods of non-hosts. However, NY crop guidelines lack rotation and residue management recommendations based on local knowledge of sclerotial survival. A field trial was established in October 2020 by deploying S. sclerotiorum sclerotia in mesh bags on the soil surface or shallowly buried (placed at 3 cm depth in the soil) at Geneva, NY. Bags were periodically collected from 67 to 769 days. At each time, sclerotial retrieval (number of sclerotia) was assessed by counting and viability evaluated through myceliogenic germination. Sclerotial retrieval was significantly affected by soil depth and was higher in those on the surface than buried. Time also affected the retrieval of sclerotia which was significantly reduced after 250 days. The interaction between burial and time had a significant effect on sclerotial viability. Approximately 15% of sclerotia placed on the surface were still viable after 769 days. After 433 days, viability of buried sclerotia was also significantly reduced compared to those on the surface. After 670 days, none of the buried sclerotia were viable. These findings suggest a rotation of at least two years between susceptible crops is required to reduce primary inoculum. However, given that low inoculum densities are sufficient to initiate a white mold outbreak, a longer rotation may be beneficial. In a cultivated system, timely tillage of crop residue to bury sclerotia after harvest to promote degradation is encouraged.

OR –Effects of rotation, soil amendment, and fumigation on potato early dying and the soil microbial community. In 2023, we continued work on two potato cropping systems experiments established in 2019 to examine how management practices including crop rotation with traditional fumigation, mustard biofumigant crop, dairy compost amendment, and a mustard biofumigant crop combined with a dairy compost amendment influence the soil abiotic and biotic properties, pathogen inoculum densities, and plant health and productivity. To date, we have established that over one multi-year rotation, it is possible to alter soil characteristics, including pathogen loads, through soil health management. Meanwhile, the effects of soil-health-promoting practices on plant health and tuber yield depended on cultivar and rotation length. These results suggest that use of alternative agricultural practices to reduce V. dahliae inoculum density in soil will take time and may be enhanced when combined with longer rotation lengths.

Objective 4. Provide outreach, education, extension and technology transfer to our clients and stakeholders- growers, biocontrol industry, graduate and undergraduate students, K-12 students and other scientists.

CA- James Borneman gave presentations to undergraduate in his Microbiomes course (MCBL 126). These presentations covered biological suppression of plant parasitic nematodes as well as root microbes that may inhibit or exacerbate Huanglongbing (HLB) disease of citrus.

CA- The target audiences of this project are producers of conventional and organic crop production systems and shippers, seed/fertilizer/pesticide/fumigant/irrigation sales and application companies, pest control advisors and Verticillium researchers. Other critical stakeholders were the California Strawberry Commission, California Leafy Greens Research Board, and others involved in crop production that also suffer from soilborne diseases. Because the status of the disease on one crop affects the crops that follow, many commodity groups will have an intense interest in the outcome of this project. The results obtained from this project will be broadly applicable to crops heavily dependent on soil fumigation in the western US as well as other states in the US.  The outcomes of this work have been presented to these audiences over the year.

CA- University of California Statewide Integrated Pest Management Program (UC IPM) recently obtained grant funding from California Department of Food and Agriculture to develop extension education materials on methods to manage soilborne pests without fumigants. According to the Pesticide Use Report recently published by California Department of Pesticide Regulation, agricultural production used 197,000,00 pounds of pesticides in 2020. Sulfur applications accounted for 24% of the total, while horticultural oils accounted for 22%, and soil fumigants 19%. Since soil fumigants pose significantly higher human health and environmental risks than sulfur or horticultural oils, focusing on alternatives to soil fumigants has significant potential benefits for California. Soil fumigants are used to manage soilborne diseases, nematodes, weeds, and insects. Research has identified several potential alternatives to fumigants including crop rotations, cover crops, mustard family crops as green manures, anaerobic soil disinfestation, soil solarization, biosolarization, steam applications, and compost amendments. Research reports and extension education materials on these individual tactics are distributed in various venues but there is no extension resource for growers to compare tactics and select the most appropriate one(s) for their crop-pest situation. In addition, there are numerous methods for monitoring of soilborne pests and ‘soil health’ more broadly. Gathering the soilborne pest and soil health monitoring methods into one extension resource will assist growers in making decisions for their situation and farming goals.

CA- UC IPM will convene an alternatives to soil fumigants workgroup to assess current soil fumigant alternatives, develop a decision support tool for growers who are seeking to use alternatives methods, develop practical biological metrics for soilborne pest and soil health monitoring, and prioritize research needs. UC Agricultural Experiment Station faculty, Cooperative Extension Specialists, Cooperative Extension Advisors working in soilborne pest management will be invited to participate in the workgroup. The target is 20-25 experts, each bringing their diverse expertise and perspectives to focus on this problem. The workgroup would meet at least four times for in-person, one-day intensive sessions and continue the collaboration through email and shared online documents between meetings. The goals are a decision-support tool for selecting alternatives to soil fumigants, descriptions of practical methods for monitoring for soilborne pests and soil health, and prioritized list of research and extension needs. These would all be available through the UC IPM website.

MT- Outputs included presentations at two field days to over 200 attendees. A graduate student presentation was also given at the International Congress of Plant Pathology, 20-25 August, Lyon, France.

NY- Outreach activities on sustainable disease management.

In 2023, Pethybridge gave 8 extension/outreach presentations on soilborne disease management to the broadacre vegetable and dry bean industry stakeholders and growers. These presentations were predominantly meetings organized by Cornell Cooperative Extension throughout NY, and the Maine Organic Farmers and Growers.

Undergraduate research experience

Pethybridge had an undergraduate summer scholar in the lab during summer 2023.

OR (Frost) – Advised one faculty research assistant, one technician, three graduate students, and one undergraduate student. In 2023, we published five refereed papers, one extension document, and four abstracts. Information has been disseminated to clientele within the region through talks at nine grower education events and two field days (14 grower education talks total), and to scientific peers via four presentations. I have provided plant disease diagnostic services via the Pathology Diagnostic Clinic at the HAREC to Oregon, southeastern Washington, Idaho, and other crop production regions in the U.S. These services result in approximately 250 direct contacts with farmers or crop managers every year. In 2023, I organized a workshop with topics including soil health for the Hermiston Farm Fair Grower education event. Editorial positions currently held include Senior Editor and Editor for the APS Journals Plant Disease and Phytofrontiers, respectively.

TN- Training graduate students and postdoctoral fellow.

Interaction with maize and sweet potato breeders on implementing metagenome-enhanced genomic prediction and understanding the modulation of complex by microbiome community members.

Working with extension faculty to evaluate the impact of microbiome on Fusarium ear and stalk rot disease.

VA- • Co-organized and launched the BBIG Boxwood Seminar series in August of 2023 with the environmental horticulture industry, public and private gardeners as well as extension and research communities as the primary audience.

• Presented biocontrol research results at the 2023 Plant Health - Annual Meeting of American Phytopathological Society in Denver, CO, 12th International Congress of Plant Pathology in Lyon, France, and 7th Partnership in Biocontrol, Biostimulant and Microbiome Conference USA in Raleigh, NC.
• Used Google group listservs for mass distribution of the latest research about boxwood blight mitigation

Peer Reviewed

Adams AK, Kristy BD, Gorman M, Balint-Kurti P, Yencho GC, Olukolu BA. (2023) Qmatey: An automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes. Briefings in Bioinformatics. 24 (6): bbad351

Adhikari T, Olukolu BA*, Paudel R, Pandey A, Halterman D, Louws F. (2023) Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in Alternaria linariae from Tomato. Phytopathology. https://doi.org/10.1094/PHYTO-07-23-0229-R

Arstingstall, K.A., DeBano, S.J., Li, X., Wooster, D., Rowland, M.M., Burrows, S. and Frost, K. 2023. Investigating the use of DNA metabarcoding to quantify bee foraging and effects of threshold selection. PLOSONE 18:e0282715 https://doi.org/10.1371/journal.pone.0282715.

Bell-Dereske LP, Benucci GM, da Costa PB, Bonito G, Friesen ML, Tiemann LK, Evans SE. Regional biogeography versus intra-annual dynamics of the root and soil microbiome. Environmental Microbiome. 2023 Jun 7;18(1):50.

Cheng, W., Xue, H., Yang, X., Huang, D., Cai, M., Huang, F., Zheng, D., Peng, D., Thomashow, L.S., Weller, D.M., Yu, Z., and Zhang, J. 2022. Multiple receptors contribute to the attractive response of C. elegans to pathogenic bacteria. EMBO Reports. 11(1). https://doi.org/10.1128/spectrum.02319-22.

Delventhal, K., Busby, P., and Frost, K.E. 2023. Tare soil alters the composition of the developing the potato rhizosphere microbiome. Phytobiomes 7:91-99

Delventhal, K., Skillman, V.^#, Li, X., Busby, P., and Frost, K.E. 2023. Characterizing variation in the bacterial and fungal tare soil microbiome of seed potato. Phytobiomes 7:78-90.

Figueroa JL, Panyala A, Colby S, Friesen M, Tiemann L, White III RA. MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data. bioRxiv. 2022 Nov 24:2022-11.

Flasco, M. T., Cieniewicz, E. J., Pethybridge, S. J., and Fuchs, M. F. 2023. Distinct red blotch disease epidemiological dynamics in two nearby vineyards. Viruses 15:1184.https://doi.org/10.3390/v15051184.

Heck, D. W., Hay, F. S., and Pethybridge, S. J. 2023. Enabling population biology studies of Stemphylium vesicarium from onion with microsatellites. Plant Dis. PDIS-04-23-0706-RE. Published First Look 17 June 2023. https://doi.org/10.1094/PDIS-04-23-0706-RE.

Heck, D. W., Sharma, P., Kikkert, J. R., and Pethybridge, S. J. 2023. Sampling, a new iOS application for assessment of damage by diseases and pests using sequential sampling plans. Plant Dis. 107:1714-1720. https://doi.org/10.1094/PDIS-04-22-0800-SR

Jernigan, A., Kao-Kniffin, J., Pethybridge, S. J., and Wickings, K. 2023. Soil microarthropod effects on plant growth and development. Plant and Soil 483:27-45.Soil microarthropod effects on plant growth and development (springer.com)

Klasek, S., Crants, J., Abbas, T., Ashley, K., Bolton, M., Caballero, J.I., Celovsky, M., Gudmestad, N.C., Hao, J., Jahn, C., Nkuekam, G.K., Lankau, R., Larkin, B., Lopez, E., Miller, J., Moore, A., Pasche, J., Ruark, M., Schroeder, B., Shan, S., Skillman, V., Srour, A., Stasko, A., Steinke, K., Stewart, J., Thornton, M., Zitnick-Anderson, K., Frost, K., Rosen, C., and Kinkel, L. 2023. Potato soil core microbiomes are regionally variable across the continental U.S. Phytobiomes (in press).

Menalled, U. D., Smith, R. G., Cordeau, S., Di Tommaso, A., Pethybridge, S. J., and Ryan, M. R. 2023. Phylogenetic relatedness can influence cover crop-based weed suppression. Scientific Rep. 13:17323. https://doi.org/10.1038/s41598-023-43987-x.

Pethybridge, S. J., Damann, K., Murphy, S. P., Diggins, K., and Gleason, M. 2023.Optimizing mesotunnels for organic acorn squash in New York. Plant Health Progress. PHP-08-23-0072-RS. Accepted 16 October 2023. On First Look. Proofs returned 7 December 2023. https://doi.org/10.1094/PHP-08-23-0072-RS.

Pethybridge, S. J., Murphy, S. P., and Kikkert, J. R. 2023. Growth manipulation of slicer carrots by foliar-applied gibberellic acid 3 in New York. HortTechnology 33:325-332. https://doi.org/10.21273/HORTTECH05231-23.

Pethybridge, S. J., Murphy, S. P., Branch, E. B., Sharma, P. S., and Kikkert. J. R. 2023. Manipulating table beet growth using exogenous gibberellic acid 3 in New York, USA. Annals of Applied Biology Published 19 September 2023. On Early View. https://doi.org/10.1111/aab.12870.

Pethybridge, S. J., Murphy, S., Lund, M., and Kikkert. J. R. 2023. Survival of Sclerotinia sclerotiorum sclerotia in central New York. Plant Disease. PDIS-10-23-2126-SC. Accepted 6 November 2023. On First Look 9 November 2023.https://doi.org/10.1094/PDIS-10-23-2126-SC.

Rivedal, H.M., Temple, T., Thomas, W.J., Ocamb, C.M., Funke, C., Skillman, V., Jackson, R., Jones, G., Shrestha, G., KC, A., Dung, J.K.S., and Frost, K.E. 2023. First report of Spiroplasma citri causing disease in field-grown hemp (Cannabis sativa L.) in the Pacific Northwest. Plant Disease (in Press).

Rodriguez-Herrera, K. D., Ma, X., Swingle, B., Pethybridge, S. J., Gonzalez-Giron, J. L., Hermann, T. Q., Damann, K., and Smart, C. D. 2023. First report of cucurbit yellow vine disease caused by Serratia marcescens in New York. Plant Dis. Published Online (First Look) 24 July 2023. https://doi.org/10.1094/PDIS-06-23-1051-PDN.

Saif, M. S., Chancia, R., Hassanzadeh, A., Pethybridge, S. J., Murphy, S. M., and van Aardt, J. 2023. Forecasting table beet root yield from spectral and textural features from hyperspectral UAS imagery. Remote Sensing 15:794. https://doi.org/10.3390/rs15030794.

Savary, S., (coordination team: Savary, S., Andrivon, D., Esker, P. D., Frey, P., Huberli, D., Kumar, J., McDonald, B. A., McRoberts, N., Nelson, A., Pethybridge, S. J., Rossi, V., Schreinemachers, P., and Willocquet, L.) 2023. A global assessment of the state of plant health. Plant Dis. PDIS-01-23-0166-FE. Published First Look 12 May 2023. https://doi.org/10.1094/PDIS-01-23-0166-FE.

Sharma, S., Strickland, D. A., Hay, F. S., and Pethybridge, S. J. 2023. First report of halo blight on hop (Humulus lupulus) caused by Diaporthe humulicola in New York. Plant Dis. 107:216. https://doi.org/10.1094/PDIS-01-22-0202-PDN

Smith Becker, J., Ruegger, P., Borneman, J., and Becker, J.O. 2023. Indigenous populations of a biological control agent in agricultural field soils predicted suppression of a plant pathogen. Phytopathology. Doi:10.1094/PHYTO-07-23-0221-R

Ulbrich TC, Rivas-Ubach A, Tiemann LK, Friesen ML, Evans SE. Plant root exudates and rhizosphere bacterial communities shift with neighbor context. Soil Biology and Biochemistry. 2022 Sep 1;172:108753.

Wen, T., Ding, Z., Thomashow, L.S., Hale, L.E., Yang, S., Xi, P., Liu, X., Wang, H., Shen, Q., and Yuan, J. 2023. Deciphering the mechanism of fungal pathogen-induced disease-suppressive soil. New Phytologist. 238(6):2634-2650. https://doi.org/10.1111/nph.18886.

White III RA, Garoutte A, Mclachlan EE, Tiemann LK, Evans S, Friesen ML. Genome-Resolved Metagenomics of Nitrogen Transformations in the Switchgrass Rhizosphere Microbiome on Marginal Lands. Agronomy. 2023 May 3;13(5):1294.

Yin, C., Hagerty, C., and Paulitz, T.C. 2022. Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen. Frontiers in Microbiology. 13. Article 908981. https://doi.org/10.3389/fmicb.2022.908981.

Yin, C., Schlatter, D.C., Hagerty, C., Hulbert, S.H., Paulitz, T.C. 2023. Disease induced assemblage of the rhizosphere fungal community in successive plantings of wheat. Phytobiomes Journal. 7 (1):100-112. https://doi.org/10.1094/PBIOMES-12-22-0101-R.

Book Chapters

Meeting presentations, abstracts and proceedings

Adams, A. K, Brandon D Kristy, Myranda S Gorman, Alhagie K Cham, Bode A Olukolu (2022). OmeSeq-qRRS/Qmatey-A platform for broad-spectrum, quantitative, and strain-level metagenomic profiling. Microbiome, Cold Spring Harbor Laboratory.

Barnes, E. M., Yin, C., Schlatter, D., Hao, P., Willmore, C., Paulitz, T., and Tringe, S. G. 2023 The Root Microbiome of Camelina in the Dryland Wheat Production Areas of Eastern Washington. Poster presented at Annual Meeting of American Society of Microbiology, Houston, TX, June 15-19, 2023.

Becker, S.J., J. Borneman, P. Ruegger, and J.O. Becker 2022. Predicting specific cyst nematode suppression in California sugar beet soils. Journal of Nematology 54: no. 1, pp. 12.

Branch, E. A., and Pethybridge, S. J. 2023. Microbial communities associated with table beets from different field sites and production practices in New York State. Plant Health 2023, Denver, Colorado, 12-16 August 2023 (Poster Presentation).

 Delgado, H., Camille Wendlandt, Maren L Friesen, Stephanie Porter.  Loci associated with differential success in nodulating contrasting host species in naturally co-evolving legume and rhizobium populations. American Phytopathology Society Meeting Aug 2023

Eaker, A. , Richard Allen White III, Maren L Friesen. Mutalism maintenance: comparative genomics of coexisting clovers. American Phytopathology Society Meeting Aug 2023

Echeverria, D., Skillman, V., Rivedal, H.M., Temple, T., and Frost, K. 2023. Identifying biotic characteristics of soils that suppress powdery scab of potato (Solanum tuberosum L.).  American Phytopathological Society Annual Meeting, August 13 – 16, Denver, CO.

Echeverria, D., Skillman, V., Rivedal, H.M., Temple, T., and Frost, K. 2023. Identifying biotic characteristics of soils that suppress powdery scab of potato (Solanum tuberosum L.). Phytopathology xx(Suppl. yy):SX.YY

Friesen, M. Can we replace synthetic nitrogen with microbes? WA SoilCon Feb 2023

Frost, K., Charlton, B., and Sathuvalli, V. Struggles with Ss and powdery scab suppression. WERA089: Potato virus and virus-like disease management working group and potato tuber necrotic virus SCRI research meeting, March 16-17, 2023, Denver, CO.

Frost, K., Klasek, S., Crants, J., Rosen, C. and Kinkel, L. 2023. Relationships between soil health, soil microbiomes, and potato yield. Annual Meeting of the Potato Association of America, July 23-27, Charlottetown, PEI, CA.

Frost, K., Klasek, S., Crants, J., Rosen, C. and Kinkel, L. 2023. Relationships between soil health, soil microbiomes, and potato yield. Annual Meeting of the Potato Association of America, July 23-27, Charlottetown, PEI, CA.

Landry, D., Alison Adams, Virginia Sykes, Tara Rickman, Heather Kelly, and Bode A. Olukolu (2022) Evaluation of Fusarium Ear Rot Resistance and Impact on Yield in non-GMO and Bt-Maize Hybrids. The Tennessee Agricultural Production Association (TAPA), Gatlinburg, TN.

Loria, K., Brockmueller, B., Darby, H., Diggins, K., Everest, E., Gomez, M., Krezinski, I., Mallory, E., Molloy, T., Moore, V., Murphy, S., Pelzer, C., Pethybridge, S. J., Ryan, M., Sharifi, A., Smith, D., and Youngerman, E. 2023. Expanding productivity and resilience of organic dry bean systems in the Northeast and upper Midwest. Bean Improvement Cooperative Conference, Greenville, SC. (Poster Presentation). 6-8 November 2023.

Luong, K. P., McFeaters, T. S., Pethybridge, S. J., and Esker, P. D. 2023. Associations of microclimates, soil, and histories, on the population structure of diversity of Sclerotinia sclerotiorum in Pennsylvania and New York. Plant Health 2023, Denver, Colorado, 12-16 August 2023 (Poster Presentation).

Luong, K. P., Pethybridge, S. J., and Esker, P. D. 2023. Developing a high-throughput method for screening fungicide sensitivity in Sclerotinia sclerotiorum. Plant Health 2023, Denver, Colorado, 12-16 August 2023 (Poster Presentation).

Moore, A., Sathuvalli, V., Frost, K., Yilma, S., Aguilar, M., and Charlton, B. 2023. Powdery scab of potato: expanding genomic resources for the pathogen and host. American Phytopathological Society Annual Meeting, August 13 – 16, Denver, CO.

Moore, A., Sathuvalli, V., Frost, K., Yilma, S., Aguilar, M., and Charlton, B. 2023. Powdery scab of potato: expanding genomic resources for the pathogen and host. Phytopathology xx(Suppl. yy):SX.YY

Odoi M, Onufrak A, Boggess S, Pantalone V, Olukolu B, Trigiano R, Hadziabdic D (2023) Compendium of plant-associated microbes on endangered whorled sunflower. American Phytopathological Society Conference, Denver, CO (August 2023).

Odoi ME, Onufrak A, Boggess SL, Pantalone V, Olukolu B, Hadziabdic D, Trigiano RN. (2022) Characterizing endophytic leaf fungal composition of whorled sunflower. Phytopathology. 112(11):178

Parks, J, Maren L Friesen. The role of microorganisms in nutrient provisioning in Peaola. WSU Plant Sciences Retreat. March 2023. Pullman, WA

Parks, J.  Maren L Friesen.  Microbial underpinnings of pea-canola intercropping success. MPS Seminar. Oct 2023. Pullman, WA

Paulitz, T. C. 2023. The Soil Microbiome & Soil Health. A 1.5-hour hands-on lab to growers at the Wheat Academy, Dec. 2023

Peng, H., Barnes, E. M., Yin, C., Schlatter, D., Willmore, C., Paulitz, T., Tringe, S. G., and Lu, C. 2023. The Root Microbiome of Camelina in the Dryland Wheat Production Areas of Eastern Washington. poster at the Department of Energy Biological Systems Science Division Meeting, Bethesda, MD, April 17-18, 2023.

Pethybridge, S. J., and Hay, F. S. 2023. Fight the blight: Stemphylium leaf blight, an emerging threat to United States onion production. National Allium Research Conference, San Antonio, TX.

Pethybridge, S. J., and Ryan, M. R. 2023. Breaking down the barriers to organic no-till soybean and dry bean production through improved white mold management. USDA NIFA Organic Programs Project Directors Meeting (Poster and Oral Presentation). Pp. 73-75.

Petipas, R.H., E.A. McNeil, J.F. Tabima, M.L. Friesen, and C.J. Jack. Prairie soil promotes wheat growth but are the effects caused by soil microbes? American Society of Naturalists Meeting, Virtual Asilomar, Asilomar, CA. January 2023

Pineros-Guerrero, N., Hay, F. S., Heck, D. W., Klein, A., Hoepting, C. A., and Pethybridge, S. J. 2023. Determining the contribution of onion transplants to the population genetics of Stemphylium vesicarium in New York, USA using microsatellite markers. Proc. International Congress of Plant Pathology, Lyon, France. 20-25 August 2023.

Ryan, M. R., Allen, J., Brockmueller, B., Loria, K., McFadden, E., Menalled, U. D., Pelzer, C. J., Pethybridge, S. J., Rowland, A., Sharifi, A., Silva, E. M., Wayman, S., and Youngerman, E. 2023. Taking out tillage with cover crops. Proc. Northeast Cover Crops Council Annual Meeting, Portland, Maine, 16 February 2023 (Poster Presentation).

Saif, M. S., Chancia, R. A., Pethybridge, S. J., Murphy, S. P., Hassanzadeh, A., and van Aardt, J. 2023. Predicting table beet yield with hyperspectral UAS imagery. STRATUS Conference, Rochester, NY, 22-24 May 2023.

Saif, M. S., Chancia, R., Sharma, P., Murphy, S. P., Pethybridge, S. J., and van Aardt, J. 2023. Detection of Cercospora leaf spot disease in table beets from UAS multispectral imagery. Proc. International Congress of Plant Pathology, Lyon, France, 20-25 August 2023.

Sauceda Padron, A. Y., Sharma, P., and Pethybridge, S. J. 2023. Determining the mating types in Cercospora beticola populations from a table beet field. Proc. 2023 Cornell AgriTech Summer Scholars Program, Cornell University, Geneva, New York, Abstract.

Sharma, P., Murphy, S., Kikkert. J. R., and Pethybridge, S. J. 2023. Effect of residue management on Cercospora leaf spot of table beet and microbiome. Proc. International Congress of Plant Pathology, Lyon, France. 20-25 August 2023.

Thornton, M., Olsen, N., Miller, J., Frost, K., Goyer, A., and Qin, R. 2023. Is plant maturity a reliable indicator of bruise susceptibility? Annual Meeting of the Potato Association of America, July 23-27, Charlottetown, PEI, CA.

Webster, C., Anita Paneru, Won-Jun Kim, Abdelrhman Mohamed, Ibrahim Bozyel, Eduardo Sanchez, Natalie Sanchez, Maren L. Friesen, and Haluk Beyenal. Electrochemically active biofilm in soil. EMSL User Meeting: Visualizing Chemical Processes Across the Environment, October 3–5, 2023

Yin, C., Larson, M., Lahr, N., and Paulitz, T. 2023. Wheat Rhizosphere-Derived Bacteria Protect Soybean Roots from Fusarium graminearum Infection. Poster presented at the Annual Meeting of the American Phytopathological Society, Denver, CO, Aug. 13-16, 2023.

Technical Bulletins and Extension Publications

Aegerter, B.J., Becker, J.O., Davis, R.M., Goodell, P.B., Henderson, D.W., Lanini, W.T., Natwick, E.T., Stapleton, J.J., Stoddard, C.S., Turini, T.A., Westerdahl, B.B. 2022.

Becker, J. O. Agriculture: Pest Management Guidelines Cucurbits. UC IPM Pest Management Guidelines: Cucurbits. UC ANR Publication 3445. Davis, CA. https://ipm.ucanr.edu/agriculture/cucurbits/

Becker, J.O. and Smith Becker, J. 2022. 35th Anniversary of the Nematode Quarantine Facility at the University of California Riverside. Topics in Subtropics 22, 7-8.

Becker, J.O. and Westerdahl, B. 2023. Citrus: Nematodes. Pp. 183-185. (revision), UC IPM Pest Management Guideline: Citrus, UC ANR Publication 3441, Publication URL:

Branch, E. B., Pethybridge, S. J., Murphy, S. M., and Kikkert. J. R. 2023. Efficacy of fungicides for control of Rhizoctonia damping-off and root rot in table beet, 2022. Plant Dis. Manage. Rep. 17:V026.

Damann, K., and Pethybridge, S. J. 2023. Hoop pending for covered agriculture. YouTube Video. 20 January 2023. The Current Cucurbit Website.

Damann, K., and Pethybridge, S. J. 2023. On-farm trials: three years of grower’s feedback.  pending for covered agriculture. YouTube Video. 20 January 2023. The Current Cucurbit Website. 20 January 2023. The Current Cucurbit Website.

Gonzalez, J., Gleason, M. R., Gonthier, D., Pethybridge, S. J., Nair, A. J., Bessin, A., Williams, M., Zhang, W., Dantzker, H., Fiske, A., Diggins, K., Mphande, K., Badilla, S., and Damann, K. 2023. Mesotunnels for improved management of cucurbit pests and diseases: Tips for growers.

Gonzalez, J., Gonthier, D., Pethybridge, S. J., Bessin, R., Nair, A., Zhang, W., Cheng, N., Fiske, K., Gauger, A., Damann, K., Murphy, S., Badilla, S., Mphande, K., and Gleason, M. 2023. Mesotunnels for organic management of cucurbit pests and diseases: Tips for growers. NCPA 038. North Central IPM Center. Pp. 8.

Govinda, S., Ocamb, C.M., Rivedal, H., KC, A., Dung, J., Frost, K., Wysocki, D., Reitz, S., and Steiner, J. 2022. State-wide needs assessment for the hemp industry in Oregon. Oregon State University Extension and Experiment Station Communications Publication EM9417. https://extension.oregonstate.edu/catalog/pub/em-9417-statewide-needs-assessment-hemp-industry-oregon. Role: Participated in the needs assessment activities, wrote and edited content.https://ipm.ucanr.edu/agriculture/citrus/nematodes/

Kikkert. J. R., Lund, M., and Pethybridge, S. J. 2023. What to do after a bad Sclerotinia white mold season. Cornell VegEdge 19(21):9.VegEdge newsletter – Vol. 19, Iss. 21, 8/30/2023 (cornell.edu)

Pethybridge, S. J. 2023. Crop insights – beets. Cornell VegEdge 19(15):5.VegEdge newsletter – Vol. 19, Iss. 15, 7/19/2023 (cornell.edu)

Pethybridge, S. J. 2023. White mold in tomato. Long Island Fruit and Vegetable Update 13 (29 June 2023). Cornell Cooperative Extension, Suffolk County. Pp. 2.

Pethybridge, S. J., and Damann, K. 2023. Feasibility of mesotunnels for muskmelon production. Mid-Atlantic Fruit and Vegetable Growers Convention, Hershey, Pennsylvania. 31 January 2022. Pp. xxx.

Pethybridge, S. J., and Murphy, S. 2023. Efficacy of fungicides for white mold control in snap bean, 2022. Plant Dis. Manage. Rep. 17:V013.

Pethybridge, S. J., and Murphy, S. M. 2023. Efficacy of fungicides for white mold control in snap bean. Mid-Atlantic Fruit and Vegetable Growers Convention, Hershey, Pennsylvania. 31 January 2022. Pp. xxx.

Pethybridge, S. J., and Murphy, S. M. 2023. Efficacy of fungicides for white mold control in snap bean. Mid-Atlantic Fruit and Vegetable Growers Convention, Hershey, Pennsylvania. 31 January 2022. Pp. xxx.

Pethybridge, S. J., Kikkert, J. R., and Telenko, D. 2023. Keep watch for tar spot in sweet corn. Cornell VegEdge 19(18):1-3.VegEdge newsletter – Vol. 19, Iss. 18, 8/9/2023 (cornell.edu)

Pethybridge, S. J., Murphy, S. M., and Damann, K. 2023. Feasibility of Mesotunnels for muskmelon production. Mid-Atlantic Fruit and Vegetable Growers Convention, Hershey, Pennsylvania. 31 January 2022. Pp. 38-40. http://www.pvga.org/23-proceedings/.

Pethybridge, S. J., Murphy, S. M., and Kikkert, J. R. 2023. Manipulating table beet and carrot production with plant growth regulators. Cornell VegEdge 19(1):6-VegEdge newsletter – Vol. 19, Iss. 1, 1/4/2023 (cornell.edu).

Pethybridge, S. J., Murphy, S. P., and Kikkert. J. R. 2023. Efficacy of conventional and OMRI-listed fungicides for Cercospora leaf spot control in table beet (2023 results). Cornell VegEdge 19(24):4-5.VegEdge newsletter – Vol. 19, Iss. 24, 11/1/2023 (cornell.edu)

Pethybridge, S. J., Murphy, S. P., and Kikkert. J. R. 2023. Efficacy of conventional and OMRI-listed fungicides for Cercospora leaf spot control in table beet. UMass Extension Vegetable Notes (November 9, 2023). VegNotes 35(24):4-6.november_9_2023_vegetable_notes.pdf (umass.edu)

Pethybridge, S. J., Murphy, S. P., Lund, M., and Kikkert, J. R. 2023. How long do sclerotia that cause white mold survive in central New York? Cornell VegEdge 19(25):4-5.VegEdge newsletter – Vol. 19, Iss. 25, 12/6/2023 (cornell.edu)

Rodriguez-Herrera, K. D., Ma, X., Swingle, B., Pethybridge, S. J., Reiners, S., Nault, B., Day, C. T. C., DuBeer, C., Herrmann, T. Q., and Smart, C. D. 2023. A new bacterial disease of cucurbits in NY: Cucurbit yellow vine disease caused by Serratia marcescens. Cornell AgriTech Factsheet.

Extension Talks/Field Days/Workshops/Consultations

Becker, J. S. P. Ruegger, J. Borneman, and J.O. Becker, Forecasting Sugar Beet Cyst Nematode Suppression in Imperial Valley Soils. University of California, Agricultural and Natural Resources Division, Statewide Conference, Fresno, CA, April 24-27, 2023.

Becker, J.O. and A. Ploeg. Non-fumigant nematicides efficacy improved against RKN by soil wetting agent. California Fresh Market Carrot Research Symposium; by Zoom, February 14, 2023.

Becker, J.O.. Avicta seed treatment: two with one blow. The 68^th Annual Conference on Soilborne Plant Pathogens and the 53^rd California Nematology Workshop 2023, Salinas, CA. March 28-30.

Borneman, J. and J.O. Becker Predicting Nematode Suppression in the Imperial Valley. Sugarbeet Research Board Meeting, Holtville, CA, March 22, 2023.

Echeverria, D., and Frost, K.E. Identifying soils and soil properties suppressive to powdery scab. OSU-HAREC Potato Field Day, Hermiston, OR, June 21, 2023 (~100)

Frost, K. E. Hermiston Farm Fair, General Session (AD). Twelve invited speakers. (~80 attendees)

Frost, K.E. Above ground problems with potato plants in the seed lots. First rating of the Washington State potato seed lot trial, Othello, WA, June 6, 2023 (~50)

Frost, K.E. Enhancing potato productivity through management practices that support soil health. 2023 Southern Rocky Mountain Ag Conference, Monta Vista, CO, February 8, 2023 (~115).

Frost, K.E. Managing soil health in potatoes: opportunities and challenges. Washington State Potato Commission: Potato Summit. Spokane, WA, December 12, 2023. (~35).

Frost, K.E. Plant disease identification, diagnosis, and management. Hermiston Ag and City Expo, Hermiston, OR, February 24, 2023. (~25).

Frost, K.E. Plant pathology program updates 2023. OSU-HAREC Potato Field Day, Hermiston, OR, June 21, 2023 (~100)

Frost, K.E. Potato soil health and soilborne disease management. Hermiston Farm Fair, Hermiston, OR, November 29, 2023 (~75).

Frost, K.E. Potato soil health: where have we been and where are we going? Washington-Oregon Potato Conference, Kennewick, WA, January 26, 2023 (~200).

Frost, K.E. Powdery scab, the environment, and implications for disease management. Hermiston Farm Fair, Hermiston, OR, November 29, 2023 (~90).

Frost, K.E. The soil environment and its effect on powdery scab of potato. 2023 Southern Rocky Mountain Ag Conference, Monta Vista, CO, February 7, 2023 (~75).

Frost, K.E., Harris, M., Mesko, J., Pavelski, R., Phillips, M., and Pink, M. Round table discussion with the Spudman Dream Team about production challenges today, how they are handled and what the future of the potato industry looks like. Panel discussion hosted by Spudman Magazine (Zoom), February 16, 2023 (~30).

Moore, A., Sathuvalli, V., and Frost, K.E. Mapping powdery scab resistance in potato. OSU-HAREC Potato Field Day, Hermiston, OR, June 21, 2023 (~100)

Parks, J, Maren L Friesen. Testing microbial mechanisms of nitrogen provisioning to canola. WA Oilseed Commission Annual Meeting. Feb 2023 Pullman, WA

Paulitz, T. C. and Garland-Campbell, K. 2023. Fusarium Crown Rot of Wheat- It’s Everywhere and Persistent. Wheat Life, Dec. 2023.

Paulitz, T. C. Fusarium Crown Rot, WSU Wheat Beat Podcast, recorded Dec. 2023.

Paulitz, T. C. Presented talk on new research at the AgExpo Farm Forum, Spokane, WA, Feb. 7, 2023.

Pethybridge, S. J. 2023. ECOBean – Industry Advisory Panel (by zoom). Attendees = 20. Duration = 2 hours. Total contact = 40 hours. 24 March 2023.

Pethybridge, S. J. 2023. Efficacy of products for white mold control in dry bean in New York. NYS Dry Bean Council Twilight Meeting, Geneva, New York. Attendees = 25. Duration = 2 h. Total contact = 50 hours. 26 September 2023.

Pethybridge, S. J. 2023. Objective 2 CC_SCRI Meeting. Activities in New York. CC_SCRI Project Advisory Panel (by zoom). Attendees = 20. Duration = 60 min. Total contact = 20 hours. 20 September 2023.

Pethybridge, S. J. 2023. Optimizing control of Cercospora leaf spot with improved scouting and disease forecasting. New York Processing Vegetable Industry Roundtable Meeting, Batavia, New York. Attendees = 60. Duration = 30 min. Total contact = 30 hours. 15 March 2023.

Pethybridge, S. J. 2023. Potential for gibberellic acid 3 to manipulate table beet and carrot growth and yield. New York Processing Vegetable Industry Roundtable Meeting, Batavia, New York. Attendees = 60. Duration = 30 min. Total contact = 30 hours. 15 March 2023.

Pethybridge, S. J. 2023. Soilborne diseases of vegetables in New York. W5147 Multistate Project (by zoom). Attendees = 30. Duration = 60 min. Total contact = 30 h. 5 December 2023.

Pethybridge, S. J. 2023. Towards a durable management strategy for white mold in dry beans in New York. NYS Dry Bean Council, Geneva, New York. Attendees = 50. Duration = 30 min. Total contact = 25 hours. 22 March 2023.

Pethybridge, S. J. 2023. When push comes to shove…what really works for organic disease management (Invited Presentation). Sugarloaf Mountain, Maine. Attendees = 50. Duration = 3 hours. Total contact = 150 hours. 5 November 2023.

Pethybridge, S. J., and Murphy, S. M. 2023. Efficacy of fungicides for white mold control in snap bean. Mid-Atlantic Fruit and Vegetable Growers Convention, Hershey, Pennsylvania. Attendees = 70. Duration = 30 min. Total contact = 35 hours. 31 January 2023.

Pethybridge, S. J., and Murphy, S. M. 2023. Feasibility of Mesotunnels for muskmelon production. Empire Expo, Syracuse, NY. Attendees = 100. Duration = 30 min. Total contact = 50 hours. 6 February 2023.

Pethybridge, S. J., and Ryan, M. R. 2023. Breaking down the barriers to organic no-till soybean and dry bean production through improved white mold management. USDA NIFA Project Directors Meeting. Attendees = 120. Duration = 30 min. Total contact = 60 hours. 18 April 2023.

Pethybridge, S. J., Hay, F. S., and Heck, D. W. 2023. Stemphylium leaf blight of onions in New York. Wisconsin Muck Growers Conference (by zoom). Attendees = 100. Duration = 30 min. Total contact = 50 hours. 8 February 2023.

Pethybridge, S. J., Murphy, S. M., and Damann, K. 2023. Feasibility of Mesotunnels for muskmelon production. Mid-Atlantic Fruit and Vegetable Growers Convention, Hershey, Pennsylvania. Attendees = 100. Duration = 30 min. Total contact = 50 hours. 31 January 2023.

Ploeg, A.  and J.O. Becker. An unusual root-knot nematode on an unusual plant. The 68^th Annual Conference on Soilborne Plant Pathogens and the 53^rd California Nematology Workshop 2023, Salinas, CA, March 28-30.

Ploeg, A.  and J.O. Becker. Nematode problems in carrots and planned trials. Carrot industry research priorities meeting; by Zoom, January 24, 2023.

Rosen, C., Frost, K.E., and McIntosh, C. Recent developments in improving soil health for potato production. Potato Expo 2023, Aurora, CO, January 5, 2023 (~100).

Smith Becker, J. J. Borneman, and J.O. Becker, Cyst nematode suppression prediction. California Nematology Workgroup Meeting, Salinas, CA, March 28, 2023.

Upadhaya, S., Mayad, E.H., Potter, T., Gleason, C., Griffin LaHue, D., Frost, K., Wheeler, D., and Paulitz, T. Comparative analysis of soil health status in agricultural and native soils in PNW region. WSU Potato Field Day, Othello, WA, June 22, 2023 (~50)

Westphal, A., Z.T.Z. Maung, and J.O. Becker, Host response to Meloidogyne floridensis of selected California perennial crops. California Nematology Workgroup Meeting, Salinas, CA, March 28, 2023.