Brief Summary of Minutes of Annual Meeting

W-4147 Agenda

Friday Dec. 2, 2022

https://wsu.zoom.us/j/97079193001

8:00AM - Introduction and remarks from Scot Hulbert, Washington State University and Amer Fayad, NIFA

Tim Paulitz – Meeting Chair: Tim discussed the agenda for the day as well as the need for everyone to submit their Annual Reports.

Introductions: All attendees briefly described what they are doing.

Amer Fayad – NIFA Representative for the project: Amer told the group that NIFA is building their staff in Washington DC and Kansas City, and most personnel have been working remotely since 2020. James Borneman asked Amer about how we could get the Biologically Based Pest Management Program resurrected – which was a USDA funding program that funded only biologically based research. Amer suggested we email him with this request and leave a comment in the website of the Pests and Beneficial Species in Agricultural Production Systems Program.

Scot Hulbert – Administrative Advisor for the project: Scot reminded the group that Appendix E needs to be filled by each member to enroll in new project (W5147) and that our new proposal looks good thus far. Scot also described a high level of interest in topics relevant to this group like soil health in Washington State. Scot informed new members of the group that they should talk to their experimental station administrator about funding for travel to the group meeting and possibly research.

8:15–10:25AM - State Reports: Each person will have 10 minutes, and can share via zoom

Jenifer McBeath – AK: Jenifer showed that Trichoderma atrovirde (Plant Helper) increased several nutrients in plant tissues. Plant helper also was shown to increase peony yields. Plant helper appears to also increase Rhodiola rosea (medicinal plant) growth. Large seasonal differences in microbial communities were also described.

James Borneman – CA: James described a project examining HLB (citrus greening) survivor trees in Florida. These trees are infected with the HLB-associated pathogen but they have either remained healthy or increased in health over the last 7 years – where the vast majority of trees have died over this same period. Several microbes and RNA transcripts were found to be more abundant in the survivor trees and non-survivor trees.

Gretchen Sassenrath – KS: Gretchen told us that it was a bad year in terms of drought and high temperatures in Kansas. Soybean yields were low and charcoal rot was the major problem. Treatments like a corn stubble layer on the soil were examined and various soil parameters including microbes were measured or assessed. Corn stubble led to the lowest soil temperatures.

Jay Hao – ME: Jay described a potato experiment with different potato genotypes, crop rotations, cover crops, compost, and soil fumigation treatments. Various soil and plant parameters are being measured. Compost and fumigation led to the best yields. Soil communities were not obviously different among the treatments thus far but this is an ongoing project. Lobster Shell Meal (LSM) is also being tested as a soil amendment and thus far it has been shown to increase growth. A phylogenetic analysis of bacterial strains from an outbreak of potato soft rot and blackleg was performed. Also, the most infectious strain had an extra copy of the Type 4 secretion system.

Kiran Mysore – OK: Kiran is examining bacterial and fungal diversity in the rhizosphere in relation to Arabidopsis PAMP mutants. No large differences in bacterial taxa were observed. There also were no large differences in fungal taxa, but Pezizaceae increased with a cerk1 mutant and many pathogens are in this taxonomic group. Also, a fls2 mutant showed a difference in bacterial beta diversity.

Emma Gachomo – CA: Emma described how California is the main producer or carrots and carrot cavity spot is a common disease caused by several Pythium species. An experiment with Ridomil and Pythium found small differences in the fungal communities via beta diversity. Ridomil also reduced several fungal taxa and increase other fungal taxa even though it is not supposed to target fungi.

Harsh Bais – DE: Harsh is examining Bacillus subtilis (UD1022) in relation to plant health. UD1022 forms biofilms and protects plants against multiple stressors. He is investigating mechanisms involving drought tolerance and soil water retention as well as microbial diversity and plant traits. Harsh showed that this bacterium can increase soil water retention. He is also examining how UD1022 or a synthetic microbial community can shape the microbiome and plant health.

Tessie Wilkerson – MS: Tessie is examining reniform nematode management strategies in cotton. She is investigating commercial reniform nematode resistant cotton lines/varieties in relation to nematode populations and crop yields. There were differences in cotton yields with various susceptible and resistant varieties with the resistant varieties in general performing better. She also discussed her educational outreach to students.

Anissa Poleatewich – NH: Anissa described the effects of different propagation substrates on plant growth in presence of root pathogens. Both cucumbers and Calibrachoa had less disease in with the Oasis substrate. She is also examining alternatives to peat moss including wood substrates. Radish grown in hammer-milled pine tree substrate had less damping off by R. solani and also increased plant growth. Wood fiber type and amount had varying effects on pathogen control and plant growth.

Eric Branch/Sarah Pethybridge – NY: Eric is examining treatments to improve the management of Rhizoctonia solani in table beets. Azoxystrobin (Quadris) and other fungicides were the treatment groups along with some biological control products. The standard treatment (Quadris) worked well and combining it with other fungicides did not improve crop yields. Biological control products were not nearly as effective as Quadris.

Bode Olukolu – TN: Bode described the use of quantitative Reduced Representation Sequencing (OmeSeq-qRRS) and the Qmatey automated pipeline for analysis of metagenomic and other types of datasets. This approach can be used to examine multipartite host-microbe interactions at the strain level including genotyping for breeding. Correlations with endosymbionts and pathogens with sweet potato and white-fly were found. Host JA-defense pathways (and others) correlated (interacted) with some of these microbes. Several different types of data can be fed into this analysis pipeline including metagenome, amplicon, genome, and others. Bode uses a library construction method that amplifies both DNA and RNA.

Tim Paulitz – WA: Tim is examining nematode communities in wheat cropping systems. Canola was shown to influence the microbiomes in a subsequent wheat crop. Canola led to increased Streptomyces as well as reductions of AMF fungi.

Maren Friesen – WA: Maren is examining rhizosphere and soil microbial communities as well as host-microbe interactions and rhizobial species in various systems. Maren's outreach includes organizing the Washington SoilCon meeting and engaging tribal communities.

Discussion of new 5-year plan: The group discussed a series of collaborative projects that we plan on performing in the next cycle of this project.

Election of secretary, discussion on next meeting site: Jay Hao will be the secretary for the 2023 meeting. Meeting locations were discussed and one possibility was in Riverside CA. The group agreed that a hybrid (virtual/in-person) meeting would be optimal, because it will enable more members to attend.

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. 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 be create and maintain soils that suppress schachtii, which we anticipate will lead to higher crop yields and profitability for the growers. This work is currently being used to write a peer-reviewed paper.

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. Vanette- We have continued to isolate microbial agents from plants, mostly from leaves and flowers, to identify microbes that have biocontrol properties against plant pathogens sourced from soils, plants or insects. Our work has focused on agricultural and natural systems, including from insects that visit and feed on plants. We have also used high throughput sequencing to identify microbial taxa that inhabit agricultural systems under multiple agricultural management regimes.

KS. Crop production fields with disease pressure were identified. Soil samples were taken and tested for diseases (Phytophthora root rot and charcoal rot) and nematodes (soybean cyst nematodes). Soil biological activity was assessed using PLFA; soil background nutrient status was also measured. Charcoal rot was identified to be a much more pervasive disease in southeast Kansas than other diseases or SCN.

OR – Soil microbiome variation in potato cropping systems. We continued work to characterize the soil microbiome as a function of metam sodium fumigation, a disease control practice commonly used in the used in potato cropping systems. We found that previous MS fumigation had negative impact on soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Predominant bacterial and fungal taxa were similar between fumigated and non-fumigated soils, but the relative abundance of bacterial and fungal genera varied with fumigation history. Also, MS fumigation altered soil bacterial and fungal co-occurrence network structure and associations. In general, legacy effects of MS fumigation are more pronounced for soil bacterial communities than they are for fungal communities. Additionally, the responses of soil microbiome to MS fumigation are context dependent and seem to vary depending on field management history.

OR – Management factors influencing the potato rhizosphere microbiome. We characterized the microbiome in soils closely associated with seed potato (tare soils) and found that the microbiome varies as a function of seed source and that a large number of potentially plant pathogenic taxa were detected by sequencing tare soil, including pathogens of plants other than potato. We also found taxa potentially beneficial to plant health. Potato rhizosphere microbiome establishment appears to be heavily influenced by the bulk soil microbial community (i.e., the microbial community of the soil in which the seed tuber is planted). This suggests that on farm management practices that influence the soil microbiome are an important contributing factor to rhizosphere microbiome establishment that could influence plant productivity. 

ME- Investigated soil biochemistry and microbial communities in improving soil health for enhancing potato production. Studied soil microbiomes and soilborne pathogens under soil fumigation. Examined microbial association in blackleg and soft rot disease of potato.

Conducted field trials and examined soil treatments with chemicals and biological products on the control of potato early dying, black scurf and pink rot of potatoes. Evaluated potato clones and varieties for pink rot resistance.

NJ- We continued research on mechanisms used by plants to extract nutrients from microbes absorbed from soils into plant tissues.

NJ- We reported the functions of plant trichomes to cultivate diazotrophic microbes and described a hypothesized mechanism for nitrogen extraction in plants.

NY- Pethybridge Lab: Characterizing the microbiome associated with table beet. To characterize the microbiome associate with table beet, samples have been collected from six organic and conventional fields across NY. DNA extractions have been conducted from samples collected in the phyllosphere, rhizosphere and bulk soil. ITS and 16s Illumina sequencing is being conducted to quantify microbial community structure, alpha and beta diversity, and differentiation in these variables based on azoxystrobin in-furrow for Rhizoctonia root rot control.

NY- Pethybridge Lab: 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. A repeat of this trial was again established in fall 2022 for monitoring in summer 2023. Results from this trial are pending.

VA- Conducted field trials evaluating biological control agents (BCAs) against boxwood blight in western North Carolina, in collaboration with NC Department of Agricultural and Consumer Services, and NC Cooperative Extension. Selected BCAs and their combos, along with a fungicide standard and a nontreated control, were included in these trials. BCAs were applied monthly starting in late May while fungicide standard was sprayed every 3 weeks.

VA- Elucidated the mechanisms by which a broad-spectrum biocontrol agent – Burkholderia sp. SSG controls boxwood blight.

VA- Analyzed, wrote and published the research data on population dynamics of the boxwood blight pathogen in garden soil of five state, in collaboration with Cornell University, Clemson University, Dominican University of California, Illinois Department of Agriculture and California Department of Food and Agriculture.

VA- Analyzed 16S amplicon sequence data, wrote and published one paper on bacterial communities in the boxwood blight pathogen suppressive garden soil under five different climatic conditions of the United States.

WA- Bacterial community abundance in the soil fluctuates over the growing season. Bacterial communities in the soil play a major role in wheat health, nutrient uptake, residue decomposition and tolerance to abiotic stress. Most previous studies look at one time point, but little is known about how populations change over the growing season. ARS scientists at Pullman, Washington, and the Cook Long Term Agroecosystems Research site sampled every two weeks during the growing season (March-November) over three years and examined bacterial communities with amplicon sequencing of the 16S gene. Some bacteria families declined during the hot and dry months (June-August), but others maintained their populations. Previous rotation crops also influenced populations. This will help growers determine soil health in their field and how management practices may be adapted to favor beneficial microbiomes and increase yield and sustainability.

WA- Camelina has a core microbiome of bacteria around its roots. 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. But nothing is known about the microbial communities on the roots, and how this may influence crop performance and nutrient uptake. ARS researchers at Pullman, Washington, and Washington State University scientists, funded by a grant from Department of Energy, grew camelina in 33 soils and extracted DNA from the bulk soil, rhizosphere, and roots. The core microbiome present in all the locations included Sphingomonas, Rhizobium, Micrococcaceae, Gemmatimonadaceae, Phenylobacterium, and Streptomyces. We have made a culture collection to isolate and test the ability of these bacteria to increase camelina health and performance in the greenhouse and field. This research will help in the adaption of this crop to eastern Washington.

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.

CA. Vanette. Work in our lab has focused on how host plant factors, including specific chemicals produced, affect microbial growth, including the growth of prospective biocontrol agents and pathogens using both field and lab experiments. We performed a large-scale field experiment to assess variation in microbial growth. In 2020, we used a field–based experiment, where we inoculated two microbial species into many individuals of 4 cultivars of the native plant Epilobium canum to examine variation in microbial growth. In addition, we sampled uninoculated plants to see if our inoculation study corresponded well with unmanipulated plants’ microbial load. From our initial analysis of the data, we found significant variation in growth among cultivars in both fungal and bacterial growth. In the lab, we tested effects of common plant defenses (peroxides, alkaloids, volatiles) on microbial growth, both for individual microbes and communities in co-inoculation. Our results reveal that these common plant constituents have species-specific effects on potential microbial colonists and can influence species interactions among microbes.

KS. Fundamental knowledge of specific environmental conditions that enhance infection of crop plants by pathogens is not known. While evidence suggests charcoal rot is more abundant in hot and dry environments, the particular environmental susceptibility of disease formation is unknown. We measured the abundance and viability of disease organisms as a function of the environmental conditions within the soil. Controlled environment studies were conducted to explore the linkages between soil conditions and microenvironment (moisture and temperature) on pathogen viability of M. phaseolina, the organism responsible for charcoal rot. Treatments were implemented in replicated field plots to measure the disease organisms under different environmental conditions in the fields. Treatments included two treatments that are likely to increase disease (soybeans and corn stubble, both hosts of disease organisms), three treatments that are likely to decrease disease (brassica cover crop, animal manure, and solarization), and a fallow control. Temperature sensors were installed in plots and temperatures were recorded continuously. Plastic sheets provide a “solarization” treatment, increasing soil temperature and potentially reducing soil microbes. Corn stubble is a potential source of pathogens, as corn is a host; alternatively, corn stubble provides more carbon for soil microbes, increasing their abundance and potentially reducing pathogens by increasing beneficial microbial populations. Animal manure would also provide a greater carbon source for the microbes, and add additional microbes to the soil, increasing the complexity of the soil microbiome. Interesting differences were observed in the environment within the soil of the different treatments. The plastic sheets raised the temperature more than 10 degrees above the fallow treatment, and temperatures remained elevated at night. Animal manure also raised the day-time temperature, but temperatures decreased at night to that of fallow. Temperatures under corn stubble greatly decreased soil temperatures throughout the day, keeping soil temperatures cooler than air temperatures during both night and day. Because of the extremely hot air temperatures in 2022, and the poor crop canopy development, soil temperatures in the crop canopy were near those of the fallow treatment. Soil samples were collected and are being analyzed for microbial activity.

NY. Smart Lab: Change in Phytophthora capsici populations in NY over time. To identify control strategies, it is important to know how a pathogen population in a field is changing over time.  Sexual, endemic populations of the heterothallic Phytophthora capsici continue to devastate vegetable crops in the northeast. Over the past year we have collected 100 isolates from fields in Western NY that have been previously sampled, as well as 70 isolates from pepper fields in California. More than 50 of the isolates from Western NY were insensitive to the commonly used fungicide mefenoxam. This is a change in the population as only 5% of isolates collected in 2012 were insensitive to this fungicide. Cultivars of pepper and squash being planted on these farms have not changed dramatically in the past decade, however growers have continued to use mefenoxam at least once (and usually 2-3 times) per year. These data indicate that mefenoxam insensitive isolates are now established in Western NY and are overwintering, as isolates were collected early in the season when symptoms first appeared.

NY- Pethybridge Lab: 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.

OR –Population dynamics of Spongospora subterranea in soils. In 2022, we repeated an observational field study first conducted in 2021. Again, pathogen inoculum changes and hourly soil water and temperature throughout the growing season were tracked in four commercial potato fields (selected based on their powdery scab disease history). Pathogen population dynamics and disease expression varied among locations and the environmental data are currently being used to model risk for powdery scab occurrence and PMTV infection. Bulk soil and potato rhizosphere soils were collected to characterize the soil microbiome and determine if microbial taxa antagonistic to S. subterranea are present in the soils. The long-term goal of the project is to develop diagnostic tools that would inform growers of their risk for losses due to powdery scab and PMTV transmission.

WA- Plant root exudates feed bacteria on roots. Plant root exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. ARS scientists at Pullman, Washington, and Mississippi State University researchers addressed this gap by characterizing the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for economically important grass family crops. RNA-seq profiling of the bacteria amended with root exudates revealed changes in the expression of genes and products that are important for the multiple benefits that Pseudomonas fluorescens provides to the plant, including protection against plant disease. These results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant host.

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

KS. Cover crops were planted in replicated blocks in the field in the fall and included: control (fallow with herbicide, no cover crop); wheat; Graza radish; annual ryegrass; spring oats; winter oat; forage collards; commercial cover crop mix; and a mix of radish + ryegrass planted both drilled and broadcast methods. Spring oats had the highest levels of NO₃-N remaining, but lower levels of NH₄-N. No consistent changes in nutrient levels for the different cover crops could be related to the measured difference in soybean yield. Bacterial percentage was the highest in all cover crop plots, with a similar pattern in percentage of actinomycetes and fungi

ME. Conducted field trials and studied fungicides with biological control agents, cover crops, and soil amendment to control soilborne diseases.

NY. Smart Lab: Efficacy of biologicals to control Phytophthora capsici in the field. To determine if products are available for control of Phytophthora capsici in organic vegetable production, we tested two products currently in development as well as three commercially available products on delecata squash. The two products in development are plant-based while the three commercially available products were Bacillius or Trichoderma-based. As a control, mefenoxam was included. None of the biological products were effective against the pathogen, while squash treated with mefenoxam showed no signs of disease. Untreated plants died within two weeks of inoculum being added to the soil.

NY. Pethybridge Lab: Efficacy of fungicides for the control of Rhizoctonia root rot in table beet. A small plot replicated field trial was conducted at Cornell AgriTech in Geneva, New York. On 18 May, table beet seed (treated with Maxim 4FS, Apron XL, and Thiram 42-S) was planted at 17 seeds/ft using a Monosem planter with the press wheels up. Fertilizer (350 lb/A 10-5-10) was banded at planting, and 300 lb/A 10-5-10 and 2 lb/A boron were broadcast and incorporated one day earlier. Open furrows were inoculated with Rhizoctonia solani AG 2.2 on infested barley at 31.2 lb/A. Fungicides were applied in a 7-inch band using a CO₂-pressurized backpack sprayer with a TeeJet 8003VS nozzle delivering 22.5 gal/A at 30 psi either just prior to furrow closing, post-emergent on 14 Jun (27 days after planting (DAP)), or on both dates. Eleven treatments (Quadris; Stargus applied once or twice; Regalia applied once or twice; Stargus + Regalia applied twice; Double Nickel applied once or twice; and Howler applied once or twice), including a nontreated control, were arranged in a randomized complete block design with four replications. Plots consisted of a 10-ft length of two rows, with 5 ft between plots in the same row and two rows between adjacent plots. Overhead sprinkler irrigation was applied as needed to ensure optimal plant growth and disease development. The total number of plants per 10 ft row was recorded. Crop stand at 19, 26, 34, 40, 48, and 61 DAP, was used to calculate area under the disease progress stairs (AUDPS) in the R package ‘Agrigolae’. At 70 DAP, all plants within a 3.2 ft transect were harvested and assessed. Disease incidence was determined based on the presence or absence of root disease symptoms. Roots were assigned a value from 0 to 5 for both exterior and internal disease severity: 0 = no diseased tissue; 1 = 1 to 10% diseased tissue; 2 = 11 to 30% diseased tissue; 3 = 31 to 60% diseased tissue; 4 = 61 to 99% diseased tissue; and 5 = 100% diseased tissue. Scores were converted to the averages within each category: 0 = 0%; 1 = 5.5%; 2 = 20.5%; 3 = 45.5%; 4 = 80%; and 5 = 100%. Weighted averages were then calculated for each root: (Exterior Rating × 0.25) + (Interior Rating × 0.75) = Weighted Average Disease Rating. The effect of treatment on AUDPS, root number, average shoulder diameter, and average root disease incidence and severity was evaluated using a generalized linear mixed model with means separated by a least significant difference test (R version 4.2.1). Nontreated plots had a Rhizoctonia root rot disease incidence of 68% and average disease severity per root of 11%. In general, the biopesticide treatments were like the nontreated control, with average disease incidence of 58%. Quadris (azoxystrobin, FRAC 11) was the only treatment to significantly decrease AUDPS and root disease incidence. Quadris reduced disease severity by 96%. Two applications of Howler, one or two applications of Double Nickel, and one application of Regalis also significantly reduced disease severity per root, but only by 61% to 82%.

OR –Effects of rotation, soil amendment, and fumigation on potato early dying and the soil microbial community. In 2022, we continued work on two four-year crop rotation studies 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. 2022 was the final year of the rotation study when all treatments were fully established and comparison could be made.

WA. Influence of greenbridge management and weeds on soilborne pathogens. In a collaborative project with Oregon State University at Pendleton, OR, field trials have been established to look at the timing of weed sprayout in the fall, on Rhizoctonia and Fusarium crown rot. This project is also looking at how weed species composition affects the carryover of diseases.

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. Borneman Accelerating Growth and Treating Disease via Metabolic Modeling of Citrus, The International Congress on Citrus Nurseries, October 3 2022, Visalia Convention Center, CA

Understanding the Survivor Tree Phenotype. Annual Meeting of Western Regional Project W4147 on Biological Control, December 2 2022, Zoom because of COVID pandemic.

James Borneman gave presentations to undergraduate and graduate students in his two Microbiomes courses (MCBL 126 & MCBL 226). 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. Vanette. Gave a plenary presentation on microbial mediation of plant-insect interactions at the Phytobiomes alliance meeting, which brought together researchers, industry, growers and students/trainees to discuss how microbes might be used in sustainable agriculture.

KS. The Spring Crops Field day was held on May 17, 2022 at the SEREC in Parsons, KS. Presentations on wheat production, crop management, and soil health were shared with 75 attendees. A Soil Health field day was held in McCune, KS on February 8, 2022. Presentations were made by experts on soil-borne diseases, agroecological system functions, soil structure, and soil biology. A Regenerative Ag field day was held on August 11, 2022 in Girard, KS. Demonstrations included information on soil formation processes, measurements of soil health, and impacts of management choices on soil health and performance.

NY. Pethybridge Lab:

Outreach activities on sustainable disease management.

In 2022, Pethybridge gave 10 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 Northeast Cover Crop Association.

Undergraduate research experience

Pethybridge had two undergraduate summer scholars in the lab during summer 2022.

NY. Smart lab - 2022

Disease management strategies for Phytophthora capsici   

In 2022, Smart gave nine talks to growers, extension educators and industry representatives including pathogen biology and disease management of Phytophthora blight and other pathogens.

Undergraduate research experience. 

Smart had two undergraduate researchers in the lab during the summer of 2022

OR (Frost) – Advised two one faculty research assistants, one technician, two graduate students, and one undergraduate students. In 2022, we published five refereed papers, one extension document, and six abstracts. Information has been disseminated to clientele within the region through talks at two grower education events and one field day, and to scientific peers via seven 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 2022, 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.

VA- Co-organized and -conducted quarterly international boxwood seminars. Co-organized a session at Cultivate’22, the largest annual educational event hosted by AmericanHort, the national trade organization with over 16,000 members, in addition to two symposia at professional conferences. Used Google groups for mass distribution of the latest research about boxwood blight mitigation.

WA- Paulitz. Served as lead organizer of the 67^th Conference on Soilborne Plant Pathogens, on zoom, March 23-24, 2022. Co-organizer of the 8^th International Cereal Nematodes Symposium, Abant, Turkey.  Sept. 26-29, 2022. Hosted a Moroccan collaborator who was awarded a Fulbright Fellowship, May-October 2022. To work on nematode communities with morphological and molecular characterization. Also collaborated on numerous manuscripts. Continued a long collaboration with CIMMYT in Turkey, Morocco, and Kazakhstan and collaborated on numerous manuscripts. Consulted with the Washington State Department of Agriculture on the crucifer quarantine and black leg of canola. Presented 1.5 hour hands-on lab on The Soil Microbiome & Soil Health to growers at the Washington Wheat Academy, Dec. 15, 2022. Section editor of the Canadian Journal of Plant Pathology. Presently supervising one PhD student, one MSc applied, and on thesis committee of 3 MSc and 2 PhD students.

WA- Friesen WSU “Intentional Inclusion: Minimizing Unconscious Bias and Microaggressions” April 5, 2022. WSU CEREO-Native American Program Seminar Series, Spring & Fall 2022 6 monthly seminars on Indigenous Knowledge

Peer Reviewed

Ahmadi, M., Mirakhorli, N., Erginbas-Orakci, G., Ansari, O., Braun, H., Paulitz, T.C., Dababat, A. 2022. Interactions among cereal cyst nematode Heterodera filipjevi, dryland crown rot Fusarium culmorum, and drought on grain yield components and disease severity in bread wheat. Canadian Journal of Plant Pathology. 44(3):415-431. https://doi.org/10.1080/07060661.2021.2013947.

Alkan, M., Bayraktar, H., Imren, M., Ozdemir, F., Lahlali, R., Mokrini, F., Paulitz, T.C., Dababat, A.A., Ozer, G. 2022. Monitoring of host suitability and defense-related genes in wheat to Bipolaris sorokiniana. The Journal of Fungi. 8(2). Article 149. https://doi.org/10.3390/jof8020149.

Blundell, R, Schmidt JE, Igwe AI, Cheung AL, Vannette RL, Gaudin A, Casteel, C 2020 Organic management promotes natural pest control through altered plant resistance to insect, Nature Plants 6 (5) 483-491. https://doi.org/10.1038/s41477-020-0656-9

Bock, C. H., Pethybridge, S. J., Barbedo, J. G. A., Esker, P. D., Mahlein, A-K., and Del Ponte, E. M. 2022. A phytopathometry glossary for the 21^st century: Towards consistency and precision in intra- and inter-disciplinary crosstalk. Trop. Plant Pathol. 47:14-24.https://doi.org/10.1007/s40858-021-00454-0.

Chen, H, White, K Malik, H Chen, Y Jin, X Yao, X Wei, C Li, Z Nan. 2022. Soil nutrient dynamics relate to Epichloë endophyte mutualism and nitrogen turnover in a low nitrogen environment. Soil Biology and Biochemistry 174, 108832

Chen, H., JF White, K Malik, F Qi, C Li. 2022. Diplocarpon mespilicola sp. nov. Associated with Entomosporium Leaf Spot on Hawthorn in China. Plant Disease 106 (11), 2884-2891

Cheng, X., Dai, T., Hu, Z., Cui, T., Wang, W., Han, P., Hu, M., Hao, J., Liu, P., and Liu, X. 2022. Cytochrome P450 and glutathione s-transferase confer metabolic resistance to SYP-14288 and multi-drugs resistance in Rhizoctonia solani. Frontiers in Microbiology 13: 806339. DOI: 10.3389/fmicb.2022.806339.

Crowell, CR, Wilkerson, DG, Bekauri, M, Cala, A, McMullen, P, Mondo, S, Andreopoulos, W, Lipzen, A, Lail, K, Yan, M, Ng, V, Grigoriev, I, Smart, LB, and Smart CD (2022) The Melampsora americana population on Salix purpurea in the Great Lakes Region is highly diverse with a contributory influence of clonality. Phytopathology 112:907-916. https://doi.org/10.1094/PHYTO-05-21-0201-R

Crowell, CR, Wilkerson, DG, Smart, LB and Smart CD (2022) Evidence of asexual overwintering of Melampsora paradoxa and mapping of stem rust host resistance in Salix. Plants 11: 2385. https://doi.org/10.3390/plants11182385

Crowley-Gall A, Trouillas FP, Niño EL, Schaeffer RN, Nouri MT, Crespo M, Vannette RL. Floral microbes suppress growth of Monilinia laxa with minimal effects on honey bee feeding. Plant Disease. 2022 Feb 28;106(2):432-8.

Curland, R.D., Mainello, A., Perry, K.L., Hao, J., Charkowski, A.O., Bull, C.T., Johnson, S., Rosenzweig, N., Secor, G.A. and Ishimaru, C.A. 2021. Species of Dickeya and Pectobacterium associated with 2015-2016 outbreaks of soft rot and blackleg of potato in Northeastern and North Central United States. Microorganisms 9(8): 1733. DOI: 10.3390/microorganisms9081733.

Del Ponte, E. M., Cazon, L. I., Alves, K. S., Pethybridge, S. J., and Bock, C. H. 2022. How much do standard area diagrams improve accuracy of visual estimates of disease severity? A systematic review and meta-analysis. Trop. Plant Pathol. 47:43-57.10.1007/s40858-021-00479-5. Online Research Compendium Including Statistical Code: DOI 10.17605/OSF.IO/T2YJW.

Delventhal, K., Busby, P., and Frost, K.E. 202X. Tare soil alters the composition of the developing the potato rhizosphere microbiome. Phytobiomes XX:XXX-XXX (Accepted November 2022 – In press).

Delventhal, K., Skillman, V., Li, X., Busby, P., and Frost, K.E. 202X. Characterizing variation in the bacterial and fungal tare soil microbiome of seed potato. Phytobiomes XX:XXX-XXX (Accepted November 2022 – In press).

Dubrow, ZE, Carpenter, SCD, Carter, ME, Grinage, A, Gris, C, Audran, C, Butchachas, J, Jacobs, JM, Smart, CD, Tancos, MA, Noel, LD, and Bogdanove, AJ (2022) Cruciferous weed isolates of Xanthomonas campestris yield insight into pathovar genomic relationships and genetic determinants of host- and tissue-specificity. Molecular Plant-Microbe Interactions 35:791-802 https://doi.org/10.1094/MPMI-01-22-0024-R

Gao, Y., Lu, X., Guo, R., Hao, J., Miao, Z., Li, Y. and Li, S. 2021. Responses of soil abiotic properties and microbial community structure to 25-year cucumber monoculture in commercial greenhouses. MDPI Agriculture 11 (4): 341. DOI: 10.3390/agriculture11040341.

Gargouri, S., Bouatrous, A., Murray, T.D., Paulitz, T.C., Khemir, E., Souissi, A., Chekali, S., Burgess, L.W. 2022. Occurrence of eyespot of cereals in Tunisia and identification of Oculimacula species and mating types. Canadian Journal of Plant Pathology. 44(3):345-353. https://doi.org/10.1080/07060661.2021.1995501.

Ge, T. Ekbataniamiri, F., Johnson, S.B., Larkin, R.P. and Hao, J. 2021. Interaction between Dickeya dianthicola and Pectobacterium parmentieri in potato infection under field conditions. Microorganisms 9: 316. DOI: 10.3390/microorganisms9020316.

Giles, G, Indermaur, EJ, Gonzalez-Giron, JL, Herrmann, TQ, Shelnutt, SS, Starr, JK, Myers, K, Jensen, SL, Bergstrom, GC, Crawford, JL, Hansen, JL, Smart, LB, and Smart CD (2023) First report of downy mildew caused by Pseudoperonospora cannabina on Cannabis sativa in New York. Plant Disease. In press https://doi.org/10.1094/PDIS-08-22-1930-PDN

Hagerty, C., Gardner, S., Kroese, D.R., Yin, C., Paulitz, T.C., Pscheidt, J.W. 2022. Occurrence of mummy berry associated with huckleberry (Vaccinium membranaceum) caused by Monilinia spp. in Oregon. Plant Disease. 106(2):357-359. https://doi.org/10.1094/PDIS-04-21-0691-SC.

Han, R., Wu, Z., Teng, L., Wang, T., Liu, P., Hao, J. and Liu, X. 2021. Tracking pesticide exposure to operating workers for risk assessment in seed coating with tebuconazole and carbofuran. Pesticide Management Science 77(6): 2820-2825. DOI: 10.1002/ps.6315.

Hao, J. and Ashley, K. 2021. Irreplaceable role of amendment-based strategies to enhance soil health and disease suppression in potato production. Microorganisms 9: 1660. DOI: 10.3390/microorganisms9081660.

Hassanzadeh, A., Zhang, F., Murphy, S. M., Pethybridge, S. J., van Aardt, J. 2022. Toward crop maturity assessment via UAS-based imaging spectroscopy – A snap bean pod size classification. IEEE Transactions on Geoscience and Remote Sensing. 60:5519717.10.1109/TGRS.2021.3134564.

Hay, F. S., Heck, D. W., Klein, A., Sharma, S., Hoepting, C. A., and Pethybridge, S. J. 2022. Spatiotemporal attributes of Stemphylium leaf blight epidemics and effects of residue management in New York onion fields. Plant Dis. 106:1381-1391. https://doi.org/10.1094/PDIS-07-21-1587-RE.

Hay, F. S., Heck, D. W., Sharma, S., Klein, A., Hoepting, C., and Pethybridge, S. J. 2022. Stemphylium leaf blight of onion. Plant Disease Lesson. The Plant Health Instructor 22: 10.1094/PHI-P-2022-0​1-0​001.

He, Y, T Chen, H Zhang, JF White, C Li. 2022. Fungal endophytes help grasses to tolerate sap-sucking herbivores through a hormone-signaling system. Journal of Plant Growth Regulation 41 (6), 2122-2137

Hong, C. X., Daughtrey, M. L., Howle, M., Schirmer, S., Kosta, K., Kong, P., Likins, M., and Suslow, K.  2022. Rapid decline of Calonectria pseudonaviculata soil population in selected gardens across the United States. Plant Disease 106:2831-2838 (https://doi.org/10.1094/PDIS-02-22-0443-RE)

Indermaur EJ, Day CTC, and Smart CD (2022) First report of Didymella rhei causing leaf spot on rhubarb in New York. Plant Disease in press https://doi.org/10.1094/PDIS-03-22-0573-PDN

Kim, D., Jeon, C., Cho, G., Thomashow, L.S., Weller, D.M., Paik, M., Lee, Y., Kwak, Y. 2021. Glutamic acid reshapes the plant microbiota to protect plants against pathogens. Microbiome. 9. Article 244. https://doi.org/10.1186/s40168-021-01186-8.

Kong, P., Li, X. P., Gouker, F., and Hong, C. X.  2022. cDNA transcriptome of Arabidopsis reveals various defense priming induced by a broad-spectrum biocontrol agent Burkholderia sp. SSG. International Journal of Molecular Sciences https://doi.org/10.3390/ijms23063151

Lange, HW, Tancos, MA and Smart, CD (2022) Investigating cruciferous weeds as reservoirs of Xanthomonas campestris in New York State. Plant Disease 106:174-181  https://doi.org/10.1094/PDIS-05-21-0998-RE

Lehner, M. S., Alves, K., Del Ponte, E. M., and Pethybridge, S. J. 2022. Comparative fungicide sensitivity of Sclerotinia sclerotiorum using mycelial growth and ascospore germination assays. Plant Dis. 106:360-363. https://doi.org/10.1094/PDIS-06-21-1234-SC.

Li, K., Wang, Y., Ge, T., Larkin, R.P., Smart, A., Johnson, S.B., and Hao, J. Risk evaluation of benzovindiflupyr resistance of Verticillium dahliae population in Maine. Plant Disease. DOI: 10.1094/PDIS-06-22-1384-RE.

Li, X. P., Kong, P., Daughtrey, M. L., Kosta, K., Schirmer, S., Howle, M., Likins, M., and Hong, C. X.  2022. Characterization of the soil bacterial community in selected boxwood gardens across the United States. Microorganisms 10, 1514 at https://www.mdpi.com/2076-2607/10/8/1514/pdf

Li, X., Petipas, R.H., Antoch, A.A., Liu, Y., Stel, H.V., Bell‐Dereske, L., Smercina, D.N., Bekkering, C., Evans, S.E., Tiemann, L.K. and Friesen, M.L., 2022. Switchgrass cropping systems affect soil carbon and nitrogen and microbial diversity and activity on marginal lands. GCB Bioenergy, 14(8), pp.918-940.

 Li, X., Skillman, V., Dung., J., and Frost, K.E. 2022. Legacy effect of fumigation on soil bacterial and fungal communities and their response to metam sodium application. Environmental Microbiome 79:59 https://doi.org/10.1186/s40793-022-00454-w.

Li, Y. Liu, Y., Zhang, Z., Shen, K., Hao, J., Luo, L. and Li, J. 2022. Characterization of the host range, sensitivity to fungicides of Trichothecium spp. associated with fruit rot in the field and harvest. Plant Pathology 71(5): 1142-1151. DOI: 10.1111/ppa.13550.

Liu, Q., Liu, Xu, Y., Wang, B., Liu, P., Hao, J. and Liu, X. 2021. Encapsulation of fluazinam to extend efficacy duration in controlling Botrytis cinerea on cucumber. Pesticide Management Science 77(6): 2836-2842. DOI: 10.1002/ps.6318.

Liu, Q.L., Q.Q. Huang, F. Zhou, P.W. Song, D.X. Li, H. Y. Hu, Y. Y. Guan, Y.A. Yu, P. Hu, Q. C. Wei, E.Y. Chen, C.W. Li and J. Hao. 2021. First report of Bacillus altitudinis causing rot of pomegranate in China. Australasian Plant Pathology 50: 427-429. DOI: 10.1007/s13313-021-00789-x.

Liu, Y., Evans, S. E., Friesen, M. L., & Tiemann, L. K. (2022). Root exudates shift how N mineralization and N fixation contribute to the plant-available N supply in low fertility soils. Soil Biology and Biochemistry, 165, 108541.

Lu, X., Zhang, X., Jiao, X., Hao, J., Li, S. and Gao, W. 2022. Genetic diversity and population structure of Cylindrocarpon-like fungi infecting ginseng roots in Northeast China. Journal of fungi 8:814 DOI: 10.3390/jof8080814.

Ma, X., Brazil, J., Rivedal, H., Frost, K., Perry, K., and Swingle, B. 2022. First report of Pectobacterium versatile causing potato soft rot of potato in Oregon and Washington. Plant Disease (Note) 106:1292.

Madden, L. V., Esker, P. D., and Pethybridge, S. J. 2022. Forrest W. Nutter Jr.: A career in phytopathometry. Tropical Plant Pathol. 47:5-13. https://doi.org/10.1007/s40858-021-00469-7.

Madsen, I. J., Parks, J. M., Friesen, M. L., & Clark, R. E. (2022). Increasing Biodiversity and Land-Use Efficiency Through Pea (Pisum aestivum)-Canola (Brassica napus) Intercropping (Peaola). Frontiers in Soil Science, 20.

McFarland, C. R., Friedrichsen, C., Tao, H., & Friesen, M. L. (2022). Working Together for Soil Health: Liberating Structures for Participatory Learning in Extension. Journal of Extension, 60(2), 7.

Micci A, Zhang Q, Chang X, Kingsley K, Park L, Chiaranunt P, Strickland R, Velazquez F, Lindert S, Elmore M, Vines PL, Crane S, Irizarry I, Kowalski KP, Johnston-Monje D, White JF. Histochemical Evidence for Nitrogen-Transfer Endosymbiosis in Non-Photosynthetic Cells of Leaves and Inflorescence Bracts of Angiosperms. Biology. 2022; 11(6):876. https://doi.org/10.3390/biology11060876

Mokrini, F., Laasli, S., Benseddik, Y., Joutei, A.B., Blenzar, A., Lakhal, H., Sbaghi, M., Imren, M., Ozer, G., Paulitz, T.C., Lahlali, R., Dababat, A.A. 2021. Potential of Moroccan entomopathogenic nematodes for the control of the Mediterranean fruit fly Ceratitis capitata Wiedemann (Diptera: Tephritidae). Scientific Reports. 10. Article 19204. https://doi.org/10.1038/s41598-020-76170-7. 

Lewis, R.W., Okubara, P.A., Sullivan, T.S., Madden, B.J., Johnson, K.L., Charlesworth, C.M., Fuerst, E.P. 2022. Proteome-wide response of dormant caryopses of the weed, Avena fatua, after colonization by a seed-decay isolate of Fusarium avenaceum. Phytopathology. 112(5):1103-1117. https://doi.org/10.1094/PHYTO-06-21-0234-R.

Nieto-Lopez, EH, Cerritos-Garcia, DG, Koch Bach, RA, Petka, A, Smart, CD, Hoepting, CA, Langston, D, Rideout, S, Dutta, B, Everhart, SE. (2023) Species identification and fungicide sensitivity of fungi causing Alternaria leaf blight and head rot in cole crops in the eastern US. Plant Disease In press. https://doi.org/10.1094/PDIS-06-22-1318-SC

Pal, G., S Saxena, K Kumar, A Verma, PK Sahu, A Pandey, JF White. 2022. Endophytic Burkholderia: Multifunctional roles in plant growth promotion and stress tolerance. Microbiological Research, 127201

Pethybridge, S. J., Murphy, S., and Kikkert, J. R. 2022. Efficacy of fungicides and plant growth regulators for foliar disease control and yield components in processing carrots, 2020. Plant Dis. Manage. Rep. 16:V040.

Pethybridge, S. J., Murphy, S., Hay, F. S., Branch, E. B., Sharma, P., and Kikkert, J. R. 2022. Control of Phoma leaf spot and root decay of table beet in New York. Plant Dis. 106:1857-1866. https://doi.org/10.1094/PDIS-11-21-2506-RE.

Pethybridge, S. J., Sharma, P., Murphy, S., and Sharma, S. 2022. Efficacy of fungicides for Cercospora leaf spot control in table beet, 2021. Plant Dis. Manage. Rep. 16:V039.

Ren, H., Ding, Y., Hao, X., Hao, J., Liu, J. and Wang, Y. Enhanced rhizoremediation of polychlorinated biphenyls by resuscitation-promoting factor stimulation linked to plant growth promotion and response of functional microbial populations. Chemosphere. In print.

Rivedal, H., Funke, C.N., and Frost, K.E. 2022. An overview of pathogens associated with biotic stresses in hemp crops in Oregon, 2019-2020. Plant Disease 106:1334-1340.

Schaeffer RN, Pfeiffer VW, Basu S, Brousil M, Strohm C, DuPont ST, Vannette RL, Crowder DW. Orchard Management and Landscape Context Mediate the Pear Floral Microbiome. Applied and Environmental Microbiology. 2021 Jul 13;87(15):e00048-21.

Schaeffer, R.N., Crowder, D.W., Illán, J.G., Beck, J.J., Fukami, T., Williams, N.M. and Vannette, R.L., 2022. Ecological dynamics of the almond floral microbiome in relation to crop management and pollination. Journal of Applied Ecology, in press. Preprint: bioRxiv. https://www.biorxiv.org/content/10.1101/2020.11.05.367003v1.full

Schmidt, JE, Igwe AI, Blundell R, Gaudin A, Casteel, C, Vannette RL, 2019Effects of agricultural management on rhizosphere microbial structure and function in processing tomato. Applied and Environmental Microbiology, AEM. 01064-19.

Schlatter, D.C., Hansen, J.C., Carlson, B.R., Leslie, I.N., Huggins, D.R., Paulitz, T.C. 2022. Are microbial communities indicators of soil health in a dryland wheat cropping system? Applied Soil Ecology. 170. Article 104302. https://doi.org/10.1016/j.apsoil.2021.104302.  

Sharma, S., Kikkert, J. R., Heck D. W., Branch, E. A., and Pethybridge, S. J. 2022. Cercospora leaf spot of table beet. Disease Lesson. The Plant Health Instructor 22: ​10.1094/PHI-P-20​​22-​02-0​101.

Spanner, R., Neubauer, J., Heick, T. M., Grusak, M. A., Hamilton, O., Rivera-Varas, V., Hamilton, O., de Jonge, R., Pethybridge, S. J., Webb, K. M., Leubner-Metzger, G., Secor, G. A., and Bolton, M. D. 2022. Seed-borne Cercospora beticola can initiate disease in sugar beet (Beta vulgaris L.). Phytopathology 112:1016-1028. https://doi.org/10.1094/PHYTO-03-21-0113-R.

Sudermann, MR, McGlip, L, Regnier, M, Rodriguez Jaramillo, A, Vogel, G, and Smart, CD (2022) The diversity of Passalora fulva isolates collected from tomato plants in US high tunnels. Phytopathology 112:1350-1360. https://doi.org/10.1094/PHYTO-06-21-0244-R

Sun, Y. Wu, H., Zhou W., Yuan, Z., Hao, J., Liu X. and Han, L. 2022. Effects of indole derivatives from Purpureocillium lilacinum in controlling tobacco mosaic virus. Pesticide Biochemistry and Physiology 183: 105077. DOI: 10.1016/j.pestbp.2022.105077.

Sun, Y., Wu, H., Xu, S., Tang, S., Hao, J., Liu, X., Zhang, H., Han, L. 2022. Roles of the EPS66A polysaccharide from Streptomyces sp. in inducing tobacco resistance to Tobacco mosaic virus. International Journal of Biological Macromolecules 209: 885-894. DOI: 10.1016/j.ijbiomac.2022.04.081.

Ulbrich, T. C., Rivas-Ubach, A., Tiemann, L. K., Friesen, M. L., & Evans, S. E. (2022). Plant root exudates and rhizosphere bacterial communities shift with neighbor context. Soil Biology and Biochemistry, 172, 108753.

Verma SK, Chen Q, White JF. 2022. Evaluation of colonization and mutualistic endophytic symbiosis of Escherichia coli with tomato and Bermuda grass seedlings. PeerJ 10:e13879 https://doi.org/10.7717/peerj.13879

Vogel, G, Giles, G, Robbins, KR, Gore, MA, and Smart CD (2022). Quantitative genetic analysis of interactions in the pepper-Phytophthora capsici pathosystem. Molecular Plant-Microbe Interactions. 35:1018-1033 https://doi.org/10.1094/MPMI-12-21-0307-R

Wang, Y., Jin, Y., Han, P., Hao, J., Pan, H. and Liu, J. 2021. Impact of soil disinfestation on soil fungal and bacterial communities in cucumber cultivation. Frontiers in Microbiology 12: 685111. DOI: 10.3389/fmicb.2021.685111.

Wang, Y., Yang, R., Hao, J., Sun, M., Wang, H. and Ren H. 2021. The impact of Pseudomonas monteilii PN1 on enhancing the alfalfa phytoextraction and responses of rhizosphere soil bacterial communities in cadmium-contaminated soil. Journal of Environmental Chemical Engineering 9(6): 106533. DOI: 10.1016/j.jece.2021.106533.

Wendlandt, C.E., Roberts, M., Nguyen, K.T., Graham, M.L., Lopez, Z., Helliwell, E.E., Friesen, M.L., Griffitts, J.S., Price, P. and Porter, S.S., 2022. Negotiating mutualism: A locus for exploitation by rhizobia has a broad effect size distribution and context‐dependent effects on legume hosts. Journal of Evolutionary Biology, 35(6), pp.844-854.

Wilkerson, DG, Crowell, CR, Carlson, CH, McMullen P, Smart, CD, and Smart LB (2022) Comparative transcriptomics and eQTL mapping of response to Melampsora americana in selected Salix purpurea F2 progeny. BMC Genomics 23, 71 https://doi.org/10.1186/s12864-021-08254-1

Wu, Z., Wang, G., Zhang, B., Dai, T., Gu, A. Li, X., Cheng, X., Liu, P., Hao, J. and Liu, X. 2021. Metabolic mechanism of plant defense against rice blast induced by probenazole. Metabolites 11(4): 246. DOI: 10.3390/metabo11040246. IF3.303.

Zhang, F., Hassanzadeh, Z., Kikkert, J. R., Pethybridge, S. J., and van Aardt, J. 2022. Evaluation of Leaf Area Index (LAI) of broadacre crops using UAS-based LiDAR point clouds and multispectral imagery. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing 15:4027-4044. 10.1109/JSTARS.2022.3172491.

Zhang, Qiuwei, Kathryn L. Kingsley, and James F. White. 2022. Endophytic Pseudomonas sp. from Agave palmeri Participate in the Rhizophagy Cycle and Act as Biostimulants in Crop Plants Biology 11, no. 12: 1790. https://doi.org/10.3390/biology11121790

Zhang, X., Li, D., Huo, H., Xing, X., Lian, Y., Yu, Z., Hao, J. 2021. Improving evaluation of potato resistance to Rhizoctonia solani infection by optimizing inoculum-based method combined with toxin-based assay. Crop Protection 144: 105544. DOI: 0.1016/j.cropro.2021.105544.

Zhao, H.D., Sassenrath, G.F., Zambreski, Z.T., Shi, L., Lollato, R., De Wolfe, E., Lin, X. Predicting winter wheat heading date: A simple model and its validation in Kansas. J. Applied Meteorology and Climatology. https://doi.org/10.1175/JAMC-D-21-0040.1.

Zhao, S, S Banerjee, JF White, JJ Liu, N Zhou, CY Tian. 2022. High salt stress increases archaeal abundance and network connectivity in saline agricultural soils. Catena 217, 106520

Book Chapters

Hay, F. S., and Pethybridge, S. J. 2022. Stemphylium leaf blight of onion. Allium Chapter in World Handbook of Vegetables. In press.

Pethybridge, S. J. 2022. Cercospora leaf spot. Chenopodiaceae Chapter in World Handbook of Vegetables. In press.

Pethybridge, S. J. 2022. Alternaria leaf spot. Chenopodiaceae Chapter in World Handbook of Vegetables. In press.

Pethybridge, S. J. 2022. Aphanomyces root rot. Chenopodiaceae Chapter in World Handbook of Vegetables. In press.

Pethybridge, S. J. 2022. Bacterial leaf spot. Chenopodiaceae Chapter in World Handbook of Vegetables. In press.

Pethybridge, S. J. 2022. Black leg. Chenopodiaceae Chapter in World Handbook of Vegetables. In press.

Pethybridge, S. J. 2022. Common scab. Chenopodiaceae Chapter in World Handbook of Vegetables. In press.

Pethybridge, S. J. 2022. Pythium root rot. Chenopodiaceae Chapter in World Handbook of Vegetables. In press.

Pethybridge, S. J. 2022. Rhizoctonia root rot. Chenopodiaceae Chapter in World Handbook of Vegetables. In press.

Pethybridge, S. J. 2022. Southern root rot. Chenopodiaceae Chapter in World Handbook of Vegetables. In press.

Quesada-Ocampo, LM, Parada-Rojas, CH, Hansen, Z, Vogel, G, Smart, CD, Hausbeck, MK, Huitema, E, Naegele, RP, Kousik, CS, Tandy, P, and Lamour, K. (2023) Phytophthora capsici: Recent progress on fundamental biology and disease management 100 years after its description. In: xxyy ed Annual Review of Phytopathology Volume x. APS Press, St. Paul.

Smart, L.B., Toth, J.A., Stack, G.M., Monserrate, L.A. and Smart, C.D. (2022) Breeding of hemp (Cannabis sativa). In: Goldman, I. ed. Plant Breeding Reviews Vol. 46, New York, NY; Wiley, pp. XX-XX. (in press).

Extension and technical bulletins

Ashley, K.A., Zhang, X.Y., Mason, M., Fan, X.W., Levasseur, P. and Hao, J. 2022. Effects of B Sure and Invigorate on the control of soilborne diseases of potato. Plant Disease Management Reports 16: V020.

Damann, K., and Pethybridge, S. J. 2022. Identification of powdery mildew on cucurbit. YouTube Video. 16 March 2022.

Damann, K., and Pethybridge, S. J. 2022. Reflecting on the 2021 mesotunnel trials in New York. Current Cucurbit (blog post). 8 March 2022.

Damann, K., and Pethybridge, S. J. 2022. Reflections on the 2022 mesotunnel research trials in NY. 1 December 2022. The Current Cucurbit Website.

Damann, K., Gleason, M., and Pethybridge, S. J. 2022. What is cucurbit powdery mildew? Extension Bulletin Infographic. 21 April 2022. The Current Cucurbit Website.Final PM Infographic.pdf (iastate.edu).

Damann, K., Gleason, M., and Pethybridge, S. J. 2022. What is cucurbit downy mildew? Extension Bulletin Infographic. 21 April 2022. The Current Cucurbit Website. DM Infographic.pdf (iastate.edu).

Dille, J., Hewitt, A., Sassenrath, G. 2022. Using cover crops to control weeds and improve soil health. Kansas Agricultural Experiment Station Research Reports. Vol. 8:Iss. 3. https://doi.org/10.4148/2378-5977.8284

Moore, A., Frost, K., Rosen, C., Knuteson, D., Ruark, M., and Steinke, K. 2022. Organic Amendments & Potatoes. USDA NIFA Enhancing Soil Health in U.S. Potato Production Systems Extension Publication.

Pethybridge, S. J., Murphy, S. M., and Kikkert, J. R. 2022. 2022 fungicide trials for white mold control in snap beans. Cornell VegEdge 18 (25):5.VegEdge newsletter – Vol. 18, Iss. 25, 12/1/2022 (cornell.edu).

Pethybridge, S. J., Murphy, S. M., and Kikkert, J. R. 2022. Manipulating table beet and carrot production with plant growth regulators. Cornell VegEdge (submitted).

Sassenrath, G., Andersen Onofre, K., Lingenfelser, J., Lin, X. 2022. Comparison of sensitivity to Fusarium head blight in soft red and hard red winter wheat varieties. Kansas Agricultural Experiment Station Research Reports Vol. 8:Iss. 3. https://doi.org/10.4148/2378-5977.8285

Smart, C.D. (2022) Tomato IPM School – so many diseases so little time. Proceedings of the Tomato IPM School and the 2022 Empire Producers Expo.

Smart, C.D. (2022) Vegetable disease issues of the 2021 growing season. Proceedings of the 2022 Empire Producers Expo.

Zhang, X.Y., Fan, X.W., Ashley, K.A., Levasseur, P., Chim, B. and Hao, J. 2022. Field evaluation of chemical and biological products on the control of Verticillium wilt of potato in Maine, 2021. Plant Disease Management Reports 16: V119.

Zhang, X.Y., Fan, X.W., Ashley, K.A., Mason, M., Ge, T., Levasseur, P. and Hao, J. 2022. Field evaluation of Actinovate for soil treatment on the control of potato black scurf in Maine, 2021. Plant Disease Management Reports 16: V116.

Zhang, X.Y., Fan, X.W., Ashley, K.A., Mason, M., Ge, T., Levasseur, P. and Hao, J. 2022. Field evaluation of four fungicides for soil treatment on the control of pink rot of potato in Maine, 2021. Plant Disease Management Reports 16: V117.

Meeting presentations and proceedings

Frost, K. Enhancing potato health through management-based optimization of plant and soil microbiomes. NC State Department of Entomology and Plant Pathology Seminar Series, April 11, 2022, Raleigh, NC. Invited.

Hao, J. Understanding the outbreak of blackleg and soft rot of potato in NE US. PEI Potato Conference, Prince Edward Island, Canada, via Zoom. Mar. 30, 2022.

Karim, S., Li, X., Skillman, V., Swisher Grimm, K., and Frost, K. 2022. Short-term response of the soil microbial community to soil applied pesticides commonly used for potato production. American Phytopathological Society Annual Meeting, August 7 - August 10, 2022, Pittsburg, PA.

Moore, A., Sathuvalli, V., Frost, K., Yilma, S., Aguilar, M., and Charlton, B. 2022. Powdery scab of potato: expanding genomic resources for the pathogen and host. Annual meeting of the Potato Association of America, July 17-21, Missoula, MT.

Ocamb, C.M., Rivedal, H.M., Gent, D.H., KC, A. N., Shrestha, G., Jones, G.B., Frost, K.E., Dung, J.K.S., Thom, W.J., Garfinkel, A.R., Claassen, B.J., Wiseman, M.S., and Massie, S.T. 2022. Disease risks associated with hemp production in the Pacific Northwest. OSU Global Hemp Innovation Center Virtual Cannabis Research Conference, August 8-11 (Online).

Paulitz, T. C. Soil Microbial Communities: Relation to Plant and Soil Health in Wheat to Southern Mississippi University, Sept. 17, 2022

Paulitz, T. C. 2022. Soil Health and Microbiomes of Dryland Wheat in the Pacific Northwest of the US. 13th Arab Congress of Plant Protection Hammamet, Tunisia 16-21 October 2022

Paulitz, T. C. 2022.  The Wheat Microbiome and Soil Health- Making the Connections 8th International Cereal Nematodes Symposium Sept. 28, 2022 Bolu, Turkey

Rivedal, H.M., Shrestha, G., Jones, G. B., KC, A., Frost, K. E., Dung, J.K.S., Zasada, I. A., Núñez, L., Gent, D. H., Garfinkel, A. R., Thomas, W., and Ocamb, C. M. 2022. A disease survey of industrial hemp grown outdoors in Oregon and Washington. American Phytopathological Society Annual Meeting, August 7 - August 10, 2022, Pittsburg, PA.

Schlatter, D., Yin, C., Hanson, J., Schillinger, W and Paulitz, T C. 2022. Rhizosphere and endosphere microbiomes associated with reduced wheat yields following canola.  Plant Health 2022, Pittsburgh, PA Aug. 6-19, 2022.

Vanette, R. Microbes mediate insect-plant interactions Phytobiomes Conference, plenary speaker, Sept 13, 2022

Vanette, R. Entomological Society of America,The impact of mighty microbes and their arthropod hosts in agro-ecosystems. Nov 13, 2022

Zeng, Y., Davidson, M., Casey, D., O’Neil, P., Pandey, B, Fulladolsa, A.C., Chim, B.K., Frost, K., Pasche, J. and Charkowski, A.O. 2022. Model-based forecasting of powdery scab risk in potato, integrating soil sporosorus inoculum, potato cultivar, and environmental monitoring data. American Phytopathological Society Annual Meeting, August 7 - August 10, 2022, Pittsburg, PA.

Zeng, Y., Davidson, M., Casey, D., O’Neil, P., Pandey, B, Fulladolsa, A.C., Chim, B.K., Frost, K., Pasche, J. and Charkowski, A.O. 2022. Integrating remote sensing and molecular pathogen detection methods for developing a risk prediction model on an emerging soilborne disease in potato. 10th International Integrated Pest Management Symposium, February 28 – March 3, Denver, CO.

Abstracts

Ashley, K., Hao, J., Larkin, R. Crop management impacts on soil health, disease, and yield in northern Maine potato production. 2022 Annual Meeting of American Phytopathological Society, August 5 – 10, 2022. Pittsburg, PA.

Ekbataniamiri, F., Ge, T., Johnson, S.B., Larkin, R. and J. Hao. 2022. Investigating surface water in association with potato blackleg and soft rot. Abstract of the paper presented at the 104th Virtual Annual Meeting of the Potato Association of America, July 20 -22, American Journal of Potato Research 100: #28. DOI: 10.1007/s12230-022-09868-1.

Karim, S., Li, X., Skillman, V., Swisher Grimm, K., and Frost, K. 2022. Short-term response of the soil microbial community to soil applied pesticides commonly used for potato production. Phytopathology xx(Suppl. yy):SX.YY.

Moore, A., Sathuvalli, V., Frost, K., Yilma, S., Aguilar, M., and Charlton, B. 2022. Powdery scab of potato: expanding genomic resources for the pathogen and host. Annual meeting of the Potato Association of America, July 17-21, Missoula, MT

Ocamb, C.M., Rivedal, H.M., Gent, D.H., KC, A. N., Shrestha, G., Jones, G.B., Frost, K.E., Dung, J.K.S., Thom, W.J., Garfinkel, A.R., Claassen, B.J., Wiseman, M.S., and Massie, S.T. 2022. Disease risks associated with hemp production in the Pacific Northwest. OSU Global Hemp Innovation Center Virtual Cannabis Research Conference, August 8-11.

Rivedal, H.M., Shrestha, G., Jones, G. B., KC, A., Frost, K. E., Dung, J.K.S., Zasada, I. A., Núñez, L., Gent, D. H., Garfinkel, A. R., Thomas, W., and Ocamb, C. M. 2022. A disease survey of industrial hemp grown outdoors in Oregon and Washington. Phytopathology xx(Suppl. yy):SX.YY.

Zeng, Y., Davidson, M., Casey, D., O’Neil, P., Pandey, B, Fulladolsa, A.C., Chim, B.K., Frost, K., Pasche, J. and Charkowski, A.O. 2022. Model-based forecasting of powdery scab risk in potato, integrating soil sporosorus inoculum, potato cultivar, and environmental monitoring data. Phytopathology 112(Suppl. 12):SX.YY.

Zeng, Y., Davidson, M., Casey, D., O’Neil, P., Pandey, B, Fulladolsa, A.C., Chim, B.K., Frost, K., Pasche, J. and Charkowski, A.O. 2022. Integrating remote sensing and molecular pathogen detection methods for developing a risk prediction model on an emerging soilborne disease in potato. 10th International Integrated Pest Management Symposium, February 28 – March 3,  Denver, CO.

Zhang, X., Ge, T., Fan, X., Chim, B.K., Johnson, S.B., Porter, G. and Hao, J. Impact of inoculation methods on potato tuber responses to Dickeya dianthicola infection. 2022 Annual Meeting of American Phytopathological Society, August 5 – 10, 2022. Pittsburg, PA.

Extension Talks/Field Days/Workshops/Consultations

Borneman, J. Accelerating Growth and Treating Disease via Metabolic Modeling of Citrus, The International Congress on Citrus Nurseries, October 3 2022, Visalia Convention Center, CA

Borneman, J. Understanding the Survivor Tree Phenotype. Annual Meeting of Western Regional Project W4147 on Biological Control, December 2 2022, Zoom because of COVID pandemic

Frost, K.E. 2022 plant disease research: fumigation, tuber blemishes, and stem canker. OSU-HAREC Potato Field Day, Hermiston, OR, June 22, 2022 (~70) Invited.

Frost, K.E. Impact of tare soils on rhizosphere microbiome establishment and implications for plant health. Hermiston Farm Fair (Virtual).  November 30, 2022 (~250). Invited.

Frost, K.E. Suppression of soilborne diseases: fumigation and crop rotations. Hermiston Farm Fair (Virtual).  December 1, 2022 (~230). Invited.

Frost, K. F. Hermiston Farm Fair, Soil Health/General Session (AD). Eight invited speakers. (~230 attendees)

Hao, J. Maine Potato Research Field Day, Aroostook Research Farm, Presque Isle, ME. Aug. 17, 2022. 100 attendees.

Paulitz T. C.  2022. The Soil Microbiome. Talk at the annual LTAR meeting at the Cook Agronomy Farm, July 13, 2022.

Paulitz, T. C.  Does canola suppress AMF infection in a following wheat crop? WA  SoilCon Feb. 23, 2022 

Paulitz, T. C. 2022. Research at USDA-ARS Wheat Health, Genetics and Quality Research Unit:  What’s New? talk at Spokane Farm Forum on New Research in Feb. 2, 2022.

Paulitz, T. C. 2022. The Soil Microbiome & Soil Health.  A 1.5 hour lab presented to growers at the Washington Wheat Academy, Dec. 15, 2022.

Paulitz, T. C. 2022.Soil Microbial Communities: Relation to Plant and Soil Health in Wheat to Walla Walla Conservation District Annual Meeting January 27, 2022.

Paulitz, T. C. Black leg of canola , Canola field day, Davenport, WA June 17, 2022.

Paulitz, T. C. Current Research at USDA-ARS Pullman Presented talk at Western Wheat Workers meeting, Pendleton, OR, June 20, 2022.

Paulitz, T. C. Determination of the Microbial Bases for Yield Decline In Wheat After Canola to Washington Oilseeds and Cropping Systems Commission, March 15, 2022, Spokane, WA.

Pedreira, B., Sassenrath, G.F. 2022. Corn production in Southeast Kansas. Kansas Corn School. Jan. 18, 2022. Parsons, KS.

Pedreira, B., Sassenrath, G.F. 2022. Wheat disease and soil health. Kansas Crop Improvement Association. Feb. 15-16. Manhattan, KS

Pethybridge, S. J. 2022. Mesotunnels for integrated pest management of organic cucurbit production. Organic Cucurbit Field Day, Cornell AgriTech, Geneva, NY. Attendees = 20. Duration = 2 hours. Total contact = 40 hours. 9 August 2022.

Pethybridge, S. J. 2022. On-farm trial results for mesotunnels for organic cucurbit

Pethybridge, S. J. 2022. Optimizing pollination in mesotunnels for cucurbit production (NY results). Iowa State University Mesotunnel Working Group. Virtual by Zoom. Attendees = 25. Duration = 60 min. Total contact = 25 hours. 25 October 2022.

Pethybridge, S. J. 2022. Potential of cereal rye mulch to suppress white mold in no-till soybean and dry bean. Northern Grain Growers Association. 2022 Grain Growers Series. University of Vermont Extension. Virtual by Zoom. Attendees = 30. Duration = 60 min. Total contact = 30 hours. 30 March 2022.

Pethybridge, S. J. 2022. Potential of cereal rye mulch to suppress white mold in no-till soybean and dry bean. Empire Expo. Virtual by Zoom. Attendees = 32. Duration = 40 min. Total contact = 21.3 hours. 9 March 2022.

Pethybridge, S. J. 2022. Potential of cereal rye mulch to suppress white mold in no-till soybean and dry bean. Northeast Cover Crop Conference. Virtual by Zoom. Attendees = 80. Duration = 45 min. Total contact = 60 hours. 10 March 2022.

Pethybridge, S. J. 2022. Stakeholder engagement. Tips for new Assistant Professors on extension. Cornell Cooperative Extension Seminar Series. Virtual by Zoom. Attendees = 42. Duration = 60 min. Total contact = 42 hours. 28 April 2022.

Pethybridge, S. J. 2022. Towards a durable management strategy for white mold in dry beans in New York: Sclerotial survival (2021/22). NYS Dry Bean Council. Virtual by Zoom. Attendees = 40. Duration = 45 min. Total contact = 30 hours. 16 March 2022.

Pethybridge, S. J. 2022. Untangling the web of cover crops and root diseases in summer crops. Organic No-Till Field Day, Hudson Valley Farm Hub, Hurley, NY. Attendees = 50. Duration = 4 hours. Total contact = 200 hours. 4 August 2022.

Pethybridge, S. J. 2022. Using mesotunnels for integrated pest management in organic cucurbit production (NY results). Iowa State University Mesotunnel Working Group. Virtual by Zoom. Attendees = 30. Duration = 60 min. Total contact = 30 hours. 11 November 2022. production (NY results). Iowa State University Mesotunnel Working Group. Virtual by Zoom. Attendees = 25. Duration = 60 min. Total contact = 25 hours. 18 November 2022.

Sassenrath, G.F. 2022. Measuring soil biology. Extension presentation. March 10, 2022. Haven, KS

Sassenrath, G.F. 2022. Soil health: Improving production and profitability. Southeast Kansas Soil Health Field Day, McCune, KS. Feb. 8, 2022.

Sassenrath, G.F. 2022. Suppressive soils for improved crop production. Radio interview with Greg Akagi, WIBW radio.

Smart, C. Alternaria leaf and head rot on broccoli research update. January 6, 2022. 2x15 minutes talks to 26 participants. Contact hours = 13

Smart, C. Empire State Producers Expo, February 25, 2022. Broccoli issues including Alternaria leaf spot. 50 minute talks and discussion with 40 participants. Contact hours = 30

Smart, C. Empire State Producers Expo, February 28, 2022. Hemp diseases – results from 2021 field trials. 30 minute talk to 40 participants. Contact hours =  20

Smart, C. Empire State Producers Expo, March 10, 2022. Tomato IPM School – so many diseases so little time. 53 participants for a 1 hour talk. Contact hours = 53

Smart, C. Empire State Producers Expo, March 10, 2022. Winter squash cultivar evaluations for resistance to powdery mildew. 15 minute talk to 40 growers. Contact hours = 10

White, J. Acres Annual Convention in Covington, KY on December 8, 2022. Title: How plants use soil and plant microbes to acquire nutrients (Plenary presentation).

White, J. Acres Healthy Soil Summit in Sacramento, CA in August 2-3, 2022. Title: Rhizophagy cycle and endophytes in plants (Plenary presentation).

White, J. Australian Biological Farming and Tradeshow (online) on December 3, 2022. Title: The rhizophagy cycle (Plenary presentation).