Brief Summary of Minutes of Annual Meeting

Scot Hulbert, W5147 Administrator, Washington State University (WA). Introduced himself and welcomed the group. Jim Farrar (Director of University of California Integrated Pest Management, UC-IPM) told the group that we should use our Impact Statements to show congress and other supporters that our work is having a real impact on agriculture, and don't just focus on listing presentations and publications. He also stated that this can include activities that we have done anytime during our careers, not just recently.

Meeting Participant Introductions. Participants gave brief summaries of where they are located and the type of research and extension activities they perform.

Amer Fayad, NIFA Administrator. Told the group that USDA officials look at our progress reports for success stories, which they then put in newsletters and also share with congress. He briefly described AFRI's 3 major programs: Foundational Program, Education and Workforce Program, and Sustainable Agricultural Systems Program. He also described a new funding program: Rapid Response to Extreme Weather (A1712).

STATE REPORTS

Jay Hao, University of Maine (ME). Jay discussed a long-term study examining different cropping rotations for potato production. Potato yields varied by crop rotation. Best treatment for potato yields included compost. Best treatment for controlling Verticillium included compost. Jay told the group that continuous fumigation produces inconsistent results in Maine. The frequent fumigation treatment had increased levels of microbes that can degrade fumigants, possibly explaining the inconsistent results growers obtain when they use fumigants.

Sarah Pethybridge, Cornell AgriTech (NY). Sarah described studies examining the use of rolled crimped cereal rye mulch in the management of Sclerotinia sclerotiorum (white mold) in organic bean production. The goal of this work is to reduce the reproduction of white mold in the top layer of soil, because this is the main source of the fungus in the disease. The mulch treatment increased yields of black beans and soybeans. A reduction of white mold was shown with the mulch treatment. Reductions of functional apothecia with the mulch treatment were also shown.

James White, Rutgers University (NJ). Jim described a hypothesis where endophytes stimulate genetic variation. In corn, microbes lead to more mutations. Xanthobacter autotrophicus was tracked in plants, which showed the bacterium moving in and out of root hairs, and into root and shoot meristem tissues. Jim also described the phenomenon of endoreduplication, which is where ethylene, nitrogen, and hormones cause plant nuclei to become polyploid. The mechanism by which endophytes could be causing genetic variation in plants is thought to involve transposons.

Gretchen Sassenrath, Kansas State University (KS). Gretchen described studies examining the effect of rotation on crop yields, pathogen densities, and soil health in soybean production. Since diseases are a major factor that reduce soybean yields, this group is examining a variety of soil and crop parameters. The goal of this work is to find variables that correlate with less disease, which is information that could be used to predict and/or control disease.

Harsh Bais, University of Delaware (DE). Harsh described studies examining the role of the root microbiome in plant health. This group is determining whether adding wild ancient microbiomes will improve plant growth and nutrient management. They also showed Bacillus subtilis UD1022 causes stomatal closure in Arabidopsis thaliana, which then inhibited invasion of a plant pathogen. This could therefore be a mechanism of disease control associated with the use of this bacterium.

Tessie Wilkerson, Mississippi State University (MI). Tessie described studies examining reniform nematodes in cotton production. Yield losses due to these nematodes can be 10 to 80% but on average are 15 to 30%. This group performed field studies to determine whether cotton breeding lines with resistance to reniform nematodes affects cotton yields, root health, and the number of nematodes.

MORNING BREAK

Ernie Osborne, University of Kentucky (KY). Ernie is a new Assistant Professor who has a microbial ecology background. He started working on a long-term tillage and fertilization study site that is examining cover crops, different levels of nitrogen inputs, and tillage in corn production. This study has been running since 1970. Soils that have not been tilled for 54 years had greater numbers of bacterial rRNA genes. The treatments examined in this long-term site were shown to affect the types of bacteria and fungi. Relative abundance of fungal pathogens were almost doubled in no till vs. conventional, but most of these pathogens targeted weeds, so they are likely not affecting corn yields. The abundance of viruses in the rhizosphere was shown to be associated with higher soil respiration.

Mike Kolomiets, Texas A&M University (TX). Mike described studies examining the mechanisms of Trichoderma virens and Pseudomonas chlororaphis in the regulation of maize resistance to anthracnose leaf blight disease and western corn rootworm. These microbes improved resistance to Colletotrichum graminicola and they reduced plant damage caused by the western corn rootworm. These microbes also inhibited the suppression of armyworms via JA accumulation.

Amita Kaundal, Utah State University (UT). Amita described studies examining native plant microbiomes. The goal of this work included finding microbes that increase plant growth as well as control pathogen populations. This group showed that native microbes improved the growth of snowbrush and they induced nodulation by Frankia. Similar studies were also performed on Buffaloberry.

James Borneman, University of California Riverside (CA). James described potential problems associated with the use of fungal Illumina amplicon sequencing, which this group is using to identify fungi that parasitize cyst nematodes. The two problems were assigning taxonomy to ASVs/OTUs and binning sequences into ASVs/OTUs. Solutions to these problems were discussed.

Ole Becker/Antoon Ploeg, University of California Riverside (CA). Ole described some of the history of cole crop production along California's Central Coast. This involved controlling cyst nematodes with 1,3-D, which were banned for 6 years in the 1990s due to its presence in a public school. While predictions of large crop losses due to the ban of this chemical were made, this did not happen, because there were no increases in cyst nematode populations. Ole described a hypothesis that might explain this phenomenon, which is that microbes, primarily Hyalorbilia spp., parasitize cyst nematodes, thereby keeping their populations at low levels.

Antoon Ploeg, University of California Riverside (CA). Antoon described a study examining damage to bentgrass on golf course greens. Roots showed galling, which is characteristic of root-knot nematode infestations. The question then became were root-knot nematodes causing this disease, and if yes, which species was responsible. Meloidogyne marylandi was determined to be the main species associated with this disease. However, even at high levels of nematodes, these nematodes did not cause damage to bentgrass when Koch's postulates experiments were performed. The current hypothesis is that the plant damage is caused by these nematodes but only in combination with higher ambient temperatures.

Emma Gachomo, University of California Riverside (CA). Emma described the ability of Bradyrhizobium japonicum to increase plant growth, which was associated with auxin levels. This same bacterium increased plant biomass and siliques in Arabidopsis, and this also occurred under drought stress. The flavonoid pathway was shown to be turned on in drought stress. Different Arabidopsis mutants in the flavonoid pathway were used to confirm that this pathway was involved in drought tolerance in the presence of B. japonicum. This bacterium was also shown to close stomata, a known mechanism of drought tolerance. A study on biofungicides was also described.

LUNCH BREAK

Bode Olukolu, University of Tennessee (TN). Bode described ways to leverage microbiomes for improving crop yields. Bode also stated that SynComs produce inconsistent results because of variation in specific microbe-microbe interactions and specific microbe-plant interactions. Metagenomic data was analyzed with plant genome data using quantitative Reduced Representation Sequences (qRRS). This approach identified associations among microbes, plant genomic features, plant health, and plant disease.

Jiue-in Yang, University of California Riverside (CA). Jiue-in described the isolation and evaluation of 14 new Hyalorbilia oviparasitica strains. She also described an isolation method that was based on a method originally developed by Jennifer Smith Becker. These strains were shown to parasitized eggs from different types of nematodes and that they also suppressed Heterodera schachtii densities by different amounts. A nematode identification method using deep learning (artificial intelligence) was also described. Different models and sub-models were tested to find the one that most accurately identified different types of nematodes. A web-based interface enabling users to identify nematodes was also described.

Jenifer McBeath, University of Alaska (AK). Jennifer described projects examining leaf spot disease on rhodiola and the growth promoting effect of Trichoderma atroviride on peonies, as well as the seasonal dynamics of microbial communities in Alaskan agriculture. She also described the diseases and pathogens of rhodiola and peonies in Alaska. She also showed T. atroviride increased the growth of rhodiola. A collaboration with Bode Olukolu examined metagenomic data to identify associations among microbes, plant genomic features, plant health, and plant disease.

Maren Friesen, Washington State University (WA). Maren described the benefits of increasing nitrogen in agriculture as well as some of the problems associated with increasing nitrogen via nitrogen fertilizer amendments. The primary question examined in the Friesen lab is, can nitrogen fertilization be replaced by biological nitrogen fixation. Several strategies were described. Crop rotations that use legumes is one strategy to increase nitrogen in soil using a biological approach. Long-term studies sites were examined in some of the studies. Associations of microbes involved in many of these processes were identified and described.

Timothy Paulitz, Washington State University (WA). Tim described research examining the microbes associated with potato production in soils that had not been cropped to potatoes in the last twenty years compared to soils that were frequently cropped to potatoes. Higher alpha diversity was detected in bulk soil compared to rhizosphere. Beta diversity was mostly influenced by location and not soil treatment (no previous recent potato production vs. frequently potato production). Drivers of beta diversity were identified and they included the amount of nitrogen. There was higher pathogen levels in soils previously cropped to potatoes compared to soils without recent potato production. A different project that created an AI-based method to identify different types of nematodes in potato production was also described.

BUSINESS DISCUSSIONS

The group discussed whether the next group meeting should be held in person or via Zoom. While several people indicated a preference for in-person meetings, the group thinks it is important to include members that are unable to travel to the annual meeting by holding hybrid meetings. The group thinks it is especially important to hold an in-person meeting when it is time to write the proposal for the project renewal. Members were asked to contact Tim Paulitz if they are interested in hosting a hybrid meeting next year and if they are interested in being the secretary for the next meeting.

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.

AK. Understanding beneficial Bacillus under Alaska cold environment. More than 53 Bacillus isolates which were adapted to cold temperature (can grow at 7 ᵒC) were isolated. Among them, 18 isolates demonstrate different degrees of antagonism against economically important pathogens. Efficacious isolates were identified as Bacillus subtilis, and B. amyloliquefaciens and they are compatible with the beneficial cold adapted Trichoderm atroviride (>4 ᵒC). [Plant Helper™]. Understanding Phoma leaf spot (new disease) found on rhodiola plants grown under the cool (10 ᵒC) and wet environmental conditions. on the leaves and stems of the diseased plants. Phoma isolates were found susceptible to Plant Helper™.Understanding seed decay of rhodiola resulted in the isolation of Fusarium spp. (new record) from the florets of rhodiola plants. Infested florets causes severely decline in rhodiola seed production.

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 H. schachtii, which we anticipate will lead to higher crop yields and profitability for the growers. This work was published in this reporting period. During the course of this work, we also created new ways to analyze fungal Illumina amplicon data, which improved the results of our research. We expect this will also improve the results for other researchers.

CA.  New biologically derived and biological agents were evaluated for their efficacy to control root-knot nematodes (RKN; Meloidogyne spp.) on vegetable crops in greenhouse and field experiments. A research project was initiated in collaboration with Ole Becker (UC Riverside), Joji Muramoto (UC Davis),  and Erin Rosskopf (USDA, FL) to test anaerobic soil disinfestation (ASD) with different organic materials as a means to manage RKN in carrot in field trials.

CA. In the 1970s and 1980s, sugar beet growing along the California coast was replaced by more profitable vegetable production. The remaining sugar beet cyst nematodes (Heterodera schachtii) significantly impacted Cole crops (Brassica oleracea), such as broccoli, cabbage, cauliflower, Brussels sprouts, and others.

Our recent survey of 88 broccoli fields detected only three fields with potentially damaging cyst nematode population levels. Repeated 3-month greenhouse experiments with 11 randomly selected broccoli field soils found 9 highly suppressive to Heterodera schachtii. We hypothesize that biological suppression was caused by various nematode-parasitic fungi, particularly Hyalorbilia spp. and Pochonia chlamydosporia.

In other greenhouse trials, we tested four nematicides and two biological control agents to determine their efficacy against Meloidogyne incognita on tomato plants in three different soils. Three new nematicides reduced more than 99% of the eggs per root. A combination of Metacordyceps chlamydosporia and Pasteuria penetrans reduced the number of eggs by 69% relative to the untreated control. Overall, the tested biological control agents did not match the nematicides' early protection of tomato transplants.

DE.  As part of objective 1, our work showed that using a synthetic community approach of administering single or consortium of microbes, we can enrich plants for nutrients and biological control. Using systems approach we used a single inoculum of a wild strain of Bacillus subtills strain UD1022 to control dollar spot disease in turfgrass. Experiments showed the efficacy of B. subtilis UD1022 against dollar spot pathogen (Clarireedia spp.) was dependent on surfactin and SpoA pathway. We also showed that application of UD1022 in dry and temperate soil cores increases soil water retention. In addition, the ability to increase soil water retention by UD1022 was found of be independent of surfactin and exopolysaccharide pathway.

DE. Towards an understanding of the role of bacterial viruses (phages) in altering host populations in soil, we examined both virulent and temperate phages of soybean bradyrhizobia (Bradyrhizobium japonicum, B. diazoefficiens, and B. elkanii.).  The complete genomes of 13 virulent phage isolates from Delaware farms were sequenced, revealing that phage species was strongly but not entirely dictated by the host species used for isolation.  These phages represented four distinct and novel species having little similarity to previously sequenced phages.  Studies of temperate phages provided strong evidence that phages (along with resident plasmids and insertion sequences) are an important component of the bacterial host’s mobilome and play a role in the evolution (via horizontal gene transfer) and potentially the symbiotic effectiveness of the Bradyrhizobium hosts with the soybean plant.  As part of the latter research, we found that a majority (~70%) of 98 Bradyrhizobium cultures in our collection spontaneously produce abundant and diverse temperate phages in routine lab culture, again suggesting these phages influence the evolution, ecology, and symbiotic effectiveness of soybean bradyrhizobia and associated crop yields.

ME. Studied effects of continuous soil fumigation on soil health, diseases, and potato yields. Studied soil microbial communities treated with biological and chemical products. Examined potato varieties and clones on the resistance to pink rot and soft rot.

NY. Effects of table beet residue management on the microbiome associated with table beet. A small plot replicated trial was again 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. Results from this trial are being combined across years (2023 and 2024) and data analysis is pending.

NY. Effects of tillage x nitrogen interactions on organic dry bean production. This trial was initiated in 2023 (fall treatments) and this season (2024) was the first cropping season. data was collected in all trials and the effect of treatment is being analyzed. Soil and root samples were also collected. The severity of root rot was evaluated, and fungal isolations were made from all samples. DNA was extracted from the fungal isolates and multilocus sequencing was conducted for species identification. Interestingly, charcoal rot caused by Macrophomina phaseolica was present at high incidence and severity, which is a new disease report for dry beans in NY. Fusarium spp. (F. oxysporum and F. solani) were present at high frequency. The effect of treatment on fungal root rot severity and isolations is being analyzed. Bulk soil and rhizosphere samples were also used for DNA extraction for analysis of the microbiome through 16S and ITS sequencing to quantify the diversity and abundance of bacterial and fungal species, respectively. 16S sequencing has been completed, and PCR reactions for the ITS sequencing are being optimized. This trial location will be planted in spring 2025 with barley to evaluate legacy effects of the treatments. This trial will also be established for the second time at a different location state in fall 2024, with a replication of the cropping season in 2025.

UT. We have isolated around 200 plant growth-promoting bacteria from the rhizosphere of native plants Cenaonthus velutinus (Snowbrush) and three species of Shepherdia (buffaloberry). We Shortlisted around 20 rhizobacteria from C. velutinus and 30 rhizobacteria from three Shepherdia sp. with plant growth-promoting activities to test on different crops, to develop as biofertilizers under different abiotic conditions, and for their biocontrol activities against various bacterial and fungal pathogens. Eight isolates were tested on Arabidopsis, wheat, tall fescue, maize, and watermelon for plant growth promotion. All isolates are being tested for biocontrol characteristics.

WA. Nematode communities can be described by DNA techniques. 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. At present, they can only be described by extracting live nematodes from the soil, and identified by morphological characters under the microscope, which few trained nematologists can do.  ARS scientists in Pullman and Corvallis and Washington State University scientists developed a database of 18s sequences for amplicon sequencing. This was validated with potato and wheat soils across eastern Washington and Oregon, including soils that have never been cropped. Nematodes were morphologically identified and sequenced with amplicon sequencing, with a high degree of correlation between the two methods.  This opens up the possibility of more extensive use of nematode communities as indicators for soil health, especially by those not skilled in nematology taxonomy.

WA. Bacterial and fungal communities in rhizosphere of camelina are driven by soil and environmental factors
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. Microbial communities on the roots may influence crop performance and nutrient uptake. ARS researchers at Pullman, Washington, and Washington State University and Montana State University scientists, funded by a grant from Department of Energy, described the microbiome of camelina from the roots of camelina grown in 33 different locations in eastern Washington and Montana. Bacterial communities were highly influenced by soil pH, Ca and Mg, while fungal communities were more affected by precipitation. Influences were stronger in the bulk soil but less in the rhizosphere and root, indicating that the plant selects the community from the soil. This is part of a larger project to identify key components of the camelina bacterial community that may play a role in increasing nutrient uptake, pathogen resistance and drought tolerance in this important biofuels crop

WA. Potato phytobiome shows the legacy of cropping systems and soil drivers. Growers have observed yield increases when virgin land is first cropped, but then declines with continuous cropping.  Are there shifts in the soil and plant microbiome that are responsible for this observation? WSU and ARS researchers sampled potato farms in the Columbia Basin and Skagit Valley of WA, with paired samples- cropped, non-cropped and virgin soil. A common garden was established in Pullman, and the bulk soil, rhizosphere, endosphere and tubersphere fungal, bacterial, protist, and nematode communities were analyzed with amplicon sequencing. Location was the strongest driver of communities with smaller effects of cropping legacy and soil factors.  Plant compartments each harbored distinctive core microbiomes. Fungal and nematode pathogens were more abundant in the cropped soils. This research has established a better understanding of the microbial communities on potato and will also provide insights for designing hypothesis-driven research on different soil communities and their associations with soil types across various potato compartments. This can help growers to adapt and refine best practices for soil health.

WA. The microbiome under intercropping. Intercropping is gaining interest as a way to increase production on the currently available landbase. Pea and canola have been found to show overyielding in the inland PNW when intercropped, but the mechanisms of this are not known. We characterized three years of peaola field trials for the plant and soil microbiomes, and found that pea and canola consistently maintained distinct microbiomes from one another, but that under intercropping there were additional bacteria present in the core microbiome that were not recruited by each crop when grown in monoculture. We also found that in one year with high intercropping replication the canola has higher tissue N when grown with pea than when grown in monoculture. These data show which bacteria each plant recruits to its rhizosphere, and could be useful in rationale design of microbiomes for biocontrol purposes.

WA.  Nitrogenase diversity. We analysed one of the conserved nitrogenase subunits, nifH, for sequence diversity in soil samples at Cook Farm LTAR and found higher diversity under business as usual, which may be due to less acidic soil pH than under no-till. We collected samples from multiple prairie and neighboring agricultural fields, as well as from the WA Soil Health Initiative baseline samples and are currently sequencing these. This data will provide a survey of nitrogen-fixing bacteria present under diverse management regimes as well as across geographic variability, and can be used to determine whether there are particular diazotrophs whose populations could be enhanced in place versus taxa that are not present and could be added to an agroecosystem through inoculation.

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.

AK. The soil microbiome studies. The metagenomes were subjected to the quantitative reduced representation sequencing (qRRS) method to understand plant pathogen-microbiome interactions in peony and in Arctic soils. Results indicated that specific microbes might function as a master-regulator of other community members in a seasonal-dependent manner in the Arctic soil metagenome.

CA  Decline of bentgrass in a Southern California golf course was investigated. High populations of RKN were associated with the decline symptoms. The RKN were isolated from affected areas, cultured and identified as Meloidogyne marylandi using morphological and molecular methods. The ability of this nematode to cause symptoms and multiply on a range of grasses and vegetable crops, and the effect of soil temperature on the reproductive rate was determined. In greenhouse trials using steam-pasteurized soil, increasing population levels of this nematode did not result in a growth reduction or decline symptoms in bentgrass.

DE. As part of objective 2, we used B. subtilis UD1022 in tomato rhizosphere to evaluate how an application of a synthetic inoculum modulates microbial ecology and interactions. We showed that a mutant of UD1022 deficient in ES and TasA production showed a diminished capacity to colonize tomato roots in soils with diluted microbial diversity. The analysis of bacterial β-diversity revealed significant differences in bacterial and fungal community structures following inoculation with either the wild-type or mutant B. subtilisstrains. Our study advances our understanding of the EPS and TasA genes, which are not only important for root colonization but also play a significant role in shaping rhizosphere microbiome assembly.

WA.  Disease-suppressive soils have a broader role in plant defense. Disease-suppressive soils are examples of natural microbial-based defense of plant roots against soilborne pathogens. They are defined as soils in which, because of their microbial makeup and activity, a pathogen does not establish or persist, establishes but causes little or no disease, or establishes and causes disease at first but then the disease declines with successive cropping of a susceptible host even though the pathogen may still persist in the soil.  Take-all decline (TAD) is a natural suppression of take-all disease of wheat (caused by Gaeumannomyces tritici) that develops during wheat monoculture and following a severe outbreak of the disease. ARS scientists at Pullman in collaboration with colleagues at Utecht University, the Netherlands determined the ability of a TAD soil from Washington state to induce systemic resistance (ISR) in Arabidopsis thaliana against Pseudomonas syringae pv. tomato (Pst) DC3000, causal agent of bacterial speck.  Arabidopsis seedlings grown in an autoclaved soil/sand mixture amended with 10% (wt/wt) TAD soil demonstrated strong induced resistance against Pst, but a non-suppressive soil did not induce resistance in Arabidopsis. This is the first report of induction of systemic resistance by a suppressive soil and indicates that TAD can have a broader role in foliar disease suppression, beyond the control of its target disease, take-all.

WA Detection of the early effects of plant disease. Phenomics imaging technologies as applied to phytopathology allow the acquisition of high-dimensional phenotypic data on morphological and physiological changes in infected plants during disease development without destructive sampling of plant parts. Spectral analysis of plants can detect rapid and subtle changes in tissues and organs before symptoms are visible. ARS scientists at Pullman and Dutch scientists used the Helios phenomics system at The Netherlands Eco-phenotyping Centre (NEPC) to describe the early phase of infection of tomato seedlings by Pseudomonas syringae pv. tomato (Pst) DC3000, causal agent of bacterial speck of tomato. Twenty days after planting in an autoclaved potting soil/sand mixture, tomato seedlings were inoculated by dipping the foliage into a suspension of Pst DC3000.  In less than 24 hrs. after inoculation, and prior to appearance of any symptoms of bacterial speck, Helios detected significant changes in the morphology and physiology of tomato plants including a significant decline in the density of leaves and stems, efficiency of energy harvesting, and leaf area. This research demonstrates how phenomics technologies can be used for early detection of foliar diseases in field- or greenhouse-grown crops, allowing more rapid removal of infected plants and preventing pathogen spread to healthy plants.  

TX. The focus of the Kolomiets lab research in the reporting period was on gaining better understanding of the biological effects of the root-colonizing fungal endophyte, Trichoderma virens, and the bacterial endophyte, Pseudomonas chlororaphis, on maize induced resistance to fungal pathogens and below- and above ground herbivores, western corn rootworm and fall armyworm, respectively. The study resulted in one refereed publication that describe the following knowledge gained:

When T. virens or P. chlororaphis was applied to maize seedlings grown in sterile soil, resistance to fall armyworm infestation was reduced due to reduced levels of wound-induced jasmonic acid biosynthesis.   This was unexpected as some literature suggested that Trichoderma species application to crops may improve resistance to leaf-chewing insects. Therefore, we tested whether such a detrimental effect would be observed in plants grown in non-sterile field soils and showed that both endophytes had no effect on resistance to fall armyworm herbivory under natural soil conditions. Unlike above-ground herbivory, colonization of roots by T. virens, resulted in strong suppression of western corn rootworm growth and development suggesting such treatment as an effective biocontrol for root-feeding pests.    Unlike resistance to herbivory, both T. virens and P. chlororaphis endophytes improved systemic resistance to anthracnose leaf blight regardless of soil condition, suggesting their strong effectiveness on improving resistance to pathogens.  Previously, T. virens was shown to secrete Sm1 and Sir1 peptides that oppositely regulate induced systemic resistance to the foliar pathogens. We generated the double mutants for the two genes and found that the disease Sir1 peptide acts as the dominant negative regulator of induced resistance against the anthracnose pathogen Colletotrichum graminicola, since the double mutant triggered greater resistance. 

TX. Brady Lab. For the peanut project, we have isolated and screened several hundred plant endophytes to identify select microbes that increase drought tolerance in peanut seedlings. Nineteen of the most impactful isolates are being characterized phenotypically and genetically. The 19 elite microbial isolates are at varying stages of intellectual property protection within the Texas A&M system. Initial functional characterization has begun. Some of the microbes interact with peanut plants through hormonal pathways and/or altered nutrient mineralization/uptake. The time it takes for greenhouse peanut seedlings to wilt after cessation of watering is doubled in plants containing some of these microbial inoculants. A replicated field trial for 7 of the elite microbial isolates is being conducted in 2024 and peanut harvest is underway currently.

UT. For the native plant project, we have isolated several hundred plant microbial endophytes from the native grass little bluestem (Schizachyrium scoparium) and we are screening the ability of those microbes to inhibit germination of the invasive grass KR bluestem (Bothriochloa ischaemum var. songarica). Ten microbes have been screened and 2 microbes with the desired effect are being characterized genetically while we are screening the remaining hundreds.

For the biochar project, we have conducted field and greenhouse experiments with wood biochar, activated wood biochar, and dairy-manure derived biochar as soil amendments in Italian ryegrass, Bermudagrass, and cowpea pots (greenhouse) and maize, sorghum, and Bermudagrass field forage production plots. We noted no negative production impacts due to biochar while finding improvements in soil including an increase in microbial diversity, an increase in soil carbon, a decrease in pathogenic microbes, a decrease in antibiotic residues and antibiotic resistance genes.

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

AK. Information for peony growers were: 1) Plant Helper™ was the only efficacious means of controlling Botrytis grey mold disease on peony under a cool (10 ᵒC) and wet conditions. 2) peony plants treated with Plant Helper™ were much more robust. Biomasses of treated peony plants were significantly larger. 3) treated peony plants demonstrated a delay in the senescence process (and maintained their photosynthesis longer).

Information for rhodiola growers were: 1) Plant Helper™ enhanced significantly the growth and development of rhodiola plants, 2) Phoma spp. and Fusarium spp. found on rhodiola plants were susceptible to cold tolerant Trichoderma. Plant Helper™ can potentially be able to protect rhodiola plants against these diseases.

CA. Plant resistance has been used effectively to manage RKN by California processing tomato growers for many years. Over the last decade however, nematode infestations in resistant varieties are being observed with increasing frequency. Such resistance-breaking populations were encountered throughout California processing fields. The majority of these populations were identified as M. incognita, although a population of M. javanica was also found to break resistance. There were no obvious differences in virulence among these populations on a range of resistant tomato varieties. Resistance to RKN in other vegetable crops was generally not compromised by these nematode populations indicating the resistance-breaking ability of these populations was specific for the tomato Mi-resistance gene. Thus, growing other RKN-resistant of non-host crops would offer a viable strategy to reduce levels of such RKN populations in processing tomato fields.

CA. A new-to-California RKN species was discovered a few years ago from almond rootstock. This RKN species (M. floridensis) is known to infest prunus rootstocks normally resistant to RKN. We tested the virulence of this nematode on several RKN-susceptible and -resistant vegetable crop varieties to determine if this nematode poses a risk to vegetable crops grown in California. Results showed that this nematode infests most of the vegetable crops and furthermore is able to overcome nematode resistance in tomato and some resistant pepper cultivars. These results further emphasize the need to eliminate or restrict the spread of this nematode outside of the original location where it was found.

KS. We conducted research to identify beneficial microbes that can naturally suppress harmful pathogens and improve soil health, leading to more resilient crops. Additionally, we engaged in extensive outreach efforts, including workshops and online resources for growers, helping them adopt sustainable practices that reduce dependence on chemical treatments and enhance crop productivity. Specifically, our studies for 2024 explored the effect of alternative production methods on a primary soybean disease, charcoal rot, caused by the fungus Macrophomina phaseolina.

Treatments that could potentially enhance or reduce disease pressure were implemented, and soil tests were conducted for nutrients, soi health properties, and disease. Much effort has been directed at Brassica juncea (Indian mustard) cover crops. Manure increased the nutrient levels in the soil, as expected, but did not control disease. Solarization increased the temperature within the plots and increased the population M. phaseolina.

NJ. We have identified several new endophytic microbes of plants that also have activity in suppression of fungal pathogens of plants. In addition, we have identified microbes that suppress seedling growth. We are exploring use of these in bioherbicides to control weeds with non-toxic herbicidal components.

ME. Studied crop rotation, cover crops, and soil amendments on soil health and disease management. Analyzed soil microbial communities under the above treatments

NY. Efficacy of fungicides for Cercospora leaf spot control in table beet, 2024. Cercospora leaf spot (CLS), caused by the fungus, Cercospora beticola, is a major constraint to table beet and sugar beet worldwide. The disease causes defoliation which deleteriously affects harvest using top-pulling machinery and reduces root weight and quality. A replicated small plot trial was conducted to evaluate selected fungicides for CLS control in table beet at Geneva, NY in 2024. The trial was a randomized complete block design with four replications of each treatment and a nontreated control. Fungicides were applied four times at 62, 72, 93, and 94 DAP. The trial was inoculated with a mycelial suspension of C. beticola at 62 DAP. Of the fungicides tested, Cevya provided superior control of CLS that outperformed the comparative FRAC 3 product, Tilt. Miravis Prime (FRAC 7 + 12) also, again, provided excellent control of CLS but Cevya provided improved control of epidemic progress. There was some evidence of differential efficacy between products containing FRAC 7 active ingredients. For example, Endura (FRAC 7 – boscalid) provided only moderate CLS control. In contrast, Tesaris that only contains the FRAC 7, fluxapyroxad, provided significantly improved CLS control compared to Endura. Considering the majority of C. beticola isolates are FRAC 11 resistant (active ingredient of Cabrio alone and Merivon), Tesaris may be useful for rotational purposes. The absence of an effect of root yield components is beneficial to abide by strict processor regulation requirements for placement into cans and jars.

NY Efficacy of OMRI-listed fungicides for white mold control in black bean in New York, 2024. A replicated small plot trial was conducted to quantify the efficacy of selected Rovensa Next products (OR-079B, OR-329H, and OR-009 EPA) in comparison to the OMRI-listed (Double Nickel LC, Badge X2, Howler and Theia) and conventional (Endura) fungicides for white mold control in dry black bean in Geneva, New York in 2024. All products significantly reduced the incidence of white mold in plants and pods compared to the nontreated control plots. OR-079B applied to the soil increased green leaf area (as measured by the Normalized Difference Vegetative Index; NDVI]) by 8.9% and decreased the incidence of white mold in pods compared to nontreated plots. Application of OR-079B (soil) followed by OR-329H at flowering, NDVI was increased by an additional 4.3% but there were no additional reductions in white mold incidence. The combined treatment of OR-079B + OR-329H (soil) followed by OR-329H + OR-009 EPA at flowering resulted in a 12.2% increase in NDVI compared to nontreated plots but was significantly less than the soil application only. The incidence of white mold on plants was not significantly different from nontreated plots and there was no additional benefit in disease control from the flowering treatment compared to the soil only products. Fungicide treatment had no significant effect on pod number and weight, and average pod weight.

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.

AK. Workshop of diseases found on peony and rhodiola and their control (including biological control) were conducted. Information for government officials, citizen scientists, stakeholders, farmers and home growers were disseminated through various venue (classroom instructions, workshops, seminars and farm bureau conferences, etc.)

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.

ME Trained 5 graduate and 2 undergraduate students. Presented results at the annual meeting of Potato Association of America. Conducted 9 field trials including studying soil microbiomes associated with soil health, disease control by applications of chemicals on soil, seed, and foliage, and varietal test of potatoes for resistance screening. Presented two talks at extension meetings. Served the industry and growers in plant disease diagnosis and detection with hundreds of disease samples.

NY Outreach activities on sustainable disease management.

In 2023, Pethybridge gave 24 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 Northeastern United States.

Undergraduate research experience

Pethybridge had an undergraduate summer scholar in the lab during summer 2024.

TX Two presentations were given at the APS Caribbean division meeting and at the virtual Genetics of Maize Microbe Interactions workshop.

TX Brady For the peanut project, we have employed two Tarleton State University undergraduate students (Claire Toalson and Taylor Duty) who have been trained in microbial isolation, plant cultivation/microbial inoculation, and massively parallel DNA sequencing. The project also supports a Ph.D. level Texas A&M graduate student (Sarah Tasmin).

For the native plant project, we hired a Tarleton State University Ph.D. level graduate student in January 2024 (Aimee Byington), and have trained her in plant cultivation, microbial cultivation, and will soon train her in microbiome studies. Two Tarleton State University undergraduate students were recently hired to assist with the project in December 2024.

For the biochar project, the research has funded one full-time technician in 2024 (Caroly Leija), and three Tarleton State University undergraduate students (Bethany Wood, Maggie Robinson, Ethan Conner-bioinformatics) and one Tarleton State University undergraduate intern (Madalyn Chavez). All personnel on the project received intensive experience and training in massively parallel DNA library construction and DNA detection including quantitative PCR and digital PCR. Additionally, a Texas A&M University Ph.D. level graduate student (Daisy Gonzalez) has begun a project to use dairy manure biochar as a bovine feed additive to suppress methane production in the animal and from the manure stream.

UT  We participated in the field day organized by the Center for Water Efficient Landscaping, USU, on August 13, 2024, and Student Organic Farm, USU, on August 26, 2024, where 85 participants, including farmers, nursery growers, and stakeholders gained knowledge about native plants and plant growth promoting bacteria and their use to develop biofertilizers and biocontrol agents.

UT  We isolated plant growth-promoting bacteria from the rhizosphere of native plants and characterized their roles in enhancing plant growth. Our research demonstrated the effectiveness of these isolates in promoting growth in Arabidopsis, tall fescue, wheat, and watermelon. We have published our findings related to Arabidopsis and tall fescue in peer-reviewed journals, and we are currently preparing manuscripts for our results on wheat and watermelon. To date, we have published three research articles, two review articles, and one editorial. Additionally, we have presented our findings at various conferences, meetings, and field days.

WA - SoilCon. We contributed to the organization of WA SoilCon 2024, which consisted of regional in-person soil health days as well as an online Global Perspectives session.

WA - Soil Health Coffee Hours. In collaboration with the PNW Farmer’s Network, we contributed to monthly online coffee hours focused on soil health in dryland cropping systems in the inland PNW.

WA - Native Youth in STEM. We contributed a nodule module to a Native Youth week-long summer camp on WSU campus in which 30 students collected plants, examined nodules, and isolated bacteria.

WA - NodCamp. We hosted 5 high school students in our lab at WSU in which they isolated and characterized bacteria from agricultural and wild (prairie) ecosystems and learned about microbial ecology and bacteriology.

WA - Phytobacteriology. We led 7 graduate students in a 3 week Bacteriology module in which they isolated and characterized bacteria from wheat rhizosphere for plant growth promotion and pathogen inhibition properties.

Peer Reviewed

Acharya BR, Gill SP, Kaundal A, and Sandhu D (2024). Strategies for combating plant salinity stress: the potential of plant growth-promoting microorganisms. Front. Plant Sci. 15:1406913. https://doi.org/10.3389/fpls.2024.1406913

Adams, A., Landry, D., Sykes, V., Richman, T., Cham, A., Timling, A, Kelly, H., McBeath, J.H., and Olukolu, B.A. 2024. Bt and Conventional Maize Kernel-associated Metagenomes reveal Potential Microbe-Microbe underlying Fusarium Ear Rot Disease. Bioinformatics Journal. http://doi.org/10.1094/PBIOMES-07-23-0074-R.

Amanda Carolina Prado de Moraes,  Kathryn Louise Kingsley,  Lucas da Silva Ribeiro,  Bianca Baccili Zanotto Vigna,  Emerson Rodrigues de Camargo,  James Francis White,  Alessandra Pereira Fávero,  Paulo Teixeira Lacava. 2024. Beneficial Bacteria Associated With Silica Nanoparticles for Growth Promotion of Paspalum notatum. Applied and Environmental Soil Science. https://doi.org/10.1155/aess/9971370

Bellanger, M., Figueroa III, J. L., Tiemann, L., Friesen, M. L., & White III, R. A. (2024). NFixDB (Nitrogen Fixation DataBase)-A Comprehensive Integrated Database for Robust'Omics Analysis of Diazotrophs. Accepted at NAR Genomics and Bioinformatics

Benjlil, H., Ihitassen, A., Idhmida, A., Ait Hamza, M., Braimi, A., Furze, J., Paulitz, T.C., Ferji, Z., Cherifi, K., Mayad, E. 2023. Nematodes associated with saffron II: Bioindication for soil health assessment and impact of agricultural practices. Applied Soil Ecology. 23(08):0929-1393. https://doi.org/10.1016/j.apsoil.2023.105111.

Benjlil, H.,et al. 2024. Nematodes associated with saffron II: Bioindication for soil health assessment and impact of agricultural practices.  Applied Soil Ecology 193: 0.1016/j.apsoil.2023.105111

Burlakoti S, Devkota AR, Poudyal S, Kaundal A. (2024).  Beneficial Plant–Microbe Interactions and Stress Tolerance in Maize. Applied Microbiology. 2024; 4(3):1000-1015. https://doi.org/10.3390/applmicrobiol4030068

Chekali, S., Ayed, S., Khemir, E., Gargouri, S., Marzougui, S., Paulitz, T.C., Gharbi, M. 2024. Response of Tunisian durum wheat vs. bread wheat to Fusarium foot and root rot under semi-arid conditions. European Journal of Plant Pathology. 2024(6). https://doi.org/10.1007/s42161-024-01659-3.

Chekali, S., Ayed, S., Khemir, E., Gharbi, M. S. Marzougui, S., Paulitz, T. and Gargouri, S.  2024. Response of durum wheat vs. bread wheat to Fusarium foot and root rot under semi-arid conditions.  Journal of Plant Pathology. 106: 1207-1220. 10.1007/s42161-024-01659-3

Chen, H., White, J. F., Malik, K., & Li, C. 2024. Molecular assessment of oat head blight fungus, including a new genus and species in a family of Nectriaceae. International Journal of Food Microbiology, 417, 110715. https://doi.org/10.1016/j.ijfoodmicro.2024.110715

Choi, G., Brady, J.A., Obayomi, O., Green, E., Leija, C., Sefcik, K., Gonzalez, D.A., Taggart, C.B., Muir, J.P., Kan, E. 2024. Wood- and manure-derived biochars reduce antibiotic residues and shift antibiotic resistance genes and microbial communities in manure applied forage-soil systems. Agronomy 14(9), 2100. https://doi.org/10.3390/agronomy14092100.

Deng, L., Huang, X., Dao, J., Xu, Y., Zhou, K., Wang, W., Liu, C., Chen, M., Zhang, S., Zhang, Y., Hao, J., Liu, X., and Yang, Y. 2024. Pectinesterase activity and gene expression correlate with pathogenesis of Phytophthora infestans. Frontiers in Plant Science 15: 1481165. DOI: 10.3389/fpls.2024.1481165.

Devkota AR, Wilson T and Kaundal A (2024). Soil and root microbiome analysis conditions and isolation of plant growth-promoting bacteria from hybrid buffaloberry  (Shepherdia utahensis ’Torrey’) across three locations. Front. Microbiol. 15:1396064. doi.org/10.3389/fmicb.2024.1396064

Devkota, A. R., Kaur, S., & Kaundal, A. (2024). Rhizobacterial Isolates from the Native Plant Ceanothus velutinus Promote Growth in Two Genotypes of Tall Fescue. Microbiology Research, 15(4), 2607-2618. https://doi.org/10.3390/microbiolres15040173

Entio, L.J., Taggart, C.B., Muir, J.P., Kan, E., Brady, J.A., and Obayomi, O. 2024. Biochar and dairy manure amendment effects on Cynodon dactylon performance and soil properties. Plants 13(2), 242. https://doi.org/10.3390/plants13020242.

Feng, Y., Hao, J., Zhang, D., Huo, H., Li, L., Xiu, Z., Yang, C., and Zhang, X. 2024. Transcriptomic analysis of sodium silicate-induced resistance against Rhizoctonia solani AG-3 in potato. Agronomy 14:1207. DOI: 10.3390/agronomy14061207.

Figueroa III, J. L., Redinbo, A., Panyala, A., Colby, S., Friesen, M. L., Tiemann, L., & White III, R. A. (2024). MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics database. Bioinformatics Advances, vbae061.

Ganesh, J., Hewitt, K., Devkota, A. R., Wilson, T., and Kaundal, A. (2024). IAA-producing plant growth promoting rhizobacteria from Ceanothus velutinus enhance cutting propagation efficiency and Arabidopsis biomass. Frontiers in Plant Science, 15. :1374877. https://doi.org/10.3389/fpls.2024.1374877

Huang P-C, Yuan P, Grunseich JM, Taylor J, Tiénébo EO, Pierson EA, Bernal JS, Kenerley CM, Kolomiets MV (2024). Trichoderma virens and Pseudomonas chlororaphis Differentially Regulate Maize Resistance to Anthracnose Leaf Blight and Insect Herbivores When Grown in Sterile versus Non-Sterile Soils. Plants 2024, 13, 1240. https://doi.org/10.3390/plants1309124

Huynh, B., Dahlquist‐Willard, R. M., Ploeg, A. T., Yang, M., Thaoxaochay, L., Kanter, J., Brar, S., Paz, J., Qaderi, S., Singh, H., Duong, T., Dinh, H., Kang, H. P., Matthews, W. C., De Souza, A., Bhatia, A., Ke, H., Ehlers, J. D., & Roberts, P. A. (2024). Registration of four pest‐resistant long bean germplasm lines. Journal of Plant Registrations, 18(2), 415–425. Portico. https://doi.org/10.1002/plr2.20361

Jernigan, A. B., Kao-Kniffin, J., Pethybridge, S. J., and Wickings, K. 2024. Spatial and temporal dynamics of Collembola (Isotomiella minor) and plant pathogenic fungi (Rhizoctonia solani) interactions. Appl. Soil Ecol. 201:105504. https://doi.org/10.1016/j.apsoil.2024.105504.

Jernigan, A., Kao-Kniffen, J., Pethybridge, S. J., and Wickings, K. 2024. Microarthropods improve oat nutritional quality and mediate the effects of fertilizers on soil biological activity. Agronomy J. 117:2007-2033. https://doi.org/10.1002/agj2.21597.

Jia, R., Yang, J., Hao, J., Wang, S., Wu, J., Lin, K., Chen, Z., and Zhang, Y. Y. 2024. First report of root rot caused by Fusarium equiseti on Syrian rue (Peganum harmala) in China. Plant Disease. DOI: 10.1094/PDIS-06-24-1297-PDN.

Jin, Y., Chen, Z., White, J. F., Malik, K., & Li, C. 2024. Interactions between Epichloë endophyte and the plant microbiome impact nitrogen responses in host Achnatherum inebrians plants. Microbiology Spectrum, 12(4), e0257423. https://doi.org/10.1128/spectrum.02574-23

Joglekar, P., Ferrell, B. D., Jarvis, T., Haramoto, K., Place, N., Dums, J. T., S. W. Polson, K. E. Wommack, and Fuhrmann, J. J.  (2023) Spontaneously produced lysogenic phages are an important component of the soybean Bradyrhizobium mobilome. mBio, 14(2).  https://doi.org/10.1128/mbio.00295-23

Jones-Held, S., & White, J. F. 2024. Effects of endophytes on early growth and ascorbate metabolism in Brassica napus. Frontiers in Plant Science, 15, 1480387. https://doi.org/10.3389/fpls.2024.1480387

Kaniz F, Zheng W, Bais HP, Jin Y (2023) Plant Growth-Promoting Rhizobacteria Mediate Soil Hydro-Physical Properties: An Investigation with Bacillus Subtilis and its Mutants. Vadose Zone J. 22 (5), e20274.

Kaundal, A.  Anoop Kumar Srivastava, and Dinesh Yadav (2024) The role of the microbiome in plant and soil health in changing climate Front. Plant Sci. Volume 15 – 2024 https://doi.org/10.3389/fpls.2024.1491438

Kaur C, Pomerleau M, Beauregard PB, Fidenza M, Ervin E, Bais HP (2023) Antifungal activity of plant growth promoting rhizobacteria Bacillus subtilis strain UD1022 against the dollar spot pathogen (Clarireedia spp.). Biological Control 105284.

Kehlet-Delgado, H., Montoya, A.P., Jensen, K.T., Wendlandt, C.E., Dexheimer, C., Roberts, M., Torres Martínez, L., Friesen, M.L., Griffitts, J.S. and Porter, S.S. (2024). The evolutionary genomics of adaptation to stress in wild rhizobium bacteria. Proceedings of the National Academy of Sciences, 121(13), e2311127121.

Khmelnitsky, O., Buck, E., and Pethybridge, S. J. 2024. First report of anthracnose on banana peppers caused by Colletotrichum scovillei in New York. Plant Dis. 108:2577.https://doi.org/10.1094/PDIS-04-24-0735-PDN.

Klasek, S., Crants, J., Abbas, T. Ashley, K., Bolton, M. Celovsky, M., Gudmestead, N. Hao, J., Ibarra Caballero, J., Jahn, C., Kamgan Nkuekam, G., Lankau, R., Larkin, R., Lopez, E., Miller, J., Moore, A., Pasche, J., Ruark, M., Schroeder, B., Shan, S., Skillman, V., Srour, A., Stasko, A., Steinke, K., and Steward, J. 2024. Potato soil core microbiomes are regionally variable across the continental US. Phytomiomes Journal 8:168-178. DOI: 10.1094/PBIOMES-07-23-0060-R.

Komondy, L., Hoepting, C. A., Fuchs, M., Pethybridge, S. J., and Nault, B. A. 2024. Identifying onion fields at risk for Iris yellow spot virus infection in New York. Plant Dis. 108:1750-1754. https://doi.org/10.1094/PDIS-10-23-2097-RE

Komondy, L., Hoepting, C., Fuchs, M., Pethybridge, S. J., and Nault, B. 2024. Spatiotemporal patterns of Iris yellow spot virus and its onion thrips vector in transplanted and seeded onion fields in New York. Plant Dis. 108:398-406. https://doi.org/10.1094/PDIS-05-23-0930-RE.

Komondy, L., Hoepting, L., Pethybridge, S. J., Fuchs, M., and Nault, B. A. 2024. Development of a sequential sampling plan for classifying Thrips tabaci (Thysanoptera: Thripidae) populations levels in onion fields. J. Econ. Entomol. 117:2151-2158. https://doi.org/10.1093/jee/toae161.

Laasli, S., E., Mokrini, F., Iraqi, D., Shataya, MJY, Amiri, S., Dababaat, A. A., Paulitz, T., Khfif, J. and Lahlali, R.  2024. Phytopathogenic nematode communities infesting Moroccan olive agroecosystems: impact of agroecological patterns.  Plant and Soil 501: 39-55. 10.1007/s11104-023-06190-5

Laasli, S., Mokrini, F., Dabaat, A.A., Paulitz, T.C., Lahali, R. 2023. Phytopathogenic nematode communities infesting Moroccan olive agroecosystems: impact of agroecological patterns. Plant and Soil. https://doi.org/10.1007/s11104 023-06190-5.

Loffredo, A., Edwards, S., Ploeg, A., and Becker, J.O. 2024. Performance of biological and chemical nematicides in different soils to control Meloidogyne incognita in tomato plants. Journal of Phytopathology 172, e13250. Doi:10.1111/jph.13250 

Ma, X., Zhang, X., Stodghill, P., Rioux, R., Shrestha, S., Babler, B., Rivedal, H.M., Frost, K., Hao, J., Secor, G., and Swingle, B. 2024. Analysis of soft rot Pectobacteriaceae population diversity in US potato growing regions between 2015 and 2022. Frontiers in Microbiology 15:1403121. DOI: 10.3389/fmicb.2024.140312.1.

Martins SJ, Pasche J, Silva H, Gijs Selten, Noah Savastano, Lucas Magalhães Abreu, Bais HP, Karen A. Garrett, Nattapol Kraisitudomsook, Corné M.J. Pieterse, Tomislav Cernava (2023) The Use of Synthetic Microbial Communities (SynComs) to improve plant health. Phytopathology 113 (8), 1369-1379.

Menalled, U., Bybee-Finley, K. A., Smith, R. G., DiTommaso, A., Darby, H. M., Pethybridge, S. J., and Ryan, M. R. 2024. Legacy effects of annual and perennial crop diversity on weed-crop competition in maize. Npj Sustain. Agric. 2:24.https://doi.org/10.1038/s44264-024-00036-y.

Nishisaka CS, Ventura JP, Prapajati V, Bais HP, Mendes R (2024) Role of Bacillus subtilis exo-polymeric molecules in modulating rhizosphere microbiome assembly. Environmental Microbiome 19 (1), 33.

Obidari, T., Wardi, M., Alaoui, I. F., Braimi, A., Paulitz, T., El Mousadik, A., and Mayad, E. 2024. Microbial communities and high trophic level nematodes in protected argan soil show strong suppressive effect against Meloidogyne spp. Global Ecology and Conservation 54: 10.1016/j.gecco.2024.e03191.

Parks, J. M., & Friesen, M. L. (2024). The role of plant-microbe interactions in legume non-legume intercropping success. Plant and Soil, 1-11.

Pethybridge, S. J., Damann, K., Murphy, S. P., Diggins, K., and Gleason, M. 2024. Optimizing mesotunnels for organic acorn squash in New York. Plant Health Progress. 25:146-155. https://doi.org/10.1094/PHP-08-23-0072-RS.

Pethybridge, S. J., Murphy, S. P., Branch, E. B., Sharma, P. S., and Kikkert. J. R. 2024. Manipulating table beet growth using exogenous gibberellic acid 3 in New York, USA. Ann. Appl. Biol. 184:196-209. https://doi.org/10.1111/aab.12870.

Pethybridge, S. J., Murphy, S., Lund, M., and Kikkert. J. R. 2024. Survival of Sclerotinia sclerotiorum sclerotia in central New York. Plant Dis. 108:1165-1168.https://doi.org/10.1094/PDIS-10-23-2126-SC.

Pethybridge, S. J., Rea, M., Gadoury, D. M., Murphy, S. P., Hay, F. S., Skinner, N. P., and Kikkert, J. R. 2023. Nighttime applications of germicidal ultraviolet light (UV-C) to suppress Cercospora leaf spot in table beet. Plant Dis. 108:2518-2529.https://doi.org/10.1094/PDIS-12-23-2715-RE.

Petipas, R. H., Antoch, A. A., Eaker, A. N., Kehlet-Delgado, H., & Friesen, M. (2024) Back to the future: Using herbarium specimens to isolate nodule associated bacteria Ecology and Evolution, 14(7), e11719.

Petipas, R. H., Peru, C., Parks, J. M., Friesen, M. L., & Jack, C. N. (2024). Prairie soil improves wheat establishment and accelerates the developmental transition to flowering compared to agricultural soils. Canadian Journal of Microbiology.

Petipas, RH, Delgado, H, Antoch, A, Friesen, ML. Genome sequences of Microvirga spp. CF3062 and CF3016 isolated from nodules found on herbarium specimens collected in 2004 and 2015 DOI: 10.1128/mra.00161-24 (accepted at MRA)

Ploeg, A. T., & Edwards, S. (2024). Host status of melon, carrot, and Meloidogyne incognita-susceptible and -resistant cotton, cowpea, pepper, and tomato for M. floridensis from California. Journal of Nematology, 56(1). https://doi.org/10.2478/jofnem-2024-0004

Ploeg, A. T., & Stoddard, C. S. (2024). A Comparison Between Meloidogyne floridensis and M. incognita from California on Susceptible and Resistant Sweetpotato Cultivars. Plant Disease, 108(6), 1577–1581. https://doi.org/10.1094/pdis-09-23-1886-re

Ploeg, A. T., Edwards, S., Loffredo, A., & Becker, J. O. (2024). Efficacy of Fluorinated Nematicides for Management of Root-knot Nematodes in California Processing Tomatoes. Journal of Nematology, 56(1). https://doi.org/10.2478/jofnem-2024-0034

Ploeg, A. T., Witte, H., Subbotin, S. A., Tandingan De Ley, I., Smith Becker, J., & Becker, J. O. (2024). Meloidogyne marylandi is Involved in, but not the Primary Cause of Creeping Bentgrass Decline of Putting Greens in Southern California. Journal of Nematology, 56(1). https://doi.org/10.2478/jofnem-2024-0046

Ren, H., Hao, X., Zhang, R., Hao, J., Ding, Y., Liu, J., Pan, H. Wang, Y. and Zhou, R. 2024. Enhanced phytoremediation of PCBs-contaminated soil by co-expressing tfdBand bphCin Arabidopsis aiding in metabolism and improving toxicity tolerance. Environmental and Experimental Botany 217: 105548. https://doi.org/10.1016/j.envexpbot.2023.105548.

Richards, V.A.; Ferrell, B.D.; Polson, S.W.; Wommack, K.E.; Fuhrmann, J.J. (2024) Soybean Bradyrhizobium spp. spontaneously produce abundant and diverse temperate phages in culture. Viruses 2024, 16, 1750. https://doi.org/10.3390/v16111750

Rosier A., Pomerleau, M., Beauregard P. B, Samac, D. A., Bias, H. P. (2023) Surfactin and Sp0A-Dependent Antagonism by Bacillus subtilis Strain UD1022 against Medicago sativa Phytopathogens. Plant 12 (5), 1007

Sassenrath, G., Waite, N., Hsiao, C.-J., and Little, C.R. 2025. Brassica juncea cover crops reduce soybean root colonization by Macrophomina phaseolina, the fungus causing charcoal rot. Plant Health Progress, Vol. 25 (https://doi.org/10.1094/PHP-05-24-0048-RS).

Savastano, N., Bais, H. P. (2024) Synergism or Antagonism: Do Arbuscular Mycorrhizal Fungi and Plant Growt-Promoting Rhizobacteria Work Together to Benefit Plants? International Journal of Plant Biology 15 (4), 944-958

Schillinger, W., Hansen, J.C., Paulitz, T.C. 2023. Canola rotation effects on soil and subsequent wheat in the Pacific Northwest USA. Agronomy Journal. 2023:115(1):314-324. https://doi.org/10.1002/agj2.21248.

Sharma, P., Murphy, S. M., Kikkert, J. R. and Pethybridge, S. J. 2024. Susceptibility of table beet cultivars to foliar diseases in New York. Plant Health Progr. 25: 399-409. https://doi.org/10.1094/PHP-01-24-0005-RS.

Smith Becker, Jennifer, Ruegger, Paul M., Borneman, James, Becker, J. Ole. 2024. Indigenous populations of a biological control agent in agricultural field soils predicted suppression of a plant pathogen. Phytopathology 114:334-339. https://doi.org/10.1094/PHYTO-07-23-0221-R

Wang, L., Liu, H., Wu, J., Lin, K., Hao, J., Jia, R., and Zhang, Y. 2024. First Report of Alternaria alternata causing leaf spot on smooth bromegrass (Bromus inermis) in China. Plant Disease 108: 2225. DOI: 10.1094/PDIS-04-24-0833-PDN.

Wang, T., Shi, X., Wu, Z., Zhang, J. Hao, J., Liu, P., and Liu, X. 2024. Carboxylesterase and cytochrome P450 confer metabolic resistance simultaneously to azoxystrobin and some other fungicides in Botrytis cinerea. Journal of Fungi 10: 261. DOI: 10.3390/jof10040261.

Webster, C, Kim, J, Reguera, G, Friesen, ML, Beyenal, H. Can bioelectrochemical sensors be used to monitor soil microbiome activity and fertility? (accepted at Current Opinion Biotechnology)

Weller, D.M., Berendsen, R.L., Thomashow, L.S., Van Bentum, S., Spooren, J., Pieterse, C.M. 2024. Plant-driven assembly of disease-suppressive soil microbiomes. Annual Review of Phytopathology. 2024.62:11.1-11.30. https://doi.org/10.1146/annurev phyto-021622-100127

Weller, D.M., Van Pelt, J.A., Thomashow, L.S., Mavrodi, D.V., Mavrodi, O., Pieterse, C.M., Bakker, P.A. 2024. Disease-suppressive soils induce systemic resistance in Arabidopsis thaliana against Pseudomonas syringae pv. tomato. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-02-24-0012-R.

Wen, N., Chen, C; Garland- Campbell, K. G., and Lu, C.  2024. First detection of Aster Yellows Associated with Phytoplasma on Camelina sativa in Montana.  Plant Disease: in press.

Wu, H., Huang, Z., Cheng, S., Zhao, J., Hao, J., and Han, L. 2024. Streptomyces changanensis sp. nov. isolated from soil in China. Current Microbiology 81(2): 1-8. https://doi.org/10.1007/s00284-023-03527-2.

Wu, H., Sun, Y., Ma, L., Cheng, S., Lu, D., Hao, J., and Han, L. 2024. Microbial exopolysaccharide EPS66A in inducing walnut (Juglans regia) resistance to bacterial blight. Food Chemistry 435: 137551. https:/doi.org/10.1016/j.foodchem.2023.137551.

Wu, Z., Bi, Y., Zhang, J., Gao, T., Li, X., Hao, J., Liu, P., and Liu, X. 2024. Multidrug resistance of Botrytis cinerea associated with its adaptation to plant secondary metabolites. mBIO 47: 126476. DOI: https://doi.org/10.1128/mbio.02237-23.

Wu, Z., Liu, Z., Hu, Z., Wang, T., Teng, L., Dai, T., Liu, P., Hao, J., and Liu, X., 2024. Utilizing metabolomic approach to study mode of action of fungicides and corresponding resistance in plant pathogens. Advanced Agrichem 3(3): 197-205. DOI: 10.1016/j.aac.2024.05.001.

Wu, Z., Yu, C., Bi, Q., Zhang, J., Hao, J., Liu, P., and Liu, X. 2024. Procymidone application contributes to multidrug resistance of Botrytis cinerea. Journal of Fungi 10(4): 261. DOI: 10.3390.jof10040261.

Yang, J., Jia, S., Li, T., Zhang, J., Zhang, Y., Hao, J., and Zhao, J. Delayed sowing reduced Verticillium wilt by enhancing beneficial rhizosphere bacteria of sunflower. 2024 Microorganisms 12 (12): 2416. DOI: 10.3390/microorganisms12122416.

Yang, M., Schlatter, D. C., LeTourneau, M. K., Wen, S., Mavrodi, D., Mavrodi, O., Thomashow, L, Kandlati, E., Rajagopalan, K., Weller, D. M., and Paulitz, T. C.  2024. Eight years in the soil: temporal dynamics of wheat-associated bacterial 3 communities under dryland and irrigated conditions.  Phytobiomes: in press

Yin, C., Larson, M., Lahr, N.D., Paulitz, T.C. 2023. Wheat rhizosphere-derived bacteria protect soybean from soilborne diseases. Plant Disease. https://doi.org/10.1094/PDIS 08-23-1713-RE.

Yin, C., T., Larson, M., Lahr, N. and Paulitz, T.  2024. Wheat Rhizosphere-Derived Bacteria Protect Soybean from Soilborne Diseases.  Plant Disease 108: 1565-1576. 10.1094/PDIS-08-23-1713-RE

Young, B., White, J. and Struwe, L. 2024. Endophytic bacteria discovered in oil body organelle of liverworts (Marchantiophyta). American Journal of Botany (In press).

Book Chapters

Meeting presentations, abstracts and proceedings

Borneman, J. Illumina Sequence Processing & Analysis. Annual Meeting of Western Regional Project W5147 on Biological Control. W5147, December 6, 2024, Zoom Meeting.

Byington, A., Speshock, J., Murray, D., and Brady, J. Utilizing microbial endophytes to inhibit germination of King Ranch bluestem (Bothriochloa ischaemum var. songarica): A novel tactic for rangeland restoration.Texas Section Society for Range Management Annual Meeting in Victoria, Texas, October 17, 2024. 

Devkota, A.  and Amita Kaundal* (2024). Comparative microbial diversity analysis and isolation of plant-promoting bacteria from roundleaf Buffaloberry (Shepherdia rotudifolia). American Society for Horticultural Science (ASHS) Annual Conference September 23-27, 2024, Honolulu, Hawaii.

Devkota, A.  and Amita Kaundal (2024). Comparative microbial diversity analysis of root and soil of Shepherdia rotundifolia from three locations in Utah. Student Research Symposium, Utah State University, April 12, 2024

Devkota, A. R. and Kaundal, A. (2024). Plant growth-promoting rhizobacteria (PGPR) from the native plant Ceanothus velutinus promote growth in Tall Fescue. Food Security and Solutions Symposium, Utah State University, April 17, 2024.

Diggins, K., Damann, K., Murphy, S. P., and Pethybridge, S. J. 2024. Enhancing organic acorn squash resilience with mesotunnel production systems. squash bug (Anasa tristis). Proc. APS Annual Meeting, Memphis, TN. P-310.

Entio, L.J., Taggart, C.B., Muir, J.P., Kan, E., Brady, J.A., Obayomi, O. Dairy effluent-saturated biochar short-term effects on Vigna unguiculata and Cynodon dactylon performance and soil properties. 77^th Southern Pastures and Forage Crop Improvement Conference, Mobile, Alabama January 2024.

Friesen, ML. 2024. WSU Crop and Soil Sciences department seminar  “Can we replace synthetic nitrogen with microbes?”, Aug 2024

Jakir Hasan, Caley Gasch, Mingchu Zhang, Jenifer McBeath, Milan Shipka, Jodie Anderson, James V. Anderson, Jinita Sthapit Kandel and David Archer. 2023. Small grain crops breeding for the sub-arctic climate in interior Alaska. 2023 Tri-Society (ASA-CSSA-SSSA) Meeting in St. Louise, MO.

Kaur, C., Bias, H. P., and Ervin, E. (2024) Evaluation of Seasonal Plant Health Products Program on Creeping Bentgrass Putting Greens (Abstract). ASA, CSSA, SSSA International Annual Meeting, San Antonio, TX. November 10^th – November 13^th, 2024

Kaur, C., Ervin, E. & Bais, H. P. (2024) Evaluation of Seasonal Plant Health Products Program on Creeping Bentgrass Putting Greens. Plant Genomics & Gene Editing Congress and Partnerships in Biocontrol, Biostimulants & Microbiome Congress, North Carolina. October 21^st – October 22^nd, 2024

Kaur, C., Ervin, E., and Bais, H. P. (2023) Plant Growth Promotion and Dollar Spot Disease Suppression by PGPR Bacillus subtilis strain UD1022 in Creeping Bentgrass. (Abstract). ASA, CSSA, SSSA International Annual Meeting, St. Louis, MO. October 29^th – November 1^st, 2023

McBeath, J.H. and Emerson, N.W. 2024. Impact of Glyphosate on cold adapted Trichoderma atroviride. American Phytopathology Society-Pacific Division annual meeting and the 69^th Annual Conference on soil-borne plant pathogens, March 26-29, 2024.Oregan State University, Corvallis, OR.

Morgese E.A., Kristal J., Li, H., Richards, V.A., Ferrell, B.D., K., Wommack, K.E., Polson, S.W., Fuhrmann, J.J. (2023) Bradyrhizobium lytic phage: Building genome to phenome connections. [Poster Presentation]. University of Delaware Microbiology Research Symposium. Newark, DE.

Morgese, E.A., Ferrell, B.D., Toth, S.C., Haramato, K., Wommack, K.E., Polson, S.W., Fuhrmann, J.J. (2024) Comparative analysis reveals host-dependent diversity in 16 novel Bradyrhizobium bacteriophages. [Poster Presentation]. University of Delaware College of Agriculture and Natural Resources Research Symposium. Newark, DE.

Morgese, E.A., Ferrell, B.D., Toth, S.C., Kristol, J., Haramato, K., Wommack, K.E., Polson, S.W., Fuhrmann, J.J. (2024) Genomic and phenotypic characteristics of 13 novel Bradyrhizobium phages. [Poster Presentation]. DENIN Environmental Research Symposium. Newark, Delaware.

Morgese, E.A., Ferrell, B.D., Toth, S.C., Kristol, J., Haramato, K., Wommack, K.E., Polson, S.W., Fuhrmann, J.J. (2023) Genomic and phenotypic characteristics of 13 novel Bradyrhizobium phages. [Poster Presentation; 1^st place award]. University of Delaware College of Agriculture and Natural Resources Research Symposium. Newark, DE.

Muir, J.P., Taggart, C.B., Hays, K.N., Brady, J.A., Kan, E., Entio, L.J., and Cooper, C.P. Short-term biochar effects in cultivated forages: ecosystems services, soil characteristics, herbage yields, and nutritive value. European Grasslands Federation 30^th General Meeting, Leeuwarden, Netherlands, June 9-13, 2024.

Paulitz, T. 2024. The Soil and Root Microbiome of Eastern Washington Crops:  Unraveling the Complexity and Meaning. Department of Crops and Soil Sciences, Washington State University, Sept. 30, 2024.

Paulitz, T. 2024. The Soil and Root Microbiome of Eastern Washington Crops:  Unraveling the Complexity and Meaning. Department of Microbiology and Plant Pathology, University of California, Riverside. October 30, 2024.

Paulitz, T. C. 2023. Canola in Rotation Influences Microbial Communities of Wheat Roots.  Invited talk at workshop at ASA/CCSA/SSSA meeting, St. Louis, MO. Oct. 30-Nov. 1, 2023.

Paulitz, T., Prihatna, C., Yan, Q., Andeer, P., Barnes, E., Northen, T., Tringe, S., Willmore, C., Peng, H., Yin, C., Craine, C., Eberly, J. and Lu, C. 2024. The Root Microbiome of Camelina: From Structure to Function. Department of Energy 2024 BSSD Biological Systems Science Division  Genomic Science Program (GSP) and Enabling Capabilities Resources (ECR) meeting, Bethesda, MD. April, 2024.

Pethybridge, S. J. 2024. Building resilient foliar disease management strategies for the organic table beet industry. USDA NIFA Organic Programs Project Directors Meeting Abstracts. Pp. 10.

Pethybridge, S. J., Khmelnitsky, O., and Buck, E. 2024. Recent outbreaks of Green Fruit Anthracnose: A threat to pepper production in the United States. Proc. International Pepper Conference, Ithaca, New York. Pp. 25.

Pineros-Guerrero, N., Hay, F. S., Heck, D. W., Klein, A., Hoepting, C., and Pethybridge, S. J. 2024. Determining the contribution of onion volunteers to the population genetics of Stemphylium vesicarium in New York, USA, using microsatellite markers. Proc. APS-North East Division Meeting, Ithaca, NY. Pp. 10. 6 March 2024.

Pineros-Guerrero, N., Hay, F. S., Heck, D. W., Klein, A., Hoepting, C., and Pethybridge, S. J. 2024. Determining the contribution of onion transplants and volunteers to the population genetics of Stemphylium vesicarium in New York. Proc. APS Annual Meeting, Memphis, TN. Phytopathology. Technical Session.

Rodgers, P., Pineros-Guerrero, N., Pethybridge, S. J., and Hay, F. S. 2024. Use of microsatellites to understand the role of onion transplants in Stemphylium leaf blight epidemics in New York. Proc. 2024 Cornell AgriTech Summer Scholars Program, Cornell University, Geneva, New York, Abstract.

Rodriguez-Herrera, K. D., Day, C. T. C., Nault, B. A., Swingle, B. M., Pethybridge, S. J., and Smart, C. D. 2024. Squash bug preference for cucurbit species and its influence on vectoring Serratia marcescens causing cucurbit yellow vine disease in New York. Proc. APS-North East Division Meeting, Ithaca, NY. Pp. 10. 6 March 2024.

Rodriguez-Herrera, K. D., Day, C. T. C., Nault, B. A., Swingle, B. M., Pethybridge, S. J., and Smart, C. D. 2024. Determining cucurbit yellow vine disease incidence influenced by the population dynamics and cucurbit species preference of its vector, the squash bug (Anasa tristis). Proc. APS Annual Meeting, Memphis, TN. Phytopathology. Technical Session.

Saif, M. S., Chancia, R., Murphy, S. P., Pethybridge, S. J., and van Aardt, J. 2024. Assessing multiseason table beet root yield from unmanned aerial systems. AGU 2024. What’s Next for Science. B007 – Advances in Remote Sensing from Small Unmanned Aerial Systems in Support of Sustainable Agricultural Research Across Working Landscapes.

Saif, M. S., Chancia, R., Murphy, S. P., Pethybridge, S. J., and van Aardt, S. J. 2024. Assessing multi-season table beet root yield from unmanned aerial systems. University of Rochester, Institute of Optics Industrial Associates Program Fall 2024 IA Meeting. 24 October 2024. 

Saif, M., Chancia, R., Pethybridge, S. J., and van Aardt, J. 2024. UAS-enabled monitoring of Cercospora leaf spot disease of table beets. 2024 Graduate Showcase at Rochester Institute of Technology, Rochester, NY. 11 April 2024.

Saif, M., Chancia, R., Sharma, P., Murphy, S., Pethybridge, S. J., and van Aardt, J. 2024. Agricultural disease management: Estimation of Cercospora leaf spot severity in table beet using UAS.  STRATUS Conference.

Sharma, P., Branch, E., Murphy, S., Kikkert, J. R., and Pethybridge, S. J. 2024. Residue management as an alternative to manage Cercospora leaf spot of table beet and its effect on the soil microbiome. Proc. APS-North East Division Meeting, Ithaca, NY. Pp. 11. 6 March 2024.

Sharma, P., Murphy, S., Kikkert, J. R., and Pethybridge, S. J. 2024. Role of infested seed as a primary inoculum source in Cercospora leaf spot epidemics in table beet. Proc. APS Annual Meeting, Memphis, TN. Phytopathology. Technical Session.

Simangunsong, R. M., Koenick, L., Murphy, S., and Pethybridge S. J. 2024. Morphology and multi-gene phylogeny of Phoma betae (syn. Neocamarosporium betae) populations in New York and Washington States, USA. Proc. APS-North East Division Meeting, Ithaca, NY. Pp. 11. 6 March 2024.

Simangunsong, R. M., Murphy, S., du Toit, L., and Pethybridge, S. J. 2024. Morphology and multi-gene phylogeny of Phoma betae (syn. Neocamarosporium betae) populations in New York and Washington States, USA. Proc. APS Annual Meeting, Memphis, TN. Phytopathology. P-495.

Toth, S.C. (2023) What insights do phage proteins provide into viral infection dynamics? [Oral Presentation]. DENIN Pitch90 Event. Newark, Delaware.

Toth, S.C., Morgese, E.A., Ferrell, B.D., Fuhrmann, J.J., Wommack, K.E., Polson, S.W. (2024) Exploring viral diversity across ecosystems: Insights from soil Bradyrhizobium phage genomics. [Poster Presentation; 1^st place award]. UD College of Agriculture and Natural Resources (CANR) Symposium. Newark, Delaware.

Toth, S.C., Morgese, E.A., Ferrell, B.D., Richards, V.A., Locke, H., Wommack, K.E., Polson, S.W., Fuhrmann, J.J. (2024) Genomic similarities reflect infectivity patterns in Bradyrhizobium lytic phages. [Poster Presentation]. UD Biology Research Day Symposium. Newark, Delaware.

Toth, S.C., Morgese, E.A., Ferrell, B.D., Richards, V.A., Locke, H., Wommack, K.E., Polson, S.W., Fuhrmann, J.J. (2023) Genomic similarities reflect infectivity patterns in Bradyrhizobium lytic phages. [Poster Presentation]. UD College of Agriculture and Natural Resources (CANR) Symposium. Newark, Delaware.

Toth, S.C., Morgese, E.A., Ferrell, B.D., Richards, V.A., Locke, H., Wommack, K.E., Polson, S.W., Fuhrmann, J.J. (2023) Genomic similarities reflect infectivity patterns in Bradyrhizobium lytic phages. [Poster Presentation]. Delaware Data Science Symposium. Newark, Delaware.

Toth, S.C., Morgese, E.A., Ferrell, B.D., Richards, V.A., Locke, H., Wommack, K.E., Polson, S.W., Fuhrmann, J.J. (2023) Genomic similarities reflect infectivity patterns in Bradyrhizobium lytic phages. [Poster Presentation]. UD Undergraduate Research Summer Symposium. Newark, Delaware.

Upadhay, S. G. C., Gleason, C., Chavoshi, S., Zasada, I., Wheeler, D. L. and Paulitz, T. C. 2024. Using Artificial Intelligence (AI) to identify plant-parasitic nematodes genera found in potato production fields.  Plant Health 2024, Memphis, TN July 27-30, 2024.

Upadhaya, S., G., G., Wheeler, D., Griffin LaHue, D., Potter, T., Gleason, C., Frost, K, Mayad, E. and Paulitz, T. 2024. The Phytobiome of Potato in Washington State: The Legacy of Cropping Systems, Soil and the Environment. International Phytobiomes Conference 2024, Nov. 19-21, 2024, St. Louis, MO.

Wiest, T.A.M., and Bais, H. (2023). Association of a marine bacteria Shewanella sp. IRI-160 with terrestrial plants to abate salt stress. [Poster Presentation] DENIN Environmental Research Symposium. Newark, Delaware.

Wiest, T.A.M., and Bais, H. (2023). Effects of marine bacteria Shewanella sp. IRI-160 on tomato seeds experiencing salt stress. [Poster Presentation] University of Delaware Microbiology Symposium. Newark, Delaware.

Wiest, T.A.M., and Bais, H. (2024). Under simulated microgravity, Salmonella enterica infection and cultivar selection may alter stomatal aperture and density in Lettuce. [Poster Presentation]. DENIN Environmental Research Symposium. Newark, Delaware.

Wiest, T.A.M., and Bais, H. (2024). Under simulated microgravity, Salmonella enterica infection and cultivar selection may alter stomatal aperture and density in Lettuce. [Poster Presentation]. InnovatHER Research Showcase. Newark, Delaware.

Wiest, T.A.M., and Bais, H. (2024). Under simulated microgravity, Salmonella enterica infection and cultivar selection may alter stomatal aperture and density in Lettuce. [Oral Presentation]. Plant Health 2024, Memphis, Tennessee.

Wiest, T.A.M., and Bais, H. (2024). Under simulated microgravity, Salmonella enterica infection and cultivar selection may alter stomatal aperture and density in Lettuce. [Oral Presentation]. The Carroll Symposium, Newark, Delaware.

Wiest, T.A.M., and Bais, H. (2024). Under simulated microgravity, Salmonella enterica infection and cultivar selection may alter stomatal aperture and density in Lettuce. [Poster Presentation]. CANR Research Symposium, Newark, Delaware.

Wilson, T.  and Amita Kaundal (2024). “Isolation of Plant-promoting bacteria from the rhizosphere of hybrid buffaloberry Shepherdia x utahensis” Food Security and Solutions Symposium, Utah State University, April 17, 2024

Wilson, T. , and Amita Kaundal (2024). “Finding and Characterizing Plant Growth-promoting Microbes from Native Desert Plants” Utah Conference on Undergraduate Research (UCUR), Utah Velley University, Orem, Utah, Feb 16, 2024.

Wilson, T. Jyosthna Ganesh, Ananta Devkota, Katie Hewitt, and Amita Kaundal (2024).  “Isolation of Native Plant’s Microbiome for Plant Growth-Promoting Bacteria” Undergraduate Research Fair, Utah State University, September 6, 2024.

Wilson, T., and Amita Kaundal (2024). “Isolation of Plant-promoting bacteria from the rhizosphere of hybrid buffaloberry Shepherdia x utahensis” National Conference on Undergraduate Research (NCUR), April 8-12, 2024, Long Beach, California

Zhang, X., Ge, T. Fan, X., Chim, B.K., Johnson, S.B., Porter, G., Larkin, R.P., and Hao, J. Taxonomic switches and interactions of bacterial species causing blackleg and soft rot of potato in the Northeastern United States. Annual Meeting of Potato Association of America, Portland, Oregon. Jul. 21-24, 2024.

Technical Bulletins and Extension Publications

Becker, J. O., Ploeg, A. T., & Westerdahl, B. B. (2024). Carrot: Nematodes. UC IPM Pest Management Guideline: Carrot, UC ANR Publication 3438. https://ipm.ucanr.edu/agriculture/carrot/nematodes/#gsc.tab=0

Becker, J.O. and J. Smith Becker 2024. Plant disease-causing nematodes in California turfgrasses. 2024 UC IPM Turfgrass and Landscape Research Field Day Proceedings, p.41-42.

Becker, J.O., Ploeg, A., and Westerdahl, B. 2024. UC IPM Pest Management Guidelines: Carrots: Nematodes. In: UC ANR Publication 3438. pp. 39-41, revised 6/2024. 

Biochar and soil health. For Texas Dairy Matters, Texas A&M AgriLife Extension video produced and distributed on youtube, 8/22/2024. https://www.youtube.com/channel/UCWYjfLTZzJbNGrIK5O4IMbQ

Diggins, K. R., Murphy, S., and Pethybridge, S. J. 2024. Efficacy of fungicides for white mold control of black bean in New York, 2023. Plant Dis. Manage. Rep. 18:V020.https://www.plantmanagementnetwork.org/pub/trial/pdmr/volume18/abstracts/V020.asp.

Diggins, K. R., Murphy, S., and Pethybridge, S. J. 2024. Efficacy of OMRI-listed fungicides for white mold control of black bean in New York, 2023. Plant Dis. Manage. Rep. 18:V021.https://www.plantmanagementnetwork.org/pub/trial/pdmr/volume18/abstracts/V021.asp.

Fan, X.W., Zhang, X., Teng, L.J., Morris, S., Gao, Y.H., Askarizadeh, M., Ashley, K.A., Chim, B.K., Zhang, X.Y., and Hao, J. 2024. Evaluation of multiple fungicides to control foliar diseases of potatoes in Maine, 2023. Plant Disease Management Reports, 18: V059.

Fan, X.W., Zhang, X.Y., Teng, L.J., Morris, S., Gao, Y.H., Askarizadeh, M., Ashley, K.A., Chim, B.K., Zhang, X., and Hao, J.J. 2024. Evaluation of fungicides for controlling foliar diseases of potatoes in Maine, 2023. Plant Disease Management Reports, 18: V060.

Gao, Y.H., Zhang, X.Y., Teng, L.J., Fan, X.W., Askarizadeh, M., Ashley, K.A., Morris, S., Zhang, X.Y., and Hao, J. 2024. Effect of seed treatment using fungicides for the control of black scurf of potato in Maine, 2023. Plant Disease Management Reports, 18: ST003.

Khmelnitsky, O., Pethybridge, S. J., Murphy, S., and Kikkert, J. R. 2024. Efficacy of fungicides for Cercospora leaf blight control in carrot, 2023. Plant Dis. Manage. Rep. 18:V023.https://www.plantmanagementnetwork.org/pub/trial/pdmr/volume18/abstracts/V023.asp

Kikkert, J. R., and Pethybridge, S. J. 2024. Tar spot of corn is widespread in our region. Cornell VegEdge 20(23):1-3.VegEdge newsletter – Vol. 20, Iss. 23, 10/2/2024 (cornell.edu)

Pethybridge, S. J., Kikkert. J., and Telenko, D. 2024. Tar spot in corn: Be Alert!! Cornell VegEdge 20(17):1-3.VegEdge newsletter – Vol. 20, Iss. 17, 7/31/2024 (cornell.edu).

Pethybridge, S. J., Murphy, S., and Kikkert, J. R. 2024. Efficacy of pesticides for bacterial leaf spot control in table beet, 2023. Plant Dis. Manage. Rep. 18:V010 https://www.plantmanagementnetwork.org/pub/trial/pdmr/volume18/abstracts/V010.asp.

Pethybridge, S. J., Sharma, P., Murphy, S., Simangunsong, R., and Kikkert, J. R. 2024. Efficacy of fungicides for Cercospora leaf spot control in table beet, 2023.  Plant Dis. Manage. Rep. 18:V022. https://www.plantmanagementnetwork.org/pub/trial/pdmr/volume18/abstracts/V022.asp.

Ploeg, A. T., & Edwards. (2024). Root-knot Nematode Populations Infecting Resistant Tomatoes. UC ANR Kern County Vegetable Crops Newsletter, February 2024. 6 pp.https://cekern.ucanr.edu/newsletters/Kern_Vegetable_Crops_Newsletter100648.pdf

Sassenrath, G.F., Little, C.R., Lin, X. 2024. Role of soil management in control of soilborne diseases. Kansas Agricultural Experiment Station Research Reports 10: Article 8. (doi.org/10.4148/2378- 5977.8577)

Sharma, P., Pethybridge, S. J., Murphy, S., and Kikkert. J. R. 2024. Susceptibility of selected table beet cultivars to foliar diseases. Cornell VegEdge 20(2):4-6.VegEdge newsletter – Vol. 20, Iss. 2, 2/7/2024 (cornell.edu)

Teng, L., J., Zhang, X., Fan, X. W. Askarizadeh, M., Ashley, K., Morris, Gao, Y.H., S., Chim, B.K., and Hao, J. 2024. Field evaluation of Orondis Gold for controlling pink rot of potato in Maine, 2023. Plant Disease Management Reports, 18: V029.

Teng, L., J., Zhang, X., Fan, X. W. Askarizadeh, M., Gao, Y.H., Ashley, K., Morris, S., Chim, B.K., Zhang, X.Y., Porter, G., and Hao, J. 2024. Examining resistance of potato variety and clones for pink rot in 2023. Plant Disease Management Reports, 18: V049.

Extension Talks/Field Days/Workshops/Consultations

Becker, J. O. California Nematology Workshop and Workgroup Meeting, Kearney Research and Extension Center, Reedley, CA, March 26, 2024. “Cyst nematodes and biocontrol agents” (invited hands-on demonstration as part of the Statewide Nematology Workshop; J.O. Becker).

Becker, J. O. PCA Nematodes Fall Update Meeting, Bakersfield, October 8, 2024. “Nematodes important in California's agriculture” (invited presentation, J.O. Becker)

Becker, J. O. PLPA 240 class field demonstration, August 27, 2024. UC ANR South Coast Research and Extension Center, Irvine. “Root-knot nematode diseases and management” (invited presentation and hands-on demonstrations, J.O. Becker).

Becker, J. O. PLPA 240 class launch meeting, August 15, 2024. UCR Alumni Center. “Plant-parasitic Nematodes Diseases and Management” (invited presentation, J.O. Becker)

Becker, J. O. Teaching one part of Simon (Niel) Groen's class NEM206. “Integrated Nematode Pest Management, June 5, 2024 (invited, J.O. Becker)

Becker, J. O. UCR Turfgrass & Landscape Research Field Day, Sept. 12, 2024. “Plant disease-causing nematodes in California turfgrass.” (invited presentation, J.O. Becker).

Diggins, K., and Pethybridge, S. J. 2024. Mesotunnel research in NY update. USDA NIFA OREI Project Meeting. Attendees = 25. Duration = 30 min. Total contact = 12.5 hours. 21 August 2024.

Diggins, K., and Pethybridge, S. J. 2024. NY field trial plans – mesotunnel research. USDA-NIFA OREI Project Advisory Meeting. By Zoom. Attendees = 25. Duration = 60 min. Total contact = 25 hours. 11 January 2024.

Friesen, ML. 2024. PNW Farmer’s Network Soil Health coffee Hour “Can we replace synthetic nitrogen with microbes?”, Sept 2024

Hao, J. “Integrating biological and chemical strategies for controlling potato diseases.” 2024 Crop Health Conference, Northeastland Hotel, Presque Isle, ME. Dec. 4, 2024.

Hao, J. “Understanding the dynamics and taxonomy of pathogens for improved management of potato soft rot.” 2024 Crop Health Conference, Northeastland Hotel, Presque Isle, ME. Dec. 4, 2024.

Hao, J. Maine Potato Research Field Day –Aroostook Research Farm, Presque Isle, ME. Aug. 14, 2024. 100 attendees.

Heck, D. W., and Pethybridge, S. J. 2024. Microbial biopesticides. Empire Expo, Syracuse, New York. Attendees = 30. Duration = 30 min. Total contact = 15 hours. 23 January 2024.

James Borneman Presentation. Predicting Cyst Nematode Suppression in the Imperial Valley & Beyond. Sugarbeet Workgroup Meeting, February 21 2024, Zoom Meeting.

Little, C. R. The project leader, C.R. Little, presented at the Southeast Research and Extension Center in Parsons, Kansas as part of the 2025 Spring Crops Meeting, a session entitled: "Soil healh and soilborne diseases," which covered the concepts of soil health, the importance of two soybean soilborne diseases (sudden death, charcoal rot), and disease management strategies including crop rotation, soil nutrition, host resistance, cover crops/green manures, and the soil microbial community.

McBeath, J.H. 2023. Challenges and Potential of Rhodiola Cultivation in Alaska. 2023 Alaska Food and Farm Festival, Nov. 10-12, 2023, Anchorage, AK.

McBeath, J.H. 2023. Peony Research Report. 2023 Alaska Food and Farm Festival, Nov. 10-12, 2023, Anchorage, AK.

McBeath, J.H. 2024. What wrong with my garden. CES Master Gardener. April, 2024

Paulitz, T. 2024.  What’s New in Root Disease Research.  Farm Forum, Spokane, WA Feb. 6, 2024.

Paulitz, T. C.   2024. Canola in Rotation Influences Microbial Communities of Wheat Roots.  ARS webinar, Feb. 16, 2024.

Paulitz, T. C.  2023.  Canola in Rotation Influences Microbial Communities of Wheat Roots. Soil Health Coffee Hour, a webinar for growers, Washington State University, Dec. 20, 2023.

Paulitz, T. C.  2023. Mycorrhizal Fungi and Plants: An Ancient Symbiotic Partnership.  Palouse Prairie Foundation,  Moscow, ID. Dec. 5, 2023.

Paulitz, T. C.  2024. The Underground World of the Potato Microbiome to 15^th Washington - Oregon Potato Conference Jan. 23-24, 2024, Pasco, WA.

Paulitz, T. C. 2023. 1.5 hour hands-on lab to growers on The Soil Microbiome & Soil Health, Washington Wheat Academy, Washington State University, Dec. 15, 2023.

Paulitz, T. C. 2024.  Fusarium crown rot of wheat.  Washington Grain Commission Feb. 13, 2024.

Paulitz, T. C. 2024. 1.5 hr podcast. 24 years of on-farm research at the Jirava Farm, Ritzville, WA.  May 1, 2024.

Pethybridge, S. J. 2024. Building resilient foliar disease management strategies for the organic table beet industry. USDA Organic Program Project Directors Meeting. Attendees = 150. Duration = 30 min. Total contact = 60 hours. 25 April 2024.

Pethybridge, S. J. 2024. Development of a preparedness strategy for tar spot of processing sweet corn in New York. New York Vegetable Research Council and Association Meeting, Batavia, New York. Attendees = 54. Duration = 30 min. Total contact = 27 hours. 18 March 2024.

Pethybridge, S. J. 2024. Dry bean disease management. University of Vermont Dry Bean Webinar Series. Attendees = 85. Duration = 90 min. Total contact = 127.5 hours. 20 February 2024.

Pethybridge, S. J. 2024. Dry beans for lunch webinar series. Mid-season disease management. University of Vermont Dry Bean Webinar Series. Attendees = 28. Duration = 60 min. Total contact = 28 hours. 19 July 2024.Beans for Lunch Webinar Series, Managing dry bean diseases in the field, July 19, 2024 (youtube.com).

Pethybridge, S. J. 2024. Efficacy of products for white mold control in dry bean in New York (2024). NYS Dry Bean Twilight Growers Meeting, Le Roy, New York. Attendees = 30. Duration = 60 min. Total contact = 30 hours. 25 September 2024.

Pethybridge, S. J. 2024. Feasibility of mesotunnels for cucurbit production. 43^rd Annual LI Agricultural Forum, Riverhead, New York. Attendees = 50. Duration = 60 min. Total contact = 100 hours. 11 January 2024.

Pethybridge, S. J. 2024. Integrated management of diseases affecting dry bean. Vermont Grain Growers Conference, Essex Junction, Vermont. Attendees = 200. Duration = 60 min. Total contact = 200 hours. 20 March 2024.

Pethybridge, S. J. 2024. Mesotunnels for cucurbit production. UConn Extension Vegetable & Small Fruit Growers’ Conference. Storrs, CT. Attendees = 175. Duration = 60 min. Total contact = 175 hours. 9 January 2024.

Pethybridge, S. J. 2024. Microbial biopesticides and other organic disease management options. Cornell University NYS Pesticide Applicator Update, Ithaca, New York. Attendees = 180. Duration = 60 min. Total contact = 180 hours. 21 March 2024.

Pethybridge, S. J. 2024. Seedborne diseases of cucurbits and chenopods caused by the bacterium, Pseudomonas syringae pv. aptata. SCRI Webinar (by zoom). Attendees = 96. Duration = 60 min. Total contact = 96 hours. 3 April 2024.

Pethybridge, S. J. 2024. Soilborne diseases of vegetables in New York – white mold in rolled cereal rye systems. W5147 Multistate Project (by zoom). Attendees = 30. Duration = 60 min. Total contact = 30 h. 6 December 2024.

Pethybridge, S. J. 2024. The new kid on the block: Tar spot of sweet corn. Empire Expo, Syracuse, New York. Attendees = 75. Duration = 30 min. Total contact = 38 hours. 24 January 2024.

Pethybridge, S. J. 2024. The new kid on the kernal, tar spot of corn. New England Fruit and Vegetable Conference, Manchester, NY. Attendees = 100. Duration = 30 min. Total contact = 50 hours. 17 December 2024.

Pethybridge, S. J. 2024. Towards a durable management strategy for foliar diseases of processing carrots in New York. New York Vegetable Research Council and Association Meeting, Batavia, New York. Attendees = 54. Duration = 30 min. Total contact = 27 hours. 18 March 2024.

Pethybridge, S. J. 2024. Towards a durable management strategy for white mold in dry beans in New York. NYS Dry Bean Council Meeting, Geneva, New York. Attendees = 50. Duration = 30 min. Total contact = 25 hours. 22 March 2024.

Pethybridge, S. J. 2024. Towards an integrated durable management strategy for diseases of carrots. New England Fruit and Vegetable Conference, Manchester, NY. Attendees = 50. Duration = 30 min. Total contact = 25 hours. 19 December 2024.

Pethybridge, S. J. 2024. Vegetable disease research at Cornell AgriTech. NY Vegetable Research Association and Council, Batavia, NY. Attendees = 33. Duration = 60 min. Total contact = 33 hours. 11 April 2024.

Pethybridge, S. J. 2024. Vegetable disease research at Cornell AgriTech. NY Vegetable Research Association and Council, Geneva, NY. Attendees = 20. Duration = 3 hours. Total contact = 60 hours. 10 December 2024.

Pethybridge, S. J., and Khmelnitsky, O. 2024. Sustainable anthracnose management in watermelons: Update from NY research. USDA-SCRI Project Meeting, Myrtle Beach, SC. Attendees = 30. Duration = 3 hours. Total contact = 1.5 hours. 4 December 2024.

Pethybridge, S. J., Khmelnitsky, O., and Buck, E. 2024. Recent outbreaks of Green Fruit Anthracnose: A threat to pepper production in the United States. International Pepper Conference, Ithaca, New York. Attendees = 50. Duration = 30 min. Total contact = 25 hours. 11 September 2024.

Pineros Guerrero, N., and Pethybridge, S. J. 2024. Update on Stemphylium leaf blight of onions. Empire Expo, Syracuse, New York. Attendees = 50. Duration = 30 min. Total contact = 25 hours. 24 January 2024.

Ploeg, A. A root-knot nematode in golf course greens. Multistate Research Project meeting, W5147. 12/2024

Ploeg, A. Nematode management strategies in annual crops. UC ANR Nematology Workgoup. Parlier, 03/2024.

Ploeg, A. Nematode population biology: Population dynamics and effects of nematodes on plants. Graduate student class lecture NEM206.05/2025

Ploeg, A. Nematodes important in California agriculture. Fall Update Meeting. Stockton, CA. 10/2024

Ploeg, A. Nematodes important in California agriculture. Fall Update Meeting. Fresno, CA. 10/2024

Ploeg, A. Nematodes important in California agriculture. Fall Update Meeting. Woodland, CA. 10/2024

Ploeg, A. Summary of 10 years of research trials with fluorinated nematicides. 35th Annual Fall Desert Crops Workshop. Holtville 12/2024.

Wilson, T. and Amita Kaundal (2024).  “Microbes from Native Plant Provide Drought Tolerance” Research on Capitol Hill, Utah State Capitol, Feb 20, 2024.

Wilson, T., Jyosthna Ganesh, Ananta Devkota, Katie Hewitt, and Amita Kaundal*(2024).  “Isolation of Native Plant’s Microbiome for Plant Growth-Promoting Bacteria” CWEL Field Day, Greenville Research Farm, August 13, 2024.

Wilson, T., Jyosthna Ganesh, Ananta Devkota, Katie Hewitt, and Amita Kaundal*(2024).  “Isolation of Native Plant’s Microbiome for Plant Growth-Promoting Bacteria” Student Organic Farm, Utah State University, August 21,2024.

White, J.  presentation in the Canadian Regenerative Agriculture and Rangeland Annual Conference (Dec. 12, 2024).