Brief Summary of Minutes of Annual Meeting

Meeting commenced at 8:00 am and finished at noon.

Antoon Ploeg discussed Mi breaking Meloidogyne in tomatoes, this widely deployed resistance gene has been overcome by many populations. He also discussed the testing of other hosts against these populations.

Ole Becker-  discussed new nematicide products, including Velum, a SDI succinate dehydrogenase inhibitor.

Tessie Wilkerson-  discussed a new Xylaria pathogen on soybean in the South

James Borneman- discussed work with Hylobilia (Dactylella)- a fungus that suppresses sugar beet cyst nemadode, and also work with HLB (citrus greening) and microbiomes.

Jenifer McBeath-  talked about work with peony pathogens, in collaboration with Gary Chastagner.

Johan Leveau-  talked about his work with the soil bacterium Collimonas, which can lyse fungi, produce antifungal compounds and is a potential biological agent for Fusarium wilt of tomato.

Jianjun Hao-  talked about soft rot pathogens of potato in Maine, including Dickya and Pectobacterium

Maren Friesen-  talked about microbiome work with Rhizobium and other projects

Tim Paulitz- talked about work to correlate soil microbiomes with soil health to identify key members of the community that function in disease suppression.

Gretchen Sassenrath-  discussed work on Macrophomina on soybeans and cover crops in SE Kansas

After lunch, attendees had a tour of the Puyallup station and Gary Chastagner’s work on Christmas trees, horticultural crops and sudden oak death and the research of Marianne Elliott. We also visited a local Christmas tree grower.

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- Efforts were made to screen for cold adapted bacillus and other biological agents for the control of Botrytis and other pathogens in Alaska. At the present, more than 100 isolates have been obtained from soils, harvested in the fall, from the rhizospheres of peony plants and from soil samples harvested from the forests. Glycerol stocks of the isolates were stored for biological control studies in the future. and will be compared with data obtained from the microbiome studies. 

CA- California (CA) is the major producer of US Cole crops. According to our analysis of the CA DPR pesticide use database, before 1990, the soil fumigant l,3-dichloropropene (1,3D), was widely used to mitigate broccoli crop damage by the sugar beet cyst nematode, Heterodera schachtii. When the permits for 1,3D use were temporarily canceled, the use of other products with nematicidal activity greatly increased. After 1,3D became available again, its use reached less than 15% of the previous demand. By 2014, none of the coastal CA broccoli fields were treated with soil fumigants or contact nematicides with no apparent adverse effect on crop yield. Our project attempts to clarify if the diminished pesticide need was caused by a change in cultural practices, the establishment of an antagonistic microbiome, or if the previous use was promoted by product marketing without thorough data collection and analysis. We conducted a sampling survey of 88 broccoli fields along the Central California coast that found Heterodera cysts in only about one-third of the locations. The cyst nematode population density was surprisingly low and averaged approximately 3.2 eggs/cm3 soil. In subsequent greenhouse experiments, substantial numbers of the collected field samples significantly suppressed cyst nematode reproduction. 

CA- We used probit regression models to show that there was a strong relationship between pre-planting population levels of the fungus Dactylella oviparasitica in sugar beet soils in the Imperial Valley (CA) and post-planting levels of the nematode Heterodera schachtii. 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. 

CA- We are currently performing experiments to examine soils used to grow members of the Brassicaceae along the west coast of California between Los Angeles and San Francisco, toward the same goal of developing 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. 

CA- We are also currently performing experiments to determine why some citrus trees in Florida do not decline rapidly (Survivor Tree Phenotype) due to Huanglongbing. Our research to date shows that soil bacteria and fungi appear to correlate best with this Survivor Tree Phenotype, including some that are putatively beneficial and some that are putatively exacerbating Huanglongbing disease. 

CA- Our project characterized bacterial and fungal communities in the rhizosphere of tomato grown under conventional or organic cultivation using 16S and ITS amplicon sequencing. In brief, organic farms hosted more diverse communities at most sites, and organic and conventionally managed plots had distinct communities of bacteria and fungi. 

CA- Experimental studies examined how soil microbes from each soil type affect tomato defense and herbivore performance. Those results are summarized in Blundell et al, available on biorxiv and in revision at Nature Communications. Briefly, soil microbiota isolated from organically managed soils were sufficient to induce resistance in tomatoes and other crops to piercing/sucking herbivores, likely mediated via increase SA-mediated defenses. This adds an additional mechanism by which soil health and organic practices can enhance IPM. 

CA- One new experiment examines if the addition of beneficial soil biota (mycorrhizal fungi) influence plant health, yield and resistance to herbivores and if its effects vary across soil management backgrounds. Initial results suggest that management mediates the outcome of AMF application but we hope to repeat this experiment again in 2020. 

CA- The discovery, characterization and application of bacteria belonging to the genus Collimonas, their antifungal properties, and their ability to work synergistically with Bacillus bacteria to protect plants from soilborne fungal pathogens (https://apsjournals.apsnet.org/doi/abs/10.1094/PBIOMES-05-19-0027-R). Long-term goal is a Collimonas-based or -fortified biocontrol product. We use a variety of complementary methods to interrogate the observed Collimonas-Bacillus biocombicontrol. These include but are not limited to: generating and screening bacterial mutants of Collimonas with reduced ability to suppress fungal growth and to contribute to 'biocombicontrol' when mixed with Bacillus; the use of miniaturized rhizotron environments to unravel the interactions of Collimonas, Bacillus, pathogenic fungi, and host plants; comparative genomics of Collimonas to identify gene clusters with potential to code for new types of antifungal chemistries. 

KS- Soil microorganisms are critical for good soil function. Inherent soil properties and management practices, including tillage and crop rotation, alter microbial structure and function in the soil profile. Research examined key soil microbial properties by under conventional and conservation management in crop production fields and a hay meadow. Vertical and temporal changes in microbial properties were measured in a corn/winter wheat/soybean rotation, including extracellular enzyme activity, microbial structure as measured by phospholipid fatty acid (PLFA), and soil chemical properties (nutrients and texture). The hay meadow had the highest activities of soil C, enzyme activities, and microbial biomass, followed by the no-till fields. Greater enzyme activities in the claypan layer resulted from both the clay-enzyme interaction and impacts from management practices. Microbial properties at the soil surface are determined by the crop (corn, wheat or soybeans) and soil management practices (conventional or conservation); in deeper soil layers, microbial activities are dependent on the interaction of management and pedogenetic properties 

KS- Continued research on the control of charcoal rot in soybeans determined that the method of managing the mustard cover crop impacted the disease presence. When the mustard cover crop was rolled instead of being incorporated with tillage, a greater reduction in colony forming units (CFUs) of the disease organisms was measured. This will further benefit soil productive capacity by providing producers with a management system that reduces use of tillage. 

ME- Established trials to examine soil biochemistry and microbial communities in improving soil health for better potato production. This 4-year project will greatly broaden the knowledge of potato cropping system in Maine. 

ME- Examined microbial association in blackleg and soft rot disease of potato. This helps researchers to understand how the outbreak of the bacterial disease occurred in order to find a better solution in disease control. 

MS- Collaborations with neighboring southern states have led to the discovery and confirmation of a pathogen which is new to soybean, Xylaria sp. causing tap root decline of soybean. Research efforts have further characterized this organism in Mississippi soybean fields and has determined to be distributed in the majority of the counties across the state. Experiments have led to determination of soybean varieties either exhibiting resistance or tolerance to the pathogen and management strategies such as seed treatment or in-furrow applications exhibiting activity at controlling the effects of the pathogen. Data from 2018 and 2019 suggest that some commercial products applied in-furrow at planting are effective at reducing the signs of tap root decline, however, additional work is needed to support these findings. To support efforts associated with varietal resistance, field experiments using the complete Mississippi State Soybean Variety Trial seed were initiated in 2019 and will be on-going to determine natural resistance to the Xylaria sp. and to determine yield differences under disease pressure. 

NH- Evaluation of cultivars for differential biocontrol efficacy. Replicated experiments were completed to evaluate four tomato cultivars for differential biocontrol activity using a rockwool assay. There was no effect of cultivar on the efficacy of the biopesticides tested. A different (and more genetically diverse cultivar panel) may be needed to see differences. If our results continue to show no interaction between cultivar and biopesticide efficacy, then this will provide evidence that biopesticide inconsistency may not be due to cultivar. 

NH- Evaluate the effect of propagation substrates on biocontrol efficacy. Two experiments were conducted using a vegetable crop (cucumber) and a floriculture crop (calibrachoa). We wanted to determine if root rot disease suppression by biopesticides is influenced by the growing media type. Three growing substrates commonly used in greenhouse propagation made from inorganic (Oasis foam) and organic (peat and coconut coir) materials were compared. Three commercially available biopesticides were tested on each of the three substrates and compared to a water control. We found that substrate influenced Pythium root rot severity. Generally, plants grown in coconut coir had higher levels of disease. We also found that substrate had an effect on biopesticide efficacy, in which disease suppression tended to be greatest in coconut coir. 

TN- Developed quantitative reduced representation sequencing (qRRS) and computational algorithms for strain-level microbiome profiling and cataloging members of microbial community in sweetpotato.

In addition to deploying an inexpensive and quantitative reduced-representation sequencing (qRRS) strategy, omeSeq, for cataloguing microbial communities, we have now developed new bioinformatic software that automates the metagenomic analysis. These bioinformatic tools implement novel algorithms that provide strain-level and quantitative profiling of microbiomes, as well as the ability to handle new features derived from the qRRS protocol that delivers high-fidelity base calls and yields that exceed Illumina’s maximum yield by as much as 50%. The new software is also backward compatibility with amplicon sequencing and shotgun sequencing of metagenomes and metatranscriptomes. 

TN- Raw NGS reads can now be processed with ngsComposer that features new algorithms and empirical-based quality filtering of NGS reads (https://github.com/ryandkuster/ngsComposer). High-fidelity base calls are particularly important for strain-level microbiome profiling that delineates taxonomic groups based on SNP level resolution. The resulting high-quality reads are used as input for microbiome/ metagenomic analyses using the Qmatey software (https://github.com/B-Kristy/Qmatey). Qmatey, Quantitative Metagenomic Alignment and Taxonomic Exact-matching, can analyze various types of metagenomic/microbiome data (shotgun, amplicon and reduced representation sequencing). 

WA- Specific groups of bacteria are associated with soil health. Despite the current interest in soil health and programs by the National Resources Conservation Service (NRCS), little is known about the specific microbial groups that play a role.  ARS scientists at Pullman, Washington used next generation sequencing at a Long Term Agricultural Research (LTAR) site to compare bacterial communities to traditional soil health tests such as Haney and Solvita.  We found significant positive correlations between grain yield and the bacterial family Caulobacteraceae and negative correlations with Micromonosporaceae.  Oxalobacteraceae, Cytophagaceae, Comamonadaceae, Verrucomicrobiaceae and Pseudomonadaceae were positively correlated with the Haney and Solvita tests. Knowledge of specific community components are critical for developing management programs to improve soil health. 

WA- Wheat plants have a core microbiome. Plant roots exude carbon, nitrogen, and other nutrients that support a microbial community on the root surface, much like the gut microbiome in humans.  Is there a finite set of core microbes on wheat roots present across a wide range of environments?  ARS scientists in Pullman sampled wheat roots across a range of precipitation zones in eastern Washington. A core set of bacteria and fungi were found in >95% of rhizosphere or bulk soil samples. The most abundant core bacteria in the wheat rhizosphere were members of Bradyrhizobium, Sphingomonadaceae, Massilia, Variovorax, Oxalobacteraceae, and Caulobacteraceae.  These bacteria may play a critical role in plant health and provide an indicator of soil health for wheat growers. WA- Bacterial communities in deep soil depths. In the Palouse region of the eastern Washington, the loess soils are very deep (10 feet or more) and wheat roots can grow down to these layers to extract water. But little is known about the bacterial communities at these depths. We sampled soils down to 5 feet and used next-generation sequencing to examine fungal communities. Bacteria in the top layer are primarily rhizosphere associated, but those in the lower layers are slow growing bacteria adapted to low carbon levels. There was also an acid-adapted community in the low pH layer right below the seed.  Although there was less richness and diversity at deeper depths, more of the sequences were undescribed, indicating that the deep depths harbor unique unknown bacteria. This work leads to a greater understanding of how bacteria may play important functions for no-till wheat growers, especially for soil and plant health 

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- Nutrient Recycling Studies: The hypothesis is that in Alaska, plant diseases can facilitate the degradation of plant tissues and hence, impact positively on the recycling of nutrients. In the fall of 2019, fallen leaves from aspen trees were collected and divided into two groups depending on the numbers of sori of Melampsora rust disease—mesh bags contained: 1) leaves with large number of Melampsora rust sori, and 2) leaves with no sori or a limited number of sori. In the spring 2020, after breakup, mesh bags will be excavated. Plant tissues in the mesh bags will be evaluated. Degradation will be evaluated by the loss of weight and minerals.  

ME- Studied in field trials on fungicide with biological control agents. Potato growers benefit from the updated results. 

TN- Pairwise correlations revealed microbe-microbe interactions that corroborate well-studied interactions. For example, levels of various Fusarium sp. pathogenic in sweetpotato had negative relationship with several species/strains of microbes whose efficacy as biocontrols have been well documented in literature (i.e. Curtobacterium sp, Cladosporium sp., Pantoea sp. and Rhodococcus sp.). The study provides a high-throughput screen to document plausible naturally occurring bio-controls and synergistic relationships. 

TN- The high-density marker data enable detection of candidate genes, which was annotated to infer plausible biological relevance underlying plant-microbe interactions. The results from this study provides a proof of concept for increasing the statistical power of detection for disease traits that are heavily impacted by biotic and abiotic factors. This quantitative microbiome profiling method will help to account and model for variation due to biotic factors, hence, improving disease prediction and alleviates difficulty with disease rating. This results also provide preliminary information on biotic factors that modulate the efficacy of biocontrols. 

WA- Microbiome shifts under fertilization. WSU researchers, in collaboration with scientists at MSU, investigated the relationship between rhizosphere microbial communities, nitrogen fertilization, plant traits, and performance in the bioenergy crop switchgrass (Panicum virgatum). The data implicate bacteria in the genus Micromonospora as being negatively correlated with root traits and plant performance, despite previous reports that this organism was able to promote plant growth. Intriguingly, this genus has also been identified in wheat as being negatively correlated with yield, suggesting that better understanding the interactions with this organism will be important in optimizing grass crops ranging from bioenergy to cereals.

WA- Phenazine producers mediate iron mineral transformation on roots. Dryland wheat on the Columbia Plateau of the Pacific Northwest selects for phenazine antibiotic-producing Pseudomonas spp. that suppress a wide range of soilborne plant pathogens. Scientists at ARS Pullman, Washington State University, and Argonne National Labs demonstrated that these phenazine producers also enhance the reactivity and mobility of Fe (iron) derived from soil minerals, providing increased quantities of bioavailable iron to crop plants. These results provide evidence that biocontrol agents provide benefits to agroecosystems that extend beyond pathogen control. 

WA- Molecular communication in the wheat rhizosphere. Plant roots secrete exudates that sustain and mediate communication with their rhizosphere microbiome, but the biochemical basis of these processes in cereals is poorly understood. ARS scientists, with collaborators at Southern Mississippi University, identified amino acids and compatible solutes in exudates of the model grass Brachypodium distachyon and the wheat cultivar Buchanan, which supports increased production on roots of the antifungal metabolite 2,4 diacetylphloroglucinol. These exudate compounds, and the technology developed to recover and analyze them, are important because they can help to explain why cultivars of wheat such as Buchanan are sensitive to colonization by diacetylphloroglucinol-producing strains suppressive of take-all throughout the Pacific Northwest. 

WA- The role of bacteriophage in disease-suppressive soils. Phage that lyse bacteria are abundant in agricultural soils, but whether they influence populations of beneficial Pseudomonas strains that suppress root diseases of wheat is unknown. ARS scientists, with collaborators at Washington State University, developed methods for the isolation of phage populations indigenous to dryland and irrigated wheat field soils throughout the Pacific Northwest. These methods will enable the characterization of bacteriophage that may either interfere with or enhance suppressive bacterial populations in wheat field soils. 

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

AK- Peony Farm Surveys: This study was designed to gain a thorough understanding of the peony farms, especially the health of peony plants and controls. Questionnaires were designed to gather information on: 1) general information (geographic location, crop history, and source of peony rhizomes/root stocks, cultivation and cultural practices), 2) environmental information, 3) disease information and management methods used. The survey was a success: out of the 77 peony farms, 72 farmers (94%) responded.  

KS- Fusarium head blight (FHB) infestations in wheat have occurred frequently in recent years, reducing yield and quality. Wheat is particularly susceptible to the disease when high rainfall or humidity occur during the flowering period, which is common in southeast Kansas. Accurate prediction of wheat phenological development is important to provide accurate and timely remediation through use of fungicides. In this research, three wheat phenological models were evaluated: APSIM, SIMPLACE, and Modified-SIMPLACE. The Modified-SIMPLACE model was the best predictor of heading date for each variety in all the locations. The results indicated that the differences between parameter characteristics for the same variety in different locations were not significant, but the varietal differences in the same location were significant. This model may be a useful tool for producers to time application of fungicide for control of FHB in wheat.

MS- Research experiments surrounding management strategies, specifically, alternate host for rotation for Xylaria are on-going. To date it has been determined that colonization of the pathogen occurs on all primary rotational crops which limits crop rotation as a management tool for this particular disease.  Management options beyond cultural practices such as crop rotation are needed to reduce taproot decline of soybean such as completely resistant cultivars.  Additional research is on-going to determine organisms present within the soil interface coexisting with Xylaria which could be a potential source of biocontrol. 

WA- Developing high-throughput assays for microbial genes involved in soil health. WSU and ARS scientists are using a new qPCR platform enabling over 5K assays to be conducted simultaneously. The first targets are soilborne fungal pathogens and nitrogen-cycling bacteria and archaea. This flexible technology could be applied in the future to any molecular targets of interest that will enable growers to conduct rapid tests for pathogens as well as beneficial microbes important for plant and soil health. 

WA- Liming and pH shifts in microbial communities. Soil acidification is an increasing problem in the dryland wheat production, because of long term use of ammonium fertilizer and nitrification. Growers are looking at using lime to raise the pH, but what effect does this have on microbial communities in the soil?  Oregon State University scientists at Pendleton, Oregon and ARS scientists in Pullman analyzed the soil microbiome in replicated field plots with addition of different levels of lime. Liming significantly increased the relative abundance of some bacterial families, including Pseudomonadaceae, Opitutaceae, and Flavobacteriaceae, while decreasing others, such as the Bradyrhizobiaceae, though this effect was often seen only at the 0-3 inch depths. This information is important for growers because liming will reshape soil communities, primarily impacting bacteria, in ways that may influence plant health. 

WA- Molecular diagnostic assays for biocontrol strains of native grape yeasts. The wine industry in Washington State and throughout the world sustains yield losses caused by Botrytis cinerea, a fungal pathogen of wine grapes, table grapes and apples. Biological control is an attractive alternative to fungicides, to which Botrytis frequently develops resistance. ARS and Washington State University scientists identified 11 yeasts from Washington vineyards that inhibited the growth of 9 isolates of Botrytis on laboratory media or on whole grape berries. Niche competition appeared to be the predominant mode of biocontrol, and inhibition was dependent on genotypes of both the yeast and the pathogen. The findings suggest that native yeasts or their products could be used in combination when deployed against vineyard Botrytis cinerea. 

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. 

Borneman gave presentations to undergraduate and graduate students in his two Microbiomes courses (MCBL 126 & MCBL 226). These presentations covered biological suppression of plant parasitic nematodes as well as root microbes that may inhibit or exacerbate Huanglongbing disease of citrus. These presentations took place in the spring quarter of 2019 at UC Riverside. Borneman was a senior editor for the journal, Phytobiomes. 

Friesen advised four postdoctoral research associates and two technicians, and served on the thesis committee of 1 MS and 6 PhD students. Friesen also co-taught a bacterial pan-genomes seminar course for undergrad and grad students, and taught the bacteriology module of a graduate lab class. Friesen and Paulitz are co-advising a USDA postdoctoral research fellow. 

Olukolu. We provided summer research experience to two high school students and a deaf and hard of hearing REU student who were interested in working on soil microbiomes that interact closely with the root system. Currently, 3 PhD students and 2 honors undergraduate student are conducting experiments in sweetpotato and maize microbiome. We are proving training on NGS library prep, NGS data quality filtering, microbiome analytics, and SNP calling/filtering to collaborators, partners and a next-generation sequencing service provider. 

McBeath- a survey was sent to the peony farmers, and were also invitations to serve as ”citizen scientists” and ”research collaborators”. Among the survey responses received, 75% of peony farmers expressed strong interest in serving as “citizen scientists”. 

Paulitz was the main organizer for the 64th Annual Conference on Soilborne Pathogens at Huntington Gardens in San Marino, CA in March, 2019. He organized a keynote session on Soil Health and Microbial Interactions. Paulitz advised two postdoctoral research associates. Advised one MSc student, co-supervised 2 PhD students (including an African American woman) and served on thesis committee of 2 MS and 1 PhD students. Paulitz hosted a Borlaug Fellow from Turkey in July and Aug., 2019.Paulitz is editor of Pythium Protocol project, an on-line publication of the American Phytopathological Society Press and senior editor of the Canadian Journal of Plant Pathology. 

Poleatewich       An undergraduate student was trained in a one-on-one setting as an independent study project. The student learned basic principles of plant pathology and experimental design. The student also gained laboratory and greenhouse skills related to culturing fungi in the lab, preparation of growth media, growing and maintaining plants in the greenhouse, collecting and analyzing data.   A masters student was trained and graduated in August 2019.

Sassenrath- Presentations on soil health, erosion, and wheat and soybean disease were given to producers at field days, extension meetings, and information coffee meetings. One radio interview on disease suppression in soybeans using the cover crop system was conducted, and broadcast through the K-State Agronomy Radio Network. This research was also the basis of a publication by the Supporters of Agricultural Research (SoAR) for their Retaking the Field publication. A second interview on general crop production formed the basis of a newspaper article. Two presentations were made at scientific meetings, and nine reports of progress were published for farmers. Two field days and demonstrations were developed and presented to farmers. Ten presentations were made to farmers, conservationists, extension agents and agronomist on crop production systems, conservation practices, and soil health. County Extension Agents were trained at an agent update held in southeast Kansas. One webinar and two short courses were given to landowners; three classroom presentations on site-specific management were given to undergraduate and graduate classes.  

Wilkerson- Participated in local educational opportunities. The primary focus of the "Pathways to Possibilities" event was to instill ideas for the future into middle school students in a fairly rural community. This outreach is very valuable to the public and private schools in the area. Many of these students are not aware of the career opportunities available and some settle for low wage jobs without the consideration of what else is out there. For instance, many don't know what soybean looks like or that they pass fields of it every day on the way to school. They see tractors in the field and beyond that image have no understanding of the many career paths agriculture has to offer. This type of presentation provides information about options beyond agriculture's historic stereotype. Washington County MS education outreach to Public and Private secondary school students • Entitled "Pathways to Possibilities" • Booths set up at "career fair" to showcase careers to area 8th grade students • 36 area schools both public and private • 1816 students • Demonstration including crop plants, fungal cultures, microscopes set up for observation. Coordination with American Phytopathology Society Foundation provided handouts, educational games ("What nematode Am I?") and stickers to handout to participants to promote the study of plant pathology. Presentations at professional meetings and field tours have provided information to colleagues, students, and growers on current issues surrounding soil pathogens such as Xylaria sp. (tap root decline of soybean). -"Taproot Decline Update" at Mississippi Agriculture Consultants Association meeting Feb, 5, 2019 Seminar entitled "Root Diseases: What Lies beneath" for EPP1001 first year seminar class-Mississippi State University November 26, 2019

Peer-reviewed 

Bell, T., K.L. Hockett, R.I. Alcalá-Briseño, M. Barbercheck, G.A. Beattie, M.A. Bruns, J.E. Carlson, T. Chung, A. Collins, B. Emmett, P. Esker, K.A. Garrett, L. Glenna, B.K. Gugino, M. del Mar Jiménez-Gasco, L. Kinkel, J. Kovac, K.P. Kowalski, G. Kuldau, J.H.J. Leveau, M.J. Michalska-Smith, J. Myrick, K. Peter, M.F. Vivanco Salazar, A. Shade, N. Stopnisek, X. Tan, A.T. Welty, K. Wickings, E. Yergeau (2019) Manipulating wild and tamed phytobiomes: challenges and opportunities. Phytobiomes Journal 3:3-21. 

Biessy, A., Novinscak, A., Blom, J., Leger, G., Thomashow, L.S., Cazorla, F.M., Josic, D., Filion, M. 2018. Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environmental Microbiology. 21:437-455. 

Blundell, R, Schmidt JE, Igwe AI, Cheung AL, Vannette RL, Gaudin A, Casteel, C 2019. “Organic management promotes natural pest control through enhanced plant resistance to insects”, in review at Nature Communications and on at biorxiv: https://www.biorxiv.org/content/10.1101/787549v1 

Cai, M., Ma, S., Hu, R., Tomberlin, J.K., Thomashow, L.S., Zheng, L., Li, W., Yu, Z., Zhang, J. 2018. Hermetia illucens mitigates antibiotic resistance risks in chicken manure bioconversion by controlling microflora and reforming environment. Environmental Microbiology. 20(11)4051-4062. 

Chen Taixiang, Chunjie Li, James F White, Zhibiao Nan. 2019.  Effect of the fungal endophyte Epichloë bromicola on polyamines in wild barley (Hordeum brevisubulatum) under salt stress. Plant and Soil 03/2019; 436:29-48., DOI:10.1007/s11104-018-03913-x

Cheng, M.Y., McBeath, J.H., Dong, J.H., Han, C.G., Zhang, Z.K., 2019. First report of Phytoplasma ‘Candidatus Phytoplansma australiense’ associated with purple top diseased potatoes (Solanum tuberosum) in Guangdong. Plant Disease 103 (5): 1015. 

Clark T, Friel C, Grman E, Friesen ML, Shachar-Hill Y. 2019. Unfair trade underground revealed by integrating data with Nash bargaining models. New Phytologist, 222(3), 1325-1337. 

CN Jack, KJ Wozniak, SS Porter, ML Friesen. 2019. Rhizobia protect their legume hosts against soil-borne microbial antagonists in a host-genotype-dependent manner. Rhizosphere 9, 47-55 

DN Smercina, SE Evans, ML Friesen, LK Tiemann. 2019. Optimization of the 15N2 incorporation and acetylene reduction methods for free-living nitrogen fixation. Plant and Soil, 1-17 

Doan, H.K., N.N. Maharaj, K.N. Kelly, E.M. Miyao, R.M. Davis, and J.H.J. Leveau (2019) Antimycotal activity of Collimonas isolates and synergy-based biocontrol of Fusarium wilt of tomato. Phytobiomes https://doi.org/10.1094/PBIOMES-05-19-0027-R. 

Dohnalkova, A.C., Tfaily, M.M., Smith, A.P., Chu, R.K., Crump, A.R., Brislawn, C.J., Varga, T., Shi, Z., Thomashow, L.S., Harsh, J.B., Keller, C.K. 2017. Molecular and microscopic insights into the persistence of soil organic matter in a red pine rhizosphere. Soil Processes. https://doi.org/10.3390/soils1010004. 

Friel, CA, Friesen, ML. Legumes modulate allocation to rhizobial nitrogen fixation in response to factorial light and nitrogen manipulation. Frontiers in Plant Science doi: 10.3389/fpls.2019.01316 

Ge, T.L., Ekbataniamiri, F., Chesley, A., Giggie, E. and Hao, J.J. 2019. Evaluation of Orondis premixes in soil or foliar applications for pink rot control in potatoes, Presque Isle, ME, 2018. Plant Disease Management Reports 13:V113. 

Ge, T.L., Ekbataniamiri, F., Chesley, A., Giggie, E. and Hao, J.J. 2019. Evaluation of BAS 750F for the control of early blight of potato, Presque Isle, ME 2018. Plant Disease Management Reports 13:V112. 

Ge, T.L., Ekbataniamiri, F., Liu, Q., Giggie, E. and Hao, J.J. 2019. Evaluation of Miravis Prime for controlling white mold and grey mold on potato, Presque Isle, ME, 2018. Plant Disease Management Reports 13:V114. 

Ge, T.L., Li, K. Ekbataniamiri, F., Giggie, E. and Hao, J.J. 2019. Evaluation of the application interval of BAS 750F for controlling early blight disease of potato, Presque Isle, ME 2018. Plant Disease Management Reports 13:V111. 

Ge, T.L., Li, K. Ekbataniamiri, F., Giggie, E. and Hao, J.J. 2019. Evaluation of seed treatments and in-furrow treatments for soilborne disease control on potato, Presque Isle, ME, 2018. Plant Disease Management Reports 13:VST006. 

Gloria M Macedo-Raygoza, Benjamín Valdez-Salas, Fernanda M Prado, Lydia F Yamaguchi, Massuo J Kato, Blondy B Canto-Canché, Carrillo -Beltrán, Paolo Di Mascio, James F White, Miguel J Beltrán-García, Katia R. Prieto. 2019. Enterobacter cloacae, an Endophyte That Establishes a Nutrient-Transfer Symbiosis With Banana Plants and Protects Against the Black Sigatoka Pathogen. Frontiers in Microbiology 03/2019;, DOI:10.3389/fmicb.2019.00804

Hansen, J.C., Schillinger, W., Sullivan, T., Paulitz, T.C. 2019. Soil microbial biomass and fungi reduced with canola introduced in long-term monoculture wheat rotations. Frontiers in Microbiology. 10:1488. https://doi.org/10.3389/fmicb.2019.01488. 

Hansen, J.C., Sullivan, T., Schillinger, W., Paulitz, T.C. 2018. Rhizosphere microbial communities of canola and wheat at six paired field sites. Applied Soil Ecology. 130:185-193. 

Hao Chen, James Francis White, Chunjie Li 2019. First Report of Epicoccum layuense Causing Brown Leaf Spot on Oat (Avena sativa ) in Northwestern China. Plant Disease 10/2019;, DOI:10.1094/PDIS-09-19-1984-PDN

Henry, P.M., A.M. Pastrana, J.H.J. Leveau, and T.R. Gordon (2019) Persistence of Fusarium oxysporum f. sp. fragariae in soil through asymptomatic colonization of rotation crops. Phytopathology 109:770-779. 

Hewavitharana, S. S., Klarer, E., Reed, A. J., Leisso, R., Poirer, B., Honaas, L., Rudell, D. R., and Mazzola, M. 2019. Temporal dynamics of the soil metabolome and microbiome during simulated anaerobic soil disinfestation. Frontiers in Microbiology doi:10.3389/fmicb.2019.02365 

Hsiao, C.-J., Sassenrath, G.F., Zeglin, L., Hettiarachchi, G.M., Rice, C.W. 2018. Vertical stratification of soil microbial properties in claypan soils. Soil Biology and Biochemistry. 121L154-164. doi.org/10.1016/j.soilbio.2018.03.012

Hsiao, C.J., Sassenrath, G.F., Zeglin, L.H., Hettiarachchi, G.M., Rice, C.W. 2019. Temporal variation of soil microbial properties in a corn-wheat-soybean system. SSSAJ. doi: 10.2136/sssaj2019.05.0160 

James F White, Kathryn L Kingsley, Rajan Verma, Nkolika Obi, Sofia Dvinskikh, Matthew T Elmore, Satish K. Verma, Surendra K Gond, Kurt P. Kowalski, Qiuwei Zhang. 2019.  Review: Endophytic Microbes and Their Potential Applications in Crop Management. Pest Management Science 09/2019; 75(10):2543-2548., DOI:10.1002/ps.5527

Jiang, H., Hwang, H., Ge, T., Cole, B., Perkins, L.B., and Hao, J. 2019. Leucine regulates zoosporic germination and infection by Phytophthora erythroseptica. Frontiers in Microbiology 10:131. DOI:10.3389/fmicb.2019.00131. 

Kim, D., Jeon, C., Shin, J., Weller, D.M., Thomashow, L.S., Kwak, Y. 2019. Function and distribution of a lantipeptide in strawberry Fusarium wilt disease suppressive soils. Molecular Plant-Microbe Interactions. 32:306-312. 

Knerr, A., Wheeler, D., Schlatter, D.C., Sharma-Poudyal, D., Du Toit, L.J., Paulitz, T.C. 2019. Arbuscular Mycorrhizal Fungal Communities in Organic and Conventional Onion Crops in the Columbia Basin of the Pacific Northwest USA. Phytobiomes Journal. 2:194-207. 

Li J, Wu R, Wang M, Borneman J, Yang J, Zhang KQ. 2019. The pH sensing receptor AopalH plays important roles in the nematophagous fungus Arthrobotrys oligospora. Fungal Biol. 123(7):547-554. 

Liang, C., Hao, J., Li, J., Baker, B., and Luo, L. 2019. Artificial microRNA-mediated resistance to cucumber green mottle mosaic virus in Nicotiana benthamiana. Planta. DIO: 10.1007/s00425-019-03252-w. 

Liang, C., Liu, H., Hao, J., Li, J., and Luo, L. Expression profiling and regulatory network of cucumber microRNAs and their putative target genes in response to cucumber green mottle mosaic virus infection. Archives of Virology. DOI: 10.1007/s00705-019-04152-w. 

Longhai Xue, Lei Zhang, Xiao xiang Yang, Xiaoqin Huang, Wenxian Wu, Xiquan Zhou, James F White, Yong Liu, Chunjie Li. 2019. Characterization, Phylogenetic Analyses, and Pathogenicity of Colletotrichum Species on Morus alba in Sichuan Province, China. Plant Disease 10/2019; 103(10):2624-2633., DOI:10.1094/PDIS-06-18-0938-RE

Lu, X.H., Gao, W., Zhang, X.M., Jiao, X, Luo, Y., Hao, J., and Zhang, X.S. 2019. Fungal complex associated with red-skin root of Panax ginseng in China. Journal of Ginseng Research. DOI: 10.1016/j.jgr.2019.01.006. 

Ma, X., Pernab, N.T., Glasner, J.D., Hao, J., Johnson, S., Charkowski, A., Perry, K.L., Stodghill, P., and Swingle, B. 2019. Complete genome sequence of the potato blackleg pathogen Dickeya dianthicola ME23. Microbiology Resource Announcements 8: e01526-18. 

Matthew T Elmore, James F White, Kathryn L Kingsley, Katherine H Diehl, Satish K Verma. 2019.  Pantoea spp. Associated with Smooth Crabgrass (Digitaria ischaemum) Seed Inhibit Competitor Plant Species. 05/2019; 2019(7):143., DOI:10.3390/microorganisms7050143

Moein, S., Mazzola, M., Ntushelo, N. S. and McLeod, A. 2018. Apple nursery trees and irrigation water as potential external inoculum sources of apple replant disease in South Africa. European Journal of Plant Pathology   https://doi.org/10.1007/s10658-018-01631-9 . 

Nyoni, M., Mazzola, M., Wessels, J.P. B. and McLeod, A. 2019. The efficacy of semi-selective chemicals and chloropicrin/1,3-dichloropropene containing fumigants in managing apple replant disease in South Africa. Plant Disease https://doi.org/PDIS-10-18-1844-RE-R1 

Okubara, P.A., Peetz, A.B., Sharpe, R.M. 2019. Cereal root interactions with soilborne pathogens--from trait to gene and back. Agronomy. 157:21-30. 

Parke, J. L., Redekar, N. R., Eberhart, J. E., and Funahashi, F. 2019. Hazard analysis for Phytophthora species in container nurseries: three case studies. HortTechnology 29: 745-755.  https://doi.org/10.21273/HORTTECH04304-19 

Peterson, E. K., Larson, E., and Parke, J. L. 2019.  Film-forming polymers and surfactants reduce infection and sporulation of Phytophthora ramorum on rhododendron. Plant Dis. 103:1148-1155. https://apsjournals.apsnet.org/doi/abs/10.1094/PDIS-05-18-0802-RE 

Peterson, E. K., Rupp, F., Eberhart, J. L., and Parke, J. L. 2019. Root rot of Juniperus and Microbiota by Phytophthora lateralis in Oregon horticultural nurseries. Plant Dis. 103: https://apsjournals.apsnet.org/doi/10.1094/PDIS-04-19-0808-RE 

Petipas RH, Bowsher A, Bekkerring C, Mclachlan E, White RA, Younginger B, Jack CN, Tiemann LK, Evans SE, Friesen ML.  Interactive effects of microbes and nitrogen on Panicum virgatum root functional traits and patterns of phenotypic selection. International Journal of Plant Sciences in press 

Pollard, A.T., Okubara, P.A. 2018. Real-time PCR quantification of Fusarium avenaceum in soil and seeds. Journal of Microbial Methods. 9(4)188. 

Porter SS., Bantay R., Ibaretta K., Friel CA., Garoutte A., Gdanetz K., Moore BM., Shetty PS., Siler E., Friesen, ML. Beneficial microbes ameliorate abiotic and biotic sources of stress on plants. Accepted at Functional Ecology 

Redekar, N. R., Eberhart, J.E., and Parke, J. L. 2019. Diversity of Phytophthora, Pythium, and Phytopythium species in recycled irrigation water in a container nursery. Phytobiomes Journal 3:31-45. https://doi.org/10.1094/PBIOMES-10-18-0043-R 

Redekar, N. R., Eberhart, J.E., Rooney-Latham, S., Blomquist, C.L., and Parke, J. L. 2019. First report of Phytophthora tropicalis causing foliar blight and shoot dieback of Pieris japonica in Oregon. Plant Dis. 103: https://apsjournals.apsnet.org/doi/10.1094/PDIS-10-19-2179-PDN 

Richard Allen White, III, Jeffrey S. Norman, Emily E. Mclachlan, Joseph P. Dunham, Aaron Garoutte, Maren L. Friesen (2019) Elucidation of the Genome of Bradyrhizobium sp. Strain USDA 3456, a Historic Agricultural Diazotroph from Cowpea (Vigna unguiculata). Microbiology Resource Announcements DOI: 10.1128/MRA.00812-19 (1,2,6) 

Richard Allen White, III, Jeffrey S. Norman, Emily E. Mclachlan, Joseph P. Dunham, Aaron Garoutte, Maren L. Friesen (2019) Revealing the Draft Genome Sequence of Bradyrhizobium sp. Strain USDA 3458, an Effective Symbiotic Diazotroph Isolated from Cowpea (Vigna unguiculata) Genotype IT82E-16. Microbiology Resource Announcements 8 (38), e00813-19 (1,2,6) 

S Hatamzadeh, K Rahnama✉, S Nasrollahnejad, Kh.-Br Fotouhifar, K Hemmati, James F White. 2018. Septoria malagutii as an endophytic fungus of Achillea millefolium from Iran. DOI:10.22043/MI.2018.120384

Sarwar, A., Latif, Z. Zhang, S., Hao, J., and Bechthold, A. 2019. A potential biocontrol agent Streptomyces violaceusniger AC12AB for managing potato common scab. Frontiers in Microbiology 10: 222. DOI: 10.3389/fmicb.2019.00202. 

Sassenrath, G.F., Farney, J., Lollato, R. 2019. Impact of fungicide and insecticide use on wheat production in a high-rainfall environment. Crop, Forage and Turfgrass Management. 5:190008. doi:10.2134/cftm2019.01.0008 

Satish K Verma, Ravindra N Kharwar, James F White. 2019. The Role of Seed-Vectored Endophytes in Seedling Development and Establishment. Symbiosis 04/2019;, DOI:10.1007/s13199-019-00619-1

Schlatter, D. C., Baugher, C., Kahl, K., Huggins, D. R. Johnson- Maynard, J., and Paulitz, T. C. 2019. Bacterial communities of soil and earthworm casts of native Palouse Prairie remnants and no-till wheat cropping systems.  Soil Biology and Biochemistry: in press 

Schlatter, D.C., Paul, N.C., Shah, D.H., Schillinger, W.F., Bary, A.L., Sharratt, B.S., Paulitz, T.C. 2019. Biosolids and tillage practices influence soil bacterial communities in dryland wheat. Microbial Ecology. https://doi.org/10.1007/s00248-019-01339-1. 

Schlatter, D.C., Reardon, C.L., Maynard-Johnson, J.L., Brooks, E., Kahl, K.B., Norby, J., Huggins, D.R., Paulitz, T.C. 2019. Mining the drilosphere: bacterial communities and denitrifier abundance in a no-till wheat cropping system. Frontiers in Microbiology. 10:1339. 

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

Schroeder, K.L., Schlatter, D.C., Paulitz, T.C. 2018. Location dependent impacts of liming and crop rotation on bacterial communities in acid soils of the Pacific Northwest. Applied Soil Ecology. 130:59-68. 

Shen, Z., Xue, C., Penton, C.R., Thomashow, L.S., Zhang, N., Wang, B., Ruan, Y., Li, R., Shen, Q. 2018. Suppression of banana Panama disease induced by soil microbiome reconstruction through an integrated agricultural strategy. Soil Biology and Biochemistry. 128:164-174. 

Shuai Zhao, Jun-Jie Liu, Samiran Banerjee, James F. White, Na Zhou, Zhen-Yong Zhao, Ke Zhang, Ming-Fang Hu, Kathryn Kingsley, Chang-Yan Tian. 2019.  Not by Salinity Alone: How Environmental Factors Shape Fungal Communities in Saline Soils. Soil Science Society of America Journal 01/2019; 83(5):1387., DOI:10.2136/sssaj2019.03.0082

Siefert A, Zillig KW, Friesen ML, Strauss SY. 2019. Mutualists stabilize the coexistence of congeneric legumes. The American Naturalist. Feb 1;193(2):200-12. 

Smercina, D., Evans, S.E., Friesen, M.L., Tiemann, L.K. 2019. To fix or not to fix: Controls on Free-living Nitrogen fixation. Accepted at Applied and Environmental Microbiology 

Thomashow, L.S., Kwak, Y., Weller, D.M. 2019. Natural antibiotics in sustainable agriculture: models, metabolites and mechanisms. Pest Management Science. https://doi.org/10.1002/ps.5406. 

Thomashow, L.S., Letourneau, M., Kwak, Y., Weller, D.M. 2018. The Soil-borne Legacy in the Age of the Holobiont. Microbial Biotechnology. https://doi.org/10.1111/1751-7915.13325. 

Vijay K Sharma, Xin-Ya Li, Guang-Li Wu, Wei-Xiao Bai, Shobhika Parmar, James F White, Hai-Yan Li. 2019. Endophytic community of Pb-Zn hyperaccumulator Arabis alpina and its role in host plants metal tolerance. Plant and Soil 02/2019;

Wang, L., and Mazzola, M. 2019. Field evaluation of reduced rate Brassicaceae seed meal amendment and rootstock genotype on the microbiome and control of apple replant disease. Phytopathology 109:1378-139. 

William Pietro-Souza, Felipe de Campos Pereira, Ivani Souza Mello, Fernando Ferrari Frutuoso Stachack, Ailton Jose Terezo, Cátia Nunes da Cunha, James Francis White, Haiyan Li, Marcos Antônio Soares. 2019. Mercury resistance and bioremediation mediated by endophytic fungi. Chemosphere 09/2019; 240:124874., DOI:10.1016/j.chemosphere.2019.124874

Younginger, BY, Friesen, ML. Connecting signals and benefits through partner choice in plant-microbe interactions. FEMS Microbiology Letters in press 

Zhang, X. M., Jiang, H. and Hao, J. 2019. Evaluation of the risk of development of fluopicolide resistance in Phytophthora erythroseptica. Plant Disease. DOI: 10.1094/PDIS-02-18-0366-RE. 

Zhengfeng Wang, ﹒chunjie Li, James F White, Zhibiao Nan. 2019. Effects of Epichloë endophyte infection on growth, physiological properties and seed germination of wild barley under saline conditions. Journal of Agronomy and Crop Science 08/2019;, DOI:10.1111/jac.12366

Zhenjiang Chen, Chunjie Li, Zhibiao Nan, Xuekai Wei, James F White. 2019. Segregation of Lolium perenne into a subpopulation with high infection by endophyte Epichloë festucae var. lolii results in improved agronomic performance. Plant and Soil 11/2019;, DOI:10.1007/s11104-019-04370-w  

Books and book chapters 

Kumar, A. E K Radhakrishnan, Samir Droby, Vipin Kumar Singh, Sandeep Kumar Singh, James Francis White: Entry, colonization and distribution of endophytic microorganisms in plants. Microbial Endophytes: Functional Biology and Applications, 05/2019; Elsevier.

Li, H-Y., Shobhika Parmar, Vijay K Sharma, James F White: Seed Endophytes and Their Potential Applications. Seed Endophytes (eds) Verma S., White, Jr J., 04/2019: pages 35-54; Springer, Cham., ISBN: Print ISBN 978-3-030-10503-7 Online ISBN 978-3-030-10504-4, DOI:10.1007/978-3-030-10504-4_3

Martinez-Rodriguez, A.  Gloria Macedo-Raygoza, Aurora X. Huerta-Robles, Ileana Reyes-Sepulveda, Jhovana Lozano-Lopez, Evelyn Y. García-Ochoa, Luis Fierro-Kong, Marisa H. G. Medeiros, Paolo Di Mascio, James Francis White, Miguel J. Beltran-Garcia: Agave Seed Endophytes: Ecology and Impacts on Root Architecture, Nutrient Acquisition, and Cold Stress Tolerance. Seed Endophytes, 04/2019: pages 139-170; , ISBN: 978-3-030-10503-7, DOI:10.1007/978-3-030-10504-4_8

Molina, M, James F White, Kathryn Kingsley, Natalia Gonzalez: SEED ENDOPHYTES OF JASIONE MONTANA: ARSENIC DETOXIFICATION WORKERS IN AN ECO-FRIENDLY FACTORY. Seed Endophytes-Biology and Biotechnology, First 06/2019: chapter 17: pages 365-384; Springer., ISBN: 978-3-030-10503-7

Molina, Maria, Luis Fernando Bautista, Ignacio Belda, Manuel Carmona, Eduardo Díaz, Gonzalo Durante-Rodríguez, Sara García-Salgado, Jaime López-Asensio, Pilar Martínez-Hidalgo, María Ángeles Quijano, James F. White, Natalia González-Benítez: Bioremediation of Soil Contaminated with Arsenic. Microbes and Enzymes in Soil Health and Bioremediation, 11/2019: pages 321-351; , ISBN: 978-981-13-9116-3, DOI:10.1007/978-981-13-9117-0_14

Pal, G. Kanchan Kumar, Anand Verma, James Francis White, Satish K. Verma: Functional Roles of Seed-Inhabiting Endophytes of Rice. Seed Endophytes, 04/2019: pages 213-236; , ISBN: 978-3-030-10503-7, DOI:10.1007/978-3-030-10504-4_11

Tadych, M. ,James F White: Endophytic Microbes. Encyclopedia of Microbiology (5th Ed.), Updated Forth Edition 09/2019: pages 123-136; Academic Press., ISBN: 9780128117378, DOI:10.1016/B978-0-12-809633-8.13036-5

Verma, S. K. Ravindra N. Kharwar, Surendra K. Gond, Kathryn L. Kingsley, James Francis White: Exploring Endophytic Communities of Plants: Methods for Assessing Diversity, Effects on Host Development and Potential Biotechnological Applications. Seed Endophytes, 04/2019: pages 55-82; , ISBN: 978-3-030-10503-7, DOI:10.1007/978-3-030-10504-4_4

White, J. F.  Satish Kumar Verma: Seed Endophytes: Biology and Biotechnology. 06/2019; Springer, ISBN: 978-3-030-10503-7, DOI:10.1007/978-3-030-10504-4

White, J. F. , Satish K. Verma: Prologue to book 'Seed Endophytes'. Seed Endophytes: Biology and Biotechnology, 06/2019; Springer., ISBN: 978-3-030-10503-7 

Extension and technical bulletins 

Coop, L. B., D. Upper, and J. Parke. 2019. Soil solarization program – for using transparent anti-condensation plastic film to manage soil-borne plant pathogens and weed seeds. Oregon State University Integrated Plant Protection Center https://uspest.org/soil/solarizeV2beta1 

Hsiao, C.J., Sassenrath, G.F., Zeglin, L., Hettiarachchi, G., Rice, C. 2019. Changes in soil microbiology under conventional and no-till production during crop rotation. Kansas Agricultural Experiment Station Research Reports: Vol. 5: Iss. 2. https://doi.org/10.4148/2378-5977.7746   https://www.yumpu.com/en/document/fullscreen/62280511/organic-farmer-dec-jan-2019

Majsztrik, J., Parke, J., Swett, C., Pitton, B., and Kumar, S. 2019 Disease Risk Model v 1.0. https://occviz.com/CW3/pathogen/pathogen.html 

Mallory-Smith, C., Wada, N., and Parke, J. L. 2019. Here comes the sun: soil solarization for weed management. Digger Magazine (Jan. issue):33-36. http://www.diggermagazine.com/here-comes-the-sun/ 

Parke, J. L., and E. Peterson. 2019. Sudden oak death, sudden larch death, and ramorum blight. The Plant Health Instructor. DOI: 10.1094/PHI-I-2019-0701-02 https://www.apsnet.org/edcenter/disandpath/oomycete/pdlessons/Pages/SuddenOakDeath.aspx   

Parke, J. L., Mallory-Smith, C., Dragila, M., Hill, B., Wada, N., Weidman, C., Coop, L., Buckland, K. 2019. Soil solarization – a potential tool for organic growers to manage weeds and improve soil health. Organic Farmer 1(4):12-18. 

Paulitz, T. C. Porter, L., Schroeder, K. L. and Du Toit, L. 2019.  Pythium seed and root. in: Compendium of Pea Diseases and Pests, Third Edition. R. Harveson, Ed. APS Press. 

Porter, L., Paulitz, T. C. and Schroeder, K. L. 2019. Pythium seed and seedling rot. Lentil Disease Diagnostic Series.  NDSU Extension Publication. PP1913 

Redekar, N. R. and J. L. Parke. 2019. Testing the waters. Digger Magazine 63(6):33-37. http://www.diggermagazine.com/testing-the-waters/ 

Rupp, J., Bruce, M. and Paulitz, T. C. 2019. Rhizoctonia seed, seedling and root rot. Lentil Disease Diagnostic Series.  NDSU Extension Publication. PP1913 

Sassenrath, G.F., Little, C., Roozeboom, K., Lin, X., Jardine, D. 2019. Controlling soil-borne disease in soybean with a mustard cover crop. Kansas Agricultural Experiment Station Research Reports: Vol. 5: Iss. 2.https://doi.org/10.4148/2378-5977.7740 

Stoven, H. and Parke, J. L. 2019. The continuing battle against nasty Nostoc. Digger Magazine 63(11):27-29. http://www.diggermagazine.com/the-continuing-battle-against-nasty-nostoc/ 

Zhao, H., Sassenrath, G.F., Lin, X., Lollato, R., De Wolf, E.D. 2019. Modeling wheat susceptibility to disease. Kansas Agricultural Experiment Station Research Reports: Vol. 5: Iss. 2. https://doi.org/10.4148/2378-5977.7742 

Meeting presentations and proceedings 

DeGenring, L. and Poleatewich, A. 2019. Effect of substrate on biopesticide efficacy to suppress Pythium in hydroponic systems. Phytopathology. 109(9): S1.26 

Friesen, M. L. “Conversations on Soil Health”, an interactive discussion facilitated by Maren L. Friesen

Clare L. Casteel*, Amélie C.M. Gaudin and Rachel L. Vannette “Soil microbes mediate enhanced pest resistance on organic farms” International Society for Chemical Ecology, Atlanta GA, June 4, 2019 CROPS (Hudson Alpha), June 2019 

Friesen, ML. 2019.  The switchgrass rhizosphere microbiome and nitrogen transformations on marginal lands. Multi-omics for Microbiomes, July 2019 

Friesen, ML. 2019.  Underground markets in nitrogen-fixing host-symbiont transactions. Microbial Population Biology Gordon Conference, July 2019 

Friesen, ML. 2019. Underground markets in nitrogen-fixing host-symbiont transactions. MIT, Civil and Environmental Engineering, October 2019 

Friesen, ML. 2019. Underground Trade: Interactions between nitrogen and microbes on root traits. Nov 4, 2019: Marco Bittelli, Markus Flury, Tarah Sullivan. Sept 30, 2019: Linda Kinkel & Bill Pan 

Paulitz, T. C. 2019. Soil Health and the Microbial Black Box. Presented invited seminar on soil health at the Western Wheat Workers Conference, Pullman, WA, July 10, 2019. 

Thomashow, L.  2019. Pseudomonas in sustainable agriculture: Models, metabolites and mechanisms. Presented an invited talk at the Pseudomonas 2019 meeting in Putrajaya Malaysia, July 20-27, 2019.

Yin, C., Schlatter, D., Kroese, D., Paulitz, T. and Hagerty, C. 2019.Acid soils in PNW wheat production and impacts on the soil microbiome.  APS Pacific Division meeting, June 27, 2019, Ft. Collins, CO 

Yin, C., Vargas, J. M. C., Schlatter, D. C. Hagerty, C. Hulbert, S. and Paulitz. T. C. 2019.  Rhizosphere community selection reveals bacteria associated with reduced root disease. 18th Congress of International-Society-for-Molecular-Plant-Microbe-Interactions (IS-MPMI), Glasgow, Scotland.

Thesis 

DeGenring, L. 2019. Effect of cultivar and substrate on efficacy of biopesticides to suppress Pythium on greenhouse crops. M.S. Thesis. University of New Hampshire. 

Hsiao, C.-J. 2018. Microbial Properties of Soils: Effects of Management and Pedogenesis. Kansas State University. https://krex.k-state.edu/dspace/handle/2097/39380 

Abstracts 

Becker, J.O., S.T. Koike, Y.Y. Chen, and J. Becker. Exploring the curious rise and fall of nematicide use for broccoli in California. Journal of Nematology 51:5. DOI: https://doi.org/10.21307/jofnem-2019-065 

Chesley, A. and Hao, J. Sensitivity of Phytophthora erythroseptica to oxathiapiprolin. 2019 University of Maine Student Symposium, Cross Insurance Center, Bangor ME, April 10, 2019. 

Chesley, A. and Hao, J. Sensitivity of Phytophthora erythroseptica to oxathiapiprolin. 2019 University of Maine Student Symposium, Cross Insurance Center, Bangor ME, April 10, 2019. 

Ge, T. and Hao, J. Microbial association in blackleg and soft rot of potato. 2019 Northeast Potato Technology Forum, Rodd Hotels & Resorts, Charlottetown, Canada. Mar. 20-21, 2019. 

Ge, T. and Hao, J. Synergistic Effect of co-inoculation with Dickeya dianthicola and Pectobacterium parmentieri on potato. 2019 University of Maine Student Symposium, Cross Insurance Center, Bangor ME, April 10, 2019. 

Ge, T. and Hao, J. Synergistic Effect of co-inoculation with Dickeya dianthicola and Pectobacterium parmentieri on potato. 2019 University of Maine Student Symposium, Cross Insurance Center, Bangor ME, April 10, 2019. 

Hao, J. and Jiang, H. Chemical regulation of zoosporic behavior of Phytophthora erythroseptica. 2019 Northeast Potato Technology Forum, Rodd Hotels & Resorts, Charlottetown, Canada. Mar. 20-21, 2019. 

Jiang, H., Ge, T. and Hao, J. 2019. Impact of signal molecules on Phytophthora erythroseptica for potato infection. Annual Meeting of Northeastern Division of American Phytopathological Society, Penn. State University, State Park, PA. Link: https://www.apsnet.org/members/community/divisions/ne/meetings/Documents/NED-APS_Program-2019_3.pdf. 

Jiang, H., Ge, T., and Hao, J. Impact of signal molecules on Phytophthora erythroseptica for potato infection. Annual Meeting of Northeastern Division of American Phytopathological Society. Days Inn, State College, PA, Apr. 3-5, 2019. 

Li, Y., Liu, Y., Zhu, S., Hao, J., Luo, L., and Li, J. 2019. Functional analysis of transient receptor potential channel in Fusarium solani causing root rot of Panax notoginseng. Annual Meeting of American Phytopathological Society, Cleveland, OH. 

Schlatter, D. C., Hansen, J., Huggins, D. R. Carlson, B., and Paulitz, T. C. 2019. Bacterial communities associated with soil health in wheat.   Phytopathology 109: S2: 151 

Secor, G., Charkowski, A., Hao, J., Johnson, S.B., and McIntosh, C. Integrating next-generation technologies for blackleg and soft rot management in the usa: a progress report. European Association for Potato Research (EAPR) Pathology and Pests Section Meeting, Neuchâtel – Switzerland, Sep. 2-5, 2019. 

Extension Talks/Field Days/Workshops/Consultations 

Adams AK, Rickman TE, Wadl PA, Yencho GC, Olukolu BA (2020) Multipartite interactions involving sweetpotato and its leaf microbiome. National Sweetpotato Collaborators Group Meeting, Nashville, TN. 

Becker, J. O. 58^th Annual Society of Nematologists meeting, Raleigh, NC, July 7-10, 2019. “Exploring the curious rise and fall of nematicide use for broccoli in California.” (poster) 

Becker, J. O. California Statewide Nematology Workgroup, Huntington Gardens, San Marino, March 26, 2019. “Hyalorbilia spp.: potential role in biological disease suppression” (presentation). 

Becker, J. O. Class with 12 graduate students (PLPA 240 Field Plant Pathology), June 3, 2019. “Nematology in Cooperative Extension” (invited presentation, discussion). 

Becker, J. O. Growers, PCAs, and Industry field day, South Coast Research and Extension Center, Irvine, CA, July 29, 2019. “Experiences with novel nematicides.” (presentation and hands-on demonstrations) 

Becker, J. O. Industry and PCA training session, UC South Coast Research and Extension Center, February 19, 2019. “California agriculture and plant-parasitic nematodes” (presentation and hands-on demonstrations) 

Becker, J. O. Plant Pathology Department Seminar, Nanning, Guangxi Province, China, Nov 13, 2019. Management of Plant-Parasitic Nematodes in California: Research & Extension (invited presentation). 

Becker, J. O. Soil-borne Diseases and Nematodes Management Symposium “Toward developing a multifaceted approach to control soil-borne diseases and nematodes”. March 13, 2019. Volcani Center, Tel Aviv, Israel. “Towards a paradigm shift in crop protection against plant-parasitic nematodes.” (invited key-note speaker) 

Becker, J. O. UC Riverside, PLPA 265. Colloquium on the Principles of Plant Pathology, May 1, 2019. “A career in Cooperative Extension.” (invited 1 hrs. lecture w/discussion), ca 30 undergraduate students. 

Becker, J. O. Undergraduate student group from Southwest University, Chongqing, China. Organized by UCR’s International Education Programs. UC Riverside Extension Center, August 2, 2019. “Plant parasitic nematodes in CA Agriculture” (2 hrs. invited presentation with discussion, 20 students). 

Becker, J. O. Visit of nematode field plots by 9 graduate students with Dr. Georgios Vidalakis (PLPA 240 Field Plant Pathology), UC South Coast Research & Extension Center, September 17, 2019. 

Borneman, J. Fraunhofer Institute Visit Meeting in Riverside CA, January 11, 2019. Title: Modeling the Interactions Between CLas, Citrus, and ACP for the Development of HLB Management Strategies 

Borneman, J. Sugarbeet Work Group Meeting, February 8 2019, Holtville CA, Title: Use of Dactylella oviparasitica to Improve the Sugarbeet Cropping Decision Model. 

Borneman, J.  Indigenous Populations of Dactylella oviparasitica Appear to Suppress Cyst Nematode Populations in Several Regions & Crops. Annual Meeting of Western Regional Project W-4147 on Biological Control, December 6 2019, Puyallup, Washington.  Attended via Zoom.

DeGenring, L. Poleatewich, A. Utilizing the power of beneficial microbes in a systems approach to plant disease management. Presentation. New England Tri-State Greenhouse Growers IPM Workshop. Durham, NH. January 2019. 

Ge, T. and Hao, J. Title: “Microbial association in blackleg and soft rot of potato.” Northeast Potato Technology Forum. Rodd Hotels & Resorts, Prince Edward Island, Canada, Mar. 20-21, 2019.

Hao, J. J.  “Updates on blackleg study.” 32^nd Maine Potato Conference, Caribou Inn, ME. Jan. 17-18, 2019. 

Hao, J. J. BASF Field Day. Aroostook Research Farm, Presque Isle, ME. Aug. 20, 2019. 30 attendees. 

Hao, J.J. Title: “Chemical regulation of zoosporic behavior of Phytophthora erythroseptica.” Northeast Potato Technology Forum. Rodd Hotels & Resorts, Prince Edward Island, Canada, Mar. 20-21, 2019. 

Hsiao, C.-J., Sassenrath, G.F., Rice, C.W., Zeglin, L.H. 2018. Long-term fertilization and tillage effects on soil microbial properties with depth. Abstract 111912. American Society of Agronomy Annual Meeting, Nov. 4-7, 2018, Baltimore, MD 

Kristy BD, Gorman MS, Rickman TE, Adams AK, Kuster RD, Olukolu BA (2019). Introducing Qmatey: A Taxonomic Profiler Capable of Robust Microbiome Analysis. Annual STEM Poster Symposium, Knoxville, TN. 

Kristy BD, Olukolu BA (2019). From Soil to Software: Using Computational Tools to Solve Biological Problems. 1794 Honors Capstone Showcase, Knoxville, TN. 

Hao, J. J. Maine Potato Research Field Day, Aroostook Research Farm, Presque Isle, ME. Aug. 20, 2019. 40 attendees. 

Paulitz, T. C.  2019.  Microbial communities in canola and wheat rotations. Washington Oilseeds and Cropping System Meeting. Feb 1, 2019, Pullman, WA. 

Paulitz, T. C.  2019. “Management of Nematode Diseases with Genetic Resistance”.  Washington Grain Commission Research Review, Pullman WA Feb. 20, 2019 

Paulitz, T. C. 2018 “Fusarium crown rot on wheat: Prebreeding and development of tools for genetic disease management”.  Washington Grain Commission Research Review, Pullman WA Feb. 20, 2019 

Paulitz, T. C. 2019.  Biosolids and Soil Microbes. Lind Field Day, Lind, WA June 15, 2019 

Paulitz, T. C. 2019.  What’s behind canola rotation effects; research updates.  Winter Canola Tour, May 30, 2019, Hartline-Almira, WA 

Paulitz, T. C. 2019. “What’s New in Research on Soilborne Plant Pathogens”. Spokane Farm Forum, Ag Expo, Spokane, Washington.   Feb. 6, 2019 

Poleatewich, A. From The Ground Up: How soil-less substrate can affect biocontrol efficacy. Presentation. Canadian Greenhouse Conference. October 2019. 

Sassenrath, G. Precision systems for crop production. Precision Ag Field Day. July 29, 2019 

Sassenrath, G. Radio Interview for Agriculture Today, hosted by Eric Atkinson. April 5, 2019. Mustard cover crop for charcoal rot control. 

Sassenrath, G. Retaking the Field: Science Breakthroughs for Thriving Farms and a Healthier Nation. Volume 4. Applying Alternatives: Leveraging the Soil Microbiome to Fight Disease. 

Sassenrath, G. Soil Health: Profitability. KSU Agronomy 655. May 7, 2019 

Sassenrath, G. Soil Variability and Cover Crops Update. Spring River WRAPS. Feb. 21, 2019 

Sassenrath, G.F., Precision Conservation Management: Targeting Soil Health for Agronomic Profitability. Soil and Water Conservation Society. July 28-31, 2019, Pittsburgh, PA. 

Vannette RL. “Soil management, mycorrhizal fungi and plant-pest interactions” Russell Ranch Field day June 12, 2019 

Wilkerson, T. "Taproot Decline Update" at Mississippi Agriculture Consultants Association Conference, Starkville, MS, Feb. 5, 2019 

Zhao, H., Sassenrath, G., Lin, X. Evaluation of winter wheat phenology models in eastern Kansas. Abstract 112183. American Society of Agronomy Annual Meeting, Nov. 4-7, 2018, Baltimore, MD 

License agreement 

USDA License No. 1787-001 and WSU Case TECH-19/3281, Real-time PCR primers for native yeasts of grape