Location: Crops Pathology and Genetics Research
2019 Annual Report
Objectives
Objective 1: Characterize the spread of trunk pathogens and other wood-infecting
fungi of grape, at the plant, field, and landscape scales. Subobjective 1.A. Evaluate alternative hosts as inoculum reservoirs.
Subobjective 1.B. Define the stages of wood colonization, in terms of the infection process and the plant response to infection.
Objective 2: Identify the physiological and genetic bases of grapevine resistance to abiotic and biotic stresses using a combination of advanced-imaging methods, nucleic acid-based analyses, light and confocal microscopy, and hydraulic physiological measurements.
Subobjective 2.A. Determine how drought stress alters the hydraulic permeability of grapevine root systems and the capacity for hydraulic redistribution among grapevine rootstocks.
Subobjective 2.B. Determine the roles that xylem network connectivity, cavitation, and embolism repair play in drought resistance of grapevine rootstocks.
Objective 3: Characterize the relationship between vineyard floor management practices (including, but not limited to, sustainable weed management) and biogeochemical cycles.
Subobjective 3.A. Quantify greenhouse gas emissions resulting from current vineyard floor management practices, to refine existing biogeochemical models.
Subobjective 3.B. Examine soil microbial communities associated with vineyard floor management, and edaphic and environmental gradients.
Subobjective 3.C. Examine weed communities associated with vineyard floor management, and edaphic and environmental gradients to develop ecologically-based weed control strategies.
Approach
Objective 1, Subojective 1.A. - Compare population genetic diversity, host specificity, and spore dispersal of E. lata among three hosts (grape, apricot, willow), in CA landscape that include vineyards, stonefruit orchards, and riparian areas.
Subobjective 1.B. - Identify unique plant-molecular responses in leaves, which coincide with the early stage of canker development, and to then develop a PCR-based assay for these plant molecular responses for use as an early detection tool.
Objective 2, Subobjective 2.A. - Combine hydraulic physiological measurements with anatomical assessments to determine how stress and rootstock genotype affect the hydraulic permeability of roots.
Subobjective 2.B. - Use HRCT to evaluate the structure and function of grapevine xylem.
Objective 3, Subobjective 3.A. - Assess the effects of pulse events (fertigation or irrigation of equal volumes in the ‘in-row’ region, 70% regulated deficit irrigation; tillage or no tillage in alleys) on CO2 and N2O emissions.
Subobjective 3.B. - Soil samples will be extracted, quantified and pooled to link landscape patterns of soil microbial communities and specific populations (e.g., nitrifiers, denitrifiers) with functions that facilitate winegrape production, specifically transformations that control nutrient availability to plants and GHG emissions.
Subobjective 3.C. - Survey weed communities in the Napa AVA up to 90 existing field sites for which grower interviews and soil data exist.
Progress Report
This report documents progress for bridging project 2032-21220-007-00D and continues research from expired 2032-21220-006-00D. See the old project report for more information.
In support of Objective 1, this research focuses on the most economically important grapevine diseases, with an emphasis on the trunk-disease complex, a worldwide problem. Every vineyard in California is eventually attacked by one or more of the following trunk diseases: Esca, Botryosphaeria dieback, Eutypa dieback, and Phomopsis dieback. Trunk diseases significantly limit the profitable lifespan of California vineyards and are thus one of the main reasons growers must replant entire vineyards on a premature basis. During the rainy season, spores are produced with rain and are then dispersed by rain or wind to infect pruning wounds, where they establish localized, chronic infections (internal cankers) in the wood. The dieback-type trunk diseases (Botryosphaeria dieback, Eutypa dieback, and Phomopsis dieback) kill the positions on the woody part of the vine canopy from which shoots are trained, which result in yield losses over time, and thus the productive life of the vineyard decreases. Esca causes a broader range of symptoms and has more variable impacts, ranging from improper ripening and subsequent poor wine quality to total vine collapse (apoplexy). Given the high start-up costs to plant vines in California ($15,000 to $30,000 per acre), preventing infection, on a routine basis starting with young vines, is expected to maximize the vineyard’s lifespan. One preventative practice is to delay pruning from December until February or later, when the period of pruning-wound susceptibility is shorter. Another approach is to apply a fungicide (protectant) to protect pruning wounds before rain. Once infections are established, however, and the symptoms become apparent months to years later, the only way to eradicate trunk pathogens is to physically cut out infected wood, a practice known as vine surgery or trunk renewal. This approach involves cutting off the vine at the base of the trunk (above the graft union) and retraining a new shoot into a new canopy. It is a labor-intensive practice that removes a vine from production for the three years it takes to retrain a new canopy, but with the help of an established root system, vines return to full production much faster than a replant would. Indeed, our economic models suggest that performing vine surgery before disease incidence reaches levels of 75 percent, typically by year 15, is a cost-effective strategy. If pruning wounds are not the main infection court, then our field trials will fall short of providing an adequate test of protectants. Similarly, if trunk pathogens are present below the graft union, then performing vine surgery will not clear vines of infection. As such, research projects established this year focused on addressing research questions on mixed infections, spore production, and infection courts, which will help fill these gaps for two of the most common trunk diseases in California and other grape-producing states of the U.S., Esca and Phomopsis dieback. A potential outcome of this objective is, thus, more effective disease management.
In support of Objective 2, which focuses on implementing deficit irrigation effectively, growers must plant grapes that better tolerate drought stress, and they need new technologies to better-quantify water use, for day-to-day irrigation scheduling. A major focus of the research is to develop precision-irrigation tools, which are tailored to the physiological responses to drought stress by the different rootstocks in accordance with the concept of genotype x environment x management. Fine roots of drought-tolerant rootstocks were found to focus their physiological resources towards the growing root tip during drought, presumably in an attempt to access soil moisture. ARS researchers in Davis, California, also worked with other ARS, university, and industry stakeholders on the project ‘Grape Remote-sensing Atmospheric Profile and Evapotranspiration eXperiment (GRAPEX)’ to evaluate a multi-scale remote sensing-based modeling system for vineyards. Physiological, micrometeorological, and biophysical data were collected throughout key stages of the growing season in vineyards throughout California. These plant data from the field coincided with the collection of airborne and satellite data. Refinements to water-use models, based on GRAPEX, are now being implemented at the field scale; this generates real-time data for growers to schedule irrigations. This team also conducted an experiment to evaluate how structural changes in leaves under drought stress can alter our interpretation of sensor measurements.
In support of Objective 3, ARS scientists collaborated with the Natural Resource Ecology Laboratory at Colorado State University of Fort Collins. DayCent, a biogeochemical model, was expanded in FY18 to accommodate grapes and other California specialty crops. These specialty-crop modules are part of CARBON management Evaluation Tool (COMET) COMET-Farm and COMET-Planner, tools used by the USDA-National Resources Conservation Service (NRCS) to assess greenhouse-gas footprints and, furthermore, support incentive-based grower programs. COMET-Planner modules for specialty crops also were used by stakeholders engaged in the Healthy Soils Program (California Department of Food and Agriculture). ARS scientists in Davis, California, posted a new report on the USDA California Climate Hub website documenting the role of conservation practices in reducing greenhouse-gas emissions and improving soil-carbon storage. The report presents total greenhouse-gas emissions from tillage, cover cropping, fertilization, and irrigation, based on calculated emission factors. Growers and policymakers alike can thus prioritize which practices best reduce greenhouse gas-emissions and improve soil health. Along similar lines, experimental work in different wine-grape regions of California revealed that cover crops, compost, and no-till practices build healthier soils. These long-term outcomes demonstrate to growers the value of adopting such practices.
The USDA Climate Hub program continues to fulfill its mission by developing region-specific, science-based resources, which enable climate-informed decision-making and supporting greater adaptive capacity for California’s agricultural and forestry systems. The California Climate Hub addresses producer-specific concerns related to drought, water efficiency, extreme heat, and other climate-mediated stressors/disturbances. This program has outreach as a focus, and is not restricted to any one crop or even to agriculture alone; our work spans specialty crops, rangelands, and forestry. Further, regular communication with federal, state, private sector, and academic partners helps leverage our efforts. This year, we completed and published a vulnerability assessment for California rangelands, specifically for use by livestock producers. In partnership with University of California Cooperative Extension, the National Drought Mitigation Center, USDA-Natural Resource Conservation Resources, and USDA-Risk Management Agency (RMA), The California Climate Hub developed and hosted four workshops across the state for livestock producers to have a behind-the-scenes look at the U.S. Drought Monitor, and an overview of local, state, and federal drought programs, weather monitoring and forecast products, and drought early-warning systems. In collaboration with the USDA-Foreign Agricultural Service (FAS), Cornell University, and Eco Agriculture Partners, The California Climate Hub created a six-module Climate Smart Agriculture curriculum for mid-level government officials. The California Climate Hub is leading the outreach and extension portion of a multi-organization research and demonstration project, funded by the California Strategic Growth Council. The objective of this Council is to evaluate various soil amendments for meeting greenhouse gas-mitigation goals. For forest managers and scientists who attended the two large symposia we organized (>200 participants each), there were presentations on the most current science to date on reforesting practices in a changing world. The California Climate Hub co-chair, the Forest Management Task Forces’ Science Advisory Panel, helped guide actions that support forest management, backed by California Climate Investments – of which other USDA agencies were engaged (namely USDA-U.S. Forest Service and USDA-Natural Resources Conservation Services).
Accomplishments
1. Evaluated surface renewal technology and radiation models for effectiveness in quantifying vineyard water use. Surface renewal (SR) uses high-frequency air temperature measurements above a plant canopy to estimate heat exchange processes, which allows for estimation of crop evapotranspiration (ET; i.e., crop water use). SR previously relied on calibration against other complicated methods (e.g., eddy covariance) to obtain accurate measurements of sensible heat flux, and this need for calibration limited the use of SR to research applications. In collaboration with University of California, Davis, researchers and industry cooperators, ARS researchers in Davis, California, developed an inexpensive, stand-alone SR system to estimate ET in from SR using measured and modeled energy balance components with those from a weighing lysimeter and the Grape Remote-sensing Atmospheric Profile and Evapotranspiration eXperiment (GRAPEX) project. Vineyard ET measured with SR was strongly and positively correlated with that of the lysimeter, eddy covariance, and a soil water budget approach in both research settings. A stress index, calculated using reference and actual ET from SR and lysimetry, was correlated to direct measurements of plant stress and volumetric soil water content measurements. The results suggest that the new SR method could provide growers with low-cost, site-specific estimates of crop water use for scheduling irrigation.
2. Pruning-wound protectants tested for managing trunk diseases in Washington vineyards. ARS researchers in Davis, California, surveyed Washington state wine-grape vineyards for Esca pathogens, as no published work has yet been done on grapevine trunk diseases in Washington, the U.S. state with the second highest grape production. The survey identified the fungi of unknown pathogenicity Cadophora margaritata and Flammulina velutipes from symptomatic vines, along with known pathogens Phaeomoniella chlamydospora and Phaeoacremonium minimum. These latter two fungi, the pathogenicity of which is unknown, are being evaluated on potted grapes in the greenhouse. ARS scientists in Davis, California, also established a field trial to test the efficacy of pruning-wound protectants, as none are registered for management of Esca or any other trunk disease in Washington. Because the high-desert climate of the State of Washington’s wine-grape region is different from that of California’s regions, it is important to determine if different species of pathogens are involved with Esca. The field trial may provide efficacy data to help register fungicides in the State of Washington, to help protect vines from infection by trunk pathogens.
Review Publications
Baumgartner, K., Hillis, V., Lubell, M., Kaplan, J. 2019. Managing grapevine trunk diseases in California’s southern San Joaquin Valley. American Journal of Enology and Viticulture. 70:267-276. https://doi.org/10.5344/ajev.2019.18075.
Galarneau, E.R., Lawrence, D.P., Travadon, R., Baumgartner, K. 2019. Drought exacerbates Botryosphaeria Dieback symptoms in grapevines and confounds host-based molecular markers of infection by Neofusicoccum parvum. Plant Disease. 103(7):1738-1745. https://doi.org/10.1094/PDIS-09-18-1549-RE.
Parry, C.K., Nieto, H., Guillevic, P., Agam, N., Kustas, W.P., Alfieri, J.G., McKee, L.G., McElrone, A.J. 2019. An intercomparison of radiation partitioning models in vineyard canopies. Irrigation Science. 37(3):239-252. https://doi.org/10.1007/s00271-019-00621-x.
