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Research Project: Resilient, Sustainable Production Strategies for Low-Input Environments

Location: Crops Pathology and Genetics Research

2024 Annual Report

Objectives
Objective 1: Develop crop production strategies that integrate water and nutrient input management and the environment for healthy, sustainable vineyards. [NP 305, Component 1, Problem Statement 1B] • Subobjective 1.A. Characterize varied responses of grapevine genotypes to drought in order to improve detection and interpretation of water stress signals for local and remote proximal sensors and to develop precision irrigation techniques tailored to genotype- specific root responses. • Subobjective 1.B. Determine the molecular basis associated with the differential responses to drought stress among grapevine genotypes. • Subobjective 1.C. Identifying threshholds for organoleptic volatile phenols and their glycosidically-bound derivatives in wine grape varieties exposed to smoke taint across different growing regions. Expected benefits include standardized chemical analyses of smoke taint compounds in exposed and unexposed vineyards for the wine varietals growing in CA, OR, and WA with the goal of identifying and quantifying genotype-specific environmental threshold levels. Objective 2: Analyze the interaction of soil health and vineyard floor management for the enhancement of vine and fruit quality. [NP 305, Component 1, Problem Statement 1B] • Subobjective 2.A. Determine relationships among soil and grape must microbiomes and their structure in the wine grape production system. Objective 3: Develop improved strategies for controlling grapevine disease using preventative and post-infection management strategies. [NP 305, Component 1, Problem Statement 1B] • Subobjective 3.A. Characterize the role of wood-decay fungi in trunk diseases, to develop post-infection practices that return vines to productivity. • Subobjective 3.B. Identify when trunk pathogens sporulate and the infection courts by which they infect, to develop preventative practices that protect susceptible host tissues.

Approach
The approaches for each objective range from experimentation under controlled conditions in the greenhouse to experimentation under natural field conditions, with commercial vineyards making up the majority of field study sites. Prior to hypothesis testing, some level of methods development (e.g., imaging water flowing through the vessels of living plants, pathogen detection from environmental samples of microscopic spores) is required for each objective, in part because grape is not a model study system. For objective 1, parallel sets of physiological experiments are focused on measuring anatomical, physiological, and transcriptional responses of leaves and fine roots, under normal levels of irrigation versus under drought stress. Whole plants of Vitis vinifera wine-grape varieties (Cabernet-Sauvignon, Chardonnay) and rootstocks with differential drought tolerance will be examined by X-ray microCT, followed by sections of leaves and roots examined by transmittance electron microscopy and Laser Capture Microdissection. RNA-seq techniques will then be used to seek out transcriptional differences at a molecular scale. For Sub-Objective 1.C.-The approach will combine field experimentation in the vineyard, winemaking and distilling processes in the experimental winery, and laboratory analyses of smoke-related compounds using, for e.g., gas chromatography/mass spectrometry (GC/MS). Compositional changes in the fruit of different cultivars, with exposure to smoke, will be characterized and quantified. Smoke-related compounds in wines made from the smoke-exposed fruit will also be characterized and quantified. Grape and wine quality analytical methods will be developed to detect key smoke-related compounds in the fruit and the wine, and acceptable limits will be established. Further, endproduct processing methods will be developed to help mitigate such compounds. For objective 2, the interaction of host genotype by environment (soil and climate, specifically) by management is examined. High-throughput amplicon sequencing of soil fungi and bacterial communities will be used to compare those of vine rows under different floor-management practices. Samples from the must will evaluate whether vineyard floor management practices impact the microbiome during fermentation. Diffuse reflectance Fourier transformed mid-infrared spectroscopy (DRIFTS) will be used to characterize changes in SOM chemical composition in particulate organic matter and other soil C fractions. For objective 3, inoculations of potted plants in the greenhouse will be used to test hypotheses at the plant scale about which combinations of pathogens and sequences of infection cause disease symptoms, and also about how differential tissue susceptibility affects whether an infection spreads throughout an individual plant. At the vineyard scale, spore trapping in diseased vineyards and evaluations of pruning-wound susceptibility will be used to determine when grapevines are at greatest risk of infection.

Progress Report
This report documents progress for project 2032-21220-008-000D "Resilient, Sustainable Production Strategies for Low-Input Environments", which started in March 2020 and continues research from 2032-21220-007-000D, "Sustainable Vineyard Production Systems". The project objectives focus on grapes and, to a limited extent, two other woody perennial crops in California (walnut, almond). The deliverables include labor-saving practices for preventing grapevine trunk diseases and technology to give growers precise measurements of water-use in real-time. Scientific advances are also an important outcome of the project, with development of novel study tools for researchers to examine the physiological bases of drought tolerance in grape rootstocks and the diversity of microbes originating in the vineyard that contribute to the fermentation of wine. The project also addresses the complex impacts of global climate change on California agriculture, namely wildfires, drought, changing rainfall patterns, less irrigation water, lower quality water, and heatwaves. In support of Sub-objective 1A, ARS researchers in Davis, California, in collaboration with colleagues from other ARS locations, universities, and industry partners, continued efforts to develop better measurements of crop water-use and stress with ground-based and remote sensing tools in commercial vineyards and orchards in California. Towers and sensor arrays replicated across varied growing regions for the Grape Remote-sensing Atmospheric Profile and Evapotranspiration eXperiment (GRAPEX) and Tree crop Remote Sensing of Evapotranspiration eXperiment (T-REX) projects were maintained throughout the year to measure water and carbon dioxide (CO2) exchange from these agroecosystems. Intensive ground-based efforts were conducted to assess the resilience of these acro-ecosystems to heat stress during increasingly intense and prolonged heat waves. Ground-based physiological, micrometeorological, and biophysical data, including lidar scanning, were collected to link physiological and stress responses at the leaf level to that of the whole canopy. This helps assure that measurements taken at various spatial scales, from one leaf to the whole vineyard, will reflect the stress status of a crop grown in different locations or even on different continents. In support of Sub-objective 1B, ARS researchers in Davis, California, successfully completed an experiment on drought-stress of grapevine. Three drought-sensitive rootstock genotypes (Riparia Gloire, 101-14, 420 A) and three drought-resistant genotypes (110R, 140 Ru, 1103 P) were selected for the drought stress test. These plants were grown in controlled conditions in an aeroponics system for approximately two months. When their roots reached 15 to 20 cm in length, plants were subject to drought stress by exposure to air for three hours, and then total RNA was extracted and purified from their roots. Transcriptomic profiling through high-through put RNA sequencing was completed, and gene-expression analysis is in progress to identify the gene-regulatory pathways in the genotypes that are related to drought sensitivity or resistance. Regulatory transcription factors that may play roles in tolerance were identified. These regulatory genes are very similar to those characterized in Myrothamnus flabellifolia (commonly known as ‘Resurrection Plant’), which is extremely resistant. These transcription factors identified from resistant grape rootstocks could serve as molecular markers to identify sources of tolerant germplasm and also to develop management practices for drought stress. For Sub-objective 1C, ARS researchers in Davis, California, constructed a ‘smoking chamber’ to experimentally expose grapes to smoke in a reproduceable manner, and then tested how different levels of smoke exposure bring about production of chemical compounds responsible for smoke taint of wine. Grapes of European wine grape cultivar Vitis vinifera ‘Cabernet-Sauvignon’ that were exposed to various amounts of smoke were later made into wines. There was a positive correlation between smoke intensity, concentrations of smoke-derived compounds (volatile phenols), and ‘smoky’ and ‘meaty’ aromas in both grapes and wines. ‘Fruity’ aromas were less detectable in wines from grapes with higher levels of smoke exposure, suggesting that the presence of smoke-derived compounds suppresses the former. Future experiments will focus on specific volatile phenols, to characterize thresholds that are associated with unfavorable sensory characteristics of wine. In support of Sub-objective 2A, ARS researchers in Davis, California, examined the spatial distribution of soil microbial communities in 15 Vitis vinifera ‘Pinot noir’ vineyards, spanning a region from southern Oregon to southern California. Soil was collected from the alleys, the vine rows (irrigated soil) and between the rows (non-irrigated soil). Soil microbial communities differed by soil type, management, and production region. Characterizing the interactive effects of soil type, climate, and microbial communities may help identify better strategies for managing the soil to promote soil health and microbial function, depending on where a vineyard is located. For Sub-objective 3A, ARS researchers in Davis, California, and Geneva, New York, developed a phenotyping assay for Phomopsis cane and leaf spot, which attacks all tissues of green shoots (leaves, stems, grapes) and woody tissues (stem/cane, cordon, trunk) of the vine, when spores of the causal fungus Diaporthe ampelina spread with spring rains. The fungus overwinters in infected green stems that mature into woody canes. Infected canes that are not pruned off during the dormant season serve as a source of inoculum for new green tissues the following spring. To determine how best to identify resistant germplasm, the fungus was inoculated to green stems and woody stems of hybrid grapes, resulting from a cross of European wine-grape Vitis vinifera ‘Chardonnay’ and North American species Vitis cinerea B9. Not all plants had consistent phenotypes between the two stem types. Given that the fungus can colonize both green and woody stems, evaluating resistance of both stem types can help identify progeny of future crosses, and can inform management decisions of which tissues to protect from infection.

Accomplishments
1. Characterizing the molecular biology of drought stress in grape. An ARS researcher in Davis, California, identified drought stress-induced transcription factors from grapevine rootstocks, which were similar to those of Myrothamnus flabellifoli (‘Resurrection plant’), an extremely drought and salt-resistant species. Plants have evolved sophisticated regulatory mechanisms for managing water stress. Regulatory proteins, such as transcription factors, play critical roles in plant resistance to drought stress and other adverse conditions. These results will help develop molecular markers to identify grape germplasm and practices for managing drought stress.

2. Wildfire smoke can affect the chemical composition of grapes, which in turn negatively impacts the sensory characteristics of a wine. Current detection methods to measure smoke-derived compounds are costly and time consuming; therefore, alternative methods are needed to measure smoke marker compounds in grapes and wines. An ARS researcher in Davis, California, in collaboration with researchers from University of California, Davis, and Clarkson University, Potsdam, New York, identified cerium oxide nanoparticles (nanoceria) as a possible detection tool to measure smoke-derived compounds (volatile phenols) in grapes. Nanoceria reacted with all volatile phenols that are currently known to be present in smoke-exposed grapes. In addition, researchers identified diffusive passive samplers as an alternative detection tool that can accurately predict the concentrations of select smoke marker compounds in grapes and wines. This research will provide an inexpensive, quick, and robust detection method, allowing growers to decide whether to harvest smoke-exposed grapes for wine production.

3. Identified unique hyperspectral reflectance patterns of asymptomatic grapevines with trunk diseases. ARS researchers in Davis, California, demonstrated that the asymptomatic leaves of grapevines with trunk diseases had different hyperspectral reflectance patterns. Detection of trunk diseases is confounded by the multi-year delay between infection of the pruning wounds by spores of the causal fungi and the first appearance of leaf symptoms. We evaluated a hyperspectral camera (Pika XC2, Resonon) to detect hyperspectral reflectance of asymptomatic leaves (wavelengths of 400 to 1,000 nm) for three months, on potted grapevines inoculated with fungi that cause Botryosphaeria dieback (Neofusicoccum parvum) or Esca (Phaeomoniella chlamydospora, Tropicoporus texanus), with non-inoculated plants as controls. Throughout the three months of the assay, leaves were asymptomatic, in spite of lesions that spread three to five cm from the inoculation site in the woody stem. Wavelengths detected from the leaves of inoculated plants had higher reflectance than that of the controls were identified within the visible and near infrared spectra, depending on the pathogen. A hyperspectral camera could be useful as a non-destructive detection tool for scanning the leaves of plants in the nursery, in order to identify and remove plants contaminated by fungi that cause trunk diseases.

4. Discovered that grape xylem collapses under mild drought stress preventing water loss from young leaves during dry atmospheric conditions. Grape growers often utilize deficit irrigation to enhance fruit quality, while conserving water. However, water stress induced by deficit irrigation can increase grapevine susceptibility to heat stress because their leaves have a lower capacity for transpirational cooling. Using X-ray imaging, an ARS researcher in Davis, California, in collaboration with university researchers, found that the water-conducting cells in leaves collapse under mild drought stress to prevent water loss. Collapse occurred more frequently in young versus fully developed leaves and may be associated with shoot tip dieback seen in grapevines at the onset of water stress. Understanding how leaves and shoots respond to water stress enables more precise ground-based and remote-sensing systems to monitor irrigation strategies under a range of climatic conditions.

5. Revealed barriers to adoption of soil management practices that improve soil health in California wine-grape vineyards. Adoption of soil management practices, such as cover cropping and no-till, is often rare in California wine-grape vineyards. ARS scientists in Davis, California, collaborated with university researchers to assess wine grape growers’ perceptions of soil health and to understand how these might influence behavior related to adoption of soil management practices. The main barriers for adoption and maintenance of soil health practices were high costs, potential economic risks, and lack of information on how these practices might influence grape yields, growth, and nutrition. Most growers were willing to adopt more soil health practices if practical information was available on outcomes of adoption, especially economic benefits. This novel study has impacted outreach activities to better communicate with wine grape growers in building and protecting soil health while achieving viticultural goals.

U.S. DEPARTMENT OF AGRICULTURE

Crops Pathology and Genetics Research: Davis, CA