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

Location: Crops Pathology and Genetics Research

2021 Annual Report

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.

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 2032-21220-008-00D Resilient, Sustainable Production Strategies for Low-Input Environments, which started in March 2020 and continues research from 2032-21220-007-00D Sustainable Vineyard Production Systems. A major focus of Sub-objective 1A is to develop precision-irrigation tools and to identify new and existing cultivars and rootstocks, which better tolerate drought stress. In support of Sub-objective 1A, ARS researchers in Davis, California, in collaboration with researchers at University of California, Davis, found that a standard and simple similar physiological analysis (i.e., pressure volume curves) can be used to differentiate the responses of commercial grapevine rootstocks to drought stress. This new application was applied in controlled experimental conditions and compared with x-ray imagery across several genotypes to evaluate their relative drought resistance. ARS researchers in Davis, California, in collaboration with a team of other ARS, university, and industry partners, continued work on the multi-scale, remote sensing-based modeling system for California vineyards ‘Grape Remote-sensing Atmospheric Profile and Evapotranspiration eXperiment (GRAPEX)’. Physiological, micrometeorological, and biophysical data were collected at the plant scale, along with airborne and satellite data at the vineyard scale in order to validate these new tools. This experiment was expanded to almonds with the establishment of the Tree crop Remote sensing of Evapotranspiration eXperiment (T-REX) project in several commercial orchards. This team also installed a Solar-Induced Fluorescence (SIF) tower in the GRAPEX site to identify stress related to both drought and heat waves in order to improve precision of scheduled irrigation practices. Data from a controlled drought experiment were used to verify SIF measurements in potted plants as well. In support of Sub-objective 1B, ARS researchers in Davis, California, developed an aeroponic system to efficiently grow grapevines for molecular studies on drought stress resistance by different varieties. Experiments progressed to identify a few genes that potentially regulate root system architecture, which could enhance drought resistance. These genes could be used as genome-editing targets using the CRISPR/CAS9 technology (Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9) and could serve as the molecular markers for screening drought stress resistance in different grape genotypes. For Sub-objective 2A, ARS researchers in Davis, California, examined the relationship between microbial communities in vineyard soil and during fermentation, with samples from 15 Vitis vinifera ‘Pinot noir’ vineyards, which are located along a transect extending from southern Oregon to southern California. An outcome of this research is to cultivate a soil microbial community that maximizes wine quality. Microbial samples were collected from soil from under the vinerows (in the irrigated ‘drip zone’) and in between the rows, and from fermenting grape juice at three days after the onset of fermentation and just prior to addition of yeast. The roles of management histories and climatic conditions were used to determine the interactive effects of climate, vineyard management, soil microbes, and juice microbes on the chemical composition of the juice, namely compounds that are indicative of wine quality. Soil microbe metagenomes will be sequenced in summer 2021 to reveal how desirable soil microbe functions can be manipulated by vineyard management practices. In support of Objective 3, ARS researchers in Davis, California, sequenced the genomes and transcriptomes of five wood-decay fungi that cause the grapevine trunk disease, Esca, in California and Texas. This research is, in the short term, valuable for researchers, who are tasked with determining when and how these five species infect vines. In the long term, this research is valuable for growers and nurseries, who do not currently have management strategies for these pathogens. Further, promising results from a field study on trunk-disease pathogens common in Washington vineyards, namely the Cytospora-dieback pathogen, Cytospora viticola, helped facilitate registration of the fungicide thiophanate-methyl in Washington for dormant-season applications to manage trunk diseases.

1. A new and rugged ground-based method estimates crop water use. Farmers in the drought-stricken western United States require better tools to improve precision irrigation management. Reliable ground-based sensors can complement efforts to quantify crop water use and stress remotely with satellites and drones. ARS researchers, along with University of California, Davis, collaborators, have found a way to utilize rugged infrared temperature sensors to measure crop water use and stress down to the single plant level. This new method determines crop water use by measuring changes in the crop temperatures captured every second that represent the energy required to evaporate water that is lost by the plant’s leaves to the air. Effectiveness of the new method was shown in vineyards and tree crop orchards by comparing measurements against gold standard, research grade methods. This breakthrough may enable the use of these durable, readily available sensors to improve precision irrigation management.

2. Characterization of fungal and bacterial microbiomes in grape must demonstrates unique identity based on vineyard location. Similar to soil microbiomes in wine grape vineyards, grape must (i.e., juice resulting from the freshly crushed fruit) microbiomes of ‘Pinot noir’ reflect their place of origin. ARS researchers in Davis, California, along with University of California, Davis, collaborators, demonstrated that grape must microbiomes in ‘Pinot noir’ measured for two production seasons in Oregon and California possess a unique identity reflective of growing region and climate. Differential abundances of specific microbial groups varied with vintage, growing season precipitation, and fruit maturity metrics. Bacterial microbiomes were most strongly influenced by precipitation and their dispersal was not limited by distances between vineyard or region. In contrast, fungal microbiomes were structured by precipitation and growing degree days and experienced dispersal limitation, indicating that the local vineyard itself was a source for abundant fungal taxa. Long-term outcomes from this work include identification of vineyard management practices and abiotic conditions that can be adjusted to manipulate the fungal and bacterial microbiomes to elicit desired grape production results.

3. Effective management of Cytospora dieback now exists for Washington wine grapes. Grape-growers in Washington now have management tools for grapevine trunk diseases. ARS researchers in Davis, California, tested two fungicides in eastern Washington, against fungal species and isolates from Washington vineyards, which were first shown in greenhouse studies to be virulent pathogens. One application of thiophanate-methyl after pruning was the most effective treatment, based on consistently lower detection rates of Cytospora-dieback pathogen, Cytospora viticola, and Esca pathogen, Phaeomoniella chlamydospora, compared to those of unprotected controls. In 2021, thiophanate-methyl was labeled for dormant-season applications against trunk diseases in Washington wine grapes. Given that Cytospora viticola appears to be a common pathogen, based on a survey of Washington vineyards, availability of thiophanate-methyl gives Washington growers the opportunity to adopt preventative practices against trunk diseases in both young, healthy vineyards and after pruning in mature vineyards.

Review Publications
Steenwerth, K.L., Morelan, I.A., Stahel, R.J., Figueroa-Balderas, R., Cantu, D., Lee, J., Runnebaum, R.C., Poret-Peterson, A.T. 2021. Fungal and bacterial communities of ‘Pinot noir’ must: effects of vintage, growing region, climate, and basic must chemistry. PeerJ. 9. Article e10836.
Miller, M., Roddy, A., Brodersen, C.R., McElrone, A.J., Johnson, D. 2020. Anatomical and hydraulic responses to desiccation in emergent conifer seedlings. American Journal of Botany. 107(8):1177-1188.
Ingel, B., Reyes, C.R., Massonnet, M., Boudreau, B., Sun, Y., Sun, Q., McElrone, A.J., Cantu, D., Roper, M. 2020. Xylella fastidiosa causes transcriptional shifts that precede tylose formation and starch depletion in xylem. Molecular Plant Pathology. 22(2):175-188.
Théroux-Rancourt, G., Roddy, A., Earles , J.M., Gilbert , M., Zwieniecki, M., Boyce, K., Tholen, D., McElrone, A.J., Simonen, K., Brodersen, C.R. 2021. Maximum CO2 diffusion inside leaves is limited by the scaling of cell size and genome size. Proceedings of the Royal Society B. 288. Article 20203145.
Chen, J., Li, Y., Li, Y., Ji, Y., Wang, Y., Jiang, C., Choisy, P., Xu, T., Cai, Y., Pei, D., Jiang, C., Gan, S., Gao, J., Ma, N. 2021. AUXIN RESPONSE FACTOR 18–HISTONE DEACETYLASE 6 module regulates floral organ identity in rose (Rosa hybrida). Plant Physiology. 186(2):1074-1087.
Cheng, C., Yu, Q., Wang, Y., Wang, H., Dong, Y., Ji, Y., Zhou, X., Li, Y., Jiang, C., Gan, S., Zhao, L., Fei, Z., Gao, J., Ma, C. 2021. Ethylene-regulated asymmetric growth of the petal base promotes flower opening in rose (Rosa hybrida). The Plant Cell. 33(4):1229-1251.
Dong, T., Yu, C., Li, G., Zhu, Z., Zhang, S., Jiang, C., Wang, Q. 2021. A novel aspartic protease inhibitor inhibits the enzymatic browning of potatoes. Postharvest Biology and Technology. 172. Article 111353.
Knipfer, T., Bambach, N., Hernandez, M.I., Bartlett, M.K., Sinclair, G., Duong, F., Kluepfel, D.A., McElrone, A.J. 2020. Predicting stomatal closure and turgor loss in woody plants using predawn and midday water potential. Plant Physiology. 184(2):881-894.
Theroux-Rancourt, G., Jenkins, M.R., Brodersen, C.R., McElrone, A.J., Forrestel, E.J., Earles, J.M. 2020. Digitally deconstructing leaves in 3D using X-ray microcomputed tomography and machine learning. Applications in Plant Sciences. 8(7). Article e11380.
McElrone, A.J., Manuck, C., Patakas, A., Pearsall, K.R., Brodersen, C.R., Williams, L.E. 2021. Functional hydraulic sectoring in grapevines as evidenced by sap flow, dye infusion, leaf removal, and micro-computed tomography. AoB Plants. 13(2). Article plab003.
Meeker, E.W., Magney, T.S., Bambach, N., Momayyezi, M., McElrone, A.J. 2020. Modification of a gas exchange system to measure active and passive chlorophyll fluorescence simultaneously under field conditions. AoB Plants. 13(1). Article plaa006.
Albuquerque, C., Scoffoni, C., Brodersen, C., Buckley, T., Sack, L., McElrone, A.J. 2020. Coordinated decline of leaf hydraulic and stomatal conductances under drought is not linked to leaf xylem embolism for different grapevine cultivars. Journal of Experimental Botany. 71(22):7286-7300.
Reingwirtz, I., Uretsky, J., Cuneo, I.F., Knipfer, T.M., Reyes, C., Walker, A.M., McElrone, A.J. 2021. Inherent and stress-induced responses of fine root morphology and anatomy in commercial grapevine rootstocks with contrasting drought resistance. Plants. 10(6). Article 1121.
Bouda, M., Windt, C., McElrone, A.J., Brodersen, C. 2019. In-vivo pressure gradient heterogeneity increases flow contribution of small diameter vessels in grapevine. Nature Communications. 10. Article 5645.
Wason, J., Bouda, M., Lee, E.F., McElrone, A.J., Phillips, R.J., Shackel, K.A., Matthews, M.A., Brodersen, C. 2021. Analysis of embolism spread in microCT-derived xylem networks of grapevines. Plant Physiology. 186(1):373-387.
Xiang, X., Chen, J., Xu, W., Qiu, J., Song, L., Wang, J., Tang, R., Chen, D., Jiang, C., Huang, Z. 2021. Dehydration-induced WRKY transcriptional factor MfWRKY70 of Myrothamnus flabellifolia enhanced drought and salinity tolerance in Arabidopsis. Biomolecules. 11(2). Article 327.
Garcia, J., Lawrence, D.P., Morales-Cruz, A., Travadon, R., Minio, A., Hernandez-Martinez, R., Rolshausen, P.E., Baumgartner, K., Cantu, D. 2021. Phylogenomics of plant-associated Botryosphaeriaceae species. Frontiers in Microbiology. 12. Article 652802.
Cuneo, I., Barrios-Masias, F., Knipfer, T., Uretsky, J., Reyes, C., Lenain, P., Brodersen, C., Walker, M., Mcelrone, A.J. 2020. Differences in grapevine rootstocks sensitivity and recovery from drought are linked to fine root cortical lacunae and root tip function. New Phytologist. 229(1):272-283.
Hugalde, I., Aguero, C.B., Barrios-Masias, F., Romero, N., Nguyen, A.V., Riaz, S., Piccoli, P., Mcelrone, A.J., Walker, M., Vila, H. 2020. Modeling vegetative vigour in grapevine: Unraveling implicated mechanisms. Heliyon. 6(12). Article e05708.
Parry, C.K., Shapland, T.M., Williams, L.E., Calderon-Orellana, A., Snyder, R.L., Kyaw, T., McElrone, A.J. 2019. Comparison of a stand-alone surface renewal method to weighing lysimetry and eddy covariance for determining vineyard evapotranspiration and vine water stress. Irrigation Science. 37:737-749.
Dayer S., Reingwirtz I., McElrone A.J., Gambetta G.A. 2019. Response and recovery of grapevine to water deficit: from genes to physiology. In: Cantu D., Walker M., editors. The Grape Genome. Compendium of Plant Genomes. Cham, Switzerland: Springer. pp. 223-245.
Griggs, R.G., Steenwerth, K.L., Mills, D.A., Cantu, D., Bokulich, N.A. 2021. Sources and assembly of microbial communities in vineyards as a functional component of winegrowing. Frontiers in Microbiology. 6(12). Article e05708.