Progress 03/01/19 to 02/29/24
Outputs
Target Audience:We have reached all of our three main target audiences during this project: Scientists working in areas of ecology, evolutionary biology, agroecology, and pest management. This audience was reached through publications, direct communication, and conference presentations. Agricultural stakeholders including apple growers, pest management professionals, cider makers, and consumers. This audience was reached primarily through industry conferences, public presentations, demonstrations at our research orchard, and direct communication with the grower-participants in our study (21 orchards). Trainees including undergraduate students and graduate students that are working directly on the project or are in courses taught by the faculty. Changes/Problems:Work on this project wassignificantly impacted by COVID-19 and related university closures, travel restrictions, and personnel challenges.Our laboratories at Virginia Tech were closed for research from March-May 2020 and operated under very limited capacity from May 2020 to May 2021 (one person at a time in the lab,no undergraduates allowed in laboratories, shared equipment use restricted). No travel was allowed to field sites outside of Blacksburg, VA, which caused us to significantly shift our timeline for this project. Our project was proposed as a five year project, largely to allow our new research orchard to be planted and enter production prior to our planned experiments. We originally planned to focus on our observational work in commercial orchards (Obj. 1) in years one and twoof the project, followed by more experimental work in the orchard (Obj. 2) in years three and four. Unfortunately, as a result of COVID-19we were unable to complete our Obj. 1 orchard surveys until the fourth year of our five year project. Our method development in the laboratory was also significantly delayed. Eventually, we were able to successfully complete all major data collection efforts proposed for the project, but theshifts in timeline as a result of COVID-19 have meant that some of our key scientific publications resulting from the work are still in the pipeline. We expect to finalize those publications over the next year. We also experienced a series of personnel challenges with our project. First, the named post-doc on our award in the Knight Lab, SeJin Song, who was also heavily involved in the proposal development, took another position early in the first year of the project. Because our budget only supported part of her salary, this created a challenge with recruiting a new post-doc with appropriate expertise and interest in the work. Meanwhile, at Virginia Tech, we originally planned to spearhead most data collection efforts with graduate students, butCOVID-19 affected our recruiting of new graduate students for Fall 2020 (in both the Whitehead and Stewart Laboratories).We re-budgeted the award to partially fund a post-doc in the Whitehead Labinstead of a graduate student, and successfully recruited and hired Loren Rivera Vega, who worked50% time on this project between 2021-22. This hire combined with relaxedrestrictions on in-person work allowed us to make strong progress on both field data collection and laboratory analysis until Dr. Rivera Vega took a permanent position in industry in May 2022. Since that time, we have worked largely withtechniciansand undergraduates to completedata collection efforts for several objectives, butprogress on bioinformatics, statistics, and scientific writing, which require more advanced training,has been slowed. Finally, another important unanticipated challenge was that once we started planning in earnest for our orchard surveys in 2022,we encounted significant challenges in located certified organic growers in the eastern US, even after reaching out to numberous existing growers contacts, university researchers and extension agents, and other apple industry professionals. The few orchards in the eastern US that are growing organically are often not certified, or they are growing on a very small scale that would make it difficult to compare to larger conventional orchards. Thus, after much consideration, we decidedto move our orchard surveystudy to the west coast of the US. While this representeda major shift in the proposed execution of the study, the scientific objectives and general experimental design remained unchanged and we feel we were better able to address our questions in a way that is relevant for scientists and stakeholders across the country. What opportunities for training and professional development has the project provided?This project has provided extensive opportunities for training and professional development across multiple disciplines central toagriculture and food systems research, including ecology, microbiology, horticulture, and food science. First, as the first major federal award in the Whitehead Lab, this project has fundamentally shaped the direction of the lab's research and established key infrastructure, skillsets, and collaborative networks that have been central to our group's success and the establishment of new partnerships across Virginia Tech. This includes the establishment of a research orchard at Virginia Tech's Kentland Farm that we expectto maintain for decades with institutional and external support. We are currently pursuingfollow-on fundingthat will utilize the orchard for additional research as well as an experiential learning program for Virginia Tech undergraduates in agroecology. We have also developed an invaluablelibrary of protocols for field sampling and safety in agricultural environments, chemical extractions, chemical analyses via HPLC-MS, DNA extractions, PCR and sequencing, and bioinformatics of both chemical and microbial data. In terms of collaborations, this project has catalyzed Whitehead Lab collaborations across the USand internationallyincluding groups in Israel,Argentina, and Germany. It has also helped us to connect directly with growers and other industry professionalsacross Virginia and on the west coast of the United States; theseinteractions with stakeholders have been essential to informing our understanding of the practical challenges faced in the apple industry andhave also formed the basis for new directions in our work. For example, we recently submitted a proposal to SSARE that included several grower-collaborators we originally met as a result of this project. Our lab is also continuing to grow and support students through the extensive datasets and samples generated by this project. The data and samples in our freezercan form the basis of many years worth of small projects that introduce students to agroecological science. Second, we have provided interdisciplinary training forthe next generation of scientists by involving and supporting three post-docs and two graduate students, three technicians, and 26+ undergraduates. All students and post-docs attended regular lab meetings and wereexposed to a wide variety of topics in plant evolutionary ecology, microbial ecology, and agroecology: Loren Rivera-Vega was a post-doc in the Whitehead Lab from Feb 2021-May 2022 (50% time on this project)and led the data collection efforts for Obj. 2 and some of Obj. 3. She learned methods in culture-independent and culture-dependent microbiome sampling and analysis, as well as chemical analyses and techniques including GC-MS and HPLC. Furthermore, she learned cutting-edge networking and machine learning approaches that are allowing us to decipher links between the microbiome and the metabolome. In May 2022 she transitioned to an industry job and is currently employed as the Plant Trait Testing Lead at Pairwise in North Carolina. Justin Shaffer was a post-docin the Knight Lab (20% time on this project 2020-23), led microbial community sequencing efforts for part of Obj. 1 and 2, and is currently leading a publication related to Objective 1. He has gained valuable skills in molecular biology method development as well as an improved background in agroecology, analytical approaches for multi-omics datasets, and spatially-explicit sampling design and analysis. He is currently an Assistant Professor at California State University in Fresno. Marlon Ac-Pagan is currently a post-doc inthe Stewart Lab. He was not directly supported on this award, but has participated in research related to Objective 3 and has gainedskills in experimental design, fermentation methods, laboratory analytical methods for cider chemical profiles, human-subjects sensory research, and data analysis and writing. He is leading a publication currently in preparation related to Objective 3. Tori Meakem (supported one semester and one summer) received her M.S. degree in the Whitehead lab 2020 and participated in data collection related to Objective 1 and the establishment of our reearch orchard. She received training and gained extensive skills in both chemical analyses and microbial community analyses, as well as best practices in modern horticulture. In addition, Tori participated in an International Workshop on the Fruit Microbiome in 2019. She is currently employed as a research scientist at the USDA Plant Genetic Resources Unit in Geneva, NY. Xavier Ozowara (supported one semester) started as an M.S. student in the Whitehead Lab in 2022 and recently transitioned to our Ph.D. program. He spearheaded field data collection for our sampling from west coast orchards, led a publication related to that project, and is currently continuing laboratory analysis and preparing manuscripts. With limited research experience at the start of his time in our program, his growth as a result of this project has been remarkable. He has gained extensive skills in experimental design, laboratory methods for analysis of phytochemical and microbiome composition, statistics and coding in R, and scientific writing. He also had the opportunity to share his work and develop industry connections atthe annual meeting of the American Cider Association (CiderCon) in 2023. Threepart-time technicians (Annie Zell, Grace Florjancic,and Morgan Haymaker)and at least 26undergraduates in the Whitehead Lab have also assisted or conducted independent projects in the orchard and lab. All of these students have learned a combination of horticultural practices (grafting, planting, pruning, irrigation, trellising, mowing, etc), laboratory skills for phytochemical analysis (extractions, HPLC, GC/MS), and microbiology (sterile technique, DNA extraction, PCR). An additional 28 students have visited the orchard for a lab in agroecology as part of Whitehead's Field Ecology Research course, and 280 students have learned about the project in Whitehead's lecture course in Ecology. These students have been broadly introduced to the potential for ecological science to contribute to more sustainable food systems that support biodiversity, ecosystem function, and healthy rural communities. How have the results been disseminated to communities of interest?Knowledge gained from this project has been shared broadly with scientists, students, apple industry stakeholders, and the general public. For scientific audiences, we have communicated our results and related foundational concepts and methods through sevenpeer-reviewed scientific articles, twobook chapters, and one M.S. thesis. These includedreviews and syntheses (e.g. Wetzel and Whitehead 2020 Ecology Letters; Whitehead et al. 2021, invited book chapter forThe Apple Genome)and empirical research articles (e.g. Teixeira et al. 2020Environmental and Experimental Botany; Abdelfattah et al. 2020Microorganisms; Ozowara & Whitehead in review atPlants, People, Planet). We havethree additional empirical articles in preparation that we expect to submit in the coming months (one each from Obj. 1, 2, and 3). We have also presented our work and gathered feedback from colleaguesat all stages from conception to results. This has included presentations atseven scientific conferences and 16 invited seminars or plenary lectures that featured this work. For students, we have communicated our work through direct interactions with 26+ undergraduatestudents that have been directly involved with this project in the Whitehead Laband an estimated350+ that have learned about the project through their involvementin other lab activitiesor courses led by PI Whitehead (Ecology and Field Ecology Research). For the apple and cider industry, we have shared our results through 10presentations orworkshops as well as direct communication with diverse stakeholders. The Stewart Lab has largely led efforts to communicate our research to stakeholders in the cider industry. These efforts included three presentations at the Virginia Association of Cider Makers in 2019 and fourpresentations at CiderCon (the annual meeting of theAmericanCider Association) across 2022-23. Our research wasalso featured ina workshop led by Stewart on fermentation methods through the Cider Institute of North America, held at Virginia Tech in 2020.In terms of direct communication, we have shared our project and gained invaluable perspective from our interactions with apple growers, cider makers, and consultants in the apple industry. These include: Our official stakeholder advisory team: Ian Merwin of Black Diamond Farm in NY (where we obtained NY fruit for Obj. 3),Chuck Shelton of Albermarle Cider Works inVA, and Michael Phillips of Lost Nation Orchard inNH (prior to his passing in 2022). Several 'unofficial advisors' we gained over the course of the project, including Bill Mackintosh (apple grower and IPM consultant),Diane Flynt of Foggy Ridge Orchard in Carroll County, VA, and Diane Kearns of Fruit Hill Orchard in Winchester,VA. Other grower-participants, including Ruth Saunders (Silver Creek Orchard in Nelson County, VA, which provided fruit for Obj. 1 and Obj. 3) and 21growers across California, Oregon, and Washington that participated in research for Obj. 1, providing access to their orchard for fruit collection and completinga survey on management practices. For the general public, we have shared our results through direct communication, two orchard demonstrations, one local news feature, and one book feature. We have directly communicated our work through our website and social media accounts (@WhiteheadLabVT) as well as to the 20+ panelistsin our cider sensory study. The Whitehead Lab led onein-person and one virtual (video and live Q&A) demonstration for the general public at our research orchard that broadly introduced the importance of the microbiomeas well as our specific research to apple growers. The in-person activity included a fruit and cider tasting that demonstrated the enormous variety in apple flavor (and links to phytochemistry) across cultivars, especially those selected for cider production. These activities were also covered by the local TV news channel for Roanoke, VA and the surrounding areas (WDBJ7). Finally, our research wasalso featured in a recent book by Diane Flynt of Foggy Ridge Orchard entitled:Wild, Tamed, Lost, and Revived: The Surprising Story of Apples in the South[pg. 244] published by the University of North Carolina Press. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Impact Statement:This project has generated new knowledge describing the diversebacterial and fungal communitiesliving on and in apple fruit. It has shown that agricultural practices, including pesticidesprays, can alter these communities. Furthermore, it has begun to uncover the importance of bacteriaand fungifor shaping the phytochemical profiles of both apple fruit and hard cider, with broad consequences for pest resistance, fruit and cider flavor,and human health. This knowledge provides a foundation formoreapplied research andmayre-shape industry practices in the long-term. It can inform efforts to produce fruit with exceptional flavor and nutrient density, thereby improving human health and nurturing cultural connections to food and the land. Stakeholders in the growing hard cider industry can also utilizeour results to inform both orchard management and fermentationpractices that aim to showcase high-quality fruit and region-specific flavor profiles. Obj. 1: Characterize variation in fruit microbiomes and model the relationships among pest management, fruit microbial communities, fruit quality, and pest resistance. Research under this objective included two major data collection efforts. First, we examinedthe spatial variation in the microbiome and metabolome of 'Pink Lady' fruit from a commercial orchard in Virginia,assessing multiple scales of variation from microsite-to-microsite within a single fruit, fruit-to-fruit within a tree, and tree-to-tree within an orchard. We found strong spatial structuring forepiphytic bacterial communities and fruit surface metabolites, but not forepiphytic or endophytic fungi. This has important implications for understanding how disease and beneficial microbes may dispersethrough orchards, and can also inform sampling methods for future studies aiming to capture microbial diversity at a particularscale. These results were recently presented by Justin Shaffer (former post-doc on our project) at the Fungal Genetics Conference and are currently being prepared for publication. Second, we comparedfruit microbial communitiesand phenolic chemistryacross across 24 commerical orchards (13organic, 11conventional)spanning from southern California to northern Washington. We sampled fruit from five 'Gala' trees in each orchard toquantifyfruit quality (weight, sugar content, firmness, maturity),phenolic composition of skin, pulp, and seeds, and fruit microbial communities (epiphytic and endophyticbacteria and fungi). Although most fruit quality traitswere not different between organic and conventional orchards, we did detecteight phenolics (mostly in skin) that were higher in organic fruit and five (mostly in seeds) that were higher in conventional. Further analyses of survey data submitted by participating growers suggested that ground management practices (e.g. herbicide use) may be key drivers of these differences. These results formed the basis of a manuscript recently submitted to the peer-reviewed journal Plants, People, Planet (Ozowara and Whitehead, 2024). A second manuscript focused on the microbial communities is still in progress. In addition to these primary data collection efforts, we were able to significantly advance thisobjective through synthesis of existing knowledge of the apple microbiome and phytochemical diversity (invited book chapters: Whitehead et al. 2021 and Wisniewski et al. 2021;peer-reviewed article: Wetzel and Whitehead 2020,Ecology Letters) and collaborative studies that addressed how the apple microbiome changes based on postharvest treatmentsand coldstorage(Abdelfattah et al. 2020, Zhimo et al. 2022). Obj. 2: Experimentally determine how specific pesticides alter fruit microbiomes and how specific fruit microbiota alter fruit quality and resistance. To address this objective, we established a newresearch orchard at Virginia Tech. The orchard includes 620 trees planted in60 replicated mixed-cultivarblocks with eight cultivars each. Once trees entered production, we conducted a large experiment in which wetreated 'GoldRush' treesthroughout fruit developmentwith either conventional fungicides (Flint Extra, Captan, or Inspire Super), organic fungicides (copper, sulfur), or a water-onlycontrol (N = 8-10 trees per treatment). From each tree, we sampled fruit at harvest to assess the epiphytic and endophytic microbiome and the phenolic content ofthe skin and pulp. For a subset of trees, we also conducted longitudinal sampling before and after sprays. All sequencing and chemical analyses have been completed for this study and we are currently preparing a manuscriptfor publication. Overall, our results suggest that, at fruit harvest, average microbial richness issimilar across treatments. However, for some treatments, especially copper, wenoted a sharp decline in diversity directly after a spray that rebounded prior to harvest.Furthermore, it was notable that the variability in communities (i.e. beta diversity) across trees was higher for copper than for any of the other treatments. We are continuing to explore how these patterns in microbial composition relate to fruit chemical composition. Also in our experimental orchard, we examined variation in the epiphytic and endophytic microbiome among all eight cultivars (genotypes)in our orchard, along withpest and pathogen damage, fruit quality (sugar content, firmness, size), and phenolic metabolites in skin and pulp. We have found large differences across cultivars in fruit quality, chemistry, and pest susceptibility. Sequencing for these samples is currently in progress and we aim to use multi-omics techniques to assess how broad differences in fruit traits across cultivars relate to microbial community composition. We also significantly advanced this objective through additional analyses of existing data(Teixeira et al. 2020; Meakem 2020 [M.S. thesis]). Overall, theseresults suggested that pesticide treatments have broad consequences for fruit quality, fruit phenolic chemistry, and fungal endophyte communities, but more work is needed to understand the variability and underlying mechanisms of these effects. Finally, the orchard site we established for this objective has also provided infrastructure for additional fundamental and applied student projects and collaborative data collection efforts. These projects includestudies on variability in plant-herbivore interactions(Robinson et al. Science), the effectiveness of lures to attract predatory insects (Rodriguez-Saona et al., in prep), and a study by the Stewart Lab to explore the use of indigenous yeasts from the orchard as a 'pied de cuve'(cider fermentation starter). Obj. 3: Determine how the fruit microbiome and associated impacts on fruit quality affect the sensory and health-promoting properties of hard cider.To address this objective, we conducted a cider fermentation and sensory study with 'GoldRush' and 'Harrison' fruit from NY and VA orchards. Fruitfrom each cultivar and region was pressed and divided into 160 individual small-scale cider fermentations with four different treatments: 1) no commercial yeasts or sulfites added (fully wild ferment), 2) commerical yeast added (semi-controlled ferment), 3) sulfites added (semi-controlled ferment), 4) commercial yeasts and sulfites added (highlycontrolled ferment). We collected over 1600 samples over the course of fermentation to assess how chemistry and microbial communities change during fermentation. With the final ciders, we conducted a sensory study that asked participants to sortciders into groupsand describe those groups using sensory attributes. Our resultsare currently being prepared for publication (Ac-Pagan et al. in prep)andsuggestthatfermentation methods, rather than cultivar or fruit origin,are the most important drivers of cider flavor profiles. Additional phenolic analysis and microbial sequencing of cider samples for this project are still in progress.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Herbivory Variability Network* , Robinson, M.L., Hahn, P.G., Inouye, B.D., Underwood, N., Whitehead, S.R., Abbott, K.C., Bruna, E.M., Cacho, N.I., Dyer, L.A. and Abdala-Roberts, L., 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science, 382(6671), pp.679-683.
- Type:
Journal Articles
Status:
Submitted
Year Published:
2024
Citation:
Ozowara, X.G and S.R. Whitehead (in review). Variability in quality and phenolic composition of apple fruit across management systems and latitudinal climate gradients. Submitted 06/28/24 to Plants, People, Planet
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Shaffer, J.P., R. Knight, and S.R. Whitehead. Spatial variability in bacterial and fungal communities of apples (Malus domestica): Unexpected patterns of nestedness and co-occurrence, from individual fruits to the orchard scale. Oral Presentation. Genetics Society of America Fungal Genetics Conference, Pacific Grove, CA
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Shaffer, J.P., R. Knight, and S.R. Whitehead. Spatial variability in fungal endophytes of apples (Malus domestica): co-occurrence with metabolites and other microbes, from individual fruits to the orchard scale. Poster Presentation. Genetics Society of America Fungal Genetics Conference, Pacific Grove, CA
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Whitehead, S.R. Are fruits incubators of phytochemical diversity? A story of plants, bugs, birds, and bats Invited Plenary Lecture for the VII Latin American Association of Chemical Ecology (ALAEQ), Buenos Aires, Argentina
- Type:
Other
Status:
Published
Year Published:
2024
Citation:
Whitehead, S.R. Fruit, frugivores, and the evolution of phytochemical diversity . University of Tennessee Knoxville Plant Research Center Seminar Series, Knoxville, TN
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Whitehead, S.R. Frutos, frug�voros y la evoluci�n de la diversidad fitoqu�mica. Instituto de Investigaciones en Biodiversidad y Medioambiente (Consejo Nacional de Investigaciones Cient�ficas y T�cnicas - Universidad Nacional del Comahue), Invited Seminar, Bariloche, Argentina
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Progress 03/01/22 to 02/28/23
Outputs
Target Audience:We have reached all of our three main target audiences during this reporting period: 1. Scientists working in areas of ecology, evolutionary biology, agroecology, and pest management. This audience was reached through publications, direct communication, and conference presentations. 2. Agricultural stakeholders including apple growers and pest management professionals. This audience was reached primarily through industry conferences, public presentations, and direct communication with growers in our network. 3. Trainees including undergraduate students and graduate students that are working directly on the project or are in courses taught by the faculty. Changes/Problems:A major challenge during this reporting period was that the main post-doc that was spearheading many of the studies supported bythis project (Loren Rivera-Vega) received anotherjob offer and accepted in May 2022. This caused significant delays to planned statistical analyses and writing, but we were able to move the field data collection and laboratory sample processingfor the project forward with a graduate student and technician supported on the project in the Whitehead Lab. PD Whitehead is currently taking the lead on analyzing data and preparing results for publication. What opportunities for training and professional development has the project provided?This project has helped to train the next generation of scientists by involving one post-doc at UCSD, one post-doc in VT Food Science and Technology, and one post-doc, onegraduate student, one technician, and two undergraduates in the Whitehead Lab who worked directly on the project. In addition, it has engaged 70 students who learned about the project in courses. The UCSD post-doc, Justin Shaffer, worked 10% time on the project during Year 4and has gained valuable skills in molecular biology method development as well as an improved background in agroecology, analytical approaches for multi-omics datasets, and spatially-explicit sampling design and analysis. One VT post-doc, Marlon Ac-Pagnan, is mentored primarily by collaborator Jake Lahne, and has worked closely with Jake Lahne and co-PD Amanda Stewart to develop sensory methods and lead the sensory study for Obj. 3. He has received training in sensory science methodology, statistical analyses, and scientific writing. OneVT post-doc, Loren Rivera Vega, worked in the Whitehead Lab fromFeb 2021-May 2022 and led the data collection efforts for Obj. 2 and some of Obj. 3. She learned methods in culture-independent and culture-dependent microbiome sampling and analysis, as well as chemical analyses and techniques including GC-MS and HPLC. Furthermore, learned cutting-edge networking and machine learning approaches that areallowing us to decipher links between the microbiome and the metabolome. One graduate student, Xavier Ozowara, began an MS degree in Jan 2022 and has now transferred to a PhD degree program in the Whitehead Lab. Thus far, his research hasfocused on Obj. 1, and he isreceiving training in experimental design, phytochemical analysis, microbiome analysis, statistical analysis, and scientific writing. Furthermore, this project has provided an opportunity for him to engage directly with a diversity of apple growers, gain exposure to orchard establishment and orchard management, and to better understand how agricultural practices affect food quality and value. In addition, one technician in the Whitehead Lab and twoundergraduates from VT have been heavily involved in orchard maintenance and field data collection and have gained valuable skills in basic horticultural practices for apples as well as experimental design and data management. All students and post-docs attend regular lab meetings and are also exposed to a wide variety of topics in plant evolutionary ecology, microbial ecology, and agroecology. Finally, this research has been featured in course content for 70 undergraduates in the Agroecology unit of an Ecology course taught by the project PD. How have the results been disseminated to communities of interest?Our research as been communicated to scientific audiences through one scientific publication and numerous invited seminars and other presentations. We havegiven a total of four scientific presentations (conference presentations, invited seminars or plenaries) to university and academic audiences from diverse disciplines, and threepresentations to cidermakers and industry professionals at CiderCon in Chicago, IL. These presentations have included results from the project as well as plans for future work, which has allowed us to gain extensive feedback on our planned work in the coming years and also develop a strong network of researchers with shared interests, from which several new collaborations are already brewing. Our work has also been communicated extensively to stakeholders and the general public, especially through our recruitment of growers forStudy 1b and our recruitment of participants for the sensory study (Study 3a). What do you plan to do during the next reporting period to accomplish the goals?Key goals for the coming reporting period are listed below under each objective. Obj. 1: Characterize variation in fruit microbiomes and model the relationships among pest management, fruit microbial communities, fruit quality, and pest resistance. Submit manuscript for spatial variability study for publication (Study 1a) Complete sample processing and statistical analysis forcommercial orchard survey (Study 1b) Obj. 2: Experimentally determine how specific pesticides alter fruit microbiomes and how specific fruit microbiota alter fruit quality and resistance. Continue maintenance of research orchard Complete sequencing and chemical analyses of samples collected during Fall 2021-2022 for the pesticide study (Experiment 2a) and genotype study (Experiment 2b) Complete statistical analysis of data and draft manuscript for pesticide study (Experiment 2a) Obj. 3: Determine how the fruit microbiome and associated impacts on fruit quality affect the sensory and healthpromoting properties of hard cider. Conduct chemical analyses and sequencing of cider samples from sensory study (Study 3a) Conduct data analysis of sensory data and draft manuscript for publication (Study 3a)
Impacts
What was accomplished under these goals?
Project Impacts: Rapidly expanding knowledge of the apple microbiome can provide unprecedented opportunities for biologically-based management in orchards, but we lack core knowledge of plant-microbe interactions and their downstream consequences in agroecosystems. In the fourthyear of our project, we have continued to generate new foundational knowledge of the apple microbiome and communicated that knowledge as well as our plans for future research to the scientific community, agricultural stakeholders, and the general public. This is evidenced by one scientific publication, four scientific presentations (conferences or invited seminars), threepresentations at an industry conference (CiderCon), and social media accounts (Twitter @WhiteheadLabVT). In addition, our project has increased research capacity at Virginia Tech by maintaining and improving infrastructure, in particular our apple research orchard located at Virginia Tech's Kentland Farm that was planted in the first year of the project. The orchard includes 8 varieties planted in 60 replicated blocks separated by buffer zones (620 trees total), with a focus on local heirloom, multi-purpose, and cider varieties that are of increasing interest for Virginia growers. We planted this orchard in Spring 2019 and have continued basic maintenance (pruning, pest management, ground management, etc.) since this time. Our secondcrop was harvested in Fall 2022. During this season, we conducted a large data collection effort that will compare the microbiome across the eight cultivars and also examine how microbial communities change during six months of post-harvest storage.We are currently processing samples from thisstudy, as well as a 2021 study focused on the effects of fungicides,for sequencing and chemical analyses. In addition, we have collected most data for a large study examining how the fruit microbiome shapes the sensory properties of hard cider. Results from this study will provide new information that can help cider-makers to understand and promote the unique regional characters of their products. Finally, our project has helped to train the next generation of scientists by involving students and post-docs at Virginia Tech and UCSD in research, including three post-docs, two graduate students, and two undergraduates. Students have been trained in experimental design, field data collection, data management, orchard maintenance, processing of samples for chemical and microbiological analysis of fruits, statistical analysis, and scientific writing. This research has also been featured in course content for 87 undergraduates in Ecology courses taught by the project PD. Specific accomplishments under each objective are described below: Obj. 1: Characterize variation in fruit microbiomes and model the relationships among pest management, fruit microbial communities, fruit quality, and pest resistance. Research planned under this objective included two main components. First, we conducted detailed spatial sampling of the multi-scale variation in the fruit microbiome and metabolome (Study 1a). Second, we are examining the variation in the fruit microbiome across 20 organic and conventional orchards (Study 2b). For Study 1a, sampling was collected in Year 1 of the project, method development in Year 2, and in Year 3 we have now completed all sequencing of the samples and are currently conducting downstream data analyses to quantify the multi-scale variation in microbial communities from within-fruit (1cm2 sections of fruit skin) to across orchard blocks. We are also applying multi-omics tools to assess how the microbiome is related to the fruit metabolome. For Study 1b, we conducted all field sampling during this project period. An MS student in the Whitehead Lab, Xavier Ozowara, led this effort and visited 24 orchards across California, Oregon, and Washington during Fall2022. He surveyed growers on their basic management practices, collected data on fruit quality, and samples fruits for chemical and microbial analyses. In addition, he collected climate data from publicly available sources for all sites. We have already completed analysis of phenolic chemistry for all samples, and are currently conducting statistical analyses to examine how fruit quality and chemistry are jointly drivenby management practices and climate. Obj. 2: Experimentally determine how specific pesticides alter fruit microbiomes and how specific fruit microbiota alter fruit quality and resistance. Research planned under this objective involved three main experiments. First, we are examining how specific pesticides affect the fruit microbiome (Experiment 2a). Second, we are examining how the microbiome varies among genotypes (Experiment 2b). Third, we will determine whether specific microbial inoculations can alter fruit quality and pest resistance (Experiment 3b). All field data collection for Experiment2a wereconducted during Year 3, and we had also collected some samples for Experiment 2b. However, we decided to repeat sampling for Experiment 2b this year (Year 4) because we had much better fruit production in our experimental orchard,and therefore more complete sampling effort across all eight cultivars. In addition, we were able to collect enough fruit to extend the study to examine how microbial communities change during six months of cold storage.Sequencing for Experiment 2a is in progress at the Knight Lab at UCSD, and chemical analyses of fruit samples is in progress in the Whitehead Lab. We have also invested in continuing to maintain the experimental orchard, including pruning, pest management, irrigation, trellis maintenance, and more. PD Whitehead has managed these activities directly with feedback from other VT researchers (including Sherif Sherif, VT Horticulture, and Keith Yoder, VT Plant Pathology) and industry consultants, especially Bill Macintosh and Raul and Mary Godinez, to ensure the orchard is managed according to best practices in modern horticulture. Obj. 3: Determine how the fruit microbiome and associated impacts on fruit quality affect the sensory and health-promoting properties of hard cider. Research planned under this objective involves two experiments. First, we are examining how regional variation in the fruit microbiome affects hard cider quality (Experiment 3a). Second, we will examine how pest management and experimental inoculations affect cider quality (Experiment 3b). For Experiment 3a, during Year 3, we sampled fruit from NY and VA orchards, conducted a controlled fermentation experiment with over 160 individual fermentations, and collected over 1600 samples over the course of fermentation to assess how chemistry and microbial communities change during fermentation. In collaboration with Jacob Lahne (VT Food Science), the Stewart Lab led a sensory study that asked participants to complete a sorting task to group ciders with similar sensory properties and describe those different groups using sensory attributes. Data analysis for this study is currently in progress using the program DISTATIS, which will allow us to identify cider groupings and their shared sensory attributes.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Zhimo, V.Y., A. Kumar, A. Biasi, A. Abdelfattah, V. Sharma, S. Salim, O. Feygenberg, R. Bartuv, S. Freilich, S.R. Whitehead, M. Wisniewski, S. Droby (2022). Assembly and dynamics of the apple carposphere microbiome during fruit development and storage. Frontiers in Microbiology 13: 928888
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Whitehead, S. R. Fruits, frugivores, and the evolution of phytochemical diversity. University of Connecticut Ecology and Evolutionary Biology Seminar Series
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Whitehead, S. R. Evolutionary ecology of chemically-mediated plant interactions. Max Planck Institute for Chemical Ecology Frontiers in Chemical Ecology International Symposium (virtual presentation)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Whitehead, S.R., E. Bass, A. Corrigan, A. Kessler, and K. Poveda. Interaction diversity explains the maintenance of phytochemical diversity. Phytochemical Society of North America, Blacksburg, VA
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Ozowara, X., A. Stewart, J. Lahne, and S.R. Whitehead. "From Stress to Press: How Microbes Shape Apple Chemistry". CiderCon: Annual Meeting of the American Cider Association. Chicago, IL
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Ac-Pangan, M., J. Lahne, and A.C. Stewart. "Influence of cultivar and fermentation strategies on chemistry, flavor and consumer valuation of ciders made from Virginia-grown apples" CiderCon: Annual Meeting of the American Cider Association. Chicago, IL
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Stewart, A.C. "Fermentation Science Research at Virginia Tech". CiderCon: Annual Meeting of the American Cider Association. Chicago, IL
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Ac-Pangan, M. , E. Cole, B. Littleson, E. Chang, C. Neill, K. Phetxumphou, A. Sandbrook, A. Stewart, J. Lahne Sensory characteristics of Virginia hard cider evaluated across multiple studies and harvesting seasons. Eurosense 2022, Turku, Finland
|
Progress 03/01/21 to 02/28/22
Outputs
Target Audience:We have reached all of our three main target audiences during this reporting period: 1. Scientists working in areas of ecology, evolutionary biology, agroecology, and pest management. This audience was reached through publications, direct communication, and conference presentations. 2. Agricultural stakeholders including apple growers and pest management professionals. This audience was reached primarily through industry conferences, public presentations, and direct communication with growers in our network. 3. Trainees including undergraduate students and graduate students that are working directly on the project or are in courses taught by the faculty. Changes/Problems:Work on this project has been significantly impacted by research and travel restrictions put in place as a result of COVID-19. Our laboratories were closed for research from March-May 2020 and operated under very limited capacity from May 2020 to May 2021 (one person at a time in the lab in the Whitehead Lab, no undergraduates are allowed in laboratories, shared equipment use is restricted). No travel was allowed to field sites outside of Blacksburg, VA, which caused us to significantly shift our timeline for this project. In addition, COVID-19 affected our recruiting of new graduate students for Fall 2020 (in both the Whitehead and Stewart Laboratories), further complicating progress on the project. These challenges forced us to greatly modify our plans for Year 2 and Year 3 of the project, however, we still expect that we can accomplish the major objectives of the project within the planned time frame of five years. During Spring 2022 we began planning in earnest for Study 1b (the survey of commercial orchards), which was originally planned for the Eastern US. However, we encounted significant challenges in located certified organic growers in the eastern US, even after reaching out to numberous existing growers contacts, university researchers and extension agents, and other apple industry professionals. The few orchards in the eastern US that are growing organically are often not certified, or they are growing on a very small scale that would make it difficult to compare to larger conventional orchards. Thus, after much consideration, we are now planning tomove this study to the west coast of the US. We have already established contacts with over 20growers that are willing to participate and are now working to optimize locations in ways that can minimize variation in climate and other factors in our organic/conventional comparisons. While this represents a major shift in the proposed execution of the study, the scientific objectives and general experimental design remain unchanged and we are confident that this shift will allow us to better addressour questions in a way that is relevant for scientists and stakeholders alike. What opportunities for training and professional development has the project provided?This project has helped to train the next generation of scientists by involving one post-doc at UCSD and many students and post-docs at Virginia Tech, including twopost-docs, two graduate students, two undergraduates, and one technician who worked directly on the project, and 70students who learned about the project in courses. The UCSD post-doc, Justin Shaffer, worked 10% time on the project during Year 3and has gained valuable skills in molecular biology method development as well as an improved background in agroecology, analytical approaches for multi-omics datasets, and spatially-explicit sampling design and analysis. The VT post-doc, Loren Rivera Vega, was hired in Feb 2021 and led the data collection efforts for Obj. 2 and some of Obj. 3. She learnedmethods in culture-independent and culture-dependent microbiome sampling and analysis, as well as chemical analyses and techniques including GC-MS and HPLC. Furthermore, she is starting to learn cutting-edge networking and machine learning approaches that will allow us to decipher links between the microbiome and the metabolome. One new graduate student, Xavier Ozowara, began a MS degree in Jan 2022 that will focus on Obj. 1. He isreceivingtraining in experimental design, phytochemical analysis, microbiome analysis, statistical analysis, and scientific writing. Furthermore, this project has provided an opportunity for himto gain exposure to orchard establishment and orchard management, and to better understand how agricultural practices affect food quality and value. In addition, two undergraduates fromVT have been heavily involved in orchard maintenance and field data collection and have gained valuable skills in basic horticultural practices for apples as well as experimental design and data management. All students and post-docs attend regular lab meetings and are also exposed to a wide variety of topics in plant evolutionary ecology, microbial ecology, and agroecology. Finally, this research has been featured in course content for 70undergraduates in the Agroecology unit of an Ecology course taught by the project PD. How have the results been disseminated to communities of interest?Our research as been communicated to scientific audiences through onescientific publication and numerous invited seminars and other presentations. PD Whitehead has given a total of fourscientific presentations (invited seminars or plenaries) to university and academic audiences from diverse disciplines, and co-PD Stewart gave one presentation to cidermakers and industry professionals at CiderCon. These presentations have included results from the project as well as plans for future work, which has allowed us to gain extensive feedback on our planned work in the coming years and also develop a strong network of researchers with shared interests, from which several new collaborations are already brewing. Our work has also been communicated extensively to stakeholders and the general public, especially through our recruitment of growers for Study 1b and our recruitment of participants for the sensory study (Study 3a). What do you plan to do during the next reporting period to accomplish the goals?Key goals for the coming reporting period are listed below under each objective. Obj. 1: Characterize variation in fruit microbiomes and model the relationships among pest management, fruit microbial communities, fruit quality, and pest resistance. • Complete statistical analysis of data (Study 1a) • Submitmanuscript for spatial variability study for publication (Study 1a) • Complete field sampling effortsfor commercial orchard survey (Study 1b) Obj. 2: Experimentally determine how specific pesticides alter fruit microbiomes and how specific fruit microbiota alter fruit quality and resistance. • Continue maintenance of research orchard • Complete sequencing and chemical analyses of samples collected during Fall 2021 for the pesticide study(Experiment 2a) and genotype study (Experiment 2b) • Complete statistical analysis of data and draft manuscript for pesticide study(Experiment2a) Obj. 3: Determine how the fruit microbiome and associated impacts on fruit quality affect the sensory and healthpromoting properties of hard cider. • Conduct chemical analyses and sequencing of cider samples from sensory study(Study 3a) • Conduct data analysis of sensory data and draft manuscript for publication(Study 3a)
Impacts
What was accomplished under these goals?
Project Impacts: Rapidly expanding knowledge of the apple microbiome can provide unprecedented opportunities for biologically-based management in orchards, but we lack core knowledge of plant-microbe interactions and their downstream consequences in agroecosystems. In the thirdyear of our project, we have continued to generate new foundational knowledge of the apple microbiome and communicated that knowledge as well as our plans for future research to the scientific community, agricultural stakeholders, and the general public. This is evidenced by onescientific publications,fourscientific presentations (conferences or invited seminars), one presentation at an industry conference (CiderCon), and social media accounts (Twitter @WhiteheadLabVT). In addition, our project has increased research capacity at Virginia Tech by maintaining and improving infrastructure, in particular our apple research orchard located at Virginia Tech's Kentland Farm that was planted in the first year of the project. The orchard includes 8 varieties planted in 60 replicated blocks separated by buffer zones (620 trees total), with a focus on local heirloom, multi-purpose, and cider varieties that are of increasing interest for Virginia growers. We planted this orchard in Spring 2019 and have continued basic maintenance (pruning, pest management, ground management, etc.) since this time. Our first crop was harvested in Fall 2021 and we were able to conduct two major studies in the orchard, one examining the effects of five common fungicides on the fruitmicrobiome, and another comparing the microbiome across the eight cultivars. We are currently processing samples from these studies for sequencing and chemical analyses. In addition, we have collected most data fora large study examining how the fruit microbiome shapes the sensory properties of hard cider. Results from this study will provide new informationthatcan help cider-makers to understand and promote the unique regional characters of their products.Finally, our project has helped to train the next generation of scientists by involving students and post-docs at Virginia Tech and UCSD in research, including threepost-docs, two graduate students, and twoundergraduates. Students have been trained in experimental design, field data collection, data management, orchard maintenance, processing of samples for chemical and microbiological analysis of fruits, statistical analysis, and scientific writing. This research has also been featured in course content for 87 undergraduates in Ecology courses taught by the project PD. Specific accomplishments under each objective are described below: Obj. 1: Characterize variation in fruit microbiomes and model the relationships among pest management, fruit microbial communities, fruit quality, and pest resistance. Research planned under this objective includedtwo main components. First, we conducteddetailed spatial sampling of the multi-scale variation in the fruit microbiome and metabolome (Study 1a). Second, we areexaminingthe variation in the fruit microbiome across 20 organic and conventional orchards(Study 2b). For Study 1a, sampling was collected in Year 1 of the project, method development in Year 2, and in Year 3 we have now completed all sequencing of the samples and are currently conducting downstream data analyses to quantify the multi-scale variation in microbial communities from within-fruit (1cm2 sections of fruit skin) to across orchard blocks. We are also applyingmulti-omics tools to assess how the microbiome is related to the fruit metabolome. For Study 1b, we have not yet begun field work due travel restrictions in place as a result of COVID-19, but we hired a new MS student to work on this aspect of the project (beginning in Jan 2022), established collaborations withgrowers, and planned a sampling regime. We are planning tocompletethe field data collection for this study in Summer/Fall 2022. Obj. 2: Experimentally determine how specific pesticides alter fruit microbiomes and how specific fruit microbiota alter fruit quality and resistance. Research planned under this objective involvedthree main experiments. First, we are examininghow specific pesticides affect the fruit microbiome (Experiment 2a). Second, we are examininghow the microbiome varies among genotypes (Experiment 2b). Third, we will determine whether specific microbial inoculations can alter fruit quality and pest resistance (Experiment 3b). All field data collection for Experiments 2a and 2b wasconducted this yearinour new research apple orchard, which was planted in Year 1 of the project and produced fruit for the first time in Fall 2021. Sequencing for this study is in progress at the Knight Lab at UCSD, and chemical analyses of fruit samplesis in progress in the Whitehead Lab. We have also invested in continuing to maintain the experimental orchard, including pruning, pest management, irrigation, trellis maintenance, and more. PD Whitehead has managed these activities directly with feedback from other VT researchers (including Sherif Sherif, VT Horticulture, and Keith Yoder, VT Plant Pathology) and industry consultants, especially Bill Macintosh and Raul and Mary Godinez, to ensure the orchard is managed according to best practices in modern horticulture. Obj. 3: Determine how the fruit microbiome and associated impacts on fruit quality affect the sensory and healthpromoting properties of hard cider. Research planned under this objective involves two experiments. First, we areexamininghow regional variation in the fruit microbiome affects hard cider quality (Experiment 3a). Second, we will examine how pest management and experimental inoculations affect cider quality (Experiment 3b). For Experiment 3a, during Year 3, we sampled fruit from NY and VA orchards, conducted a controlled fermentation experiment with over 160 individual fermentations, and collected over 1600 samples over the course of fermentation to assess how chemistry and microbial communities change during fermentation. In collaboration with Jacob Lahne (VT Food Science), the Stewart Lab led a sensory study that asked participants to complete a sorting task to group ciders with similar sensory properties and describe those different groups using sensory attributes. Data analysis for this study is currently in progress using the program DISTATIS, which will allow us to identify cider groupings and their shared sensory attributes.
Publications
- Type:
Journal Articles
Status:
Submitted
Year Published:
2022
Citation:
Zhimo, V.Y., A. Kumar, A. Biasi, A. Abdelfattah, V. Sharma, S. Salim, O. Feygenberg, R. Bartuv, S. Freilich, S.R. Whitehead, M. Wisniewski, S. Droby (in review). Assembly and dynamics of the apple carposphere microbiome during fruit development and storage (Submitted 04/26/22 to Frontiers in Microbiology)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Whitehead, S.R. Plants, bugs, bats, and birds: how plant interaction diversity shapes phytochemical diversity ; University of Florida Department of Entomology seminar series (virtual presentation)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Whitehead, S.R. Rewards, toxins, and trade-offs: the chemical ecology of seed dispersal . German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig seminar series (virtual presentation)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Whitehead, S.R. Fruit, frugivores, and the evolution of phytochemical diversity . University of British Columbia Biodiversity Research Centre seminar series (virtual presentation)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Whitehead, S.R. Attracting friends and avoiding foes: how plant interaction diversity shapes phytochemical diversity. Invited Plenary Lecture for International Workshop on Evolution of Chemodiversity, Leipzig, Germany
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Stewart, A. "Cider Production Research: How Chemistry and Sensory Parameters Lead to Style Outcomes" Invited Lecture for CiderCon, Richmond, VA
|
Progress 03/01/20 to 02/28/21
Outputs
Target Audience:We have reached all of our three main target audiences during this reporting period: 1. Scientists working in areas of ecology, evolutionary biology, agroecology, and pest management. This audience was reached through publications, direct communication, and conference presentations. 2. Agricultural stakeholders including apple growers and pest management professionals. This audience was reached primarily through industry conferences, public presentations, and direct communication with growers in our network. 3. Trainees including undergraduate students and graduate students that are working directly on the project or are in courses taught by the faculty. Changes/Problems:Work on this project has been significantly impacted by research and travel restrictions put in place as a result of COVID-19. Our laboratories wereclosed for research fromMarch-May 2020 and operated under very limited capacityfrom May 2020 to May 2021(one person at a time in the lab in the Whitehead Lab, no undergraduates are allowed in laboratories, shared equipment use is restricted). No travel was allowed to field sites outside of Blacksburg, VA. Just in the past week (as of 05/21/21), we are now finally lifting restrictions as lab members are all fully vaccinated and community transmission is low, and are able to work with multiple people in the lab at one time.In addition, COVID-19 affected our recruiting of new graduate students for Fall 2020 (in both the Whitehead and Stewart Laboratories), further complicating progress on the project. These challenges forced us to greatly modify our plans for Year 2 of the project. We were forced to postpone plans for Study 1b (the survey of commercial orchards across the Eastern US), which was originally intended to be the major focus of Year 2 and would have involved extensive travel across the Eastern US during Summer/Fall 2020. Currently, we expect that this survey will take place in Summer/Fall 2022. Were-budgetedthe award to partially fund a post-doc on the project instead of a graduate student in the Whitehead Lab, and successfully recruited and hired Loren Rivera Vega, who began in Feb 2021 and isfunded 50% time on this project and 50% on another project in the Whitehead Lab. This new hire combined with the lifting of lab distancingrestrictions is allowing us to now make significant progress on various aspects of the project, including laboratoryanalyses of samples and field work. Despite these challenges, we have made significant progress with project goals that could be accomplished remotely, i.e. data analysis and writing manuscripts, recruiting grower participants, method development, data management, and developing data pipelines for analysis of microbiome and chemical data. Currently, we still expect that we can accomplishthe major objectives of the project within the planned time frame of five years. What opportunities for training and professional development has the project provided?This project has helped to train the next generation of scientists by involvingone post-doc at UCSD and many students and post-docs at Virginia Tech, including one post-doc, two graduate students, twoundergraduates, and onetechnician who worked directly on the project, and 87students who learned about the project in courses. The UCSD post-doc, Justin Shaffer, worked10% time on the project during Year 2 and has gainedvaluable skills in molecular biology method development as well as an improved background in agroecology, analytical approaches formulti-omics datasets,and spatially-explicit sampling design and analysis.The VT post-doc, Loren Rivera Vega, was hired in Feb 2021 and will continue on the project over the next two years. She is learning methods in culture-independent and culture-dependent microbiome sampling and analysis, as well as chemical analyses and techniques including GC-MS and HPLC. Furthermore, she is starting to learn cutting-edge networking and machine learning approaches that will allow us to decipher links between the microbiome and the metabolome.One graduate student, Tori Meakem, completed her MS degree in May 2020 and has worked extensively on the project during Year 1-2. She received training in experimental design, phytochemical analysis, microbiome analysis, statistical analysis, and scientific writing.A second graduate student, Brenna Littleson, is advised by co-PD Stewart and has worked on cider fermentation studiesfor Obj. 3 of the project. She has received training in fermentation methods, chemical analyses, and sensory studies. Furthermore, this project has provided an opportunity for her to gain exposure to orchard establishment and orchard management, and to better understand how agricultural practices affect food quality and value. In addition, onetechnician and twoundergraduates in the VT Horticulture program have been heavily involved in orchard maintenance and field data collection and have gained valuable skills in basic horticultural practices for apples as well as experimental design and data management. All students and technicians attend regular lab meetings and are also exposed to a wide variety of topics in plant evolutionary ecology, microbial ecology, and agroecology. Finally, this research has been featured in course content for 87undergraduates in the Agroecology unit of anEcology coursetaught by the project PD. How have the results been disseminated to communities of interest?Our research as been communicated to scientific audiences through fourscientific publications, including Whitehead et al. (2021) in Ecology Letters (Impact Factor: 8.66), Abedelfattah et al. (2021) in Microorganisms, and two invited book chapters Wisniewski et al. (2021) and Whitehead et al. (in press). The book chapter by Whitehead et al. will be published in a book titled "The Apple Genome" edited by Schuyler Korban and represents a comprehensive review of our current knowledge of the microbiome associated with apple trees. This will be an important resource to bring researchers together working on different aspects of the apple microbiome (rhizosphere, flowers, leaves, fruit, etc).In addition, PD Whitehead hasgiven a total of fivescientific presentations (conferences or invited seminars) to university and academic audiences from diverse disciplines. These presentations have included results from the project as well as plans for future work, which has allowed us to gain extensive feedback on our planned work in the coming years and also develop a strong network of researchers with shared interests, from which several new collaborations are already brewing. Our work has also been communicated extensively to stakeholders and the general public. Co-PD Stewart gave industry presentations that explained the goals of the project and described methods and preliminary results. Whitehead also gave one public virtual presentation/orchard tour at Virginia Tech's Kentland Farm to approximately 100 participants. Finally, we have communicated the project plans informally through numerous meetings with Virginia growers and industry professionals, who will be essential participants in future stages of the project. What do you plan to do during the next reporting period to accomplish the goals?Key goals for the coming reporting period are listed below under each objective. Obj. 1: Characterize variation in fruit microbiomes and model the relationships among pest management, fruit microbial communities, fruit quality, and pest resistance. Complete laboratory analysis of all samples collected for the spatial variability study (Study 1a), including microbiome analysis (Knight Lab), surface exudate analysis (Whitehead Lab), and phenolic analysis (Whitehead Lab). Complete statistical analysis of data and draft manuscript for spatial variability study (Study 1a) Continue developing network and recruit participants for commercial orchard survey (Study 1b) Obj. 2: Experimentally determine how specific pesticides alter fruit microbiomes and how specific fruit microbiota alter fruit quality and resistance. Complete data analysis and submit manuscript examining how experimental pest management treatments affect fungal endophytes, fruit chemistry, and pest resistance Continue maintenance of research orchard Conduct experiment in VT orchard to determine how pesticides (Experiment 2a) and genotype (Experiment 2b) impact the microbial communities associated with apples Obj. 3: Determine how the fruit microbiome and associated impacts on fruit quality affect the sensory and healthpromoting properties of hard cider. Collect samples from NY and VA orchards to conduct native fermentation experiment (Study 3a) Conduct chemical and sensory analyses of ciders (Study 3a)
Impacts
What was accomplished under these goals?
Project Impacts:Rapidly expanding knowledge of the apple microbiome can provide unprecedented opportunities for biologically-based management in orchards, but we lack core knowledge of plant-microbe interactions and their downstream consequences in agroecosystems. In the secondyear of our project, we have continued to generatenew foundational knowledge of the apple microbiome and communicated that knowledge as well as our plans for future research to the scientific community, agricultural stakeholders, and the general public. This is evidenced by fourscientific publications, fivescientific presentations (conferences or invited seminars), oneindustry presentation, one public presentation/orchard tour, and social media accounts (Twitter @WhiteheadLabVT). In addition, our project has increased research capacity at Virginia Tech by maintaining and improvinginfrastructure, in particularourapple research orchard located at Virginia Tech's Kentland Farm that was planted in the first year of the project. The orchard includes 8 varieties planted in 60 replicated blocks separated by buffer zones (620 trees total), with a focus on local heirloom, multi-purpose, and cider varieties that are of increasing interest for Virginia growers. We planted this orchard in Spring 2019 and this year we replaced approximately 10% of the trees (which were expected losses in the first year) and continued basic maintenance (pruning, pest management, ground management, etc.) and expect our initial fruit crop in Fall 2021. Finally, our project has helped to train the next generation of scientists by involving students and post-docs at Virginia Tech and UCSD in research, including two post-docs, two graduate students, and 3undergraduates. Students have been trained in experimental design, field data collection, data management, orchard maintenance,processing of samples for chemical and microbiological analysis of fruits, statistical analysis, and scientific writing. This research has also been featured in course content for 87undergraduates in Ecology courses taught by the project PD. Specific accomplishments under each objective are described below: Obj. 1: Characterize variation in fruit microbiomes and model the relationships among pest management, fruit microbial communities, fruit quality, and pest resistance. Research planned under this objective includes two main components. First, we are conducting detailed spatial sampling of the multi-scale variation in the fruit microbiome and metabolome (Study 1a). Second, we will examine the variation in the fruit microbiome across 20 organic and conventional orchards in the Eastern US (Study 2b). For Study 1a, sampling was collected in Year 1 of the project, and this year we have worked to develop methods for both themicrobiome analyses (Knight Lab) and the chemical analyses of fruits (Whitehead Lab). Part of the goal for this study was to quantify small-scall variation in microbial communities across a single fruit (1cm2 sections of fruit skin), andthe Knight Lab has developed a method and pipeline for obtaining high quality sequences from these low biomass DNA samples. In addition, they have developed methods for blocking plant DNA from the apple tissue samples that will allow us to better understand the endophytic microbes that are associated with different fruit tissues. A few more details of this method development are still in progress, and we expect to start the main sequencing in June 2021. In the Whitehead Lab, we have developed a GC/MS-based metabolomics method to analyze metabolites on the apple surface at the same small scale that the microbial samples were taken (1cm2), which will allow us to examine how small-scale variations in microbial communities may be linked to chemical environments. For Study 1b,we have not yet begun field work due travel restrictions in place as a result of COVID-19, but we have continued to plan methods details and now anticipate completing this study in Summer/Fall 2022. Obj. 2: Experimentally determine how specific pesticides alter fruit microbiomes and how specific fruit microbiota alter fruit quality and resistance. Research planned under this objective involves three main experiments. First, we will examine how specific pesticides affect the fruit microbiome (Experiment 2a). Second, we will determine how the microbiome varies among genotypes (Experiment 2b). Third, we will determine whether specific microbial inoculations can alter fruit quality and pest resistance (Experiment 3b). These experiments will be conducted in our new research apple orchard, which was planted in Year 1 of the project and should start producing fruits during Year 3. Thus, our main work under this objective has been to maintainthe experimental orchard. During Spring 2020, we replaced trees that had died during Year 1, pruned, notched trees to encourage lateral branching, planned and executed a pest management regime, and maintained irrigation equipment and the trellis system. PD Whitehead has managed these activities directly with feedback from other VT researchers (including Sherif Sherif, VT Horticulture, and Keith Yoder, VT Plant Pathology) and industryconsultants, especially Bill Macintosh and Raul and Mary Godinez, to ensure the orchard is managed according to best practices in modern horticulture. We are currently planning our first experiments forSummer/Fall 2021. In addition to field work and data collection, we have worked to further analyze data collected in a preliminary study relevant to this objective. This study compared the fungal endophyte community, fruit chemistry, and fruit quality in fruits treated under different pest management regimes in an existing VT orchard. We show distinct communities of fungal endophytes in trees treated with different regimes, and a positive relationship between fungal endophyte diversity and phenolic diversity in fruits. This work formed part of Meakem's MS thesis (submitted 05/2019) and this year we have worked to further characterize fruit chemistry and use networking analyses and machine learning to determine how the microbial communities are linked to fruit chemical traits. This work is currently being prepared for publication. Obj. 3: Determine how the fruit microbiome and associated impacts on fruit quality affect the sensory and healthpromoting properties of hard cider. Research planned under this objective will involve two experiments. First, we will examine how regional variation in the fruit microbiome affects hard cider quality (Experiment 3a). Second, we will examine how pest management and experimental inoculations affect cider quality (Experiment 3b). For Experiment 3a, during Year 2, MS student Brenna Littleson, co-PD Stewart, and collaborator Jacob Lahne leda study to determine how wild fermentation with local microbiota in our experimental orchard (versus fermentation with commercial yeast) impacts the fermentation and sensory properties of hard cider. There wereclear differences in the sensory profiles of cider produced with wild and commercial yeast. Furthermore, a comparison of two important local apple cultivars, GoldRush and Harrison, showed interactions between fermentation method and cultivar such that wild ferments had very different results for the two cultivars. A full sensory descriptive analysis was performed with trained panels to describe these differences. This work formed part of a MS thesis by Brenna Littleson (submitted 05/2021) and is currently being prepared for publication.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Whitehead, S.R., E. Bass, A. Corrigan, A. Kessler, and K. Poveda (2021). Interaction diversity explains the maintenance of phytochemical diversity. Ecology Letters 24(6): 1205-1214
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Abdelfattah, A., S.R. Whitehead, D. Macarisin, J. Liu, E. Burchard, S. Freilich, C. Dardick, S. Droby and M. Wisniewski (2020). Effect of washing, waxing, and low-temperature storage on the postharvest microbiome of apple. Microorganisms 8(6): 944
- Type:
Book Chapters
Status:
Published
Year Published:
2021
Citation:
Wisniewski, M., S. Droby, A. Abdelfattah, J. Liu, S.R. Whitehead, S. Freilich and C. Dardick (2021). Spatial and compositional diversity in the microbiota of harvested fruits: what can it tell us about biological control of postharvest diseases. pp 63-72 In Postharvest Pathology: Next Generation Solutions to Reducing Losses and Enhancing Safety ed. D. Spadaro, S. Droby, and M. Lodovica Gullino, Springer Nature (invited book chapter)
- Type:
Book Chapters
Status:
Awaiting Publication
Year Published:
2021
Citation:
Whitehead, S.R., M. Wisniewski, S. Droby, A. Abdelfattah, S. Freilich, M. Mazzola (in press). The apple microbiome: structure, function, and manipulation for improved plant health. In The Apple Genome ed. S.S. Korban, Springer-Nature (invited book chapter)
- Type:
Other
Status:
Other
Year Published:
2020
Citation:
Whitehead, S.R. Pest management impacts on the apple microbiome and downstream consequences for fruit quality and cider production , Virginia Tech Department of Food Science and Technology Invited Seminar (virtual presentation)
- Type:
Other
Status:
Other
Year Published:
2021
Citation:
Whitehead, S.R. Pest management impacts on the apple microbiome and downstream consequences for fruit quality ; Microbiology Without Borders Seminar Series; Universidad Aut�noma de Quer�taro, Mexico Invited Seminar (virtual presentation)
- Type:
Other
Status:
Other
Year Published:
2021
Citation:
Whitehead, S.R. Fruits, frugivores, and the evolution of phytochemical diversity ; Max Planck Institute for Chemical Ecology in Jena, Germany Invited Seminar (virtual presentation)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Whitehead, S.R. The diversity unseen: phytochemical complexity and seed dispersal. Invited Plenary at the 7th Frugivores and Seed Dispersal International Symposium, March 2020, Corbett Landscape, India
- Type:
Other
Status:
Other
Year Published:
2021
Citation:
Whitehead, S.R. Fruits, frugivores, and the evolution of phytochemical diversity . Invited Plenary at Iowa State University EEB Graduate Symposium, Feb 2021, Virtual Presentation
- Type:
Other
Status:
Other
Year Published:
2020
Citation:
Whitehead, S.R. "A Whole World in an Apple: Microbes, Fruit Flavor, Pest Resistance, and Human Health" video presentation and live Q&A for growers and general public at Kentland Farm Field Day https://video.vt.edu/playlist/details/1_8i25tiqr
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2020
Citation:
Meakem V. Induced defenses in apple fruits: linking fruit chemistry, quality, and plant-insect-microbe interactions (Master's thesis, Virginia Tech, supervised by Dr. Susan Whitehead). https://vtechworks.lib.vt.edu/handle/10919/99100
- Type:
Other
Status:
Other
Year Published:
2020
Citation:
Stewart, A.C. "Current research in cider orchard management and fermentation." Cider Institute of North America - Foundations of Cidermaking Workshop, Blacksburg, VA.
|
Progress 03/01/19 to 02/29/20
Outputs
Target Audience:We have reached all of ourthree main target audiences during this reporting period: 1. Scientists working in areas of ecology, evolutionary biology, agroecology, and pest management. This audience wasreachedthrough publications, direct communication, and conference presentations. 2. Agricultural stakeholders including apple growers and pest management professionals. This audience wasreached primarily through industry conferences, public presentations, and direct communication with growers in our network. 3. Trainees including undergraduate students and graduate students that are working directly on the project or are in courses taught by the faculty. Changes/Problems:Work on this project has beensignificantly impacted by research and travel restrictions put in place as a result of COVID-19. Our laboratories have been closed for research since March 2019. We expect that some restrictions will be lifted beginning in June, butactivities in campus laboratories will be heavily restricted(i.e. no undergraduates are allowed in laboratories, shared equipment use is restricted, students cannot be working in proximity). Furthermore, non-essential travel forfield-work is currently prohibited, and we expect these restrictions to remain in place for months.In addition, COVID-19 affected our recruiting of new graduate students for Fall 2020 (in both the Whitehead and Stewart Laboratories), further adding to the uncertainty of when we will have the required personnel to move the work forward efficiently.These challengeshaverequired us to greatly modify our plans forYear 2 of the project, but we have a plan that we believe will allow us to largely stay on track to accomplish our goals within the five-year project period. We wereforced topostpone plans for Study 1b (the survey of commercial orchards across the Eastern US), which was originally intended to be the major focus of Year 2 and would have involved extensive travel across the Eastern US during Summer/Fall 2020. Currently, we expect that this survey will take place inSummer/Fall 2021. We are also considering re-budgeting the award to partially fund a post-doc on the project instead of a graduate student, likely starting toward the end of Year 2 (e.g. Jan 2021). The post-doc would be funded 50% time on this project and 50% on another project in the Whitehead Lab. Ideally, this will reduce the time required for training a new student, allow moreflexibility in a start date (i.e. we can recruit as soon as travel/research restrictions are relaxed), and more flexible time for off-campus field research. We believe that a post-doc could move forward with Study 1b (originally planned for Summer 2020) and Studies2a/2b (originally planned for Summer 2021) simultaneously during Summer 2021.Meanwhile, we are moving forward with parts of the project that can be completed remotely, i.e. data analysis and writing manuscripts, recruiting grower participants, method development, data management, and developing data pipelines for analysis of microbiome and chemicaldata. We have obtained "essential worker" status for PD Whitehead and personnel involved in orchard maintenance and are continuing to maintain the research orchard. We also expect that we will be able to resume some lab work (i.e. microbiome analysis in the Knight Lab, chemical analyses in the Whitehead Lab, and fermentations in the Stewart Lab) in the coming months and can complete laboratory analysis this year for Study 1a. If limited travel can be safely completedin Oct/Nov 2019, we will also complete field data collection and fermentations for Study 3a (the role of native microbiota in fermentation). What opportunities for training and professional development has the project provided?Traning Activities This project has helped to train the next generation of scientists byinvolvingmany students at Virginia Tech in research, including twograduate students and 19 undergraduates who worked directly on the project, and 139 students who learned about the project in courses. One graduate student, Tori Meakem, completed her MS degree in May 2020 and has worked extensively on the project over the last year. She has received training in experimental design, phytochemical analysis, microbiome analysis, statistical analysis, and scientific writing. This training has come from PDWhitehead, collaborator Wisniewski, and many other faculty and students at Virginia Tech through her coursework and other activities. A second graduate student, Brenna Littleson, is advised by co-PD Stewart and has worked on method development for Obj. 3 of the project. She has received training in fermentation methods, chemical analyses, and sensory studies that will be used in Study 3a and 3b.Furthermore, this project has provided an opportunity for herto gain exposure to orchard establishment and orchard management, and to better understand how agricultural practices affect food quality and value. In addition, 12undergraduates, 2 graduate students, and one post-doc were involved in planting the orchard; six of these students and one other have participated in other aspects of the project, including orchard maintenance, field data collection, and processing of samples for chemical and microbiological analysis of fruits. Two students, in particular, have worked extensively on the project (100+ hours each), one largely on orchard maintenance (Zach Fisher), and one on both orchard maintenance and laboratory work (Grace Florjancic). One of these students graduated in Dec. 2019 and is continuing to assist with the project as a research technician. Finally, this research has been featured in course content for 139undergraduates in Ecology courses taught by the project PD. This has included 125 students in Ecology lecture who learned about the research in a lecture unit on Agrocecology, and 14 students in her Field Ecology Research course, who visited the orchard and were introduced first-hand to the goals of the project and theexperimental design for Objective 2. These students also learned about the biology and propagation of apple trees and skills in identification of insect herbivores and tree pathogens. Professional Development This project also has supported extensive professional development activities, particularly for PDWhitehead and MS student Tori Meakem. Whitehead has learned extensive skills in orchard care and maintenance that will help her to directly understand the needs of growers, and has developed an extensive network of advisors and advocates in the apple industry. She has also improved her conceptual background and learned important new scientificskills (laboratory techniques, analytical methods)in several areas of research related to this interdisciplinary project, including microbiology, microbial ecology, metabolomics, and fruit/frugivore interactions through conferences (e.g. the International Fruit Microbiome Conference), direct interactions with collaborators (co-PD Knight and collaborator Wisniewski), and individual study. Meakem has also learned extensive new skills through relevant coursework (e.g. Bioinformatics, Chemical Ecology) and participation in conferences and symposia (the International Fruit Microbiome Conference, VT Translational Plant Sciences symposium, VT Biological Sciences symposium). In addition, this project provided an important professional development opportunity for Dr. Gustavo Teixeira, Visiting Professor in the Whitehead Lab from the Universidade Estadual Paulistain Brazil. Dr. Teixeira participated in various aspects of the project and learned valuable new skills, including fruitchemical analyses andorchard maintenance. He also gained new conceptual background in agricultural ecology and microbiome studies that can translate to many aspects of his research. While in the lab, Dr.Teixeira helped to lead fieldwork associated with the project, manage undergraduate researchers, and alsoled the publication of a paper in Environmental and Experimental Botany. How have the results been disseminated to communities of interest?Our research as been communicated to scientific audiences through threescientific publications, including Wetzel and Whitehead (2020) in Ecology Letters(Impact Factor: 8.699), Teixeira et al. (2020) inEnvironmental and Experimental Botany, and Wisniewski et al. (in review) in a bookentitled "Postharvest Pathology: Next Generation Solutions to Reducing Losses and Enhancing Safety". In addition, PD Whitehead and graduate student Meakem have given a total of sixscientific presentations (conferences orinvited seminars) to university and academic audiences from diverse disciplines. These presentations have included results from the project as well as plans for future work, which has allowed us to gain extensive feedback on our planned work in the coming years and also develop a strong network of researchers with shared interests, from which several new collaborations are already brewing. Our work has also been communicated extensively to stakeholders and the general public. Both PDWhitehead and co-PD Stewart gave industry presentations at the Virginia Association of Cider Makers meeting that explainedthe goals of the project and describedmethods and preliminary results. Whitehead also gaveonepublic presentation/orchard tour at Virginia Tech's Kentland Farm to approximately 120 participants. Our research has also been featured in aVirginia Techpress release, a local televised news feature (WDBJ7, Roanoke, VA), and through social media accounts (Twitter @WhiteheadLabVT). Finally, we have communicated the project plans informally through numerous meetings with Virginia growers and industry professionals, who will be essential participants in future stages of the project. What do you plan to do during the next reporting period to accomplish the goals?Key goals for the coming reporting period are listed below under each objective. Obj. 1: Characterize variation in fruit microbiomes and model the relationships among pest management, fruit microbial communities, fruit quality, and pest resistance. Finalize method development and complete laboratory analysis of all samples collected for the spatial variability study (Study 1a), including microbiome analysis (Knight Lab), surface exudate analysis (Whitehead Lab), and phenolic analysis (Whitehead Lab). Complete statistical analysis of data and draft manuscript for spatial variability study (Study 1a) Continue developing network and recruit participants for commercial orchard survey (Study 1b) Obj. 2:Experimentally determine how specific pesticides alter fruit microbiomes and how specific fruit microbiota alter fruit quality and resistance. Complete data analysis and submit manuscript examining how experimental pest management treatments affect fungal endophytes, fruit chemistry, and pest resistance Continue maintenance ofresearch orchard Obj. 3:Determine how the fruit microbiome and associated impacts on fruit quality affect the sensory and health-promoting properties of hard cider. Finalize methods for native fermentation experiment (Study 3a) Collect samples from NY and VA orchards and complete fermentation trials(Study 3a) Conduct chemical analyses of ciders(Study 3a)
Impacts
What was accomplished under these goals?
Project Impacts Rapidly expanding knowledge of the applemicrobiomecanprovideunprecedented opportunities for biologically-based management in orchards, but we lackcore knowledge of plant-microbe interactions and their downstream consequences in agroecosystems. In the first year of our project, we have generated new foundational knowledge of the apple microbiome and communicated thatknowledge as well as our plans for future research to the scientific community, agricultural stakeholders, and the general public. This is evidenced by threescientific publications, sixscientific presentations (conferences orinvited seminars), threeindustry presentations, onepublic presentation/orchard tour, oneVirginia Techpress release, a local televised news feature, and social media accounts (Twitter @WhiteheadLabVT).In addition, our project has increasedresearch capacity at Virginia Tech by establishing newinfrastructure, most importantly anew apple research orchard located at Virginia Tech's Kentland Farm. The orchard includes 8 varieties planted in 60 replicated blocks separated by buffer zones (620 trees total), with a focus on local heirloom, multi-purpose, and cider varieties that are of increasing interest for Virginiagrowers. We planted thisorchard in Spring 2019 and we plan tomaintain the orchardbeyond the course of the funded project to support many future research activities. Finally, our project has helped to train the next generation of scientists byinvolvingmany students at Virginia Tech in research, including twograduate students and 13undergraduates. Students have been trained inorchard maintenance, field data collection, and processing of samples for chemical and microbiological analysis of fruits, statistical analysis, and scientific writing. This research has also been featured in course content for 139undergraduates in Ecology courses taught by the project PD. Specific accomplishments under each objective are described below: Obj. 1: Characterize variation in fruit microbiomes and model the relationships among pest management, fruit microbial communities, fruit quality, and pest resistance. Research planned under this objective includestwo main components. First, we areconducting detailed spatial sampling of the multi-scale variation in the fruit microbiome and metabolome (Study 1a). Second, we willexamine the variation in the fruit microbiome across 20 organic and conventional orchards in the Eastern US (Study 2b). For Study 1a, we completed all field samplingin October2019 atSilver CreekOrchards in Tyro, Virginia. Weconducted spatially-explicit sampling at three scales: across different microsites within a single fruit, across different fruits within a tree, and across different trees within an orchard block. Sampling focused on one variety (cv. 'Pink Lady'). For the within-fruit sampling, we producedspatially explicit 3-D mapsof each focal fruit (3 fruits total) and then collected samples from 50 distinct microsites per fruit to quantify variation in the epiphytic microbiome, endophytic microbiome, and fruit chemistry. In addition, we sampledfor epiphytes, endophytes and metabolites on 16additional fruits on the focal tree and from 16 additional trees across the orchard block (~200m x 90m), all of which were spatially-mapped.We are currently developing methods for both the microbiome analyses (Knight Lab) and the chemical analyses of fruits (Whitehead Lab).Analyses of these samples will take place during Year 2 of the project. For Study 1b, we have not yet begun field work, but we have made important progressbuilding our network of growers and met with many VA growers to gather their feedback on the project.PDWhitehead has met with a number of VA growers and industryprofessionals including Bill Mackintosh (Nutrien Ag Solutions), Raul and Mary Godinez (Countryside Farm and Nursery),Ruth Saunders (Silver Creek Orchards), Diane Flynt (Foggy Ridge), Diane Kearns (Fruit Hill Orchard), the Shelton Family (Vintage Virginia Apples and Albemarle CiderWorks), and many additional growers and cider makers at the Virginia Association of Cider Makers annual meeting. We have also collated a list of 200+ potential organic and conventional orchards in North Carolina, Virginia, Maryland, Pennsylvania, New York, Vermont, Massachusets, and New Hampshire from which we can recruit participants for the field study. In addition to data collection efforts, important conceptual progress has been made toward Obj. 1through the writingof synthesis and review papers.PDWhitehead and collaborator Wisniewski submitteda book chapter discussing existing knowledge on the spatial variability in the fruit microbiome (Wisniewski et al. in review), and Whitehead published a conceptual paper on phytochemical variation, including spatial variation and methods for analysis (Wetzel and Whitehead, 2020). Obj. 2:Experimentally determine how specific pesticides alter fruit microbiomes and how specific fruit microbiota alter fruit quality and resistance. Research planned under this objective involvesthree main experiments. First, we will examine how specific pesticides affect the fruit microbiome (Experiment 2a). Second, we will determine how the microbiome varies among genotypes (Experiment 2b). Third, we will determine whether specific microbial inoculations canalter fruit quality and pest resistance (Experiment 3b). These experiments will be conducted in our new research apple orchard, which was planted in Year 1 of the project and should start producing fruits during Year 3. Thus, our main work under this objective has been to establish the experimental orchard. During Spring 2019, we prepared the orchard site (removing an existing planting, amended soil, etc.), installed perimeter deer fencing, and installed a trellis system. We alsofinalized plans for rootstock andvariety selection in the orchard in consultation with local growers, sourced bench-grafted trees from a local nursery, planted 696 trees, and managed all orchard maintenance (pesticides, ground management, pruning, etc.). PDWhitehead has sought feedback from other VT researchers (including Sherif Sherif, VT Horticulture, and Keith Yoder, VT Plant Pathology) and worked closely with established growers and consultants, especially Bill Mackintosh and Raul and Mary Godinez, to ensure the orchard is managed according to best practices in modern horticulture. In addition to field work and data collection, wehave worked to further analyze data collected in a preliminary study relevant to this objective. This study compared the fungal endophyte community, fruit chemistry, and fruit qualityin fruits treated under different pest management regimes in an existing VT orchard. We showdistinct communities of fungal endophytes in trees treated with different regimes, and a positive relationship between fungal endophyte diversity and phenolic diversity in fruits. This work formed part of Meakem's MS thesis (submitted 05/2019) and is currently being prepared for publication. In addition, we published one paper (Teixeira et al. 2020) focused on the effects of pesticides on fruit quality. Obj. 3:Determine how the fruit microbiome and associated impacts on fruit quality affect the sensory and health-promoting properties of hard cider. Research planned under this objective will involve two experiments. First, we will examine how regional variation in the fruit microbiome affects hard cider quality (Experiment 3a). Second, we will examine how pest management and experimental inoculations affect cider quality (Experiment 3b). During2019, co-PD Stewart trained one MS student in Food Science on methods used to conduct laboratory and pilot-scale cider fermentation, and methods for the chemical analysis of cider. The student also worked with Dr. Jacob Lahne's sensory group to learn and apply various approaches in sensory evaluation for the assessment of cider sensory characteristics and cider quality.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Wetzel, W.C. and S.R. Whitehead (2020). The many dimensions of phytochemical diversity: linking theory to practice. Ecology Letters 23: 16-32
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Teixeira, G.H., V. Meakem, C. de L. M. de Morais, K.M.G. de Lima, and S.R. Whitehead (2020). Conventional and alternative pre-harvest treatments affect the quality of Golden delicious and Yorkapple fruit. Environmental and Experimental Botany 173 (2020): 104005.
- Type:
Book Chapters
Status:
Under Review
Year Published:
2020
Citation:
Wisniewski, M., S. Droby, A. Abdelfattah, J. Liu, S.R. Whitehead, S. Freilich and C. Dardick (in review). Spatial and compositional diversity in the microbiota of harvested fruits: what can it tell us about biological control of postharvest diseases. In Postharvest Pathology: Next Generation Solutions to Reducing Losses and Enhancing Safety ed. D. Spadaro, S. Droby, and M. Lodovica Gullino, Springer Nature
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Whitehead, S.R. "Pest management practices impact the apple microbiome with downstream consequences for fruit quality and insect resistance" Invited Speaker for International Workshop: The Fruit Microbiome: A New Frontier, Sept. 2019, Washington, D.C.
- Type:
Other
Status:
Other
Year Published:
2019
Citation:
Whitehead, S.R. "What's in a fruit? Phytochemical complexity and seed dispersal" Invited Seminar, Oct. 2019, University of Miami Department of Biology
- Type:
Other
Status:
Other
Year Published:
2019
Citation:
Whitehead, S.R, Plants, pests, and people: how crop domestication has shaped plant-insect interactions . Invited Seminar, May 2019, Oakland University Department of Biology
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Whitehead, S.R., "Plant chemistry links plant-herbivore and plant-microbe interactions"; Chemical Ecology Multistate Annual Meeting, State College, PA, Oct. 2019
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Whitehead, S.R. A Whole World in an Apple: Microbiome Contributions to Cider Quality Invited Presentation at the Virginia Association of Cider Makers (VACM) Summer Meeting at Albemarle Cider Works, Albemarle, VA. July 22, 2019
- Type:
Other
Status:
Other
Year Published:
2019
Citation:
Whitehead, S.R. New VT Research on Apple Production: The Role of the Microbiome ; Led presentation and tour for growers and general public at VT Kentland Farm Field Day Sept. 17, 2019
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Meakem,V. G. Teixeira, and S.R. Whitehead (2020), The impact of a biotic interaction diversity gradient on apple fruit chemistry. Poster presentation for Virginia Tech Biological Sciences Research Day Symposium. Feb 2020, Blacksburg, VA
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
V. Meakem and S.R. Whitehead (2019) Pesticide-based management practices and the apple fruit microbiome. Poster presentation for International Workshop: The Fruit Microbiome: A New Frontier, Sept. 2019, Washington, D.C.
- Type:
Other
Status:
Other
Year Published:
2019
Citation:
Payne, Neesey, WDBJ7 Local News Report Oct. 15, 2019 "Grown Here at Home: Kentland Farm Field Day giving farmers latest on research, production tools" https://www.wdbj7.com/content/news/559451291.html?jwsource=cl
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Stewart, A.C. Virginia Tech Cider Research Update. Invited Presentation and Panel Discussion at the Virginia Association of Cider Makers (VACM) Summer Meeting at Albemarle Cider Works, Albemarle, VA. July 22, 2019
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Stewart, A.C. Cidermaking vs. Winemaking: Fruit Chemistry Considerations for Cider Fermentation Invited Presentation at the Virginia Association of Cider Makers (VACM) Summer Meeting at Albemarle Cider Works, Albemarle, VA. July 22, 2019
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