Source: CORNELL UNIVERSITY submitted to NRP
LEVERAGING SOIL MICROBIOMES TO PROMOTE CLIMATE CHANGE RESILIENCE AND ADOPTION OF ORGANIC AGRICULTURE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1029059
Grant No.
2022-51106-38007
Cumulative Award Amt.
$749,606.00
Proposal No.
2022-04685
Multistate No.
(N/A)
Project Start Date
Sep 1, 2022
Project End Date
Aug 31, 2026
Grant Year
2022
Program Code
[112.E]- Organic Transitions
Recipient Organization
CORNELL UNIVERSITY
(N/A)
ITHACA,NY 14853
Performing Department
(N/A)
Non Technical Summary
Current problem:Farmers are grappling with the impacts of climate change globally, including increased extreme weather events and pest and pathogen outbreaks. While some organic farms are predicted to be more resilient to climate change compared to others, the mechanisms underlying these differences are still poorly understood. Our prior work indicates that changes in the soil microbiome on organic farms mediate ecosystem services, such as crop resilience, however, microbiome-mediate ecosystem services varied across farms. It is also still unknown how time in organic management and farming practices interact to influence different functions of the soil microbiome. Thus, the long-term goal of this projectis to promote the adoption of organic practices by determining which aspects of organic management promote microbiome-mediated resilience and providing tools for growers to leverage this knowledge.Methods and approach:In objective 1, we will collect soil and data on farm characteristic from organic farms across New York. The soil microbiome will be sequenced and soil fertility determined for each sample. This data will then be used to determine specific practices and the amount of time in organic required for optimal soil microbe conservation. In objective two we will identify specific microbiomes that promote climate resilience using different genotypes of plants, the soil samples collected from across New York, and common garden experiments. In objective 3, we develop a soil microbiome sequencing lab and decision support tool app. Organic growers will be able to submit soil samples for sequencing and recieve results using the app. The app will also assist growers in interpreting their data and making management decisions related to soil microbiome conservation. Results and resources from our project will be developed in to webinars with the help of eOrgancics and through communication with extension agents, our farmer advisory committee, and though the publication of peer-reviewed journal articles.Impacts and benefits to society:Over 25% of the earth's vegetative land has undergone soil degradation largely due to increases in agricultural production. As agricultural production continues to increase globally, growers will also be forced to utilize more and more marginal land. Thus, adoption of agricultural management practices that increase soil health, such as organic methods, is critical to sustainable food production and will be fundamental to maintain productivity for all agricultural systems in an uncertain future.The long-range implications of this study include the conservation of soil microbiomes, climate change education for all farmers, and increased adoption of organic agriculture. This will lead to a more sustainable agroecological food system in the United States as soil health increases and the economic costs associated with climate change and yield losses are alleviated
Animal Health Component
30%
Research Effort Categories
Basic
70%
Applied
30%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1321499107033%
2111499107033%
2054099107034%
Knowledge Area
211 - Insects, Mites, and Other Arthropods Affecting Plants; 205 - Plant Management Systems; 132 - Weather and Climate;

Subject Of Investigation
1499 - Vegetables, general/other; 4099 - Microorganisms, general/other;

Field Of Science
1070 - Ecology;
Goals / Objectives
1)Evaluate the benefits of long-term organic management for microbiome conservation2)Identify microbiomes that promote climate change resilience in crops3)Provide a microbiome decision support tool for organic farmers
Project Methods
Objective1: Determine thebenefits of long-term organic management for microbiome conservation We will collect soil from a network of 85 organic farms accross NYS that range in location, practices used, and time in organic. Soil ferility will be characterized at the Cornell Soil Health Lab.DNA will be extracted from soil samples, the 16S and ITS regions sequenced, and microbiome characterized as in (Blundell et al 2019). We will calculate loss and replacement of microbe taxa across long-term organic and transitioning sites andfor farming practices used across the paired fields. We will also include two-way interactions between each term characterizing changes in farming practices across fields and time in organic management. To extend our results we will develop a 45-minute webinar on microbiome conservation in organic farming systems in partnership with eOrganic. Objective 2: Microbiomes that promote climate change resilience in crops identifiedWe will use a manipulative experimental approach to evaluate ecosystem services provided by the microbiome of organic farming systems across NYS. Specifically, we will evaluate microbiome-mediated resilience to abiotic (drought) and biotic (herbivory) aspects of climate change using microbiome transplant experiments and greenhouse experiments. To determine the impact of plant-microbiome genotype matches on ecosystem serviceswe will also grow seeds from 7 different seed producers in theirnatal microbiomes(extracted from the farm where they were produced) and inforeign microbiomes(extracted from paired transitioning and long-term organic farms across NYS). Natal and foreign microbiomes will be sequenced and plant resilience to drought and herbivorywill be evaluated in a common garden greenhouseexperiment. To extend our results we will develop a 45-minute webinar with the help of eOrganics that highlights our stakeholder's efforts to produce regionally adapted seed crops that are climate change resilient. We will describe how plant-microbe interactions mediate climate change resilience.Objective 3: Provide a microbiome decision support tool for organic farmersWe will set up a regional organic soil sequencing lab using theMinION long-read sequencing platform and by developing a low cost high-throughput DNA extraction and sequeincing protocol for NY soils. We will develop a platform to deliver sequencing results using an descision support tool app we design. Focus groups will be conducted with growers to determine message framing for the app and promotional materials. We will use machine learning algorithums and our soil microbiome databaseto predict the relationships between microbiome taxa and farming practices (e.g., no-till), farm characteristics (long-term organic and transitioning), measures of plant performance (normal conditions and droughted), and pest suppression. In the final year of the project we will trial the tool with farmer submitted soil samples and data on user experience will be collected. To extend our results from this objectivewe will make a finaleOrganic webinar highlighingcurrent resources on the Climate Smart Farming available at Cornell University andourfor rapid microbiome sequencing and our decision support tool piolet program.Evaluation plan:First, we will track the number of organic farmers using our decision support tool. Second, we will track the number of attendees and asynchronous views for our eOrganic webinars. Third we will evaluate the effectiveness of our webinars by asking attendees to fill out a brief survey regarding their experience. We will then follow up 1 year after the webinar to determine if any attendees made changes to their farm to promote microbiome conservation and climate change resilience.Finally, the project team will have quarterly conferences and the annual stakeholder advisory committee meeting to evaluate the project and make modifications if needed.We expect the number of organic farms withcharacterizedsoil microbiomesin NYS toincrease. We expect farmer knowledge on the benefits of organic agriculture for soil microbiome conservation and climate resilliencewill increase.Finally we expect farmers using organic practices thatconserve soil microbiomes that enhanceclimate resiliencewill increase.

Progress 09/01/23 to 08/31/24

Outputs
Target Audience:Farmer Stakeholder Engagement:During the reporting period, we engaged with our regional farmer stakeholders (n = 7) in the collection of soil samples and market ready seeds (2×) for climate change bioassays (see Obj 2). National Audience: To promote engagement on the national level, we developed an eOrganic webinar (n = 1) highlighting the findings of Obj 1 and our SAC. The webinar engaged 120 attendees from 36 US states, and 7 international attendees from Mexico, India, Canada, and Spain. Our audience breakdown was as follows: 10 agricultural professionals, 13 extension agents, 18 farmers, 24 government agency researchers, 16 nonprofit organization staff, 3 organic certifiers and inspectors, 22 university researchers, and 14 participants representing other aspects of food systems (e.g., gardeners). The webinar is permanently posted to eOrganic and freely available on YouTube. In ≈2mo, the recording has received > 280 views and 11 likes (≈140 views/mo). Extension Agents:We are currently preparing individualized microbiome reports for farmers who participated in Obj 1. We will leverage our previously described target audience of 18 Cornell University extension personnel in the validation of reports before farmer delivery, ensuring reports are understood by non-academic audiences. Report delivery to 85 farmers who make up a core audience is planned for January 2025. Scientists and Academics: Our research was shared with academics 8X in the reporting period. Specifically, our research was shared at the Entomology Society of America (National Harbor Maryland); American Society of Plant Biologists (Honolulu, HI), University of California (Riverside, CA); X2 Pennsylvania State University (State College, PA); X2 Cornell University (Ithaca Campus), and Cornell University AgriTech (Geneva, NY). Total engagement for the academic environment was ≈350 individuals. Interdisciplinary Researchers: In preparation for the development of the decision support tool, we consulted with Alison Chatrchyan (Cornell University, Senior Research Associate, Earth and Atmospheric Sciences) and Arthur Degaetano (Cornell University, Director of Undergraduate Studies for Atmospheric Sciences). Through these consultations we developed a timeline and framework for the development and deployment of the decision support tool which will have a broad target audience (n ≈ 280 organic vegetable farmers in NYS). Social media: We promoted the publication of our research, eOrganic webinar, and seminars on X (formerly Twitter), generating 818 impressions (views), 54 engagements, and 21 profile visits. Project results will continue to be shared via social media during the final reporting period, and beyond our project completion date. Undergraduate, post-baccalaureate, and graduate student researchers: We successfully recruited 1× full-time research technician with a background in bioinformatics to develop our rapid soil microbiome sequencing resource (see Obj 3), and 1× part-time undergraduate researcher to assist with climate change experiments (see Obj 2). Via these activities each technician is gaining skills useful for career advancement. We plan to recruit 1× graduate student to assist with project completion and the continuation of our research in the final reporting period. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training activities: Manipulative experimental design 2× (drought, cover cropping lab experiments ); Insect rearing, colony management, and handling 5× (1 research technician, 2 undergraduate researchers, 2 graduate students); Microbiome extraction 3× (1 research technician, 2 undergraduate researchers); PCR, library preparation, long read sequencing, and bioinformatics 2× (1 research technician, 1 postdoc); Phytohormone extraction 2× (1 research technician, 1 undergraduate researcher); Phytohormone quantification and interpretation (1× postdoc); Structural equation modeling (1x postdoc). Professional development:Conferences presentations by junior scientists 2× (ASPB/EntSoc); Seminar presentations conducted by project team 8x; DEI Trainings 4x; (Project Biodiversity Affiliates; Wellbeing in Academia Lab Meeting; Introduction to Inclusive & Equity-Minded Mentoring and the Faculty Advancing Inclusive Mentoring, What was that? Identifying bias workshop) 2×; IDP (Individual development plan) for junior and senior scientists 4×; Graduate student training for senior scientists 2×. How have the results been disseminated to communities of interest?Results for organic farming practices that mediate the microbiome, plant defenses, and pest suppression were extended through a 1.5hr eOrganic webinar (Obj 1). This webinar included 4× 15min presentations (2× researchers; 2× members of the SAC) along with a robust 30min question period. Statistics on engagement include: 120 attendees from 36 states. Of the attendees 7 were engaged internationally (Mexico 2×, India 1×, Canada 3×, and Spain 1×). We engaged participants from 8 professional backgrounds (agricultural professionals 10×, extension 13×, farmers 18×, government researchers 24×, nonprofit staff 16×, organic certifiers and inspectors 3×, university researchers 22×). 97% of attendees indicated an improved understanding of soil microbiomes, and 75% indicated that they were greater than somewhat likely to apply the knowledge they gained. Feedback suggests 72% of participants felt the presentation was appropriate in terms of technical information. The webinar has been permanently posted to our eOrganic community of practice website (https://eorganic.info/soilmicrobiome) and YouTube where it has received 297 views and 11 likes in < 2mo. What do you plan to do during the next reporting period to accomplish the goals?Objective 1: Evaluate the benefits of long-term organic management for microbiome conservation Our results will be extended to 85 farmers through microbiome reports. We will leverage our previously described target audience of 18 Cornell University extension personnel in the validation of reports before farmer delivery, ensuring reports are understood by non-academic audiences. Report delivery to 85 farmers who make up a core audience is planned for January 2025. Feedback from farmers will be gathered to determine changes in practice adoption. Two additional manuscripts on the impacts of compost application and cover cropping are in preparation. Objective 2: Identify microbiomes that promote climate change resilience in crops We will continue conducting experiments and will construct our GEM model. These experiments will expand our seed sources to additional members of our SAC (n = 3), allowing us to determine the generality of our findings across microbiomes and seed sources. Long read microbiome sequencing for soil samples will be performed, along with plant hormone induction quantification. These data along with the sequencing conducted for the 85 farms in our network (Obj 1) will be used to parameterize our rapid microbiome sequencing decision support tool (Obj 3) by July 2025. A manuscript describing the relationship between the microbiome and crop fitness under drought will be prepared. The results of these analyses will be shared in a 1.5hr eOrganic webinar given with 2 members of the SAC. Objective 3: Provide a microbiome decision support tool for organic farmers We will refine our rapid long read microbiome sequencing approach and bioinformatics pipeline. We will then use our pipeline to sequence the soil microbiome of our 85 organic farmer network and the soil microbiomes of the SAC farms. Combining these data with our bioassays (Obj 2) we will use machine learning to determine relationships between farming practices, microbiome taxa, and measures of plant performance under climate change scenarios. In Fall 2025, we will promote our rapid sequencing resource and decision support tool. Farmers indicating interest in using the decision support tool will be sent a soil sampling guide, sample bags, and return postage. Within 1 week of receiving a submission to our rapid sequencing resource we will send the participant a QR code to access a CSV file with their microbiome results and a link to try our decision support tool. The decision support tool will be built as a web application with Shiny and hosted on the Climate Smart Farming website. At the conclusion of the rapid sequencing resource pilot program, all submissions will be used to cross-validate our models. Participants will be emailed a report detailing the validity of our results and any changes in our suggestions based on this cross-validation in December 2025. Prior to launching our decision support tool, focus group interviews with our SAC will be used to evaluate decision support tool messaging frames for microbiome conservation and climate change. Results from focus groups and the pilot program of our decision support tool will be published in peer-review journals and developed into informative content to be delivered via eOrganic. In our final 1.5hr eOrganic webinar, we will highlight the current resources for climate smart farming. We will then highlight our pilot program for rapid microbiome sequencing and our decision support tool. Members of our SAC will reflect on the usefulness of the decision support tool and barriers to implementation will be discussed.

Impacts
What was accomplished under these goals? Issue: Functional relationships between the soil microbiomes on organic farms, specific farming practices, and climate change resilience remains largely unresolved. We seek to determine functional microbiome relationships, provide rapid microbiome decision support, and promote climate change resilience in transitioning and long-term organic farms. Objective 1: Major activities. During year 2 we used machine learning and structural equation modeling to determine how farming practices mediate the microbiome, plant defenses, and pest suppression. To confirm these models, we then conducted bioassays manipulating cover cropping and compost applications. Different cover crop species (canola and cereal rye) were found to mediate unique phytohormone pathways via changes in the microbiome, resulting in pest fitness differences for taxa with chewing and piercing sucking mouthparts. The results of these activities were extended to farmers via a 1.5hr eOrganic webinar. Data collected: Using a field soil microbiome survey of 85 farms, we evaluated nine aspects of microbiome alpha and beta diversity for both the fungal and bacterial sequences. To determine which taxa may be driving changes in microbiome diversity and function, we evaluated links between farming practice adoption and the abundance of specific microbial OTUs. Then we establish correlations between farming practices, plant defenses, and pest suppression, by inoculating sterilized potting media with the soil microbiome of farms from across NYS. Finally, we used structural equation models to test the impact of farming practices and farm characteristics (time in organic) on microbiome-mediated pest suppression. Summary statistics and discussion: The adoption of 3 management variables was correlated with decreases in alpha diversity for fungi and bacteria, including pre-planting practices (e.g., tarping and solarization), mineral fertilizer use; and no tillage. Five management practices (diversified cropping, cover cropping with grasses, cover cropping with legumes, compost application, and precision irrigation) correlated with changes in microbiome beta diversity. Twelve practices correlated with changes in specific OTUs across farms (no tillage, vegetative fertilizer, compost application, animal manures, mineral fertilizer, cover cropping with herbs, cover cropping with grasses, synthetic mulch, biological mulch, pesticides, broadcast irrigation, targeted irrigation). Of these microbiome changes, only 2 microbiome beta diversity measures and 3 OTUs were also linked with changes in jasmonic and salicylic acid, two important plant defense related compounds. In combination, our findings suggest the adoption of compost applications and organic pesticides increases crop susceptibility, while the adoption of grass cover cropping, targeted irrigation, and no tillage decreases plant susceptibility, via soil microbiome changes. Key outcomes.Change in Knowledge:Evidence linking 17 farming practices with microbiome diversity, plant defenses, and pest suppression 1×; Change in Action:Adoption of five key practices (no tillage, cover cropping, precision irrigation, compost application, and soil pesticides) linked with pest suppression and plant defenses via the microbiome; Change in condition:Highlighted key areas of improvement for long term organic management including increased adoption of cover cropping and no-tillage 1×; Extension of findings via eOrganic 1× Objective 2: Major activities.Soil sampling was conducted at the 7 organic seed farms in our stakeholder advisory committee. Seeds produced at farms and farming system practices at the site of soil sampling were also collected. Approximately 50ml of soil per sample was stored at -20° C for use in microbiome sequencing (see Obj 3). Data collected.Lab assays: Three 5-week assays were conducted. Bioassays began by extracting the live soil microbiome from each farm (n = 7 microbiomes). These microbiome extractions were applied to triple sterilize potting soil, beginning at the time of seeding, and continuing 2× per week for four weeks. Drought treatments were established by elevating plants on wicking foam blocks above a water reservoir with an approximate depth. The reservoir for well-watered treatments was filled daily, whereas the reservoir for drought treatments was filled 3× per week (≈2.3× less frequently compared to well-watered controls). After 4 weeks, microbiome applications ceased as did supplemental watering for the drought treatments for 8 days. During this 8-day period, plants (either received a cage control (no aphid), 10 aphids for 48hrs to assess induction responses, or 1 aphid for the full 8-day period to assess reproduction (6 replicates per measure). At the end of ≈5w we counted aphid progeny, measured plant biomass, collected leaf tissue samples for phytohormone quantification, sampled soil for microbiome characterization, and used a probe to record the percent soil moisture in each replicate. Plant tissues were then oven dried to determine the actual biomass and water content of plants. Summary statistics and discussion. Across our experiments, the microbiomes of the 7 seed farms provided consistent pest suppression benefits compared to a no microbiome control under droughted and well-watered conditions. These preliminary results suggest soil microbiomes are important for crop resilience to stress. In the next reporting period we will construct a Genotype × Environment × Microbiome (GEM) model to evaluate the impact of local versus foreign microbiomes (environment) on different crops (genotypes). Key outcomes.Change in Knowledge:Increased evidence that organic crops are adapted to local conditions and microbiomes 1×; Change in Action:Indicates importance of historical production characteristics in seed choice and future propagation regardless of microbiome 1×;Change in condition:Farmers may be able to align microbiomes and production practices to promote pest suppression under climate change conditions 1×. Objective 3: Major activities.We conducted a literature review for soil fungi and bacteria sequencing conducted with the ONT MinION device. Based on this review, we developed nanopore a long-read metabarcoding library preparation protocol and metabarcoding data analysis pipeline for downstream analyses. Data collected. A preliminary sequencing run was conducted on 12 of 85 field soil samples collected on NY organic farms, some of which were replicated, along with cell and DNA mock community controls. Following de-multiplexing we evaluated simplex and duplex base called reads for each sample, filtered, and aligned sequences. Summary statistics and discussion: By adjusting filtering, we have reduced false positive alignments for control samples and can now correctly assign taxonomy to the genus level of the mock community controls. We are currently modifying our filtering and clustering approach to further improve alignment. Key outcomes.Change in Knowledge:Developed novel in-laboratory sequencing pipeline for soil microbiomes 1×; Change in Action:Ability to rapidly sequence soil microbiomes of organic farms 1×;Change in condition:Farmers can submit soil samples for rapid microbiome sequencing and decision support in final reporting period 1×.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Exploring the Chemical and Molecular Ecology of Plant and Microbes: Interactions, Advances, and Future Directions. (2024) International Chemical Ecology Short Course. Pennsylvania State University, College Park, PA. Published presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Casteel CL. Exploring the Chemical and Molecular Ecology of Plant-Microbe-Insect Interactions. (2024) Plant Breeding and Genetics Department Seminar Series, Cornell University, Ithaca, NY. Published presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Casteel CL. Adoption of sustainable soil management practices, crop defense capacity, and the soil microbiome. (2024) USDA NIFA Annual Chemical Ecology Multistate Meeting, Cornell University, Ithaca, NY.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Casteel CL. Adoption of sustainable soil management practices, crop defense capacity, and the soil microbiome. (2024) Cornell AgriTech Seminar Series, Cornell University, Geneva, NY.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Bloom EH, Economos Z, Casteel CL (2024) How Organic Practices Affect the Soil Microbiome. eOrganic. Webinar.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Bloom EH, Casteel CL (2024) The causes of soil microbiome mediated insect pest suppression in organic agroecosystems. Entomology Society of America. National Harbor, MD.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Bloom EH (2024) A novel socio-ecological approach for promoting areawide adoption of organic farming practices that enhance microbially mediated pest control. Eco-spatial summit, State College, PA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Economos Z, (2024). Cereal rye and canola cover crops uniquely influence dry bean pest resistance through microbiome mediation. American Society of Plant Biologists. Honolulu, HI. Published poster.


Progress 09/01/22 to 08/31/23

Outputs
Target Audience:New York State Farmers:During project initiation, we described our intent to consult and engage with a group of organic farmers and educators interested in microbiome conservation, soil health, localization of food systems, and climate change resilience. This included 85 commercial organic farmers and a select group of farmers in a stakeholder advisory committee (SAC). In YR1 we met with our SAC advisory committee to generate preliminary feedback on study design and prepare for our YR1 sampling effort. Meeting attendees (n = 7) included Steven Crist (Hudson Valley Seed Company/Four-Fold Farm); Zaid Kurdieh (Norwich Meadows Farm); Zach Pickens (Row 7 Seed Co.); Lia Babitch (Turtle Tree Biodynamic Seed Initiative); Elijah Goodwin (Stone Barns Center); Jason Grauer (Stone Barns Center), and Isabel Hoyos (Stone Barns Center). Our SAC represents a broad range of organic and transitioning farmers in NYS and minoritized groups. For example, our collaborator at Turtle Tree Biodynamic Seeds works extensively with a community of people with developmental differences. This SAC meeting informed our experimental approach for our climate change experiments (seeObj 2). National Farms:Our project is relevant to all US organic farmers (US organic operations ≈ 28,000). To promote engagement on the national level, we are working closely with eOrganic in the development of extension materials including a website and webinars (1 webinar per project year = 3 webinars total). With the support of Alice Formiga at eOrganic we have developed a website showcasing the project, highlighting the SAC, and providing resources on our research to the general public (https://eorganic.info/soilmicrobiome). This website will serve as a repository for products (e.g., webinars, manuscripts, extension manuals) generated by the project. Extension Agents:Through our prior microbiome research (see Grant Number: 2021-67012-35042) we have a target audience of 18 Cornell University extension personnel that have assisted with the development of organic farmer survey tools for the microbiome. We will continue to engage with these extension agents as we deliver the results of our microbiome assessment conducted (see Obj 1) in YR2 to our 85 commercial organic farmer collaborators. We also promoted our research with extension agents at the annual "All Hands" Cornell Cooperative Extension meeting (Ithaca, NY). Scientists and Academics:During the reporting period, our research was shared in 4x lectures for post graduate academics and graduate and undergraduate students (see Products). Total engagement for the academic environment was ≈150 individuals;In YR1, the results of our research were shared with academics at the Frontiers in Chemical Ecology Symposium (Max Planck Institute, Jena, Germany) and the American Society of Plant Biologists (ASPB) (Savannah, Georgia) Social media:Posts regarding our research and recruitment for the project on Twitter generated 2768 impressions (views); 215 engagements; 2 new followers; and 114 profile visits. Project results will continue to be shared via social media during the following reporting periods. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training activities:Microbiome extraction, sequencing, and analysis 1×; Phytohormone extraction and interpretation 2×; Machine learning 1×; Structural equation modeling 1×;Professional development:Conferences for junior scientists 2× (ASPB/EntSoc); Junior scientists co-hosted seminar series 1×; Grant writing and development for junior scientists 1×; Seminar presentations conducted by project team 4×; DEI Trainings (Project Biodiversify, Adult Mental Health First Aid,Fostering Well-being in Racialized Mentoring Environments) 3×; Mentoring (Graduate Mentoring and Well-being: Translating Research into Practice,Introduction to Equity-MindedMentoring,Creating Cultures of Mentoring and Well-being) 3X;IDP (Individual development plan) for junior and senior scientists 3×; Graduate student training for senior scientists 2×. How have the results been disseminated to communities of interest?Dissemination of results is integrated in Objectives 1-3 through the production of eOrganic webinars. In the next reporting period, we will detail the results of these Webinars. In our final reporting period, we will also discuss focus groups that will be hosted to determine appropriate messaging frames for a climate change resilience decision support tool (Sub-objective 3b) and the dissemination of information through rapid microbiome sequencing (Sib-objective 3c). In preparation for dissemination of information we have established an eOrganic community of practice website (https://eorganic.info/soilmicrobiome); conducted a meeting with our stakeholder advisory committee (SAC); presented our preliminary results at conferences and seminars (7×); and met with vegetable extension personnel to discuss the project and potential impacts. What do you plan to do during the next reporting period to accomplish the goals?Objective 1: Evaluate the benefits of long-term organic management for microbiome conservation We are developing two modeling approaches to improve our analysis. One uses machine learning, stability selection, and stepwise AIC to select farming practices that are influential on microbiome alpha and beta diversity, and differential abundance. The second uses structural equation modeling to the direct and indirect effects of economics, soil conditions, and farm characteristics on the microbiome, as mediate by farming practice adoption. Objective 2: Identify microbiomes that promote climate change resilience in crops From fall 2023 - winter 2024, we will collect cleaned market ready seed and soil from our SAC, along with characterizations of their farming practices. Microbiome sequencing for soil samples will be performed. Seeds will then be randomly selected from the lot and used in microbiome transplant experiments and climate change resilience evaluated. In brief, we will extract soil microbes which will be added to OMRI certified sterile (autoclaved) potting soil. Seeds from each of the SAC members will be planted in their natal microbiome, and sterilized controls. Because the same seeds are not produced by all of our stakeholders, multiple plant species (legumes, nightshades, and brassicas) will be evaluated in diverse microbiomes, which will also broaden the impact of our results. In the first experiment we will examine crop resilience to insect outbreak using aphids. A second set of experiments will examine crop resilience to drought stress. We are in the process of developing the methods to induce drought now. The experiments will be repeated at least three times and staggered over a 12-month period from spring 2024 - winter 2025. We will develop a 45-minute webinar that highlights our stakeholder's efforts to produce regionally adapted seed crops that are climate change resilient. Objective 3: Provide a microbiome decision support tool for organic farmers In the next reporting period, we will begin developing the hardware and standard operating procedures for a high throughput long read sequencing facility and decision support tool. We are currently in the process of hiring a highly skilled researcher to assist in decision support tool development. In brief, we will purchase the MinION long-read sequencing platform. Via these new sequencing resources, we will pilot a decision support tool in our final reporting period allowing NYS organic farmers to receive rapid microbiome sequencing.

Impacts
What was accomplished under these goals? Impact Statement. Issue:Farmers are grappling with the impacts of climate change globally, including increased extreme weather events and pest and pathogen outbreaks. We are using soil samples, laboratory and field experiments, and rapid sequencing to link the microbiome with climate change resilience in organic farms through plant health and inform farmer management through decision support. Methods/Preliminary Results:We characterized paired microbiome samples from 85 organic farms in New York State (NYS), and related microbiome characteristics (e.g., diversity) with specific farming practices. The preliminary analysis suggest soil microbiome diversity is highly dependent on the use of no-tillage, pre-planting practices (e.g., solarization), and fertilizer regimes (e.g., the use of mineral fertilizers). We are developing two modeling approaches to improve our analysis. One uses machine learning, stability selection, and stepwise AIC to select farming practices that are influential on microbiome alpha and beta diversity, and differential abundance. The second uses structural equation modeling to the direct and indirect effects of economics, soil conditions, and farm characteristics on the microbiome, as mediate by farming practice adoption. We also conducted a series of field and manipulative studies with combinations of cash and cover crops to assess the induction of plant hormones (ABA) that mediate climate change resilience. In our field and manipulative experiments, we found the microbiomes associated with some cover crops (cereal rye and hairy vetch) may reduce plant stress related to climate change in cash crops, as measured by abscisic acid concentrations in leaf tissues. In the next reporting period, we will work to identify microbiomes that promote climate change resilience in crops and start to develop a microbiome decision support tool for organic farmers. Taken together, our studies will determine if long-term organic management interacts with farming practices to predictably alter the microbiome and ecosystem services related to climate change. Broader outcomes.Climate change is now affecting agroecosystems in all regions of the world, through rising temperatures, changes in precipitation patterns, and increased pest and pathogen outbreaks. Our research is broadly applicable to any agroecosystem interested in leveraging soil microbiome conservation to promote climate change resilience. Details of Work done Toward Each Objective: Objective 1: Evaluate the benefits of long-term organic management for microbiome conservation Major activities.We created a survey tool to assess farm characteristics (time in organic management), farming practices, and collected soil samples from farmers accross New York State. We received 138 usable soil samples from 85 farming systems throughout NYS. We sequenced the soil microbiome of 85 NYS organic farms at MiSeq at Dalhousie University (Halifax, Nova Scotia). Preliminary analysis examiningthe impact of farm organic characteristics and practices on microbiome diversity was conducted. Data collected.DNA sequences:The V4-V5 region of the 16SrRNA, a region of the 18S SSU, and the ITS region of the rRNA gene was sequenced from DNA extracted from each soil sample to characterize the bacterial and fungal communities, respectively. Read preprocessing, data clustering, and post clustering were conducted, yielding the final set of 9,343 and 6,740 OTUs for bacteria and fungi, respectively. Taxonomy was then assigned yielded OTU and taxonomy tables for the soil samples. Phylogenetic tree construction was conducted.Farm and soil properties:Farm characteristics (time in organic management) and farming practices, for each sample were collected in the survey tool. We used the gridded soil survey geographic (gSSURGO) database rasters to retrieved representative values for the following soil properties: pH; available water content; organic matter; percent sand, silt, and clay; and erodibility. Summary statistics and discussion.We detected 6740 and 9343 unique OTUs for fungi and bacteria, respectively. OTU richness ranged from 651.13-1638.13 (mean = 1122.43; median = 1089.23) for fungi and 1078.18-6067.78 (mean = 4534.90; median = 4561.07) for bacteria. Fungi and bacteria were composed of 18 and 51 unique phyla, respectively. For fungi, 56.86% and 21.25% of OTUs belonged to the phyla Ascomycota and Basidiomycota. We observed OTUs were more evenly distributed across phyla for bacteria, with 24.79%, 12.85%, and 12.67% of OTUs belonging to the phyla Planctomycetota, Proteobacteria, and Chloroflexota, respectively.Our work with these microbiomes may indicate idiosyncratic relationships between diversity and ecosystem function, questioning whether conserving microbiome diversity per se is key for promoting biotic and abiotic resistance in farms. In the next reporting period, we may describe these idiosyncrasies in greater detail and the suites of practices that mediate microbiome diversity across farms and practices. Key outcomes.Change in Knowledge:Increased evidence for the factors mediating microbiome diversity in organic farming systems1×;Change in Action:Increase development of research related to the adoption of farming practices found to promote the microbiome and ecosystem function 1×; Increase extension tools geared towards the microbiome1×;Change in condition:Developed a basic understanding of the relationship between time in organic management, farming practices, and the microbiome 1×. Objective 2: Identify microbiomes that promote climate change resilience in crops Major activities.Randomized plots were constructed at two research farms in Upstate NY, Musgrave Research Station (CUAES) and Hudson Valley Farmhub. A cover crop treatment was grown for one season prior to the experiment, and then crimped. Tilled control plots were included. Then, each cash crop was planted within cover crop each treatment. Data collected.Field trials:Rhizosphere soil was sampled, bulked, and frozen for each treatment. Then, cash crop tissue was sampled for at least three plants per treatment plot and frozen in liquid nitrogen when the plants reached maturity before flowering/seeding. To extract the phytohormones, the tissue was lyophilized, then the metabolites were extracted. The concentration of abscisic acid (ABA), a hormone related with drought and climate change resistance in plants, was measured in field collected plants using HPLC/LCMS.Lab Trials:Microbiomes were transferred from the rhizosphere soil samples for each cover crop treatment. Cash crops were planted at the first soil microbe inoculation, then the microbiome slurries were re-applied to the soil twice a week. Then, metabolites were extracted using the same protocol from the field trials. Summary statistics and discussion.Cereal rye & hairy vetch cover crop residues reduced abscisic acid levels in multiple cash crops in both the field and laboratory experiments.Our results indicate that cover cropping may promote microbiomes that aid plants in hormonal responses linked with climate change resilience. In our next reporting period, we will be conducting a series of abiotic and biotic experiments to further link the microbiome with climate change resilience in organic farming systems. Key outcomes.Change in Knowledge:Increased evidence that cover cropping mediates the microbiome and climate change resilience on organic farms 1×;Change in Action:Identified specific cash and cover crop combinations that promote the microbiome and climate change resilience 1×;Change in condition:Farmers may be able to select cash and cover crops that promote the microbiome and climate change resilience 1×. Objective 3: Provide a microbiome decision support tool for organic farmers

Publications

  • Type: Peer Reviewed Journal Articles Status: Other Year Published: 2023 Citation: Bloom EH, Atallah SS, Casteel CL (2023) The causes of soil microbiome mediated insect pest suppression in organic agroecosystems. In prep.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Casteel CL (2023) Frontiers in microbial reprogramming of the plant defense system during plant-insect interactions. Frontiers in Chemical Ecology Symposium. Max Planck Institute of Chemical Ecology, Jena, Germany. Published presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Casteel CL (2023) Microbial remodeling of plant-insect interactions. Entomology Seminar Series, Cornell University, Ithaca, NY. Published presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Casteel CL (2023) Microbial remodeling of the plant to enhance vector performance. University of Georgia, Athens, GA. Published presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Casteel CL (2023) Microbial remodeling of plant-insect interactions. Biology Department, EGE University, Ismir, Turkey. Published presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Economos ZC, Bloom EH, Eddy EH, Menalled UD, Ryan MR, Casteel CL (2023) Cover-crop conditioned microbiomes show promise as tools to manage cash crop stress responses. Savannah, Georgia.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Bloom EH, Atallah SS, Casteel CL (2023) A novel socio-ecological approach for promoting areawide adoption of organic farming practices that enhance microbially mediated pest control. PPPMB Lecture Series, Ithaca, NY.