Current Research in Farming Systems and Agroecological Science


    Anaerobic Soil Disinfestation (ASD) to Control Verticillium and Weed Seed Germination

  • ASD was developed in the Netherlands and Japan independently and through the work of UCSC researchers and their partners is being optimized for California strawberries. The first successful ASD trial in the US was conducted at the CASFS farm to control Verticillium wilt in organic strawberries in 2003. In the 2014-15 season, over 1,000 acres of strawberries and cane berries in California, of which 80% are organic fields and 20% conventional (buffer zone), are being produced using ASD.

    ASD starves pathogens and weeds of oxygen. Researchers introduce a carbon source such as chopped cover crops, wheat bran, or molasses to the strawberry bed, then irrigate and tarp the beds to create temporary anaerobic conditions. This technique, known as anaerobic soil disinfestation (ASD), has been tested for a number of seasons at the CASFS/UCSC Farm and has been shown to control the soil pathogen Verticillium dahliae, a major diseases of strawberries.

    Several studies funded by grants from the US Department of Agriculture and the California Strawberry Commission have expanded this initial work to examine the efficacy of various carbon sources, irrigation techniques, tarp types, and tarping periods to create sufficient anaerobic conditions to control weed seed germination and V. dahliae. Research is underway at the UCSC Farm and at cooperator farms in the Central Coast region focusing on understanding the mechanisms of how ASD works, and how to optimize its use and effectiveness in terms of timing, soil temperature, and carbon source used for specific target pathogens. A 2017 grant of $2.5 million from the USDA will expand this effort to locations in Florida, North Carolina, and Tennessee to help fine tune the ASD technique in different climate zones and crops.

    Read about the 2017 USDA Grant to expand ASD research

    Learn more about ASD research on the Shennan Lab Group's website.

    Watch a video about the CalCORE project to improve organic vegetable and strawberry rotation systems in the Monterey Bay region. 

    CASFS/UCSC participants: Joji Muramato, Carol Shennan, Darryl Wong, Graeme Baird, Marguerite Zavatta. Cooperators: Mark Bolda, Karen Klonsky, Steve Koike, UC Cooperative Extension, Farm Fuel, Inc. Funding: U.S. Department of Agriculture.

    Selected related publications – 

    • Butler, D.M., E.N. Rosskoph, N. Kokalis-Burelle, J. MuramotoC. Shennan, S. Koike, M. Bolda and O. Daugovish. 2009. Impact of Anaerobic Soil Disinfestation on introduced inoculum of Phytophthora capsici and Verticillium dahliaePhytopathology 99:S18
    • Coombs, Amy. 2013. Growing berries without bromideSanta Cruz Good Times.
    • Fennimore, S., et al. 2013. TIF film, substrates and nonfumigant soil disinfestation maintain fruit yields. California Agriculture 67:3, 139–146.
    • Lasnier, G. 2011 UCSC wins $2.6 million grant for orgnanic farming research. UCSC News.
     Muramoto, J., C. Shennan, G. Baird, M. Zavatta, S. T. Koike, O. Daugovish, M. P. Bolda, S. K. Dara, K. Klonsky, and M. Mazzola. 2014. Optimizing anaerobic soil disinfestation for California strawberries. Acta Horticulturae 1044:215-220.
    • Rosskopf, E., Serrano-Pérez, P, Hong, J., Shrestha, U., del Carmen Rodríguez-Molina, M., Martin, K., Kokalis-Burelle, N., Shennan, C., Muramoto, J. and D. Butler. 2016. Anaerobic soil disinfestation and soil borne pest management.  In: Organic Amendments and Soil Suppressiveness in Plant Disease Management.
    • Shennan, C., J. Muramoto, G. Baird et al. 2016. CAL-collaborative organic research and extension network: on-farm research to improve strawberry/vegetable rotation systems in coastal California. Acta Hortic. 1137. Proc. Int. Symp. on Innovation in Integrated and Organic Horticulture (INNOHORT) Eds.: S. Bellon et al.
    • Shennan, C., J. Muramoto, M. Mazzola, D. Butler, E. Rosskoph, N. Kokalis-Burelle, K. Momma, Y. Kobara, J. Lamers. 2014. Anaerobic soil disinfestation for soil borne disease control in strawberry and vegetable systems: Current knowledge and future directions. Acta Horticulturae 1044:165-175.
    • Shennan, C., Muramoto, J., Koike, S., Bolda, M., Daugovish, O., Mochizuki, M., Rosskopf, E., Kokalis-Burelle, N., and Butler, D. 2010 Optimizing anaerobic soil disinfestation for strawberry production in California. Proceedings of the Annual International Research Conference on Methyl Bromide Alternatives and Emissions Reductions, Orlando, FL. p 23.1 - 23.4
    • Shennan, C., J. Muramoto, M. Bolda, S. T. Koike, O. Daugovish, E. Rosskopf, N. Kokalis-Burelle, and K. Klonsky. 2007. Optimizing anaerobic soil disinfestation: an alternative to soil fumigation. Page 40-1 to 40-4 in Proceedings, Annual International Research Conference on Methyl Bromide Alternatives and Emission Reduction, San Diego, CA.
    • Shennan C., J. Muramoto J., G. Baird, et al. 2011. Anaerobic soil disinfestation: California. In: Proceedings, Annual International Research Conference on Methyl Bromide Alternatives and Emissions Reductions, Oct. 31–Nov. 2, 2011. San Diego, CA. Abstr. 44.


  • Organic Seedling Production, Demonstration, and Training for Annual Vegetable, Flower and Herb Growers

  • Producing quality organic seedlings for vegetable, flower, and herb production is challenging for seasoned growers, and more so for beginning farmers and nursery operators. This project will increase the viability of vegetable, herb, and flower growers and nursery operators by improving the success and sustainability of their seedling production. This project takes place at the UCSC Farm and builds on over forty years of organic specialty crop production and training. Through trials and improved practices, the project will demonstrate and teach increased efficiency, quality, and sustainability in seedling production.

    The project includes a soil mix trial comparing a standard commercial organic soil mix, soil mix amended with sifted compost, and soil mix amended with compost and bone meal, using broccoli, peppers, and sunflowers as test crops. Data on germination, seedling size, "holding" success, and other factors will be collected.

    CASFS/UCSC participants: Christof Bernau, Kellee Matsushita-Teng, Skye McIntire. Funding: California Department of Food & Agriculture Specialty Crop Block Grant.

    Selected related publication –
    CDFA grant supports organic greenhouse production and training, UCSC News


  • Phylogenetic Disease Ecology of Plants

  • Pathogens can often attack multiple species. This could affect how pathogens spread and the impact of the diseases they cause. Two host species are more likely to share a pathogen when they are closely related to each other.  This multi-year research project explores three important predictions that follow from this simple idea. The first is that in nature, the complex networks of plants and their pathogens will be structured in predictable ways that reflect the evolutionary relationships among the species. Second, when a new plant species (such as a crop) is introduced into an area, pathogens will “spill over” from close relatives already growing there. Third, because pathogens are less likely to spread between species that are not closely related, mixtures of crop species could be designed to suppress disease pressure in agriculture. In the process of testing these predictions, the we will develop new analytical tools for the study of plant disease and for the protection of agriculture and other plant resources. The large training component of this project will include high school classes, college classes, senior thesis students, and PhD students. Participating students will engage in active, experiential learning in forest ecology, ecological monitoring, agroecology and ecological horticulture, and both laboratory and bioinformatics aspects of metagenomics.

    For each of the three components of the project, we will take advantage of a quantitative model previously developed and validated that predicts how pathogen host ranges are constrained by the evolutionary relationships among host plants. In a novel application of network theory, we will incorporate phylogenetic structure into network models for plant-pathogen interactions. We will use a metagenomics approach (identifying all fungal species growing inside plants by extracting and sequencing their DNA, sometimes called an eDNA approach) to characterize the plant-pathogen networks of three plant communities and will test predictions against the empirical networks. Novel hosts will be used in a transplant experiment in the field and an inoculation experiment in the laboratory to measure which local fungi colonize novel hosts, and how the phylogenetic structure of local plant-fungus networks affects fungal spillover to novel hosts. Finally, collaborating with the CASFS certified organic research farm, we will test whether the “Dilution Effect” lowers disease pressure in cover crop mixtures, and whether greater phylogenetic distance among intercropped species suppresses disease.

    CASFS/UCSC participants: Ingrid Parker, Greg Gilbert, Darryl Wong. Funding: National Science Foundation (NSF DEB-1655896) 2017-2020

    Selected related publication –
    Diverse campus landscapes are ideal outdoor laboratories—and classrooms, UCSC News


  • CDFA 2014 Specialty Crop Block Grant Program—Specialty Crop Farmer Training and Toolkit for a Sustainable Future

  • This project builds on over 40 years of organic specialty crop production and training of beginning farmers at the 30 acre farm and three acre market garden of the Center for Agroecology & Sustainable Food Systems (CASFS) at the University of California, Santa Cruz (UCSC). It also builds on a CASFS-led regional collaboration for beginning farmer training and the CASFS online curriculum for agriculture educators. This new project will produce a specialty crop Toolkit featuring eight to ten Grower Guides in English and Spanish on specific crops grown using organic and sustainable production practices. These crops will be demonstrated at the CASFS farm, with distinct blocks of mixed vegetables and cut flowers providing data for publications covering varietal choices, production practices, and economic analysis. Specialty crop classes, field days, and mentoring sessions using these materials and demonstration blocks will be delivered to over 250 new and beginning small-scale farmers during the project. 

    See the Grower Guides series developed as part of this specialty crops grant.

    CASFS/UCSC participants: Christof Bernau, Martha Brown, Kirstin Comerchero, Sky DeMuro, Orin Martin, Eliza Milio, Jan Perez, Darryl Wong Funding: California Department of Food and Agriculture Specialty Crops Block Grant Program


  • Implementing Anaerobic Soil Disinfestation for Soilborne Disease Control in Strawberries and Apple Nurseries

  • Anaerobic soil disinfestation (ASD) controls soilborne disease by acid fermentation process through anaerobic decomposition of incorporated carbon sources (see above). Rice bran is the most typical carbon source for ASD in California. However the cost of rice bran is increasing and the use of cover crop as a carbon source may be able to reduce the cost and the carbon footprint of the practice.

    This 3-year grant supports an ongoing pilot study iat the CASFS/UCSC Farm comparing Sudan grass or wheat as cover crop, each cover crop plus reduced rate of rice bran, rice bran only, and un-treated check. Soil N dynamics and strawberry yield are being monitored.

    CASFS/UCSC participants: Carol Shennan, Joji Muramoto

    Funding Source: US Department of Agriculture Methyl Bromide Transition Program


  • Insect Biodiversity in Santa Cruz Area Urban Gardens: Baseline Date and an Opportunity for Undergraduate Research

  • Urbanization threatens biodiversity, but urban gardens may provide an oasis for biodiversity while also  providing social and economic benefits. Anecdotal and empirical evidence suggests that urban gardens provide habitat and improve air quality and protect nearby residents from flooding. Gardens can increase multiculturalism, cross-cultural exchange, and provide spaces for meetings and recreational activities.  Gardens have been linked to increased health of residents and garden produce can sometimes be sold, contributing to local economies. Insects are diverse and abundant organisms.

    In agroecosystems, including urban gardens, insects provide important services, such as pollination and pest control. However, few studies have examined the drivers of insect biodiversity in urban gardens, and the implications of this diversity for pollination and pest control services.

    This project examines insect biodiversity in 19 urban gardens in the Central Coast region, including the handworked gardens at the UCSC Farm and UCSC’s Alan Chadwick Garden. Garden study sites capture a range of landscape diversity (e.g. forest, farmland, pasture, or urban sprawl), a range of economic status, and a large degree of cultural diversity. Insect sampling focuses on 5 groups including one group of pollinators (bees), and four groups of organisms that provide pest control services (ants, spiders, wasps, and ground beetles). UCSC undergraduates are assisting with sampling insects and plants, and students with interest in Geographic Information Systems (GIS) are examining the landscapes surrounding each study site.

    Project goals include collecting preliminary data on insect biodiversity in gardens in communities that differ in surrounding landscape, economic status, and ethnic backgrounds; laying the groundwork for a research program investigating biodiversity and ecosystem services in urban habitats; and providing a research umbrella under which UCSC undergraduates can complete senior exit internships and theses.

    CASFS/UCSC participants: Stacy Philpott, UCSC Research Specialist Peter Bichier, UCSC undergraduate students Simone Albuquerque, Stephanie Coronado, Michelle Otoshi, Robyn Quistberg, and Casey Wing. Cooperators: City of San Jose Community Gardens, City of Santa Cruz City Gardens, Salinas Chinatown Garden, ME Earth, Our Green Thumb at Monterey Institute of International Studies, Seaside Giving Garden, Mi Jardin Verde, Homeless Garden Project, Live Oak Grange, Aptos Community Garden, Salinas Community Garden, The Forge at Santa Clara University. Funding: UCSC New Faculty Research Grant.


  • Natural Enemies in the Garden

  • In urban agroecosystems, ecological functions such as pest predation by insect natural enemies result in ecosystem services that increase crop life and production. This study examines drivers of pest predation services in urban gardens and correlate services with garden features. Observational and manipulative research on the relationship between aphid pests and ladybeetle predators are used to ask: 1) what local or landscape characteristics of gardens correlate with abundance and taxonomic and functional diversity of predators in urban gardens? 2) What features of gardens or predator communities enhance predation services? 3) What local pest management strategies do practitioners employ in each respective urban garden?

    This research aims to contribute to understanding impacts of community biodiversity and composition on ecosystem services, and of potential ecological mechanisms and social practices enhancing services in urban agroecosystems.

    CASFS/UCSC Participants: Monika Egerer, Stacy Philpott  Funding : Heller Agroecology Graduate Student Research Grant

See Also