Sponsoring Institution
National Institute of Food and Agriculture
Project Status
Funding Source
Reporting Frequency
Accession No.
Grant No.
Project No.
Proposal No.
Multistate No.
Program Code
Project Start Date
Sep 1, 2023
Project End Date
Aug 31, 2027
Grant Year
Project Director
Pires, A. F.
Recipient Organization
DAVIS,CA 95616-8671
Performing Department
Non Technical Summary
Grazing sheep or other animals to convert cover crops to manure infield has a number of practical benefits such as negating labor and costs associated with manure transport, reducing pests, and increasing soil fertility and soil health. Given these benefits, there has been increased interest in the use of cover crops and livestock grazing in nut orchards (almonds, walnuts and pistachios). However, grazing livestock are natural reservoirs for foodborne pathogens, and diet type can increase foodborne pathogen shedding in manure and affect their survival in the soil. While many growers consider livestock grazing of cover-crops on orchards as a way to enhance soil health and environmental benefits, recent concerns about microbial food safety are limiting expansion of this practice because livestock grazing may introduce pathogens into soil with a potential for transfer to nuts. Therefore, we are proposing a multi-regional integrated research-extension approach to fully assess the benefits of livestock integration via cover-crop grazing on bacterial population dynamics, soil health, pest control and economic outcomes to enhance the value of cover crops while limiting food safety risks in organic orchards in two distinct agroecological regions in California. The overall goal of this proposal is to improve the microbial food safety and productivity of organic nuts while maintaining the value of integration of livestock and cover crops in nut production while limiting food safety risks and environmental impacts, and promoting sustainability and biodiversity.
Animal Health Component
Research Effort Categories

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
Goals / Objectives
Our long-term goal is to facilitate adoption of organicintegrated crop-livestock systems (ICLS) practices within nut and fruit agriculture throughout the United States, by leveraging the research outputs described in this proposal to create a decision analysis tools encompassing food safety risk, economic cost/benefit, soil enhancement, water conservation, and pest management. These tools would be employed by a diverse range of stakeholders (growers, educators, policymakers, certifiers) to implement and regulate these systems in an evidence-based, economical, and sustainable fashion.The overall objective of this proposal is to develop on-farm research plots in which livestock are integrated into perennial nut crop systems in major production zones to quantify the impacts of sheep grazing of cover crops in organic orchards on soil ecosystems, suppression of common pests of high economic importance, food safety risks, and socioeconomic metrics. Our specific objectives are to measure effects of integrated crop-livestock systems (ICLS) on 1) N availability and soil health (Activity 1); 2) presence and persistence of navel orangeworm (Activity 2); 3) determination of the optimal time-interval between grazing and nut harvesting as a function of environmental & soil parameters to reduce foodborne contamination (Activity 3); 4) determination of the economic costs and benefits of grazing sheep in organic tree nut orchards (Activity 4); and 5) development of an outreach program to guide the implementation of ICL systems in nut production (Activity 5).
Project Methods
Field sites: We will establish field research trials in mature commercial almond, walnut and pistachio orchards located in the Sacramento Valley (SV) and the San Joaquin Valley (SJV) (n=6 trials). Experimental design and management: Four treatments will be established in a randomized split block design with three replicates. Winter cover as main plot treatments and grazing as subplots will be implemented to tease out impacts of cover crop and grazing in isolation or combined. Treatment at the main plot level will consist of 1) planted cover crop (CC) or 2) spontaneous resident vegetation (RV). Grazing treatments will consist of (3) one high density short duration grazing event to terminate cover (G) or 4) ungrazed vegetation (NG), established on subplots by fencing. Plots will be established across the orchard alley on both sides of three tree rows (6 middles). Tree berms will be managed according to grower practices and NG winter covers will be terminated at the time of grazing by mowing. A similar cover crop mix adequate for grazing and to these production zones will be planted at all orchards. Activity 1: Above-ground vegetation biomass and litter quality will be measured before grazing or mowing. Total C and N content of dried above ground plant samples will be measured. Composite soil samples will be taken and analyzed for: Total C and N , POM, pH, CEC, soil inorganic N pools, dissolved Organic C and N pools, Microbial biomass C and N, and Potential Mineralized Nitrogen.Soil samples will be taken in the alleyways at the interface between tree roots and the orchard middles at termination and four weeks following termination to capture shifts in soil health chemical and physical metrics relevant for assessing salinity (EC), compaction (bulk density) and water capture (infiltration rates). Activity 2: Each year in late October and March, all plots at all orchard sites will be surveyed to determine the abundance of remnant nuts prior to ground cover development and sheep grazing activity and post grazing. Each year in early November, cohorts of remnant nuts infested with navel orangeworm will be placed into the various experimental plots. Each year around March 1 a series of egg traps will be placed into the experimental plots to measure egg deposition by first flight navel orangeworm females. Activity 3: A repeated cross-sectional sampling scheme will be conducted in almond, walnut and pistachios orchards (3 nut types X 2 regions X 3 years),following the treatment : 1) planted cover crop (CC), 2) spontaneous resident vegetation (RV) [main plots] and 3) high density grazing (G) and ungrazed vegetation (NG) (planted cover crop (CC), spontaneous resident vegetation (NG) [subplots]. Each orchard will be sampled six times following the growing cycle. Soil, fecal, air and leaf samples will be collected and tested for E. coli O157:H7, non-O157 STEC, Salmonella and indicators of fecal contamination. Further molecular analysis ( WGS of isolates and microbiota analysis) will be conducted from a subset of the samples. Environmental factors, treatment and orchard effect will be analysed using multilevel logistic regression models. A decision- making tool using Bayesian Belief Networs. Activity 4: To quantify associated economic costs and benefits, we will begin by conducting three Cost and Returns Studies for organic almond, pistachio and walnut orchards. Once the cost and returns studies are completed for each crop, we will develop an interactive decision tool that incorporates partial budget analysis methods to analyze a producer's decision of whether to incorporate animal grazing into their organic tree nut production system. Acomprehensive online and in-person (mixed model) outreach program will be developed to provide training for organic producers adopting crop-livestock integration, and industry leaders who seek to purchase from sustainable suppliers.