INTEGRATING COVER CROPS AND SHEEP GRAZING IN ALMOND ORCHARDS

Progress report for OW23-376

Project Type: Professional + Producer
Funds awarded in 2023: $75,000.00
Projected End Date: 03/31/2026
Grant Recipient: The Regents of the University of California, Agriculture and Natural Resoruces
Region: Western
State: California
Principal Investigator:
Julie Finzel
The Regents of the University of California, Agriculture and Natural Resoruces
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Project Information

Summary:

Interest in integrating cover crops and grazing into conventional almond farming practices is growing. However, almonds are harvested by shaking the nuts onto the ground, sweeping them to row middles and mechanically collecting them. Since about 70% of almonds are not pasteurized, the presence of grazing animals and manure on the orchard floor raises concerns about food safety; the industry standard to maintain food safety is to avoid grazing in almond orchards. 

Documented benefits of cover crops in orchards include more effective nutrient cycling, reduced fertilizer use, and increased water infiltration. Grazing further enhances these benefits by reducing herbicide use, synthetic fertilizers, and fuel for tractors. However, the actual food safety risks of sheep grazing in almond orchards are unknown. We propose to assess the presence of foodborne pathogens in orchard soils where cover crops are grazed by sheep.

For broader adoption of sheep grazing, in addition to data on food safety risks, producers need to know the economic feasibility of using sheep to manage vegetation in orchards. Currently, there is no cost analysis of grazing in orchards. There is a perception that grazing will cost more than conventional methods. It is also possible that grazing may cost less, or that higher returns could offset increased costs. A cost analysis will help producers understand the tradeoffs and make the best decision for their operations. We will compare the costs and returns of conventional almond production to the costs and returns in a livestock-integrated almond orchard system.

Project Objectives:
  1. Test for the prevalence and die-off of fecal pathogens in the soil of almond orchards grazed by sheep to understand the food safety risk of ground-harvested almonds in a grazed system.
  2. Complete a cost analysis comparing the costs and returns of conventional almond production to the costs and returns from a livestock and crop integrated almond production system.

Cooperators

Click linked name(s) to expand/collapse or show everyone's info
  • Dr. Edward R. Atwill (Researcher)
  • Theresa Becchetti (Researcher)
  • Rosie Burroughs - Technical Advisor - Producer
  • Julie Finzel - Technical Advisor (Researcher)
  • Dr. Brittney Goodrich (Researcher)
  • Steve Kistler - Producer
  • Dr. Fadzayi Mashiri (Researcher)
  • Rebecca Ozeran (Researcher)
  • Dr. Alda Pires (Researcher)
  • Bret Sill - Producer
  • Donald Thomas - Producer
  • Kaleb Thomas - Producer
  • Dr. Mohammad Yaghmour (Researcher)
  • Cameron Zuber (Researcher)

Research

Materials and methods:

Research objectives

  1. Test for the prevalence and die-off of fecal pathogens in the soil of almond orchards grazed by sheep to understand the food safety risk of ground-harvested almonds in a grazed system.
  2. Complete a cost analysis comparing the costs and returns of conventional almond production to the costs and returns from a livestock and crop integrated almond production system.

Project sites

The soil samples were collected from two orchards. The first is owned by the Burroughs family who own both the almond orchard and the sheep that graze the orchard floors. The site is located in Merced County and comprises two farms. Combined, the Burroughs have a total of 610 acres of almond orchards, 850 acres of rangeland and 770 acres irrigated pasture. Their products have been certified 100% organic for almost 20 years, though the farm has been implementing regenerative practices (including ICLS) even longer. The Burroughs graze their almond orchards primarily for weed control. As part of a very diversified farming operation, the Burroughs own their own flock of sheep. Flaming is used to clear the orchard floors for harvesting. The main soils on the farms are sandy loam soils of the Montpelier and Pents series.

The second almond orchard, in Kern County, is owned by Mr. Sill and was historically operated as a conventional almond orchard. In fall 2022, Mr. Sill began implementing regenerative agricultural practices including cover crops and sheep grazing in a portion of his almond orchard. Mr. Sill has incorporated biochar into his soil treatments and is seeking to reduce his reliance on herbicides and improve soil health and water infiltration in his orchards.

Research design, Data collection, and Analysis Methods

Treatments

All almond orchard acreage we include in our study was planted with cover crops. Within these orchard systems we established a grazed and ungrazed treatment. The ungrazed treatment was about one-quarter the size of the grazed treatment. Ungrazed treatment areas were mowed.

Randomization of sample locations within each orchard

Pathogen persistence and population size in soil is affected by several environmental factors like weather; soil temperature, moisture, and texture; organic matter; etc. (Sharma et al., 2019, Topp et al., 2003, and Underthun et al, 2018). In an almond orchard there are two micro-climate zones where these factors differ significantly. The wetting zone is a moist-temperate zone where soil remains moist due to irrigation, and temperature fluctuations may be more minimal due to shading from the canopy. Outside the wetting zone is a dry-arid zone where the soil will remain drier through the growing season and temperature fluctuations may be more severe due to higher sun exposure. These zones also represent two primary locations for potential contamination during harvest. The wetting zone is where almonds will first contact the soil when shaken from the trees, and may remain as the crop dries. The almonds are then blown and swept into the dry-arid zone in between the trees where they will be picked up from the ground and mixed with the soil in this area.

The Produce Safety Rule of the Food Safety Modernization Act (FSMA) addresses concerns about the feasibility of compliance for farms that rely on grazing animals, but does not require establishing waiting periods between grazing and harvest. However, farmers are encouraged to voluntarily consider applying intervals appropriate for the farm’s commodities and practices. Organic farmers follow the National Organic Program standards for raw animal manure, applying a 90-120 day interval between incorporating raw manure into the soil and harvest. Moreover, third-party food safety auditors have directed attention toward these integrated crop-livestock farms due to the possible contamination risk of nuts.

We characterized the longitudinal profile of the occurrence of bacterial pathogens and indicator species in orchard soils from cessation of sheep grazing until almond harvest. Seven pairs of sample locations were selected in the grazed treatment and three pairs of sample locations were selected in the ungrazed treatment. For each paired sample, one of the paired sample locations was within the wetting zone of irrigation; the second was outside the wetting zone. A random number generator in Excel identified the tree row to be sampled and the tree to be sampled. Tree rows on the external edge of an orchard were excluded from the randomization to reduce edge effects. Samples were collected at 0, 7, 14, 30, 60, 90, and 120 days post-grazing in both treatments. In the grazed treatment seven trees were selected at each sampling interval (different trees at every sampling) (7 trees = 14 paired samples; 14 x 7 sampling dates = 98 samples/year/orchard). In the ungrazed treatment three trees were selected at each sampling interval (3 trees = 6 paired samples; 6 x 7 sampling dates = 42 samples/year/orchard). Post-grazing samples totaled to 560 samples each year. Forty pre-grazing samples were collected in the same manner, 20 in Year 1 and 20 in Year 2 (10 paired samples in each orchard per year). Two paired samples in the ungrazed treatment (2 trees = 4 paired samples) and 3 paired samples (3 trees = 6 paired samples) in the grazed treatment.

Soil sampling

Trees were divided into quadrants based on cardinal directions - northwest, northeast, southeast, and southwest - and soil sub-samples were taken under each tree from three quadrants. Soil sub-samples from under each tree were placed in resealable plastic bags and mixed. Samples from the row middles were collected from either the south or west side of the tree. Actual sampling depended on which direction the rows ran. For example, if the almond trees were in rows that ran north to south, the row middles fell on the west and east sides of the trees. In that case, soil sub-samples were collected from the west side of the tree. Similar to the soil samples from under the trees, three sub-samples were mixed together. Using the example above in which tree rows ran north to south, three soil sub-samples were collected from north to south, at least one meter apart.

At each sample location within the orchard, a sterile sampling scoop (Spectrum, New Jersey, USA) was used to collect three or four soil subsamples of about 50 grams each from the upper 2 inches of soil, soil samples were placed into resealable plastic sample bags and shipped overnight on ice to the University of California, Davis.

Bacterial analyses

UC Davis provided analyses on pathogens of interest for food safety as well as indicator bacteria that sheep fecal matter may host.

Detection of Pathogens (Atwill Lab)

For each sample location and sampling date, 25 grams of mixed soil were placed into a 710 ml Whirl-Pak(R) Homogenizer Blender Filter Bag (MilliporeSigma, Darmstadt, Germany) and incubated in 225 ml tryptic soy broth (TSB; Difco, San Jose, CA) on a shaking incubator (50 rpm) at 25° C for 2 hr followed by 42° C for 8 hrs. Then, 0.5 ml of the TSB enrichment were transferred into 4.5 ml of TSB and modified Enterohemorrhagic E. coli broth (mEHEC). These secondary TSB and mEHEC (BioControl Systems, Inc., Bellevue, WA) enrichments were screened for E. coli O157, stx 1/2 genes, and Salmonella using quantitative-PCR (qPCR) (Atwill et al., 2015; Baker et al., 2019; Suo et al., 2010). All suspect positives from the qPCR screen were plated onto their respective selective agar and suspect colonies qPCR-confirmed for E. coli O157 and Salmonella as previously described (Atwill et al., 2015; Gorski et al., 2011). Suspect shigatoxin producing E. coli (STEC) colonies were confirmed using multiplex conventional PCR to identify O26, O45, O103, O111, O121, O145 and O157 serogroups of E. coli (Paddock et al., 2012).

Generic E. coli Most Probable Number (MPN) (Pires Lab)

A subset of soil samples were cultured for indicators of contamination and generic E. coli quantification. To quantify E. coli in soil, we used a standard tube method with serial dilutions up to 10-6 in quadruplicate followed by streaking onto CHROMagar ECC to quantify E. coli as described previously (Patterson et al., 2018). At least one presumptive positive isolate per sample was purified and confirmed using a standard PCR method (Chen and Griffiths, 1998). MPN series cell densities were calculated based on dilution to extinction using an MPN Calculator (Curiale, 2004). Fecal coliforms were assayed using the USEPA 1680 protocol (Reynnells et al., 2014).

Almond yield assessment

Yield per acre for the different treatments was assessed in August after trees were shaken. For each replicate, almond fruit was collected from the ground following standard on-ground commercial harvesting techniques. Subsamples of a minimum of five pounds of harvested nuts from each replicate were collected to run a turnout analysis to separate almond kernels from other materials such as hulls, shells, dried leaves, wood sticks, soil particles, etc. This allowed us to determine the percentage of almond kernels in the gross weights and extrapolate the values to yield per acre based on the harvested area. Yield from each orchard was compared to historical average almond yields per orchard.

Quantifying economic impacts

We used partial budget analysis methods to evaluate the changes in economic costs and benefits from integrating livestock into almond orchards in comparison to using conventional methods. We gathered information for cost and benefit estimates through conversations with participating growers and fellow Co-PIs and collaborators on this proposal. As a baseline for the conventional methods, we used the most recent Almond Cost and Returns Studies and updated costs and returns where necessary (https://coststudies.ucdavis.edu/en/current/commodity/almonds/ ). The Almond Cost and Returns Studies were updated in 2023. Potential increased costs associated with integrating livestock include: contract grazing fees and repairs to irrigation equipment. Potential benefits include: decreased herbicide use and decreased labor for mowing and/or navel orangeworm sanitation. Quantifying these benefits and costs helps growers evaluate their current practices in comparison to integrating livestock. 

Manure pellet counts

Just prior to harvest, after the orchard floor is cleaned, we surveyed for manure pellets under 50 trees in each orchard. We used the same Excel program as mentioned above to randomly identify the trees sampled. Under each tree sampled a one meter square quadrat was placed three times: 1) under the tree, right next to the trunk; 2) under the tree canopy, near the dripline, and; 3) in the row middle. Each time the quadrat was placed a visual survey for manure pellets was conducted and manure pellets were counted

Research results and discussion:
Partial Budget Analysis Summary Table
Partial Budget Analysis Summary Table

1st year Results

  • Fecal Samples
    • 20 samples collected on both farms
    • Farm A – 6 out of 20 positive for Coli O157:H7
    • Farm B – 9 out of 20 positive for STEC (Shiga Toxin E. Coli – potential to cause disease)
  • Soil Samples – 280 samples total
    • Farm A – 1 positive for STEC on Day 0 (wet zone)
    • Farm B – 2 positive, one for E. coli and one for STEC, both on Day 60, same sample (wet zone)
  • Manure surveys – surveyed under 50 trees at both farms
    • Farm A – 4 whole and 2 partial; wildlife scat noted
    • Farm B – data not available
Participation Summary
2 Producers participating in research

Research Outcomes

Recommendations for sustainable agricultural production and future research:

Soil-borne Fecal Pathogen Testing

We recently began collection of our second year of data. Preliminary results from the first year of data collection support the current rule to remove grazing animals 120 days prior to harvest. Our data show fecal pathogens present at Day 0 at the site in Kern County and Day 60 at the site in Merced County. No other positive samples were found. All samples that tested positive were found in the 'wetting zone' or irrigated area under the trees. This data is preliminary information that demonstrates that sheep grazing in almond orchards does not increase the risk of food-borne pathogen contamination in ground-harvested almonds.

Partial Budget Analysis - Benefits and Trade-offs of Integrating Sheep Grazing in Almond Orchards

Dr. Goodrich completed data collection for the partial budget analysis and summarized results. Increased costs include paying the sheep producer $60/acre for two grazing passes in an orchard, plus labor spent coordinating timing of grazing for a total of $151/acre increased cost. Reduced costs include less mowing, less herbicide use, and less compost application for a total of $158/acre less. Net change is $7 increase in profit per acre. It should be noted that mowing the orchards is not always necessary, particularly in drought years.

I have tried to update the cooperators on this project, but I am not able to modify the list. It should be noted that Dr. Brittney Goodrich and Rebecca Ozeran have moved on from their positions with UCANR and are no longer part of the project. Dr. Goodrich completed her portion of the project before leaving, the partial budget analysis. Rebecca's primary role was to provide connections among livestock producers and almond growers in Fresno County. Rebecca shared her contacts before her departure. As a result, we do not anticipate any negative impacts from the change in our team.

Education and Outreach

1 Consultations
1 Curricula, factsheets or educational tools
2 Webinars / talks / presentations
3 Workshop field days

Participation Summary:

35 Farmers participated
Education and outreach methods and analyses:
  • We held a field day in the fall of 2023 to share information about sheep grazing in orchards as an option for cover crop and weed management. At that meeting we presented an overview of the objectives and methods for this project. The meeting was well-attended by producers and pest control advisors. (Workshop/field day)
  • We also held an introductory meeting for our grower cooperators at the Burroughs Family Farm in the fall of 2023. This meeting was well-attended and included question and answer and discussion time for our grower cooperators. (workshop/field day)
  • We presented a poster in December 2024 at the annual Almond Board Conference in Sacramento showcasing this project and our findings to date. More than 3,600 people attended the three-day event. ABC2024.Poster.Finzel (educational tool)
  • In the fall of 2024 we held an update meeting for our grower cooperators at the UC Cooperative Extension office in Merced County. We shared with our grower cooperators the results from Year 1 sampling, discussed the project to date and answered questions. (workshop/field day)
  • PI Finzel was contacted regarding sheep grazing in a pistachio orchard as a result of her work on this project. This included an hour long phone consultation and a site visit to the orchard. (consultation)
Education and outreach results:

No results to date. Surveys were not conducted after the workshops/field days, however, anecdotal feedback and interest after the field days was strong and attendees asked insightful questions that showed significant interest in using sheep as a management tool in orchards.

Education and Outreach Outcomes

Recommendations for education and outreach:

With the first year of data collection complete we were excited to start sharing some preliminary findings. We organized a meeting (mentioned above) for our grower cooperators to share updates and ask questions. We presented a poster at the annual Almond Board Conference in December 2024 in Sacramento. The American Sheep Industry has requested that we present the findings of this project at their annual meeting in January 2026. Currently we are planning an in-person cooperator meeting early May 2025 and we were invited to present a summary of the project internally to UCANR academics and administration in late April 2025.

The partial budget analysis is essentially complete and we have shared a summary of those results at the meetings listed above. We plan to publish the results of the partial budget analysis as part of the food safety findings from this study, so we have not prepared any educational materials to share this data at this time.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and should not be construed to represent any official USDA or U.S. Government determination or policy.