INTEGRATING COVER CROPS AND SHEEP GRAZING IN ALMOND ORCHARDS

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 will be 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 will be planted with cover crops. Within these orchard systems we will establish a grazed and ungrazed treatment. The ungrazed treatment will be about one-quarter the size of the grazed treatment. Ungrazed treatment areas will be 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 will characterize 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 will be selected in the grazed treatment and three pairs of sample locations will be selected in the ungrazed treatment. For each paired sample, one of the paired sample locations will be within the wetting zone of irrigation; the second will be outside the wetting zone. A random number generator in Excel will identify the tree row to be sampled and the tree to be sampled. Tree rows on the external edge of an orchard will be excluded from the randomization to reduce edge effects. Samples will be collected at 0, 7, 14, 30, 60, 90, and 120 days post-grazing in both treatments. In the grazed treatment seven trees will be selected each year (7 trees = 14 paired samples; 14 x 7 sampling dates = 98 samples/year/orchard). In the ungrazed treatment three trees will be selected each year (3 trees = 6 paired samples; 6 x 7 sampling dates = 42 samples/year/orchard). These samples total to 560 samples. Using Excel, 40 additional samples will be randomly selected and sampled without regard to treatment; five paired samples per orchard per year.

Soil sampling

Trees will be divided into quadrants based on cardinal directions - northwest, northeast, southeast, and southwest - and soil sub-samples will be taken under each tree from three quadrants. Soil sub-samples from under each tree will be placed in resealable plastic bags and mixed. Samples from the row middles will be collected from either the south or west side of the tree. Actual sampling will depend on which direction the rows run. For example, if the almond trees are in rows that run north to south, the row middles will fall on the west and east sides of the trees. In that case, soil sub-samples will be collected from the west side of the tree. Similar to the soil samples from under the trees, three sub-samples will be mixed together. Using the example above in which tree rows run north to south, three soil sub-samples will be 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) is used to collect three soil subsamples of about 50 grams each of the upper 2 inches of soil which are placed into resealable plastic sample bags and shipped overnight on ice to the University of California, Davis.

Bacterial analyses

UC Davis will provide 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 are 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 are 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 are then 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 are 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 are 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 will be cultured for indicators of contamination and generic E. coli quantification. To quantify E. coli in soil, we will use 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 will be purified and confirmed using a standard PCR method (Chen and Griffiths, 1998). MPN series cell densities will be calculated based on dilution to extinction using an MPN Calculator (Curiale, 2004). Fecal coliforms will be assayed using the USEPA 1680 protocol (Reynnells et al., 2014).

Almond yield assessment

Yield per acre for the different treatments will be assessed in August after trees have been shaken. For each replicate, almond fruit will be collected from the ground following standard on-ground commercial harvesting techniques. Subsamples of a minimum of five pounds of harvested nuts from each replicate will be 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 will allow 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 will be compared to their historical average almond yields.

Quantifying economic impacts

We will use 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 will gather 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 will use the most recent Almond Cost and Returns Studies and will update costs and returns where necessary (https://coststudies.ucdavis.edu/en/current/commodity/almonds/ ). The Almond Cost and Returns Studies are planned to be 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 will allow growers to evaluate their current practices in comparison to integrating livestock. If the costs of integrating livestock outweigh the economic benefits, it’s important to note that growers may also receive premiums for almonds marketed that were produced using regenerative practices, such as integrating livestock. In this case, we will be able to calculate the minimum premium necessary to justify livestock integration. 

Addressing additional grower concerns

Motion-triggered trail cameras will provide photos and/or videos of sheep grazing behavior in orchards. Cameras can help to identify the frequency of concerning impacts such as damage to drip lines or excessive impacts to tree bark. They can also record daily images to record cover crop consumption as an indicator of grazing efficacy. Images and videos can be used in field days to share information about sheep behavior with growers interested in grazing orchards.

Manure pellet counts and sieving 

After sheep are removed from the orchards sheep pellets will be counted at 0 and 120 days. Areas with high, medium, and low density of manure will be identified. For example, water trough and bedding areas are expected to receive high manure deposition. Half-meter belt transects will be used in high-, medium-, and low-density representative areas using a clicker counter to count manure pellets.

Subsamples from harvested nuts will also be processed to assess presence of manure and pellets at harvest. Subsamples will be weighed and then air dried at room temperature. Air dried weight will be recorded and then subsamples will be sieved using U.S. standard sieves (Thermo Fisher Scientific, Fresno, CA). Sieve mesh sizes will be selected to separate large material (e.g., almond fruits, sticks, etc.) and small material (e.g., soil) from manure pellets. Each subsample will be mechanically sieved at the same strength and time. Each portion will then be weighed to estimate the amount of manure pellets compared to other harvested material.