Progress 06/01/24 to 05/31/25
Outputs
Target Audience:The goal of the Chick-EES project is to quantify the ecosystem services and disservices of pastured chickens on farms, as well as to develop tools and materials for growers managing chickens, and other livestock, alongside crops. Our target audience is small-scale chicken growers who manage their chickens in organic, integrated crop-livestock, or other alternative production systems. These growers stand to gain the most from potential biological control and soil health benefits of pastured chickens, but must also manage food safety risks that livestock present. In the fall of 2024, we visited 15 small-scale farms across the southeastern US (Georgia, Florida, and South Carolina), all of which had outdoor flocks of chickens, and many of which also managed produce and other livestock. We collected chicken fecal samples at each farm to evaluate chicken diet and bacterial prevalence, and also collected farm management information and arthropod sweep net samples. These datasets are providing insights into 1) outdoor-access chickens' diets, and the effects of pastured chickens on arthropod (spiders and insect) communities that could have biological control potential; 2) bacterial prevalence and food safety risks of outdoor-access chickens; and 3) how farm management and geography can mediate these potential benefits and risks. These data are the first to assess ecosystem services and disservices of outdoor-access chickens in the southeast. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Two graduate students (Sofie Varriano and Avery Ryan) as well as one undergraduate assistant (Kariana Colon) are currently being trained on this project. Sofie Varriano is examining the biological control potential of chicken through diet analysis and coordinating the Chicken Dinner project and grower survey. Sofie defended her thesis in March 2025 and is transitioning to a postdoctoral research position on this project for 2025-2026. Avery Ryan is examining how chicken grazing affects arthropod and plant communities and soil health. Avery will also be trained in molecular techniques in order to run bacterial diagnostic PCRs. Kariana Colon is assisting with arthropod identification and molecular work. Kariana has been awarded the UGA CURO Symposium Research Award and UGA Undergraduate College of Agriculture and the Environment (CAES) Research Initiative award for her work on this project and presented this work at the UGA CURO Symposium and UGA CAES Undergraduate Symposium in April 2025. How have the results been disseminated to communities of interest? We have established our Chicken Dinner website (https://chickendinner.uga.edu/), the first component of our diagnostic chicken diet lab. Growers are welcome to send in fecal samples from their chickens to learn what they are eating. We are planning to present the initial results of this project at a grower-oriented conference in 2025. What do you plan to do during the next reporting period to accomplish the goals?Objective 1: Detail chickens' feeding on pest and beneficial insects, and weeds, through molecular analysis of dietary-DNA remains in chicken feces. Our next two on-farm collection periods are scheduled for spring and fall 2025. Sofie Varriano and Avery Ryan will be travelling back to our cooperating 15 farms each of these collection periods to collect another 150 chicken fecal samples and 120 sweep net samples. We will also be expanding our on-farm collection plan to better characterize chicken grazing effects on arthropods and plants. On each collection trip, we will collect 120 pitfall traps to assess ground-dwelling arthropod communities, 120 above-ground plant biomass samples, and 120 seed bank samples to assess plant communities. Our seed bank samples will be grown out in the greenhouse this summer to identify abundance and richness of plant seeds in chicken-grazing and chicken-free areas. We will compare arthropod and plant communities in chicken-grazing and chicken-free areas to assess the biological control potential of chickens. We will finish DNA extraction from our 2024 fecal samples and start to identify and analyze this data to characterize chicken diet. We have already established a diet-item identification pipeline to expediate this process. We will start advertising and receiving Chicken Dinner mail kits. We will start DNA extraction from these samples as well as compiling results from our grower survey for analysis. Objective 2: Track likely sources of chicken exposure to Salmonella and Campylobacter bacteria using whole-genome pathogen sequencing and landscape analysis. We will culture all of our fecal samples from our 2025 collection periods to assess Salmonella and Campylobacter prevalence. We will send any Salmonella positive samples for CRISPR Sero-Seq analysis and whole genome sequencing and start to analyze this data from our 2024 samples to trace pathogen sources. We will continue to work on establishing a qPCR protocol for Salmonella and Campylobacter detection in our lab. We will hire an additional undergraduate worker to help expediate this process. Objective 3: Quantify the birds' net impacts on arthropods, weeds, and soil microbes, through on-farm chicken exclusion experiments. We will conduct our chicken exclusion experiment summer 2025. We will extract DNA from soil samples collected during this experiment and quantify plant biomass from plots.
Impacts
What was accomplished under these goals?
Objective 1: Detail chickens' feeding on pest and beneficial insects, and weeds, through molecular analysis of dietary-DNA remains in chicken feces. During our first fall of field work (Aug-Sept. 2024), we collected 8 sweep net samples from each of 15 farms producing outdoor-access chickens and chicken products (n=120). These 8 sweep net samples were taken from chicken-grazed areas (n=4) and chicken-free areas (n=4) to allow us to assess the impacts of chickens on arthropods. Each sample was taken along a 20 m transect. We have started counting arthropods from these samples and identifying them to family. We have counted 338 arthropods from 22 samples and identified 51 families; the most abundant families were fruit flies (Chloropidae, n=61), leafhoppers (Cicadellidae, n=46), and aphids (Aphidae, n=29). From each of the same 15 farms, we collected 10 chicken fecal samples (n=150). Fecal samples were collected in the early morning before 9:00 am. Fecal samples were manually homogenized, and approximately 2mL scooped into an 8 mL vial filled with ethanol. We extracted DNA from half of these ethanol-stored fecal samples using the KingFisher Flex System and are preparing to send these DNA samples to Novogene for DNA sequencing in order to assess chicken diet. We built the Chicken Dinner website (https://chickendinner.uga.edu/) to start soliciting samples for growers across the country for our Chicken Dinner project. We finalized our grower survey to evaluate grower attitudes and perceptions towards integrated crop-livestock systems and obtained IRB approval for distribution (IRB ID: PROJECT00009975). We built our Chicken Dinner mail kits and are planning to start advertising and distribution both kits and survey. Objective 2: Track likely sources of chicken exposure to Salmonella and Campylobacter bacteria using whole-genome pathogen sequencing and landscape analysis. The fecal material not placed in ethanol (see above) was shipped to UGA's Poultry Diagnostic and Research Center for bacterial culturing. We cultured each of our 150 fecal samples for Salmonella and Campylobacter, two of the most common foodborne bacteria, to assess food safety risks. Samples were divided in half and enriched separately for either Salmonella (BPW) or Campylobacter (Bolton's broth). BPW cultures were inoculated into TT and MSRV broth before streaking onto XLT-4 plates, while Bolton's broth was streaked onto Cefex plates. Bacterial presence was determined by counting colonies on plates. Campylobacter isolates were molecularly confirmed with a 16S colony PCR. We detected Salmonella in 26/150 samples (17.3%) and Campylobacter in 9/150 (6%) of samples. We have sent our Salmonella-positive samples for CRISPR Ser-Seq and whole-genome sequencing in order to trace pathogen source. We obtained IBC approval (Protocol # 2024-0031) to run diagnostic PCRs on these same samples to detect Campylobacter and Salmonella presence. Culture-based methods can only detect viable bacteria, while PCR methods can detect both viable and non-living bacteria. Using these two methods in conjunction can give us a more complete picture of food safety risks. We gathered weather data for the seven days preceding sample collection from the nearest weather station on the Weather Underground site (https://www.wunderground.com/). We tested for preliminary associations between weather variables (mean temperature, humidity, precipitation, and wind speed) and Salmonella prevalence as determined by culturing. We did not find any association between Salmonella prevalence and weather variables, but we are planning to re-run this analysis after receiving our PCR assay results. Objective 3: Quantify the birds' net impacts on arthropods, weeds, and soil microbes, through on-farm chicken exclusion experiments. We have recruited growers for our chicken exclusion experiment and are planning for a start date of summer 2025.
Publications
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