Scratching the surface

Two researchers crouch in a field surrounded by a flock of brown, pastured chickens while they collect fecal samples for testing.

Leniha Lagarde (left) and Sofia Varriano collect feces samples from pastured chickens at Foster Brady Farms in Madison, Georgia.

Researchers in the University of Georgia’s College of Agricultural and Environmental Sciences are using molecular genetics to determine how pastured and free-range chickens influence the ecosystem on farms where crops and livestock are raised together.

Supported by a $749,000 grant from the U.S. Department of Agriculture’s National Institute of Food and Agriculture, entomology doctoral student Sofia Varriano and her thesis advisor, agroecologist and systems biology Professor Bill Snyder, are testing the promise of integrated crop-livestock agriculture to increase the sustainability of smaller farms.

“We're interested in this group of farmers that have livestock and crop production within the same farms for their operation. Nowadays we call that integrated crop-livestock agriculture, but 100 years ago what did we call that? We called it farming,” Snyder said. “Every farm, pretty much everywhere in the world, had that model. We’re interested in whether there are aspects of that farming approach that can be useful in a modern setting.”

Using DNA analysis to demystify diets

Called “Chicken Ecology and Ecosystem Services,” or ChickEES, the three-year project will detail what the birds on each farm are consuming by analyzing the DNA remains in chicken feces. With this information, producers can determine how their chickens are helping to control pest insects and weeds.

While research on poultry nutrition in controlled production facilities is plentiful, Snyder said there is little available information on what chickens on smaller farms with integrated poultry production practices are eating in a natural setting.

“That got us interested in what these chickens eat. Chickens are what we call generalist predators, which means they're hungry, and they don't care what they eat, whether it's a plant or a spider or an aphid or a pest caterpillar — they eat everything. Likewise, they eat things like earthworms, which are beneficial to the soil,” he explained. “Do they mostly eat pests? What weeds do they eat? Are there particular pest species or particular weed species that they prefer? These are the questions we're interested in.”

Natural pest control and soil amendment benefits

With this knowledge, producers can modify their weed and pest control practices to work in tandem with pastured or free-range chickens.

“The farmers we're working with have these diversified farms, and a lot of them intuitively feel that it probably has some pest control advantage. This will answer that,” Snyder added. “The other thing the animals do is poop, so that's manure, that's fertilizer. The animals and the crops can kind of complement one another in that way.”

Varriano, who came to CAES to study wild birds, pivoted to poultry research when the pandemic closed labs in 2020.

This project focuses on chickens with outdoor access, whether they are pastured, free-range or otherwise have the ability to roam outside. DNA samples collected from the chickens are sent off for analysis to identify arthropods and plants through sequencing. By comparing the sequences to a species database, researchers aim to determine what the chickens are consuming, Varriano explained.

“The end goal with these data is to give growers this information so it can benefit whatever farming they're doing. One system helps support the other. Using chickens to control pests and enrich the soil to benefit your crops would be one integrative strategy,” Varriano said.

“We want to help growers take full advantage of the chickens that they have on their farms.”

A woman in a black shirt and white sweatpants uses a large net to sweep for insects in a pasture where chickens roam.

A female researcher uses a large net to sweep for insects in a pasture where chickens roam while another female researcher watches

Lagarde sweeps for insects while Varriano waits to collect whatever insects are captured.

A farmer fills narrow troughs with grain for pastured chickens.

Clay Brady fills narrow troughs with grain for his pastured chickens.

Researchers are surrounded by pastured chickens as they collect fecal samples.

Lagarde and Varriano collect samples in a field where chickens are pastured.

Two female researchers use a yellow tape to measure out an area for insect collection in a farm pasture surrounded by free-ranging chickens.

Varriano and Lagarde measure out an area for insect collection in a farm pasture at Foster Brady Farms.

Three people stand together in front of a farm field fence.

Legarde, Varriano and Brady at Foster Brady Farms after sample collection in September 2024.

Tracking pathogens in free-range and pastured systems

In addition to DNA sampling, the project will uncover likely sources of chicken exposure to Salmonella and Campylobacter bacteria, which can make people sick, using whole-genome pathogen sequencing and landscape modeling. Exploring technology to help small farmers improve and diversify their production practices is one step toward improving the sustainability of smaller-scale producers.

“The farmers we're working with are often selling directly to restaurants, farmers markets and the public through community-supported agriculture. To bring people to their farms or serve the needs of restaurants or fill their stand at the farmer’s market, they need to have all different types of products,” Snyder explained. “The diversity of products helps to make their farms more sustainable.”

A pilot study Varriano performed in Georgia revealed that chickens can consume hundreds of different types of prey on farms.

The team has performed similar work in the Western U.S. between Southern California and Canada to create a broad footprint in different climates to determine what is typical for the Southeast versus other regions.

“If you have a chicken that’s stationary versus a chicken that is free-roaming, we’re trying to predict what their differences in diet will be. In a certain setting, are they going to really focus on one certain pest or weed?” Snyder said.

Gathering data from smaller flocks through citizen science

Later in the study, Varriano and Snyder will solicit citizen-scientist input to the study by asking farmers throughout the region to self-submit information about their operations as well as fecal samples from their chickens.

Providing kits similar to those used for genetic genealogy, the researchers will solicit samples from small or backyard flocks.

“We'll extract the DNA and do the sequencing, and then we'll be able to tell them exactly what chickens on their farms — these are the five top weeds they're eating, these are the five top pests and insects that they're eating,” Snyder said. “That helps the farmers because they usually don't know what additional benefit they are really getting from these systems; we’ll be able to tell them that.”

The team plans to create a service center with testing technology to quickly analyze the DNA samples and the many contributors to each sample, whether plant or insect.

“We can get back, from one farm, more than 200 weeds and insects and other arthropods that the chickens are eating, so we are trying to automate that process,” he said, adding that preliminary studies in Georgia have shown that chickens are eating Palmer amaranth, one of the most damaging weeds for producers.

“It does really seem like there are some certain things they really are picking out. When they're really confined, chickens do just clear out everything. But when they're foraging freely, it does seem like chickens have things they really like, such as pest caterpillars,” Snyder said.

Examining how diversification contributes to sustainable farming

The researchers also will monitor how soil quality changes when pastured chickens are moved from area to area on farms by performing full soil-quality tests to look at the weed seed bank and extracting DNA from the soil to look at microbial biodiversity.

“Chickens, presumably, when they're coming through and pooping, they're dropping a lot of nitrogen, and that's probably changing the soil microbiome. And is that beneficial? Is it building up?” Snyder said. “There's some decent evidence that when you have greater biodiversity and microbes, it makes it harder for pathogens to persist. So are they actually building up the health of the soil in a really general way, not just with nitrogen, but also microbial biodiversity.”

A collaborator in the UGA College of Veterinary Medicine, Nikki Shariat, an associate professor in the Department of Population Health, Poultry Diagnostic and Research Center, will test samples for the presence of Salmonella and Campylobacter. By performing whole-genome sequencing on the bacteria, they can determine where the foodborne illness-causing bacteria originated in the farm environment.

“Where on the farm might they be picking these things up? We want to see how often they are present to get some idea of what the incidence would be," Snyder added. "We want to give the growers a full picture — here are the pests the chickens are eating, here are the beneficials they're eating, here's your food safety risk.”

Enhancing local food systems and farm profitability

The findings have the potential to benefit growing local food systems in populated areas.

“Economically, if you have 10 acres that you're farming instead of 1,000 acres, you have to know how to generate enough income. That comes down to diversification,” Snyder said, adding that “chickens in these systems are providing eggs or meat that you can sell, they’re providing fertilizer and they’re providing pest and weed control.

“When you're trying to keep costs low and reduce off-farm inputs as much as you can, if more of that can be produced on farm, it's better for the producer. We are helping those things work together,” he said.

“The better these producers can function, the more opportunity they have for people in the public to enjoy what they're doing and for them to make a profit.”