Tucked into the rolling hills of Stone Valley, Cole Farm seems like a typical central Pennsylvania farm. A gravel driveway slopes down to a steel and wood-plank bridge that spans Shaver’s Creek. The path continues relatively flat, past a murky green retention pond and two barns, to a log farmhouse nestled at the base of a hill. A spring trickles through the wooded swale west of the house. Sloping fields are flush with alfalfa, corn, hay grass, and wheat.

It’s easy to overlook the four soil sampling pits, one gas measurement tower, 12 wells, and 115 sensors and instruments deployed across the 160-acre property. These and other, more portable, pieces of equipment are helping Penn State researchers understand the effects that farming has on the critical zone, the slice of Earth’s surface that extends from bedrock to treetops.

The critical zone is the porous boundary layer where rock, water, soil, air, and living organisms interact to form terrestrial habitats. The National Science Foundation calls it "the zone where rock meets life." It’s also where humans get their drinking water, grow crops, graze livestock, and extract resources like lumber, granite, and iron ore — activities that can have consequences including soil erosion, nutrient depletion, and pollution of waterways.

Cole Farm provides an outdoor laboratory where researchers can learn about critical zone processes, and how to manage boundary-layer resources in environmentally and economically sustainable ways.

“This farm is part of a critical zone observatory,” said Susan Brantley, distinguished professor of geosciences and director of the Earth and Environmental Systems Institute at Penn State. “We are testing if we go to one place and try to measure all the different processes happening there at the surface, maybe we can put those all back together and really understand how they fit.”

Forest to farmland

The Susquehanna Shale Hills Critical Zone Observatory (CZO) was one of three sites funded by NSF in 2007 as part of a program to study how fresh water affects surface processes. NSF chose the Penn State proposal, Brantley said, because it included a research team of top scientists from across the University and a site that had been studied by investigators in the College of Agricultural Sciences as early as the 1960s: Shale Hills, a 20-acre tract in Penn State’s Stone Valley Forest.

Shale Hills sits on Rose Hill shale, one of the most common rock formations on Earth, but little was known about how soil forms and what controls water flow in this type of landscape. The site has experienced two major changes in recent geologic history: thawing, after the last glacial period, and deforestation, during colonial and early industrial times. Scientists wanted to understand how these short- and long-term changes have affected what goes on there.

As the CZO program expanded to nine locations across the United States and Puerto Rico, the Shale Hills site grew, too. A 2014 expansion incorporated the entirety of the 64-square mile Shaver’s Creek watershed. In 2017, research began at Cole Farm. The larger site includes new geologies — in addition to Rose Hill shale, the watershed sits atop limestone, sandstone, and calcareous shale at various points — and, at least as importantly, a new land-use model.

“We’re interested in looking at how cultivation changes some of the same chemical and biological processes we’ve been studying in Shale Hills,” said Brantley, the project’s lead investigator.

In the past, she said, scientists working here would study only the aspects directly related to their field. A critical zone approach combines disciplines, challenging researchers to step across boundaries and broaden their thinking. The collaborations they form can help them see the bigger picture, and better predict complex processes like air flow, soil fertility, and the rate of nutrient loss in streams.

Ongoing work at Cole Farm includes hydrology, geology, soil science, ecology, and atmospheric sciences, underscoring just how interconnected these fields are, especially in a boundary region. It also demonstrates how scientists working together can apply their findings to benefit rural communities.

What happens in central Pennsylvania flows south

Shaver’s Creek enters Cole Farm from the northeast and travels south through a forested area bordering fields of corn and winter wheat. It continues west, just below a grassy drainage field, then flows along a wooded boundary at the farm’s entrance, running for another 600 yards through field and forest before exiting near the southwest corner of the property, beneath the two-lane blacktop of PA Route 305.

Graduate students drive out to collect water samples at the wood-plank bridge and the spring near the farmhouse. They also sample the farm’s 12 wells, dug to monitor the shallow flow paths that groundwater takes through the first few feet of soil, as well as the deeper traces that extend down to bedrock. Back in the laboratory, they analyze the water for nutrient concentrations, tracking nitrate as it leaches from fertilizer, enters the creek, and travels downstream — into the Juniata River, then the Susquehanna, and on to the Chesapeake Bay. Excess nitrate is a serious pollution problem, choking out marine ecosystems and sometimes contaminating drinking water supplies.

“Looking at the whole watershed, we can get a pretty good general idea of how nutrients are being transported,” said Mike Forgeng, a graduate student in geosciences. “But zeroing in on Cole Farm offers a high-resolution view.”

One thing their sampling efforts have shown is that the farmhouse spring contains fairly high nitrate concentrations, likely from the manure applied seasonally to the surrounding fields. But something happens when that spring water flows into the retention pond that sits beside the creek.

The pond, built in the mid-1980s to capture excess nutrients, is sealed with clay and sediment; even so, the water that fills it eventually leaks out and enters the creek. When it enters the pond, however, that water measures high in nitrate, and when it hits the creek it measures low.

This shows the filtering effect of the surrounding soil, Brantley said: When there’s enough organic matter present to catalyze the reaction, bacteria in soil and mud can change nitrate into nitrogen gas. She suspects the pond, with all its organic matter, is accelerating this process. The water flowing in stays long enough to allow the nitrate to diffuse, over days and weeks, into the mud at the bottom of the pond, she explained. “There’s time for the nitrate to be ‘breathed’ by micro-organisms living in the mud.”

A retention pond can indeed be a useful tool for removing nitrate from water moving in shallow flow paths, she concludes. But a deeper flow path can avoid such a trap altogether, carrying nitrate underneath the pond and directly into the creek. To understand what’s happening in these deeper paths, the team relies on sampling wells.

Most of the wells at Cole Farm are paired, with one well 6.5 feet deep beside another drilled to about 15 feet, to account for both shallow and deeper flow paths. A lone well drilled to 200 feet allows the researchers to see how nutrient levels change at greater depth. What the wells reveal, Forgeng said, is that there’s less nitrate deep in the groundwater than there is near the surface — and where the nitrate level decreases, sulfate tends to increase. Something down below is promoting denitrification.

That something, they suggest, is the underlying geology. The southeast portion of Cole Farm sits atop the Clinton Group, a formation that includes iron pyrite. “As nitrate reacts with pyrite,” Forgeng suggested, “it could oxidize the pyrite, and one of the byproducts is sulfuric acid,” or sulfate.

In large quantity, oxidized pyrite can be a serious problem; it’s the major source of acid mine drainage. In this case, Brantley said, there’s only a small amount of the mineral present, so the reaction releases only tiny amounts of acid. That acid dissolves nearby carbonate rock, including limestone, which acts as a base and neutralizes the acid.

Here, then, the presence of small amounts of pyrite may be having a positive effect on nutrient runoff. If the researchers can confirm this hypothesis, and if they can accurately determine where pyrite is present, they may be able to use that information to help farmers, Brantley said. “Planting crops in fields where we understand how water flows into rocks with and without pyrite might be another way to prevent nitrate from entering waterways.”

Digging deeper

Jason Kaye, professor of soil biogeochemistry, has spent much of his career working with farmers to improve agricultural practices and reduce nutrient pollution. Over the years, almost all of his work has focused on the top 20 inches of soil. Cole Farm has taught him he needs to dig deeper.

“Management practices that affect shallow soil processes are just one part of the picture,” said Kaye. “At Cole Farm I’ve learned to think about deep groundwater flow paths and collaborate with people who work in this area.”

One such collaboration focuses on riparian zones — forested strips planted as environmental buffers between farm fields and streams. The idea behind riparian zones is that tree roots and organic matter in the soil will filter nitrate from water coming off the field before it reaches the stream. In practice, riparian buffers work well in some places but not in others.

In large part, it’s again the geology that determines the flow paths of water underground, Kaye explained. Where the underlying rock directs that water through a shallow path, the forest soil can act as a filter. But the rock’s structure can also dictate a deeper flow, allowing nitrate to enter a stream unimpeded. In some cases, however, as where the water interacts with pyrite, the rock’s composition may cause chemical reactions that lessen nutrient concentrations.

“We don’t really think about geologic processes as being important for removing nitrate,” Kaye said. However, “given that pyrite is a common component of the rocks in the Chesapeake Bay watershed, having a better understanding of how that pyrite-nitrate reaction is affecting our water quality really changes how we manage nitrate and where we apply biological management practices.”

Considering the geology can lead to more strategic placement of riparian buffers, said Brantley, which can in turn lead to less frustration for farmers looking for ways to reduce nutrient pollution.

Soil and climate

People don’t tend to think of soil as a living organism, but it breathes and eats like one. Roots and soil microbes take in oxygen and use it to convert organic carbon into carbon dioxide, which they then exhale. This process of aerobic respiration releases lots of carbon dioxide into the atmosphere — the largest such transfer from terrestrial ecosystems — but some percentage of that carbon remains in the soil. A clearer understanding of how much gets held back, Brantley said, is vital to accurate carbon cycle modeling.

Caitlin Hodges, a doctoral student in soil science, is measuring carbon dioxide and oxygen concentrations in the soil at three different depths at three hillside locations at Cole Farm. She is also taking measurements of soil pore water chemistry, which show the products of weathering reactions.

Hodges and her co-advisers, Kaye and Brantley, have found that these reactions have a profound effect on the amount of carbon dioxide released into the atmosphere versus how much is retained in the soil.

“When CO₂ reacts with water and soil, it becomes a weak acid,” Hodges explained. “That weak acid can dissolve soil minerals. When it does, instead of leaving the soil system as a gas, it leaves as bicarbonate, a solute in soil water or groundwater.

“The traditional way of measuring soil respiration only measures the CO­₂ that leaves the soil as a gas,” Hodges continued, “which leads to underestimating respiration rates by a third to a half. This weathering process hasn’t really been considered important on the shorter timescales that ecologists are interested in. But it is important. It’s something people should take into account.”

Community engagement

Research in the Shaver’s Creek watershed depends on the cooperation of the local community. Among the many factors that led to the CZO’s expansion in 2014, finding a suitable farm and a sympathetic landowner were of utmost importance.

“We looked for a long time to find a farm situated on the right kind of landscape,” said Brantley. “It had to be actively farmed and about the right size. The person that lived there had to be amenable to having us come in.”

Cole Farm was the perfect fit. The farm’s owner, Herb Cole, is an emeritus professor of plant pathology and environmental microbiology at Penn State, and a strong advocate of sustainable farming practices. “Herb was very excited about having us study his site,” said Brantley.

Watershed specialist Brandon Forsythe works with Cole and the local farmer who leases the land to coordinate site visits and decide where to place instruments and drill new wells. He also helps researchers gain permissions from other nearby landowners for water sampling on their properties.

“Generally, we’ve had positive interactions,” said Forsythe. “Most of the landowners allow us to take samples as long as we’re not damaging their property or their crops.”

Outreach events have helped to build and maintain ties with local residents. In 2015, Forsythe and graduate student Beth Hoagland went to the heart of the community — Petersburg Bethel Presbyterian Church — to spread awareness of the scientists’ work. They attended a Sunday service and afterward addressed the congregation and two youth groups about their water monitoring efforts and its importance for the health of the watershed.

In September 2019, Forgeng organized a watershed “snapshot” day, an event funded by Penn State alumna and geoscientist Marilyn Fogel. About 50 volunteers — Penn State students, landowners, and citizen scientists alike — took water samples at 55 sites throughout the watershed, including on private lands and farms. The researchers plan to use the data to map nitrate transport, and to share their results with farmers.

Forgeng said he understands why some farmers might be hesitant to work with CZO researchers, especially when those farmers may already be struggling to adapt their traditional practices to changing environmental regulations. But he added that the ultimate aim is to work with farmers to find practical solutions.

“Our goal is to help develop a management plan that farmers will be enthusiastic to implement, something that will help them reduce nutrient loss without having to make financial sacrifices,” he said. “It has to be something that works for them.”

After ten years of research focused mainly on natural landscapes, the future of critical zone science, Brantley said, is exactly the type of research now being conducted at Cole Farm, with its emphasis on human impacts.

“Everybody is interested in improving their ability to model what humans are doing to landscapes, and to predict future scenarios,” she said. “This project has been wonderful for us because Dr. Cole really allows us to work on an operating farm and try to understand what’s happening here.”

Federal funding for the Susquehanna Shale Hills CZO will end in 2021, but the researchers don’t plan to stop their interdisciplinary work anytime soon. Kaye is spearheading an initiative with units across Penn State to continue the research efforts in collaboration with Shaver’s Creek Environmental Center and the Penn State Sustainable Forest. Members of the research team, in coordination with Shaver’s Creek, will also offer classes to Penn State students and citizen scientists that focus on teaching many of the sampling techniques the researchers use at Cole Farm, preparing the next generation of scientists to continue their work measuring humanity’s impact on the critical zone.