Digging into the past: Forgotten soil samples are opportunity for new research

UNIVERSITY PARK, Pa. — While most time capsules found on campus feature pop-culture relics like vintage copies of the Daily Collegian newspaper, the College of Agricultural Sciences has unearthed a different kind of relic: sealed jars of soil samples collected by Penn State researchers in 1915 and 1933.

Recently, the first jar was opened by a group of researchers, who said because the samples were taken before many of the changes in agricultural and industrial practices throughout the past century, they offer the chance to study how these changes have affected the microorganisms that live within the soil.

Estelle Couradeau, assistant professor of soils and environmental microbiology, said because the samples pre-date the "Green Revolution" — the period between the 1940s and 1980s during which agricultural technology greatly accelerated — they can, for example, give scientists a window into what soils were like before the broad adoption of chemical fertilizers and pesticides.

“I suspect that these practices have influenced the microbial functional diversity of modern agroecosystems over the last several decades,” Couradeau said. “If we can use the data from these samples as a baseline, we can compare it to data from modern soils and start to learn just how big that influence is.”

Laura Weyrich, associate professor of anthropology and bioethics, said these lessons from the past may also help give scientists a peek into the future.

“These microbes are critical for effectively growing crops and can be indicators of contamination from pollutants and heavy metals,” Weyrich said. “The microbes that still exist in these jars are like a time capsule, preserving information about how our environment changed over time and how we might predict it to change in the future.”

Bringing history into the lab

According to Rita Graef, director of the Pasto Agricultural Museum, the sample jars were found in 2020 in a storage closet at the Agronomy Research Farm, located at Penn State’s Russell E. Larson Agricultural Research Center about 10 miles from campus.

Using binders containing research findings that accompanied the samples in the time capsule, and published research from the time period, the scientists were able to discover that the jars were part of a long-running study that took place on the University Park campus from 1881 to the 1950s, on what were known as the Jordan soil fertility plots. These plots were located on the land where the Millennium Science Center and Life Sciences Bridge are located, today.

Because the study included experiments on how adding different substances to the soil affected crop yields, it was necessary for the researchers to collect soil samples frequently — both for testing and to provide a record. Graef  said she believes the samples were stored away and gradually forgotten over the years as they were moved from building to building.

Graef added that while the University Library Archives already keeps a trove of information on the history of the Jordan soil fertility trials — including published papers and bulletins and details about the experiments — there is still much to be learned. She said she is excited to see how current Penn State scientists continue research on the soil in the 21st century.

“The project offers the opportunity to engage the public in what we know about soils now and what we knew at the time these samples were taken,” Graef said. “It’s also the chance to share how our scientists think about the samples in these Mason jars and, more broadly, how they work to solve larger questions affecting agriculture, the environment and our food supply today.”

Testing out first steps

Now that the first jar has been opened and the soil has been transferred into several other sterile jars, the team said they will run a variety of tests and analyses on the samples.

Couradeau’s lab is planning to do culture assays and cell counts with a flow cytometer, which will provide a count of intact cells left in the soil. The lab performed culture enrichment from these soils, and taxonomic identification of three fast-growing bacterial strains is pending.

Meanwhile, Weyrich’s lab will sequence the DNA within the soil to identify what microbes are there and then try to grow those microbes in the lab with the goal of understanding what, if anything, has survived. Then, the researchers will regroup to review what they’ve learned and how they want to proceed.

“These first tests will act as a pilot and will help inform our next steps with the other 52 still-unopened jars,” Couradeau said. “I really enjoy thinking about the scientist who put these samples in jars almost 100 years ago and probably did not imagine us extracting nucleic acids and performing next-generation sequencing on them!”

Additionally, as the project continues, Graef said some of the artifacts will be displayed at the Pasto Agricultural Museum, along with their history and what the researchers continue to learn from the samples.

Overall, the team said the project is a great opportunity to bring together researchers for collaborations that otherwise might not have happened.

“It’s a great example of how outreach through museums like the Pasto Agricultural Museum can be developed into interdisciplinary research collaborations,” Weyrich said. “These collaborations are critical if we are to understand the past and get the next generation of scientists interested in the work we do here at Penn State.”