Soil pathogen hot spots reveal risk across the United States

New research from Virginia Tech digs deeper into American soil to find where soil-borne pathogens may be hiding and how they spread.

Recently published in GeoHealth, the study examined soil samples from across the United States to identify where disease-causing microbes occur and how environmental conditions may influence human exposure. The study represents one of the first to examine natural reservoirs of pathogen communities in soil at a national scale. 

“At the most basic level, bacteria that can make us sick can naturally exist in soil,” said Emily Matthews, a Ph.D. student in civil and environmental engineering and lead author of the publication. “Whenever people engage in outdoor activities — gardening, hiking, farming — they may come into contact with these organisms. That baseline risk exists everywhere, but what we don’t yet know is how that risk varies geographically.”

By overlapping the presence of pathogens and environmental and social risks, the researchers identified the southeastern United States as a potential hot spot. Researchers say this is from a combination of forests, humid soils, and climate conditions as well as the social vulnerability of rural populations and limited access to health care. They also found pathogens tend to be more abundant in areas closer to surface water, which may increase exposure risk during flooding events.

“We were looking for places where several risks overlap,” said Ryan Calder, assistant professor of environmental health and policy. “Where soil pathogens are present, where environmental conditions could move them, and where people may be more vulnerable to exposure.”

With funding from the Institute for Society, Culture, and Environment’s Scholars program, the research team, led by Jingqiu Liao, examined natural soil samples from 42 of the 48 contiguous states and identified which microbes, or small living organisms, are present in a given environment and how environmental conditions, such as flooding and wind, can mobilize them.

To determine which microbes were present in each location, the researchers analyzed datasets they had previously collected from 622 soil samples from natural environments across the United States. Using sequencing technology, they characterized microbial communities in each sample and compared the results with databases that contain information about known human pathogens to identify microbes that could potentially cause disease.

“Sequencing technology allows us to see the full microbial community in soil,” said Liao, civil and environmental engineering assistant professor. “From there, we can identify which microbes may have the potential to cause disease. By combining microbial data with environmental measurements, we can identify which soil conditions help putative pathogens survive and persist in the soil.”

With those microbes identified, the researchers were able overlay that information with data from the Centers for Disease Control and Prevention’s Social Vulnerability Index and the First Street Foundation, a nonprofit research organization that models climate and environmental risks across the United States and provides standardized risk scores for hazards such as flooding, wildfire, extreme heat, and wind.

The team then examined such environmental risks and their potential to move soil-borne pathogens through the environment and influence where people might be exposed.

As the next phase of research begins, the team will focus on collecting additional soil samples in regions identified as potential hot spots, especially in the Southeast. More detailed sampling will help better understand the mechanisms behind pathogen transmission, such as specific environmental events. The team hopes the findings can help scientists and public health officials identify where to focus future research, monitoring, and prevention efforts in these hot spot areas.

The team is also preparing a proposal to the National Science Foundation to expand the project and support a more comprehensive, mechanistic understanding of how soil-borne pathogens survive, persist, and spread in the environment.

“The role of naturally occurring soil pathogens has rarely been studied,” Calder said. “Now that we have begun identifying where potential hot spots exist, the next step is to zoom in on those regions to better understand how environmental changes influence pathogen movement and what it may mean for public health.”