Microbes and Pathogen Genes Fill New York City Soil

Noah Fierer collects soil samples in New York City’s Central Park. Photo courtesy of Noah Fierer.

With all the attention to and other pathogens floating around in bodily fluids and the air, we may not be aware that the dirt beneath our feet is home to thousands of and other microorganisms. Even the soil in New York City, which we might think is somewhat lifeless given the preponderance of concrete and pollution, is as full of life as soils in tropical rain forests and rich grasslands. It is also home to more pathogenic genes than any of those places.

Those surprising conclusions come from published this week in . A team of scientists took soil samples at 596 sites across New York’s famous (and large) Central Park—all in a single, 12-hour blitz. They brought their dirt back to the lab and analyzed the genetic makeup of every bit of lifelike material they could find. They uncovered an astounding 167,000 different kinds of bacteria, archaea (single-celled organisms that do not have cell nuclei) and eukaryotes (organisms whose cells contain nuclei).

They then compared the genetics of their critters to those living in soils from 52 places around the world. The Central Park soil had as much or than soils from rain forests in Hawaii and Peru, woodlands in California, and the Mojave Desert and valleys in Antarctica. “The amount of biodiversity in Central Park, and how comparable it is to soils around the globe, was surprising,” says team leader and microbial ecologist , who was at Colorado State University when the samples were taken and is now a postdoctoral scholar at the Netherlands Institute of Ecology in Wageningen.

Ramirez also emphasized that “we know so little” about what’s living in the universe beneath our feet. Although the park soil had tremendous biodiversity, only 16 percent of the bacteria and archaea gene sequences matched those in soils from around the world in the Greengenes database. Only 8.5 percent of the eukaryotes matched those from global soils in the SILVA database. Ramirez is eager to add the New York City results to the Global Soil Biodiversity Initiative, which is trying to broaden the world’s knowledge of dirt.

She also emphasized that scientists know very little about how organisms in soil interact with one another, which is crucial to maintaining soil health. “We are only beginning to unravel what each group of organisms’ role is,” she says. Healthy soil is crucial for robust plant life, and therefore for healthy ecosystems.

GoogleMaps plot of 596 soil sample locations. Image courtesy of Kelly Ramirez.

Soil can also be a help or harm to human health. Therein lies perhaps the biggest surprise of the Central Park study. Although the researchers did not find many complete human pathogens in the soil, they found an abundance of genetic sequences that were close matches—more than twice as many as in soils around the globe. In particular, they found high levels of close matches to Staph, Salmonella and Citrobacter bacteria—all causes of prevalent and potentially serious human diseases—as well as anthrax spores (which occur naturally in addition to weaponized forms).

The paper contains a careful note about that: “We want to stress that the presence of potential pathogen sequences does not indicate the presence of a disease-causing organism in the soil, rather this finding highlights a significant difference between soil bacterial communities found in more natural systems and those found in Central Park.” Ramirez says her team cannot explain for sure why the pathogen sequences are higher, but she assumes it is because so many people are crisscrossing the park each day.

Ramirez hopes the Central Park results “wave the flag” that scientists are only beginning to understand what roles the many soil organisms play in maintaining biodiversity. More insight could help farmers tweak soil to reduce pathogens that can destroy crops, and help scientists track whether soils can migrate as climate changes, how much plants determine the traits of soils, and whether plants can change soils to help themselves as they, too, migrate to warmer, wetter or drier places.