New York City Park Soil Contains Wealth of Pathogen-fighting Microbes

Using bacteria to fight bacteria is not a new approach to fighting pathogens; researchers are increasingly finding new ways to fight infections with microbes, and now, a team of researchers in New York City have made an important discovery in urban soil.

While soil microbiota can transfer antibiotic resistance genes to clinical pathogens, studies have also found that environmental bacteria in soil and plant ecosystems naturally produce antibiotic compounds against competitive microorganisms. In light of the growing problem of antibiotic-resistant bacteria and the decline of new drugs to fight them, harnessing that natural process to develop new antibiotic treatments has been an important part of the research going into the development of novel antibiotics. According to a 2016 report from The Pew Charitable Trusts, every antibiotic in use today is derived from a class of antimicrobials found between 1900 and 1984, highlighting what has been a static drug market in medically dynamic times.

A team of molecular researchers at The Rockefeller University recently studied the soil in New York City and found that it contains some promising beneficial bacteria. Their paper, recently published in Proceedings of the National Academy of Sciences, details their discovery on what they call bacterial natural products (NP). The authors site previous studies on soil microbe diversity that have yielded powerful medical agents capable of killing tumor cells and fighting viruses. Much of that research has focused on samples collected from natural environments with rich biodiversity rather than urban areas, noted the authors. For their study, though, the researchers collected soil samples from New York’s city parks for metagenomic sequencing, gathering 275 topsoil samples from locations in the city’s park system representing a variety of ecosystems. The work was done in cooperation with a team of high school students involved with the university’s Science Outreach Program, along with researchers at Barnard College, Columbia University, and the Natural Areas Conservancy.

The soil samples the researchers collected contained an array of microbes, which the team found to be rich in biosynthetic diversity. In addition, these microbes were found to include an array of living organisms capable of forming chemical compounds that were distinct from samples collected from non-urban settings. In an effort to avoid the problem of encountering difficulties growing soil bacteria in a lab, the team looked directly at the bacterial DNA in the soil samples instead, and scientists at Barnard isolated and sequenced the DNA. In comparing their city topsoil samples to those collected from natural environments around the world, the team found that the New York samples contained bacteria producing the same families of antibiotics, antifungals, and anticancer agents that are so clinically important to today’s medical research. In just one sample collected from Prospect Park in Brooklyn, the researchers found genes believed to encode 25 molecules that previous studies have found to show potential for use as antibiotics and other drugs.

“The sheer diversity we saw suggests there are many more potentially valuable compounds out there awaiting discovery—even in a place as mundane as urban soil,” said Rockefeller associate professor and senior author Sean F. Brady, PhD, head of Rockefeller’s Laboratory of Genetically Encoded Small Molecules, in a recent press release. “By sequencing and analyzing genes within soil samples, we found the genetic instructions for making a wide range of natural products that have the potential to become treatments for various conditions, from cancer to bacterial or fungal infections, or that are already being used as drugs.”

While the research team was happy to find known soil bacteria producing known compounds, much of their findings were of unfamiliar genes. “Less than one percent of molecule-encoding sequences matched up to the known genes to which we compared them,” said author Zachary Charlop-Powers, in the Rockefeller press release. “Similar efforts in soil collected elsewhere have also shown that novel molecule-encoding sequences vastly outnumber those we recognize. This suggests there are many as yet-unidentified genes out there, and among these, some are likely to have potentially useful biological activity.”

The results of their investigation shows that city microbiomes are home to rich biosynthetic diversity. “Contrary to traditional NP discovery efforts that involve shallow explorations of diverse environments, our data suggest that a deeper exploration of local microbiomes may prove equally, if not, more productive,” noted the authors in their paper. “The identification of new bacterial NPs often centers on the systematic exploration of bacteria present in natural environments. Here, we find that the soil microbiomes found in large cities likely hold similar promise as rich unexplored sources of clinically relevant NPs.”