Johns Hopkins University geneticists and a small army of researchers across the country, including students, are working to catalog the vast and largely unknown soil microbiome of the United States.
The project, one of the biggest microbiome studies ever attempted, that's tapping the latest DNA-analysis technology, has already resulted in the discovery of more than 1,000 new strains of bacteria and never-before-seen microbes—still just a tiny fraction of the microbial dark matter.
"This scientific void we're trying to fill on microbial diversity could only be accomplished by having this network of scientists and students across the United States," said senior author Michael Schatz , a leading genomics expert who has helped map the human genome, as well as the genomes for many other species of animals and plants. "The soil is the most biologically active environment on the planet, yet we've sampled only a tiny fraction of the life that lives inside it."
The federally-funded project is outlined in Nature Genetics .
Soil is the most biodiverse habitat on the planet, home to more than half of all existing species, including vertebrates, arthropods, annelids, nematodes, plants, and fungi, as well as millions of bacteria, archaea, bacteriophages, and other microbial species.
Certain microorganisms within soil are key to ecological functions that human, animal and plant life depend on. Others foster antimicrobial resistance, which threatens human health by allowing bacteria and viruses to become immune to antibiotics and other drugs.
An estimated 99% of soil microorganisms remain unstudied, or part of what scientists refer to as microbial "dark matter." With scores of researchers across most states in the country, armed with the latest in DNA analysis technology, this team hopes to make headway.
The BioDiversity and Informatics for Genomics Scholars (BioDIGS) consortium spans more than 40 sites across the country. The team of about 150 people includes researchers from dozens of institutions, including many students.
The project was partly inspired by the MetaSUB Consortium , a study launched in 2010 to collect and study microbes from each subway station in New York City, that eventually evolved into a global effort.
The expansive team gathers soil samples from urban and rural locations and then analyzes them, looking for genetic relationships and patterns between the soil, the environment, and human health. Recent advances in technology used to study DNA, particularly long-read sequencing, make it possible. The team is leveraging the same sophisticated technology used to unlock the final portions of the human genome.
BioDIGS has collected samples from all corners of the country, from a vast variety of terrains. Around Baltimore, teams have collected samples from playgrounds, wooded streams and popular hiking trails. The team from Spelman University in Atlanta collected samples near a Superfund hazardous waste site. Others have looked to everything from farms and lawns to wild grasslands, forests and parks.
Emily Biggane, who leads the collection effort at United Tribes Technical College in North Dakota said BioDIGS has "expanded the reach of science. UTTC students collected samples in an open part of their campus that could be developed.
"Our students have a deep connection to the land and this project offered an opportunity to explore the properties of something celebrated and honored," said Biggane, who is a research faculty member. "Students learned about the microscopic living things that call the soil home and it's been a holistic experience to better understand the soil that supports us."
While working to address knowledge gaps in soil biodiversity, BioDIGS is also encouraging the next generation of genetic scientists, and strengthening genetics course materials at participating schools. To date more than 100 student researchers have contributed to the project and organizers expect to engage many more as the work expands.
"Students can be very sophisticated data scientists," Schatz said. "They were involved with sample collection and now we're leaning on them to help build out the reference genomes of the microbes, to scan and ID genes—everything. We knew we couldn't do it alone."
Corresponding authors include Emily Biggane from United Tribes Technical College in North Dakota; Mentewab Ayalew from Spelman College; Karla Fuller of the City University of New York; Ava M. Hoffman of the Fred Hutch Data Science Lab; and Xianfa Xie of Virginia State University. There are dozens of additional authors.
