Below Our Feet, a World of Hidden Life The soil teems with billions of hidden microbes. Researchers have begun to catalog how these organisms are changing the world.
Janet Jansson first started to wonder about the vast universe of underground life as a student at New Mexico State University in the late 1970s. A handful of soil contains about 10 billion bacteria, but at the time, earth scientists knew very little about what these microbes were and what they did. Later, as a young microbial ecologist at Stockholm University in Sweden, she started to catalog the microorganisms she collected during soil sampling trips, deciphering their genetic code so she could understand both their internal workings and how they fit into their underground habitat.
As Jansson dug, though, she kept running into a problem. The main method then used to amplify and analyze stretches of DNA wasn’t powerful enough to reveal all the workings of a single microorganism, much less an entire community of them. “You could get information about specific genes, but sequencing technologies were very slow,” said Jansson, now a division director of biological sciences at Pacific Northwest National Laboratory (PNNL) in Richland, Wash. She knew the layers of sediment she studied held a treasure trove of biological finds, but she didn’t yet have the tools she needed to unearth them.
Then, soon after the turn of the century, new high-octane DNA sequencing methods made it possible to sequence thousands or even millions of genes almost instantly. These new, speedier methods meant researchers could easily sequence the collective genomes of the sample, known as a metagenome, for the first time. Suddenly, it was possible to scan the overall composition of habitats as diverse as stagnant bogs and frozen tundra, producing a detailed portrait of the microbial life they held. The gene and protein sequences from these wide-ranging scans — the first of their kind — would, once decoded, illuminate what the microbes were actually doing within each ecosystem. The data would help researchers understand how microbes capture and store carbon dioxide from the atmosphere, how they break down organic matter so that plants can access its nutrients, and how they neutralize soil toxins known to threaten human health. “You can just sequence everything,” Jansson said. “That’s where the metagenomic approach has really been an advantage.”
Almost everything about Jansson’s current surroundings is big and bold: the 600 acres of sycamore-studded PNNL campus rolling across eastern Washington, the endless blue sky she can see through her picture window, the fridge-size gene sequencing machine where her team deposits soil samples. But, as ever, what drives Jansson is the lure of the microscopic and the unseen — the challenge of mapping the contents of the soil microbiome, a teeming global community whose functions have never been fully understood. “Soil,” Jansson said, flashing a grin, “is the ultimate complex system.”