Scientists uncover dominant new microbe group deep in Earth's soil

Scientists uncover dominant new microbe group deep in Earth's soil
by Clarence Oxford
Los Angeles CA (SPX) Apr 10, 2025

Leonardo da Vinci once remarked that humanity understands the heavens better than the earth beneath its feet. James Tiedje at Michigan State University echoes that sentiment, but he's working to change it through groundbreaking research into Earth's Critical Zone-a dynamic layer stretching from treetops to bedrock.

"The Critical Zone extends from the tops of trees down through the soil to depths up to 700 feet," Tiedje said. "This zone supports most life on the planet as it regulates essential processes like soil formation, water cycling and nutrient cycling, which are vital for food production, water quality and ecosystem health. Despite its importance, the deep Critical Zone is a new frontier because it's a major part of the Earth that is relatively unexplored."

Tiedje, a University Distinguished Professor Emeritus with dual appointments in Microbiology, Genetics and Immunology and in Plant, Soil and Microbial Sciences, has helped reveal a previously unknown microbial phylum, CSP1-3. Unearthed from soil cores as deep as 70 feet in Iowa and China, these microbes appear to have a broad geographic presence due to the similar deep soil conditions in both regions.

By extracting DNA from these depths, Tiedje's team discovered that CSP1-3 originated in aquatic environments such as hot springs and freshwater habitats. Over evolutionary time, they transitioned into terrestrial ecosystems, moving from surface soils to deeper layers.

Far from being dormant, CSP1-3 microbes are metabolically active. "Most people would think that these organisms are just like spores or dormant," Tiedje said. "But one of our key findings we found through examining their DNA is that these microbes are active and slowly growing."

In an unexpected twist, CSP1-3 are not minor players in the microbial community but often dominate, accounting for more than half of the population in some deep soil samples-a pattern not observed in surface soils.

"I believe this occurred because the deep soil is such a different environment, and this group of organisms has evolved over a long period of time to adapt to this impoverished soil environment," Tiedje added.

The research also highlights CSP1-3's role in natural water filtration. As rainwater percolates down, it passes through the nutrient-rich topsoil quickly but slows in the deeper layers, where CSP1-3 reside. Here, they metabolize residual carbon and nitrogen, further purifying the water.

"CSP1-3 are the scavengers cleaning up what got through the surface layer of soil," Tiedje said. "They have a job to do."

The next challenge is to grow these elusive microbes in laboratory conditions to better understand their physiology. Tiedje's team is exploring high-temperature cultivation, inspired by the microbes' hot spring ancestry, as one of several potential approaches.

If successful, this could lead to the discovery of novel biochemical pathways or genetic traits with applications beyond soil science. "CSP1-3's physiology, driven by their biochemistry is different, so there may be some interesting genes of value for other purposes," he said. "For example, we don't know their capacities for metabolizing tough pollutants and, if we could learn that, we can help solve one of the Earth's most pressing problems."

Research Report:Diversification, niche adaptation and evolution of a candidate phylum thriving in the deep Critical Zone