A new category of lifeform has been discovered within Earth’s Critical Zone, the planet’s near-surface “skin” that stretches from tree canopies down to bedrock, offering fresh insights into what’s hidden beneath Earth’s soil.
Michigan State University microbiologist James Tiedje led the research, which explored a poorly understood yet vital part of the global ecosystem. The team uncovered a previously unknown form of microbe representing an entirely new phylum—a major taxonomic rank just below kingdom in the classification of life on Earth.
“The Critical Zone extends from the tops of trees down through the soil to depths up to 700 feet,” Tiedje explained. “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 said.
A previously unknown group of microbes, Tiedje and his team have designated these organisms CSP1-3. The scope of the discovery became clear when soil samples taken from a depth of 70 feet in both Iowa and China—despite their geographic distance—each contained CSP1-3 microbes. The shared presence of these organisms in similar deep soil environments highlighted their surprising global distribution.
DNA Reveals Microbial Evolution
By analyzing DNA extracted from the soil, the researchers found that CSP1-3 likely evolved from aquatic organisms that once lived in hot springs and freshwater environments millions of years ago. Over time, these microbes adapted to new environments—starting with surface soils and eventually colonizing deeper layers. Remarkably, the team also determined that CSP1-3 are not dormant.
“Most people would think that these organisms are just like spores or dormant,” he said. “But one of our key findings we found through examining their DNA is that these microbes are active and slowly growing.”
Contrary to expectations, CSP1-3 are not rare but dominant, making up more than half the microbial population in deep soil layers.
“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.
Lifeforms as Water Purifiers
These microbes also play an important role in purifying Earth’s water. As water travels downward from the surface, past plant roots, and into deeper soil layers, CSP1-3 consume the carbon and nitrogen compounds that remain, acting as a final filter in the natural purification process.
“CSP1-3 are the scavengers cleaning up what got through the surface layer of soil,” Tiedje said. “They have a job to do.”
Future Research Plans
Tiedje now plans to bring the discovery from the field into the lab, to culture CSP1-3 in controlled conditions. If successful, researchers would be able to study the microbes’ unique physiologies in greater detail to understand what makes them thrive in such extreme environments.
However, this will be no small task. Laboratory efforts to replicate deep-soil habitats are notoriously difficult, and few such microbes have been successfully grown. Tiedje plans to begin by mimicking the high-temperature conditions of the organisms’ evolutionary origins in hot springs.
“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.”
The paper “Diversification, Niche Adaptation, and Evolution of a Candidate Phylum Thriving in the Deep Critical Zone” appeared in Proceedings of the National Academy of Sciences on April 11, 2025.
Ryan Whalen covers science and technology for The Debrief. He holds an MA in History and a Master of Library and Information Science with a certificate in Data Science. He can be contacted at ryan@thedebrief.org, and follow him on Twitter @mdntwvlf.