New microbes could purify global water supply

April 11, 2025

Scientists in the US have discovered a newly identified phylum of microbes thriving up to 70 feet underground, which help purify groundwater and could offer clues for filtering pollutants from drinking water.

The study, led by James Tiedje, PhD, a university distinguished professor emeritus and director of the Michigan State University (MSU) Center for Microbial Ecology, identified the microbe phylum called CSP1-3 in soil samples from Iowa and China in Earth’s Critical Zone.

Both sites have deep, similar soils, which can help determine whether the microbes occur more broadly than in just one location. “The Critical Zone extends from the tops of trees down through the soil to depth up to 700 feet,” Tiedje says.

“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,” he continues. “Despite its importance, the deep Critical Zone is a new frontier because it’s a major part of the Earth that is relatively unexplored.”

Digging deeper into the findings

Tiedje and his team extracted DNA from deep soil samples for the study. They discovered that the phylum’s ancestors lived in aquatic environments such as hot springs and freshwater millions of years ago.

They underwent at least one major habitat transition during their evolutionary history, moving from water to topsoil and eventually to deep soils, where Tiedje observed that they were still metabolically active.

“Most people would think that these organisms are just like spores or dormant,” he states. “But one of our key findings we found through examining their DNA is that these microbes are active and slowly growing.”

The lead researcher was also surprised to discover that these microbes were not just rare exceptions but dominant members of the deep soil community, making up 50 percent or more in some cases, a previously unseen phenomenon 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 says.

Water purifying activity

Soil is Earth’s largest natural water filter, which cleans it through different physical, chemical, and biological processes. However, while surface soil only handles a small volume and rapid flow, deep soil retains significantly more water, providing the environment where CSP1-3 becomes active.

Since carbon and nitrogen wash down from the topsoil, the phylum feeds on these elements to help complete the water purification process. “CSP1-3 are the scavengers cleaning up what got through the surface layer of soil,” Tiedje explains. “They have a job to do.”

Now, the team aims to culture some of these microbes in the lab to learn more about the unique physiologies that make them well-adapted to the deep soil environment.

However, Tiedje notes that the experiment will be difficult, as most microbes have never been cultured in the lab due to the extreme difficulty of mimicking the precise conditions required to live and grow.

“CSP1-3’s physiology, driven by their biochemistry is different, so there may be some interesting genes of value for other purposes,” Tiedje concludes in a press release. “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.”