New microbes found deep underground in the 'Critical Zone' help clean our water

Microbes live all around us, but some of the most important ones are hidden far beneath our feet. They are part of a world that plays a critical role in keeping our ecosystems healthy.

Recent discoveries have revealed that a previously unknown group of microbes is thriving in this deep soil – and they’re quietly helping to clean the water that becomes our drinking supply.

Researchers at Michigan State University are exploring one of the least understood parts of our planet – a vast underground zone that quietly supports life above.

What goes on in this zone helps regulate essential processes like water purification, soil formation, and nutrient cycling. Despite how vital it is, scientists still know very little about it, especially at its deepest levels.

What is the Critical Zone?

“The Critical Zone extends from the tops of trees down through the soil to depths up to 700 feet,” explained James Tiedje, a world-renowned expert in microbiology from Michigan State University.

“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,” said Tiedje.

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

By analyzing deep soil samples from Iowa and China – two places known for their rich and deep soils – the team discovered something extraordinary: a whole new phylum of microbes, which they named CSP1-3.

A phylum is a major category in biological classification, so this is not just a new species or strain – it’s a completely different branch of microbial life.

The team selected Iowa and China to see whether these microbes are widespread or limited to specific regions. Their findings suggest CSP1-3 might be more common than anyone realized.

History of the new microbes

The researchers extracted DNA from these deep soils and traced the evolutionary journey of CSP1-3. It turns out these microbes have a long history.

Their ancestors once lived in aquatic environments, including freshwater habitats and hot springs, millions of years ago. Over time, they adapted to life in soil, first moving into surface layers and eventually into deeper regions.

But perhaps the most surprising discovery isn’t just that they exist – it is that they are thriving.

“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.”

Not only are they active, they’re dominant. In some samples, CSP1-3 made up over half of the microbial community, which is a rare occurrence in soil ecosystems.

“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.

How microbes help purify water

Soil isn’t just dirt – it’s the Earth’s largest water filter.

As rainwater moves down through the layers of soil, it’s cleaned by a combination of physical, chemical, and biological processes.

While the surface soil does part of the job, much of the water purification actually happens deeper down – and that’s where CSP1-3 comes in.

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

These microbes feed on leftover carbon and nitrogen that percolates down from the topsoil. In doing so, they help purify groundwater before it reaches the aquifers that supply our drinking water.

What scientists plan to do next

The next step for the research team is to grow CSP1-3 in the lab. Culturing deep-soil microbes in the lab is notoriously difficult because their native environment is hard to replicate. However, the researchers are hopeful.

Knowing that CSP1-3’s ancestors once lived in hot springs, they’re experimenting with high-temperature conditions to encourage growth.

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

“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.”

As Leonardo da Vinci once said, “We know more about the movement of celestial bodies than about the soil underfoot.” With discoveries like this, we’re starting to change that – one layer at a time.

The full study was published in the journal Proceedings of the National Academy of Sciences.

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