Deep soil — ranging from below 30 cm (12 inches) to hundreds of meters, depending on soil type and region — is a neglected ecosystem within Earth’s Critical Zone. Biologists have now discovered a widespread and relatively abundant bacterial phylum, named CSP1-3, in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history.
A diagram showing the evolutionary history from an aquatic organism and adaptive traits of CSP1-3 phylum for each habitat. Image credit: Michigan State University.
“The Critical Zone extends from the tops of trees down through the soil to depths up to 213 m (700 feet),” said Michigan State University’s Professor James Tiedje.
“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.”
Professor Tiedje and his colleagues discovered in this huge, unexplored microbial world a completely different phylum of microbes called CSP1-3.
This new phylum was identified in soil samples from both Iowa and China at depths down to 21 m (70 feet).
“Why Iowa and China? Because these two areas have very deep and similar soils and we want to know if their occurrence is more general and not just in one area,” Professor Tiedje said.
The researchers extracted DNA from these deep soils and found that CSP1-3’s ancestors lived in the water — hot springs and fresh water — many millions of years ago.
They underwent at least one major habitat transition to colonize soil environments — first topsoil and, later, deep soils, during its evolutionary history.
The scientists also found that the CSP1-3 microbes were active.
“Most people would think that these organisms are just like spores or dormant,” Professor Tiedje said.
“But one of our key findings we found through examining their DNA is that these microbes are active and slowly growing.”
The authors also were surprised to find these microbes were not rare members of the community, but were dominant; in some cases they made up 50% or more of the community, which is never the case 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,” Professor Tiedje said.
A paper describing the findings was published on March 18 in the Proceedings of the National Academy of Sciences.
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Wenlu Feng et al. 2025. Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone. PNAS 122 (12): e2424463122; doi: 10.1073/pnas.2424463122
