Groundwater often gets treated like a simple thing, even though microbes fill it and shape how it behaves. It flows through cracks, fills wells, and ends up in a glass on the kitchen table.
Beneath that calm surface is a crowded world of microscopic life doing quiet but serious work.
For years, scientists mostly studied the microbes drifting freely in groundwater. They were easy to collect. Researchers could scoop the water, study what was floating in it, and move on. That approach felt reasonable, but it missed something big.
Most underground microbes are not drifting at all. They cling to rock surfaces, forming dense biofilms. These attached microbes can be up to a thousand times more abundant than the ones swimming freely. Ignoring them means ignoring most of the action.
Microbial worlds share aquifers
To get a better look, researchers studied a natural aquifer in the Thuringian Hainich region. They focused on carbonate rock, a common type of underground stone that groundwater flows through.
Microbial communities living on the rock were compared with those living in the surrounding water, using modern genomic analysis tools.
The results were striking. The microbes attached to rock and those floating in water formed two very different ecosystems. They lived side by side, yet had very different roles and abilities.
Alisha Sharma conducted the study as part of her doctoral thesis at Friedrich Schiller University Jena.
“The lifestyle of the microorganisms – attached to rock or floating free in the water – has a stronger influence on the structure of the community than environmental factors, such as the availability of oxygen,” said Sharma.
What rock microbes actually do
The microbes attached to rock are not just hanging on for stability. They are highly specialized workers.
Instead of feeding on organic material, many of the microbes pull energy from inorganic substances like iron or sulfur. While doing this, they also bind carbon dioxide.
That means they actively store carbon underground – a process that may be far more significant than scientists once realized.
Carbon binding in the subsurface affects how carbon moves through the planet, making these microbes relevant not only to groundwater chemistry but also to climate models and studies of natural carbon sinks.
What happens underground does not stay underground when it comes to long-term climate balance.
“If we ignore the community attached to rock, we overlook an important functional actor in the groundwater system,” said Dr. Martin Taubert, a research group leader at the University of Jena.
“These microorganisms make an important contribution to central chemical processes such as the carbon cycle.”
Microbes help protect groundwater
Groundwater is one of the most important sources of drinking water on Earth. Nearly half of the global population depends on groundwater for everyday household use, and protecting it means protecting the microbial life within it.
The chemistry of that water doesn’t just depend on rocks and flow rates. It depends on microbes changing substances as water moves underground.
Understanding attached microbial communities helps scientists better judge how groundwater cleans itself naturally.
It also helps explain how certain chemicals break down or get trapped before reaching wells and springs. That knowledge matters for water safety and long-term water management.
Active microbes underground
This research fits into the broader goals of the Cluster of Excellence “Balance of the Microverse.”
The team focuses on how microbial communities shape their environments and how environmental changes push back on those communities.
“Microorganisms keep many natural systems in balance without us noticing,” said Professor Kirsten Küsel. “By unlocking their hidden habitats, we better understand how stable – or vulnerable – these systems really are.”
The takeaway is simple but easy to miss. Microbes in the subsurface are not passive background noise. They are active players shaping water quality, carbon storage, and chemical cycles.
Most of them are not floating past each other. They are anchored to stone, doing their work in place, every hour of every day.
The full study was published in the journal Microbiome.
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