Far below the Earth’s surface, deep inside cracks and pores in solid rock, vast communities of microorganisms are quietly at work.
These microscopic organisms are invisible to us, yet they play a crucial role in shaping groundwater quality and regulating major chemical cycles on our planet.
New research shows that where these microbes live—on rock surfaces or floating freely in water—matters far more than scientists previously realized.
A research team led by Dr. Martin Taubert from the University of Jena has discovered that underground microbial life follows two very different survival strategies, with important consequences for environmental science, water management, and climate research.
The study was carried out as part of the Cluster of Excellence “Balance of the Microverse” and published in the journal Microbiome.
For many years, scientists studying groundwater microbes mainly focused on organisms that float freely in water. These microbes are easier to collect and analyze.
However, earlier hints suggested that this approach was missing most of the story.
The new research confirms that suspicion. In underground environments, the overwhelming majority of microorganisms do not drift in the water at all. Instead, they form dense biofilms that cling tightly to rock surfaces, where they can be up to a thousand times more abundant than free-living cells.
To better understand these rock-attached microbes, the team studied a natural groundwater system in the Thuringian Hainich region of central Germany.
They examined microorganisms growing on carbonate rock and compared them with microbes living freely in the same groundwater. Using advanced genetic techniques, the researchers were able to identify which species were present and what functions they performed.
The results revealed two sharply different microbial worlds existing side by side. Even though the microbes live very close to one another and may interact, the communities attached to rock and those floating in water are made up of very different organisms with very different abilities.
Surprisingly, the researchers found that lifestyle—whether a microbe is attached or free-living—has a stronger influence on the community than environmental factors such as oxygen levels.
The microbes living on rock surfaces are highly specialized. Many can extract energy from inorganic substances like iron or sulfur. At the same time, they are able to capture carbon dioxide and turn it into organic material, effectively storing carbon underground. This means they actively contribute to the carbon cycle and may help lock away carbon for long periods.
In contrast, the microbes floating in groundwater appear to have a much narrower range of functions. While they still play a role in the ecosystem, they cannot match the chemical versatility of their rock-bound counterparts.
According to Dr. Taubert, overlooking the microbes attached to rock surfaces means ignoring one of the most important players in underground ecosystems. These organisms help drive key chemical processes, including those that influence water quality and carbon storage.
The findings have real-world implications. Groundwater is a vital source of drinking water for much of the world, and understanding how microbes transform chemicals underground can improve assessments of natural water purification. The study also suggests that groundwater systems in carbonate rocks may store more carbon dioxide than previously thought, an insight that could affect climate models and our understanding of natural carbon sinks.
In short, life hidden on rock surfaces deep underground is quietly shaping both our water and our planet’s carbon balance—and scientists are only just beginning to appreciate its full impact.
