Previous work on groundwater microbiology has focused mainly on cells suspended in the water column because they are easier to sample and analyze. Early indications, however, suggested that this approach captured only a fraction of the subsurface biosphere. The new study confirms that most microorganisms in the subsurface actually live as biofilms tightly attached to rock, where they can be up to a thousand times more abundant than free-living cells.
To probe this hidden lifestyle, the researchers deployed passive samplers in a natural carbonate aquifer in Germany's Thuringian Hainich region. Over time, microbial communities colonized rock material in the samplers, allowing direct comparison between rock-attached communities and those freely suspended in the same groundwater system. Using modern genome-based techniques, the team analyzed community composition and metabolic potential in both habitats.
The results reveal two sharply contrasting microbial ecosystems coexisting in close physical proximity. Rock-attached communities and free-living communities host very different sets of species and functions. According to first author and doctoral researcher Alisha Sharma, the way microbes live, whether fixed to rock or drifting in water, exerts a stronger influence on community structure than environmental factors such as oxygen availability.
On rock surfaces, microbes form highly specialized communities capable of tapping inorganic energy sources such as iron and sulfur. By oxidizing these compounds, they can fix carbon dioxide and build biomass, effectively turning the subsurface into an active carbon sink. These metabolic capabilities allow rock-bound microbes to play a central role in transforming chemicals and sequestering carbon in the underground.
In contrast, the free-living microorganisms in groundwater appear functionally more constrained. They lack the same breadth of metabolic tools seen in rock-attached communities and contribute less to key processes such as carbon fixation. The researchers argue that focusing solely on planktonic cells leads to a distorted view of how groundwater ecosystems function and evolve over time.
"If we ignore the community attached to rock, we overlook an important functional actor in the groundwater system," explains research group leader Martin Taubert from the Cluster of Excellence. He notes that these attached microorganisms are deeply involved in central chemical processes, particularly the carbon cycle, that shape groundwater quality and geochemistry. Recognizing their role is essential for realistic models of subsurface environments.
The findings carry direct relevance for environmental protection, drinking water safety and climate assessments. Groundwater is one of the world's most important sources of drinking water, and an improved understanding of subsurface microbial processes can refine estimates of natural self-purification and contaminant breakdown. The work also suggests that carbonate rock aquifers may lock away significantly more carbon dioxide than previously assumed, a factor that could influence how natural carbon sinks are represented in climate models.
Beyond their immediate environmental implications, the results contribute to the broader goals of the Balance of the Microverse Cluster of Excellence. The initiative seeks to understand how microbial communities shape their surroundings and how environmental conditions in turn regulate microbial balance. Aquatic geomicrobiologist and cluster speaker Kirsten Kuesel emphasizes that microorganisms act as quiet stabilizers of many natural systems, often without human awareness.
By revealing the distinct strategies of rock-attached and free-living microbes in the subsurface, the study underscores that microbial life underground is not merely a passive backdrop. Instead, it is an active architect of groundwater composition, carbon cycling and ecosystem stability. Unlocking these hidden habitats helps researchers gauge how robust or fragile subsurface systems may be in the face of environmental change.
Research Report:Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere
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