Resilience of deep aquifer microbial communities to seasonal hydrological fluctuations

Abstract

The influence of seasonal variations in temperature and precipitation on subsurface biogeochemical processes remains poorly understood. In the Lavey-les-Bains thermal system in the Swiss Alps, annual variations in electrical conductivity are observed to depths of 500 m, suggesting a potential link to surface environmental changes. Here we show, through year-round analyses of stable water isotopes, noble gases, and conductivity, that seasonally varying contributions of shallow groundwater from the Rhône alluvial aquifer mix with deep groundwater. Despite vertically similar fluid geochemical compositions suggesting high hydrological connectivity, microbial communities exhibit significant depth-dependent variation with minimal seasonal change. This decoupling of dynamic water source partitioning and stable microbial community structure has not been previously observed and fills a critical gap in our understanding of geothermal systems and microbial life in the deep subsurface. At 200 m, the communities are dominated by sulfur-disproportionating Bacteria (Dissulfurispira) and Micrarchaeota, while at 500 m the major groups include sulfate- and iron-reducers and/or hydrogen-oxidizers (Thermales, Thermodesulfobacteriota, and Bathyarchaeota). Our study highlights the resilience of terrestrial subsurface microbial communities to temporal variations in water sources and fluid composition. We propose that intrinsic environmental properties-such as temperature-are more critical drivers of microbial community structure in hydrologically connected deep aquifers than seasonal hydrological changes.

Keywords: deep microbial communities; geomicrobiological; noble gases; thermal aquifer.

Fig. 1.

(A) Weekly measurements of electrical conductivity (K₂₀) (mS/cm) for wells P600 (black) and P201 (red), highlighting seasonal variations. Despite the clear offset, both curves appear to be temporally correlated. (B) Normalized partial pressures (R_i) of CO₂ (blue) and CH₄ (black) relative to N₂ in well P201 (solid line). The data show daily averages of measurements taken with a time resolution of about 10 min. The dotted line models the sinusoidal fluctuations over a period of 365 d, with shaded areas indicating the deviation between the model and observed data.

Fig. 2.

Geographic mapping of water sampling in the Lavey-les-Bains region (Top) and stable isotopic composition (Bottom): the isotopic signatures of all samples from various water sources, including local precipitations, river water, drinking water, and thermal springs, plot closely along the global meteoric water line (GMWL), bracketed by local meteoric water lines (LMWL) from Sion at 482 m ASL and Grimsel at 1,950 m ASL. This alignment indicates that the thermal waters of Lavey-les-Bains and other local water sources originate from recent meteoric water that has fallen in the Rhône valley and the Aiguilles Rouges massif. Compared to Lavey-les-Bains, wells in Saint-Gervais-les-Bains and Val d’Illiez, which are believed to recharge in the same area as the Lavey-les-Bains’ thermal waters (33), indeed have similar isotopic composition as the thermal waters at P600. Furthermore, drinking water springs near the village of Salvan (SI Appendix, Table S1), which range in elevation from 900 m ASL to 1,950 m ASL in the supposed recharge area, display isotopic values that lie between those of P600 and AP. Map sources: satellite imagery (34); digital elevation model (35); boundaries (36); EPSG:3035.

Fig. 3.

Analysis of the relative abundance of microbial communities based on 16S rRNA gene sequencing from Lavey-les-Bains wells. Bacterial (Left) and archaeal (Right) community compositions at the phylum level; predominant phyla (dashed squares) are further categorized by their dominant orders to detail the community structure. For wells P201 and P600, triplicate samples are arranged in chronological order based on their sampling dates from Table 1, with the earliest sampling at the Top.