Fig. 1: Groundwater sampling design.

a Groundwater sampling was conducted in 2019 and 2022 at the Hainich Critical Zone Exploratory (CZE) located in Thuringia, Germany (indicated by the red star in the map to the left; 51°6′N, 10°25′E). Photographs show the field sampling equipment and a close-up of one of the groundwater wells. b A schematic cross-section of the Hainich CZE sampling site. Groundwater wells (represented by vertical red lines) were installed at various depths within a hillslope area. The groundwater monitoring transects span approximately 6 km. The multistorey aquifer system comprises a lower, karstified main aquifer (shown in blue, and labeled HTL for Hainich transect lower aquifer) and an upper mudstone-dominated aquifer (shown in teal, and labeled HTU for Hainich transect upper aquifer). Groundwater samples were collected using a sequential filtration through 0.2- (diamond symbol) and 0.1-µm (circle symbol) pore size filters. The figure is modified from Kohlhepp et al.³⁴. c Selected hydrochemical parameters of the groundwater of the seven wells are presented. For well H43, water level values were obtained from the two subsequent measurement campaigns, as no data were available during the metagenome sampling period. Complete and additional parameters are provided in Supplementary Data 7.