Subsurface microbiology

One aspect of subsurface microbiology is to understand microbial surface-subsurface links in the Earth’s Critical Zone (CZ). The CZ is defined as the Earth’s near-surface layer ranging from the vegetation canopy down to saturated and unsaturated bedrock, including the pedosphere and aquifers. Groundwater is a keyhole to study the subsurface, it is an essential resource for drinking water and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome functioning is crucial for our understanding of these important ecosystem services.

Motivation and selected findings

What are facors that control groundwater microbiomes, how are groundwater microbiomes formed? Through metagenomics and -transcriptomics, we could show that groundwater microbiomes are mainly driven by nitrogen- and to a lesser extent sulfur cycling, depending on local hydrochemical differences between groundwater wells (Figure 5) (Wegner et al., 2019). Surprisingly, we also noted a constitutive expression of carbohydrate-active enzymes along the groundwater flowpath, suggesting that organic carbon turnover complements lithoautotrophic carbon assimilation pathways.

Microbial community functions along the Hainich CZE aquifer assemblages are dominated by chemolithoautotrophic processes. H2-H5 = position of wells along the monitoring transect, numbers in circles = different wells accessing the aquifer assemblages. Modified based on

We studied the formation of a groundwater microbiome, by tracing the input of microorganisms from recharge areas into fractured aquifers focusing on the ultra-small and potentially symbiotic Cand. Patescibacteria, which are part of the “candidate phyla radiation” (CPR) and often abundant in groundwater (Herrmann et al., 2019). Co-occurence network analysis revealed a central role for Cand. Patescibacteria in groundwater microbial communities and links to chemolithoautotrophic taxa involved in iron-, sulfur- and nitrogen-cycling. Apparently, import from soil, and community differentiation driven by hydrochemical conditions (Figure 2), including the availability of organic resources and potential partner microorganisms, determine Cand. Patescibacteria success in groundwater.

Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments. Subsurface biomass estimates are flawed by uncertainties due to poorly understood parameters such as the ratio between surface-attached and endolithic to pelagic groundwater cells, for which assumptions range between 10000 and 1. By adapting methods from microbial archaeology and paleogenomics, we were able to successfully recover genomic DNA from rock cores originating from limestone and mudstone from the vadose zone, and deep aquitards (down to 293 meters below ground level) (Wegner et al., 2023). DNA damage pattern analysis, for the first time carried out for subsurface and endolithic rock material, revealed paleome signatures (genetic records of past microbial communities) for three rock specimen (H22-8, H22-30, KS36-H32, Figure 6). Taxonomic and functional profiling suggested a high relevance of chemolithoautotrophy for endolithic microbiomes, but also the utilization of sedimentary organic carbon in the past. We propose that limestones can function as archives for genetic records of past microbial communities, due to their specific conditions facilitating long‑term DNA preservation.