Metagenomics/Metatranscriptomics of the Hainich CZE. Metagenomics/Metatranscriptomics of shallow, oligotrophic aquifers

Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-“omic” profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, anammox) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), dependent on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Dominated by few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes, encoded by different microbiome members, along the groundwater flow path. The turnover of organic carbon apparently complements four lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome dependent on the availability of oxygen and inorganic electron donors like ammonium. The differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells.