Is there a distinct microbiome within the deep aeration zone?

We applied in situ incubation of bedrock fragments in a 47 m deep aeration zone well that underwent pronounced seasonal fluctuation of oligotrophic groundwater. After groundwater-saturated colonization, and successional exposure to natural de-saturation and re-saturation, we analyzed the bacterial and archaeal 16S rRNA diversity and applied a statistical-based source tracking for identifying the relationship to groundwater-suspended sources. In our interdisciplinary study, we monitored the dynamic environmental conditions in the fractured mixed carbonate-/siliciclastic alternations as well. Mimicking large fracture habitats, the incubated rock fragments were colonized by a diverse bacterial, and less diverse archaeal community, both including persistent genera that withstand harsh environmental changes. Similar to local mature fracture-surfaces, our freshly colonized rock fragments were dominated by Gammaproteobacteria. Compositional differences to communities within contrasting endolithic habitats of the phreatic zone, viz. groundwater and rock matrices, and communities within soil, point to a distinct and adapted microbiome within the deep aeration zone. Its persistent, although cosmopolitan genera like Pseudomonas, Sulfuritalea, Cand. Nitrosoarchaeum possess functional potentials for cycling surface-sourced nutrients. Even though they are hardly represented by ecological surveys that solely utilize groundwater or rock samples, endolithic niches within the deep aeration zone may significantly contribute to biogeochemical cycling and groundwater quality. We suggest that in situ-incubation that was barely applied under water-unsaturated conditions so far, is an appropriate tool, especially for discovering the unknown microbial dynamics and services within large aeration zones.