A glimpse of the paleome in endolithic microbial communities

Microbiome - Tập 11 - Trang 1-18 - 2023
Carl-Eric Wegner1, Raphaela Stahl2, Irina Velsko2, Alex Hübner2, Zandra Fagernäs2, Christina Warinner2,3,4, Robert Lehmann5, Thomas Ritschel5, Kai U. Totsche4,5, Kirsten Küsel1,4,6
1Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
2Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
3Department of Anthropology, Harvard University, Cambridge, USA
4Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
5Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Jena, Germany
6German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany

Tóm tắt

The terrestrial subsurface is home to a significant proportion of the Earth’s microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards. By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g−1 rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past. Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation.

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