A glimpse of the paleome in endolithic microbial communities

Microbiome

Research

Carl-Eric Wegner¹  Kirsten Küsel²  Kai U. Totsche³  Alex Hübner⁴  Raphaela Stahl⁴  Irina Velsko⁴  Zandra Fagernäs⁴  Christina Warinner⁵  Robert Lehmann⁶  Thomas Ritschel⁶ 

[1] Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany;Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany;Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany;German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany;Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany;Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany;Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany;Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany;Department of Anthropology, Harvard University, Cambridge, MA, USA;Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany;Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany;

关键词: Subsurface;    Metagenomics;    Endolithic;    DNA damage;    Chemolithotrophy;   

DOI  :  10.1186/s40168-023-01647-2

 received in 2022-10-12, accepted in 2023-08-09,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsBy 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.ConclusionsOur 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.5FvsXWM5isfqTEMW9i73VYVideo Abstract

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

【 图 表 】

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