Microbial Communities in the Terrestrial Subsurface
Cumulative thesis
Date of Examination:2024-10-15
Date of issue:2025-01-23
Advisor:Prof. Dr. Thomas Friedl
Referee:Prof. Dr. Dirk Wagner
Referee:Prof. Dr. Thomas Scholten
Referee:PD Dr. Michael Hoppert
Referee:Prof. Dr. Rolf Daniel
Referee:Prof. Dr. Jan-Peter Duda
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Abstract
English
Terrestrial subsurface habitats represent a significant portion of Earth's prokaryotic biomass. However, our understanding of microbial diversity and functions in these environments, particularly in arid regions, remains limited. Using 16S rRNA gene sequencing and metagenomic analyses, this thesis explores the microbial communities in the deeper subsurface of Chile's Coastal Cordillera. Focusing on two distinct geological settings within the Atacama Desert — the salt-containing sediments of a hyperarid basin in Yungay and the granitic bedrock beneath the arid hillslope of Pan de Azúcar — the research presented here provides the first assessment of microbial biodiversity in arid subsurface environments. Additionally, by comparing the microbial composition and ecology of the arid sites to subsurface communities from the humid environment of Nahuelbuta, characteristic traits of the arid deep biosphere were identified. The findings revealed distinct arid subsurface communities influenced by geological factors. In Yungay, an established desert soil community composed of specialized Actinobacteriota, which were buried over the last 19,000 years, was observed. This community probably persisted by gaining water from the gypsum content of the sediments, combined with the communities' mixotrophic capacities which were initially acquired to adapt to desiccation conditions in desert surface environments. In Pan de Azúcar, Proteobacteria-dominated community composition is mainly controlled by igneous deep biosphere dynamics, including the granitic bedrock lithology, and the nutrient supply and colonization pattern determined by fractures. Comparing these communities to the humid bedrock communities in Nahuelbuta highlighted the role of isolation in shaping arid subsurface ecosystems, with chemolithoautotrophic and mixotrophic taxa in Yungay and Pan de Azúcar sustaining life in nutrient-limited conditions just meters below the surface in contrast to the humid deep biosphere in Nahuelbuta. The application of an improved iDNA extraction method demonstrated its potential for characterizing living microbial communities in low biomass environments, especially desert environments. Furthermore, applying an EDTA-containing buffer from the improved iDNA method enabled the molecular assessment of iron-rich granite samples recovered from the deep biosphere. This offered a more thorough characterization of these environments than previous investigations, which are mostly based on the molecular analysis of fracture fluids and groundwater. These findings show that highly adapted microorganisms can inhabit arid subsurface environments down to a depth of at least 55 m. This extends our understanding of microbial diversity and ecological dynamics not only of the terrestrial deep biosphere but also arid environments. The finding of these two arid subsurface niches emphasizes the need for further studies investigating the microbial composition of deeper arid environments for a comprehensive assessment of arid subsurface biodiversity. Furthermore, the findings highlight the importance and potential of refining DNA extraction methods to enhance the exploration of challenging oligotrophic, desert, and deep biosphere environments.
Keywords: Terrestrial Subsurface; Microbial Diversity; Desert environments; Chemolithoautotrophy; Deep Biosphere; Rock weathering; Gypsum