Microbial communities inhabit spaces in soils and rock from the surface extending deep into Earth. Though these environments seem homogeneous, they record inherent complexity in the system, incorporating hydrology, mineralogy, biology, and ecological succession. A challenge to understanding rock-hosted microbial ecosystems is describing this complexity and its relationship to resident microbial communities. Highly sensitive tools have been developed over the past decade to describe the physical and biogeochemical environment in rock pore spaces, as well as microbes and their functions in natural ecosystems. This is key for microbes in extreme environments that are can’t be studied in pure culture. Rock-hosted habitats associated with serpentinization, the aqueous alteration of ultramafic rock, are an exciting avenue to explore as they’ve been present throughout Earth’s history, are abundant in the solar system, and create energy and organic molecules that may fuel microbial growth. Chapter 2 describes the subsampling and molecular, biological and mineralogical analyses of a large hydrothermal vent chimney structure from the Lost City Hydrothermal Field (LCHF) near the Mid-Atlantic Ridge. LCHF is strongly influenced by serpentinization, resulting in high pH, methane and hydrogen rich fluids. Although the chimney structures contain three minerals, aragonite, brucite and calcite, their distribution provided highlight which parts of the structure were directly in contact with alkaline hydrothermal fluids. Using these minerals as proxies for discrete hydrothermal regions, correlations were drawn between microbes, genes and minerals, making a coarse map of the domains of taxa and their metabolisms across a complicated marine extreme environment. In chapter 3, LCHF chimneys samples were embedded in resin and sectioned for multi-modal analyses using Raman microspectroscopy, laser-ablation ICP-MS, and fluorescence confocal microscopy. This localized relationships between microbial biofilms, pore spaces, and the microenvironment. We identified an abundance of microbial biofilms in brucite-lined pore channels, indicating contact with and adaptation to vent fluids. Further, the work showed that these channels were enriched in trace metals near biofilms critical to metabolism in chimney structures. Microscopy complemented by metagenomic analyses of biofilms showed active metal cycling pathways responsive to nearby metals with a possible biotic mechanism for their deposition through efflux systems. Chapter 4 looked at a different type of serpentinite-hosted ecosystem within an ophiolite complex in Northern California. Forming in the Earth’s upper mantle, ultramafic ophiolites are enriched in heavy metals such as Ni, Cr, and Co. Here, metal toxicity rather than limitation plays a key role in the ecosystem’s organization. As these rocks weather into serpentine soils they host unique endemic fauna. The trace metal content of groundwater, rocks, and soils were compared to the diversity and function of microbial populations. Analysis showed Ni, Cr, and Co increase with depth, and high concentrations of Ni and Cr in high pH groundwater. Examining amplicon sequence data showed no correlations to Ni, Cr or Co but an adapted community overall. Analysis of metagenomic and metatranscriptomic data showed metal efflux systems abundant within the system. These data point to the adaptation of serpentinite-hosted microbiota to Ni and Cr rich environments, and additional resource demands imposed by this stressor. This work provides important knowledge necessary to better understand micro-habitats in rock-hosted environments influenced by serpentinization. These data help to illuminate the microbial ecology of modern-day ecosystems and may guide future cultivation efforts while at same time providing an important point of comparison to models of the early evolution of life on Earth in places like the LCHF, and the potential for life elsewhere.
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