Distinct Microbial Communities in the Soils, Waters, and Speleothems of a Hyperalkaline Cave System

Shen, J. and Smith, A.C. and Barnett, M.J. and Morgan, A. and Wynn, P.M. (2022) Distinct Microbial Communities in the Soils, Waters, and Speleothems of a Hyperalkaline Cave System. Journal of Geophysical Research: Biogeosciences, 127 (9): e2022JG006. ISSN 2169-8953

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Abstract

Caves are complex ecosystems with various microbial habitats. Understanding the individual community structures in the key source environments (soils, waters) and those in the sinks (speleothems, cave muds) can help elucidate the extent to which in-cave communities are a function of their source communities, or if they can successfully adapt and diversify locally. Here, we assess the network of microbial communities existing within a unique British cave system. Poole's Cavern is characterized by alkalinity or even hyperalkalinity (pH > 9) in its drip waters, creating a series of challenging ecological niches for microbes to survive. Samples of soil, drip water, speleothem, and cave sediment were collected for chemical characterization, cell culture assays and DNA sequencing analysis. We show that microbial abundance and diversity were highest in the soils proximal to the cave, and the microbiotas of the hyperalkaline cave chamber were less abundant and less diverse than the cave chamber with lower pH. Proteobacteria and Planctomycetota were the most prevalent bacterial phyla throughout the cave system irrespective of pH, indicating their members are comparatively more metabolically versatile. Predicted essential metabolic pathways were still dominant within all sampling sites, and microorganisms were shown to be capable of utilizing various inorganic or simple organic compounds to survive. Interestingly, co-occurrence between Poole's samples was limited, never demonstrating more than 50% similarity. This work highlights the diversity of microbial communities within this extreme environment and the development of microbial niches which reflects the adaptation strategy of microorganisms under alkaline-hyperalkaline conditions.