Microbial ecology of the deep terrestrial subsurface

Abstract

The terrestrial subsurface hosts microbial communities that, collectively, are predicted to comprise as many microbial cells as global surface soils. Although initially thought to be associated with deposited organic matter, deep subsurface microbial communities are supported by chemolithoautotrophic primary production, with hydrogen serving as an important source of electrons. Despite recent progress, relatively little is known about the deep terrestrial subsurface compared to more commonly studied environments. Understanding the composition of deep terrestrial subsurface microbial communities and the factors that influence them is of importance because of human-associated activities including long-term storage of used nuclear fuel, carbon capture, and storage of hydrogen for use as an energy vector. In addition to identifying deep subsurface microorganisms, recent research focuses on identifying the roles of microorganisms in subsurface communities, as well as elucidating myriad interactions-syntrophic, episymbiotic, and viral-that occur among community members. In recent years, entirely new groups of microorganisms (i.e. candidate phyla radiation bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoloarchaeota, Nanoarchaeota archaea) have been discovered in deep terrestrial subsurface environments, suggesting that much remains unknown about this biosphere. This review explores the historical context for deep terrestrial subsurface microbial ecology and highlights recent discoveries that shape current ecological understanding of this poorly explored microbial habitat. Additionally, we highlight the need for multifaceted experimental approaches to observe phenomena such as cryptic cycles, complex interactions, and episymbiosis, which may not be apparent when using single approaches in isolation, but are nonetheless critical to advancing our understanding of this deep biosphere.

Keywords: deep subsurface; groundwater; microbial ecology; microbiology; subsurface.

Figure 1

Schematic of a terrestrial subsurface environment. The top layer of the subsurface is generally unsaturated, with saturated layers below. Most aquifers exist in the saturated zone, within the top 100 m from the subsurface. The saturated zone consists of aquifers in permeable rock, loose material, or fractured rock. Outside of aquifers, rock fractures within the saturated zone are often water-filled. As depth increases, so do the temperature and pressure, whereas microbial diversity and abundance are highest closer to the surface. Organic carbon, water, and oxygen become increasingly unavailable with depth, whereas H₂, CO₂, and CH₄ gases are abundant in the deep subsurface.

Figure 2

Schematic of deep subsurface microbial metabolisms fueled by organic carbon (A) and H₂ gas (B), and the sources of electron donors and acceptors in subsurface environments (C). The oxidation of organic carbon compounds can support methylotrophic methanogenesis (1), acetoclastic methanogenesis (2), iron reduction (3), sulfate reduction (4), fermentation, potentially involving episymbiotic relationships (e.g. CPR bacteria and DPANN archaea and their hosts; 5), and nitrate reduction (6). The oxidation of H₂ gas can support iron reduction (7), acetogenesis (8), sulfate reduction (9), and methanogenesis (10), and the reduced iron, sulfate, and carbon dioxide, and electrons (dashed arrow) produced through these processes can act as electron donors for sulfide oxidation (11), nitrate reduction (12), and anaerobic oxidation of methane (13). Water can be reduced to H₂, coupled to the oxidation of CO to CO₂ through the process of carboxydotrophy (14). The metabolisms presented within have been predicted from metagenomic studies [23, 24, 64, 68, 82].