Linking Surface and Subsurface: The Biogeochemical Basis of Cave Microbial Ecosystem Services

Most caves form by the dissolution of soluble rock (typically limestone or dolomite, but occasionally halite or gypsum), and occur within karst landscapes, where dissolution is the dominant geomorphic process (Ford and Williams 2007). Karst landscapes occupy approximately 20% of terrestrial ice-free areas globally and are major geomorphological features in North America, Europe, the Middle East, Asia and Australia (Figure 1) (Palmer 1991; Goldscheider et al. 2020; Chen et al. 2017). Caves also occur within insoluble rocks, where they form by a variety of processes. Caves within basalt lava flows form as internal conduits (tubes) (White, Culver, and Pipan 2019). Lava tubes are much less common than limestone caves but are found worldwide, scattered within basalt lava fields in every continent and on volcanic islands such as New Zealand, Hawaii, the Azores, Galapagos and the Canary Islands (Figure 1) (Espinasa-Pereña 2006; Greeley and Hyde 1972; Middleton et al. 2023; Webb 2023).

Cave environments are typically classified as oligotrophic ecosystems, where traces of surface-derived organic carbon and nutrients enter the cave via sinking streams or water percolation (Simon, Pipan, and Culver 2007; Ravn, Michelsen, and Reboleira 2020; Jones and Macalady 2016). Yet, despite this energy limitation, caves harbour diverse microbial communities which live on cave walls and speleothems (particularly, flowstone and rimstone dams) as biofilms and in allochthonous sediments on the cave floor (Figure 2). Dominant bacterial phyla frequently described in cave surveys include Pseudomonadota, Actinobacteriota, Acidobacteriota, Chloroflexota and Bacteroidota, while the more prevalent archaeon is Thermoproteota (Engel 2010; Zhu et al. 2019; Luis-Vargas et al. 2019). Recent studies have also identified fungi, especially those from the phylum Basidiomycota, which play a significant role in organic matter degradation and nutrient cycling (Martin-Pozas et al. 2022). Most microbial communities depend on the heterotrophic breakdown of allochthonous carbon sources for energy (Engel 2010; Stevens 1997). However, chemolithoautotrophs, bacteria and archaea, which couple the oxidation of inorganic compounds to CO₂ fixation, have also been reported. As cave primary producers, these microorganisms play key roles in subterranean carbon and nutrient cycles (Zhu, Jiang, and Liu 2022). Conventional chemolithoautotrophs that are commonly reported include nitrifying microorganisms, such as ammonia-oxidising bacteria and archaea, as well as sulphide and iron oxidisers (Tetu et al. 2013; Ortiz et al. 2014; Chen et al. 2009; Jones and Northup 2021).

Caves provide microbial life with a relatively stable climate, which is characterised by relatively small variations in temperature and moisture content of the cave air (de Freitas and Littlejohn 1987). In the absence of atmospheric exchange with the surface, cave climates reflect the temperature and moisture content of their host rock. However, most caves frequently exchange air with the surface in response to changes in atmospheric pressure and air movements (Wigley 1967). This realisation has led to the discovery that, besides reduced nitrogen, sulphur, and iron compounds, cave bacteria also use reduced atmospheric gases as an energy source, such as hydrogen (H₂), carbon monoxide (CO) and methane (CH₄). At the surface, soil bacteria are a major biogeochemical sink for these trace gases, accounting for net losses of approximately 75%, 15% and 4%, respectively (Greening and Grinter 2022). Indeed, trace gas oxidisers are widespread across various grassland, forest, wetland and dryland ecosystems (Bay, Dong, et al. 2021), but little is known about their prevalence and ecological role in caves.

Methane has a global impact as a powerful greenhouse gas and its oxidation by cave microbes has received increasing attention. Indeed, high-affinity aerobic methanotrophs, bacteria which use atmospheric methane as both carbon and energy source, have been shown to rapidly consume this gas across diverse cave ecosystems (Cheng et al. 2022; Mattey et al. 2013; Nguyễn-Thuỳ et al. 2017; McDonough et al. 2016; Allenby et al. 2022; Waring et al. 2017; Fernandez-Cortes et al. 2015). These findings are supported by a preprint study showing that both aerobic high-affinity methanotrophs and hydrogenotrophs, bacteria which can couple the oxidation of atmospheric H₂ to CO₂ fixation, act as major primary producers (Bay et al. 2024). Reflecting the fact that the atmospheric energy source is used for carbon assimilation and fixation, the study termed these microbes as ‘aerotrophs’. The study further shows that cave aerotrophs are supported by other groups, such as nitrifiers and to a lesser extend sulphide oxidisers, to support energy requirements independent from surface-derived organic carbon sources (Figure 2).

Caves provide numerous provisioning, regulating, supporting and cultural ecosystem services (Goldscheider 2019). Most of these services are mediated by microbial communities which drive the biogeochemical processes underlying them (Table 1). In turn, these processes affect the air, water and soil of surface ecosystems through groundwater flows, aeolian transport and atmospheric exchange (Goldscheider 2019; Bennett, Peterson, and Gordon 2009). Supporting services, such as the microbial degradation of surface-derived organic matter, are relatively well understood (Simon, Pipan, and Culver 2007; Ravn, Michelsen, and Reboleira 2020; Dong et al. 2024). This process converts nitrogen and phosphorous from dissolved and particulate organic carbon into more usable forms, such as ammonium and phosphorus. These compounds can serve as the energetic basis for other processes, such as nitrification, or benefit surface ecosystems, which are supplied by groundwater flow (Ravn, Michelsen, and Reboleira 2020). However, services such as chemolithoautotrophic primary production, sustained by various lithic and atmospheric energy sources, are much less known. For example, bacteria and archaea involved in stepwise nitrification are important mediators of nitrogen cycling. They can use energy from the oxidation of ammonium to fix CO₂ using various carbon fixation pathways (Tetu et al. 2013; Ortiz et al. 2014; Zhao et al. 2017; Silva Marques et al. 2018). Similarly, atmospheric trace gases can fuel hydrogenotrophic CO₂ fixation and methanotrophic carbon assimilation, which provide a hidden energy source that can sustain primary production independent from sunlight. Overall, this suggests that cave ecosystems may be more productive than previously thought (Stevens 1997; Bay et al. 2024). While sulphur and iron oxidisers are less common in aerated caves, they are an important group of primary producers in caves where these substrates are abundant from either mineral or geothermal sources (Chen et al. 2009; Macalady et al. 2008).

Among regulating services, caves are potentially a major overlooked biogeochemical sink for climate-active trace gases, including H₂, CO, CH₄ and CO₂. Mediated by various lithoheterotrophic and chemotrophic processes, microorganisms use H₂, CO and CH₄ as ubiquitous and potentially unlimited energy sources to support both cellular maintenance and, in the case of ‘arotrophs’, primary production. Similar modes of energy conservation and primary production driven by trace gases have been described in other challenging ecosystems such as deserts (Ji et al. 2017; Bay, Waite, et al. 2021; Jordaan et al. 2020; Ortiz et al. 2021; Ray et al. 2022). However, caves appear unique in that they facilitate these processes continuously, reflecting the relatively stable cave climate. Caves also act as major sinks for CO₂. The uptake is primarily driven by chemoautotrophic CO₂ fixation and the interaction of atmospheric CO₂ from various sources, including microbial respiration, with meteorological water, forming carbonic acid, which reacts with carbonate rock to form dissolved calcium cations and bicarbonate anions (Figure 2) (Goldscheider 2019). Moreover, karst systems are crucial in many regions as underground water reservoirs where microorganisms drive provisioning services such as the degradation of pollutants (Goldscheider 2019). Overall, these microbial ecosystem services form a connection between surface and subsurface ecosystems which are central to climatic regulation, agricultural productivity and biodiversity.

S.K.B. conceptualised the article, writing, reviewing and editing. M.N.L.V. writing of original draft, writing, reviewing and editing, visualising main figures. J.W. and S.W. reviewing and editing.

The authors declare no conflicts of interest.