# Microbial Activity in Subterranean Ecosystems: Recent Advances
## 1 Introduction  
Karst is the term used to describe terrains underlain by soluble rock and characterized by the occurrence of caves, sinkholes, sinking streams, and an assortment of other landforms carved on thebedrock. Shallow karst ecosystems cover up to 25% of the Earth's land surface [1] and differ from the surface environments because of their limited energy and available nutrients. Caves, in general, are characterized by a constant temperature, humidity, and high carbon dioxide (CO\({}_{2}\)) concentration the year round, as well as absence of light and scarcity of nutrients. Microorganisms occupy all the niches of the biosphere, including the subsurface, as a part of the critical zone, the heterogeneous near surface environment in which complex interactions involve rock, soil, water, air, and living organisms [2]. Earth's subsurface contains an active microbiota colonizing rock surfaces. In this environment, microorganisms are forced to adapt their metabolism for surviving in extreme conditions, and the low input of carbon, nitrogen and phosphorus as well as the chemical composition of the rock has a direct impact on the community diversity. In fact, one of the main reservoirs of microbial life, even at great depths, where life is not dependent on solar energy and photosynthesis for its primary energy supply is the terrestrial subsurface [3]. The colonization of substrates in caves is not homogeneous. Microorganisms colonize speleothems, host rock, detrital sediments, and/or speleosols with different compositions (clays, carbonate minerals, etc.) and/or textures (crystal habit, grain size, permeability, etc.). Microbial colonization is ultimately a complex and dynamic process that is determined and controlled by physicochemical properties (temperature, pH, redox potential, salinity) and biochemical factors (bioreceptors, nutrient or electron acceptor availability, carbon, nitrogen and phosphorous concentrations, etc.) [4]. Therefore, the collective metabolic processes of microorganisms are decisive in the biogeochemical cycles of the biosphere: C and N fixation, CH\({}_{4}\) metabolism, S oxide reduction, etc. It is well-known that dissolution and precipitation of carbonates are the main processes involved in the mobilization of carbon in subterranean environments. Cave microorganisms are able to induce the precipitation of carbonates, via biomineralization processes [5] and also dissolution processes due to the excretion of acids [6]. There is a wide array of literature on the study of bio-induced mineral formations in subterranean environments [7] and on the microbial-rock interaction related to the CO\({}_{2}\) uptake or release processes [8]. In this context, previous studies have confirmed that _Actinobacteria_ biofilms developing on cave walls promote uptake of CO\({}_{2}\), dissolve the rock, and produce calcite crystals in periods of lower humidity and/or CO\({}_{2}\)[8]. However, the interactions of microbes with the air-water-rock interfaces in subterranean ecosystems and the biological mechanisms by which microorganisms adjust to new environments or changes in their current environment are poorly understood. Low energy subsurface environments are uniquely positioned for examining minimum energetic requirements and adaptations for chemolithotrophic life and become a suitable environment to study the origins of life on Earth and may also serve as analogs to explore subsurface life in extraterrestrial bodies [9]. Furthermore, the microbiota from shallow subsurface environments (karst cavities, lava tubes) are becoming a target of increasing interest in different research fields, including biodiversity [10], mineral formation and dissolution [7], cultural and natural heritage conservation [11], and paleoclimatology [12]. In addition, other important uses of microorganisms are the production of bioactive compounds valuable for medicine and enzymes for bioremediation [13]. The extensive literature about microbial diversity and activity of cave microorganisms has been reviewed by many authors.