Microbial roles in cave biogeochemical cycling

Abstract

Among fundamental research questions in subterranean biology, the role of subterranean microbiomes playing in key elements cycling is a top-priority one. Karst caves are widely distributed subsurface ecosystems, and cave microbes get more and more attention as they could drive cave evolution and biogeochemical cycling. Research have demonstrated the existence of diverse microbes and their participance in biogeochemical cycling of elements in cave environments. However, there are still gaps in how these microbes sustain in caves with limited nutrients and interact with cave environment. Cultivation of novel cave bacteria with certain functions is still a challenging assignment. This review summarized the role of microbes in cave evolution and mineral deposition, and intended to inspire further exploration of microbial performances on C/N/S biogeocycles.

The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives

“…The TOC concentration determines the nutrient availability across the cave zones, and it should be determined in the groundwater and sediments. Standard physicochemical characterization of the environmental matrices (e.g., groundwater, rock, air, sediment) would aid in understanding the metabolic activity of microbial inhabitants and the local biogeochemical cycling ( D’Angeli et al, 2019b ; Zada et al, 2022 ; Zhu et al, 2022 ). For instance, portable spectrophotometers and Fourier Transform Infrared (FTIR) spectroscopes can detect the presence of some organic and inorganic compounds (e.g., heavy metals) potentially involved in microbial metabolism ( Macalady et al, 2008 ).…”

“…Therefore, cave microbiology has emerged as a new field of geomicrobiology, continuously improving thanks to scientific and technological advances in environmental microbiome studies. The complexity of microbial life implicated in key processes of cave ecosystems, such as nutritional and biogeochemical cycles, has recently been highlighted ( Zhu et al, 2022 ). Microorganisms constitute the majority of rock-associated biomass in caves, capable of colonizing any cave habitat, including extremely oligotrophic environments ( Reboleira et al, 2022 ).…”

“…In parallel, high-magnification and fluorescence microscopies have contributed to unveiling biofilm-like structures on cave surfaces, identifying and quantifying specific taxa composing these communities, and studying the functional properties of individual microbial components ( Jones et al, 2023 ). Cave microbiology has masterly been reviewed in the past, with an emphasis on geomicrobiology ( Northup and Lavoie, 2001 ; Barton, 2006 ; Barton and Northup, 2007 ), anthropic impact (e.g., Bontemps et al, 2022 ), biogeochemical cycling (e.g., Zhu et al, 2022 ), biodiversity and functional roles of microbial communities ( Engel, 2010 ; Kosznik-Kwaśnicka et al, 2022 ).…”

Unravelling the hidden diversity of cave mycobiota in Thailand’s Satun Geopark

“…Fungi in caves have adapted to low nutrient availability, darkness, coolness, and humidity, making them unique environments for studying extreme-adapted fungi 5 , 6 . Karst cave fungi are essential in biogeochemical cycling, speleothem formation, and the development of caves 7 , 8 .…”

Seasonal variations of microbial community structure, assembly processes, and influencing factors in karst river

“…As the most active component of the aquatic ecosystem, microorganisms acquire nutrients and energy to survive in an oligotrophic environment via numerous metabolic pathways, which are crucial to the elemental cycling of the karst ecosystem ( Webster et al, 2018 ; Xue et al, 2020 ; Zhu et al, 2022 ). According to several studies, Proteobacterium, Bacteroides, and Firmicutes were the most common phyla in karst aquifers ( Li et al, 2017 ; Danczak et al, 2018 ; Tang et al, 2019 ; Li Q. et al, 2020 ), and there were shifts in both geographical and seasonal composition of microbial communities ( Opalički Slabe et al, 2021 ).…”