Microbial Diversity and Ecological Dynamics in Cave Ecosystems

Cave ecosystems represent oligotrophic environments shaped by perpetual darkness, stable temperature and high humidity. Within these subterranean habitats, microorganisms underpin primary production, mediate mineral transformations and sustain food webs in the absence of sunlight. Diversity spans Bacteria, Archaea and Fungi, with dominant bacterial phyla including Proteobacteria, Actinobacteria, Chloroflexi and Nitrospirae. Spatial heterogeneity arises across zones of entrance, twilight and dark, as well as in sediments, water films and mineral deposits. Biogeochemical cycles of carbon, nitrogen, sulphur and iron are driven by specialised taxa exhibiting chemoautotrophy, methylotrophy, iron oxidation and sulphide oxidation. Keystone species form modular networks, structuring community assembly and facilitating resilience to environmental perturbation. Recent advances in high-throughput sequencing and metagenomic assembly have revealed previously unrecognised lineages and novel metabolic pathways, highlighting caves as reservoirs of microbial novelty and biotechnological potential. Understanding these ecological dynamics informs conservation of subterranean heritage sites, guides bioprospecting for novel metabolites and offers analogues for life in extreme planetary environments.

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Microbial Diversity and Ecological Dynamics in Cave Ecosystems publication trend

The graph below shows the total number of articles in microbial diversity and ecological dynamics in cave ecosystems across all publications each year (not limited to Nature Index journals).

Technical terms

Metagenomics: High-throughput sequencing of genetic material directly extracted from environmental samples to characterise community composition and functional potential.

Metabarcoding: Targeted sequencing of phylogenetic marker genes (e.g. 16S rRNA) to assess taxonomic diversity and relative abundance of microbial communities.

Oligotrophic environment: A habitat with low concentrations of nutrients, often resulting in specialised microbial adaptations for survival.

Speleothem: Secondary mineral deposit formed within caves, including stalactites, stalagmites and moonmilk, often influenced by microbial activity.

Chemoautotrophy: Metabolic process by which organisms derive energy from inorganic chemical reactions and fix carbon dioxide to build biomass.

Metagenome-assembled genome (MAG): A draft genome reconstructed from metagenomic sequencing data, representing an organism’s genetic blueprint without the need for cultivation.

Biosynthetic gene cluster (BGC): A contiguous set of genes that collectively encode enzymes responsible for the biosynthesis of specialised metabolites, such as antibiotics or pigments.

References

1. Dark-zone alterations expand throughout Paleolithic Lascaux Cave despite spatial heterogeneity of the cave microbiome. Environmental Microbiome (2023).
2. A first insight into the Polish Bochnia Salt Mine metagenome. Environmental Science and Pollution Research (2023).
3. The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification. Frontiers in Microbiology (2016).
4. Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle. BMC Microbiology (2017).
5. Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System. Frontiers in Microbiology (2019).