Abstract
Omics technologies are revolutionizing researchers’ understanding of life’s composition, function and evolution across ecosystems. Omics have been used in terrestrial and aquatic environments for decades but their application to subterranean ecosystems, such as caves and groundwaters, is more emergent. Since their initial applications in the 2010s, subterranean omics research has uncovered remarkable insights into both fauna and microbial communities with ecological and evolutionary implications. This Review highlights the growing capacity of omics to detect cryptic diversity, reconstruct evolutionary histories, and identify the genetic and functional basis of subterranean adaptation. Omics applications facilitate the assessment of subterranean biodiversity and ecosystem functions as well as informing what evolutionary trajectories shape life underground. Insights from subterranean omics offer potential to elucidate the molecular basis of subterranean phenotypes and can help to improve conservation strategies for highly vulnerable and understudied subterranean metazoans and microbiota. Finally, we explore the future of subterranean omics applications. The emerging potential of integrating omics with other disciplines is becoming clear, not only to illuminate life in subterranean ecosystems but also to advance understanding of broader global processes, such as water and carbon cycles, at a time of accelerated environmental change.
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Acknowledgements
H.B. has been supported by the Croatian Science Foundation under project number IP-2024-05-2868. I.B. was funded by the programme LOEWE–Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz of Hesse’s Ministry of Higher Education, Research, and the Arts, through the Centre for Translational Biodiversity Genomics (LOEWE-TBG). S.J.B.C. was funded by Australian Research Council grants (DP230100731, LP190100555 and DP180103851). S.M. was funded by the P.R.I.N. 2022 projects ‘DEEPCHANGE’ (2022MJSYF8) and NBFC, funded by the Italian Ministry of University and Research, P.N.R.R., Missione 4 Componente 2, ‘Dalla ricerca all’impresa’, Investimento 1.4, Project CN00000033. The authors acknowledge additional support provided by Biodiversa+, the European Biodiversity Partnership under the 2021–2022 BiodivProtect joint call for research proposals, co-funded by the European Commission (GA No. 101052342), and the funding organizations Ministry of Universities and Research (Italy), Agencia Estatal de Investigación – Fundación Biodiversidad (Spain), Fundo Regional para a Ciência e Tecnologia (Azores, Portugal), Suomen Akatemia – Ministry of the Environment (Finland), Belgian Science Policy Office (Belgium), Agence Nationale de la Recherche (France), Deutsche Forschungsgemeinschaft e.V. (Germany), Schweizerischer Nationalfonds (Grant No. 31BD30_209583, Switzerland), Fonds zur Förderung der Wissenschaftlichen Forschung (Austria), Ministry of Higher Education, Science and Innovation (Slovenia), and the Executive Agency for Higher Education, Research, Development and Innovation Funding (Romania). M. Couton was supported by the ALIQUOT project (ANR 22-PEXO-0011, France Relance 2023, OneWater programme). H.R. was funded by the European Commission H2020 MSCA Fellowship 897695 and by the Slovenian Research and Innovation Agency (ARIS) Core Funding P1-0184. M.T. is supported by the Western Australian Biodiversity Science Institute (WABSI). M.S. acknowledges support from the School of Molecular and Life Science at Curtin University and the BHP-Curtin alliance within the framework of the ‘eDNA for Global Environment Studies (eDGES)’ programme.
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P.B.-G. and M.S. conceived the review article. M.T. and M.S. prepared the introduction. P.B.-G., M.T. and M.S. prepared Fig. 1 and Fig. 2. M.B., M. Cappelletti, M. Couton, J.-F.F., M.T.G., C.K., S.M.S. and M.S. prepared the ‘Omics for subterranean biodiversity’ section. P.B.-G., I.B., S.J.B.C. and S.R. prepared the ‘Evolutionary genomics of subterranean fauna’ section. P.B.-G. prepared Fig. 3 and Supplementary Table 1. P.B.-G., H.B. and H.R. prepared the ‘Omics of subterranean fauna phenotypes’ section. S.M. prepared the ‘Omics for subterranean conservation’ section. P.B.-G., M. Campbell, T.L. and M.S. prepared the discussion section. P.B.-G. drafted the manuscript. All authors contributed to the final version of the manuscript.
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Glossary
- Amplicon sequencing
Sequencing of PCR-amplified DNA regions to study specific genes or taxonomic markers in environmental or clinical samples.
- ATAC-seq
Assay for transposase-accessible chromatin using sequencing, mapping open chromatin regions genome-wide.
- ChIP–seq
Chromatin immunoprecipitation followed by sequencing, used to identify protein–DNA interactions.
- Cis-regulatory element
Non-coding DNA sequences controlling gene transcription, including promoters and enhancers.
- ddRAD
Double-digest restriction-site-associated DNA sequencing, a method for genotyping thousands of loci across individuals.
- DNA methylation
Addition of methyl groups to DNA, often regulating gene expression and chromatin structure.
- Epigenetic regulation
Modifications affecting gene expression without changing DNA sequence, for example, methylation and histone modifications.
- Exon capture
Targeted sequencing of coding regions (exons) to study the variation, evolution and function of protein-coding genes.
- Genetic assimilation
Process by which environmentally induced traits become genetically fixed through selection over generations.
- Genetic drift
Random changes in allele frequencies in populations, particularly influential in small or isolated populations.
- Long-read sequencing
Sequencing technologies, such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), producing reads thousands of bases long, facilitating genome assembly and structural variation detection.
- Nonsynonymous-to-synonymous substitution
Ratio comparing mutations that alter amino acids (nonsynonymous) versus silent mutations (synonymous), indicating selection strength, often named as dN/dS ratio.
- Phylogenomic
Analysis combining phylogenetics and genomics to infer evolutionary relationships using genome-scale data.
- Premature termination codons
(PTCs). Mutations introducing stop codons in coding sequences, often leading to truncated, nonfunctional proteins.
- Pseudogenes
Nonfunctional gene copies arising from mutation or duplication events.
- Relaxed purifying selection
Reduction in selective pressure maintaining gene function, allowing accumulation of mildly deleterious mutations.
- Single-cell RNA sequencing
Transcriptomic profiling of individual cells to resolve heterogeneity in gene expression.
- Troglomorphic
Traits evolved in subterranean-adapted organisms, often including reduced eyes, pigmentation or enhanced sensory structures.
- Tyrosine catabolism
Metabolic pathway breaking down tyrosine — an amino acid involved in neurotransmitter, melanin and hormone production — into energy or other metabolic intermediates.
- Ultraconserved elements
(UCEs). Highly conserved DNA sequences across distant species, often used as phylogenetic markers.
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Balart-García, P., Bilandžija, H., Bista, I. et al. Advances, challenges and frontiers for omics in subterranean ecosystems.
Nat. Rev. Biodivers. (2026). https://doi.org/10.1038/s44358-026-00151-3
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DOI: https://doi.org/10.1038/s44358-026-00151-3
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