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Ghost-rock karst systems in particular represent unexplored microbial niches. Here, we provide the first genome-resolved metagenomic comparison of ghost-rock and groundwater microbial communities from the Sterkfontein karst system (South Africa). Ghost-rock and groundwater communities host distinct taxonomic and metabolic assemblages. Groundwater communities are dominated by chemolithotrophs capable of oxidizing sulfur- and nitrogen-bearing compounds, and by heterotrophs degrading refractory, plant-derived organic matter. In contrast, primary producers in ghost-rocks likely rely on atmospheric chemosynthesis via trace gas oxidation, while glycogen metabolism and necromass recycling point to adaptations to oligotrophic and fluctuating hydrological conditions. Groundwater taxa with metal-interacting pathways may initiate bedrock colonization via metal oxidation, whereas ghost-rock communities include potential metal reducers that could drive iron and manganese oxide dissolution and influence trace element mobility. Together, these results underscore ghost-rocks as active microbial and geochemical hot spots within karst systems that may play a non-negligible role on biomineralization\/bioweathering processes and on shaping (sub)terrestrial landscapes and global biogeochemical cycles.<\/jats:p>","DOI":"10.1093\/femsec\/fiag047","type":"journal-article","created":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T11:34:22Z","timestamp":1781004862000},"source":"Crossref","is-referenced-by-count":0,"title":["Ghost-rocks\u2019 microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater"],"prefix":"10.1093","volume":"102","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3180-4653","authenticated-orcid":false,"given":"Guillaume","family":"Peugnet","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9, Institut de physique du globe de Paris, CNRS , 75005 Paris 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