ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Microbiological Chemistry and Geomicrobiology
This article is part of the Research TopicMicrobes in Caves: Biomes, Activities, and Potential ApplicationsView all articles
Metabolic traits of sediment bacteria in karst caves in the light of environmental changes
Provisionally accepted
- 1Research Centre of the Slovenian Academy of Sciences and Arts, Ljubljana, Slovenia
- 2Sarajevska skola nauke i tehnologije Sarajevo Medicinska skola, Sarajevo, Bosnia and Herzegovina
- 3Univerza v Novi Gorici Laboratorij za raziskave materialov, Nova Gorica, Slovenia
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Karst subterranean systems are vulnerable ecosystems that have not yet been studied adequately at the microbial functional level. Cave sediments deposited over different time periods host diverse microbial communities that play a critical role in nutrient cycling and pollutant degradation. In this study, we investigated microbial diversity and metabolic capacity in recently deposited alluvial sediments and an ancient palaeo-river deposit in a karst cave system. Using 16S rRNA gene amplicon metagenomic analysis, community-level physiological profiling (CLPP), and chemical characteristics of the environment, the influence of key environmental factors on microbial community composition and substrate degradation, concentrating particularly upon sediment age, oxygen availability, and temperature, was assessed. The results showed different microbiome compositions and metabolic characteristics between sites. The old alluvial sediment exhibited low taxonomic and functional diversity, accompanied by elevated heavy-metal concentrations, suggesting that sediment age might act as a geochemical filter, limiting microbial function. In contrast, a periodically flooded site showed high metabolic versatility and taxonomic diversity, emphasising the ecological role of hydrological pulses in maintaining functional microbial diversity. CLPP metrics linked community structure to functional potential, revealing adaptive traits in key taxa such as Polaromonas, Methylibium, and Beggiatoa. These results demonstrated the value of integrating functional and taxonomic approaches in subsurface environments and provide insights into microbial resilience, biogeochemical processes, and the potential for applied environmental use.
Keywords: 16S rRNA gene amplicon sequencing, cave sediment microbiome, Community-level physiological profiling, diversity, ecosystem resilience
Received: 15 Oct 2025; Accepted: 27 Nov 2025.
Copyright: © 2025 Mulec, Pasic and Oarga-Mulec. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Janez Mulec
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