The absence of photosynthetic activity, stable temperature, high relative humidity, low rates of evaporation and limited supply of organic material create an environment that determines the distribution and population density of cave biota including microorganisms. Microbes are an important source of organic matter in subterranean environments, with a significant role in geomorphological processes and speleogenesis. Moreover, chemolithoautotrophic primary production provides the usage of sulfur-, ammonium- or nitrite-based chemolithotrophy and autochthonous organic carbon. These ecosystems are often characterized by the unique biodiversity of microbial communities, which possess specialized metabolisms that remain largely unexplored for their potential for biotechnological applications.
Marine caves are known as biodiversity reservoirs and refuge habitats, often inhabited by rare species, even living fossils, whose microbiome is almost unknown. Similarly, microbial biodiversity and microbiomes in freshwater and anchialine caves have not been well studied/characterized. Cave environments are prime sites for interdisciplinary studies, combining microbial biology and biogeochemistry to characterize the role of microbes and to explore potentially beneficial bioprocesses. Cave ecosystems are sensitive to environmental impacts including anthropogenic pollution and thus conservation is an important issue. We believe that studies of the biodiversity, biochemistry and molecular biology, and biotechnological potential of microbes in caves help balance their biological stability and reveal beneficial active molecules and new discoveries and visions of bioprocesses.

Microbial metabolism and interactions in caves pose challenges at many levels of sampling and research. These habitats possess biodiversity with proven and uncharted potential for biotechnology, potentially yielding new biologically active molecules. Studies of these microbial communities may reveal novel aspects of the phylogeny and evolution, connecting them with technology and applications. A deep understanding of the structure and function of these habitats, based on the complex intra- and interspecies interactions, could provide plenty of new opportunities and challenges in biotechnology. Additionally, it could uncover novel aspects of the phylogeny and evolution of microbial communities, especially modifications in their biosynthetic gene clusters (BGCs).
This Research Topic welcomes manuscripts on all aspects of microbial processes and their promising biotechnological potential in natural and man-made dark ecosystems.

We encourage manuscript submissions on all subjects of cave microbiology. The following are some examples of areas relevant to the scope of this collection:
• microbial diversity and interactions: communities, biofilms, invertebrate symbionts;
• metabolic engineering, central and secondary metabolites;
• discovery of novel bioactive compounds through culturable and nonculturable approaches (e.g.,
metagenomics, metabolomics and genome mining);
• biodegradation of xenobiotic compounds;
• biomineralization and solid phase transformations;
• microbial consumption and production of gases;
• elemental cycling and stratifications;
• modeling and AI of the microbial cave ecosystems.

This Research Topic brings together fundamental and applied research on microbes, their biology and bioprocesses in caves and is open for papers on caves in terrestrial and aquatic (freshwater, anchialine, marine) environments. Review manuscripts of all aspects of these topics are also welcome.
We seek manuscripts that are hypothesis-driven and report experimental studies on cave microbes. Manuscripts on in silico screening on 16S rDNA metagenomics or shotgun data mining must include experimental work or cross-disciplinary discoveries that will help to better understand and probe the biological potential of these unique environments.

Are you interested in contributing a manuscript to this Research Topic?

Microbes in Caves: Biomes, Activities, and Potential Applications