FUNCTIONAL POTENTIAL AND DIVERSITY OF THE BACTERIAL FAMILY PSEUDONOCARDIACEAE FROM CAVES

Dark, humid, and nutrient-depleted conditions inside caves set limitations on their habitability, which results in microbial diversity and community structures that differ from surface environments. Recent studies that investigated cave microbiomes reveal that Pseudonocardiaceae, a family of bacteria belonging to the phylum Actinomycetota, are abundant in cave sediment and on rocks as subaerial biofilms. This study applied metagenomics to characterize the functional potential of uncultured Pseudonocardiaceae and associated microbes from a cave in Knox County, Tennessee, which complemented past research that assessed microbial diversity using 16S rRNA gene surveys. From metagenomic data, several Metagenome Assembled Genomes (MAGs) were recovered and assigned to Pseudonocardiaceae. The closest relatives to these MAGs belong to the genus, Actinoalloteichus. The Pseudonocardiaceae MAG with the highest quality was 98.22% complete and had 3.83% contamination. Functions of interest to evaluate from the MAGs included carbon and nitrogen metabolism, antimicrobial strategies, and metabolisms that could affect microbe-mineral interactions. Analyses revealed the potential for chemolithoautotrophic CO₂ fixation, denitrification, trace gas uptake, specifically carbon monoxide, antimicrobial defenses, and capability to affect carbonate precipitation. The Pseudonocardiaceae likely play a crucial role in the cave environments by producing organic carbon at the base of the food web, acting as a sink for trace gas in cave air, limiting microbial interactions within subaerial biofilms, and participating in microbe-mineral interactions that could lead to speleothem formation. This investigation reinforces the connection between microbial ecology and the biogeochemistry of cave environments and raises interests for possible applications in biotechnology from the cave microbiome.