121-1 Chemolithoautotrophic Pseudonocardiaceae from Cave-wall Biofilms

Session: Caves and Karst Through Space and Time: Biogeochemistry, Climate, and Astrobiology

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Colorful (i.e., yellow, blue, pink, or white) colonies and biofilms are commonly observed growing under nutrient-limited and relatively dry conditions on subaerial surfaces in caves. For decades, cave-wall biofilms from geographically separated caves formed in different bedrock lithologies (e.g., basalt, limestone, quartzite, iron ore) have been studied, with the shared result being that biofilms are predominately comprised of microbes from the Actinomycetota phylum and, more specifically, routinely related to genera within the Pseudonocardiaceae family. The metabolism of these taxa is generally unknown, but the prevailing dogma has been that they are heterotrophic or chemoorganotrophic. However, in recent years, there is growing evidence that some Pseudonocardiaceae from desert and cold environments appear capable of ammonium and nitrate use, H₂ and CO oxidation, CO₂ fixation, and methanotrophy. To assess the metabolic capabilities of cave-dwelling Pseudonocardiaceae, several studies were conducted that included geochemical measurements, stable isotope ratio analyses, isotope mixing models, 16S rRNA gene profiles, and metagenome sequencing and evaluation from cave-wall biofilms in limestone caves of eastern Tennessee. Pseudonocardiaceae-dominated biofilms had δ¹³C values that were more negative than would be predicted if biomass resulted solely from heterotrophic assimilation of surface-derived organic carbon (e.g., from soil). Instead, biofilm biomass was likely produced from CO₂-derived carbon, with the potential for biomass to also result from CH₄-derived carbon. Annotations from near-complete, high-quality metagenome-assembled genomes (MAGs) taxonomically assigned to the Pseudonocardiaceae, albeit to uncultured representatives, revealed putative autotrophic carbon and energy acquisition pathways consistent with trace gas (i.e., H₂, CO) uptake, as well as pathways for DNA repair mechanisms, biofilm formation, antimicrobial defense, and antimicrobial toxin production. MAGs also showed the potential for carbonic anhydrase production, which has been associated with microbially-induced carbonate precipitation. Collectively, these results provide strong evidence that Pseudonocardiaceae are critical for subsurface ecosystems by forming biofilms and potentially serving as primary producers using trace gases. By participating in, if not mediating, carbonate precipitation, these taxa may also be responsible for biosignature development and preservation. Considering the ubiquity of Pseudonocardiaceae in caves globally, these findings emphasize the potential that chemolithoautotrophically-derived carbon is more prevalent in subsurface ecosystems than previously recognized.

Geological Society of America Abstracts with Programs. Vol. 57, No. 6, 2025

doi: 10.1130/abs/2025AM-9902

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