Genomic evidence for aerotrophy as a defining trait of Ktedonobacteria inhabiting silica-rich oligotrophic caves

Abstract

Members of the class Ktedonobacteria (phylum Chloroflexota) are widespread across various terrestrial environments, including oligotrophic caves, although the genomic basis underlying this distribution remains unclear. Here, we present a systematic genomic analysis of Ktedonobacteria across ecosystems, with a focus on oligotrophic caves. Cave Ktedonobacteria belong to novel genera within the Ktedonobacteraceae and harbour genes associated with a mixotrophic metabolism combining the use of organic and inorganic substrates as energy and carbon sources. Comparative analyses of all available Ktedonobacteria genomes from diverse environments showed that most metabolic traits, including those associated with atmospheric gas oxidation, are primarily conserved among members of the same family. In contrast, genes involved in CO₂ fixation are enriched in Ktedonobacteria inhabiting caves. Phylogenetic analysis indicated that the RuBisCO of Ktedonobacteria likely represents a novel Form I subtype (named group IG) encompassing thermophilic and acidophilic bacteria from six different phyla that often inhabit similar extreme environments. The presence of this subtype across distinct lineages in comparable habitats suggests that it may confer a selective advantage in nutrient-poor settings (like caves) and that its distribution may be influenced by horizontal gene transfer. This inferred autotrophic capacity is associated with a transaldolase variant of the Calvin–Benson–Bassham cycle that was previously described only in one Firmicutes species. Overall, this study provides genetic evidence for the potential coupling of atmospheric gas oxidation with dark CO₂ fixation in Ktedonobacteria, highlighting their possible role in sustaining primary production in oligotrophic ecosystems, including caves.