The majority of bacteria within aerated environments exist within a variety of dormant forms (1). In this state, bacteria adapt to adverse environmental conditions such as organic carbon starvation by reducing metabolic expenditure and potentially using alternative energy sources (2,3). In this study, we investigated the energy sources that could sustain persistence of the environmentally widespread and abundant bacterial phylum Chloroflexi. We provide evidence that three strains from this phylum can persist during organic carbon limitation by scavenging trace concentrations of molecular hydrogen (H2) and carbon monoxide (CO) found within the atmosphere. Phylogenetic analysis shows that the enzymes required for atmospheric H2 and CO oxidation, namely the group 1h [NiFe]-hydrogenase and carbon monoxide dehydrogenase, are widely distributed in aerobic heterotrophic strains of Chloroflexi. Studies focusing on Thermomicrobium roseum as a model organism showed that the operons encoding these enzymes are significantly upregulated during the transition from active growth to persistence. We validated by gas chromatography that this strain oxidises atmospheric H2 and CO during organic carbon starvation. Moreover, we validated that the sporulating strains, Ktedonobacter racemifer and Thermogemmatispora T81, also mediate scavenge of these gases during persistence. This study demonstrates for the first time the ability of Chloroflexi, the sixth most dominant soil phylum (4), persist by using atmospheric energy sources and uncovers new sinks in the biogeochemical cycles of H2 and CO. Our findings also suggest that trace gas oxidation is present in more bacterial phyla than previously thought.