Abstract
Hydrogenogenic carbon monoxide (CO)-oxidizing bacteria (hereafter referred to as CO-oxidizing bacteria) conserve energy using an anaerobic CO dehydrogenase containing Ni (Ni-CODH) and hydrogen-producing hydrogenase (ECH). In this study, we promoted the exploration and isolation of undescribed microbial species by using the established enrichment culture method in which the gas phase is replaced by CO to expand the culture strain collection as a genetic resource. Parageobacillus sp. strain G301 was successfully isolated from the sediment of Unagi-ike Lake in Kagoshima Prefecture, Japan, and closely related to Parageobacillus toebii, which lacks CODH/ECH. Furthermore, the genome of strain G301 encoded a gene cluster for aerobic CODH containing Mo (Mo-CODH). Culture experiments demonstrated that the strain enabled both hydrogenic anaerobic and aerobic CO oxidation, which had not been previously reported. We also obtained a CO oxidizing bacterial isolate of Thermolongibacillus altinsuensis which has not been reported to be capable of CO oxidation, from a sediment sample from the bottom of Lake Biwa. A comprehensive search in public metagenomes showed that Ni-CODH was distributed in a wide range of prokaryotes spanning 55 bacterial and 11 archaeal phyla. Although Ni-CODH is a universal enzyme that exists in a wide variety of microbiome, including aquatic environments such as oceans, artificial environments, and mammalian microflora including humans, Ni-CODH responsible for hydrogenogenic CO oxidation was rarely found in the metagenomic data, suggesting the importance of the isolation and cultivation. We also found an acetyl CoA production pathway, in which Ni-CODH is a key enzyme, in heterotrophic, human gut-derived enterobacteria, and expanded the genomic database of potential aerobic marine CO-oxidizing bacteria in the ocean. These results in this study could expand our knowledge on Ni-CODH and CO oxidizers and are expected to provide a basis not only for utilization as a genetic resource, but also for elucidating unpreceded metabolisms of CO-oxidizing bacteria and their ecological functions on the surrounding environment.
