Significance Termites are textbook examples of the “extended phenotype” given their ability to construct complex mounds and regulate environments. Here, we show that termites also control microbial composition and biogeochemical cycling in their mounds through their emissions of hydrogen. These emissions drive remarkable enrichments of mound bacteria that use hydrogen to drive aerobic respiration and sometimes carbon fixation (i.e., lithoautotrophs). Such mound communities efficiently consume all termite-produced hydrogen and even mediate atmospheric uptake, while termite-produced methane escapes to the atmosphere. This provides further evidence that hydrogen is a major substrate for aerobic bacteria and that the terrestrial hydrogen sink is highly responsive to elevated emissions.