Despite the extreme conditions in terrestrial Antarctica, surprisingly diverse and abundant microbial communities thrive. Until recently, in arid, Antarctic desert sites that lack phototrophs, an enduring question was what primary production strategy was supporting these communities. Through metagenomics and biochemical analysis, we discovered that a novel form of microbial-mediated chemoautotrophy was filling this gap, which we coined ‘atmospheric chemosynthesis’. In this overlooked process, the oxidation of atmospheric H2 and CO gas by high-affinity enzymes supports bacterial growth through the RuBisCO form IE-driven Calvin-Benson-Bassham cycle. Here, we will describe the broad distribution of the genetic markers of this process - RuBisCO form I and high-affinity hydrogenases- across cold deserts spanning the Antarctic, Arctic, and Tibetan Plateau, with increasing abundances of critical taxa and genetic indicators with lower moisture, carbon and nitrogen availability. Through the analysis of 18 metagenomes, 230 dereplicated metagenome-assembled-genomes and 24,080 publicly available genomes, we uncovered a growing number of phyla genetically capable of this process alongside a high diversity of RuBisCO form I and high-affinity hydrogenases. Finally, we quantified multispecies responses to environmental changes along edaphic gradients in the Windmill Islands region, eastern Antarctica. We predicted high rates of compositional turnover at the soil moisture threshold of 10-12%, with phototrophs likely to be the ‘winners’ in a progressively warmer and wetter climate at the expense of the functionally important but usually rare bacterial phyla implicated in atmospheric chemosynthesis - Ca. Dormibacterota and Eremiobacterota. In a second dataset, after a decade of change, we found, as predicted, increasing relative abundances of photosynthetic taxa with increased soil moisture at the expense of Ca. Dormibacterota and Eremiobacterota. We believe that future shifts in environmental conditions to a wetter, milder climate scenario could lead to the loss of these rare bacterial phyla that are well suited to dry environments, with long-term monitoring of these Windmill Islands sites now critical to future conservation planning in the region.