Desert Spring Microbiomes from the Great Basin

Desert springs are aquatic oases that provide critical habitat for aquatic and riparian species in otherwise arid landscapes. However, our knowledge of microorganisms in these ecosystems is limited in scope and scale. We surveyed 16S rRNA gene amplicons in 683 samples from 73 springs across the southern hydrographic Great Basin, USA, within the context of extensive hydrogeochemical data, along with metagenomes from 18 springs. We reveal a strong differentiation between microbiomes of (i) local springs, characterized by cold, young, and dilute waters; (ii) regional springs, characterized by warmer, older, and more evolved waters; and (iii) saline springs. Of 115,877 amplicon sequence variants (ASVs) and 3,213 high- and medium-quality metagenome-assembled genomes (MAGs), >93% and >88% were unique to one spring type. By comparison to the Earth Microbiome Project (EMP), local spring microbiomes resembled soil and rhizosphere communities and hosted predominantly aerobic or facultatively anaerobic, saprophytic microbial communities. Regional spring microbiomes were less diverse, more unique, with abundant Cyanobacteriota. Saline springs hosted abundant Desulfurobacterota, Halobacterota, and Nanoarchaeota. Distance-decay relationships suggest desert spring microbiomes are shaped by a combination of dispersal limitation and environmental filtering that work together to drive the development of region-specific microbiomes punctuated by high rates of apparent endemism, with 42% of ASVs and 50% of MAGs unique to each spring. Our study reveals the importance of spring residence time and salinity as dominant controls of desert spring microbiomes, suggesting diversification of these microbiomes via tectonic extension of the Great Basin during the Miocene. More incisive community ecology studies may reveal functional consequences of spring microbiome diversification.