Microbial communities of selected regions of the Deep Springs Lake aquifer system.

Deep Springs Lake is a small, isolated, highly alkaline soda lake in Inyo County of Eastern California, USA. It is a seasonally filled salt lake or playa, and is part of a closed aquifer system. Such closed systems are globally rare, occurring only in arid zones where annual evaporation is greater than annual rainfall. Deep Springs Lake's hydrology and geology have been well studied, and it is home to a unique toad species, but its microbiome remains unexplored. Here we perform 16S, 18S, and ITS amplicon sequencing of the lake water, dried salt crust at the edges the lake, and nearby feeder springs to investigate the community composition of prokaryotes, eukaryotes, and fungi. Bacterial communities in the lake water consist predominantly of Pseudomonadota and Bacteroidota. Nearby springs and salt crust contain different genera of Pseudomonadota than the lake water but similar Bacteroidota, along with an abundant population of Chlorobiota. Noticeably rare in the lake itself but abundant in the biofilms and crust are populations of photosynthetic Cyanobacteria. Archaea are found only in the lake water, largely Halobacterota. Fungi are mostly Ascomycota, with some Chytridiomycota and Rozellomycota; chytrid fungi show no evidence of pathogens related to amphibian die-offs. Eukaryotes in the lake water consist mostly of flagellates, notably the photosynthetic