Motivation
Extreme environments such as hot springs hold great promise for discovering deeply branching prokaryotic taxa of industrial and scientific interest, for multiple reasons. First, these environments exert strong selective pressures on resident microorganisms. For example, the industrially important heat-stable Taq polymerase was first isolated from a hot spring bacterium. Second, hot springs likely resemble some of the earliest life-harboring environments on Earth. Third, prokaryotes found in hot springs are known to exhibit much stronger geographic endemism than those in many other environments such as soil or the ocean. In fact, speciation is thought to occur even within individual hot springs, which resemble "isolated islands" of microbial biogeography. In the Great Basin area in Western US, a largely desert-like region, intense faulting and volcanic activity have resulted in hundreds of hot springs, making it one the regions with the highest density of geothermal activity worldwide. Yet, very few studies exist on the microbial diversity in this region, and existing studies are largely restricted to morphological descriptions and 16S rRNA amplicon sequences.

Methodology
In this study we surveyed the microbiomes of dozens of hot springs, using genome-resolved metagenomics. Our goal was to shed light on the functional structure of these microbiomes, i.e., in terms of the abundances of various metabolic pathways, as well as to reconstruct and examine the genomes of the dominant resident microbial populations. To this end, we analyzed 500 microbial mat and sediment samples collected during the years 2020-2024. Shotgun Illumina metagenomic sequencing yielded over 11 billion raw short DNA sequences. Coassembly by hot spring yielded over 17 million contigs of length ≥500 bp, and over 250,000 contigs of length ≥10000 bp. Binning of contigs into metagenome-assembled genomes (MAGs) yielded 780 high-quality bacterial and archaeal MAGs (completeness ≥80%, contamination ≤5%).