Microbial dark matter and their metabolic potential in terrestrial hot springs

Terrestrial hot springs have persisted throughout Earth’s history, offering valuable insights into the origin and evolution of life. However, these ecosystems are facing significant biodiversity loss due to global climate change and anthropogenic activities. This underscores the urgency and necessity of documenting the microbiomes, exploring biosynthetic potentials, and dissecting the ecological interactions within them. By analyzing 1,100 hot spring metagenomes worldwide, we constructed the Genomes from Hot Spring’s Microbiomes (GHM) catalog. This catalog comprises 18,386 microbial metagenome-assembled genomes and reveals a vast and unprecedented novel bacterial and archaeal lineage. Additionally, we predicted over 20 million non-redundant protein-coding genes, which not only showcase the functional landscape of hot spring microbiomes but also highlight their ecological significance and adaptation mechanisms to extreme environments. We identified a substantial diversity of novel viral lineages and provided insights into virus-host interactions, particularly through auxiliary metabolic genes that reprogram host metabolic networks and modulate key cellular processes in geothermal ecosystems. The GHM catalog serves as a vital resource for capturing microbial dark matter and understanding the ecology and evolution in terrestrial hot springs.