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Nanoarchaeota are obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence ofNanoarchaeota in high-temperature (∼90°C), acidic (pH ≈ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposedNanobsidianus stetteri from a more neutral YNP hot spring than to the marineNanoarchaeum equitans . Single-cell and catalyzed reporter deposition-fluorescencein situ hybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNPNanoarchaeota as aSulfolobales species known to inhabit the hot springs. Furthermore, we demonstrate thatNanoarchaeota are widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within oneNanoarchaeota single-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNPNanoarchaeota .

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs