Viruses associated with Nitrososphaerota archaea: diversity, evolution and horizontal gene transfers

Nitrososphaerota, an archaeal phylum mainly containing Thaumarchaea and Aigarchaea, is an ecological widespread archaeal lineage belonging to TACK super-phylum. However, viral diversity and evolution associated with this archaeal lineage, especially for extremophilic Thaumarchaea and Aigarchaea, remain uncharacterized. Here, we reveal the neglected diversity of the Thaumarchaea virome by identifying 152 species-level viral and mobile genetic element (MGE) sequences associated with extremophilic Thaumarchaea, which mainly colonize in hyperthermophilic environments, deep sea, and acidic soils. Importantly, we identified 263 previously unrecognized species-level viral/MGE sequences associated with Aigarchaea, including a novel rod-shaped viral family uniquely characterized by capsid heterodimers, thereby filling a long-standing gap in the viral diversity of the TACK super-phylum. Phylogenetic analysis revealed close evolutionary relationships between Aigarchaea-associated rod-shaped viruses and Methanophagales (ANME-1) rod-shaped viruses, suggesting that they may have evolved from a common rod-shaped viral ancestor. In contrast, Aigarchaea-associated head-tailed viruses formed three distinct monophyletic clades compared to other viruses, representing previously undiscovered evolutionary lineages within virosphere. Gene functional analysis identified 32 viral-encoded genes potentially involved in supplementing host metabolism, including, for the first time, genes that confer selective advantages to their extremophilic archaeal hosts, such as those involved in oxidative stress adaptation and antibiotic synthesis. Approximately 54% of 6,505 horizontal gene transfers (HGTs) occur bidirectionally between Nitrososphaerota and viruses/MGEs, highlight the significant role of viruses/MGEs in facilitating gene exchange within the archaeal communities. Collectively, this work sheds light on the previously unknown Aigarchaea-associated viromes, and unveils the underexplored diversity, evolution, functional repertoires, and HGTs of Nitrososphearota-associated viruses.