New lineages provide insights into the convergent evolution of extreme salt adaptation within symbiotic Archaea

Environmental genomics has led to the discovery of many new lineages of archaea, including “DPANN” (or Nanobdellati), comprising organisms with small genomes, reduced gene content, and potentially symbiotic or parasitic lifestyles. DPANN live in various environments, and several lineages have been identified that are adapted to extremely high-salt concentrations, including the Nanohaloarchaeota. Since it was long thought that the Haloarchaea (within “Euryarchaeota”) were the only high salt-adapted archaea, the origins of these genome-reduced halophiles have been debated. Here, we used phylogenetic, comparative genomic, and gene tree-species tree reconciliation approaches to resolve the evolution of halophily within DPANN, making use of recently published genomes that help to inform the phylogenetic placement and genome evolution of salt-adapted lineages. Phylogenetic analysis placed Nanohaloarchaeota sister to a previously uncharacterized lineage, which we here refer to as Terrarchaeota. Terrarchaeota appear to be predominantly anaerobic thermophiles that are not adapted to high-salt concentrations, indicating that adaptation to high salt evolved after their divergence from Nanohaloarchaeota. Furthermore, our analyses identified genomic hallmarks of salt adaptation in another recently discovered halophilic DPANN lineage within Aenigmatarchaeota, the Haloaenigmatarchaeaceae. We found that the Nanohaloarchaeota and Haloaenigmatarchaeaceae have distinct sets of proteins that enable life at high salt concentrations but share a common mechanism of evolutionary adaptation, in which niche-relevant genes were acquired horizontally from their halophilic hosts. This work provides the first detailed investigation into the enigmatic Terrarchaeota, and new insights into the convergent evolution of high salt adaptation within symbiotic clades of Archaea.