A novel order-level lineage of ammonia-oxidizingThaumarchaeotais widespread in marine and terrestrial environments

AbstractAmmonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant groups of Archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those of marine and soil AOA. We here report a novel AOA orderCandidatusNitrosomirales that forms a deeply branching basal sister lineage to the thermophilicCa.Nitrosocaldales. Metagenomic and 16S rRNA gene read mapping demonstrates the dominant presence ofNitrosomiralesAOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Notably, terrestrialNitrosomiralesAOA show the genetic capacity of using formate as an alternative source of reductant and appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including the genes encoding urease, nitrite reductase, and V-type ATPase. Potential metabolic versatility and acquired functions may facilitate their radiation into a variety of subsurface, marine, and soil environments. Molecular thermometer-based evolutionary analysis suggests thatNitrosomiralesoriginated from thermophilic environments and transitioned into temperate habitats in parallel withNitrososphaeralesandNitrosopumilales. We also provide evidence that terrestrial-marine habitat transitions occurred within each one of the four AOA orders, which reveals a more complex evolutionary trajectory of major AOA lineages than previously proposed. Together, these findings establish a robust taxonomic and evolutionary framework of AOA and provide new insights into the ecology and evolution of this globally abundant functional guild.