High occurrence of <i>Pacearchaeota</i> and <i>Woesearchaeota</i> (<scp>A</scp>rchaea superphylum <scp>DPANN</scp>) in the surface waters of oligotrophic high‐altitude lakes

<jats:title>Summary</jats:title><jats:p>We carried out a regional survey on the archaea composition from surface waters of > 300 high‐altitude <jats:styled-content style="fixed-case">P</jats:styled-content>yrenean lakes (average altitude 2300 m, <jats:styled-content style="fixed-case">pH</jats:styled-content> range 4.4–10.1) by 16<jats:styled-content style="fixed-case">S</jats:styled-content> r<jats:styled-content style="fixed-case">RNA</jats:styled-content> gene tag sequencing. Relative <jats:styled-content style="fixed-case">A</jats:styled-content>rchaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (<jats:styled-content style="fixed-case">PCR</jats:styled-content>) mixture, and we detected 769 operational taxonomic units (<jats:styled-content style="fixed-case">OTUs</jats:styled-content>; grouped at 97% identity) that split into 13 different lineages, with altitude and <jats:styled-content style="fixed-case">pH</jats:styled-content> having a significant effect on the community composition. Woesearchaeota and <jats:styled-content style="fixed-case">P</jats:styled-content>acearchaeota (formerly <jats:styled-content style="fixed-case">E</jats:styled-content>uryarchaeota <jats:styled-content style="fixed-case">DHVEG</jats:styled-content>‐6 cluster) dominated the data set (83% of total <jats:styled-content style="fixed-case">OTUS</jats:styled-content>), showed a high occurrence (presence in <jats:italic>c.</jats:italic> 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota–Diapherotrites (formerly <jats:styled-content style="fixed-case">E</jats:styled-content>uryarchaeota <jats:styled-content style="fixed-case">MEG</jats:styled-content> cluster), Methanomicrobia, Thermoplasmata and ammonia‐oxidizing thaumarchaeota (<jats:styled-content style="fixed-case">AOA</jats:styled-content>) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were <jats:styled-content style="fixed-case">SM1K</jats:styled-content>20, Aenigmarchaeota (formerly <jats:styled-content style="fixed-case">E</jats:styled-content>uryarchaeota <jats:styled-content style="fixed-case">DSEG</jats:styled-content> cluster), <jats:styled-content style="fixed-case">M</jats:styled-content>ethanobacteria, Bathyarchaeota and <jats:styled-content style="fixed-case">SCG</jats:styled-content>. Environmental preferences substantially differed among lineages, with <jats:styled-content style="fixed-case">A</jats:styled-content>enigmarchaeota and <jats:styled-content style="fixed-case">M</jats:styled-content>ethanomicrobia having the largest habitat breadth, and Thermoplasmata, <jats:styled-content style="fixed-case">AOA</jats:styled-content> and <jats:styled-content style="fixed-case">M</jats:styled-content>icrarchaeota having the smallest. Pacearchaeota and <jats:styled-content style="fixed-case">W</jats:styled-content>oesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.</jats:p>