Genomic diversity, lifestyles and evolutionary origins of DPANN archaea

Abstract

Archaea—a primary domain of life besides Bacteria—have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.

Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area

“…the Methanonatronoarchaeia (20,21) or Candidate Divison MSBL1, thought to encompass methanogens (22) and/or sugar-fermentors (23), but also other archaeal groups not specifically associated with salty systems. These included Thermoplasmata and Archaeoglobi within 45 Euryarchaeota, Woesearchaeota and other lineages (Aenigmarchaeota, Altiarchaeales) usually grouped as DPANN (24)(25)(26) and Thaumarchaeota and Crenarchaeota (Sulfolobales) within the TACK/Proteoarchaeota (27) ( Fig. 3a; Supplementary Data S2).…”

“…3c, red dots) failed to amplify Nanohaloarchaeota and other divergent DPANN lineages. These likely encompass ectosymbionts/parasites (24)(25)(26)28). Given their relative abundance and co-occurrence in these and other ecosystems, it is tempting to hypothesize that Nanohaloarchaeota are (ecto)symbionts of Halobacteria; likewise, Woesearchaeota might potentially be associated with Thermoplasma-like archaea.…”

Differential polysaccharide utilization is the basis for a nanohaloarchaeon : haloarchaeon symbiosis

“…Halophilic fermentative bacteria are known to play a role in chitin mineralization in hypersaline habitats worldwide 5-7 , and more recently it was shown that haloarchaea also take part in the primary degradation of polymeric organic matter in many of the same habitats 8-11 . Here we reveal the role of haloarchaea as chitinotrophic hosts for nanohaloarchaea, the extremely halophilic members of the DPANN superphylum 12-15 .…”

Undinarchaeota illuminate the evolution of DPANN archaea

“…The DPANN radiation 12 , named after the first members of this group (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) 11 , comprises one of these recently proposed archaeal clades and is now thought to be comprised of at least ten and (according to NCBI taxonomy) putative phylum-level lineages 13,14 . Most members of the DPANN archaea are characterized by small cell sizes and reduced genomes, which code for a limited set of metabolic proteins 13 .…”

“…In particular, analyses focusing on the placement of selected DPANN lineages in isolation, such as Nanoarchaeota and Parvarchaeota, relative to other Archaea, have led to the conclusion that these represent fast-evolving Euryarchaeota 28,29 . Furthermore, it is debated whether the free-living Altiarchaeota belong to the DPANN radiation, form an independent lineage or belong to Euryarchaeota 8,9,14,30,31 . A potential cause for these conflicting topologies is that DPANN are often found on long branches in phylogenetic trees; these long branches might result from compositional biases or fast evolutionary rates 32,33 (as seen for obligate bacterial endosymbionts 34,35 ) or might reflect genomic under sampling of the true diversity of this group 9 .…”