DPANN

DPANN is a superphylum of Archaea first proposed in 2013.[2] Many members show novel signs of horizontal gene transfer from other domains of life.[2] They are known as nanoarchaea or ultra-small archaea due to their smaller size (nanometric) compared to other archaea.

DPANN
Parvarchaeum acidiphilum
Scientific classification
Domain: Archaea
Superphylum: DPANN
Rinke et al. 2013
Phyla[1]

DPANN is an acronym formed by the initials of the first five groups discovered, Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota. Later Woesearchaeota and Pacearchaeota were discovered and proposed within the DPANN superphylum.[3] In 2017, another phylum Altiarchaeota was placed into this superphylum.[4] The monophyly of DPANN is not considered established until now, due to the high mutation rate of the included phyla, which can lead to the artifact of the long branch attraction (LBA) where the lineages are grouped basally or artificially at the base of the phylogenetic tree without being related.[5][6] These analyzes instead suggest that DPANN belongs to Euryarchaeota or is polyphyletic occupying various positions within Euryarchaeota.[5][6][7]

The DPANN groups together different phyla with a variety of environmental distribution and metabolism, ranging from symbiotic and thermophilic forms such as Nanoarchaeota, acidophiles like Parvarchaeota and non-extremophiles like Aenigmarchaeota and Diapherotrites. DPANN was also detected in nitrate-rich groundwater, on the water surface but not below, indicating that these taxa are still quite difficult to locate.[8]

Characteristics

They are characterized by being small in size compared to other archaea (nanometric size) and in keeping with their small genome, they have limited but sufficient catabolic capacities to lead a free life, although many are episymbionts that depend on a symbiotic or parasitic association with other organisms. Many of their characteristics are similar or analogous to those of ultra-small bacteria (CPR group).[3]

Limited metabolic capacities are a product of the small genome and are reflected in the fact that many lack central biosynthetic pathways for nucleotides, aminoacids, and lipids; hence most DPANN archaea, such as ARMAN archaea, which rely on other microbes to meet their biological requirements. But those that have the potential to live freely are fermentative and aerobic heterotrophs.[3]

They are mostly anaerobic and cannot be cultivated. They live in extreme environments such as thermophilic, hyperacidophilic, hyperhalophilic or metal-resistant; or also in the temperate environment of marine and lake sediments. They are rarely found on the ground or in the open ocean.[3]

Classification
  • Diapherotrites. Found by phylogenetic analysis of the genomes recovered from the groundwater filtration of a gold mine abandoned in the USA.[9][10]
  • Parvarchaeota and Micrarchaeota. Discovered in 2006 in acidic mine drainage from a US mine.[11][12][13] They are of very small size and provisionally called ARMAN (Archaeal Richmond Mine acidophilic nanoorganisms).
  • Woesearchaeota and Pacearchaeota. They have been identified both in sediments and in surface waters of aquifers and lakes, abounding especially in saline conditions.[3][14]
  • Aenigmarchaeota. Found in wastewater from mines and in sediments from hot springs.[15]
  • Nanohalarchaeota. Distributed in environments with high salinity.[16]
  • Nanoarchaeota. They were the first discovered (in 2002) in a hydrothermal source next to the coast of Iceland. They live as symbionts of other archaea.[17][18]

Phylogeny
Tom A. Williams et al. 2017,[19] Castelle et al. 2015[3] and Dombrowski et al. 2020.[20] Jordan et al. 2017[7] Cavalier-Smith2020[6] and Feng et al 2021.[21]

DPANN may be the first divergent clade of archaea according to some phylogenetic analyses. Recent phylogenetic analyses have found the following phylogeny between phyla.[3][19][20]

 

Bacteria

 
Archaea
 
DPANN
 
 

Altarchaeota

 
 
 

Diapherotrites

 
 

Micrarchaeota

 
 
 
 
 

Undinarchaeota

 
 
 

Aenigmatarchaeota

 
 
 

Nanohaloarchaeota

 
 
 
 

Nanoarchaeota

 
 

Parvarchaeota

 
 
 
 

Mamarchaeota

 
 
 

Pacearchaeota

 
 

Woesearchaeota

 
 
 
 
 
 
 
 
 
 

Euryarchaeota

 
Proteoarchaeota
 

TACK

 
Asgard
 
 

Lokiarchaeota

 
 
 

Odinarchaeota

 
 

Thorarchaeota

 
 
 
 
 

Heimdallarchaeota

 
(+α─Proteobacteria)

Eukaryota

 
 
 
 
 
 
 

Other phylogenetic analyzes have suggested that DPANN could belong to Euryarchaeota or that it may even be polyphyletic occupying different positions within Euryarchaeota. It is also debated whether the phylum Altiarchaeota should be classified in DPANN or Euryarchaeota.[20][5] An alternative location for DPANN in the phylogenetic tree is as follows.[7][6][21] The groups marked in quotes are lineages assigned to DPANN, but phylogenetically separated from the rest.

 

Bacteria

 
Archaea
Euryarchaeota
 

Thermococci

 
 
 

Hadesarchaea

 
 
 
 

Methanobacteria

 
 
 

Methanopyri

 
 

Methanococci

 
 
 
 
 
 

Thermoplasmata

 
 
 

Archaeoglobi

 
 
 

Methanomicrobia

 
 
 

"Nanohaloarchaeota"

 
 

Haloarchaea

 
 
 
 
 
 
 

"Altarchaeota"

 
DPANN
 
 

Diapherotrites

 
 

Micrarchaeota

 
 
 
 

Undinarchaeota

 
 
 

Aenigmatarchaeota

 
 
 
 

Nanoarchaeota

 
 

Parvarchaeota

 
 
 
 

Mamarchaeota

 
 
 

Pacearchaeota

 
 

Woesearchaeota

 
 
 
 
 
 
 
 
 
 
 
 
Proteoarchaeota
 

TACK

 
Asgard
 
 

Lokiarchaeota

 
 
 

Odinarchaeota

 
 

Thorarchaeota

 
 
 
 
 

Heimdallarchaeota

 
(+α─Proteobacteria)

Eukaryota

 
 
 
 
 

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[22] and National Center for Biotechnology Information (NCBI).[23]

GTDB phylogeny of "DPANN" (fitted to accepted taxonomy)[24][25][26]


DPANN
 
"Altarchaeota"
"Altarchaeia"

"Altarchaeales"

 
 
 
"Iainarchaeota"
"Iainarchaeia"
 

0-14-0-20-30-16

 
 

"Iainarchaeales"

 
 
 
"Micrarchaeota"
"Micrarchaeia"
 

"Norongarragalinales"

 
 
 

"Micrarchaeales"

 
 
 
 

"Burarchaeales"

 
 

"Fermentimicrarchaeales"

 
 
 
 

"Gugararchaeales"

 
 

"Anstonellales"

 
 
 
 
 
 
 
 
 
"Undinarchaeota"
"Undinarchaeia"

"Undinarchaeales"

 
 
 
"Huberarchaeaota"
"Huberarchaeia"

"Huberarchaeales"

 
 
 
 
"Aenigmarchaeota"
"Aenigmarchaeia"

"Aenigmarchaeales"

 
 
"Nanohalarchaeota"
"Nanohalobiia"

"Nanohalobiales"

 
 
 
"Nanoarchaeota"
"Nanoarchaeia"
 

"Nanoarchaeales"

 
 
 
 

"Pacearchaeales"

 
 

"Woesearchaeales"

 
 
 
 

"Tiddalikarchaeales"

 
 

"Parvarchaeales"

 
 
 
 
 
 
 
 
 

Super Phylum "DPANN" Rinke et al. 2013

  • Phylum Altarchaeota Probst et al. 2018 (SM1)
    • Class "Altarchaeia" corrig. Probst et al. 2014
      • Order "Altarchaeales" corrig. Probst et al. 2014
  • Phylum "Iainarchaeota" ["Diapherotrites" Rinke et al. 2013] (DUSEL-3)
    • Class "Iainarchaeia" Rinke et al. 2020
      • "Candidatus Forterrea" Probst & Banfield 2017 {0-14-0-20-30-16: CSSED10-239}
      • Order "Iainarchaeales" Rinke et al. 2020
  • Phylum "Micrarchaeota" Baker & Dick 2013
    • Class "Micrarchaeia" Vazquez-Campos et al. 2021
      • Order "Anstonellales" Vazquez-Campos et al. 2021 (LFWA-IIIc)
      • Order "Burarchaeales" Vazquez-Campos et al. 2021 (LFWA-IIIb)
      • Order "Fermentimicrarchaeales" Kadnikov et al. 2020
      • Order "Gugararchaeales" Vazquez-Campos et al. 2021 (LFWA-IIIa)
      • Order "Micrarchaeales" Vazquez-Campos et al. 2021
      • Order "Norongarragalinales" Vazquez-Campos et al. 2021 (LFWA-II)
  • Phylum "Undinarchaeota" Dombrowski et al. 2020
    • Class "Undinarchaeia" Dombrowski et al. 2020
      • Order "Undinarchaeales" Dombrowski et al. 2020
  • Phylum "Huberarchaeota" Probst et al. 2019
    • Class "Huberarchaeia" corrig. Probst et al. 2019
      • Order "Huberarchaeales" Rinke et al. 2020
  • Phylum "Aenigmatarchaeota" corrig. Rinke et al. 2013 (DSEG, DUSEL2)
    • Class "Aenigmatarchaeia" corrig. Rinke et al. 2020
      • Order "Aenigmatarchaeales" corrig. Rinke et al. 2020
  • Phylum "Nanohalarchaeota" corrig. Rinke et al. 2013
    • Class "Nanohalobiia" corrig.La Cono et al. 2020
      • Order "Nanohalobiales" La Cono et al. 2020
    • Class ?"Nanohalarchaeia" corrig. Narasingarao et al. 2012
      • Order "Nanohalarchaeales"
  • Phylum "Nanoarchaeota" Huber et al. 2002
    • Class "Nanoarchaeia" Vazquez-Campos et al. 2021
      • Order "Nanoarchaeales" Huber et al. 2011
      • Order "Pacearchaeales" (DHVE-5, DUSEL-1)
      • Order "Parvarchaeales" Rinke et al. 2020 (ARMAN 4 & 5)
      • Order "Tiddalikarchaeales" Vazquez-Campos et al. 2021 (LFW-252_1)
      • Order "Woesearchaeales" (DHVE-6)
  • Phylum ?"Mamarchaeota"
  • Order ?"Wiannamattarchaeales"

See also

References
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