Biology:DPANN
| DPANN | |
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| Parvarchaeum acidiphilum | |
Scientific classification 
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| Domain: | Archaea |
| Superphylum: | DPANN Rinke et al. 2013 |
| Phyla[1] | |
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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 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 yet considered established, 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 have not been 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] | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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]
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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.
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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"[24][25][26] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Super Phylum "DPANN" Rinke et al. 2013
- Phylum "Undinarchaeota" Dombrowski et al. 2020
- Class "Undinarchaeia" Dombrowski et al. 2020
- Order "Undinarchaeales" Dombrowski et al. 2020
- Class "Undinarchaeia" Dombrowski et al. 2020
- Phylum "Huberarchaeota" Probst et al. 2019
- Class "Huberarchaeia" corrig. Probst et al. 2019
- Order "Huberarchaeales" Rinke et al. 2020
- Class "Huberarchaeia" corrig. Probst et al. 2019
- Phylum "Aenigmatarchaeota" corrig. Rinke et al. 2013 (DSEG, DUSEL2)
- Class "Aenigmatarchaeia" corrig. Rinke et al. 2020
- Order "Aenigmatarchaeales" corrig. Rinke et al. 2020
- Class "Aenigmatarchaeia" 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"
- Class "Nanohalobiia" corrig.La Cono et al. 2020
- Phylum Altarchaeota Probst et al. 2018 (SM1)
- Class "Altarchaeia" corrig. Probst et al. 2014
- Order "Altarchaeales" corrig. Probst et al. 2014
- Class "Altarchaeia" corrig. Probst et al. 2014
- Phylum "Iainarchaeota" ["Diapherotrites" Rinke et al. 2013] (DUSEL-3)
- Class "Iainarchaeia" Rinke et al. 2020
- Order "Forterreales" Probst & Banfield 2017
- Order "Iainarchaeales" Rinke et al. 2020
- Class "Iainarchaeia" 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)
- Class "Micrarchaeia" Vazquez-Campos et al. 2021
- Phylum "Nanoarchaeota" Huber et al. 2002
- Class "Nanoarchaeia" Vazquez-Campos et al. 2021
- Order "Jingweiarchaeales" Rao et al. 2023 [DTBS01]
- 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)
- Class "Nanoarchaeia" Vazquez-Campos et al. 2021
- Phylum ?"Mamarchaeota"
- Order ?"Wiannamattarchaeales"
See also
References
- ↑ "Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life". Cell 172 (6): 1181–1197. 2018. doi:10.1016/j.cell.2018.02.016. PMID 29522741.
- ↑ 2.0 2.1 "Insights into the phylogeny and coding potential of microbial dark matter" (in En). Nature 499 (7459): 431–437. July 2013. doi:10.1038/nature12352. PMID 23851394. Bibcode: 2013Natur.499..431R. https://cloudfront.escholarship.org/dist/prd/content/qt86x4g4qw/qt86x4g4qw.pdf.
- ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 "Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling". Current Biology 25 (6): 690–701. March 2015. doi:10.1016/j.cub.2015.01.014. PMID 25702576.
- ↑ "Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life". Science 357 (6351): eaaf3883. August 2017. doi:10.1126/science.aaf3883. PMID 28798101.
- ↑ 5.0 5.1 5.2 Nina Dombrowski, Jun-Hoe Lee, Tom A Williams, Pierre Offre, Anja Spang (2019). Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. Nature.
- ↑ 6.0 6.1 6.2 6.3 Cavalier-Smith, Thomas; Chao, Ema E-Yung (2020). "Multidomain ribosomal protein trees and the planctobacterial origin of neomura (Eukaryotes, archaebacteria)". Protoplasma 257 (3): 621–753. doi:10.1007/s00709-019-01442-7. PMID 31900730.
- ↑ 7.0 7.1 7.2 Jordan T. Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar, Karen G. Lloyd (2017). Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales. Frontiers.
- ↑ "Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater". PLOS ONE 12 (4): e0174930. 2017-04-06. doi:10.1371/journal.pone.0174930. PMID 28384184.
- ↑ Genomes Online Database
- ↑ "Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon". The ISME Journal 3 (2): 159–167. February 2009. doi:10.1038/ismej.2008.99. PMID 18946497.
- ↑ "Lineages of acidophilic archaea revealed by community genomic analysis". Science 314 (5807): 1933–1935. December 2006. doi:10.1126/science.1132690. PMID 17185602.
- ↑ "Metatranscriptomic analysis of microbes in an Oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation". Applied and Environmental Microbiology 78 (4): 1015–1022. February 2012. doi:10.1128/AEM.06811-11. PMID 22156430.
- ↑ "Enigmatic, ultrasmall, uncultivated Archaea". Proceedings of the National Academy of Sciences of the United States of America 107 (19): 8806–8811. May 2010. doi:10.1073/pnas.0914470107. PMID 20421484.
- ↑ "High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes". Environmental Microbiology Reports 8 (2): 210–217. April 2016. doi:10.1111/1758-2229.12370. PMID 26711582.
- ↑ "Archaeal diversity in waters from deep South African gold mines". Applied and Environmental Microbiology 67 (12): 5750–5760. December 2001. doi:10.1128/AEM.67.21.5750-5760.2001. PMID 11722932.
- ↑ "De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities". The ISME Journal 6 (1): 81–93. January 2012. doi:10.1038/ismej.2011.78. PMID 21716304.
- ↑ "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". Proceedings of the National Academy of Sciences of the United States of America 100 (22): 12984–12988. October 2003. doi:10.1073/pnas.1735403100. PMID 14566062.
- ↑ "Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park.". Biology Direct 8 (1): 9. December 2013. doi:10.1186/1745-6150-8-9. PMID 23607440.
- ↑ 19.0 19.1 "Integrative modeling of gene and genome evolution roots the archaeal tree of life". Proceedings of the National Academy of Sciences of the United States of America 114 (23): E4602–E4611. June 2017. doi:10.1073/pnas.1618463114. PMID 28533395.
- ↑ 20.0 20.1 20.2 "Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution". Nature Communications 11 (1): 3939. August 2020. doi:10.1038/s41467-020-17408-w. PMID 32770105.
- ↑ 21.0 21.1 Yutian Feng, Uri Neri, Sean Gosselin, Artemis S Louyakis, R Thane Papke, Uri Gophna, Johann Peter Gogarten (2021). The Evolutionary Origins of Extreme Halophilic Archaeal Lineages. Oxford Academic.
- ↑ J.P. Euzéby. "Parvarchaeota". List of Prokaryotic names with Standing in Nomenclature (LPSN). https://lpsn.dsmz.de/phylum/parvarchaeota.
- ↑ Sayers. "Parvarchaeota". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=1462422&lvl=3&lin=f&keep=1&srchmode=1&unlock. Retrieved 2021-03-20.
- ↑ "GTDB release 08-RS214". https://gtdb.ecogenomic.org/about#4%7C.
- ↑ "ar53_r214.sp_label". https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/ar53_r214.sp_labels.tree.
- ↑ "Taxon History". https://gtdb.ecogenomic.org/taxon_history/.
External links
Wikidata ☰ Q24862848 entry
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