Biology:Lokiarchaeum primum

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Candidatus Lokiarchaeum primum
Scientific classification
Domain:
Archaea
Kingdom:
Promethearchaeati
Phylum:
Promethearchaeota
Class:
Promethearchaeia
Order:
Promethearchaeales
Family:
Promethearchaeaceae
Genus:
Candidatus Lokiarchaeum
Species:
Ca. L. primum
Binomial name
Candidatus Lokiarchaeum primum
Spang et al. 2015

Candidatus Lokiarchaeum primum,[1] synonym Lokiarchaeon,[2] is a currently uncultured deep-sea archaeal species. Discovered in marine sediment near the Loki's Castle deep-sea vent, Lokiarchaeon is believed to be a close ancestor of eukaryotes. An anaerobic lithoautotroph, it is believed to share key traits with eukaryotes, forming the basis for the Asgard archaea systematic grouping.

Taxonomic classification

Initial metagenomic analysis found Lokiarchaeon most closely related to eukaryotic lineages.[3] Large-scale metagenomic analysis further categorized Lokiarchaeon as Asgard archaea, a grouping of archaeal lineages possessing key eukaryotic proteins, suggesting that eukaryotes diverged from Asgard archaea.[4] Lokiarchaeum is believed to share a common ancestor with eukaryotes.[5][6][7] More specifically, Lokiarchaeon is a member of the Deep-Sea Archaeal Group[3] within the Asgard archaea, a sister group to the TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota) archaeal superphylum.[4] As determined from phylogenies built on conserved ribosomal proteins, Candidatus Lokiarchaeum ossiferum is considered the closest known species relative of Lokiarchaeon.[8]

Discovery

Lokiarchaeon was discovered by researchers Aja Spang, Jimmy H. Saw, Steffen L. Jørgensen, Katarzyna Zaremba-Niedzwiedzka, Joran Martjin, Anders E. Lind, Roel Van Eijk, Christa Schleper, Lionel Guy, and Thijs J. G. Ettema.[3] While investigating the microbial diversity of deep-sea sediments near the Arctic Mid-Ocean Ridge, researchers extracted 16S rRNA gene sequences from an unknown species of Deep-Sea Archaea. Sequences were gathered from a gravity core sample, a geological sampling technique used to extract a "core" of deep-sea sediment, located about 15 km from the active hydrothermal vent site, Loki's Castle.[3] Acquired in the summer of 2010, samples were immediately collected for analysis, with the core stored for later use once the team reached port.[3] The researchers used methods such as metagenomic sequencing, single-gene phylogenies, and binning of selected metagenomes to discover Lokiarchaeon.[3]

Physiology and morphology

Although uncultured in a laboratory setting, the Lokiarchaeon metagenome encodes eukaryotic signature proteins (ESPs) that have been traditionally associated with eukaryotes. Upon its discovery, Lokiarchaeon was predicted to possess enzymes of the broad class of GTPases, membrane-bound transport vesicles, and an actin-based cytoskeleton, necessary for intracellular nutrient transport, movement, and structural integrity.[3] While the exact morphology of Lokiarchaeon is unknown, isolated cultures of close Asgard archaea relatives Ca. L. ossiferum, Promethearchaeum syntrophicum, and Nerearchaeum marumarumayae have small, coccoid cell bodies with extracellular protrusions and vesicle formation,[8][9][10] traits that the uncultured Lokiarchaeon can potentially share.

Genomics

The Lokiarchaeon genome has only been sequenced from metagenomic analysis, not from pure culture. Thus, the "composite" genome sequence is not considered "complete" and contains some genetic information from related strains. The genome is 5.1 megabase pairs with 5413 genes, of which 5384 encode proteins.[3][11] About 30% of each of the two Lokiarchaeon lineage genome sequences determined from the metagenomic analysis were either G or C nucleotide bases.[3] Of all Lokiarchaeon proteins, 26% were similar to other archaeal proteins and 29% were similar to other bacterial proteins.[3] 32% of proteins were unique to Lokiarchaeon, while 3.3% were related to eukaryotic proteins such as ubiquitin, GTPases, and proteins required for endosome formation.[3]

Metabolism

Organisms in the Lokiarchaeum family are considered organoheterotrophs that extract energy from carbohydrates.[12] Lokiarchaeon in deep-sea samples were found to be lithoautotrophic anaerobes, using hydrogen and carbon dioxide to synthesize acetate for energy production.[13] This finding supports previous evidence suggesting that Lokiarchaeon uses hydrogen to reduce CO2 to CH3 in early stages of acetate synthesis.[2] According to metagenome assemblies of Asgard phyla, Lokiarchaeon is suggested to synthesize lipids.[14] Based on observed co-cultures of other Asgard archaea with bacteria, it is possible Lokiarchaeon engages in syntrophic relationships with bacteria, potentially allowing it to degrade amino acids and exchange metabolites such as H2 (a product of fermentative metabolism).[8][9][10]

Ecology

Discovered in Arctic deep-sea vent sediment, Lokiarchaeon is one of the most common Asgard archaea in high-salinity marine sediment environments.[14][15] Aside from the deep-sea environment of Loki's Castle, the Lokiarchaeon family has been found in salt lagoons in Baja California, in a wide pH range of 5-9.[14] As part of the Asgards, Lokiarchaeon likely co-occurs with other microbes.[15] The Lokiarchaeon family's proliferation in subsurface sediment has been attributed to the physical protection the niche provides, favoring slow growth and cell division, and protecting the structures of cell protrusions.[16]

Significance for eukaryogenesis

The discovery of Ca. L. primum implicates a highly complex archaeon as the eukaryotic ancestor.[3] Supported by the identification of Lokiarchaeon ESPs, phylogenetic studies of Lokiarchaeon have clearly established that eukaryotes originated from an Asgard archaeal ancestor within the Archaea domain. This new phylogeny presents a paradigm shift away from the three-domain model of life (Eukarya, Archaea, and Bacteria) towards the two-domain model that eliminates Eukarya as a unique domain, given its Asgard archaeal ancestor. Based on the discovery of Lokiarchaeon and Asgard archaea, models for eukaryogenesis fundamentally involve an Asgard archaeon engulfing an alphaproteobacterium that evolved into modern mitochondria.[17][18] Asgard ESPs, particularly the actin cytoskeleton, might have been necessary for the mechanism of endosymbiosis of the mitochondrial ancestor,[3] thus paving the way for the acquisition of key eukaryotic traits. Current discourse centers on the timeline of eukaryogenesis, i.e., whether an archaeon acquired the mitochondrial ancestor early or late in eukaryote evolution.[17] Despite general consensus on the two-domain model,[5][17] there is some debate that the Lokiarchaeon phylogeny suffers from tree-building errors as a result of missing taxa, supporting the three-domain model.[19]

References

  1. ↑ Göker, Markus (2026). "Species: Lokiarchaeum primum" (in en). doi:10.83108/rn.68747. https://lpsn.dsmz.de/species/lokiarchaeum-primum. 
  2. ↑ 2.0 2.1 Sousa, Filipa L.; Neukirchen, Sinje; Allen, John F.; Lane, Nick; Martin, William F. (2016-04-04). "Lokiarchaeon is hydrogen dependent" (in en). Nature Microbiology 1 (5): 16034. doi:10.1038/nmicrobiol.2016.34. ISSN 2058-5276. PMID 27572645. Bibcode: 2016NatMb...116034S. https://www.nature.com/articles/nmicrobiol201634. 
  3. ↑ 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 3.11 3.12 Spang, Anja; Saw, Jimmy H.; Jørgensen, Steffen L.; Zaremba-Niedzwiedzka, Katarzyna; Martijn, Joran; Lind, Anders E.; van Eijk, Roel; Schleper, Christa et al. (2015-05-06). "Complex archaea that bridge the gap between prokaryotes and eukaryotes" (in en). Nature 521 (7551): 173–179. doi:10.1038/nature14447. ISSN 1476-4687. PMID 25945739. Bibcode: 2015Natur.521..173S. 
  4. ↑ 4.0 4.1 Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F.; Saw, Jimmy H.; Bäckström, Disa; Juzokaite, Lina; Vancaester, Emmelien; Seitz, Kiley W.; Anantharaman, Karthik et al. (2017-01-11). "Asgard archaea illuminate the origin of eukaryotic cellular complexity" (in en). Nature 541 (7637): 353–358. doi:10.1038/nature21031. ISSN 1476-4687. PMID 28077874. Bibcode: 2017Natur.541..353Z. https://www.nature.com/articles/nature21031. 
  5. ↑ 5.0 5.1 Williams, Tom A.; Cox, Cymon J.; Foster, Peter G.; Szöllősi, Gergely J.; Embley, T. Martin (2019-12-09). "Phylogenomics provides robust support for a two-domains tree of life" (in en). Nature Ecology & Evolution 4 (1): 138–147. doi:10.1038/s41559-019-1040-x. ISSN 2397-334X. PMID 31819234. 
  6. ↑ Eme, Laura; Tamarit, Daniel; Caceres, Eva F.; Stairs, Courtney W.; De Anda, Valerie; Schön, Max E.; Seitz, Kiley W.; Dombrowski, Nina et al. (2023-06-14). "Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes" (in en). Nature 618 (7967): 992–999. doi:10.1038/s41586-023-06186-2. ISSN 1476-4687. PMID 37316666. Bibcode: 2023Natur.618..992E. 
  7. ↑ Zhang, Jiawei; Feng, Xiaoyuan; Li, Meng; Liu, Yang; Liu, Min; Hou, Li-Jun; Dong, Hong-Po (2025-05-07). "Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota" (in en). Nature 642 (8069): 990–998. doi:10.1038/s41586-025-08955-7. ISSN 1476-4687. PMID 40335687. Bibcode: 2025Natur.642..990Z. 
  8. ↑ 8.0 8.1 8.2 Rodrigues-Oliveira, Thiago; Wollweber, Florian; Ponce-Toledo, Rafael I.; Xu, Jingwei; Rittmann, Simon K.-M. R.; Klingl, Andreas; Pilhofer, Martin; Schleper, Christa (2022-12-21). "Actin cytoskeleton and complex cell architecture in an Asgard archaeon" (in en). Nature 613 (7943): 332–339. doi:10.1038/s41586-022-05550-y. ISSN 1476-4687. PMID 36544020. 
  9. ↑ 9.0 9.1 Imachi, Hiroyuki; Nobu, Masaru K.; Nakahara, Nozomi; Morono, Yuki; Ogawara, Miyuki; Takaki, Yoshihiro; Takano, Yoshinori; Uematsu, Katsuyuki et al. (2020-01-15). "Isolation of an archaeon at the prokaryote–eukaryote interface" (in en). Nature 577 (7791): 519–525. doi:10.1038/s41586-019-1916-6. ISSN 1476-4687. PMID 31942073. Bibcode: 2020Natur.577..519I. 
  10. ↑ 10.0 10.1 Nobs, Stephanie-Jane; Johnson, Matthew D.; Williams, Timothy J.; Meltzer, Julia; Vázquez-Campos, Xabier; MacLeod, Fraser I.; Rowell, Keiran; Pitt, Miranda et al. (2026-04-20). "An Asgard archaeon from a modern analog of ancient microbial mats" (in English). Current Biology 36 (8): 2090–2103.e7. doi:10.1016/j.cub.2026.03.041. ISSN 0960-9822. PMID 41962538. https://www.cell.com/current-biology/abstract/S0960-9822(26)00330-1. 
  11. ↑ "Candidatus Lokiarchaeum sp. GC14_75 genome assembly ASM98684v1" (in en). https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000986845.1/. 
  12. ↑ Spang, Anja; Stairs, Courtney W.; Dombrowski, Nina; Eme, Laura; Lombard, Jonathan; Caceres, Eva F.; Greening, Chris; Baker, Brett J. et al. (2019-04-01). "Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism" (in en). Nature Microbiology 4 (7): 1138–1148. doi:10.1038/s41564-019-0406-9. ISSN 2058-5276. PMID 30936488. Bibcode: 2019NatMb...4.1138S. https://www.nature.com/articles/s41564-019-0406-9. 
  13. ↑ Orsi, William D.; Vuillemin, Aurèle; Rodriguez, Paula; Coskun, Ömer K.; Gomez-Saez, Gonzalo V.; Lavik, Gaute; Mohrholz, Volker; Ferdelman, Timothy G. (2019-12-23). "Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments" (in en). Nature Microbiology 5 (2): 248–255. doi:10.1038/s41564-019-0630-3. ISSN 2058-5276. PMID 31873205. Bibcode: 2019NatMb...5..248O. https://www.nature.com/articles/s41564-019-0630-3. 
  14. ↑ 14.0 14.1 14.2 Manoharan, Lokeshwaran; Kozlowski, Jessica A.; Murdoch, Robert W.; Löffler, Frank E.; Sousa, Filipa L.; Schleper, Christa (2019-09-10). Moran, Mary Ann. ed. Laura Hug, Simonetta Gribaldo. "Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki - and Thorarchaeota" (in en). mBio 10 (5). doi:10.1128/mBio.02039-19. ISSN 2161-2129. PMID 31506313. 
  15. ↑ 15.0 15.1 Cai, Mingwei; Richter-Heitmann, Tim; Yin, Xiuran; Huang, Wen-Cong; Yang, Yuchun; Zhang, Cuijing; Duan, Changhai; Pan, Jie et al. (2021-03-01). "Ecological features and global distribution of Asgard archaea". Science of the Total Environment 758. doi:10.1016/j.scitotenv.2020.143581. ISSN 0048-9697. PMID 33223169. Bibcode: 2021ScTEn.75843581C. https://www.sciencedirect.com/science/article/pii/S0048969720371126. 
  16. ↑ Smith, Lovell; Lloyd, Karen G. (2026-04-06). "Ecological drivers of Promethearchaeati's specialization for deep subsurface environments" (in en). Communications Biology 9 (1): 490. doi:10.1038/s42003-026-09786-6. ISSN 2399-3642. PMID 41942770. 
  17. ↑ 17.0 17.1 17.2 Donoghue, Philip C. J.; Kay, Chris; Spang, Anja; Szöllősi, Gergely; Nenarokova, Anna; Moody, Edmund R. R.; Pisani, Davide; Williams, Tom A. (2023-09-11). "Defining eukaryotes to dissect eukaryogenesis" (in English). Current Biology 33 (17): R919–R929. doi:10.1016/j.cub.2023.07.048. ISSN 0960-9822. PMID 37699353. Bibcode: 2023CBio...33R.919D. https://www.cell.com/current-biology/abstract/S0960-9822(23)00987-9. 
  18. ↑ Roger, Andrew J.; Muñoz-Gómez, Sergio A.; Kamikawa, Ryoma (2017-11-06). "The Origin and Diversification of Mitochondria" (in English). Current Biology 27 (21): R1177–R1192. doi:10.1016/j.cub.2017.09.015. ISSN 0960-9822. PMID 29112874. Bibcode: 2017CBio...27R1177R. https://www.cell.com/current-biology/abstract/S0960-9822(17)31179-X. 
  19. ↑ Cunha, Violette Da; Gaia, Morgan; Gadelle, Daniele; Nasir, Arshan; Forterre, Patrick (2017-06-12). "Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes" (in en). PLOS Genetics 13 (6). doi:10.1371/journal.pgen.1006810. ISSN 1553-7404. PMID 28604769. 



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