Genomic diversity, lifestyles and evolutionary origins of DPANN archaea
Open accessAbstract
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.
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Phylogenetic artifacts are expected to particularly affect microbial lineages comprised predominantly of symbiotic members such as the CPR bacteria and DPANN archaea.
“These artifacts are expected to particularly affect microbial lineages comprised predominantly of symbiotic members such as the CPR bacteria and DPANN archaea, as genomes of known symbionts are often compositionally biased and characterized by faster evolutionary rates (Dombrowski et al. 2019).”
From The Emergence of Life (2019) · cites this paper as Dombrowski et al. 2019
In “The challenge of determining the phylogenetic placement of symbionts” (page unavailable), the paper says host association can bring faster sequence evolution and extreme GC content, creating phylogenetic artifacts; it specifically raises this concern for DPANN. But it treats the effect on DPANN as a possibility, and the Conclusion and Outlook (page unavailable) does not establish that CPR is predominantly symbiotic or particularly susceptible to these artifacts. (LLM, conf=0.83)
Experimental — accuracy not yet measuredSome prokaryotes, including members of the DPANN archaea, lack functional ATP synthase homologs, and these absences are present across related lineages, suggesting a genuine loss rather than metagenome-assembled genome incompleteness.
“These absences are present across related lineages, suggesting a genuine loss, rather than metagenome-assembled genome incompleteness.”
From ATP synthase evolution on a cross-braced dated tree of life (2023) · cites this paper as [59]
In “The metabolic potential of DPANN archaea” (page unavailable), the paper reports that several DPANN archaea encode putative ATP synthase subunits whose complexes might not always be functional. It does not establish that ATP synthase absences recur across related lineages or distinguish genuine gene loss from metagenome-assembled genome incompleteness. (LLM, conf=0.81)
Experimental — accuracy not yet measuredATP synthases are not as essential as previously assumed, with loss in DPANN and CPR lineages likely being the result of genome streamlining processes consistent with their predicted host-dependent lifestyles.
“This finding suggests that ATP synthases are not as essential as previously assumed32,33,45,65 with loss in DPANN and CPR lineages likely being the result of genome streamlining processes consistent with their predicted host-dependent lifestyles58,59.”
From ATP synthase evolution on a cross-braced dated tree of life (2023) · cites this paper as [59]
In “The metabolic potential of DPANN archaea” (page unavailable), the paper says many DPANN genomes lack components needed to drive membrane-bound ATP synthesis and that some putative ATP synthases may not be functional. It also describes reduced metabolic capabilities and host dependence, but does not establish that ATP synthase loss resulted from genome streamlining or make that claim for CPR lineages. The preceding claim about how essential ATP synthases are is attached to other citations. (LLM, conf=0.84)
Experimental — accuracy not yet measured
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Self-citationAn early origin of iron–sulfur cluster biosynthesis machineries before Earth oxygenation
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Hyperdiverse archaea near life limits at the polyextreme geothermal Dallol area
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“These artifacts are expected to particularly affect microbial lineages comprised predominantly of symbiotic members such as the CPR bacteria and DPANN archaea, as genomes of known symbionts are often compositionally biased and characterized by faster evolutionary rates (Dombrowski et al. 2019).”
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Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'.
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The Evolutionary Origins of Extreme Halophilic Archaeal Lineages
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Gulf of Mexico blue hole harbors high levels of novel microbial lineages
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The role of microbiomes in gastrointestinal cancers: new insights
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Self-citationEssential gene complement of Planctopirus limnophila from the bacterial phylum Planctomycetes
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Iron-Fueled Life in the Continental Subsurface: Deep Mine Microbial Observatory, South Dakota, USA
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- Authors
- Dombrowski, N., Lee, J.-H., Williams, T. A., Offre, P., & Spang, A.
- Affiliations
- Utrecht University (NL)
- Uppsala University (SE)
- University of Bristol (GB)
- Corresponding author
- Spang, Anja
- Venue
- FEMS Microbiology Letters
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-01-01
- Volume
- 366
- Issue
- 2
- ISSN
- 0378-1097 (ISSN-L)
- 1574-6968
- PMC
- PMC6349945
- OpenAlex
- W2910961041
- Cited by
- 230
- References
- 110
- Citations by year
- 2026: 20 · 2025: 25 · 2024: 34 · 2023: 30 · 2022: 43 · 2021: 39 · 2020: 28 · 2019: 11
- FWCI
- 2.19
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- FEMS Microbiology Letters (publishedVersion, cc-by)
- NIOZ Publications (Royal Netherlands Institute for Sea Research) (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Bristol Research (University of Bristol) (publishedVersion, cc-by)
- Flanders Marine Institute (Flanders Marine Institute) (submittedVersion, other-oa)
- KTH Publication Database DiVA (KTH Royal Institute of Technology) (submittedVersion, other-oa)
- Explore Bristol Research (submittedVersion, cc-by)
- Funders
- Swedish Research Council (2016-03559)
- Netherlands Organisation for Scientific Research
- Royal Society University Research
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Keywords
- DPANN archaea, genomic diversity, symbiosis, obligate symbionts, gene repertoire, tree of life, unculturable microorganisms
- MeSH terms
- Archaea, Phylogeny, Genetic Variation, Evolution, Molecular, Genome, Archaeal
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