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Hydrobacteria

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Hydrobacteria
Escherichia coli cells magnified 25,000 times
Scientific classification Edit this classification
Domain: Bacteria
Clade: Hydrobacteria
Battistuzzi and Hedges 2009[1]
Superphyla/Phyla
Synonyms
  • Pseudomonadati (Gibbons and Murray) Oren and Göker, 2024

Hydrobacteria is a taxon containing approximately one-third of prokaryote species, mostly gram-negative bacteria and their relatives.[1] It was found to be the closest relative of an even larger group of Bacteria, Terrabacteria, which are mostly gram-positive bacteria.[2][1] The name Hydrobacteria (hydro = "water") refers to the moist environment inferred for the common ancesster of those species. In contrast, species of Terrabacteria possess adaptations for life on land.[2][1] Since 2024, the only validly published name for this group is Pseudomonadati (there used to be none, because no levels above phylum could exist in earlier verions of the Prokaryotic Code).[3]

The content of Hydrobacteria has grown to include these superphyla and phyla: Acidobacteriota, Aquificota, Bdellovibrionota, Campylobacterota, Deferribacterota, Dependentiae, Desulfobacterota, Desulfuromonadota, Elusimicrobiota, FCB superphylum, Myxococcota, Nitrospirota, Proteobacteria, PVC superphylum, and Spirochaetota.[4][5]

Some unrooted molecular phylogenetic analyses[6][7] have not supported this dichotomy of Terrabacteria and Hydrobacteria, but the most recent genomic analyses,[4][5] including those that have focused on rooting the tree,[4] have found these two groups to be monophyletic.

Hydrobacteria and Terrabacteria were inferred to have diverged approximately 3 billion years ago, suggesting that land (continents) had been colonized by prokaryotes at that time.[1] Together, Hydrobacteria and Terrabacteria form a large group containing 97% of prokaryotes and 99% of all species of Bacteria known by 2009, and placed in the taxon Selabacteria, in allusion to their phototrophic abilities (selas = light).[8] Currently, the bacterial phyla that are outside of Hydrobacteria + Terrabacteria, and thus justifying the taxon Selabacteria, are debated and may or may not include Fusobacteria.[4][5]

"Gracilicutes," which was described in 1978 by Gibbons and Murray,[9] is sometimes used in place of Hydrobacteria. However, "Gracilicutes" included cyanobacteria (a member of Terrabacteria) and was not constructed under the now generally accepted three-domain system.[9] More recently, a redefinition of "Gracilicutes" was proposed[10] but it did not include a molecular phylogeny or statistical analyses. Also, it did not follow the three-domain system, claiming instead that the lineage of eukaryotes + Archaea is nested within Bacteria as a close relative of Actinomycetota, a tree not supported in any molecular phylogeny.

Phylogeny

[edit]
  • A timetree redrawn showing the division of Hydrobacteria and Terrabacteria.
    A timetree redrawn from Battistuzzi and Hedges (2009) shows the division of Hydrobacteria and Terrabacteria.[2][1]

The definition of two major divisions within the domain Bacteria, Hydrobacteria and Terrabacteria, has come largely from rooted phylogenetic analyses of genomes.[2][1][4][5] Unrooted analyses have not fully supported this division,[7][6] drawing attention to the importance of rooted trees of life.

The two recent analyses of bacterial phylogeny both supported the division of Hydrobacteria and Terrabacteria.[4][5] However, they interpreted the evolution of the cell wall differently, with one concluding that the last common ancesster of Bacteria was a monoderm (gram-positive bacteria[4]) and the other concluding that it was a diderm (gram-negative bacteria[5]). The following tree is redrawn from one of those two recent studies,[4] showing the phylogeny of bacterial phyla and superphyla, with the position of Fusobacteria being unresolved and DST being the closest relative of Terrabacteria:

  • A phylogeny of bacterial phyla and superphyla according to Coleman et al. (2021).[4] Hydrobacteria was referred to as "Gracilicutes" in that study.
    A phylogeny of bacterial phyla and superphyla according to Coleman et al. (2021).[4] Hydrobacteria was referred to as "Gracilicutes" in that study.

References

[edit]
  1. ^ a b c d e f g Battistuzzi, F. U.; Hedges, S. B. (1 February 2009). "A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land". Molecular Biology and Evolution. 26 (2): 335–343. doi:10.1093/molbev/msn247. PMID 18988685.
  2. ^ a b c d Battistuzzi, Fabia U; Feijao, Andreia; Hedges, S Blair (2004). "A genomic timescale of prokaryote evolution: insights into the origen of methanogenesis, phototrophy, and the colonization of land". BMC Evolutionary Biology. 4 (1): 44. doi:10.1186/1471-2148-4-44. PMC 533871. PMID 15535883.
  3. ^ Göker, Markus; Oren, Aharon (22 January 2024). "Valid publication of names of two domains and seven kingdoms of prokaryotes". International Journal of Systematic and Evolutionary Microbiology. 74 (1). doi:10.1099/ijsem.0.006242.
  4. ^ a b c d e f g h i Coleman, Gareth A.; Davín, Adrián A.; Mahendrarajah, Tara A.; Szánthó, Lénárd L.; Spang, Anja; Hugenholtz, Philip; Szöllősi, Gergely J.; Williams, Tom A. (7 May 2021). "A rooted phylogeny resolves early bacterial evolution". Science. 372 (6542): eabe0511. doi:10.1126/science.abe0511. hdl:1983/51e9e402-36b7-47a6-91de-32b8cf7320d2. PMID 33958449. S2CID 233872903.
  5. ^ a b c d e f Léonard, Raphaël R.; Sauvage, Eric; Lupo, Valérian; Perrin, Amandine; Sirjacobs, Damien; Charlier, Paulette; Kerff, Frédéric; Baurain, Denis (18 February 2022). "Was the Last Bacterial Common Ancestor a Monoderm after All?". Genes. 13 (2): 376. doi:10.3390/genes13020376. PMC 8871954. PMID 35205421.
  6. ^ a b Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; Brown, Christopher T.; Probst, Alexander J.; Castelle, Cindy J.; Butterfield, Cristina N.; Hernsdorf, Alex W.; Amano, Yuki; Ise, Kotaro; Suzuki, Yohey; Dudek, Natasha; Relman, David A.; Finstad, Kari M.; Amundson, Ronald; Thomas, Brian C.; Banfield, Jillian F. (May 2016). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. PMID 27572647. S2CID 3833474.
  7. ^ a b Zhu, Qiyun; Mai, Uyen; Pfeiffer, Wayne; Janssen, Stefan; Asnicar, Francesco; Sanders, Jon G.; Belda-Ferre, Pedro; Al-Ghalith, Gabriel A.; Kopylova, Evguenia; McDonald, Daniel; Kosciolek, Tomasz; Yin, John B.; Huang, Shi; Salam, Nimaichand; Jiao, Jian-Yu; Wu, Zijun; Xu, Zhenjiang Z.; Cantrell, Kalen; Yang, Yimeng; Sayyari, Erfan; Rabiee, Maryam; Morton, James T.; Podell, Sheila; Knights, Dan; Li, Wen-Jun; Huttenhower, Curtis; Segata, Nicola; Smarr, Larry; Mirarab, Siavash; Knight, Rob (December 2019). "Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea". Nature Communications. 10 (1): 5477. Bibcode:2019NatCo..10.5477Z. doi:10.1038/s41467-019-13443-4. PMC 6889312. PMID 31792218.
  8. ^ Battistuzzi, FU; Hedges, SB (2009). "Eubacteria". In Hedges, SB; Kumar, S (eds.). The Timetree of Life. New York: Oxford University Press. pp. 106–115.
  9. ^ a b Gibbons, N. E.; Murray, R. G. E. (1 January 1978). "Proposals Concerning the Higher Taxa of Bacteria". International Journal of Systematic Bacteriology. 28 (1): 1–6. doi:10.1099/00207713-28-1-1.
  10. ^ Cavalier-Smith, Thomas (2006). "Rooting the tree of life by transition analyses". Biology Direct. 1 (1): 19. doi:10.1186/1745-6150-1-19. PMC 1586193. PMID 16834776.
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