Terrabacteria Explained

Terrabacteria is a taxon containing approximately two-thirds of prokaryote species, including those in the gram positive phyla (Actinomycetota and Bacillota) as well as the phyla "Cyanobacteria", Chloroflexota, and Deinococcota.[1] [2]

It derives its name (terra = "land") from the evolutionary pressures of life on land. Terrabacteria possess important adaptations such as resistance to environmental hazards (e.g., desiccation, ultraviolet radiation, and high salinity) and oxygenic photosynthesis. Also, the unique properties of the cell wall in gram-positive taxa, which likely evolved in response to terrestrial conditions, have contributed toward pathogenicity in many species. These results now leave open the possibility that terrestrial adaptations may have played a larger role in prokaryote evolution than currently understood.

Terrabacteria was proposed in 2004 for Actinomycetota, "Cyanobacteria", and Deinococcota and was expanded later to include Bacillota and Chloroflexota. Other phylogenetic analyses [3] have supported the close relationships of these phyla. Most species of prokaryotes not placed in Terrabacteria were assigned to the taxon Hydrobacteria, in reference to the moist environment inferred for the common ancestor of those species. Some molecular phylogenetic analyses [4] [5] have not supported this dichotomy of Terrabacteria and Hydrobacteria, but the most recent genomic analyses,[6] [7] including those that have focused on rooting the tree, have found these two groups to be monophyletic.

Terrabacteria and Hydrobacteria were inferred to have diverged approximately 3 billion years ago, suggesting that land (continents) had been colonized by prokaryotes at that time. Together, Terrabacteria and Hydrobacteria 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 Terrabacteria + Hydrobacteria, and thus justifying the taxon Selabacteria, are debated and may or may not include Fusobacteria.

The name “Glidobacteria” [9] included some members of Terrabacteria but excluded the large gram positive groups, Bacillota and Actinomycetota, and is not supported by molecular phylogenetic data. Moreover, the article naming Glidobacteria did not include a molecular phylogeny or statistical analyses and did not follow the widely used three-domain system. For example, it claimed that eukaryotes split from Archaea very recently (~900 Mya), which is contradicted by the fossil record,[10] and that lineage of eukaryotes + Archaea was nested within Bacteria as a close relative of Actinomycetota.

In 2022, new rules were introduced for kingdom-level taxa of prokaryotes, and the same two authors who proposed those new rules, proposed new names in 2024.[11] They concluded that “the taxonomically preferable solution for bacterial kingdoms seems to be to accept the subdivision apparent in the study by Battistuzzi and Hedges,” with refinement. However, instead of using the existing names Terrabacteria and Hydrobacteria, or those names with modified (kingdom-level) endings, Terrabacteriati and Hydrobacteriati, they coined their own new names, Bacillati and Pseudomonadati, respectively. As an action that creates more instability than stability, it is likely to be challenged.    

Phylogeny

The phylogenetic tree according to the phylogenetic analyses of Battistuzzi and Hedges (2009) is the following and with a molecular clock calibration.

Recent molecular analyses have found roughly the following relationships including other phyla, whose relationships were uncertain.[12] [13] [14] [15] [16] [17]

On the other hand, Coleman et al. named the clade composed of Thermotogota, Deinococcota, Synergistota and related as DST and furthermore the analysis suggests that ultra-small bacteria (CPR group) may belong to Terrabacteria being more closely related to Chloroflexota. According to this study the phylum Aquificota sometimes included belongs to Hydrobacteria and that the phylum Fusobacteriota can belong to both Terrabacteria and Hydrobacteria. The result was the following:

Notes and References

  1. Battistuzzi FU, Feijao A, Hedges SB . A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land . BMC Evolutionary Biology . 4 . 44 . November 2004 . 15535883 . 533871 . 10.1186/1471-2148-4-44 . free .
  2. Battistuzzi FU, Hedges SB . A major clade of prokaryotes with ancient adaptations to life on land . Molecular Biology and Evolution . 26 . 2 . 335–343 . February 2009 . 18988685 . 10.1093/molbev/msn247 .
  3. Bern M, Goldberg D . Automatic selection of representative proteins for bacterial phylogeny . BMC Evolutionary Biology . 5 . 1 . 34 . May 2005 . 15927057 . 1175084 . 10.1186/1471-2148-5-34 . free .
  4. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF . 6 . A new view of the tree of life . Nature Microbiology . 1 . 5. 16048 . April 2016 . 27572647 . 10.1038/nmicrobiol.2016.48 . 3833474 . free .
  5. Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R . 6 . Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea . Nature Communications . 10 . 1 . 5477 . December 2019 . 31792218 . 6889312 . 10.1038/s41467-019-13443-4 . 2019NatCo..10.5477Z .
  6. Coleman GA, Davín AA, Mahendrarajah TA, Szánthó LL, Spang A, Hugenholtz P, Szöllősi GJ, Williams TA . 6 . A rooted phylogeny resolves early bacterial evolution . Science . 372 . 6542 . eabe0511 . May 2021 . 33958449 . 10.1126/science.abe0511 . 233872903 . 1983/51e9e402-36b7-47a6-91de-32b8cf7320d2 . free .
  7. Léonard RR, Sauvage E, Lupo V, Perrin A, Sirjacobs D, Charlier P, Kerff F, Baurain D . 6 . Was the Last Bacterial Common Ancestor a Monoderm after All? . Genes . 13 . 2 . 376 . February 2022 . 35205421 . 8871954 . 10.3390/genes13020376 . free .
  8. Book: Battistuzzi FU, Hedges SB . 2009 . Eubacteria . 106–115 . The Timetree of Life . Hedges SB, Kumar S . Oxford University Press . New York .
  9. Cavalier-Smith T . Rooting the tree of life by transition analyses . Biology Direct . 1 . 1 . 19 . July 2006 . 16834776 . 1586193 . 10.1186/1745-6150-1-19 . free .
  10. Book: Knoll AH . Life on a Young Planet : The First Three Billion Years of Evolution on Earth - Updated Edition . 2003 . 0-691-00978-3 . 1303471348.
  11. Göker . Markus . Oren . Aharon . 2024-01-22 . Valid publication of names of two domains and seven kingdoms of prokaryotes . International Journal of Systematic and Evolutionary Microbiology . en . 74 . 1 . 10.1099/ijsem.0.006242 . 1466-5026.
  12. Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF . 6 . Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system . Nature Communications . 7 . 13219 . October 2016 . 27774985 . 5079060 . 10.1038/ncomms13219 . 2016NatCo...713219A .
  13. Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF . 6 . Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria . Nature Communications . 10 . 1 . 463 . January 2019 . 30692531 . 6349859 . 10.1038/s41467-018-08246-y . 2019NatCo..10..463M .
  14. Ji M, Greening C, Vanwonterghem I, Carere CR, Bay SK, Steen JA, Montgomery K, Lines T, Beardall J, van Dorst J, Snape I, Stott MB, Hugenholtz P, Ferrari BC . 6 . Atmospheric trace gases support primary production in Antarctic desert surface soil . Nature . 552 . 7685 . 400–403 . December 2017 . 29211716 . 10.1038/nature25014 . 2017Natur.552..400J . 4394421 . free . 2440/124244 . free .
  15. Tahon G, Tytgat B, Lebbe L, Carlier A, Willems A . Abditibacterium utsteinense sp. nov., the first cultivated member of candidate phylum FBP, isolated from ice-free Antarctic soil samples . Systematic and Applied Microbiology . 41 . 4 . 279–290 . July 2018 . 29475572 . 10.1016/j.syapm.2018.01.009 . 3515091 .
  16. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T . 6 . Insights into the phylogeny and coding potential of microbial dark matter . Nature . 499 . 7459 . 431–437 . July 2013 . 23851394 . 10.1038/nature12352 . 2013Natur.499..431R . 4394530 . free . 10453/27467 . free .
  17. Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Dekas AE, Grasby SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmstrom R, Pati A, Pett-Ridge J, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN . 6 . Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs . Nature Communications . 7 . 10476 . January 2016 . 26814032 . 4737851 . 10.1038/ncomms10476 . 2016NatCo...710476E .

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