Actinomycetota

The Actinomycetota (or Actinobacteria) are a diverse phylum of Gram-positive bacteria with high G+C content.[4] They can be terrestrial or aquatic.[5] They are of great economic importance to humans because agriculture and forests depend on their contributions to soil systems. In soil they help to decompose the organic matter of dead organisms so the molecules can be taken up anew by plants. While this role is also played by fungi, Actinomycetota are much smaller and likely do not occupy the same ecological niche. In this role the colonies often grow extensive mycelia, like a fungus would, and the name of an important order of the phylum, Actinomycetales (the actinomycetes), reflects that they were long believed to be fungi. Some soil actinomycetota (such as Frankia) live symbiotically with the plants whose roots pervade the soil, fixing nitrogen for the plants in exchange for access to some of the plant's saccharides. Other species, such as many members of the genus Mycobacterium, are important pathogens.

Actinomycetota
Scanning electron micrograph of Actinomyces israelii.
Scientific classification Edit this classification
Domain: Bacteria
Clade: Terrabacteria
Phylum: Actinomycetota
Goodfellow 2021[1]
Type genus
Actinomyces
Harz 1877 (Approved Lists 1980)
Classes[2]
Synonyms
  • "Actinobacteraeota" Oren et al. 2015
  • "Actinobacteria" Goodfellow 2012[3]
  • "Actinobacteria" Margulis 1974 ex Cavalier-Smith 2020
  • "Actinobacteria" Stackebrandt, Rainey & Ward-Rainey 1997
  • "Actinobacteriota" Whitman et al. 2018
  • "Actinomycetes" Krasil'nikov 1949

Beyond the great interest in Actinomycetota for their soil role, much is yet to be learned about them. Although currently understood primarily as soil bacteria, they might be more abundant in fresh waters.[6] Actinomycetota is one of the dominant bacterial phyla and contains one of the largest of bacterial genera, Streptomyces.[7] Streptomyces and other actinomycetota are major contributors to biological buffering of soils.[8] They are also the source of many antibiotics.

The Actinomycetota genus Bifidobacterium is the most common bacteria in the microbiome of human infants.[9] Although adults have fewer bifidobacteria, intestinal bifidobacteria help maintain the mucosal barrier and reduce lipopolysaccharide in the intestine.[10]

Although some of the largest and most complex bacterial cells belong to the Actinomycetota, the group of marine Actinomarinales has been described as possessing the smallest free-living prokaryotic cells.[11]

Some Siberian or Antarctic Actinomycetota is said to be the oldest living organism on Earth, frozen in permafrost at around half a million years ago.[12][13] The symptoms of life were detected by CO2 release from permafrost samples 640 kya or younger.[14]

General

Most Actinomycetota of medical or economic significance are in class Actinomycetia, and belong to the order Actinomycetales. While many of these cause disease in humans, Streptomyces is notable as a source of antibiotics.

Of those Actinomycetota not in the Actinomycetales, Gardnerella is one of the most researched. Classification of Gardnerella is controversial, and MeSH catalogues it as both a Gram-positive and Gram-negative organism.[15]

Actinomycetota, especially Streptomyces spp., are recognized as the producers of many bioactive metabolites that are useful to humans in medicine, such as antibacterials,[16] antifungals,[17] antivirals, antithrombotics, immunomodifiers, antitumor drugs, and enzyme inhibitors; and in agriculture, including insecticides, herbicides, fungicides, and growth-promoting substances for plants and animals.[18] Actinomycetota-derived antibiotics that are important in medicine include aminoglycosides, anthracyclines, chloramphenicol, macrolide, tetracyclines, etc.

Actinomycetota have high guanine and cytosine content in their DNA.[19] The G+C content of Actinomycetota can be as high as 70%, though some may have a low G+C content.[20]

Analysis of glutamine synthetase sequence has been suggested for phylogenetic analysis of the Actinomycetota.[21]

Phylogeny
Whole-genome based phylogeny[22] 16S rRNA based LTP_12_2021[23][24][25] GTDB 08-RS214[26][27][28]
Actinomycetota

Rubrobacteria

Thermoleophilia

Coriobacteriia

Acidimicrobiia

Nitriliruptoria

Actinomycetia

outgroup

Chloroflexota

Rubrobacteria

Thermoleophilia

Coriobacteriia

Acidimicrobiia

Nitriliruptoria

Actinomycetia

"Humimicrobiia"

"Aquicultoria"

Coriobacteriia

"Geothermincolia"

Rubrobacteria

Thermoleophilia

Acidimicrobiia

Actinomycetia

Nitriliruptoridae

Actinobacteridae

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[2] and National Center for Biotechnology Information (NCBI).[29]

See also

References
  1. Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987. S2CID 239887308.
  2. Euzéby JP, Parte AC. "Actinobacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). Archived from the original on May 6, 2021. Retrieved June 7, 2021.
  3. Goodfellow M (2012). "Phylum XXVI. Actinobacteria phyl. nov.". In Goodfellow M, Kämpfer P, Trujillo ME, Suzuki K, Ludwig W, Whitman WB (eds.). Bergey's Manual of Systematic Bacteriology. Vol. 5 (2nd ed.). New York, NY: Springer. pp. 33–34.
  4. Gao B, Gupta RS (March 2012). "Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria". Microbiology and Molecular Biology Reviews. 76 (1): 66–112. doi:10.1128/MMBR.05011-11. PMC 3294427. PMID 22390973.
  5. Servin JA, Herbold CW, Skophammer RG, Lake JA (January 2008). "Evidence excluding the root of the tree of life from the actinobacteria". Mol. Biol. Evol. 25 (1): 1–4. doi:10.1093/molbev/msm249. PMID 18003601.
  6. Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R, Cristina Souza de Oliveira T, et al. (2011). Lopez-Garcia P (ed.). "Metagenomics of the water column in the pristine upper course of the Amazon river". PLOS ONE. 6 (8): e23785. Bibcode:2011PLoSO...623785G. doi:10.1371/journal.pone.0023785. PMC 3158796. PMID 21915244.
  7. Hogan CM (2010). "Bacteria". In Draggan S, Cleveland CJ (eds.). Encyclopedia of Earth. Washington DC: National Council for Science and the Environment. Archived from the original on 2011-05-11.
  8. Ningthoujam DS, Sanasam S, Tamreihao K, Nimaichand S (November 2009). "Antagonistic activities of local actinomycete isolates against rice fungal pathogens". African Journal of Microbiology Research. 3 (11): 737–742.
  9. Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, Claesson MJ, Kerr C, Hourihane J, Murray D, Fuligni F, Gueimonde M, Margolles A, De Bellis G, O'Toole PW, van Sinderen D, Marchesi JR, Ventura M (2012-05-11). "Diversity of bifidobacteria within the infant gut microbiota". PLOS ONE. 7 (5): e36957. Bibcode:2012PLoSO...736957T. doi:10.1371/journal.pone.0036957. PMC 3350489. PMID 22606315.
  10. Pinzone MR, Celesia BM, Di Rosa M, Cacopardo B, Nunnari G (2012). "Microbial translocation in chronic liver diseases". International Journal of Microbiology. 2012: 694629. doi:10.1155/2012/694629. PMC 3405644. PMID 22848224.
  11. Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F (2013). "Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria". Scientific Reports. 3: 2471. Bibcode:2013NatSR...3E2471G. doi:10.1038/srep02471. PMC 3747508. PMID 23959135.
  12. Sample I (2 May 2010). "The oldest living organisms: ancient survivors with a fragile future". The Guardian. Archived from the original on 2013-03-02.
  13. Hanson J. "The oldest living thing in the world". It's Okay to be Smart. Archived from the original on 2018-07-13. Retrieved 2018-07-13.
  14. Johnson SS, Hebsgaard MB, Christensen TR, Mastepanov M, Nielsen R, Munch K, et al. (September 2007). "Ancient bacteria show evidence of DNA repair". Proceedings of the National Academy of Sciences of the United States of America. 104 (36): 14401–14405. Bibcode:2007PNAS..10414401J. doi:10.1073/pnas.0706787104. PMC 1958816. PMID 17728401.
  15. Gardnerella at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
  16. Mahajan GB (2012). "Antibacterial agents from actinomycetes - a review". Frontiers in Bioscience. 4: 240–53. doi:10.2741/e373.
  17. Gupte M, Kulkarni P, Ganguli BN (January 2002). "Antifungal antibiotics". Applied Microbiology and Biotechnology. 58 (1): 46–57. doi:10.1007/s002530100822. PMID 11831475. S2CID 8015426.
  18. Bressan W (2003). "Biological control of maize seed pathogenic fungi by use of actinomycetes". Biocontrol. 48 (2): 233–240. doi:10.1023/a:1022673226324. S2CID 29320215.
  19. Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D (September 2007). "Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum". Microbiology and Molecular Biology Reviews. 71 (3): 495–548. doi:10.1128/MMBR.00005-07. hdl:11381/1721088. PMC 2168647. PMID 17804669.
  20. Ghai R, McMahon KD, Rodriguez-Valera F (February 2012). "Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC". Environmental Microbiology Reports. 4 (1): 29–35. doi:10.1111/j.1758-2229.2011.00274.x. PMID 23757226.
  21. Hayward D, van Helden PD, Wiid IJ (2009). "Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinomycetota speciation". BMC Evol. Biol. 9: 48. doi:10.1186/1471-2148-9-48. PMC 2667176. PMID 19245690.
  22. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Markus Göker M (2018). "Genome-Based Taxonomic Classification of the Phylum Actinobacteria". Front. Microbiol. 9: 2007. doi:10.3389/fmicb.2018.02007. PMC 6113628. PMID 30186281.
  23. "The LTP". Archived from the original on 14 June 2021. Retrieved 23 February 2021.
  24. "LTP_all tree in newick format". Archived from the original on 28 February 2022. Retrieved 23 February 2021.
  25. "LTP_12_2021 Release Notes" (PDF). Archived (PDF) from the original on 28 February 2022. Retrieved 23 February 2021.
  26. "GTDB release 08-RS214". Genome Taxonomy Database. Archived from the original on 26 October 2022. Retrieved 10 May 2023.
  27. "bac120_r214.sp_label". Genome Taxonomy Database. Archived from the original on 16 May 2023. Retrieved 10 May 2023.
  28. "Taxon History". Genome Taxonomy Database. Archived from the original on 1 November 2021. Retrieved 10 May 2023.
  29. Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, et al. "Actinobacteria". National Center for Biotechnology Information (NCBI) taxonomy database. Archived from the original on 2021-04-17. Retrieved 2021-03-20.

Further reading
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