Actinomycetota

The Actinomycetota (or Actinobacteria) are a phylum of mostly gram-positive bacteria. They can be terrestrial or aquatic.[4] 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
Domain: Bacteria
(unranked): Terrabacteria
Phylum: Actinomycetota
Goodfellow 2021[1]
Type genus
Actinomyces
Harz 1877 (Approved Lists 1980)
Classes[2]
  • "Aquicultoria"
  • "Geothermincolia"
  • "Humimicrobiia"
  • Acidimicrobiia
  • Actinomycetia
  • Coriobacteriia
  • Nitriliruptoria
  • Rubrobacteria
  • Thermoleophilia
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.[5] Actinomycetota is one of the dominant bacterial phyla and contains one of the largest of bacterial genera, Streptomyces.[6] Streptomyces and other actinomycetota are major contributors to biological buffering of soils.[7] They are also the source of many antibiotics.

The Actinomycetota genus Bifidobacterium is the most common bacteria in the microbiome of human infants.[8] Although adults have fewer bifidobacteria, intestinal bifidobacteria help maintain the mucosal barrier and reduce lipopolysaccharide in the intestine.[9]

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.[10]

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.[11][12] The symptoms of life were detected by CO2 release from permafrost samples 640 kya or younger. [13]

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.[14]

Actinomycetota, especially Streptomyces spp., are recognized as the producers of many bioactive metabolites that are useful to humans in medicine, such as antibacterials,[15] antifungals,[16] antivirals, antithrombotics, immunomodifiers, antitumor drugs, and enzyme inhibitors; and in agriculture, including insecticides, herbicides, fungicides, and growth-promoting substances for plants and animals.[17][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 07-RS207 by Genome Taxonomy Database[26][27][28]
 
Actinomycetota
 

Rubrobacteria

 
 
 

Thermoleophilia

 
 
 

Coriobacteriia

 
 
 

Acidimicrobiia

 
 
 

Nitriliruptoria

 
 

Actinomycetia

 
 
 
 
 
 
outgroup

Chloroflexota

 
 
 
 

Rubrobacteria

 
 
 

Thermoleophilia

 
 
 

Coriobacteriia

 
 
 
 

Acidimicrobiia

 
 

Nitriliruptoria

 
 
 

Actinomycetia

 
 
 
 
 
 
 
 
 

"Geothermincolia"

 
 
 

"Humimicrobiia"

 
 

"Aquicultoria"

 
 
 
 

Coriobacteriia

 
 
 
 
 

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]

  • Class ?"Syntrophaliphaticia" corrig. Liu et al. 2020
  • Class "Aquicultoria" Jiao et al. 2021
  • Class "Geothermincolia" Jiao et al. 2021
  • Class "Humimicrobiia" Jiao et al. 2021
  • Class Acidimicrobiia Norris 2013
  • Class Actinomycetia (Stackebrandt et al. 1997) Salam et al. 2020 (Nitriliruptoria Ludwig et al. 2013)
    • Subclass Actinobacteridae Stackebrandt, Rainey & Ward-Rainey 1997
    • Subclass Nitriliruptoridae Kurahashi et al. 2010
  • Class Coriobacteriia König 2013
  • Class Rubrobacteria Suzuki 2013
  • Class Thermoleophilia Suzuki and Whitman 2013

See also
  • List of bacteria genera
  • List of bacterial orders
  • List of bacterial vaginosis microbiota

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). 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. 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.
  5. Ghai R, Rodriguez-Valera F, McMahon KD, 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.
  6. C.Michael Hogan.. 2010. Bacteria. Encyclopedia of Earth. eds. Sidney Draggan and C.J.Cleveland, National Council for Science and the Environment, Washington DC Archived 2011-05-11 at the Wayback Machine
  7. Ningthoujam, Debananda S.; Sanasam, Suchitra; Tamreihao, K; Nimaichand, Salam (November 2009). "Antagonistic activities of local actinomycete isolates against rice fungal pathogens". African Journal of Microbiology Research. 3 (11): 737–742.
  8. 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.
  9. 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.
  10. 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.
  11. Sussman: Oldest Plants, The Guardian, 2 May 2010
  12. "It's Okay to be Smart • the oldest living thing in the world: These". Archived from the original on 2018-07-13. Retrieved 2018-07-13.
  13. Johnson, S. S.; Hebsgaard, M. B.; Christensen, T. R.; Mastepanov, M.; Nielsen, R.; Munch, K.; Brand, T.; Gilbert, M. T. P.; Zuber, M. T.; Bunce, M.; Ronn, R.; Gilichinsky, D.; Froese, D.; Willerslev, E. (2007). "Ancient bacteria show evidence of DNA repair". Proceedings of the National Academy of Sciences. 104 (36): 14401–14405. Bibcode:2007PNAS..10414401J. doi:10.1073/pnas.0706787104. PMC 1958816. PMID 17728401.
  14. Gardnerella at the US National Library of Medicine Medical Subject Headings (MeSH)
  15. Mahajan, GB (2012). "Antibacterial agents from actinomycetes - a review". Frontiers in Bioscience. 4: 240–53. doi:10.2741/e373.
  16. Gupte, M.; Kulkarni, P.; Ganguli, B.N. (2002). "Antifungal Antibiotics". Appl. Microbiol. Biotechnol. 58 (1): 46–57. doi:10.1007/s002530100822. PMID 11831475. S2CID 8015426.
  17. 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.
  18. Atta, M.A (2009). "Antimycin-A Antibiotic Biosynthesis Produced by Streptomyces Sp. AZ-AR-262: Taxonomy, Fermentation, Purification and Biological Activities". Austral. J. Basic and Appl. Sci. 3: 126–135.
  19. Ventura, M.; Canchaya, C.; Tauch, A.; Chandra, G.; Fitzgerald, G. F.; Chater, K. F.; van Sinderen, D. (5 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 (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". Retrieved 23 February 2021.
  24. "LTP_all tree in newick format". Retrieved 23 February 2021.
  25. "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
  26. "GTDB release 07-RS207". Genome Taxonomy Database. Retrieved 20 June 2022.
  27. "ar53_r207.sp_label". Genome Taxonomy Database. Retrieved 20 June 2022.
  28. "Taxon History". Genome Taxonomy Database. Retrieved 20 June 2022.
  29. Sayers; et al. "Actinobacteria". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2021-03-20.

Further reading
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