Actinomycetota

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Actinomycetota
Actinomyces israelii.jpg
Scanning electron micrograph of Actinomyces israelii .
Scientific classification OOjs UI icon edit-ltr.svg
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

The Actinomycetota (or Actinobacteria) are a diverse phylum of Gram-positive bacteria with high GC content. [4] They can be terrestrial or aquatic. [5] They are of great importance to land flora because of 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, as fungi do, 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.

Contents

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. [9] [10]

The Actinomycetota genus Bifidobacterium is the most common bacteria in the microbiome of human infants. [11] Although adults have fewer bifidobacteria, intestinal bifidobacteria help maintain the mucosal barrier and reduce lipopolysaccharide in the intestine. [12]

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. [13]

Some Siberian or Antarctic Actinomycetota are said to be the oldest living organism on Earth, frozen in permafrost at around half a million years ago. [14] [15] The symptoms of life were detected by CO2 release from permafrost samples 640 kya or younger. [16]

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. [10]

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. [17]

Actinomycetota, especially Streptomyces spp., are recognized as the producers of many bioactive metabolites that are useful to humans in medicine, such as antibacterials, [18] antifungals, [19] antivirals, antithrombotics, immunomodifiers, antitumor drugs, and enzyme inhibitors; and in agriculture, including insecticides, herbicides, fungicides, and growth-promoting substances for plants and animals. [20] Actinomycetota-derived antibiotics that are important in medicine include aminoglycosides, anthracyclines, chloramphenicol, macrolide, tetracyclines, etc.[ citation needed ]

Actinomycetota have high guanine and cytosine content in their DNA. [21] The G+C content of Actinomycetota can be as high as 70%, though some may have a low G+C content. [22]

Analysis of glutamine synthetase sequence has been suggested for phylogenetic analysis of the Actinomycetota. [23]

Phylogeny

Whole-genome based phylogeny [24] 16S rRNA based LTP_12_2021 [25] [26] [27] GTDB 08-RS214 [28] [29] [30]

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). [31]

See also

Related Research Articles

The Thermomicrobia is a group of thermophilic green non-sulfur bacteria. Based on species Thermomicrobium roseum and Sphaerobacter thermophilus, this bacteria class has the following description:

<span class="mw-page-title-main">Micromonosporaceae</span> Family of bacteria

Micromonosporaceae is a family of bacteria of the class Actinomycetia. They are gram-positive, spore-forming soil organisms that form a true mycelium.

<i>Streptomyces</i> Genus of bacteria

Streptomyces is the largest genus of Actinomycetota, and the type genus of the family Streptomycetaceae. Over 700 species of Streptomyces bacteria have been described. As with the other Actinomycetota, streptomycetes are gram-positive, and have very large genomes with high GC content. Found predominantly in soil and decaying vegetation, most streptomycetes produce spores, and are noted for their distinct "earthy" odor that results from production of a volatile metabolite, geosmin. Different strains of the same species may colonize very diverse environments.

<span class="mw-page-title-main">Actinomycetales</span> Order of Actinomycota

The Actinomycetales is an order of Actinomycetota. A member of the order is often called an actinomycete. Actinomycetales are generally gram-positive and anaerobic and have mycelia in a filamentous and branching growth pattern. Some actinomycetes can form rod- or coccoid-shaped forms, while others can form spores on aerial hyphae. Actinomycetales bacteria can be infected by bacteriophages, which are called actinophages. Actinomycetales can range from harmless bacteria to pathogens with resistance to antibiotics.

<span class="mw-page-title-main">Actinomycetia</span> Class of bacteria

The Actinomycetia are a class of bacteria.

<span class="mw-page-title-main">Bifidobacteriaceae</span> Family of bacteria

The Bifidobacteriaceae are the only family of bacteria in the order Bifidobacteriales. According to the 16S rRNA-based LTP release 106 published by 'The All-Species Living Tree' Project, the order Bifidobacteriales is a clade nested within the suborder Micrococcineae, also the genus Bifidobacterium is paraphyletic to the other genera within the family, i.e. the other genera are nested within Bifidobacterium.

<span class="mw-page-title-main">Streptomycetaceae</span> Family of bacteria

Streptomycetaceae is a family of the class Actinomycetota, making up the monotypic order Streptomycetales. It includes the important genus Streptomyces. This was the original source of many antibiotics, namely streptomycin, the first antibiotic against tuberculosis.

The Actinomycetaceae are a family of bacteria in the order Actinomycetales that contains the medically important genus Actinomyces. These organisms are closely related to the mycobacteria, but were originally classified as fungi because they were thought to be transitional forms between bacteria and fungi.

<span class="mw-page-title-main">Bacterial phyla</span> Phyla or divisions of the domain Bacteria

Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.

Acrocarpospora is a genus of bacteria in the phylum Actinomycetota. The major respiratory quinone is menaquinone MK-9(H ) and use madurose, an actinomycete whole-cell sugar.

Actinospica is a genus in the phylum Actinomycetota (Bacteria).

Cryptosporangium is a genus of bacteria in the phylum Actinomycetota.

The Jiangellaceae are the only family of the order Jiangellales, which is a part of the phylum Actinomycetota.

The Cryptosporangiaceae are the only family of the order Cryptosporangiales, which is a part of the phylum Actinomycetota.

Aestuariimicrobium is a singleton genus in the phylum Actinomycetota (Bacteria), whose first member, namely Aestuariimicrobium kwangyangense, was isolated from a diesel contaminated coastal site. Like all Actinobacteria, it is gram-positive and with a high CG content (69%). It is rod/coccoid shaped bacterium whose main quinone is menaquinone-7 (MK7).

<i>Streptomyces antibioticus</i> Species of bacterium

Streptomyces antibioticus is a gram-positive bacterium discovered in 1941 by Nobel-prize-winner Selman Waksman and H. Boyd Woodruff. Its name is derived from the Greek "strepto-" meaning "twisted", alluding to this genus' chain-like spore production, and "antibioticus", referring to this species' extensive antibiotic production. Upon its first characterization, it was noted that S. antibioticus produces a distinct soil odor.

The Coriobacteriia are a class of Gram-positive bacteria within the Actinomycetota phylum. Species within this group are nonsporulating, strict or facultative anaerobes that are capable of thriving in a diverse set of ecological niches. Gordonibacter species are the only members capable of motility by means of flagella within the class. Several species within the Coriobacteriia class have been implicated with human diseases that range in severity. Atopobium, Olsenella, and Cryptobacterium species have responsible for human oral infections including periodontitis, halitosis, and other endodontic infections. Eggerthella species have been associated with severe blood bacteraemia and ulcerative colitis.

<span class="mw-page-title-main">Mycobacteriales</span> Order of bacteria

The Mycobacteriales are an order of bacteria. The current description is genome-based, per Gupta 2019 emendation. Most members produce mycolic acids.

Modestobacter is a Gram-positive genus of bacteria from the phylum Actinomycetota.

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. 1 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. ↑ Donald, Lavinia; Pipite, Atanas; Subramani, Ramesh; Owen, Jeremy; Keyzers, Robert A.; Taufa, Taitusi (2022). "Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective". Microbiology Research. 13 (3): 418–465. doi: 10.3390/microbiolres13030031 . ISSN   2036-7481.
  10. 1 2 Procópio, Rudi Emerson de Lima; Silva, Ingrid Reis da; Martins, Mayra Kassawara; Azevedo, João Lúcio de; Araújo, Janete Magali de (2012). "Antibiotics produced by Streptomyces". The Brazilian Journal of Infectious Diseases. 16 (5): 466–471. doi: 10.1016/j.bjid.2012.08.014 . ISSN   1678-4391. PMID   22975171.
  11. ↑ 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.
  12. ↑ 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.
  13. ↑ 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.
  14. ↑ 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.
  15. ↑ 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.
  16. ↑ 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.
  17. ↑ Gardnerella at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
  18. ↑ Mahajan GB (2012). "Antibacterial agents from actinomycetes - a review". Frontiers in Bioscience. 4: 240–53. doi:10.2741/e373.
  19. ↑ 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.
  20. ↑ 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.
  21. ↑ 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.
  22. ↑ 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. Bibcode:2012EnvMR...4...29G. doi:10.1111/j.1758-2229.2011.00274.x. PMID   23757226.
  23. ↑ 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.
  24. ↑ 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.
  25. ↑ "The LTP". Archived from the original on 14 June 2021. Retrieved 23 February 2021.
  26. ↑ "LTP_all tree in newick format". Archived from the original on 28 February 2022. Retrieved 23 February 2021.
  27. ↑ "LTP_12_2021 Release Notes" (PDF). Archived (PDF) from the original on 28 February 2022. Retrieved 23 February 2021.
  28. ↑ "GTDB release 08-RS214". Genome Taxonomy Database . Archived from the original on 26 October 2022. Retrieved 10 May 2023.
  29. ↑ "bac120_r214.sp_label". Genome Taxonomy Database . Archived from the original on 16 May 2023. Retrieved 10 May 2023.
  30. ↑ "Taxon History". Genome Taxonomy Database . Archived from the original on 1 November 2021. Retrieved 10 May 2023.
  31. ↑ 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.

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