Chloroflexota

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Chloroflexota
Scientific classification Edit this classification
Domain: Bacteria
Clade: Terrabacteria
Phylum: Chloroflexota
Garrity and Holt 2021[1]
Classes
Synonyms
  • "Chlorobacteria"
    Cavalier-Smith
    2006
  • "Chloroflexi" Garrity and Holt 2001
  • "Eobacteria" Cavalier-Smith 2002
  • "Chloroflexota" Whitman et al. 2018
  • "Chloroflexaeota" Oren et al. 2015
  • Thermomicrobiota
    Oren & Garrity 2021

The Chloroflexota are a

ethenes and polychlorinated biphenyls
) as electron acceptors.

The members of the phylum Chloroflexota are

gram-negative, whereas well-known monoderms that stain Gram-positive include Firmicutes (or Bacillota) (low G+C gram-positives), Actinomycetota (high-G+C gram-positives) and Deinococcota
(gram-positive diderms with thick peptidoglycan).

History

See also: Bacterial taxonomy and Bacterial phyla

The taxon name was created in the 2001 edition of Volume 1 of

Chloroflexus, the name of the type genus of the phylum, a common practice.[3]

In 1987,

Chloroflexus, Herpetosiphon and Thermomicrobium into the "green non-sulfur bacteria and relatives",[4][5] which was temporarily renamed as "Chloroflexi" in Volume One of Bergey's Manual of Systematic Bacteriology.[6]

Chloroflexota being a deep branching phylum (see Bacterial phyla), it was considered in Volume One of Bergey's Manual of Systematic Bacteriology to include a single class with the same name.[6] Since 2001, however, new classes have been created thanks to newly discovered species, and the phylum Chloroflexi is now divided into several classes.

"

Dehalococcoidetes" is a placeholder name given by Hugenholtz & Stackebrandt, 2004,[7] after "Dehalococcoides ethenogenes" a species partially described in 1997.[8] The first species fully described was Dehalogenimonas lykanthroporepellens, by Moe et al. 2009,[9] but in the description of that species the class was not made official nor were families or orders laid out as the two species share only 90% 16S ribosomal RNA identity, meaning that they could fall in different families or even orders.[9]

Recent phylogenetic analysis of the Chloroflexota has found very weak support for the grouping together of the different classes currently part of the phylum.[10] The six classes that make up the phylum did not consistently form a well-supported clade in phylogenetic trees based on concatenated sequences for large datasets of proteins, and no conserved signature indels were identified that were uniquely shared by the entire phylum.[10] However, the classes Chloroflexi and Thermomicrobia were found to group together consistently by both the usual phylogenetic means and the identification of shared conserved signature indels in the 50S ribosomal protein L19 and the enzyme UDP-glucose 4-epimerase.[10] It has been suggested that the phylum Chloroflexi sensu stricto should comprise only the classes Chloroflexi and Thermomicrobia, and the other four classes ("Dehalococcoidetes," Anaerolineae, Caldilineae and Ktedonobacteria) may represent one or more independent phyla branching in the neighborhood of the Chloroflexi.[10]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[11] and National Center for Biotechnology Information (NCBI).[12]

16S rRNA based
LTP_08_2023[13][14][15]
 120 marker proteins based GTDB 08-RS214 (28th April 2023).[16][17][18]
Tepidiformia
Tepidiformales
Tepidiformaceae

Tepidiforma

Dehalococcoidia
Dehalococcoidales
Dehalococcoidaceae
"Caldilineia"
Caldilineales
Caldilineaceae
Ktedonobacteria
Thermogemmatisporales
Thermogemmatisporaceae

Thermogemmatispora

Ktedonobacteriales
Thermosporotrichaceae

Thermosporothrix

Ktedonobacteraceae

Ktedonobacter

Ktedonosporobacteraceae

Ktedonosporobacter

Reticulibacteraceae

Reticulibacter

Dictyobacteraceae
Thermoflexia
Thermoflexales
Thermoflexaceae

Thermoflexus

"Thermomicrobiia"
Sphaerobacterales
Sphaerobacteraceae
Thermomicrobiales
Chloroflexia
Kallotenuales
Kallotenuaceae

Kallotenue

Herpetosiphonales
Herpetosiphonaceae

Herpetosiphon

Chloroflexales
Roseiflexaceae

Roseiflexus

Chloroflexaceae

Heliothrix

Oscillochloris

Chloroflexus
"Limnocylindria"
"Limnocylindrales"
"Limnocylindraceae"

"Ca Aquidulcis"

Ktedonobacteria
Dehalococcoidia
Tepidiformales
Tepidiformaceae

Tepidiforma

Dehalococcoidales
Dehalococcoidaceae
"Caldilineia"
⊞
⊟
Ardenticatenales
Ardenticatenaceae

Ardenticatena

"Caldilineidae"
Caldilineales
Caldilineaceae
"Anaerolineidae"
J036
"Roseilineaceae"

"Ca. Roseilinea"

Thermoflexales
Thermoflexaceae

Thermoflexus

"Promineofilales"
"Promineofilaceae"

"Ca. Promineifilum"

Chloroflexia
"Thermobaculales"
"Thermobaculaceae"

Thermobaculum

Thermomicrobiales
Chloroflexales
Herpetosiphonaceae

Herpetosiphon

Roseiflexaceae
Chloroflexaceae

Chloroflexus

Taxonomy

Genus "Candidatus Caldibacter" corrig. Spieck et al. 2020
Genus "Candidatus Chlorotrichoides" corrig. Oren et al. 2020 ["Candidatus Chlorothrix" Klappenbach & Pierson 2004 non Dyar 1921 non Berger-Perrot 1982[22]]
Genus "Candidatus Nitrocaldera" Spieck et al. 2020
Genus "Candidatus Nitrotheca" Spieck et al. 2020
Genus "Candidatus Poriflexus" Kogawa et al. 2022
Class "Limnocylindria" Mehrshad et al. 2018

Class Ktedonobacteria Cavaletti et al. 2007 emend. Yabe et al. 2010

Class "Umbricyclopia" Mehrshad et al. 2018

Class "Bathosphaeria" Mehrshad et al. 2018

Class Tepidiformia Kochetkova et al. 2020

Class

Dehalococcoidia
Löffler et al. 2013

  • Order
    Dehalococcoidales
    Löffler et al. 2013

Class "Thermofontia" corrig. Ward et al. 2018

Class Ardenticatenia Kawaichi et al. 2013

Class "Caldilineia" Oren, Parte & Garrity 2016 ex Cavalier-Smith 2020

Class Thermoflexia Dodsworth et al. 2014

Class "Anaerolineia" Oren, Parte & Garrity 2016

Class Thermomicrobiia Oren, Parte & Garrity 2016

Class "Spiritibacteria" Williams et al. 2024

Class "Martimicrobia" Williams et al. 2024

Class "Tarhunnaeia" Williams et al. 2024

Class "Uliximicrobia" Williams et al. 2024

Class Chloroflexia Gupta et al. 2013

Etymology

The name Chloroflexi is a Neolatin nominative case masculine plural of

Chlorobiota, whereas "Cyanobacteria" has the root cyanos (κύανος), meaning "blue-green."[29]

Unlike some other phyla, there is no theme root in the name of genera of Chloroflexota, and in fact many genera beginning with "Chloro-" or ending in "-chloris" are either cyanobacteria or chlorobi.

See also

References

  1. S2CID 239887308
    .
  2. PMID 20637628
    .
  3. ISBN 978-0-387-24143-2
    . British Library no. GBA561951.
  4. ^ Holland L. (22 May 1990). "Woese,Carl in the forefront of bacterial evolution revolution". Scientist. 4 (10).
  5. PMID 2439888
    .
  6. ^
    ISBN 978-0-387-24143-2
    . British Library no. GBA561951.
  7. PMID 15545432
    .
  8. PMID 9171062
    .
  9. ^
    PMID 19625421
    .
  10. ^
    S2CID 17656551
    .
  11. ^ J.P. Euzéby. "Chloroflexi". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2018-07-20.
  12. ^ Sayers; et al. "Chloroflexi". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2014-03-20.
  13. ^ "The LTP". Retrieved 20 November 2023.
  14. ^ "LTP_all tree in newick format". Retrieved 20 November 2023.
  15. ^ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
  16. ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  17. ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  18. ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
  19. ^
    PMID 16738111
    .
  20. PMID 14657113
    .
  21. ^
    PMID 17911301
    .
  22. S2CID 23854988
    .
  23. PMID 20495028
    .
  24. PMID 19767365
    .
  25. PMID 21621938
    .
  26. PMID 11823222
    .
  27. Perseus Project
  28. ^ Lewis & Short...
  29. Perseus Project
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