Chloroflexia

The Chloroflexia are a class of bacteria in the phylum Chloroflexota, known as filamentous green non-sulfur bacteria. They use light for energy and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes.

Chloroflexia
Scientific classification
Domain: Bacteria
Phylum: Chloroflexota
Class: Chloroflexia
corrig. Gupta et al. 2013
Orders
Synonyms
  • "Chloroflexia" Castenholz 2001
  • "Chlorobacteria" Cavalier-Smith 2002
  • "Chloroflexi" Gupta et al. 2013

Chloroflexia are typically filamentous, and can move about through bacterial gliding. They are facultatively aerobic, but do not produce oxygen in the process of producing energy from light, or phototrophy. Additionally, Chloroflexia have a different method of phototrophy (photoheterotrophy) than true photosynthetic bacteria.

Etymology

The name "Chloroflexi" is a Neolatin plural of "Chloroflexus", which is the name of the first genus described. The noun is a combination of the Greek chloros (χλωρός)[1] meaning "greenish-yellow" and the Latin flexus (of flecto)[2] meaning "bent" to mean "a green bending".[3] The name is not due to chlorine, an element confirmed as such in 1810 by Sir Humphry Davy and named after its pale green colour.

Taxonomy and molecular signatures
See also: Genomics and Conserved signature indels

The Chloroflexia class is a group of deep branching photosynthetic bacteria (with the exception of Herpetosiphon and Kallotenue species) that currently consist of three orders: Chloroflexales, Herpetosiphonales, and Kallotenuales.[4][5][6][7][8] The Herpetosiphonales and Kallotenuales each consist of a single genus within its own family, Herpetosiphonaceae (Herpetosiphon) and Kallotenuaceae (Kallotenue), respectively, whereas the Chloroflexales are more phylogenetically diverse.[4][5][7]

Microscopic distinguishing characteristics

Members of the phylum Chloroflexota are monoderms and stain mostly Gram negative, whereas most bacteria species are diderms and stain Gram negative, with the Gram positive exceptions of the Bacillota (low GC Gram positives), Actinomycetota (high GC, Gram positives), and the Deinococcota (Gram positive, diderms with thick peptidoglycan).[9][10][11]

Genetic distinguishing characteristics

Comparative genomic analysis has recently refined the taxonomy of the class Chloroflexia, dividing the Chloroflexales into the suborder Chloroflexineae consisting of the families Oscillachloridaceae and Chloroflexaceae, and the suborder Roseiflexineae containing family Roseiflexaceae.[4] The revised taxonomy was based on the identification of a number of conserved signature indels (CSIs) which serve as highly reliable molecular markers of shared ancestry.[12][13][14][15]

Physiological distinguishing characteristics

Additional support for the division of the Chloroflexales into two suborders is the observed differences in physiological characteristics where each suborder is characterized by distinct carotenoids, quinones, and fatty acid profiles that are consistently absent in the other suborder.[4][16][17]

In addition to demarcating taxonomic ranks, CSIs may play a role in the unique characteristics of members within the clade: In particular, a four-amino-acid insert in the protein pyruvate flavodoxin/ferredoxin oxidoreductase, a protein which plays important roles in photosynthetic organisms, has been found exclusively among all members in the genus Chloroflexus, and is thought to play an important functional role.[18][19]

Additional work has been done using CSIs to demarcate the phylogenetic position of Chloroflexia relative to neighbouring photosynthetic groups such as the Cyanobacteria.[20]

Chloroflexota species form a distinct lineage with Chlorobiota species, their closest phylogenetic relatives. A CSI has been found to be shared among both Chloroflexota and Chlorobiota members, which has been interpreted as the result of a horizontal gene transfer event between the two relatives.[21]

Phylogeny
16S rRNA based LTP_12_2021[22][23][24] 120 marker proteins based GTDB 07-RS207[25][26][27]
 
"Thermomicrobiia"
Sphaerobacterales
Sphaerobacteraceae
 

Nitrolancea

 
 

Sphaerobacter

 
 
 
Thermomicrobiales
Thermomicrobiaceae
 

Thermomicrobium

 
 

Thermorudis

 
 
 
 
Chloroflexia
 

Kallotenue {Kallotenuales: Kallotenuaceae}

 
 
Herpetosiphonales
Herpetosiphonaceae

Herpetosiphon

 
 
Chloroflexales
Roseiflexaceae

Roseiflexus

 
Chloroflexaceae
 

Heliothrix

 
 
 

Oscillochloris

 
 

Chloroflexus

 
 
 
 
 
 
 
Chloroflexia
 
"Thermobaculales"
"Thermobaculaceae"

Thermobaculum

 
 
Thermomicrobiales
Thermomicrobiaceae
 
 

Nitrolancea

 
 

Sphaerobacter

 
 
 
 

Thermomicrobium

 
 

Thermorudis

 
 
 
 
 
Chloroflexales
 

Herpetosiphon {Herpetosiphonaceae}

 
 
Roseiflexaceae
 

"Kouleothrix"

 
 

Roseiflexus

 
 
Chloroflexaceae
 

Chloroflexus

 
 
 

Oscillochloris

 
 
 

"Ca. Chloroploca"

 
 

"Ca. Viridilinea"

 
 
 
 
 
 
 

Taxonomy
See also: Bacterial taxonomy

The currently accepted taxonomy is as follows:[4][5][28]

Class Chloroflexia Gupta et al. 2013

  • Genus "Dehalobium" Wu et al. 2002[29]
  • Genus "Candidatus Lithoflexus" Saghai et al. 2020
  • Genus "Candidatus Sarcinithrix" Nierychlo et al. 2019
  • Order "Thermobaculales"
    • Family "Thermobaculaceae"
      • Genus "Thermobaculum" Botero et al. 2004
  • Order Kallotenuales Cole et al. 2013
    • F amily Kallotenuaceae Cole et al. 2013
      • Genus Kallotenue Cole et al. 2013
  • Order Herpetosiphonales Gupta et al. 2013
  • Order Chloroflexales Gupta et al. 2013
    • Suborder Roseiflexineae Gupta et al. 2013
      • Family Roseiflexaceae Gupta et al. 2013 ["Kouleotrichaceae" Mehrshad et al. 2018]
        • Genus "Kouleothrix" Kohno et al. 2002
        • Genus Heliothrix Pierson et al. 1986
        • Genus Roseiflexus Hanada et al. 2002
    • Suborder Chloroflexineae Gupta et al. 2013
      • Family Chloroflexaceae Gupta et al. 2013
        • Genus Candidatus Chloranaerofilum Thiel et al. 2016
        • Genus Chloroflexus Pierson & Castenholz 1974 ["Chlorocrinis"]
      • Family Oscillochloridaceae Gupta et al. 2013
        • Genus Candidatus Chloroploca Gorlenko et al. 2014
        • Genus Chloronema ♪ Dubinina & Gorlenko 1975
        • Genus Oscillochloris Gorlenko & Pivovarova 1989
        • Genus Candidatus Viridilinea Grouzdev et al. 2018

See also

References
  1. χλωρός. Liddell, Henry George; Scott, Robert; A Greek–English Lexicon at the Perseus Project
  2. Lewis, Charlton T. and Charles Short, A Latin Dictionary. Oxford: Clarendon Press, 1879. Online version at Perseus
  3. Brenner, Don J.; Krieg, Noel R.; James T. Staley (July 26, 2005) [1984]. "Introductory Essays". In Garrity, George M. (ed.). Bergey's Manual of Systematic Bacteriology. Vol. 2A (2nd ed.). New York: Springer (orig-pub London: Williams & Wilkins). p. 304. ISBN 978-0-387-24143-2. British Library no. GBA561951.
  4. Gupta RS, Chander P, George S (2013). "Phylogenetic framework and molecular signatures for the class Chloroflexia and its different clades; proposal for division of the class Chloroflexia class. nov. [corrected] into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov". Antonie van Leeuwenhoek. 103 (1): 99–119. doi:10.1007/s10482-012-9790-3. PMID 22903492.
  5. Cole JK, Gieler BA, Heisler DL, Palisoc MM, Williams AJ, Dohnalkova AC, Ming H, Yu TT, Dodsworth JA, Li WJ, Hedlund BP (2013). "Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic and filamentous thermophile that represents a novel lineage (Kallotenuales ord. nov., Kallotenuaceae fam. nov.) within the class Chloroflexia". Int. J. Syst. Evol. Microbiol. 63 (Part 12): 4675–82. doi:10.1099/ijs.0.053348-0. PMID 23950149.
  6. Gupta RS, Mukhtar T, Singh B (1999). "Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): Implications regarding the origin of photosynthesis". Mol Microbiol. 32 (5): 893–906. doi:10.1046/j.1365-2958.1999.01417.x. PMID 10361294.
  7. Sayers; et al. "Chloroflexia". taxonomy database. National Center for Biotechnology Information (NCBI). Retrieved 25 October 2016.
  8. Euzeby J (2013). "List of new names and new combinations previously effectively, but not validly, published". Int. J. Syst. Evol. Microbiol. 63: 1577–1580. doi:10.1099/ijs.0.052571-0.
  9. Sutcliffe, I.C. (2010). "A phylum level perspective on bacterial cell envelope architecture". Trends in Microbiology. 18 (10): 464–470. doi:10.1016/j.tim.2010.06.005. PMID 20637628.
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  11. Gupta RS (2003). "Evolutionary relationships among photosynthetic bacteria". Photosynth Res. 76 (1–3): 173–183. doi:10.1023/A:1024999314839. PMID 16228576.
  12. Gupta, R.S. (2016). "Impact of genomics on the understanding of microbial evolution and classification: The importance of Darwin's views on classification". FEMS Microbiol. Rev. 40 (4): 520–553. doi:10.1093/femsre/fuw011. PMID 27279642.
  13. Gupta, R.S. (1998). "Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes". Microbiology and Molecular Biology Reviews. 62 (4): 1435–1491. doi:10.1128/MMBR.62.4.1435-1491.1998. PMC 98952. PMID 9841678.
  14. Rokas, A.; Holland, P.W. (2000). "Rare genomic changes as a tool for phylogenetics". Trends in Ecology & Evolution. 15 (11): 454–459. doi:10.1016/S0169-5347(00)01967-4. PMID 11050348.
  15. Gupta, R.S.; Griffiths, E. (2002). "Critical issues in bacterial phylogeny". Theoretical Population Biology. 61 (4): 423–434. doi:10.1006/tpbi.2002.1589. PMID 12167362.
  16. Hanada, S.; Pierson, B.K. (2006). "The Family Chloroflexaceae". In Dworkin, M.; Falkow, S.; Rosenberg, E.; Schleifer, K.H.; Stackebrandt, E. (eds.). The Prokaryotes: A handbook on the biology of bacteria. New York: Springer. pp. 815–842.
  17. Pierson, B.K.; Castenholz, R.W. (1992). "The Family Chloroflexaceae". In Balows, A.; Truper, H.G.; Dworkin, M.; Harder, W.; Schleifer, K.H. (eds.). The Prokaryotes. New York: Springer. pp. 3754–3775.
  18. Gupta RS (2010). "Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups". Photosynth. Res. 104 (2–3): 357–372. doi:10.1007/s11120-010-9553-9. PMID 20414806.
  19. Stolz, F.M.; Hansmann, I. (1990). "An MspI RFLP detected by probe pFMS76 D20S23 isolated from a flow-sorted chromosome 20-specific DNA library". Nucleic Acids Research. 18 (7): 1929. doi:10.1093/nar/18.7.1929. PMC 330654. PMID 1692410.
  20. Khadka B, Adeolu M, Blankenship RE, Gupta RS (2016). "Novel insights into the origin and diversification of photosynthesis based on analyses of conserved indels in the core reaction center proteins". Photosynth Res. 131 (2): 159–171. doi:10.1007/s11120-016-0307-1. PMID 27638319.
  21. Gupta RS (2012). "Origin and spread of photosynthesis based upon conserved sequence features in key bacteriochlorophyll biosynthesis proteins". Mol Biol Evol. 29 (11): 3397–412. doi:10.1093/molbev/mss145. PMID 22628531.
  22. "The LTP". Retrieved 23 February 2021.
  23. "LTP_all tree in newick format". Retrieved 23 February 2021.
  24. "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
  25. "GTDB release 07-RS207". Genome Taxonomy Database. Retrieved 20 June 2022.
  26. "bac120_r207.sp_labels". Genome Taxonomy Database. Retrieved 20 June 2022.
  27. "Taxon History". Genome Taxonomy Database. Retrieved 20 June 2022.
  28. Classification of Chloroflexi entry in LPSN; Euzéby, J.P. (1997). "List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet". International Journal of Systematic and Evolutionary Microbiology. 47 (2): 590–2. doi:10.1099/00207713-47-2-590. PMID 9103655.
  29. Wu, Q.; Watts, J. E. M.; Sowers, K. R.; May, H. D. (2002). "Identification of a Bacterium That Specifically Catalyzes the Reductive Dechlorination of Polychlorinated Biphenyls with Doubly Flanked Chlorines". Applied and Environmental Microbiology. 68 (2): 807–812. doi:10.1128/AEM.68.2.807-812.2002. PMC 126686. PMID 11823222.

Further reading
  • Garrity GM, Holt JG (2001). "Phylum BVI. Chloroflexi phy. nov". In Boone, D.R., Castenholz, R.W. (eds.). The Archaea and the deeply branching and phototrophic Bacteria. Bergey's Manual of Systematic Bacteriology. Vol. 1 (2nd ed.). New York: Springer Verlag. p. 169. ISBN 978-0-387-98771-2.
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