Chloroflexia

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){{LSJ|xlwro/s|χλωρός|ref}} meaning "greenish-yellow" and the Latin flexus (of flecto)Lewis, Charlton T. and Charles Short, A Latin Dictionary. Oxford: Clarendon Press, 1879. [https://www.perseus.tufts.edu/cgi-bin/resolveform?lang=Latin Online version at Perseus] meaning "bent" to mean "a green bending".{{cite book |title=Bergey's Manual of Systematic Bacteriology |volume=2A |article=Introductory Essays |editor-first=George M. |editor-last=Garrity |first1=Don J. |last1=Brenner |first2=Noel R. |last2=Krieg |author3=James T. Staley |publisher=Springer (orig-pub London: Williams & Wilkins) |location=New York |edition=2nd |isbn=978-0-387-24143-2 |page=304 |url=https://www.springer.com/life+sciences/book/978-0-387-24143-2 |date=July 26, 2005 |orig-year=1984 |id=British Library no. GBA561951}} 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.

{{see also|Genomics|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.{{cite journal |vauthors=Gupta RS, Chander P, George S |title=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. |journal= Antonie van Leeuwenhoek |volume=103|issue=1|pages=99–119 |date=2013|pmid=22903492 |doi=10.1007/s10482-012-9790-3 }}{{cite journal |vauthors=Cole JK, Gieler BA, Heisler DL, Palisoc MM, Williams AJ, Dohnalkova AC, Ming H, Yu TT, Dodsworth JA, Li WJ, Hedlund BP |title=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 |journal=Int. J. Syst. Evol. Microbiol. |volume=63 |issue=Part 12 |pages=4675–82 |year=2013 |pmid=23950149 |doi=10.1099/ijs.0.053348-0}}{{cite journal |vauthors=Gupta RS, Mukhtar T, Singh B |title=Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): Implications regarding the origin of photosynthesis |journal=Mol Microbiol |volume=32 |issue=5 |pages=893–906 |year=1999 |pmid=10361294 |doi=10.1046/j.1365-2958.1999.01417.x}}{{cite web |author1=Sayers |url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=32061&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&srchmode=1&keep=1&unlock |title=Chloroflexia |publisher=National Center for Biotechnology Information (NCBI) |series=taxonomy database |accessdate=2016-10-25 |df=dmy-all |display-authors=etal}}{{cite journal |vauthors=Euzeby J |title= List of new names and new combinations previously effectively, but not validly, published |journal=Int. J. Syst. Evol. Microbiol. |volume=63 |pages=1577–1580 |year=2013 |doi=10.1099/ijs.0.052571-0 |pmc=}} 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.

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).{{cite journal |last1=Sutcliffe |first1=I.C. |title=A phylum level perspective on bacterial cell envelope architecture |doi=10.1016/j.tim.2010.06.005 |journal=Trends in Microbiology |volume=18 |issue=10 |pages=464–470 |year=2010 |pmid=20637628}}{{cite journal |vauthors=Campbell C, Sutcliffe IC, Gupta RS |title= Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria |journal=Arch. Microbiol. |volume=196 |issue=4 |pages=307–310 |year=2014 |pmid=24535491 |doi=10.1007/s00203-014-0964-4 |url=http://nrl.northumbria.ac.uk/16439/1/AOMI-D-14-00009.pdf}}{{cite journal |vauthors=Gupta RS |title=Evolutionary relationships among photosynthetic bacteria |journal=Photosynth Res |volume=76 |issue=1–3 |pages=173–183 |date=2003 |pmid=16228576 |doi=10.1023/A:1024999314839 |url=http://ovidsp.ovid.com/ovidweb.cgi?T=JS&PAGE=linkout&SEARCH=16228576.ui}}

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. 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.{{cite journal |author=Gupta, R.S. |title=Impact of genomics on the understanding of microbial evolution and classification: The importance of Darwin's views on classification |journal=FEMS Microbiol. Rev. |volume=40 |issue=4 |pages=520–553 |year=2016 |pmid=27279642 |doi=10.1093/femsre/fuw011 |doi-access=free }}{{cite journal |last1=Gupta |first1=R.S. |title=Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes |journal=Microbiology and Molecular Biology Reviews |volume=62 |issue=4 |pages=1435–1491 |year=1998 |pmid=9841678 |pmc=98952 |doi=10.1128/MMBR.62.4.1435-1491.1998

}}{{cite journal |last1=Rokas |first1=A. |last2=Holland |first2=P.W. |title=Rare genomic changes as a tool for phylogenetics |journal=Trends in Ecology & Evolution |volume=15 |issue=11 |pages=454–459 |year=2000 |pmid=11050348 |doi=10.1016/S0169-5347(00)01967-4

}}{{cite journal |last1=Gupta |first1=R.S. |last2=Griffiths |first2=E. |title=Critical issues in bacterial phylogeny |journal=Theoretical Population Biology |volume=61 |issue=4 |pages=423–434 |year=2002 |pmid=12167362 |doi=10.1006/tpbi.2002.1589

}}

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.{{cite book |author1=Hanada, S. |author2=Pierson, B.K. |year=2006 |article=The Family Chloroflexaceae |title=The Prokaryotes: A handbook on the biology of bacteria |pages=815–842 |editor1=Dworkin, M. |editor2=Falkow, S. |editor3=Rosenberg, E. |editor4=Schleifer, K.H. |editor5=Stackebrandt, E. |publisher=Springer |place=New York}}{{cite book |author1=Pierson, B.K. |author2=Castenholz, R.W. |year=1992 |article=The Family Chloroflexaceae |title=The Prokaryotes |pages=3754–3775 |editor1=Balows, A. |editor2=Truper, H.G. |editor3=Dworkin, M. |editor4=Harder, W. |editor5=Schleifer, K.H. |publisher=Springer |place=New York}}

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.{{cite journal |vauthors=Gupta RS |title=Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups |journal=Photosynth. Res. |volume=104 |issue=2–3 |pages=357–372 |year=2010 |pmid=20414806 |doi=10.1007/s11120-010-9553-9}}{{cite journal |last1=Stolz |first1=F.M. |last2=Hansmann |first2=I. |title=An MspI RFLP detected by probe pFMS76 D20S23 isolated from a flow-sorted chromosome 20-specific DNA library |journal=Nucleic Acids Research |volume=18 |issue=7 |page=1929 |year=1990 |pmid=1692410 |pmc=330654 |doi=10.1093/nar/18.7.1929}}

Additional work has been done using CSIs to demarcate the phylogenetic position of Chloroflexia relative to other photosynthetic groups such as the Cyanobacteria.{{cite journal|author3-link=Robert E. Blankenship |vauthors=Khadka B, Adeolu M, Blankenship RE, Gupta RS |title=Novel insights into the origin and diversification of photosynthesis based on analyses of conserved indels in the core reaction center proteins |journal=Photosynth Res |volume=131 |issue=2 |pages=159–171 |year=2016 |pmid=27638319 |doi=10.1007/s11120-016-0307-1}} Chloroflexia shares a number of CSIs with Chlorobiota in the chlorophyll-synthesizing proteins. As the two lineages are not otherwise closely related, the interpretation is that the CSIs are the result of a horizontal gene transfer event between the two. Chloroflexia in turn acquired these proteins by another HGT from a "Clade C" marine cyanobacteria.{{cite journal |vauthors=Gupta RS |title=Origin and spread of photosynthesis based upon conserved sequence features in key bacteriochlorophyll biosynthesis proteins |journal=Mol Biol Evol |volume=29 |issue=11 |pages=3397–412 |date=2012 |pmid=22628531 |doi=10.1093/molbev/mss145 |doi-access=free }}

{{see also|Bacterial taxonomy}}

The currently accepted taxonomy is as follows:{{lpsn|classifphyla|Classification of Chloroflexi}}

Class Chloroflexia Gupta et al. 2013

• Genus ?"Candidatus Chlorohelix" Tsuji et al. 2024
• Genus ?"Dehalobium" Wu et al. 2002{{Cite journal | last1 = Wu | first1 = Q. | last2 = Watts | first2 = J. E. M. | last3 = Sowers | first3 = K. R. | last4 = May | first4 = H. D. | title = Identification of a Bacterium That Specifically Catalyzes the Reductive Dechlorination of Polychlorinated Biphenyls with Doubly Flanked Chlorines | doi = 10.1128/AEM.68.2.807-812.2002 | journal = Applied and Environmental Microbiology | volume = 68 | issue = 2 | pages = 807–812 | year = 2002 | pmid = 11823222| pmc =126686 | bibcode = 2002ApEnM..68..807W }}
• Genus ?"Candidatus Lithoflexus" Saghai et al. 2020
• Genus ?"Candidatus Sarcinithrix" Nierychlo et al. 2019
• Order "Thermobaculales" Chuvochina et al. 2023
• Family "Thermobaculaceae" Chuvochina et al. 2023
• Genus "Thermobaculum" Botero et al. 2004
• Order Kallotenuales] Cole et al. 2013
• Family Kallotenuaceae Cole et al. 2013
• Genus Kallotenue Cole et al. 2013
• Order Herpetosiphonales Gupta et al. 2013
• Family Herpetosiphonaceae Gupta et al. 2013
• Genus "Candidatus Anthektikosiphon" Ward, Fischer & McGlynn 2020
• Genus Herpetosiphon Holt & Lewin 1968
• Order Chloroflexales Gupta et al. 2013
• Suborder Roseiflexineae Gupta et al. 2013
• Family Roseiflexaceae Gupta et al. 2013 ["Kouleotrichaceae" Mehrshad et al. 2018]
• Genus ?Heliothrix Pierson et al. 1986
• Genus "Kouleothrix" Kohno et al. 2002
• Genus "Candidatus Ribeiella" Petriglieri et al. 2023
• 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"Ward et al. 1998]
• Family Oscillochloridaceae Gupta et al. 2013
• Genus ?Chloronema ♪ Dubinina & Gorlenko 1975
• Genus "Candidatus Chloroploca" Gorlenko et al. 2014
• Genus Oscillochloris Gorlenko & Pivovarova 1989
• Genus "Candidatus Viridilinea" Grouzdev et al. 2018

• List of bacteria genera
• List of bacterial orders
• Green sulfur bacteria

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• {{cite book |vauthors=Garrity GM, Holt JG |year=2001 |chapter=Phylum BVI. Chloroflexi phy. nov |series=Bergey's Manual of Systematic Bacteriology |volume=1 |title=The Archaea and the deeply branching and phototrophic Bacteria |edition=2nd |editor1=Boone, D.R. |editor2=Castenholz, R.W. |page=[https://archive.org/details/bergeysmanualofs00boon/page/169 169] |chapter-url=https://archive.org/details/bergeysmanualofs00boon |publisher=Springer Verlag |location=New York |isbn=978-0-387-98771-2 |chapter-url-access=registration}}

{{Wikispecies}}

{{Bacteria classification}}

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Category:Phototrophic bacteria