Chloroflexi (class)

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Chloroflexia
Scientific classification
Domain:
Bacteria
Phylum:
Chloroflexi
Class:
Chloroflexia

Gupta et al. 2013
Orders & Suborders

Herpetosiphonales
Chloroflexales

Synonyms

Chloroflexia Castenholz 2001

The Chloroflexia are one of six classes of bacteria in the phylum Chloroflexi, 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.

Contents

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

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 Chloroflexi are monoderms and stain mostly Gram negative, whereas most bacteria species are diderms and stain Gram negative, with the Gram positive exceptions of the Firmicutes (low GC Gram positives), Actinobacteria (high GC, Gram positives), and the Deinococcus-Thermus group (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]

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

Taxonomy

The currently accepted taxonomy is as follows: [4] [5] [22]

Additionally, "Kouleothrix aurantiaca" and "Dehalobium chlorocoercia" have not been fully described.

Related Research Articles

Gram-positive bacteria Bacteria that give a positive result in the Gram stain test

In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.

Spirochaete Phylum of bacteria

A spirochaete or spirochete is a member of the phylum Spirochaetes, which contains distinctive diderm (double-membrane) gram-negative bacteria, most of which have long, helically coiled cells. Spirochaetes are chemoheterotrophic in nature, with lengths between 3 and 500 μm and diameters around 0.09 to at least 3 μm.

Green sulfur bacteria Family of bacteria

The green sulfur bacteria (Chlorobiaceae) are a family of obligately anaerobic photoautotrophic bacteria. Together with the non-photosynthetic Ignavibacteriaceae, they form the phylum Chlorobi.

The Aquificota phylum is a diverse collection of bacteria that live in harsh environmental settings. The name Aquificota was given to this phylum based on an early genus identified within this group, Aquifex, which is able to produce water by oxidizing hydrogen. They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods. They are true bacteria as opposed to the other inhabitants of extreme environments, the Archaea.

Deinococcota Phylum of Gram-negative bacteria

Deinococcota is a phylum of bacteria with a single order, Deinococci, that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria. Cavalier-Smith calls this clade Hadobacteria.

<i>Chloroflexus aurantiacus</i> Species of bacterium

Chloroflexus aurantiacus is a photosynthetic bacterium isolated from hot springs, belonging to the green non-sulfur bacteria. This organism is thermophilic and can grow at temperatures from 35 °C to 70 °C. Chloroflexus aurantiacus can survive in the dark if oxygen is available. When grown in the dark, Chloroflexus aurantiacus has a dark orange color. When grown in sunlight it is dark green. The individual bacteria tend to form filamentous colonies enclosed in sheaths, which are known as trichomes.

Verrucomicrobia Phylum of bacteria

Verrucomicrobia is a phylum of Gram-negative bacteria that contains only a few described species. The species identified have been isolated from fresh water, marine and soil environments and human faeces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes residing in their gametes.

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:

The Thermotogae are a phylum of the domain Bacteria. The phylum Thermotogae is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.

A chlorosome is a photosynthetic antenna complex found in green sulfur bacteria (GSB) and some green filamentous anoxygenic phototrophs (FAP). They differ from other antenna complexes by their large size and lack of protein matrix supporting the photosynthetic pigments. Green sulfur bacteria are a group of organisms that generally live in extremely low-light environments, such as at depths of 100 metres in the Black Sea. The ability to capture light energy and rapidly deliver it to where it needs to go is essential to these bacteria, some of which see only a few photons of light per chlorophyll per day. To achieve this, the bacteria contain chlorosome structures, which contain up to 250,000 chlorophyll molecules. Chlorosomes are ellipsoidal bodies, in GSB their length varies from 100 to 200 nm, width of 50-100 nm and height of 15 - 30 nm, in FAP the chlorosomes are somewhat smaller.

The Gemmatimonadetes are a phylum of bacteria established in 2003. The phylum contains two classes Gemmatimonadetes and Longimicrobia.

The Synergistetes is a recently recognized phylum of anaerobic bacteria that show Gram-negative staining and have rod/vibrioid cell shape. Although Synergistetes have a diderm cell envelope, the genes for various proteins involved in lipopolysaccharides biosynthesis have not yet been detected in Synergistetes, indicating that they may have an atypical outer cell envelope. The Synergistetes inhabit a majority of anaerobic environments including animal gastrointestinal tracts, soil, oil wells, and wastewater treatment plants and they are also present in sites of human diseases such as cysts, abscesses, and areas of periodontal disease. Due to their presence at illness related sites, the Synergistetes are suggested to be opportunistic pathogens but they can also be found in healthy individuals in the microbiome of the umbilicus and in normal vaginal flora. Species within this phylum have also been implicated in periodontal disease, gastrointestinal infections and soft tissue infections. Other species from this phylum have been identified as significant contributors in the degradation of sludge for production of biogas in anaerobic digesters and are potential candidates for use in renewable energy production through their production of hydrogen gas. All of the known Synergistetes species and genera are presently part of a single class (Synergistia), order (Synergistiales) and family (Synergistaceae).

The Chloroflexi or Chlorobacteria are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for photosynthesis ; and anaerobic halorespirers, which uses halogenated organics as electron acceptors.

Terrabacteria Taxon of land bacteria

Terrabacteria is a taxon containing approximately two-thirds of prokaryote species, including those in the gram positive phyla as well as the phyla Cyanobacteria, Chloroflexi, and Deinococcus-Thermus.

Bacterial phyla 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.

The Negativicutes are a class of bacteria in the phylum Firmicutes, whose members have a peculiar cell wall with a lipopolysaccharide outer membrane which stains gram-negative, unlike most other members of the Firmicutes. Although several neighbouring Clostridia species also stain gram-negative, the proteins responsible for the unusual diderm structure of the Negativicutes may have actually been laterally acquired from Proteobacteria. Additional research is required to confirm the origin of the diderm cell envelope in the Negativicutes.

Armatimonadota is a phylum of gram-negative bacteria.

The Desulfurobacteriaceae family are bacteria belonging to the Aquificota phylum.

The Coriobacteriia are a class of Gram-positive bacteria within the Actinobacteria 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.

The Eggerthellaceae are a family of Gram-positive, rod- or coccus-shaped Actinobacteria. It is the sole family within the order Eggerthellales.

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. 1 2 3 4 5 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. 1 2 3 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. 1 2 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.
  10. ↑ Campbell C, Sutcliffe IC, Gupta RS (2014). "Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria" (PDF). Arch. Microbiol. 196 (4): 307–310. doi:10.1007/s00203-014-0964-4. PMID   24535491.
  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. ↑ 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.

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