Chloroflexota

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Chloroflexota
Scientific classification OOjs UI icon edit-ltr.svg
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 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 (green non-sulfur bacteria); and anaerobic halorespirers, which uses halogenated organics (such as the toxic chlorinated ethenes and polychlorinated biphenyls) as electron acceptors.

Contents

The members of the phylum Chloroflexota are monoderms (that is, have one cell membrane with no outer membrane), but they stain mostly gram-negative. [2] Many well-studied phyla of bacteria are diderms and stain 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

The taxon name was created in the 2001 edition of Volume 1 of Bergey's Manual of Systematic Bacteriology and is the Latin plural of the name Chloroflexus , the name of the type genus of the phylum, a common practice. [3]

In 1987, Carl Woese, regarded as one of the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences and grouped the genera 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_10_2024 [13] [14] [15] 120 marker proteins based GTDB 09-RS220 [16] [17] [18]
Thermoflexia
Thermoflexales
Thermoflexaceae

Thermoflexus

Chloroflexota
"Thermomicrobiia"
Chloroflexia
Kallotenuales
Kallotenuaceae

Kallotenue

Herpetosiphonales
Herpetosiphonaceae

Herpetosiphon

Ktedonobacteria
Thermogemmatisporales
Thermogemmatisporaceae

Thermogemmatispora

Ktedonobacteriales
Thermosporotrichaceae

Thermosporothrix

Ktedonosporobacteraceae

Ktedonosporobacter

Reticulibacteraceae

Reticulibacter

Ktedonobacteraceae
Dictyobacteraceae
"Caldilineia"
Caldilineales
Caldilineaceae
Ardenticatenia
Aggregatilineales
Aggregatilineaceae

Aggregatilinea

Ardenticatenales
Ardenticatenaceae

Ardenticatena

"Anaerolineia"
"Dormibacteria"
"Dormibacterales"
"Dormibacteraceae"

"Ca Dormiibacter"

"Limnocylindria"
"Limnocylindrales"
"Limnocylindraceae"

"Ca Aquidulcis"

Chloroflexia
"Thermobaculales"
"Thermobaculaceae"

Thermobaculum

Thermomicrobiales
Chloroflexales
Kallotenuaceae

Kallotenue

Herpetosiphonaceae

Herpetosiphon

Roseiflexaceae
Chloroflexaceae
Dehalococcoidia
Tepidiformales
Tepidiformaceae
"Lucifugimonadales"
"Lucifugimonadaceae"

"Ca. Lucifugimonas" [SAR202; UBA1151]

"Australimonadales"
"Australimonadaceae"

"Ca. Australimonas" [UBA2963]

"Monstramariales"
"Monstramariaceae"

" Carboxydicoccus " [UBA11650]

"Caldilineia"
Ardenticatenales
Ardenticatenaceae

Ardenticatena

"Epilineales"
"Epilineaceae"

"Ca. Avedoeria"

"Ca. Epilinea"

"Caldilineidae"
Caldilineales
Caldilineaceae
"Anaerolineidae"
J036
"Roseilineaceae"
Thermoflexales
Thermoflexaceae

Thermoflexus

"Promineofilales"
"Promineofilaceae"

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
Class "Bathosphaeria" Mehrshad et al. 2018

Class "Martimicrobia" Williams et al. 2024

Class "Poriflexia" Mehrshad et al. 2018

Class "Spiritibacteria" Williams et al. 2024

Class "Tarhunnaeia" Williams et al. 2024

Class "Uliximicrobia" Williams et al. 2024

Class "Umbricyclopia" Mehrshad et al. 2018

Class "Limnocylindria" Mehrshad et al. 2018

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

Class Thermomicrobiia Oren, Parte & Garrity 2016

Class Chloroflexia Gupta et al. 2013

Class Tepidiformia Kochetkova et al. 2020

Class Dehalococcoidia Löffler et al. 2013

Class Ardenticatenia Kawaichi et al. 2013

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

Class Thermoflexia Dodsworth et al. 2014

Class "Thermofontia" corrig. Ward et al. 2018

Class "Anaerolineia" Oren, Parte & Garrity 2016

Etymology

The name Chloroflexi is a Neolatin nominative case masculine plural of Chloroflexus , which is the name of the first genus described. The noun is a combination of the Greek adjective chloros, -a, on (χλωρός, -ά, -όν), [27] meaning "greenish-yellow," and the Latin masculine passive perfect participle flexus (of flecto), [28] meaning "bent." [6] The etymology is unrelated to chlorine, an element that was discovered in 1810 by Sir Humphry Davy and named after its pale green colour. Another phylum with the same root is 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

Related Research Articles

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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.

<span class="mw-page-title-main">Spirochaete</span> Phylum of bacteria

A spirochaete or spirochete is a member of the phylum Spirochaetota, 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.

The Chloroflexia are a class of bacteria in the phylum Chloroflexota. Chloroflexia are typically filamentous, and can move about through bacterial gliding. It is named after the order Chloroflexales.

<span class="mw-page-title-main">Verrucomicrobiota</span> Phylum of bacteria

Verrucomicrobiota 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 from genus Xiphinema, residing in their gametes. The verrucomicrobial bacterium Akkermansia muciniphila is a human intestinal symbiotic bacterium that is considered as a promising probiotic.

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">Chlamydiota</span> Phylum of bacteria

The Chlamydiota are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. Historically it was believed that all Chlamydiota had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins.

Fibrobacterota is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus Fibrobacter was removed from the genus Bacteroides in 1988.

Nitrospirota is a phylum of bacteria. It includes multiple genera, such as Nitrospira, the largest. The first member of this phylum, Nitrospira marina, was discovered in 1985. The second member, Nitrospira moscoviensis, was discovered in 1995.

Armatimonadota is a phylum of gram-negative bacteria.

Dehalococcoidia is a class of Chloroflexota, a phylum of Bacteria. It is also known as the DHC group.

There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.

Chloroflexales is an order of bacteria in the class Chloroflexia. The clade is also known as filamentous anoxygenic phototrophic bacteria (FAP), as the order contains phototrophs that do not produce oxygen. These bacteria are facultative aerobic. They generally use chemotrophy when oxygen is present and switch to light-derived energy when otherwise. Most species are heterotrophs, but a few are capable of photoautotrophy.

Anaerolineaceae is a family of bacteria from the order of Anaerolineales. Anaerolineaceae bacteria occur in marine sediments. There are a total of twelve genera in this family, most of which only encompass one species. All known members of the family are Gram-negative and non-motile. They also do not form bacterial spores and are either mesophilic or thermophilic obligate anaerobes. It is also known that all species in this family are chemoheterotrophs.

Bellilinea is a thermophilic bacteria genus from the family of Anaerolineaceae with one known species. Bellilinea caldifistulae has been isolated from thermophilic digester sludge from Niigata in Japan.

Flexilinea is a bacterial genus from the family of Anaerolineaceae with one known species. Flexilinea flocculi has been isolated from methanogenic granular sludge.

Leptolinea is a bacteria genus from the family of Anaerolineaceae with one known species.

Levilinea is a bacteria genus from the family of Anaerolineaceae with one known species.

Longilinea is a bacteria genus from the family of Anaerolineaceae with one known species.

Nitrospinota is a bacterial phylum. Despite only few described species, members of this phylum are major nitrite-oxidizing bacteria in surface waters in oceans. By oxidation of nitrite to nitrate they are important in the process of nitrification in marine environments.

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