Thermoplasmata: Difference between revisions

Thermoplasmata
	Cuniculiplasma divulgatum
Scientific classification
Domain:	Archaea
Phylum:	Methanobacteriota
Class:	Thermoplasmata; Reysenbach, 2002
Orders
	"Aciduliprofundales"; "Gimiplasmatales"; "Halarchaeoplasmatales"; "Lunaplasmatales"; "Lutacidiplasmatales"; Methanomassiliicoccales; "Proteinoplasmatales"; "Sysuiplasmatales"; Thermoplasmatales; "Yaplasmatales";
Synonyms
	Picrophilea Cavalier-Smith 2002; "Thermoplasmatia" Oren, Parte & Garrity 2016; "Thermoplasmia" Cavalier-Smith 2020;

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In taxonomy, the Thermoplasmata are a class of the Euryarchaeota.^[1]

All are acidophiles, growing optimally at pH below 2. Picrophilus is currently the most acidophilic of all known organisms growing at a minimum pH of 0.06. Many of these organisms do not contain a cell wall, although this is not true in the case of Picrophilus. Most members of Thermoplasmata are thermophilic.

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)^[2] and National Center for Biotechnology Information (NCBI).^[1]

16S rRNA based LTP_06_2022^[3]^[4]^[5]

53 marker proteins based GTDB 09-RS220^[6]^[7]^[8]

Methanomassiliicoccales

Methanomassiliicoccaceae

	Picrophilaceae

	Ferroplasmataceae

	"Proteinoplasmatales" (SG8-5)

	"Yaplasmatales" [RBG-16-68-12]

"Gimiplasmatales"	"Gimiplasmataceae" (UA10834)

"Sysuiplasmatales"

"Sysuiplasmataceae"

Methanomassiliicoccales

	Methanomassiliicoccaceae

	Methanomethylophilaceae

"Halarchaeoplasmatales"	"Halarchaeoplasmataceae" (PWKY01)

"Lutacidiplasmatales"	"Lutacidiplasmataceae" (GCA_022750295)

"Aciduliprofundales"	"Aciduliprofundaceae"

Thermoplasmatales	Thermoplasmataceae

References

^ ^a ^b Sayers; et al. "Thermoplasmata". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2015-08-20.
^ J.P. Euzéby. "Thermoplasmata". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2015-08-20.
^ "The LTP". Retrieved 10 May 2023.
^ "LTP_all tree in newick format". Retrieved 10 May 2023.
^ "LTP_06_2022 Release Notes" (PDF). Retrieved 10 May 2023.
^ "GTDB release 09-RS220". Genome Taxonomy Database. Retrieved 10 May 2024.
^ "ar53_r220.sp_label". Genome Taxonomy Database. Retrieved 10 May 2024.
^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2024.

External links

This Euryarchaeota-related article is a stub. You can help Wikipedia by expanding it.

[NCBI-1] Sayers; et al. "Thermoplasmata". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2015-08-20.

[2] J.P. Euzéby. "Thermoplasmata". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2015-08-20.

[3] "The LTP". Retrieved 10 May 2023.

[4] "LTP_all tree in newick format". Retrieved 10 May 2023.

[5] "LTP_06_2022 Release Notes" (PDF). Retrieved 10 May 2023.

[about-6] "GTDB release 09-RS220". Genome Taxonomy Database. Retrieved 10 May 2024.

[tree-7] "ar53_r220.sp_label". Genome Taxonomy Database. Retrieved 10 May 2024.

[taxon_history-8] "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2024.

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@@ Line 1: / Line 1: @@
+{{Short description|Class of archaea}}
-{{Taxobox
+{{Automatic taxobox
-| domain = [[Archaea]]
+| image = 41598 2016 Article BFsrep39034 Fig2 HTML.webp
-| regnum = [[Euryarchaeota]]
+| image_caption = ''Cuniculiplasma divulgatum''
-| phylum = [[Euryarchaeota]]
-| classis = '''Thermoplasmata''' <small>Reysenbach 2002</small>
+| taxon = Thermoplasmata
+| authority = Reysenbach, 2002
-| subdivision_ranks = [[Order (biology)|Order]]
+| subdivision_ranks = Orders
 | subdivision =
+* "Aciduliprofundales"
-* [[Methanomassiliicoccales]] <small>Iino et al. 2013</small>
+* "Gimiplasmatales"
-** [[Methanomassiliicoccaceae]] <small>Iino et al. 2013</small>
+* "Halarchaeoplasmatales"
-* [[Thermoplasmatales]] <small>Reysenbach 2002</small>
+* "Lunaplasmatales"
-** ''[[Thermogymnomonas]]'' <small>Itoh et al. 2007</small>
+* "Lutacidiplasmatales"
-** [[Ferroplasmaceae]] <small>Golyshina et al. 2000</small>
+* [[Methanomassiliicoccales]]
-** [[Picrophilaceae]] <small>Schleper et al. 1996</small>
+* "Proteinoplasmatales"
-** [[Thermoplasmataceae]] <small>Reysenbach 2002</small>
+* "Sysuiplasmatales"
+* [[Thermoplasmatales]]
+* "Yaplasmatales"
+| synonyms =
+* Picrophilea <small>Cavalier-Smith 2002</small>
+* "Thermoplasmatia" <small>Oren, Parte & Garrity 2016</small>
+* "Thermoplasmia" <small>Cavalier-Smith 2020</small>
 }}
-In [[alpha taxonomy|taxonomy]], the '''Thermoplasmata''' are a [[class (biology)|class]] of the [[Euryarchaeota]].<ref>See the [[National Center for Biotechnology Information|NCBI]] [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=183967 webpage on Thermoplasmata].  Data extracted from the {{cite web | url=ftp://ftp.ncbi.nih.gov/pub/taxonomy/ | title=NCBI taxonomy resources | publisher=[[National Center for Biotechnology Information]] | accessdate=2007-03-19}}</ref>
+In [[alpha taxonomy|taxonomy]], the '''Thermoplasmata''' are a [[class (biology)|class]] of the [[Euryarchaeota]].<ref name=NCBI></ref>
-All are [[acidophile]]s, growing optimally at pH below 2. ''[[Picrophilus]]'' is currently the most [[acidophile|acidophilic]] of all known organisms growing at a minimum pH of 0.06. Many of these organisms do not contain a cell wall, although this is not true in the case of ''[[Picrophilus]]''. Most members of Thermotoplasmata are [[thermophilic]].
+All are [[acidophile]]s, growing optimally at pH below 2. ''[[Picrophilus]]'' is currently the most [[acidophile|acidophilic]] of all known organisms growing at a minimum pH of 0.06. Many of these organisms do not contain a cell wall, although this is not true in the case of ''[[Picrophilus]]''. Most members of Thermoplasmata are [[thermophilic]].
 ==Phylogeny==
-The currently accepted taxonomy is based on the [[List of Prokaryotic names with Standing in Nomenclature]] (LPSN)<ref>{{cite web |author = J.P. Euzéby | url=http://www.bacterio.cict.fr/classifphyla.html#Euryarchaeota |title=Thermoplasmataceae | accessdate=2015-08-20 |publisher=[[List of Prokaryotic names with Standing in Nomenclature]] (LPSN) [http://www.bacterio.cict.fr/introduction.html]}}</ref> and [[National Center for Biotechnology Information]] (NCBI)<ref>{{cite web |author = Sayers|display-authors = etal| url=http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=183967&lvl=4&lin=f&keep=1&srchmode=1&unlock |title=Thermoplasmata |accessdate=2015-08-20 |publisher=[[National Center for Biotechnology Information]] (NCBI) taxonomy database [http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi]}}</ref>
+The currently accepted taxonomy is based on the [[List of Prokaryotic names with Standing in Nomenclature]] (LPSN)<ref>{{cite web | author=J.P. Euzéby | url=https://lpsn.dsmz.de/class/thermoplasmata | title=Thermoplasmata | access-date=2015-08-20 | publisher=[[List of Prokaryotic names with Standing in Nomenclature]] (LPSN)}}</ref> and [[National Center for Biotechnology Information]] (NCBI).<ref name=NCBI>{{cite web |author = Sayers|display-authors = etal| url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=183967&lvl=4&lin=f&keep=1&srchmode=1&unlock |title=Thermoplasmata |access-date=2015-08-20 |publisher=[[National Center for Biotechnology Information]] (NCBI) taxonomy database}}</ref>
-and the phylogeny is based on 16S rRNA-based LTP release 121 by [['The All-Species Living Tree' Project]].<ref>[[All-Species Living Tree Project]].{{cite web | url=http://www.arb-silva.de/fileadmin/silva_databases/living_tree/LTP_release_121/LTPs121_SSU_tree.pdf | title=16S rRNA-based LTP release 121 (full tree) | publisher=[[Silva Comprehensive Ribosomal RNA Database]] [http://www.arb-silva.de/projects/living-tree] | accessdate=2015-08-20}}</ref>
+{| class="wikitable"
-{{Clade | style=font-size:100%;line-height:80%
+|-
-|label1=[[Methanomassiliicoccales]]
+! colspan=1 | 16S rRNA based [[The All-Species Living Tree Project|LTP]]_06_2022<ref>{{cite web|title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=10 May 2023}}</ref><ref>{{cite web|title=LTP_all tree in newick format| url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_06_2022.ntree |access-date=10 May 2023}}</ref><ref>{{cite web|title=LTP_06_2022 Release Notes| url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_06_2022_release_notes.pdf |access-date=10 May 2023}}</ref>
+! colspan=1 | 53 marker proteins based [[Genome Taxonomy Database|GTDB]] 09-RS220<ref name="about">{{cite web |title=GTDB release 09-RS220 |url=https://gtdb.ecogenomic.org/about#4%7C |website=[[Genome Taxonomy Database]]|access-date=10 May 2024}}</ref><ref name="tree">{{cite web |title=ar53_r220.sp_label |url=https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/ar53_r220.sp_labels.tree |website=[[Genome Taxonomy Database]]|access-date=10 May 2024}}</ref><ref name="taxon_history">{{cite web |title=Taxon History |url=https://gtdb.ecogenomic.org/taxon_history/ |website=[[Genome Taxonomy Database]]|access-date=10 May 2024}}</ref>
+|-
+| style="vertical-align:top|
+{{Clade|style=font-size:90%; line-height:90%
 |1={{clade
+  |label1=[[Methanomassiliicoccales]]
-  |1=''Candidatus'' [[Methanogranum caenicola]] <small>Iino et al. 2013</small>
+  |1=[[Methanomassiliicoccaceae]]
-  |2=''Candidatus'' [[Methanomethylophilus alvus]] <small>Borrel et al. 2012</small>
+  |label2=[[Thermoplasmatales]]
-  |3=''Candidatus'' [[Methanoplasma termitum]] <small>Lang et al. 2015</small>
+  |2={{clade
-  |label4=''[[Methanomassiliicoccus]]''
+    |1=[[Thermoplasmataceae]]
-  |4={{clade
+    |2={{clade
-    |1=''Ca.'' [[Methanomassiliicoccus intestinalis|M. intestinalis]] <small>Borrel et al. 2013</small>
+      |1=''[[Thermogymnomonas]]''
-    |2=''[[Methanomassiliicoccus luminyensis|M. luminyensis]]'' <small>Dridi et al. 2012</small>
+      |2={{clade
+        |1=[[Cuniculiplasmataceae]]
+        |2={{clade
+          |1=[[Picrophilaceae]]
+          |2=[[Ferroplasmataceae]]
+           }}
+         }}
+       }}
      }}
    }}
+}}
-|label2=[[Thermoplasmatales]]
+|
-|2={{clade
+{{Clade|style=font-size:90%; line-height:90%
+|1={{clade
   |1={{clade
+    |1={{clade
-    |1=''[[Thermogymnomonas acidicola]]'' <small>Itoh et al. 2007</small>
+      |1="Proteinoplasmatales" (SG8-5)
+      |2="Yaplasmatales" [RBG-16-68-12]
+       }}
     |2={{clade
-      |label1= ''[[Thermoplasma]]''
       |1={{clade
+        |label1="Gimiplasmatales"
-        |1=''[[Thermoplasma acidophilum|T. acidophilum]]'' <small>Darland et al. 1970</small> (type sp.)
+        |1="Gimiplasmataceae" (UA10834)
-        |2=''[[Thermoplasma volcanium|T. volcanium]]'' <small>Segerer et al. 1988</small>
          }}
       |2={{clade
-        |label1= ''[[Picrophilus]]''
+        |label1="Sysuiplasmatales"
-        |1={{clade
+        |1="Sysuiplasmataceae"
+        |label2=[[Methanomassiliicoccales]]
-          |1=''[[Picrophilus oshimae|P. oshimae]]'' <small>Schleper et al. 1996</small> (type sp.)
-          |2=''[[Picrophilus torridus|P. torridus]]'' <small>Zillig et al. 1996</small>
-           }}
-        |label2= [[Ferroplasmaceae]]
         |2={{clade
-          |label1= ''[[Acidiplasma]]''
+          |1=[[Methanomassiliicoccaceae]]
-          |1={{clade
+          |2=[[Methanomethylophilaceae]]
-            |1=''[[Acidiplasma aeolicum|A. aeolicum]]'' <small>Golyshina et al. 2009</small> (type sp.)
-            |2=''[[Acidiplasma cupricumulans|A. cupricumulans]]'' <small>(Hawkes et al. 2008) Golyshina et al. 2009</small>
-             }}
-          |label2= ''[[Ferroplasma]]''
-          |2={{clade
-            |1=?''[[Ferroplasma acidarmanus|F. acidarmanus]]'' ♠ <small>Dopson et al. 2004</small>
-            |2=?''[[Ferroplasma thermophilum|F. thermophilum]]'' ♠ <small>Zhou et al. 2008</small>
-            |3=''[[Ferroplasma acidiphilum|F. acidiphilum]]'' <small>Golyshina et al. 2000</small> (type sp.)
-             }}
            }}
+         }}
+       }}
+     }}
+  |2={{clade
+    |1={{clade
+      |label1="Halarchaeoplasmatales"
+      |1="Halarchaeoplasmataceae" (PWKY01)
+       }}
+    |2={{clade
+      |1={{clade
+        |label1="Lutacidiplasmatales"
+        |1="Lutacidiplasmataceae" (GCA_022750295)
+         }}
+      |2={{clade
+        |label1="Aciduliprofundales"
+        |1="[[Aciduliprofundaceae]]"
+        |label2=[[Thermoplasmatales]]
+        |2=[[Thermoplasmataceae]]
          }}
        }}
@@ Line 70: / Line 100: @@
    }}
 }}
+|}
-Notes:<br>
-♠ Strains found at the [[National Center for Biotechnology Information]] (NCBI) but not listed in the [[List of Prokaryotic names with Standing in Nomenclature]] LPSN
+==See also==
+* [[List of Archaea genera]]
 ==References==
+{{Reflist|1}}
-{{reflist|1}}
 ==Further reading==
 ===Scientific journals===
-* {{cite journal|last1=Li|first1=Chao Lun|last2=Jiang|first2=Yun Tao|last3=Liu|first3=Da Li|last4=Qian|first4=JieLei|last5=Liang|first5=Jing Ping|last6=Shu|first6=Rong|title=Prevalence and quantification of the uncommon Archaea phylotype Thermoplasmata in chronic periodontitis|journal=Archives of Oral Biology|date=August 2014|volume=59|issue=8|pages=822–828|doi=10.1016/j.archoralbio.2014.05.011}}
+* {{cite journal|last1=Li|first1=Chao Lun|last2=Jiang|first2=Yun Tao|last3=Liu|first3=Da Li|last4=Qian|first4=JieLei|last5=Liang|first5=Jing Ping|last6=Shu|first6=Rong|title=Prevalence and quantification of the uncommon Archaea phylotype Thermoplasmata in chronic periodontitis|journal=Archives of Oral Biology|date=August 2014|volume=59|issue=8|pages=822–828|doi=10.1016/j.archoralbio.2014.05.011|pmid=24859768}}
+* {{cite journal|last1=Poulsen|first1=Morten|last2=Schwab|first2=Clarissa|last3=Jensen|first3=Bent Borg|last4=Engberg|first4=Ricarda M.|last5=Spang|first5=Anja|last6=Canibe|first6=Nuria|last7=Hojberg|first7=Ole|title=Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen|journal=Nature Communications|date=June 2013|volume=4|issue=1428|page=1947 |doi=10.1038/ncomms2847|bibcode=2013NatCo...4.1947P|doi-access=free}}
+* {{cite journal | last = Cavalier-Smith | first = T | date = 2002 | title = The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification | journal = Int. J. Syst. Evol. Microbiol. | volume = 52 | pages = 7–76 | pmid = 11837318 | issue = Pt 1 | doi=10.1099/00207713-52-1-7| doi-access = free }}
-* {{cite journal|last1=Poulsen|first1=Morten|last2=Schwab|first2=Clarissa|last3=Jensen|first3=Bent Borg|last4=Engberg|first4=Ricarda M.|last5=Spang|first5=Anja|last6=Canibe|first6=Nuria|last7=Hojberg|first7=Ole|title=Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen|journal=NATURE COMMUNICATIONS|date=June 2013|volume=4|issue=1428|doi=10.1038/ncomms2847}}
-* {{cite journal | last = Cavalier-Smith | first = T | date = 2002 | title = The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification | journal =  Int. J. Syst. Evol. Microbiol.  | volume =  52 | pages = 7–76 | pmid = 11837318 | issue = Pt 1}}
+* {{cite journal | last = Woese | first = CR |author2=Kandler O |author3=Wheelis ML | date = 1990 | title = Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya | journal = Proc. Natl. Acad. Sci. USA | volume = 87 | pages = 4576–4579 | pmid = 2112744 | doi = 10.1073/pnas.87.12.4576 | issue = 12 | pmc = 54159 | bibcode=1990PNAS...87.4576W| doi-access = free }}
-* {{cite journal | last = Woese | first = CR |author2=Kandler O |author3=Wheelis ML  | date = 1990 | title = Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya | journal =  Proc. Natl. Acad. Sci. USA  | volume =  87 | pages = 4576–4579 | pmid = 2112744 | doi = 10.1073/pnas.87.12.4576 | issue = 12 | pmc = 54159 | bibcode=1990PNAS...87.4576W}}
 ===Scientific books===
+* {{cite book | last = Reysenbach | first = AL | date = 2001 | chapter = Class IV. Thermoplasmata class. nov. | title = Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria | edition = 2nd | editor = DR Boone | editor2 = RW Castenholz | publisher = Springer Verlag | location = New York | isbn = 978-0-387-98771-2 | page = [https://archive.org/details/bergeysmanualofs00boon/page/169 169] | chapter-url-access = registration | chapter-url = https://archive.org/details/bergeysmanualofs00boon/page/169 }}
-* {{cite book | last = Reysenbach | first = AL | date = 2001 | chapter = Class IV. Thermoplasmata class. nov. | title = Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria | edition = 2nd | editor = DR Boone | editor2 = RW Castenholz | publisher = Springer Verlag | location = New York | isbn = 978-0-387-98771-2 | page = 169 }}
+* {{cite book | author = Garrity GM | author2 = Holt JG | date = 2001 | chapter = Phylum AII. Euryarchaeota phy. nov. | title = Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria | edition = 2nd | editor = DR Boone | editor2 = RW Castenholz | publisher = Springer Verlag | location = New York | isbn = 978-0-387-98771-2 | page = [https://archive.org/details/bergeysmanualofs00boon/page/169 169] | chapter-url-access = registration | chapter-url = https://archive.org/details/bergeysmanualofs00boon/page/169 }}
-* {{cite book | author = Garrity GM | author2 =  Holt JG | date = 2001 | chapter = Phylum AII. Euryarchaeota phy. nov. | title = Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria | edition = 2nd | editor = DR Boone | editor2 = RW Castenholz | publisher = Springer Verlag | location = New York | isbn = 978-0-387-98771-2 | page = 169 }}
-===Scientific databases===
-{{Taxonomic references|taxon=Thermoplasmata}}
 ==External links==
-{{Taxonomic links|microbe=yes|NCBI_taxID=183967|taxoname=Thermoplasmata|LSPN_letter=t|LSPN_taxoname=thermoplasmata}}
 {{Archaea classification}}
+{{Taxonbar|from=Q1135456}}
-[[Category:Archaea taxonomic classes]]
+[[Category:Archaea classes]]
 [[Category:Euryarchaeota]]
 {{Euryarchaeota-stub}}