Thermoplasmatales: Difference between revisions

Thermoplasmatales
	Cuniculiplasma divulgatum
Scientific classification
Domain:	Archaea
Kingdom:	Euryarchaeota
Phylum:	Euryarchaeota
Class:	Thermoplasmata
Order:	Thermoplasmatales; Reysenbach 2002
Families
	Thermogymnomonas; Cuniculiplasmataceae; Ferroplasmataceae; Picrophilaceae; Thermoplasmataceae;
Synonyms
	Picrophilales Cavalier-Smith 2002;

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In taxonomy, the Thermoplasmatales are an order of the Thermoplasmata.^[1] All are acidophiles, growing optimally at pH below 2. Picrophilus is currently the most acidophilic of all known organisms, being capable of growing at a pH of -0.06.^[2] Many of these organisms do not contain a cell wall, although this is not true in the case of Picrophilus. Most members of the Thermotoplasmata are thermophilic.

Phylogeny[edit]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)^[3] and National Center for Biotechnology Information (NCBI).^[1]

16S rRNA based LTP_06_2022^[4]^[5]^[6]

53 marker proteins based GTDB 08-RS214^[7]^[8]^[9]

Thermoplasmatales

Thermoplasmataceae	Thermoplasma

Thermogymnomonas

Cuniculiplasmataceae	Cuniculiplasma

Picrophilaceae

Picrophilus

Ferroplasmataceae

	Acidiplasma

	Ferroplasma

Thermoplasmataceae

Thermoplasma

	Cuniculiplasma

	Thermogymnomonas

Picrophilus

	Acidiplasma

	Ferroplasma

References[edit]

^ ^a ^b Sayers; et al. "Thermoplasmataceae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2011-06-05.
^ Life in the Universe: Expectations and Constraints
^ J.P. Euzéby. "Thermoplasmataceae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Archived from the original on 2011-06-13. Retrieved 2011-11-17.
^ "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 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
^ "ar53_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.

Madigan, M.T. & Martinko, J.M. (2005). Brock Biology of Microorganisms (11th ed.). Pearson Prentice Hall.

Further reading[edit]

Scientific journals[edit]

Hubrt, Harald; Stetter, Karl O. (2006). Prokaryotes. pp. 101–102. doi:10.1007/0-387-30743-5_7. ISBN 978-0-387-25493-7. {{cite book}}: |journal= ignored (help)
Oueriaghli, Nahid; Bejar, Victoria; Quesada, Emilia; Martinez-Checa, Fernando (2013). "Molecular Ecology Techniques Reveal Both Spatial and Temporal Variations in the Diversity of Archaeal Communities within the Athalassohaline Environment of Rambla Salada, Spain". Microbial Ecology. 66 (2): 297–311. doi:10.1007/s00248-013-0176-5. PMID 23354292. S2CID 18200481.
Paul, Kristina; Nonoh, James O.; Mikulski, Lena; Brune, Andreas (2012). ""Methanoplasmatales," Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens". Applied and Environmental Microbiology. 78 (23): 8245–8253. Bibcode:2012ApEnM..78.8245P. doi:10.1128/AEM.02193-12. PMC 3497382. PMID 23001661.
Snelling, Timothy J; Genc, Bugra; McKain, Nest; Watson, Mick; Waters, Sinead M.; Creevey, Christopher J.; Wallace, R. John (2014). "Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods". PLOS ONE. 9 (9): e106491. Bibcode:2014PLoSO...9j6491S. doi:10.1371/journal.pone.0106491. PMC 4175461. PMID 25250654.

Scientific books[edit]

Reysenbach, A-L (2001). "Order I. Thermoplasmatales ord. nov.". In DR Boone; RW Castenholz (eds.). Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria (2nd ed.). New York: Springer Verlag. p. 169. ISBN 978-0-387-98771-2.
Reysenbach, A-L (2001). "Class IV. Thermoplasmata class. nov.". In DR Boone; RW Castenholz (eds.). Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria (2nd ed.). New York: Springer Verlag. p. 169. ISBN 978-0-387-98771-2.

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

[NCBI-1] Sayers; et al. "Thermoplasmataceae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2011-06-05.

[2] Life in the Universe: Expectations and Constraints

[3] J.P. Euzéby. "Thermoplasmataceae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Archived from the original on 2011-06-13. Retrieved 2011-11-17.

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

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

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

[about-7] "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.

[tree-8] "ar53_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.

[taxon_history-9] "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.

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@@ Line 1: / Line 1: @@
+{{Short description|Order of archaea}}
 {{Taxobox
+| image = 41598 2016 Article BFsrep39034 Fig2 HTML.webp
+| image_caption = ''Cuniculiplasma divulgatum''
 | domain = [[Archaea]]
 | regnum = [[Euryarchaeota]]
 | phylum = [[Euryarchaeota]]
-| classis = [[Thermoplasmata]] <small>Reysenbach 2002</small>
+| classis = [[Thermoplasmata]]
-| ordo = '''Thermoplasmatales''' <small>Reysenbach 2002<small>
+| ordo = '''Thermoplasmatales'''
-| ordo_authority =
+| ordo_authority = Reysenbach 2002
 | subdivision_ranks = [[Family (biology)|Families]]
 | subdivision =
-*''[[Thermogymnomonas]]'' <small>Itoh et al. 2007</small>
+* ''[[Thermogymnomonas]]''
+* [[Cuniculiplasmataceae]]
-*[[Ferroplasmaceae]] <small>Golyshina et al. 2000</small>
+* [[Ferroplasmataceae]]
-**''[[Acidiplasma]]'' <small>Golyshina et al. 2009</small>
+* [[Picrophilaceae]]
-**''[[Ferroplasma]]'' <small>Golyshina et al. 2000 emend. Hawkes et al. 2008</small>
+* [[Thermoplasmataceae]]
-*[[Picrophilaceae]] <small>Schleper et al. 1996</small>
+| synonyms =
-**''[[Picrophilus]]'' <small>Schleper et al. 1996</small>
-*[[Thermoplasmataceae]] <small>Reysenbach 2002</small>
+* Picrophilales <small>Cavalier-Smith 2002</small>
-**''[[Thermoplasma]]'' <small>Darland et al. 1970</small>
 }}
-In [[alpha taxonomy|taxonomy]], the '''Thermoplasmatales''' are an [[order (biology)|order]] of the [[Thermoplasmata]].<ref>See the [[National Center for Biotechnology Information|NCBI]] [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2301 webpage on Thermoplasmatales].  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>  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.<ref>[http://books.google.com/books?id=qdjoTGAvrkkC&pg=PA57&lpg=PA57&dq=picrophilus+%22-0.06%22&source=bl&ots=-QoE-Gm98d&sig=S6509kGJi7kliQ0pQXoGpNrB1Ys&hl=ja&ei=Q57MSpP5K4zm6gOY2_GHAw&sa=X&oi=book_result&ct=result&resnum=34#v=onepage&q=picrophilus%20%22-0.06%22&f=false Life in the Universe: Expectations and Constraints ]</ref> Many of these organisms do not contain a cell wall, although this is not true in the case of ''[[Picrophilus]]''. Most of members of the Thermotoplasmata are [[thermophilic]].
+In [[alpha taxonomy|taxonomy]], the '''Thermoplasmatales''' are an [[order (biology)|order]] of the [[Thermoplasmata]].<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, being capable of growing at a pH of -0.06.<ref>[https://books.google.com/books?id=qdjoTGAvrkkC&dq=picrophilus+%22-0.06%22&pg=PA57 Life in the Universe: Expectations and Constraints ]</ref> Many of these organisms do not contain a cell wall, although this is not true in the case of ''[[Picrophilus]]''. Most members of the Thermotoplasmata 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=2011-11-17 |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 et al.| url=http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=183967&lvl=4&lin |title=Thermoplasmataceae |accessdate=2011-06-05 |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=http://www.bacterio.cict.fr/classifphyla.html#Euryarchaeota | title=Thermoplasmataceae | access-date=2011-11-17 | publisher=[[List of Prokaryotic names with Standing in Nomenclature]] (LPSN) | url-status=dead | archiveurl=https://web.archive.org/web/20110613224152/http://www.bacterio.cict.fr/classifphyla.html#Euryarchaeota | archivedate=2011-06-13 }}</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=Undef&id=183967&lvl=4&lin |title=Thermoplasmataceae |access-date=2011-06-05 |publisher=[[National Center for Biotechnology Information]] (NCBI) taxonomy database}}</ref>
-and the phylogeny is based on 16S rRNA-based LTP release 106 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_106/LTPs106_SSU_tree.pdf | title=16S rRNA-based LTP release 106 (full tree) | publisher=[[Silva Comprehensive Ribosomal RNA Database]] [http://www.arb-silva.de/projects/living-tree] | accessdate=2011-11-17}}</ref>
+{| class="wikitable"
-{{Clade
+|-
+! 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]] 08-RS214<ref name="about">{{cite web |title=GTDB release 08-RS214 |url=https://gtdb.ecogenomic.org/about#4%7C |website=[[Genome Taxonomy Database]]|access-date=10 May 2023}}</ref><ref name="tree">{{cite web |title=ar53_r214.sp_label |url=https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/ar53_r214.sp_labels.tree |website=[[Genome Taxonomy Database]]|access-date=10 May 2023}}</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 2023}}</ref>
+|-
+| style="vertical-align:top|
+{{Clade|style=font-size:90%; line-height:90%
+|label1=Thermoplasmatales
 |1={{clade
+  |1={{clade
-  |1=''[[Thermogymnomonas acidicola]]'' <small>Itoh et al. 2007</small>
+    |label1=[[Thermoplasmataceae]]
+    |1=''[[Thermoplasma]]''
+     }}
   |2={{clade
-    |label1=&nbsp; ''[[Thermoplasma]]''
+    |1=''[[Thermogymnomonas]]''
-    |1={{clade
-      |1=''[[Thermoplasma acidophilum|T. acidophilum]]'' <small>Darland et al. 1970</small> (type sp.)
-      |2=''[[Thermoplasma volcanium|T. volcanium]]'' <small>Segerer et al. 1988</small>
-       }}
     |2={{clade
-      |label1=&nbsp; ''[[Picrophilus]]''
       |1={{clade
+        |label1=[[Cuniculiplasmataceae]]
-        |1=''[[Picrophilus oshimae|P. oshimae]]'' <small>Schleper et al. 1996</small> (type sp.)
-        |2=''[[Picrophilus torridus|P. torridus]]'' <small>Zillig et al. 1996</small>
+        |1=''[[Cuniculiplasma]]''
          }}
-      |label2=&nbsp; [[Ferroplasmaceae]]
       |2={{clade
-        |label1=&nbsp; ''[[Acidiplasma]]''
+        |label1=[[Picrophilaceae]]
-        |1={{clade
+        |1=''[[Picrophilus]]''
+        |label2= [[Ferroplasmaceae|Ferroplasmataceae]]
-          |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=&nbsp; ''[[Ferroplasma]]''
         |2={{clade
-          |1=?''[[Ferroplasma acidarmanus|F. acidarmanus]]'' ♠ <small>Dopson et al. 2004</small>
+          |1=''[[Acidiplasma]]''
-          |2=?''[[Ferroplasma thermophilum|F. thermophilum]]'' ♠ <small>Zhou et al. 2008</small>
+          |2=''[[Ferroplasma]]''
-          |3=''[[Ferroplasma acidiphilum|F. acidiphilum]]'' <small>Golyshina et al. 2000</small> (type sp.)
            }}
          }}
@@ Line 57: / Line 58: @@
    }}
 }}
+|
-Notes:<br>
+{{Clade|style=font-size:90%; line-height:90%
-♠ Strains found at the [[National Center for Biotechnology Information]] (NCBI) but not listed in the [[List of Prokaryotic names with Standing in Nomenclature]] LPSN
+|label1=[[Thermoplasmataceae]]
+|1={{clade
+  |1=''[[Thermoplasma]]''
+  |2={{clade
+    |1={{clade
+      |1=''[[Cuniculiplasma]]''
+      |2=''[[Thermogymnomonas]]''
+       }}
+    |2={{clade
+      |1=''[[Picrophilus]]''
+      |2={{clade
+        |1=''[[Acidiplasma]]''
+        |2=''[[Ferroplasma]]''
+         }}
+       }}
+     }}
+   }}
+}}
+|}
+==See also==
+* [[List of Archaea genera]]
 ==References==
+{{Reflist|1}}
+* {{cite book | author=Madigan, M.T. | author2=Martinko, J.M. | name-list-style=amp | title=Brock Biology of Microorganisms | edition=11th | publisher=Pearson Prentice Hall | date=2005 }}
-{{reflist|1}}
-* {{cite book | author=Madigan, M.T. and Martinko, J.M. | title=Brock Biology of Microorganisms, 11th Ed. | publisher=Pearson Prentice Hall | year=2005 }}
 ==Further reading==
 ===Scientific journals===
+* {{cite book|last1=Hubrt|first1=Harald|last2=Stetter|first2=Karl O.|title=Prokaryotes|journal=Thermoplasmatales|date=2006|issue=The Prokaryotes|pages=101–102|doi=10.1007/0-387-30743-5_7|isbn=978-0-387-25493-7}}
+* {{cite journal|last1=Oueriaghli|first1=Nahid|last2=Bejar|first2=Victoria|last3=Quesada|first3=Emilia|last4=Martinez-Checa|first4=Fernando|title=Molecular Ecology Techniques Reveal Both Spatial and Temporal Variations in the Diversity of Archaeal Communities within the Athalassohaline Environment of Rambla Salada, Spain|journal=Microbial Ecology|volume=66|issue=2|pages=297–311|doi=10.1007/s00248-013-0176-5|pmid=23354292|year=2013|s2cid=18200481}}<!--|accessdate=12 November 2014-->
+* {{cite journal|last1=Paul|first1=Kristina|last2=Nonoh|first2=James O.|last3=Mikulski|first3=Lena|last4=Brune|first4=Andreas|title="Methanoplasmatales," Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens|journal=Applied and Environmental Microbiology|volume=78|issue=23|pages=8245–8253|doi=10.1128/AEM.02193-12|pmid=23001661|pmc=3497382|year=2012|bibcode=2012ApEnM..78.8245P}}
+* {{cite journal|last1=Snelling|first1=Timothy J|last2=Genc|first2=Bugra|last3=McKain|first3=Nest|last4=Watson|first4=Mick|last5=Waters|first5=Sinead M.|last6=Creevey|first6=Christopher J.|last7=Wallace|first7=R. John|title=Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods|volume=9|issue=9|page=e106491|doi=10.1371/journal.pone.0106491|pmid=25250654|pmc=4175461|journal=PLOS ONE|bibcode=2014PLoSO...9j6491S|year=2014|doi-access=free}}
 ===Scientific books===
+* {{cite book | last = Reysenbach | first = A-L | date = 2001 | chapter = Order I. Thermoplasmatales ord. 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 = https://archive.org/details/bergeysmanualofs00boon/page/169 }}
+* {{cite book | last = Reysenbach | first = A-L | 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 = https://archive.org/details/bergeysmanualofs00boon/page/169 }}
+{{Archaea classification}}
-* {{cite book | last = Reysenbach | first = A-L | year = 2001 | chapter = Order I. Thermoplasmatales ord. nov. | title = Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the deeply branching and phototrophic Bacteria | edition = 2nd ed. | editor = DR Boone and RW Castenholz, eds. | publisher = Springer Verlag | location = New York | isbn = 978-0-387-98771-2 | page = 169 }}
+{{Taxonbar|from=Q742437}}
-* {{cite book | last = Reysenbach | first = A-L | year = 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 ed. | editor = DR Boone and RW Castenholz, eds. | publisher = Springer Verlag | location = New York | isbn = 978-0-387-98771-2 | page = 169 }}
-===Scientific databases===
-{{Taxonomic references|taxon=Thermoplasmatales}}
-==External links==
-{{Taxonomic links|microbe=yes|NCBI_taxID=2301|taxoname=Thermoplasmatales|LSPN_letter=t|LSPN_taxoname=thermoplasmatales}}
 [[Category:Archaea taxonomic orders]]
+[[Category:Euryarchaeota]]
-{{archaea-stub}}
+{{Euryarchaeota-stub}}
-[[de:Thermoplasmatales]]
-[[uk:Thermoplasmatales]]