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''Thermomicrobia'' class. nov. | veditors = Boone DR, Castenholz RW, ((Garrity GM.)) | title = Bergey's Manual of Systematic Bacteriology | edition = 2nd | volume = 1 (The Archaea and the Deeply Branching and Phototrophic Bacteria) | publisher = Springer | location = New York, NY | year = 2001 | pages = 447–450}}</ref> | subdivision_ranks = Orders | subdivision = * [[Sphaerobacterales]] * [[Thermomicrobiales]] | synonyms = * Thermomicrobia: ** "Thermomicrobia" <small>Garrity and Holt 2001</small> ** "Thermomicrobiota" <small>Whitman et al. 2018</small> ** "Thermomicrobaeota" <small>Oren et al. 2015</small> }} The '''Thermomicrobia''' is a group of [[thermophilic]] green non-sulfur [[bacteria]]. Based on species ''Thermomicrobium roseum'' (type species) and ''Sphaerobacter thermophilus'', this bacteria class has the following description:<ref name=":0">{{cite book|title=Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, The Archaea and the Deeply Branching and Phototrophic Bacteria| vauthors = Garrity GM, Holt JG |publisher=Springer|year=2001 | veditors = Boone DR, Castenholz RW, Garrity GM |location=New York|chapter=Phylum BVII. Thermomicrobia phy. nov.}}</ref><ref name=":1">{{cite journal | vauthors = Hugenholtz P, Stackebrandt E | title = Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description) | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 54 | issue = Pt 6 | pages = 2049–51 | date = November 2004 | pmid = 15545432 | doi = 10.1099/ijs.0.03028-0 | doi-access = free }}</ref> The class Thermomicrobia subdivides into two orders with validly published names: ''Thermomicrobiales'' <small>Garrity and Holt 2001</small> and ''Sphaerobacterales'' <small>Stackebrandt,</small> <small>Rainey and Ward-Rainey 1997</small>. Gram negative. Pleomorphic, non-motile, non-spore-forming rods. Non-sporulating. No [[diamino acid]] present. No peptidoglycan in significant amount. Atypical proteinaceous cell walls. Hyper-thermophilic, optimum growth temperature at 70-75&nbsp;°C. Obligatory aerobic and chemoorganotrophic. <ref group=note name=note_2 /> As thermophilic bacteria, members of this class are usually found in environments which are distant from human activity.<ref name="Houghton_2015" /> However, they have features like improved growth in antibiotics and CO oxidizing activity, making them interesting topics of research (e.g. for biotechnology application). == History == In 1973, a strain of rose-pink thermophilic bacteria was isolated from Toadstool Spring in Yellowstone National Park, which was later named ''Thermomicrobium roseum'' and proposed as a novel species of the novel genus ''Thermomicrobium''.<ref name = "Jackson_1973">{{cite journal | vauthors = Jackson TJ, Ramaley RF, Meinschein WG | title = Thermomicrobium, a new genus of extremely thermophilic bacteria. | journal = International Journal of Systematic and Evolutionary Microbiology | date = January 1973 | volume = 23 | issue = 1 | pages = 28–36 | doi = 10.1099/00207713-23-1-28 | doi-access = free }}</ref> At that time the genus was categorized under family Achromobacteraceae, but it became a distinct phylum by 2001.<ref name=":0" /> In 2004, it was proposed, on the basis of an analysis of genetic affiliations, that the Thermomicrobia should more properly be reclassified as a [[class (biology)|class]] belonging to the phylum [[Chloroflexota]] (formerly Chloroflexi). The bacteria ''Sphaerobacter thermophilus'' originally described as an Actinobacteria is now considered a Thermomicrobia.<ref name=":1" /><ref>{{cite journal | vauthors = Boone DR, Baker CC | title = Validation of publication of new names and new combinations previously effectively published outside the IJSEM. | journal = International Journal of Systematic and Evolutionary Microbiology | date = 2002 | volume = 52 | issue = Pt 3 | pages = 685–90 | url = http://ijs.sgmjournals.org/cgi/reprint/52/3/685 | archive-url = https://web.archive.org/web/20100606222954/http://ijs.sgmjournals.org/cgi/reprint/52/3/685 | archive-date = 6 June 2010 | url-status = dead | doi = 10.1099/ijs.0.02358-0 | pmid = 12054225 }}</ref> In the same year, another strain of rose-pink thermophilic bacteria was isolated from Yellowstone National Park, which was named ''Thermobaculum terrenum''.<ref name = "Botero_2004">{{cite journal | vauthors = Botero LM, Brown KB, Brumefield S, Burr M, Castenholz RW, Young M, McDermott TR | title = Thermobaculum terrenum gen. nov., sp. nov.: a non-phototrophic gram-positive thermophile representing an environmental clone group related to the Chloroflexi (green non-sulfur bacteria) and Thermomicrobia | journal = Archives of Microbiology | volume = 181 | issue = 4 | pages = 269–77 | date = April 2004 | pmid = 14745485 | doi = 10.1007/s00203-004-0647-7 | s2cid = 31431143 }}</ref> Later analysis based on genome put this species under Thermomicrobia class.<ref>{{cite journal | vauthors = Kunisawa T | title = The phylogenetic placement of the non-phototrophic, Gram-positive thermophile 'Thermobaculum terrenum' and branching orders within the phylum 'Chloroflexi' inferred from gene order comparisons | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 61 | issue = Pt 8 | pages = 1944–53 | date = August 2011 | pmid = 20833875 | doi = 10.1099/ijs.0.026088-0 | doi-access = free }}</ref> However, the current standing of ''Thermobaculum terrenum'' is disputed.<ref name=":2" /> In 2012, a thermo-tolerant nitrite-oxidizing bacterium was isolated from a bioreactor, which was named ''Nitrolancetus hollandica'' and proposed as a novel species later in 2014.<ref name=":4">{{Cite journal | vauthors = Sorokin DY, Vejmelkova D, Lücker S, Streshinskaya GM, Rijpstra WI, Damste JS, Kleerbezem R, van Loosdrecht M, Muyzer G, Daims H | title = Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi | date = June 2014 |journal=International Journal of Systematic and Evolutionary Microbiology |volume=64 |issue=6 |pages=1859–1865 |doi=10.1099/ijs.0.062232-0 | pmid = 24573161 |doi-access= }}</ref> While it has nitrite-oxidizing activity, which is unique in the Thermomicrobia class, it is placed under the Thermomicrobia class based on 16s rRNA phylogeny.<ref name = "Sorokin_2012">{{cite journal | vauthors = Sorokin DY, Lücker S, Vejmelkova D, Kostrikina NA, Kleerebezem R, Rijpstra WI, Damsté JS, Le Paslier D, Muyzer G, Wagner M, van Loosdrecht MC, Daims H | title = Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi | journal = The ISME Journal | volume = 6 | issue = 12 | pages = 2245–56 | date = December 2012 | pmid = 22763649 | pmc = 3504966 | doi = 10.1038/ismej.2012.70 }}</ref> In 2014, two thermophilic, Gram-positive, rod-shaped, non-spore-forming bacteria (strains KI3<sup>T</sup> and KI4<sup>T</sup>) isolated from geothermally heated biofilms growing on a tumulus in the Kilauea Iki pit crater on the flank of Kilauea Volcano (Hawai'i) were proposed as representatives of new species based on 16s rRNA phylogeny. The KI3<sup>T</sup> strain, later named as ''Thermomicrobium carboxidum'', is closely related to ''Thermomicrobium roseum''. The KI4<sup>T</sup> strain, later named as ''Thermorudis peleae'', was proposed as a type strain of new genus ''Thermorudis''.<ref name="King_2014">{{cite journal | vauthors = King CE, King GM | title = Thermomicrobium carboxidum sp. nov., and Thermorudis peleae gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 64 | issue = Pt 8 | pages = 2586–92 | date = August 2014 | pmid = 24814334 | doi = 10.1099/ijs.0.060327-0 | doi-access = free }}</ref> In 2015, a thermophilic bacteria strain WKT50.2 isolated from geothermal soil in Waitike (New Zealand) was proposed to be a novel species, later named ''Thermorudis pharmacophila''. Phylogenic analysis based on 16s rRNA place it within Thermomicrobia class, as close relative to ''Thermorudis peleae''.<ref name="Houghton_2015" /> == Characteristics == === Living environment === Members of the class Thermomicrobia are broadly distributed across a wide range of both aquatic and terrestrial habitats. ''Thermomicrobium roseum'' was found in geothermally heated hot springs, ''Thermorudis pharmacophila'' and ''Thermobaculum terrenum'' from heated soils, and ''Thermomicrobium carboxidum'' and ''Thermorudis peleae'' from heated sediments<ref name="King_2014"/><ref name="Houghton_2015" /><ref>{{cite journal | vauthors = Costa KC, Navarro JB, Shock EL, Zhang CL, Soukup D, Hedlund BP | title = Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin | journal = Extremophiles | volume = 13 | issue = 3 | pages = 447–59 | date = May 2009 | pmid = 19247786 | doi = 10.1007/s00792-009-0230-x | s2cid = 24375281 }}</ref> In addition, ''Sphaerobacter thermophilus'' was found in sewage sludge that went through thermophilic treatment.<ref name="Demharter_1989" /> The common features of their habitats include temperature ranging from around 65~75&nbsp;°C and a pH around 6.0~8.0 (except for Nitrolancea hollandica which grow around 40&nbsp;°C<ref name=":4" />). === Metabolism === Members of Thermomicrobia class have variation in their basic metabolism. ''Nitrolancetus hollandica'' has nitrifying activity that utilize NO<sub>2</sub><sup>−</sup> as energy source, which is unique in the whole [[Chloroflexota]] phylum.<ref name="Sorokin_2012" /> ''Thermomicrobium spp.'' and ''Sphaerobacter thermophilus'' have constitutive CO oxidizing not found in other species in this class.<ref name="King_2014" /><ref>{{cite journal | vauthors = Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA | title = Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum | journal = PLOS ONE | volume = 4 | issue = 1 | pages = e4207 | date = 2009-01-16 | pmid = 19148287 | pmc = 2615216 | doi = 10.1371/journal.pone.0004207 | bibcode = 2009PLoSO...4.4207W | doi-access = free }}</ref> However, species of this class do share some features, as listed below: * All members except ''Thermobaculum terrenum'' have inability to utilize some common [[monosaccharide]]s (e.g. [[glucose]], [[fructose]], etc.) as sole carbon source''.''<ref name="Jackson_1973" /><ref name="Sorokin_2012" /><ref name="King_2014"/><ref name="Houghton_2015" /> The mechanisms behind this inability are currently unknown. === Antibiotic resistance === Members of Thermomicrobia class exhibit certain level of resistance against [[metronidazole]] and/or [[trimethoprim]], which are clinically relevant for humans.<ref>{{Cite news|url=https://www.drugs.com/monograph/metronidazole.html|title=Metronidazole Monograph for Professionals - Drugs.com|work=Drugs.com|access-date=2018-10-11|language=en-US}}</ref><ref>{{Cite news|url=https://www.drugs.com/monograph/trimethoprim.html|title=Trimethoprim Monograph for Professionals - Drugs.com|work=Drugs.com|access-date=2018-10-11|language=en-US}}</ref> ''Thermomicrobium carboxidum'' and ''Thermorudis peleae'' show resistance against both of those antibiotics, while ''Sphaerobacter thermophilus'' shows resistance against only [[metronidazole]].<ref name="Houghton_2015" /> Interestingly, ''Thermomicrobium roseum'' and ''Thermorudis pharmacophila'' have an increased growth in both [[metronidazole]] and [[trimethoprim]], a rare trait even within antibiotic resistant bacteria.<ref name="Houghton_2015" /> The mechanisms behind are currently undocumented, and further study is required on this topic. === Cell envelope structure === Members of Thermomicrobia class have various [[Gram stain|Gram-staining]] results. ''Thermomicrobium roseum'', ''Sphaerobacter thermophilus'' and ''Thermorudis pharmacophila'' are reported to be Gram-negative and have a typical layered [[Gram-negative bacteria|diderm]] [[cell envelope]] structure.<ref name=":0" /><ref name=":1" /><ref name="Houghton_2015" /> However, their cell envelope composition are atypical compared to typical Gram-negative bacteria. Cell envelope of ''Thermomicrobium roseum'' lacks significant amount of peptidoglycan, which is fundamental for typical Gram-negative bacteria, while being rich in protein.<ref name=":0" /> Membrane lipids of ''Thermomicrobium roseum'' are mostly long chain [[diol]]s instead of glycerol-based lipids commonly found in bacteria.<ref>{{cite journal | vauthors = Pond JL, Langworthy TA, Holzer G | title = Long-chain diols: a new class of membrane lipids from a thermophilic bacterium | journal = Science | volume = 231 | issue = 4742 | pages = 1134–6 | date = March 1986 | pmid = 17818542 | doi = 10.1126/science.231.4742.1134 | jstor = 1696788 | bibcode = 1986Sci...231.1134P | s2cid = 42023577 }}</ref> The same feature was found in ''Sphaerobacter thermophilus'' and ''Thermorudis pharmacophila.''<ref name="Houghton_2015" /> It was suggested that the high-protein and diol-based lipid composition are responsible for heat resistance of these bacteria.<ref name=":1" /><ref>{{cite journal | vauthors = Pond JL, Langworthy TA | title = Effect of growth temperature on the long-chain diols and fatty acids of Thermomicrobium roseum | journal = Journal of Bacteriology | volume = 169 | issue = 3 | pages = 1328–30 | date = March 1987 | pmid = 3818547 | doi = 10.1128/jb.169.3.1328-1330.1987 | pmc = 211939 }}</ref> Meanwhile, other members of Thermomicrobia class are reported to be Gram-positive and have typical monoderm cell envelope.<ref name="Botero_2004" /><ref name="Sorokin_2012" /><ref name="King_2014"/> There are some possible explanations of the inconsistency of Gram-staining result within the class. For ''Thermorudis pharmacophila'', a possible explanation suggested by Houghton et al. is that it is actually an atypical [[Gram-positive bacteria|monoderm]] bacterium, because its cell envelope contains amino acids usually associated with Gram-positive bacteria, have reaction to KOH, [[vancomycin]] and [[ampicillin]], and lacks genes responsible for diderm formation.<ref name="Houghton_2015" /> It is also suggested that further study is required to resolve this problem, since the inconsistent reports of cell envelope structure are found for the whole Chloroflexota phylum. ==Phylogeny== {| class="wikitable" |- ! colspan=1 | 16S rRNA based [[The All-Species Living Tree Project|LTP]]_08_2023<ref name=LTP>{{cite web|title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=20 November 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_08_2023.ntree |access-date=20 November 2023}}</ref><ref>{{cite web|title=LTP_08_2023 Release Notes| url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_08_2023_release_notes.pdf |access-date=20 November 2023}}</ref> ! colspan=1 | 120 marker proteins based [[Genome Taxonomy Database|GTDB]] 08-RS214 (28th April 2023).<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=bac120_r214.sp_label |url=https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/bac120_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:80% |label1=Thermomicrobia |1={{clade |label1=[[Sphaerobacterales]] |1={{clade |1=''[[Nitrolancea]]'' |2=''[[Sphaerobacter]]'' }} |label2=Thermomicrobiales |2={{clade |1=''[[Thermalbibacter]]'' |2={{clade |1=''[[Thermomicrobium]]'' |2=''[[Thermorudis]]'' }} }} }} }} | {{clade|style=font-size:90%;line-height:80% |label1=Thermomicrobiales |1={{clade |label1=Thermomicrobiaceae |1={{clade |1={{clade |1=''[[Nitrolancea]]'' |2=''[[Sphaerobacter]]'' }} |2={{clade |1=''[[Thermomicrobium]]'' |2=''[[Thermorudis]]'' }} }} }} }} |} == Taxonomy == 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/thermomicrobia |title=Thermomicrobia |publisher=[[List of Prokaryotic names with Standing in Nomenclature]] (LPSN) |access-date=2022-07-20}}</ref> and [[National Center for Biotechnology Information]] (NCBI).<ref>{{cite web |author = Sayers| url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=189775&lvl=3&lin=f&keep=1&srchmode=1&unlock |title=Thermomicrobia |access-date=2022-03-20 |publisher=[[National Center for Biotechnology Information]] (NCBI) taxonomy database |display-authors=etal}}</ref> * '''Order [[Sphaerobacterales]]''' <small>Stackebrandt, Rainey & Ward-Rainey 1997</small> ** '''Family [[Sphaerobacteraceae]]''' <small>Stackebrandt, Rainey & Ward-Rainey 1997</small> *** Genus ''[[Sphaerobacter]]'' <small>Demharter et al. 1989</small><ref name = "Demharter_1989" /> **** ''[[Sphaerobacter thermophilus|S. thermophilus]]'' <small>Demharter et al. 1989</small><ref name = "Demharter_1989" /> *** Genus ''[[Nitrolancea]]'' <small>Sorokin et al. 2014</small><ref group=note name=note_1 /><ref name = "Sorokin_2012" /> **** ''N. hollandica'' <small>Sorokin et al. 2014</small><ref group=note name=note_1 /><ref name = "Sorokin_2012" /> **** "''Ca.'' N. copahuensis" <small>Spieck et al. 2020</small> * '''Order [[Thermomicrobiales]]''' <small>Garrity & Holt 2002</small> ** '''Family [[Thermomicrobiaceae]]''' <small>Garrity & Holt 2002</small> *** Genus ''[[Thermalbibacter]]'' <small>Zhao et al. 2023</small> **** ''T. longus'' <small>Zhao et al. 2023</small> *** Genus ''[[Thermomicrobium]]'' <small>Jackson, Ramaley & Meinschein 1973</small><ref name = "Jackson_1973" /> **** ''T. carboxidum'' <small>King & King 2014</small><ref name="King_2014"/> **** ''T. roseum'' <small>Jackson, Ramaley & Meinschein 1973</small><ref name = "Jackson_1973" /> *** Genus ''[[Thermorudis]]'' <small>King & King 2014</small><ref name="King_2014"/> **** ''T. peleae'' <small>King & King 2014</small><ref name="King_2014"/> **** ''T. pharmacophila'' <small>Houghton et al. 2015</small><ref name="Houghton_2015" /> ==See also== * [[List of bacteria genera]] * [[List of bacterial orders]] ==Notes== {{reflist|group=note|refs= <ref name=note_1>Strain found at the [[National Center for Biotechnology Information]] (NCBI) but has no standing with the [[Bacteriological Code]] (1990 and subsequent Revision) as detailed by [[List of Prokaryotic names with Standing in Nomenclature]] (LPSN) as a result of the following reasons: * No pure culture isolated or available for prokaryotes. * Not validly published because the effective publication only documents deposit of the type strain in a single recognized culture collection. * Not approved and published by the [[International Journal of Systematic Bacteriology]] or the [[International Journal of Systematic and Evolutionary Microbiology]] (IJSB/IJSEM).</ref> <ref name=note_2>The above description does not take newly discovered species after 2004 into account.</ref> }} == References == {{reflist|32em|refs = <ref name=":2">See the [[National Center for Biotechnology Information|NCBI]] [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=189775 webpage on] [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=1859062&lvl=3&lin=f&keep=1&srchmode=1&unlock unclassified Terrabacteria group] Data extracted from the {{cite web| url= https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi |title=NCBI Taxonomy Browser |publisher=[[National Center for Biotechnology Information]] |access-date=2018-10-01}}</ref> <ref name = "Demharter_1989">{{cite journal | vauthors = Demharter W, Hensel R, Smida J, Stackebrandt E | title = Sphaerobacter thermophilus gen. nov., sp. nov. A deeply rooting member of the actinomycetes subdivision isolated from thermophilically treated sewage sludge. | journal = Systematic and Applied Microbiology | date = May 1989 | volume = 11 | issue = 3 | pages = 261–6 | doi = 10.1016/S0723-2020(89)80023-2 }}</ref> <ref name="Houghton_2015">{{cite journal | vauthors = Houghton KM, Morgan XC, Lagutin K, MacKenzie AD, Vyssotskii M, Mitchell KA, McDonald IR, Morgan HW, Power JF, Moreau JW, Hanssen E, Stott MB | title = Thermorudis pharmacophila sp. nov., a novel member of the class Thermomicrobia isolated from geothermal soil, and emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 65 | issue = 12 | pages = 4479–87 | date = December 2015 | pmid = 26374291 | doi = 10.1099/ijsem.0.000598 | hdl = 10289/11806 | doi-access = free | hdl-access = free }}</ref> <ref name="King_2014">{{cite journal | vauthors = King CE, King GM | title = Thermomicrobium carboxidum sp. nov., and Thermorudis peleae gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 64 | issue = Pt 8 | pages = 2586–92 | date = August 2014 | pmid = 24814334 | doi = 10.1099/ijs.0.060327-0 | doi-access = free }}</ref> }} {{Bacteria classification}} {{Life on Earth}} {{Taxonbar|from1=Q1349847|from2=Q123631188}} [[Category:Bacteria]] [[Category:Bacteria classes]] </textarea><div class="templatesUsed"><div class="mw-templatesUsedExplanation"><p><span id="templatesused">Pages transcluded onto the current version of this page<span class="posteditwindowhelplinks"> (<a href="/wiki/Help:Transclusion" title="Help:Transclusion">help</a>)</span>:</span> </p></div><ul> <li><a href="/wiki/Template:;" title="Template:;">Template:;</a> (<a 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