Caryophanaceae: Difference between revisions
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{{Short description|Family of bacteria}} |
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{{Taxobox_begin | color = lightgrey | name = Caryophanaceae}} |
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{{Taxobox |
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| color = lightgrey |
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{{Taxobox_regnum_entry | taxon = [[Bacterium|Bacteria]]}} |
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| name = Caryophanaceae |
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{{Taxobox_divisio_entry | taxon = [[Firmicutes]]}} |
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| domain = [[Bacteria]] |
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{{Taxobox_classis_entry | taxon = [[Bacilli]]}} |
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| phylum = [[Bacillota]] |
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{{Taxobox_ordo_entry | taxon = [[Bacillales]]}} |
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| classis = [[Bacilli]] |
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| ordo = [[Bacillales|Caryophanales]] |
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{{Taxobox_end_placement}} |
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{{Taxobox_section_subdivision | color = lightgrey | plural_taxon = Genera}} |
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| familia_authority = Peshkoff, 1939 |
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| subdivision_ranks = Genera |
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{{Taxobox_end}} |
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| subdivision = |
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*''[[Bhargavaea]]'' |
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*''[[Chryseomicrobium]]'' |
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*''[[Chungangia]]'' |
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*''[[Filibacter]]'' |
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*''[[Indiicoccus]]'' |
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*''[[Jeotgalibacillus]]'' |
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*''[[Kurthia]]'' |
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*''[[Lysinibacillus]]'' |
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*''[[Marinibacillus]]'' |
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*''[[Metalysinibacillus]]'' |
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*''[[Metaplanococcus]]'' |
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*''[[Metasolibacillus]]'' |
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*''[[Paenisporosarcina]]'' |
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*''[[Planococcus (bacterium)|Planococcus]]'' |
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*''[[Psychrobacillus]]'' |
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*''[[Rummeliibacillus]]'' |
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*''[[Savagea]]'' |
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*''[[Solibacillus]]'' |
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*''[[Sporosarcina]]'' |
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*''[[Ureibacillus]]'' |
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}} |
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The '''''Caryophanaceae''''' is a [[family (taxonomy)|family]] of [[Gram-positive]] [[bacteria]]. In 2020, the now defunct family ''[[Planococcaceae]]'' was merged into ''Caryophanaceae'' to rectify a nomenclature anomaly.<ref name=":0">{{Cite journal|last1=Gupta|first1=Radhey S.|last2=Patel|first2=Sudip|date=2020-01-14|title=Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures|journal=Frontiers in Microbiology|volume=10|page=2821 | pmid=32010063|doi=10.3389/fmicb.2019.02821|issn=1664-302X|pmc=6971209|doi-access=free }}</ref> The type genus of this family is ''[[Caryophanon]].''<ref name=":1">{{Cite web|title=Family: Caryophanaceae|url=https://lpsn.dsmz.de/family/caryophanaceae|access-date=2021-06-05|website=lpsn.dsmz.de|language=en}}</ref> |
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The family ''Planococcacae'' was validly published in 1949, however it contained within it another family level taxonomic rank, the family ''Caryophanaceae,'' which was validly published in 1939.<ref name=":2">{{Cite journal|last=Tindall|first=B. J.|date=2019-08-01|title=When treated as heterotypic synonyms the names Caryophanaceae Peshkoff 1939 (Approved Lists 1980) and Caryophanales Peshkoff 1939 (Approved Lists 1980) have priority over the names Planococcaceae Krasil'nikov 1949 (Approved Lists 1980) and Bacillales Prévot 1953 (Approved Lists 1980) and Bacillales Prévot 1953 (Approved Lists 1980), respectively|journal=International Journal of Systematic and Evolutionary Microbiology|volume=69|issue=8|pages=2187–2195|doi=10.1099/ijsem.0.003354|pmid=30896383 |issn=1466-5026|doi-access=free}}</ref> According to the [[International Code of Nomenclature of Prokaryotes|International Code of Nomenclature of Prokaryotes (ICNP)]], the name ''Caryophanacaeae'' has higher priority than ''Planococcaceae'' because of its earlier publication.<ref name=":2" /> Therefore, the emended family retained the name ''Caryophanaceae''. |
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'''Caryophanaceae''' is a [[family (taxonomy)|family]] of [[Gram positive]] [[bacteria]]. There is only one genus, ''[[Caryophanon]]'', represented by this family. |
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The name ''Caryophanaceae'' is derived from the Latin term ''Caryophanon'', referring the type genus of the family and the suffix "-aceae", an ending used to denote a family. Together, ''Caryophanaceae'' refers to a family whose nomenclatural type is the genus ''Caryophanon''.<ref name=":0" /> |
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== Biochemical Characteristics and Molecular Signatures == |
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Cells from members of the family ''Caryophanaceae'' can be cocci or rods, sometimes forming filaments or trichomes. Most species are strictly aerobic heterotrophs, although some are also facultatively aerobes. Cells are generally motile by flagella or gliding and they may or may not form endospores. Most species are catalase-positive and oxidase positive or negative.<ref name=":0" /> |
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Analyses of genome sequences from ''Caryophanaceae'' species identified 13 [[conserved signature indels]] (CSIs) that are uniquely present in this family in the proteins [[Phenylalanine—tRNA ligase|phenylalanine–tRNA ligase]] subunit alpha, [[chaperonin]] GroEL, ribosome maturation factor RimP, BrxA/BrxB family bacilliredoxin, [[RNA methyltransferase]], Rhomboid family intramembrane serine protease, [[ATP-dependent Clp protease]] ATP-binding subunit, [[DNA-directed RNA polymerase]] subunit beta, [[chorismate synthase]], stage IV sporulation protein A, [[peptidase]], KinB-signaling pathway activation protein, and DUF423 domain-containing protein.<ref name=":0" /> These CSIs serve as a reliable molecular means of demarcating members ''Caryophanaceae'' from other families within the order ''Caryophanales'' and other bacteria. |
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== Historical Systematics and Current Taxonomy == |
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''Caryophanaceae'', as of 2021, contains 19 validly published genera.<ref name=":1" /> |
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In addition to the nomenclature anomaly, ''Caryophanaceae'' also encompassed over 100 species that had varying morphology/biochemical characteristics, demonstrating that they were phylogenetically unrelated.<ref name=":4">{{Cite journal|last1=Ludwig|first1=Wolfgang|last2=Schleifer|first2=Karl‐Heinz|last3=Whitman|first3=William B.|date=2015-09-14|title=Planococcaceae|url=http://dx.doi.org/10.1002/9781118960608.fbm00116|journal=Bergey's Manual of Systematics of Archaea and Bacteria|pages=1|doi=10.1002/9781118960608.fbm00116|isbn=9781118960608 }}</ref> The original assignment of species into the family ''Caryophanaceae'' was largely based on 16S rRNA genome sequence analyses, which is known to have low discriminatory power and the results of which changes depends on the algorithm and organism information used. Despite this, the analyses still exhibited polyphyletic branching, indicating the presence of distinct subgroups within the family.<ref name=":4" /> |
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In 2020, Gupta and Patel proposed the emendation of ''Caryophanaceae,'' specifically the unification with ''Planoccocacae'', the proposal of 3 new genera as well as the transfer of a number of misclassified species into the appropriate genera.<ref name=":0" /> The changes were proposed based on various phylogenetic trees constructed based on multiple large datasets of protein sequences and the identification of unique molecular markers known as [[Conserved signature indels|conserved signatures indels]] in multiple proteins.<ref name=":0" /> |
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==References== |
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{{Reflist}} |
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{{Taxonbar|from=Q3661019}} |
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[[Category:Bacillales]] |
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Latest revision as of 01:45, 30 September 2024
| Caryophanaceae | |
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| Family: | Caryophanaceae Peshkoff, 1939
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| Genera | |
The Caryophanaceae is a family of Gram-positive bacteria. In 2020, the now defunct family Planococcaceae was merged into Caryophanaceae to rectify a nomenclature anomaly.[1] The type genus of this family is Caryophanon.[2]
The family Planococcacae was validly published in 1949, however it contained within it another family level taxonomic rank, the family Caryophanaceae, which was validly published in 1939.[3] According to the International Code of Nomenclature of Prokaryotes (ICNP), the name Caryophanacaeae has higher priority than Planococcaceae because of its earlier publication.[3] Therefore, the emended family retained the name Caryophanaceae.
The name Caryophanaceae is derived from the Latin term Caryophanon, referring the type genus of the family and the suffix "-aceae", an ending used to denote a family. Together, Caryophanaceae refers to a family whose nomenclatural type is the genus Caryophanon.[1]
Biochemical Characteristics and Molecular Signatures
[edit]Cells from members of the family Caryophanaceae can be cocci or rods, sometimes forming filaments or trichomes. Most species are strictly aerobic heterotrophs, although some are also facultatively aerobes. Cells are generally motile by flagella or gliding and they may or may not form endospores. Most species are catalase-positive and oxidase positive or negative.[1]
Analyses of genome sequences from Caryophanaceae species identified 13 conserved signature indels (CSIs) that are uniquely present in this family in the proteins phenylalanine–tRNA ligase subunit alpha, chaperonin GroEL, ribosome maturation factor RimP, BrxA/BrxB family bacilliredoxin, RNA methyltransferase, Rhomboid family intramembrane serine protease, ATP-dependent Clp protease ATP-binding subunit, DNA-directed RNA polymerase subunit beta, chorismate synthase, stage IV sporulation protein A, peptidase, KinB-signaling pathway activation protein, and DUF423 domain-containing protein.[1] These CSIs serve as a reliable molecular means of demarcating members Caryophanaceae from other families within the order Caryophanales and other bacteria.
Historical Systematics and Current Taxonomy
[edit]Caryophanaceae, as of 2021, contains 19 validly published genera.[2]
In addition to the nomenclature anomaly, Caryophanaceae also encompassed over 100 species that had varying morphology/biochemical characteristics, demonstrating that they were phylogenetically unrelated.[4] The original assignment of species into the family Caryophanaceae was largely based on 16S rRNA genome sequence analyses, which is known to have low discriminatory power and the results of which changes depends on the algorithm and organism information used. Despite this, the analyses still exhibited polyphyletic branching, indicating the presence of distinct subgroups within the family.[4]
In 2020, Gupta and Patel proposed the emendation of Caryophanaceae, specifically the unification with Planoccocacae, the proposal of 3 new genera as well as the transfer of a number of misclassified species into the appropriate genera.[1] The changes were proposed based on various phylogenetic trees constructed based on multiple large datasets of protein sequences and the identification of unique molecular markers known as conserved signatures indels in multiple proteins.[1]
References
[edit]- ^ a b c d e f Gupta, Radhey S.; Patel, Sudip (2020-01-14). "Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures". Frontiers in Microbiology. 10: 2821. doi:10.3389/fmicb.2019.02821. ISSN 1664-302X. PMC 6971209. PMID 32010063.
- ^ a b "Family: Caryophanaceae". lpsn.dsmz.de. Retrieved 2021-06-05.
- ^ a b Tindall, B. J. (2019-08-01). "When treated as heterotypic synonyms the names Caryophanaceae Peshkoff 1939 (Approved Lists 1980) and Caryophanales Peshkoff 1939 (Approved Lists 1980) have priority over the names Planococcaceae Krasil'nikov 1949 (Approved Lists 1980) and Bacillales Prévot 1953 (Approved Lists 1980) and Bacillales Prévot 1953 (Approved Lists 1980), respectively". International Journal of Systematic and Evolutionary Microbiology. 69 (8): 2187–2195. doi:10.1099/ijsem.0.003354. ISSN 1466-5026. PMID 30896383.
- ^ a b Ludwig, Wolfgang; Schleifer, Karl‐Heinz; Whitman, William B. (2015-09-14). "Planococcaceae". Bergey's Manual of Systematics of Archaea and Bacteria: 1. doi:10.1002/9781118960608.fbm00116. ISBN 9781118960608.
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