{{Short description|Family of bacteria}} {{Automatic taxobox | image = Sporosarcina highlanderae.jpg | image_caption = ''[[Sporosarcina highlanderae]]'' | taxon = Caryophanaceae | authority = Peshkoff, 1939<ref name=LPSN/> | subdivision_ranks = Genera | subdivision = *''[[Bhargavaea]]'' *''[[Caryophanon]]'' *''[[Chryseomicrobium]]'' *''[[Chungangia]]'' *''[[Indiicoccus]]'' *''[[Jeotgalibacillus]]'' *''[[Kurthia]]'' *''[[Lysinibacillus]]'' *''[[Metalysinibacillus]]'' *''[[Metaplanococcus]]'' *''[[Metasolibacillus]]'' *''[[Paenisporosarcina]]'' *''[[Planococcus (bacterium)|Planococcus]]'' *''[[Psychrobacillus]]'' *''[[Rummeliibacillus]]'' *''[[Savagea]]'' *''[[Solibacillus]]'' *''[[Sporosarcina]]'' *''[[Ureibacillus]]'' | synonyms = * Planococcaceae <small>Krassilnikov 1949</small> * "Sporosarcineae" <small>Kluyver & van Niel 1936</small> * "Zopfieae" <small>Winslow et al. 1920</small> }}
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=LPSN></ref>
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''.
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" />
== Biochemical characteristics and molecular signatures == 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" />
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.
== Historical systematics and current taxonomy == ''Caryophanaceae'', as of 2021, contains 19 validly published genera.<ref name=LPSN/>
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 |url-access=subscription}}</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" />
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" />
==Phylogeny== The currently accepted taxonomy is based on the [[List of Prokaryotic names with Standing in Nomenclature]] (LPSN)<ref name=LPSN>{{cite web |author=J.P. Euzéby |url=https://lpsn.dsmz.de/family/Caryophanaceae |title=Caryophanaceae |access-date=2022-09-09 |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 |url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=186818&lvl=3&lin=f&keep=1&srchmode=1&unlock |title=Caryophanaceae |access-date=2022-09-09 |publisher=[[National Center for Biotechnology Information]] (NCBI) taxonomy database |display-authors=et al.}}</ref>
{| class="wikitable" |- ! colspan=1 | 16S rRNA based [[The All-Species Living Tree Project|LTP]]_10_2024<ref>{{cite web |title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=10 December 2024}}</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_10_2024.ntree |access-date=10 December 2024}}</ref><ref>{{cite web |title=LTP_10_2024 Release Notes |url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_10_2024_release_notes.pdf |access-date=10 December 2024}}</ref> ! colspan=1 | 120 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=bac120_r220.sp_labels |url=https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/bac120_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:80% |label1= |1={{clade |1=''[[Bhargavaea]]'' <small>Manorama et al. 2009</small> |2={{clade |1={{clade |1={{clade |1="''[[Planococcus lenghuensis]]''" <small>Yang et al. 2020</small> |2=''[[Indiicoccus]]'' <small>Pal et al. 2019</small> }} |2=''[[Planococcus (bacterium)|Planococcus]]'' }} |2={{clade |1=''[[Ureibacillus]]'' <small>Fortina et al. 2001</small> |2={{clade |1={{clade |1=''[[Chungangia]]'' <small>Kim et al. 2012</small> |2=''[[Sporosarcina]]'' <small>Orla-Jensen 1909</small> [incl. ''[[Savagea]]'' <small>Whitehead et al. 2015</small>] }} |2={{clade |1=''[[Chryseomicrobium deserti]]'' <small>Lin et al. 2017</small> |2={{clade |1=''[[Paenisporosarcina]]'' <small>Krishnamurthi et al. 2009</small> |2={{clade |1={{clade |1=''[[Chryseomicrobium]]'' <small>Arora et al. 2011</small> |2=''[[Psychrobacillus]]'' <small>Krishnamurthi et al. 2011</small> }} |2={{clade |1={{clade |1=''[[Viridibacillus]]'' <small>Albert et al. 2007</small> |2={{clade |1=''[[Rummeliibacillus]]'' <small>Vaishampayan et al. 2009</small> |2=''[[Kurthia]]'' <small>(Kurth 1883) Trevisan 1885</small> }} }} |2={{clade |1={{clade |1=''[[Lysinibacillus alkalisoli]]'' <small>Sun, Xu & Wu 2017</small> |2=''[[Metalysinibacillus]]'' <small>Gupta & Patel 2020</small> }} |2={{clade |1={{clade |1=''[[Lysinibacillus odysseyi]]'' <small>(La Duc, Satomi & Venkateswaran <br/>2004) Jung et al. 2012</small> |2={{clade |1=''[[Metasolibacillus]]'' <small>Gupta & Patel 2020</small> |2=''[[Ureibacillus]]'' ~1, ''Ureibacillus'' ~2, ''[[Lysinibacillus]]'' ~1 <br/>& ''Lysinibacillus'' ~2 }} }} |2={{clade |1=''[[Bacillus decisifrondis]]'' <small>Zhang et al. 2007</small> |2=''[[Lysinibacillus]]'' <small>Ahmed et al. 2007</small> [incl. ''[[Caryophanon]]'' <br/><small>Peshkoff 1939</small> & ''[[Solibacillus]]'' <small>Krishnamurthi et al. 2009</small>] }} }} }} }} }} }} }} }} }} }} }} }} | {{Clade | style=font-size:90%;line-height:80% |label1= |1={{clade |1={{clade |1={{clade |1="''[[Edaphobacillus]]''" <small>Lal et al. 2013</small> |2=''[[Bhargavaea]]'' }} |2={{clade |1=''[[Savagea]]'' |2=''[[Sporosarcina]]'' }} }} |2={{clade |1={{clade |1=''[[Indiicoccus]]'' [incl. "''Planococcus lenghuensis''"] |2=''[[Planococcus (bacterium)|Planococcus]]'' <small>Migula 1894 non Ferris 1950</small> }} |2={{clade |1={{clade |1=''[[Paenisporosarcina]]'' |2={{clade |1=''[[Chryseomicrobium]]'' |2=''[[Psychrobacillus]]'' }} }} |2={{clade |1={{clade |1=''[[Viridibacillus]]'' |2={{clade |1=''[[Rummeliibacillus]]'' |2=''[[Kurthia]]'' }} }} |2={{clade |1=''[[Metalysinibacillus]]'' [incl. ''[[Lysinibacillus alkalisoli]]''] |2={{clade |1=''[[Lysinibacillus]]'' |2={{clade |1=''[[Caryophanon]]'' |2={{clade |1={{clade |1=''[[Metasolibacillus]]'' |2={{clade |1=''[[Lysinibacillus odysseyi]]'' |2=''[[Solibacillus]]'' }} }} |2=''[[Ureibacillus]]'' }} }} }} }} }} }} }} }} }} |} Unassigned genera: * "''[[Crocinobacterium]]''" <small>Lee 2006</small> * ''[[Metaplanococcus]]'' <small>Gupta & Patel 2020</small> * "''[[Stomatostreptococcus]]''" <small>Ping et al. 1998</small>
==References== {{Reflist}}
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[[Category:Bacillales]] [[Category:Bacteria families]]