Biology:Caryophanaceae

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. The type genus of this family is Caryophanon.

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. According to the International Code of Nomenclature of Prokaryotes (ICNP), the name Caryophanacaeae has higher priority than Planococcaceae because of its earlier publication. 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.

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.

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. 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.

In addition to the nomenclature anomaly, Caryophanaceae also encompassed over 100 species that had varying morphology/biochemical characteristics, demonstrating that they were phylogenetically unrelated. 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.

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. 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.

Phylogeny

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

16S rRNA based LTP_10_2024

120 marker proteins based GTDB 09-RS220

Bhargavaea Manorama et al. 2009           "Planococcus lenghuensis" Yang et al. 2020     Indiicoccus Pal et al. 2019       Planococcus         Ureibacillus Fortina et al. 2001         Chungangia Kim et al. 2012     Sporosarcina Orla-Jensen 1909 [incl. Savagea Whitehead et al. 2015]         Chryseomicrobium deserti Lin et al. 2017       Paenisporosarcina Krishnamurthi et al. 2009         Chryseomicrobium Arora et al. 2011     Psychrobacillus Krishnamurthi et al. 2011           Viridibacillus Albert et al. 2007       Rummeliibacillus Vaishampayan et al. 2009     Kurthia (Kurth 1883) Trevisan 1885             Lysinibacillus alkalisoli Sun, Xu & Wu 2017     Metalysinibacillus Gupta & Patel 2020           Lysinibacillus odysseyi (La Duc, Satomi & Venkateswaran 2004) Jung et al. 2012       Metasolibacillus Gupta & Patel 2020     Ureibacillus ~1, Ureibacillus ~2, Lysinibacillus ~1 & Lysinibacillus ~2           Bacillus decisifrondis Zhang et al. 2007     Lysinibacillus Ahmed et al. 2007 [incl. Caryophanon Peshkoff 1939 & Solibacillus Krishnamurthi et al. 2009]

"Edaphobacillus" Lal et al. 2013     Bhargavaea         Savagea     Sporosarcina             Indiicoccus [incl. "Planococcus lenghuensis"]     Planococcus Migula 1894 non Ferris 1950           Paenisporosarcina       Chryseomicrobium     Psychrobacillus             Viridibacillus       Rummeliibacillus     Kurthia           Metalysinibacillus [incl. Lysinibacillus alkalisoli]       Lysinibacillus       Caryophanon         Metasolibacillus       Lysinibacillus odysseyi     Solibacillus         Ureibacillus

Unassigned genera:

• "Crocinobacterium" Lee 2006
• Metaplanococcus Gupta & Patel 2020
• "Stomatostreptococcus" Ping et al. 1998

References

Wikidata ☰ Q3661019 entry