Proposal for the creation of a new genus Musicola gen. nov., reclassification of Dickeya paradisiaca (Samson et al. 2005) as Musicola paradisiaca comb. nov. and description of a new species Musicola keenii sp. nov.
The Pectobacteriaceae family of important plant pathogens includes the genus Dickeya. There are currently 12 described species of Dickeya, although some are poorly characterized at the genomic level. Only two genomes of Dickeya paradisiaca, the type strain CFBP 4178T and strain Ech703, have previously been sequenced. Members of this species are mostly of tropical or subtropical origin. During an investigation of strains present in our laboratory collection we sequenced the atypical strain A3967, registered as CFBP 722, isolated from Solanum lycopersicum (tomato) in the South of France in 1965. The genome of strain A3967 shares digital DNA–DNA hybridization and average nucleotide identity (ANI) values of 68 and 96 %, respectively, with the D. paradisiaca type strain CFBP 4178T. However, ANI analysis showed that D. paradisiaca strains are significantly dissimilar to the other Dickeya species, such that less than one third of their genomes align to any other Dickeya genome. On phenotypic, phylogenetic and genomic grounds, we propose a reassignment of D. paradisiaca to the genus level, for which we propose the name Musicola gen. nov., with Musicola paradisiaca as the type species and CFBP 4178T (NCPPB 2511T) as the type strain. Phenotypic analysis showed differences between strain A3967T and CFBP 4178T, such as for the assimilation of melibiose, raffinose and myo-inositol. These results support the description of two novel species, namely Musicola paradisiaca comb. nov. and Musicola keenii sp. nov., with CFBP 4178T (NCPPB 2511T=LMG 2542T) and A3967T (CFBP 8732T=LMG 31880T) as the type strains, respectively.
CharkowskiA, BlancoC, CondemineG, ExpertD, FranzaT et al. The role of secretion systems and small molecules in soft-rot Enterobacteriaceae pathogenicity. Annu Rev Phytopathol2012; 50:425–449 [View Article] [PubMed]
WinslowCE, BroadhurstJ, BuchananRE, KrumwiedeC, RogersLA et al. The families and genera of the bacteria. Final report of the Committee of the Society of American Bacteriologists on characterization and classification of bacterial types. J Bacteriol1920; 5:191–229 [View Article] [PubMed]
VictoriaJ, BarrosO. Etiologia de una neuva enfermdad bacterial del platano (Musa paradisiaca L.) en Colombia. Inst Colomb Agropecu Revista ICA1969; 4:173–190
BrennerDJ, SteigerwaltAG, MiklosGV, FanningGR. Deoxyribonucleic acid relatedness among erwiniae and other Enterobacteriaceae: the soft-rot organisms (genus Pectobacterium Waldee). Int J Syst Bacteriol1973; 23:205–216 [View Article]
HaubenL, MooreERB, VauterinL, SteenackersM, MergaertJ et al. Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst Appl Microbiol1998; 21:384–397 [View Article] [PubMed]
SamsonR, LegendreJB, ChristenR, Fischer-Le SauxM, AchouakW. Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. Int J Syst Evol Microbiol2005; 55:1415–1427 [View Article] [PubMed]
BradyCL, CleenwerckI, DenmanS, VenterSN, Rodrıguez-PalenzuelaP et al. Proposal to reclassify Brenneria quercina (Hildebrand & Schroth 1967) Hauben et al. 1999 into a novel genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., descriptions of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. Iberica subsp. nov., and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiae as Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii. Int J Syst Evol Microbiol2012; 62:1592–1602
SlawiakM, van BeckhovenJ, SpeksnijderA, CzajkowskiR, GrabeG et al. Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe. Eur J Plant Pathol2009; 125:245–261
AličŠ, Van GijsegemF, PédronJ, RavnikarM, DreoT. Diversity within the novel Dickeya fangzhongdai sp., isolated from infected orchids, water and pears. Plant Pathol2018; 67:1612–1620
WangX, HeSW, GuoHB, HanJG, ThinKK et al.Dickeya oryzae sp. nov., isolated from the roots of rice. Int J Syst Evol Microbiol2020; 70:4171–4178 [View Article]
Hugouvieux-Cotte-PattatN, Jacot-des-CombesC, BriolayJ. Dickeya lacustris sp. nov., a water-living pectinolytic bacterium isolated from lakes in France. Int J Syst Evol Microbiol2019; 69:721–726 [View Article] [PubMed]
OulghaziS, PédronJ, CignaJ, LauYY, MoumniM et al.Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia. Int J Syst Evol Microbiol2019; 69:2440–2444 [View Article] [PubMed]
DupreyA, TaibN, LeonardS, GarinT, FlandroisJP et al. The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity. Environ Microbiol2019; 21:2809–2835 [View Article] [PubMed]
DickeyRS, VictoriaJI. Taxonomy and emended description of strains of Erwinia isolated from Musa paradisiaca Lineaus. Int J Syst Bacteriol1980; 30:129–134
Fernandez-BorreroO, Lopez-DuquesS. Pudricion acuosa del suedo tallo del platana (Musa paradisiaca) causade por Erwinia paradisiaca n. sp. Cenicafe1970; 21:3–44
MarreroG, SchneiderKL, JenkinsDM, AlvarezAM. Phylogeny and classification of Dickeya based on multilocus sequence analysis. Int J Syst Evol Microbiol2013; 63:3524–3539 [View Article]
RichterM, Rosselló-MóraR. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A2009; 106:19126–19131 [View Article] [PubMed]
BankevichA, NurkS, AntipovD, GurevichAA, DvorkinM. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol2012; 19:455–477 [View Article] [PubMed]
BarcoRA, GarrityGM, ScottJJ, AmendJP, NealsonKH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio2020; 11:e02475 [View Article]
KozlovAM, DarribaD, FlouriT, MorelB, StamatakisA. RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics2019btz305 [View Article]
Proposal for the creation of a new genus Musicola gen. nov., reclassification of Dickeya paradisiaca (Samson et al. 2005) as Musicola paradisiaca comb. nov. and description of a new species Musicola keenii sp. nov.