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Nocardiopsis dassonvillei subsp. crassaminis subsp. nov., isolated from freshwater sediment, and reappraisal of Nocardiopsis alborubida Grund and Kroppenstedt 1990 emend. Nouioui et al. 2018

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Abstract
An actinomycete, strain D1(T), was isolated from a freshwater sediment sample collected from the San Pablo river in the La Risuena community, Santiago de Cuba province, Cuba. The strain was identified as a member of the genus Nocardiopsis by means of a polyphasic taxonomic study. It produced a light yellow non-fragmented substrate mycelium, a white well-developed aerial mycelium and straight to flexuous hyphae. No specific spore chains were observed. Strain D1(T) contained meso-diaminopimelic acid, no diagnostic sugars, and MK-10(H-2), MK-10(H-4), MK-10 and MK-10(H-6) as predominant menaquinones, but not phosphatidylcholine as diagnostic polar lipid of the genus Nocardiopsis. The predominant fatty acids were iso-C-16:0, 10-methyl-C-18:0 and anteiso-C-17:0. Strain D1(T) showed the highest degree of 16S rRNA gene sequence similarity to Nocardiopsis synnematoformans DSM 44143(T) (99.8 %), Nocardiopsis dassonvillei subsp. albirubida NBRC 13392(T) (99.8 %) and Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111(T) (99.6 %). A genomic OrthoANIu value between D1(T) and N. dassonvillei subsp. dassonvillei DSM 43111(T) of 97.63% and a dDDH value of 78.9% indicated that strain D1(T) should be classified in N. dassonvillei. However, phenotypic characteristics distinguished strain D1(T) from its nearest neighbour taxon. On basis of these results we propose to classify strain D1(T) (=LMG 30468(T)=CECT 30033(T)) as a representative of a novel subspecies of the genus Nocardiopsis, for which the name Nocardiopsis dassonvillei subsp. crassaminis subsp. nov. is proposed. In addition, the genomic distance between N. dassonvillei subsp. albirubida NBRC 13392(T) and N. dassonvillei subsp. dassonvillei DSM 43111(T) as determined through OrthoANIu (93.64 %) and dDDH (53.40%), along with considerable phenotypic and chemotaxonomic differences reported in earlier studies, indicated that the classification of this taxon as Nocardiopsis alborubida Grund and Kroppenstedt 1990 is to be preferred over its classification as N. dassonvillei subsp. albirubida Evtushenko et al. 2000.
Keywords
Ecology, Evolution, Behavior and Systematics, Microbiology, General Medicine, Nocardiopsis, freshwater environment, polyphasic taxonomy, OrthoANIu, dDDH, GENOME SEQUENCE, SALINE SOIL, PHYLOGENIES, ALGORITHM, DATABASE, GENUS

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MLA
Camacho Pozo, Miladis Isabel, et al. “Nocardiopsis Dassonvillei Subsp. Crassaminis Subsp. Nov., Isolated from Freshwater Sediment, and Reappraisal of Nocardiopsis Alborubida Grund and Kroppenstedt 1990 Emend. Nouioui et Al. 2018.” INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol. 70, no. 12, 2020, pp. 6172–79, doi:10.1099/ijsem.0.004514.
APA
Camacho Pozo, M. I., Wieme, A., Pérez, S. R., Llauradó Maury, G., Snauwaert, C., Lescaylle Veranes, Y., … Vandamme, P. (2020). Nocardiopsis dassonvillei subsp. crassaminis subsp. nov., isolated from freshwater sediment, and reappraisal of Nocardiopsis alborubida Grund and Kroppenstedt 1990 emend. Nouioui et al. 2018. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 70(12), 6172–6179. https://doi.org/10.1099/ijsem.0.004514
Chicago author-date
Camacho Pozo, Miladis Isabel, Anneleen Wieme, Suyén Rodríguez Pérez, Gabriel Llauradó Maury, Cindy Snauwaert, Yaneisy Lescaylle Veranes, Leonor Peña Zamora, Peter Schumann, and Peter Vandamme. 2020. “Nocardiopsis Dassonvillei Subsp. Crassaminis Subsp. Nov., Isolated from Freshwater Sediment, and Reappraisal of Nocardiopsis Alborubida Grund and Kroppenstedt 1990 Emend. Nouioui et Al. 2018.” INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 70 (12): 6172–79. https://doi.org/10.1099/ijsem.0.004514.
Chicago author-date (all authors)
Camacho Pozo, Miladis Isabel, Anneleen Wieme, Suyén Rodríguez Pérez, Gabriel Llauradó Maury, Cindy Snauwaert, Yaneisy Lescaylle Veranes, Leonor Peña Zamora, Peter Schumann, and Peter Vandamme. 2020. “Nocardiopsis Dassonvillei Subsp. Crassaminis Subsp. Nov., Isolated from Freshwater Sediment, and Reappraisal of Nocardiopsis Alborubida Grund and Kroppenstedt 1990 Emend. Nouioui et Al. 2018.” INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 70 (12): 6172–6179. doi:10.1099/ijsem.0.004514.
Vancouver
1.
Camacho Pozo MI, Wieme A, Pérez SR, Llauradó Maury G, Snauwaert C, Lescaylle Veranes Y, et al. Nocardiopsis dassonvillei subsp. crassaminis subsp. nov., isolated from freshwater sediment, and reappraisal of Nocardiopsis alborubida Grund and Kroppenstedt 1990 emend. Nouioui et al. 2018. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. 2020;70(12):6172–9.
IEEE
[1]
M. I. Camacho Pozo et al., “Nocardiopsis dassonvillei subsp. crassaminis subsp. nov., isolated from freshwater sediment, and reappraisal of Nocardiopsis alborubida Grund and Kroppenstedt 1990 emend. Nouioui et al. 2018,” INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol. 70, no. 12, pp. 6172–6179, 2020.
@article{8685297,
  abstract     = {An actinomycete, strain D1(T), was isolated from a freshwater sediment sample collected from the San Pablo river in the La Risuena community, Santiago de Cuba province, Cuba. The strain was identified as a member of the genus Nocardiopsis by means of a polyphasic taxonomic study. It produced a light yellow non-fragmented substrate mycelium, a white well-developed aerial mycelium and straight to flexuous hyphae. No specific spore chains were observed. Strain D1(T) contained meso-diaminopimelic acid, no diagnostic sugars, and MK-10(H-2), MK-10(H-4), MK-10 and MK-10(H-6) as predominant menaquinones, but not phosphatidylcholine as diagnostic polar lipid of the genus Nocardiopsis. The predominant fatty acids were iso-C-16:0, 10-methyl-C-18:0 and anteiso-C-17:0. Strain D1(T) showed the highest degree of 16S rRNA gene sequence similarity to Nocardiopsis synnematoformans DSM 44143(T) (99.8 %), Nocardiopsis dassonvillei subsp. albirubida NBRC 13392(T) (99.8 %) and Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111(T) (99.6 %). A genomic OrthoANIu value between D1(T) and N. dassonvillei subsp. dassonvillei DSM 43111(T) of 97.63% and a dDDH value of 78.9% indicated that strain D1(T) should be classified in N. dassonvillei. However, phenotypic characteristics distinguished strain D1(T) from its nearest neighbour taxon. On basis of these results we propose to classify strain D1(T) (=LMG 30468(T)=CECT 30033(T)) as a representative of a novel subspecies of the genus Nocardiopsis, for which the name Nocardiopsis dassonvillei subsp. crassaminis subsp. nov. is proposed. In addition, the genomic distance between N. dassonvillei subsp. albirubida NBRC 13392(T) and N. dassonvillei subsp. dassonvillei DSM 43111(T) as determined through OrthoANIu (93.64 %) and dDDH (53.40%), along with considerable phenotypic and chemotaxonomic differences reported in earlier studies, indicated that the classification of this taxon as Nocardiopsis alborubida Grund and Kroppenstedt 1990 is to be preferred over its classification as N. dassonvillei subsp. albirubida Evtushenko et al. 2000.},
  author       = {Camacho Pozo, Miladis Isabel and Wieme, Anneleen and Pérez, Suyén Rodríguez and Llauradó Maury, Gabriel and Snauwaert, Cindy and Lescaylle Veranes, Yaneisy and Peña Zamora, Leonor and Schumann, Peter and Vandamme, Peter},
  issn         = {1466-5026},
  journal      = {INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY},
  keywords     = {Ecology,Evolution,Behavior and Systematics,Microbiology,General Medicine,Nocardiopsis,freshwater environment,polyphasic taxonomy,OrthoANIu,dDDH,GENOME SEQUENCE,SALINE SOIL,PHYLOGENIES,ALGORITHM,DATABASE,GENUS},
  language     = {eng},
  number       = {12},
  pages        = {6172--6179},
  title        = {Nocardiopsis dassonvillei subsp. crassaminis subsp. nov., isolated from freshwater sediment, and reappraisal of Nocardiopsis alborubida Grund and Kroppenstedt 1990 emend. Nouioui et al. 2018},
  url          = {http://dx.doi.org/10.1099/ijsem.0.004514},
  volume       = {70},
  year         = {2020},
}

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