Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil

Abstract

<jats:p>The taxonomic status of a <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.7526" xlink:type="simple">Nocardiopsis</jats:ext-link> </jats:named-content> </jats:italic> strain, designated H13<jats:sup>T</jats:sup>, isolated from a high altitude Atacama Desert soil, was established by using a polyphasic approach. The strain was found to have chemotaxonomic, cultural and morphological characteristics consistent with its classification within the genus <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.7526" xlink:type="simple">Nocardiopsis</jats:ext-link> </jats:named-content> </jats:italic> and formed a well-supported clade in the <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.7526" xlink:type="simple">Nocardiopsis</jats:ext-link> </jats:named-content> </jats:italic> phylogenomic tree together with the type strains of <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.7534" xlink:type="simple">Nocardiopsis alborubida</jats:ext-link> </jats:named-content> </jats:italic>, <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.10904" xlink:type="simple">Nocardiopsis dassonvillei</jats:ext-link> </jats:named-content> </jats:italic> and <jats:italic>Nocardiopsis synnematoformans</jats:italic>. Strain H13<jats:sup>T</jats:sup> was distinguished from its closest relatives by low average nucleotide identity (93.2–94.9 %) and <jats:italic>in silico</jats:italic> DNA–DNA hybridization (52.5–62.4 %) values calculated from draft genome assemblies and by a range of phenotypic properties. On the basis of these results, it is proposed that the isolate be assigned to the genus <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.7526" xlink:type="simple">Nocardiopsis</jats:ext-link> </jats:named-content> </jats:italic> as <jats:italic>Nocardiopsis deserti</jats:italic> sp. nov. with isolate H13<jats:sup>T</jats:sup> (=CGMCC 4.7585<jats:sup>T</jats:sup>=KCTC 49249<jats:sup>T</jats:sup>) as the type strain.</jats:p>

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

“…dassonvillei DSM 43111 T as determined through dDDH was near the dDDH threshold (79-80 %) proposed for delineating subspecies within bacterial and archaeal species [49]. Together, phenotypic and genomic differences justify the classification of strain D1 T as a new ) the species delineation threshold, the whole genome sequence based divergence values detected in the present study (Table 1) and by Nouioui et al [33] and Asem et al [34] were clearly below those of the whole genomic sequence based thresholds [29,30] and demonstrate that the classification of this taxon as a distinct Nocardiopsis species is more appropriate. The latter classification is also in line with differences in menaquinone and cell wall teichoic acid content, and in several growth and physiological characteristics [6,34].…”

“…It also showed that N. dassonvillei subsp. albirubida DSM 40465 T formed a distinct lineage as previously demonstrated by Asem et al [34].…”

“…Together, phenotypic and genomic differences justify the classification of strain D1 T as a new ) the species delineation threshold, the whole genome sequence based divergence values detected in the present study (Table 1) and by Nouioui et al [33] and Asem et al [34] were clearly below those of the whole genomic sequence based thresholds [29,30] and demonstrate that the classification of this taxon as a distinct Nocardiopsis species is more appropriate. The latter classification is also in line with differences in menaquinone and cell wall teichoic acid content, and in several growth and physiological characteristics [6,34]. Although we realize that both classifications and thus names of this taxon are valid and that the use of a specific nomenclature is subject to taxonomic opinion, we support that the whole genome sequence data demonstrate that the classification as N. The type strain, D1 T (=LMG 30468 T =CECT 30033 T ), was isolated from sediment of the San Pablo river situated in the La Risueña community, Santiago de Cuba province, Cuba.…”

“…albirubida DSM 40465 T ( Table 1), confirming that the genomic divergence between these strains warrants the classification of N. dassonvillei subsp. albirubida DSM 40465 T as a distinct species [31][32][33][34]. This result was again corroborated through dDDH analyses which revealed a dDDH value of 53.40 % (confidence interval, 50.7-56.1 %) between N. dassonvillei subsp.…”

“…While the present study was under review, a novel Nocardiopsis species, i.e. Nocardiopsis deserti, was described [34]. Strain D1 T can be differentiated from N. deserti H13 T by a range of biochemical characteristics including the former's capacity to grow at 42 °C, to use myo-inositol, raffinose, trehalose, l-arabinose (weakly) and cellulose (weakly) as carbon sources, and to degrade Tween 20 and 40, and by the lack of growth in the presence of 10 % NaCl and of acid production from fructose ([34], Table 2).…”