Pseudonocardia spirodelae sp. nov., isolated from duckweed and formal proposal to reclassify Pseudonocardia antarctica as a later heterotypic synonym of Pseudonocardia alni and reclassify Pseudonocardia carboxydivorans as Pseudonocardia alni subsp. carboxydivorans.
{"title":"<i>Pseudonocardia spirodelae</i> sp. nov., isolated from duckweed and formal proposal to reclassify <i>Pseudonocardia antarctica</i> as a later heterotypic synonym of <i>Pseudonocardia alni</i> and reclassify <i>Pseudonocardia carboxydivorans</i> as <i>Pseudonocardia alni</i> subsp. <i>carboxydivorans</i>.","authors":"Waranya Butdee, Yuparat Saimee, Chanwit Suriyachadkun, Kannika Duangmal","doi":"10.1099/ijsem.0.006608","DOIUrl":null,"url":null,"abstract":"<p><p>A novel <i>Pseudonocardia</i> strain DW16-2<sup>T</sup>, isolated from duckweed (<i>Spirodela polyrhiza</i>), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to <i>Pseudonocardia carboxydivorans</i> Y8<sup>T</sup> (98.8%), followed by <i>Pseudonocardia tropica</i> YIM 61452<sup>T</sup> (98.7%), <i>Pseudonocardia antarctica</i> DVS 5a1<sup>T</sup> (98.7%) and <i>Pseudonocardia alni</i> DSM 44104<sup>T</sup> (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2<sup>T</sup> and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2<sup>T</sup> were typical for the genus <i>Pseudonocardia</i> by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2<sup>T</sup> contained <i>meso</i>-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H<sub>4</sub>). The cellular fatty acids (>5 %) were <i>iso</i>-C<sub>16 : 0</sub>, <i>iso</i>-C<sub>16 : 1</sub> H, summed feature 3: C<sub>16 : 1</sub> ω7c/C<sub>16 : 1</sub> ω6c; C<sub>16 : 1</sub> ω6c/C<sub>16 : 1</sub> ω7c, C<sub>17 : 1</sub> ω8c and <i>anteiso</i>-C<sub>17 : 0</sub>. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2<sup>T</sup> represents a novel species of the genus <i>Pseudonocardia</i>, for which the name <i>Pseudonocardia spirodelae</i> sp. nov. (type strain DW16-2<sup>T</sup> = TBRC 16418<sup>T</sup> = NBRC 115857<sup>T</sup>) is proprosed. In addition, the comparison of the whole genome sequences suggested that <i>P. alni</i> and <i>P. antarctica</i> belong to the same species and <i>P. carboxydivorans</i> is a subspecies of <i>P. alni</i>. Therefore, it is proposed that <i>P. antarctica</i> Prabahar <i>et al</i>. 2004 is reclassified as a later heterotypic synonym of <i>P. alni</i> (Evtushenko <i>et al</i>. 1989) Warwick <i>et al</i>. 1994, and <i>P. carboxydivorans</i> Park <i>et al</i>. 2008 is proposed as a subspecies of <i>P. alni</i> (Evtushenko <i>et al</i>. 1989) Warwick <i>et al</i>. 1994.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 1","pages":""},"PeriodicalIF":2.0000,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"International journal of systematic and evolutionary microbiology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1099/ijsem.0.006608","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
A novel Pseudonocardia strain DW16-2T, isolated from duckweed (Spirodela polyrhiza), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Pseudonocardia carboxydivorans Y8T (98.8%), followed by Pseudonocardia tropica YIM 61452T (98.7%), Pseudonocardia antarctica DVS 5a1T (98.7%) and Pseudonocardia alni DSM 44104T (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2T and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2T were typical for the genus Pseudonocardia by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H4). The cellular fatty acids (>5 %) were iso-C16 : 0, iso-C16 : 1 H, summed feature 3: C16 : 1 ω7c/C16 : 1 ω6c; C16 : 1 ω6c/C16 : 1 ω7c, C17 : 1 ω8c and anteiso-C17 : 0. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia spirodelae sp. nov. (type strain DW16-2T = TBRC 16418T = NBRC 115857T) is proprosed. In addition, the comparison of the whole genome sequences suggested that P. alni and P. antarctica belong to the same species and P. carboxydivorans is a subspecies of P. alni. Therefore, it is proposed that P. antarctica Prabahar et al. 2004 is reclassified as a later heterotypic synonym of P. alni (Evtushenko et al. 1989) Warwick et al. 1994, and P. carboxydivorans Park et al. 2008 is proposed as a subspecies of P. alni (Evtushenko et al. 1989) Warwick et al. 1994.
期刊介绍:
Published by the Microbiology Society and owned by the International Committee on Systematics of Prokaryotes (ICSP), a committee of the Bacteriology and Applied Microbiology Division of the International Union of Microbiological Societies, International Journal of Systematic and Evolutionary Microbiology is the leading forum for the publication of novel microbial taxa and the ICSP’s official journal of record for prokaryotic names.
The journal welcomes high-quality research on all aspects of microbial evolution, phylogenetics and systematics, encouraging submissions on all prokaryotes, yeasts, microfungi, protozoa and microalgae across the full breadth of systematics including:
Identification, characterisation and culture preservation
Microbial evolution and biodiversity
Molecular environmental work with strong taxonomic or evolutionary content
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Taxonomy and phylogenetics.