Rhodococcus oryzae sp. nov., a novel actinobacterium isolated from rhizosphere soil of rice (Oryza sativa L.)

Abstract

<jats:p>A Gram-stain-positive, non-motile, creamy-white actinobacterium, which has an elementary branching rod-coccus life cycle was isolated from the rhizosphere soil of rice (<jats:italic>Oryza sativa</jats:italic> L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and its taxonomic status was examined by using a polyphasic approach. Results from the 16S rRNA gene sequence study showed that the isolate, designated strain NEAU-CX67<jats:sup>T</jats:sup>, belonged 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.6471" xlink:type="simple">Rhodococcus</jats:ext-link> </jats:named-content> </jats:italic> and formed a cluster with <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.6488" xlink:type="simple">Rhodococcus maanshanensis</jats:ext-link> </jats:named-content> </jats:italic> DSM 44675<jats:sup>T</jats:sup>, <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.26294" xlink:type="simple">Rhodococcus kronopolitis</jats:ext-link> </jats:named-content> </jats:italic> NEAU-ML12<jats:sup>T</jats:sup> and <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.6501" xlink:type="simple">Rhodococcus tukisamuensis</jats:ext-link> </jats:named-content> </jats:italic> JCM 11308<jats:sup>T</jats:sup> (98.3, 98.1 and 97.7% gene sequence similarity, respectively). The major fatty acids were C<jats:sub>16 : 0</jats:sub>, 10-methyl C<jats:sub>18 : 0</jats:sub>, C<jats:sub>18 : 1</jats:sub> ω9<jats:italic>c</jats:italic> and C<jats:sub>16 : 1</jats:sub> ω7<jats:italic>c</jats:italic>. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major isoprenoid quinone was MK-8(H<jats:sub>2</jats:sub>). Whole-cell hydrolysates contained <jats:italic>meso</jats:italic>-diaminopimelic acid. Arabinose, galactose and ribose were detected as diagnostic sugars from whole-cell hydrolysates. Mycolic acids were detected. The genomic DNA G+C content of strain NEAU-CX67<jats:sup>T</jats:sup> was 64.6 mol%. Strain NEAU-CX67<jats:sup>T</jats:sup> exhibited low average nucleotide identity and digital DNA–DNA hybridization values with <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.6488" xlink:type="simple">R. maanshanensis</jats:ext-link> </jats:named-content> </jats:italic> DSM 44675<jats:sup>T</jats:sup> (92.1 and 45.4 %) and <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.6501" xlink:type="simple">R. tukisamuensis</jats:ext-link> </jats:named-content> </jats:italic> JCM 11308<jats:sup>T</jats:sup> (81.9 and 24.4 %). On the basis of results of phylogenetic, genotypic, physiological and chemotaxonomic analysis, strain NEAU-CX67<jats:sup>T</jats:sup> is considered to represent a novel species of 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.6471" xlink:type="simple">Rhodococcus</jats:ext-link> </jats:named-content> </jats:italic> for which the name <jats:italic>Rhodococcus oryzae</jats:italic> sp. nov. is proposed. The type strain is NEAU-CX67<jats:sup>T</jats:sup> (=DSM 107701<jats:sup>T</jats:sup>=CCTCC AB 2018233<jats:sup>T</jats:sup>).</jats:p>

A stable home for an equine pathogen: valid publication of the binomial Prescottella equi gen. nov., comb. nov., and reclassification of four rhodococcal species into the genus Prescottella.

“…subtropicus as close relatives of each other and of R. equi , although some instability is observed and not all studies include all type strains [8, 16, 20–22, 26–30]. In addition to the five validly published names for species belonging to Group A ( Prescottella ), strain 86–07, originally isolated from a patient with bacteraemia and initially identified as R.…”

“…In addition to the phylogenomic evidence presented in Fig. 1, multiple 16S rRNA phylogenetic analyses typically place R. agglutinans, R. defluvii, R. soli and R. subtropicus as close relatives of each other and of R. equi, although some instability is observed and not all studies include all type strains [8,16,[20][21][22][26][27][28][29][30]. In addition to the five validly published names for species belonging to Group A (Prescottella), strain 86-07, originally isolated from a patient with bacteraemia and initially identified as R. equi [31], was recovered as a distinct species level lineage.…”

Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species

“…Rhodococci have been detected in rhizosphere and phyllosphere microbiota [ 61 , 62 , 63 , 64 , 65 ]. Associated with plants, rhodococci can not only stimulate their productivity [ 66 ], but also cause pathology.…”