Rhodococcus pseudokoreensis sp. nov. isolated from the rhizosphere of young M26 apple rootstocks

Abstract

The Gram-positive strain R79T, isolated from the rhizosphere of young M26 apple rootstocks, was investigated by a polyphasic taxonomic approach. Phylogenetic identification based on the full-length 16S rRNA gene sequence revealed highest 16S rRNA gene sequence similarity to the type strains of Rhodococcus wratislaviensis (99.6%) and Rhodococcus opacus (99.2%) followed by Rhodococcus imtechensis (98.9%). All other 16S rRNA gene sequence similarities were below 98.65%. A phylogenomic tree calculated based on a whole-genome sequence also showed a distinct clustering with the type strain of Rhodococcus koreensis. Average nucleotide identity (ANI) values between whole-genome sequences of R79T and the closest related type strains were below 95% supported the novel species status. The DNA G + C content of R79T was 67.24% mol. Predominant fatty acids were C16:0, C15:0 and C17:1ω8c. The strain contained MK8-H2 as the major respiratory quinone. The polar lipid profile consists of diphosphatidylglycerol and phosphatidylethanolamine, as well as of some unidentified lipids. The peptidoglycan type of the strain is A1γ meso-diaminopimelic acid. Based on the obtained genotypic and phenotypic, including chemotaxonomic data, we conclude that R79T represents a novel species of the genus Rhodococcus, for which the name Rhodococcus pseudokoreensis sp. nov. is proposed. The type strain is R79T (= DSM 113102T = LMG 32444T = CCM 9183T).

Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus electrodiphilus (Ramaprasad et al. 2018) as a later heterotypic synonym of Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980)

“…electrodiphilus LMG 29881 T and R. ruber DSM 43338 T were examined for phenotypic properties known to be of value in rhodococcal systematics [23–25]. Biochemical, degradation and physiological properties were acquired using media and methods described by Williams et al [67] and enzymatic profiles using API-ZYM strips (bioMérieux).…”

“…Isolate CSLK01-03 T , R. aetherivorans DSM 44752 T , R. electrodiphilus LMG 29881 T and R. ruber DSM 43338 T were examined for phenotypic properties known to be of value in rhodococcal systematics [23][24][25]. Biochemical, degradation and physiological Fig.…”

“…Given the changes outlined above, the genus Rhodococcus contains around 50 validly named species (https://lpsn.dsmz.de/genus/rhodococcus) including R. rhodochrous , the type species, and the recently described Rhodococcus oxybenzonivorans [24], Rhodococcus pseudokoreansis [25], Rhodococcus spelaei [23] and Rhodococcus spongicola [26]. The revised genus encompasses aerobic, Gram-stain-positive to Gram-stain-variable, nonmotile, partially acid-fast actinomycetes with a rod–coccus growth cycle.…”

“…Draft genome sizes range from 3.9 to 10.4 Mbp and DNA G+C contents from 61.8 to 70.7 mol% [11, 13, 26]. Rhodococci are common in diverse natural habitats [25, 27], and are a source of valuable bioactive compounds, such as antimicrobial agents, bioflocculants, biosurfactants and enzymes [28–30]. Some are pathogens of animals, including humans [27, 31] and others are serious plant pathogens [32].…”

“…The revised genus encompasses aerobic, Gram-stain-positive to Gram-stain-variable, nonmotile, partially acid-fast actinomycetes with a rod-coccus growth cycle. Whole-organism hydrolysates are rich in meso-2.6-diaminopimelic acid, arabinose and galactose, muramic acid moieties are N-glycolated, the predominant menaquinone is MK-8 (H 2 ), the major phospholipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol mannosides, mycolic acids are present, and fatty acids consist of major proportions of straight-chain saturated, monounsaturated and 10-methyl branched chain components [23][24][25][26]. Draft genome sizes range from 3.9 to 10.4 Mbp and DNA G+C contents from 61.8 to 70.7 mol% [11,13,26].…”