Rhodococcus oxybenzonivorans sp. nov., a benzophenone-3-degrading bacterium, isolated from stream sediment

Abstract

A Gram-stain-positive, facultative aerobic, oxidase-negative, catalase-positive, non-sporulating, and non-motile bacterium, which degraded benzophenone-3, was isolated from stream sediment collected in the Republic of Korea and designated as strain S2-17T. Cells of this strain were rod-shaped during the early growth phase but became coccoid after the late exponential growth phase. Bacterial growth was observed at 15–37 °C (optimum, 25–30 °C) and pH 6.0–9.5 (optimum, pH 7.5–8.5) and in the presence of 0–9.0 % (w/v) NaCl (optimum, 0–1.0 %). Menaquinone-8 (H2) was the sole isoprenoid quinone, and C16 : 0, C17 : 1 ω8c, summed feature 3 (comprising C16 : 1 ω7c/C16 : 1 ω6c) and C18 : 1 ω9c were the major fatty acids. The cell wall of strain S2-17T contained meso-diaminopimelic acid, and arabinose, galactose and mycolic acid were found in whole-cell hydrolysates, suggesting a chemotype IV cell wall. The G+C content of the genome was 65.6 mol%. Phylogenetic analyses revealed that strain S2-17T formed a phyletic lineage within the genus Rhodococcus and was most closely related to Rhodococcus jostii DSM 44719T (99.2 % 16S rRNA gene sequence similarity). Average nucleotide identity and digital DNA–DNA hybridization values between strain S2-17T and R. jostii DSM 44719T were 82.6 and 26.5 %, respectively, indicating differences between the species. Based on its phenotypic, chemotaxonomic and molecular features, strain S2-17T represents a novel species of the genus Rhodococcus , for which the name Rhodococcus oxybenzonivorans sp. nov. is proposed. The type strain is S2-17T (=KACC 19281T=JCM 32046T).

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.…”

“…The isolate exhibited chemotaxonomic, cultural and micromorphological properties typical of Rhodococcus strains [18,20,23,24,27]. The organism proved to be an aerobic, Gram-stain-positive, partially acid-alcohol-fast, nonmotile actinomycete which was shown to form rod-and coccoid-like elements and orange red colonies on ISP3 agar (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.…”

“…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].…”