Epilithonimonas ginsengisoli sp. nov., isolated from soil of a ginseng field

Abstract

A novel Gram-staining-negative, rod-shaped bacterium, designated DCY78 T , was isolated from soil of a ginseng field in Yeon-cheon province (386 049 000 N 1266 579 000 E), Republic of Korea. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain DCY78 T belonged to the genus Epilithonimonas and was most closely related to Epilithonimonas lactis DSM 19921 T (98.5 % sequence similarity) and Epilithonimonas tenax DSM 16811 T (97.8 %). Growth occurred at 10-30 6C with an optimum temperature of 28 6C. The pH range for growth was pH 5.5-8.0. The major polar lipids were found to be phosphatidylethanolamine three unidentified amino lipids and one unidentified polar lipid. The only predominant quinone was MK-6. The major polyamines were sym-homospermidine and spermidine. The major fatty acids were summed feature 3 (comprising C 16 : 1 v6c and/or C 16 : 1 v7c), iso-C 15 : 0 and iso-C 17 : 0 3-OH. The DNA G+C content was 37.9 mol%. On the basis of the phenotypic and genotypic analysis, the isolate is classified as representative of a novel species in the genus Epilithonimonas, for which the name Epilithonimonas ginsengisoli is proposed. The type strain is DCY78 T (5KCTC 32174 T 5JCM 19896 T ).

Genome-Based Taxonomic Classification of Bacteroidetes

“…The polar-lipid patterns of Epilithonimonas also fit very well to that revision of Chryseobacterium (Table 2); the sole exception is E. psychrophila , for which only phosphatidylethanolamine and a single unknown lipid were reported; given its well-supported position within a core group of four Epilithonimonas species and the general faintness of the published thin-layer chromatogram (Ge et al, 2015), this can hardly be regarded as an argument against the unification of the genera. Moreover, the two genera have overlapping habitats and other interesting features in common, such as the production of indole-3-acetic acid for promoting plant growth (Montero-Calasanz et al, 2014; Hoang et al, 2015). Thus, the three physiological features that conflict between the original description of Chryseobacterium (Vandamme et al, 1994) and some or all of the Epilithonimonas species rather call for an emendation of Chryseobacterium .…”

“…A single star indicates slightly misinterpreted summed features according to the corrected description of Chryseobacterium (Montero-Calasanz et al, 2014); two stars indicate more strongly misinterpreted summed features. Values in parentheses are those not included in the respective species descriptions (O'Sullivan et al, 2006; Shakéd et al, 2010; Feng et al, 2014; Ge et al, 2015; Hoang et al, 2015). Physiological data for Chryseobacterium are from its original description (Vandamme et al, 1994).…”

“…The description is the same as for Epilithonimonas ginsengisoli (Hoang et al, 2015) with the following modification. Summed feature 3 should be interpreted as iso-C 15:0 2-OH (Montero-Calasanz et al, 2014).…”

Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens

“…The genus Planobacterium was created with the description of Planobacterium taklimakanense [11], which was later proposed to belong to the genus Chryseobacterium on the basis of 16S rRNA gene sequence similarity [12]. The genus Epilithonimonas was created to accommodate the species Epilithonimonas tenax [13], and by 2015 the genus had grown to contain four more species [14–17]. The species of the genus Epilithonimonas were subsequently transferred to the genus Chryseobacterium [18], despite the recognition that this would cause the genus Chryseobacterium to contain three separate lineages.…”

Epilithonimonas psychrotolerans sp. nov., isolated from alpine permafrost

“…A second recognized species of the genus was then described, Epilithonimonas lactis (Shakéd et al , 2010), which was isolated from untreated cow's milk. Recently, two novel species have been established: Epilithonimonas xixisoli (Feng et al , 2014), isolated from wetland, and Epilithonimonas ginsengisoli (Hoang et al , 2015), isolated from ginseng rhizophere soil. Members of the genus Epilithonimonas are distributed in different freshwater and soil ecosystems.…”