Sphingomonas daechungensis sp. nov., isolated from sediment of a eutrophic reservoir

Abstract

Strain CH15-11T , isolated from a sediment sample taken from Daechung Reservoir, SouthKorea, during the late-blooming period of cyanobacteria, was found to be a Gram-stain-negative, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain CH15-11 T grew optimally at pH 7 and 28-30 6C. According to a phylogenetic tree based on 16S rRNA gene sequences, strain CH15-11 T belonged to the genus Sphingomonas and clustered withSphingomonas sediminicola Dae 20 T , with which it shared the highest 16S rRNA gene sequence similarity (97.6 %). Chemotaxonomic analysis showed that strain CH15-11T had characteristics typical of members of the genus Sphingomonas, such as the presence of sphingoglycolipid, ubiquinone Q-10 and sym-homospermidine. Plus, strain CH15-11 T included summed feature 8 (C 18 : 1 v7c and/or C 18 : 1 v6c) and C 16 : 0 as the major fatty acids. The genomic DNA G+C content was 65.6 mol%. Sequence data showed that strain CH15-11 T was most closely related to Sphingomonas sediminicola Dae 20 T (97.6 %), Sphingomonas ginsengisoli Gsoil 634 T (97.2 %) and Sphingomonas jaspi TDMA-16 T (97.0 %). However, the DNA-DNA relatedness values between strain CH15-11 T and the most closely related type strains were within a range of 35-59 %. Thus, based on the phylogenetic, phenotypic and genetic data, strain CH15-11 T wasclassified as a member of the genus Sphingomonas as a representative of a novel species, for which the name Sphingomonas daechungensis sp. nov. is proposed. The type strain is CH15-11 T (5KCTC 23718 T 5JCM 17887 T ).The genus Sphingomonas was first proposed by Yabuuchi et al. (1990) and the genus description has been subsequently emended by Takeuchi et al. (2001), Yabuuchi et al. (2002 and Busse et al. (2003). A taxonomic study classified the genus as part of the family Sphingomonadaceae of the class Alphaproteobacteria. Based on the 16S rRNA gene sequences, polyamine patterns and polar lipid profiles, Takeuchi et al. (2001) proposed that the genus Sphingomonas should be divided into four genera, Sphingomonas, Novosphingobium, Sphingobium and Sphingopyxis. At the time of writing, the genus Sphingomonas consists of more than 60 species with validly published names. Members of the genus Sphingomonas are aerobic, rodshaped, Gram-reaction-negative, yellow-to orange-or redpigmented colonies and display the presence of 2-hydroxy fatty acids (C 14 : 0 2-OH) and the absence of 3-hydroxy fatty acids. The species of the genus also contain ubiquinone Q-10, sphingoglycolipid and homospermidine as the major respiratory quinone, polar lipid and polyamine, respectively. The present study reports on the taxonomic characterization of a Sphingomonas-like bacterial strain, CH15-11 T , which was isolated from a shoreline area, Chusori, of Daechung Reservoir in the central region of South Korea during the late-blooming period of cyanobacteria in summer. The isolated strain was identified using the EzTaxon-e database (http://eztaxon-e.ezbiocloud.et/; Kim et al., 2012) on the basis of 16S rRNA gene sequence data....

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

“…Sphingomonas species are commonly found in contaminated soil, albeit those containing high levels of polycyclic aromatic hydrocarbon in particular (due to their capacity to utilize these compounds as a carbon source). The 17 sub-OTUs sequences shared 87% identical sites and were similar to isolated species from Korea: Sphingomonas flava (Gyeonggi Province; Du et al, 2015 ), S. daechungensis , S. sediminicola (Daecheong Dam; An et al, 2013 ; Huy et al, 2014 ), S. oryziterrae (Jinju Province; Chung et al, 2011 ), and S. vulcanisoli (Gotjawal Forest; Lee et al, 2015 ) as well as Japan: S. jaspsi Tottori ( Asker et al, 2007 ) ( Supplementary File 3 ).…”

Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth

“…Members of the genus Sphingomonas are yellow-pigmented, rod-shaped, nonsporulating, Gram-negative, chemoheterotrophic, and aerobic bacteria that belong to class Alphaproteobacteria within the phylum Proteobacteria (Busse et al 2003 ). Sphingomonas species have been isolated from several different environments; novel strains have recently been isolated from abandoned heavy metal sites (Feng et al 2014 ), forest soil (Kim et al 2014 ), indoor air of pharmaceutical environments (Park et al 2015 ), purplish paddy soil (Huang et al 2014 ), glaciers (Miteva et al 2004 ), volcano-associated lakes (Farias et al 2011 ), space shuttles (Pan et al 2016b ), permafrost (Piao et al 2016 ), and the sediment of a eutrophic reservoir (Huy et al 2014 ). However, there are few reports describing Sphingomonas species as endophytes.…”

Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand

“…At the time of this writing, 161 species have been validly published according to the List of Prokaryotic names with Standing in Nomenclature (LPSN; https://lpsn.dsmz.de/genus/sphingomonas). Species of Sphingomonas have been known to inhabit a wide range of environments and have been isolated from sources such as clinical specimens [3, 6], sand [7, 8], rhizospheres [9], reservoir sediments [10] and lead−zinc mines [11, 12].…”

“…de/ genus/ sphingomonas). Species of Sphingomonas have been known to inhabit a wide range of environments and have been isolated from sources such as clinical specimens [3,6], sand [7,8], rhizospheres [9], reservoir sediments [10] and lead−zinc mines [11,12].…”