Abstract
A novel bacterial strain designated CJ43T was isolated from fresh water located in Gangwon-do, South Korea, displaying multi-drug resistance. The isolate was Gram-stain-negative, aerobic, orange-pigmented, and rod-shaped. Strain CJ43T grew optimally at 30°C and pH 7 on R2A agar in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain CJ43T belonged to the genus Pedobacter in the family Sphingobacteriaceae and was most closely related to Pedobacter puniceum HX-22-1T and P. glucosidilyticus 1-2T (98.3 and 98.1% sequence similarity). The genome size of strain CJ43T was 3.9Mb in a single contig with DNA G + C content of 34.9%. The genome included 3144 predicted protein-coding genes, as well as 55 tRNA, 9 rRNA and 3 ncRNA genes. The genome also contained 128 putative antibiotic resistance genes, reflecting its phenotypes. The average nucleotide identity values between strain CJ43T and two closely related strains P. puniceum HX-22-1T and P. glucosidilyticus 1-2T were 91.0 and 88.7%, respectively. In silico digital DNA-DNA hybridization results between strain CJ43T and the related strains were 42.8 and 38.6%, respectively. The major fatty acids of strain CJ43T were iso-C15:0, iso-C17:0 3-OH, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). Strain CJ43T contained phosphatidylethanolamine as the major polar lipid and menaquinone-7 as the sole respiratory quinone. Based on the polyphasic taxonomy data, strain CJ43T represents a novel species of the genus Pedobacter, for which the name Pedobacter aquae sp. nov. is proposed with the type strain CJ43T (= KACC 21350T = JCM 33709T).
Highlights
The genus Pedobacter, first proposed by Steyn et al (1998), belongs to the family Sphingobacteriaceae comprising four species
As inferred from the phylogenetic tree (Fig. 1), strain CJ43T formed a robust cluster with Pedobacter glucosidilyticus 1-2T, which has the highest 16S rRNA gene sequence similarity (98.1%), followed by P. rivuli HME8457T (94.4%) and P. pituitosus MIC2002T (93.6%)
Based on the observed pairwise 16S rRNA gene sequence identities below the established threshold (Stackebrandt and Ebers 2006; Kim et al 2014; Rosselló-Móra and Amann 2015), strain CJ43T represents a novel species within the genus Pedobacter
Summary
The genus Pedobacter, first proposed by Steyn et al (1998), belongs to the family Sphingobacteriaceae comprising four species. Members of the genus Pedobacter were recovered from various environmental habitats, including water (Gallego et al 2006; Baik et al 2007; An et al 2009; Urios et al 2013; Chun et al 2014; Kang et al 2014; Joung et al 2018), plant rhizosphere (Kwon et al 2007, 2011), sediment (Gordon et al 2009), activated sludge (Zhang et al 2018), glaciers (Shivaji et al 2005; Qiu et al 2014), and arctic tundra soil (Zhou et al 2019). We establish the taxonomic position of strain CJ43T, isolated from fresh water at Gangwon-do, South Korea, using polyphasic taxonomy and genomics approaches
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