Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter

Abstract

Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter Two Gram-stain-negative, yellow, aerobic and rod-shaped bacterial isolates, designated THG-DN3.18 T and THG-DN3.19 T , were isolated from an ancient tree trunk from Daejeon, South Korea. 16S rRNA gene sequence similarity showed that both strains belong to the genus Pedobacter within the family Sphingobacteriaceae. Strain THG-DN3.18 T exhibited maximum sequence similarity with Pedobacter boryungensis KCTC 23344 T (98.5 %) while strain THG-DN3.19 T exhibited maximum sequence similarity with Pedobacter nyackensis LMG 24260 T (97.3 %). In DNA-DNA hybridization tests, the two strains showed less than 35 % relatedness with respect to closely related species of the genus Pedobacter. Both strains contained iso-C 15 : 0 and C 16 : 1 v6c and/or C 16 : 1 v7c (summed feature 3) as the predominant fatty acids and MK-7 as the major isoprenoid quinone. The DNA G+C contents of strains THG-DN3.18 T and THG-DN3.19 T were 35.5 and 40.1 mol%, respectively. The genotypic analysis, biochemical properties, and phenotypic and chemotaxonomic characteristics indicate that strains THG-DN3.18 T and THG-DN3.19 T represent novel species of the genus Pedobacter, for which the names Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov. are proposed. The type strains are THG-DN3.18 T (5KCTC 42230 T 5JCM 30352 T ) and THG-DN3.19 T (5KCTC 42233 T 5JCM 30353 T ), respectively.The genus Pedobacter was first described by Steyn et al. (1998) and belongs to the family Sphingobacteriaceae and order Sphingobacteriales. The genus Pedobacter comprises 46 species with validly published names (http://www. bacterio.net/pedobacter.html) isolated from various environments, most frequently soils (Yoon et al., 2007;Luo et al., 2010;Zhou et al., 2012; Oh et al., 2013). Members of the genus Pedobacter are Gram-negative, rod-shaped bacteria, non-motile or motile by gliding with MK-7 as the major isoprenoid quinone and DNA G+C contents of 36.0-45.0 mol% (Qiu et al., 2014). Recently, the DNA G+C content range of the genus has been revised by Kook et al. (2014) as 36.0-47.5 mol%. The major fatty acids are iso-C 15 : 0 , iso-C 15 : 1 G, iso-C 17 : 0 and iso-C 17 : 0 3-OH. In this study we determined the exact taxonomic position of strains THG-DN3.18 T and THG-DN3.19 T by means of a polyphasic approach. On the basis of chemotaxonomic and physiological data obtained in this study we report on the new isolates THG-DN3.18 T and THG-DN3.19 T belonging to the genus Pedobacter, isolated from an ancient tree trunk from Daejeon, South Korea.Samples from different places in Daejeon, South Korea, including an ancient tree trunk were collected in a sterile ziplock bag. The samples were suspended in 0.85 % (w/v) saline solution, vortexed, serially diluted and spread on plates of nutrient agar (NA; Difco). The plates were incubated at 28 u C for 7 days. Single colonies were purified by continuous subculturing on NA. Two bacte...

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

“…Indeed, Pedobacter (Steyn et al, 1998; Vanparys et al, 2005; Gallego et al, 2006; Hwang et al, 2006; Zhou et al, 2012; Farfán et al, 2014; Kook et al, 2014; Du et al, 2015) appeared as paraphyletic in the GBDP tree because several species, P. arcticus (Zhou et al, 2012), P. bauzanensis (Zhang et al, 2010b) , P. glucosidilyticus (Luo et al, 2010; Zhou et al, 2012; Hahnke R. L. et al, 2016) , P. luteus (Oh et al, 2013), P. oryza (Jeon et al, 2009), P. psychrophilus (Švec et al, 2017), and P. ruber (Margesin and Zhang, 2013) were placed apart from the clade containing the type species, P. heparinus (Steyn et al, 1998; Zhou et al, 2012) with high support (Figure 4). The ULT also strongly supported the paraphyly of Pedobacter ; the URT showed the same albeit with lower support (Supplementary Data Sheet 1).…”

Nine novel psychrotolerant species of the genus Pedobacter isolated from Arctic soil with potential antioxidant activities

“…This genus currently comprises 79 species with validly published names (http://www.bacterio.net/pedobacter.html). The description of the genus Pedobacter has been frequently emended, with the recent emendation by Du et al adding oxidase-positive and oxidase-negative species [2]. Members of the genus Pedobacter are non-motile or motile by gliding, Gram-stain-negative, rod-shaped, yellow or pink and contain MK-7 as the predominant isoprenoid quinone; summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ), iso-C 15 : 0 and iso-C 17 : 0 3-OH as major fatty acids; and DNA G+C content ranges from 36 to 47.5 mol% [1–4].…”

“…The description of the genus Pedobacter has been frequently emended, with the recent emendation by Du et al adding oxidase-positive and oxidase-negative species [2]. Members of the genus Pedobacter are non-motile or motile by gliding, Gram-stain-negative, rod-shaped, yellow or pink and contain MK-7 as the predominant isoprenoid quinone; summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ), iso-C 15 : 0 and iso-C 17 : 0 3-OH as major fatty acids; and DNA G+C content ranges from 36 to 47.5 mol% [1–4]. Species of the genus Pedobacter are cosmopolitan in habitat, and psychrophilic and psychrotolerant members have been isolated from soil, glacier, rock and cryoconite samples [4–10].…”

“…Moreover, the presence of unidentified aminolipids, amniophospholipids, phosphoglycolipids, glycolipids and polar lipids differentiate the proposed novel species from closely related species of the genus Pedobacter (Fig. S6) [2, 4, 42].…”

Pedobacter lignilitoris sp. nov., isolated from wood falls

“…The genus Pedobacter , a member of the family Sphingobacteriaceae of the phylum Bacteroidetes (Margesin & Shivaji, 2010), was proposed by Steyn et al (1998) with the reclassification of Sphingobacterium heparinum and Sphingobacterium piscium and the descriptions of two novel species, Pedobacter africanus and Pedobacter saltans . At the time of writing, the genus comprised at least 52 species with validly published names (http://www.bacterio.net/pedobacter.html; Euzéby, 1997; Du et al , 2015; Ngo et al , 2015; Park et al , 2015). Members of the genus Pedobacter have been isolated from a variety of habitats, including temperate and Antarctic soils, glacial cryoconites and foreland samples, activated sludge, fish, aquatic environments, a nitrifying inoculum, compost, chilled food and tree material (Steyn et al , 1998; Margesin et al , 2003; Vanparys et al , 2005; Baik et al , 2007; Muurholm et al , 2007; Gordon et al , 2009; Lee et al , 2009; Zhou et al , 2012; Derichs et al , 2014; Farfán et al , 2014; Qiu et al , 2014; Du et al , 2015).…”