Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica

Abstract

A red-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, strain R2-28 T , was isolated from a soil sample collected from Ardley Island, South Shetland Islands, Antarctica, and was characterized taxonomically by using a polyphasic approach. The organism grew optimally at 18 8C in TSB. On the basis of phylogenetic analyses of the 16S rRNA gene sequence, strain R2-28 T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae. The highest levels of 16S rRNA gene sequence similarity were found with respect to Pedobacter alluvionis NWER-II11 T (95.6 %) and Pedobacter terrae DS-57 T (95.2 %). The DNA G+C content was 39.9 mol%, and MK-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine and a sphingolipid. The predominant cellular fatty acids were iso-C 15 : 0 , anteiso-C 15 : 0 , iso-C 17 : 0 3-OH and summed feature 3 (comprising C 16 : 1 v7c and/or C 16 : 1 v6c). These chemotaxonomic and phylogenetic data supported the allocation of strain R2-28 T to the genus Pedobacter. Additionally, the results of physiological and biochemical tests allowed phenotypic differentiation of strain R2-28 T from species of the genus Pedobacter with validly published names. Therefore, strain R2-28 T represents a novel species within the genus Pedobacter, for which the name Pedobacter ardleyensis sp. nov. is proposed. The type strain is R2-28 T (5CCTCC AB 2013365 T 5LMG 28255 T ).The genus Pedobacter and the family Sphingobacteriaceae were described by Steyn et al. (1998). Subsequently, the description of the genus has been emended by Vanparys et al. (2005), Hwang et al. (2006, Gallego et al. (2006) and Zhou et al. (2012). At the time of writing, the genus Pedobacter comprised 46 species. All members of the genus are obligately aerobic, non-endospore-forming, Gram-stain-negative rods that lack flagella and are negative for urease, gelatinase and indole production (Margesin & Zhang, 2013). All members of the genus Pedobacter contain menaquinone 7 (MK-7) as the major respiratory quinone and have DNA G+C contents in the range 36-45 mol%. Furthermore, they have been confirmed to possess phosphatidylethanolamine and sphingolipids (Zhou et al., 2012). Members of the genus Pedobacter have been isolated from various terrestrial and aquatic environments such as soil, drinking water, activated sludge, glacier cryoconite, glacial water, a nitrifying inoculum, a hypertrophic pond and sediment (Hwang et al., 2006;An et al., 2009;Gallego et al., 2006; Kwon et al., 2007Kwon et al., , 2011Lee et al., 2009;Luo et al., 2010;Margesin et al., 2003;Roh et al., 2008;Shivaji et al., 2005;Tang et al., 2010;Vanparys et al., 2005). In this study, an Antarctic bacterial isolate was subjected to a polyphasic analysis and was identified as a novel member of the genus Pedobacter.The soil sample was collected from a penguin colony on Ardley Island, Antarctica (628 12.6889 S 588 55.7289 W). At the time of sampling, the soil had a pH of 6.0 and a temperature of 3.0 8C at 5 cm below the surface. T...

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

“…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]. Most of the psychrotolerant and psychrophilic isolates are from Arctic and Antarctic regions.…”

Lactobacillus enshiensis sp. nov., a novel arsenic-resistant bacterium

“…To determine the optimal conditions for strain HBUAS57009 T , growth of cultures in mMRS broth was compared at a range of: temperatures (4, 10, 15, 20, 25, 28, 30, 35, 37, and 40 °C); pH values (pH 3.0–10.0 in 0.5 pH unit intervals); and NaCl concentrations (0–15 % NaCl, w/v, in 1 % intervals]. Appropriate biological buffers were used to achieve the pH ranges evaluated, specifically: citrate buffer, pH 3.0–5.0; phosphate buffer, pH 6.0–8.0; and NaHCO 3 /Na 2 CO 3 buffer, pH 9.0-10.0 [20]. Alcohol tolerance was determined from growth measurements made in the presence of alcohol at different concentrations (0–16 vol%, in 2 vol% unit intervals) in mMRS broth.…”

Hymenobacter terrestris sp. nov. and Hymenobacter lapidiphilus sp. nov., isolated from regoliths in Antarctica

“…Growth at different temperatures (1, 5, 10, 15, 20, 25 and 30 °C) and tolerance to various NaCl concentrations (0.5, 1, 2 and 3%, w/v) were determined based on cultivation on R2A agar plates for up to 4 days [13]. The pH range for growth was tested on R2A agar plates adjusted to pH 6.0–9.0 using different buffer systems (pH 6.0–8.0, 0.1 M KH 2 PO 4 /0.1 M NaOH; pH 9.0, 0.1 M NaHCO 3 /0.1 M Na 2 CO 3 ; at intervals of 1 pH unit) for 1 week at 15 °C [40]. Liquid cultures were not used, because of the poor growth of hymenobacter isolates in broth media [19].…”