Sphingopyxis italica sp. nov., isolated from Roman catacombs

Abstract

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, strain SC13E-S71 T , was isolated from tuff, volcanic rock, where the Roman catacombs of Saint Callixtus in Rome, Italy, was excavated. Analysis of 16S rRNA gene sequences revealed that strain SC13E-S71 T belongs to the genus Sphingopyxis, and that it shows the greatest sequence similarity with Sphingopyxis chilensis DSM 14889 T (98.72 %), Sphingopyxis taejonensis DSM 15583 T (98.65 %), Sphingopyxis ginsengisoli LMG 23390 T (98.16 %), Sphingopyxis panaciterrae KCTC 12580 T (98.09 %), Sphingopyxis alaskensis DSM 13593 T (98.09 %), Sphingopyxis witflariensis DSM 14551 T (98.09 %), Sphingopyxis bauzanensis DSM 22271 T (98.02 %), Sphingopyxis granuli KCTC 12209 T (97.73 %), Sphingopyxis macrogoltabida KACC 10927 T (97.49 %), Sphingopyxis ummariensis DSM 24316 T (97.37 %) and Sphingopyxis panaciterrulae KCTC 22112 T (97.09 %). The predominant fatty acids were C 18 : 1 v7c, summed feature 3 (iso-C 15 : 0 2-OH and/ or C 16 : 1 v7c), C 14 : 0 2-OH and C 16 : 0 . The predominant menaquinone was MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. These chemotaxonomic data are common to members of the genus Sphingopyxis. However, a polyphasic approach using physiological tests, DNA base ratios, DNA-DNA hybridization and 16S rRNA gene sequence comparisons showed that the isolate SC13E-S71 T belongs to a novel species within the genus Sphingopyxis, for which the name Sphingopyxis italica sp. nov. is proposed. The type strain is SC13E-S71 T (5DSM 25229 T 5CECT 8016 T ).The genus Sphingopyxis was proposed by Takeuchi et al. (2001) to include the type species Sphingopyxis macrogoltabida and Sphingopyxis terrae, which Takeuchi et al. (1993) had previously described as Sphingomonas macrogoltabidus and Sphingomonas terrae. At the time of writing, the genus Sphingopyxis comprises 16 species: Sphingopyxis macrogoltabida (Takeuchi et al., 1993, Sphingopyxis terrae (Takeuchi et al., 1993 et al., 2013) and Sphingopyxis wooponensis (Baik et al., 2013). Members of this genus are Gram-negative, non-spore-forming, aerobic, chemo-organotrophic, catalase-positive, yellow or whitish-brown-pigmented bacteria with a DNA G+C content of 58.0-69.2 mol%. The type strains of these species have been isolated from sediment, soil, sludge and water; however, novel species of Sphingopyxis have not yet been described either in subterranean environments or volcanic rock. In this study, we describe strain SC13E-S71 T retrieved from tuff, a volcanic rock from the Roman catacombs of Saint Callixtus in Rome, Italy. A polyphasic approach showed that this isolate belongs to a novel species within the genus Sphingopyxis.Strain SC13E-S71 T was isolated on tryptose soy agar (TSA; Oxoid) after 2 weeks at 28 u C. The methods used in this study have been described previously (Jurado et al., 2005a, b), unless indicated otherwise. Morphological, physiological and chemotaxonomic studies were carried out in trip...

Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid

“…Additionally, small amounts of phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, a further aminolipid and an unidentified lipid were identified. These lipids have also been reported for other species of the genera Sphingomonas and Sphingopyxis (Alias-Villegas et al , 2013; Busse et al , 1999; Zhang et al , 2010). Ubiquinone Q-10 (100 %) was the major respiratory quinone of strain Kp5.2 T , which is in accordance with other members of the genera Sphingopyxis , Sphingobium and Sphingomonas (Busse et al , 1999; Takeuchi et al , 2001).…”

“…Strain Kp5.2 T was stored on mineral medium plates (modified from Dorn et al , 1974) in the presence of 20 g glucose l − 1 at 30 °C for preservation (Oelschlägel et al , 2012, 2014). Cultures grown on this solid medium were additionally used for the determination of Gram behaviour by staining (based on Gerhardt et al , 1981; Gram, 1884) and the KOH method (Halebian et al , 1981), of catalase activity by a method described by Alias-Villegas et al (2013) and of cytochrome oxidase activity by streaking out biomass on a filter paper that was previously dropped with a 2 : 3 mixture of 1 % (w/v) 1-naphthol (in ethanol) and 1 % (w/v) N , N -dimethyl p -phenylene diammonium dichloride (modified from Gaby & Hadley, 1957). Additionally, cells from these solid medium-grown colonies were used to determine the temperature-dependence of growth as well as morphology and motility by phase-contrast microscopy (Fig.…”

“…To determine further enzyme activities and the assimilation of different substrates, API 20 NE and API ZYM strips (bioMérieux) were used and interpreted according to the instructions of the manufacturer. For this purpose, strain Kp5.2 T and the reference strains Sphingopyxis italica DSM 25229 T (Alias-Villegas et al , 2013), Sphingopyxis panaciterrae DSM 27164 T (Lee et al , 2008), Sphingopyxis chilensis DSM 14889 T (Godoy et al , 2003) and Sphingopyxis bauzanensis DSM 22271 T (Zhang et al , 2010) were cultivated on lysogeny broth (LB) medium plates (Sambrook et al , 2001) at 30 °C. After 7 days, the colonies were applied directly for the API assay.…”

Nocardioides marinquilinus sp. nov., isolated from coastal seawater

“…The genus Nocardioides , first described by Prauser (1976), belongs to the family Nocardioidaceae , in the suborder Propionibacterineae (Zhi et al , 2009). At the time of writing, the genus Nocardioides comprised 62 species including 58 with validly published names in the List of Prokaryotic Names with Standing in Nomenclature (http://www.bacterio.cict.fr) and four species in press, with names which have been validly published during the processing of this manuscript, Nocardioides albertanoniae isolated from Roman catacombs (Alias-Villegas et al , 2013), Nocardioides perillae isolated from the surface-sterilized root of Perilla frutescens (Du et al , 2013) and Nocardioides szechwanensis and Nocardioides psychrotolerans isolated from Hailuogou glacier in Szechwan, China (Liu et al , 2013). Some members in the genus Nocardioides have been isolated from various environments and ten species have been discovered from various marine environments: Nocardioides aestuarii (Yi & Chun, 2004a) and Nocardioides ganghwensis (Yi & Chun, 2004b) from tidal flat sediment, Nocardioides basaltis (Kim et al , 2009), Nocardioides dokdonensis (Park et al , 2008), Nocardioides marinisabuli (Lee et al , 2007), Nocardioides furvisabuli (Lee, 2007) and Nocardioides hwasunensis (Lee et al , 2008) from beach sand, Nocardioides marinus (Choi et al , 2007) from seawater, Nocardioides salarius from seawater enriched with zooplankton (Kim et al , 2008) and Nocardioides caricicola (Song et al , 2011) from a halophyte growing on a sand dune.…”

Rhodococcus yananensis sp. nov., a novel denitrification actinobacterium isolated from microbial fermentation bed material from a pig farm

“…Oxidase activity was determined using 1% N , N -dimethyl- p -phenylenediamine dihydrochloride and 1 % α-naphthol ethanol liquor. The catalase activity test was performed by the observation of the formation of bubbles using a commercial dropper catalase reagent (bioMérieux) [15]. Nitrate reduction and denitrification were determined by Griess reagent after 5 days of liquid culture.…”