Stakelama pacifica gen. nov., sp. nov., a new member of the family Sphingomonadaceae isolated from the Pacific Ocean

Abstract

Stakelama pacifica gen. nov., sp. nov., a new member of the family Sphingomonadaceae isolated from the Pacific Ocean Strain JLT832 T was isolated from the surface of the Pacific Ocean at 174 u 21.709 E 20 u 34.449 N and formed a deep branch within the family Sphingomonadaceae. In this study, we characterized strain JLT832T by using a polyphasic approach. Strain JLT832T was initially isolated with seawater medium (SW) containing (per litre seawater filtered by 0.2 mm film) 1 g peptone, 1 g yeast extract, 20 mg vitamin B 12 and 1 ml of a trace element solution (ES) as described by Drews (1983). The strain was identified by growing on modified rich organic (RO) medium (Yurkov et al., 1999) Cell morphology was examined using light microscopy (BX61; Olympus) and TEM (H600; Hitachi). The Gram Abbreviations: UPLC-Q-TOF-MS, ultra-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry; MR, methyl red; VP, Voges-Proskauer.The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain JLT832T is EU581829.A transmission electron micrograph of negatively stained cells and polar lipid profiles of strain JLT832 T are available as supplementary material with the online version of this paper.

Hephaestia caeni gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from activated sludge

“…Since fatty acid profile analysis has played a central role in the pioneering taxonomic studies of the family Sphingomonadaceae (Busse et al, 1999;Takeuchi et al, 2001;Yabuuchi et al, 2002), besides the most closely related type strains shown in Table 1, all type species of closely related genera were involved in our comparative analysis (Table 2). In members of the family Sphingomonadaceae, C 18 : 1 v7c is the characteristic predominant fatty acid and the presence of 2-hydroxy fatty acids, mainly C 14 : 0 2-OH, is common, while C 17 : 1 v6c is usually present in lower amounts or is even absent (Busse et al, 1999;Takeuchi et al, 2001;Maruyama et al, 2006;Huang et al, 2009;Chen et al, 2010;Liang & Lloyd-Jones, 2010;Kämpfer et al, 2012;Uchida et al, 2012). This latter compound was found in high amounts in ERB1-3 T (29.2 %) compared with the most closely related type strains, and in ERB1-3 T , C 15 : 0 2-OH was another characteristic hydroxy fatty acid (representing .5 %).…”

“…Later, this genus was subdivided into four genera, Sphingomonas sensu stricto, Sphingobium, Novosphingobium and Sphingopyxis (Takeuchi et al, 2001), and in recent years, several additional new genera have been described and assigned to the family Sphingomonadaceae (e.g. Parasphingopyxis, Sphingosinicella, Sphingomicrobium and Stakelama; Maruyama et al, 2006;Chen et al, 2010;Kämpfer et al, 2012;Uchida et al, 2012). Sphingomonads are widely distributed in nature and have been isolated from different aqueous and terrestrial habitats as well as from clinical specimens (Balkwill et al, 2006).…”

“…Sphingomonads are widely distributed in nature and have been isolated from different aqueous and terrestrial habitats as well as from clinical specimens (Balkwill et al, 2006). Furthermore, these bacteria are metabolically versatile and are able to utilize a wide range of naturally occurring or refractory organic compounds (Balkwill et al, 2006 (5DSM 25059 T ), were maintained on TSA, nutrient (medium 1, DSMZ) and seawater agar (Chen et al, 2010), respectively, at the same temperature. Temperature, pH and salt concentration optima were determined in the corresponding media given above.…”

Sphingoaurantiacus polygranulatus gen. nov., sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of the genera Sandarakinorhabdus, Polymorphobacter and Rhizorhabdus and the species Sandarakinorhabdus limnophila, Rhizorhabdus argentea and Sphingomonas wittichii

“…, Blastomonas (Sly & Cahill, 1997), Sandaracinobacter (Yurkov et al, 1997), Sphingosinicella (Maruyama et al, 2006), Sandarakinorhabdus (Gich & Overmann, 2006), Stakelama (Chen et al, 2010), Parasphingopyxis (Uchida et al, 2012), Sphingomicrobium (Kämpfer et al, 2012), Sphingorhabdus (Jogler et al, 2013) Hephaestia (Felföldi et al, 2014, Polymorphobacter (Fukuda et al, 2014) and Rhizorhabdus and Rhizorhapis (Francis et al, 2014). These members of the family Sphingomonadaceae share several phenotypic features, such as a polar lipid pattern containing sphingoglycolipids, the presence of Q-10 as their predominant respiratory quinone (Balkwill et al, 2006;Yabuuchi et al, 1990), a fatty acid profile containing C 14 : 0 2-OH fatty acid and a polyamine pattern with either spermidine or homospermidine as the major component.…”

Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae , and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.

“…Yabuuchi et al (2002) and Yabuuchi & Kosako (2005) continued to use the genus name Sphingomonas, since the new combinations created by Takeuchi et al (2001) were also homotypic synonyms of species names within the genus Sphingomonas. Recently, three additional genera were classified within the family Sphingomonadaceae, namely Sphingosinicella (Maruyama et al, 2006), Stakelama (Chen et al, 2010) and Sphingomicrobium (Kämpfer et al, 2012). It should be noted, however, that Takeuchi et al (2001) did not alter the nomenclature of Rhizomonas suberifaciens van Bruggen et al 1990, indicating that they considered this species to be a member of a separate genus.…”