Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera

Abstract

A bacterial strain, designated SW6 T , was isolated from the reef-building coral Isopora palifera, collected from seawater off the coast of southern Taiwan, and characterized using a polyphasic taxonomic approach. Strain SW6T was Gram-negative, aerobic, beige coloured, rod-shaped and motile by monopolar flagella. 16S rRNA gene sequence studies showed that the strain clustered closely with Shimia marina JCM 13038 T (97.9 % 16S rRNA gene sequence similarity). Strain SW6 T required NaCl for growth and exhibited optimal growth at 25-30 6C and 3-4 % NaCl. The predominant cellular fatty acid was summed feature 8 (C 18 : 1 v7c/C 18 : 1 v6c; 64.1 %). The major respiratory quinone was ubiquinone Q-10 and the DNA G+C content was 54.9 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from previously described species of the genus Shimia. It is evident from the genotypic, phenotypic and chemotaxonomic data that the new strain should be classified as a representative of a novel species in the genus Shimia. The name proposed for this taxon is Shimia isoporae sp. nov.; the type strain is SW6 T (5LMG 25377 T 5BCRC 80085 T ).The genus Shimia, first proposed by Choi & Cho (2006), belongs to the family Rhodobacteraceae of the order Rhodobacterales, class Alphaproteobacteria, phylum 'Proteobacteria', and currently comprises only one species with a validly published name, Shimia marina. S. marina was isolated from a biofilm formed on an acrylic slide submerged for 1 month in surface water on a coastal fish farm in Tongyeong, South Korea (Choi & Cho, 2006). The aim of the present study was to determine the taxonomic position of a Shimia-like bacterial strain, SW6 T , isolated from the reef-building coral Isopora palifera, collected off the coast of southern Taiwan.A coral sample (50 g) was collected in a sterile bag from the Kenting coast (Pingtung County, southern Taiwan) at a depth of 3-8 m (GPS location: 21 u 569 290 N 120 u 449 700 E), stored at 4 u C and transported to the laboratory within 3-4 h. The coral sample was completely ground and plated on marine agar 2216 (MA; BD Difco) using the standard dilution-plating method. After incubation of the plates at 25 u C for 5 days, strain SW6T was purified as a single colony.The strain was preserved at 280 uC as a 20 % (v/v) glycerol suspension in marine broth 2216 (MB; BD Difco) or by lyophilization with 20 % (w/v) skimmed milk. The type strain of S. marina JCM 13038 T was obtained from the Japan Collection of Microorganisms and used as a reference strain for phenotypic and genotypic tests.The bacterial cells were observed by phase-contrast microscopy (DM 2000; Leica) in the lag, exponential and stationary phases of growth to ascertain morphology. Cell motility was tested by the hanging drop and semi-solid agar methods. The Spot Test flagella stain (BD Difco) was used to stain any flagella that might be present. The Gram Stain Set S kit (BD Difco) and the Ryu non-staining KOH method (Powers, 1995) were adopted for testi...

Characteristics and Evolutionary analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from streamlined plasmids to chromids

“…Prior to the isolation of Shimia sp. wx04, Shimia were thought to be strict chemoorganotrophs based upon culture-dependent investigations (Choi and Cho, 2006; Chen et al , 2011; Hameed et al , 2013; Hyun et al , 2013; Nogi et al , 2015). Lastly, N. ignava DSM 16093 was isolated from waters of the Mediterranean and is the sole species currently described for the Nereida (Pujalte et al , 2005; Arahal et al , 2016).…”

Nitropelagi marinus gen. nov., sp. nov., Isolated From Seawater, Je-bu island, South Korea

“…Motility was observed using the semi-solid agar media [54]. Strain JB22 T was cultivated at various temperatures (5,10,15,20,25,28,30,37, and 45°C) to measure optimal temperature and temperature range for growth. The pH range for growth was determined in marine broth adjusted 3.0-10.0 (at increments of 1 pH units) by using sodium acetate buffer and Tris-HCl buffer.…”

Lacimonas salitolerans gen. nov., sp. nov., isolated from surface water of a saline lake

“…The DNA base Table 1. Differential characteristics of strain TS-T30 T and phylogenetically related genera Genera: 1, Lacimonas (strain TS-T30 T , data from this study); 2, Lutimaribacter (Iwaki et al, 2013;Yoon et al, 2009a;Yuan et al, 2009); 3, Poseidonocella (Romanenko et al, 2012); 4, Ruegeria (Huo et al, 2011;Kämpfer et al, 2013;Kim et al, 2012bKim et al, , 2014Lee et al, 2012;Muramatsu et al, 2007;Oh et al, 2011;Park & Yoon, 2012;Uchino et al, 1998;Vandecandelaere et al, 2008;Yi et al, 2007); 5, Marivita (Hwang et al, 2009;Yoon et al, 2010Yoon et al, , 2012Yoon et al, , 2013a; 6, Seohaeicola (Yoon et al, 2009b); 7, Sediminimonas (Wang et al, 2009); 8, Shimia (Chen et al, 2011;Choi & Cho, 2006;Hameed et al, 2013;…”