Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm

Sheu

International Journal of Systematic and Evolutionary Microbiology

et al. 2012

A bacterial strain, isolated from a sample of reef-building coral (Isopora palifera) collected off the coast of southern Taiwan, was characterized using a polyphasic taxonomic approach. The strain, designated sw-2T, was Gram-staining-negative, aerobic, rod-shaped and motile, with subpolar flagella, and formed greyish pink colonies. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain sw-2T was most closely related to Roseivivax halodurans Och 239T (97.4 % sequence similarity) and Roseivivax halotolerans Och 210T (96.4 %). The novel strain did not require NaCl for growth and exhibited optimal growth at 35–40 °C, at pH 7.5–8.0 and with 3–7 % (w/v) NaCl. It produced bacteriochlorophyll a under aerobic conditions. Summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 63.7 %) predominated in the cellular fatty acid profile. The novel strain’s major respiratory quinone was ubiquinone Q-10 and its genomic DNA G+C content was 68.8 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, sulfo-quinovosyl diacylglycerol and three uncharacterized phospholipids. The level of DNA–DNA relatedness between strain sw-2T and Roseivivax halodurans Och 239T was only 15.0 %. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of the novel strain from all established species of the genus Roseivivax . Based on the genotypic, phenotypic and chemotaxonomic data, strain sw-2T represents a novel species in the genus Roseivivax , for which the name Roseivivax isoporae sp. nov. is proposed. The type strain is sw-2T ( = LMG 25204T = BCRC 17966T).

mentioning

confidence: 99%

Roseivivax isoporae sp. nov., isolated from a reef-building coral, and emended description of the genus Roseivivax

Sheu

International Journal of Systematic and Evolutionary Microbiology

et al. 2012

“…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.…”

mentioning

confidence: 99%

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

Sheu

International Journal of Systematic and Evolutionary Microbiology

et al. 2011

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...

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

“…At the time of writing, this clade contains more than 35 genera (Buchan et al, 2005). Bacterial species affiliated with the Roseobacter clade have been isolated from various marine environments, such as seawater, sediment, marine algae, hypersaline microbial mats and marine biofilms (Buchan et al, 2005;Choi & Cho, 2006a;Dai et al, 2006). Their physiological properties are highly diverse, including aerobic anoxygenic photosynthesis, aerobic sulfite oxidation, organic sulfur compound degradation, lignin degradation, methylotrophy and antibiotic production (Buchan et al, 2005;Martens et al, 2006).…”

mentioning

confidence: 99%

Ponticoccus litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae

Hwang

Cho

2008

A Gram-negative, coccoid to rod-shaped, strictly aerobic bacterium, strain CL-GR66 T , was isolated from coastal seawater collected off Korea. The strain grew optimally in the presence of 3-5 % sea salts, at a temperature of 30 6C and at pH 7. The polar lipid profile of strain CL-GR66T comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminolipids, an unidentified glycolipid and an unidentified lipid. The major fatty acids were C 18 : 1 v7c (71.4 %), 11-methyl C 18 : 1 v7c (11.3 %), C 16 : 0 (6.4 %) , C 18 : 0 (4.6 %) and C 12 : 1 3-OH (3.0 %). Ubiquinone 10 was the major quinone. The DNA G+C content was 67.9 mol%. 16S rRNA gene sequence analysis revealed that strain CL-GR66 T belonged to the Roseobacter clade within the family Rhodobacteraceae. Strain CL-GR66 T was related most closely to the type strain of Marinovum algicola (95.5 % 16S rRNA gene sequence similarity), and sequence similarities between strain CL-GR66 T and other type species of the Roseobacter clade ranged from 91.8 to 95.4 %. Phylogenetic analyses of 16S rRNA gene sequences showed that strain CL-GR66 T was not associated with any known genus in the family Rhodobacteraceae.The distinct phylogenetic position of strain CL-GR66