Pelagibius litoralis gen. nov., sp nov., a marine bacterium in the family Rhodospirillaceae isolated from coastal seawater
ABSTRACT A Gram-negative, strictly aerobic, slightly curved rod-shaped bacterial strain, designated CL-UU02(T), was isolated from coastal seawater off the east coast of Korea. 16S rRNA gene sequence analysis revealed a clear affiliation of this novel strain with the family Rhodospirillaceae. Strain CL-UU02(T) formed a robust cluster with the type strains of species of the genus Rhodovibrio at 16S rRNA gene sequence similarity levels of 89.9-90.4 %. Strain CL-UU02(T) shared no more than 89 % 16S rRNA gene sequence similarity with the type strains of other species in the family Rhodospirillaceae. Strain CL-UU02(T) was able to grow in the presence of 2-6 % sea salts, and grew optimally at 28-30 degrees C and pH 7-8. The DNA G+C content of strain CL-UU02(T) was 66.3 mol%. On the basis of phylogenetic analyses and chemotaxonomic and physiological data, strain CL-UU02(T) is considered to represent a novel species of a new genus in the family Rhodospirillaceae, for which the name Pelagibius litoralis gen. nov., sp. nov. is proposed. The type strain of Pelagibius litoralis is CL-UU02(T) (=KCCM 42323(T)=JCM 15426(T)).
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ABSTRACT: Phytoplankton blooms in surface waters of the oceans are known to influence the food web and impact microbial as well as zooplankton communities. Numerous studies have investigated the fate of phytoplankton-derived organic matter in surface waters and shelf sediments, however, little is known about the effect of sinking algal biomass on microbial communities in deep-sea sediments. Here, we analyzed sediments of four regions in the South Atlantic Ocean along the Antarctic Polar Front that had different exposures to phytoplankton bloom derived organic matter. We investigated the microbial communities in these sediments using high-throughput sequencing of 16 S rRNA molecules to determine microorganisms that were active and catalyzed reporter deposition fluorescence in situ hybridization to infer their abundance and distribution. The sediments along the Antarctic Polar Front harbored microbial communities that were highly diverse and contained microbial clades that seem to preferably occur in regions of high primary productivity. We showed that organisms affiliated with the gammaproteobacterial clade NOR5/OM60, which is known from surface waters and coastal sediments, thrive in the deep-sea. Benthic deep-sea NOR5 were abundant, diverse, distinct from pelagic NOR5 and likely specialized on the degradation of phytoplankton-derived organic matter, occupying a similar niche as their pelagic relatives. Algal detritus seemed to not only fuel the benthic microbial communities of vast areas in the deep-sea, but also to influence communities locally, as we found a peak in Flavobacteriaceae-related clades that also include degraders of algal biomass. The results strongly suggest that phytoplankton-derived organic matter was rapidly exported to the deep-sea, fuelled distinct benthic microbial communities and seemed to be the main energy source for microbial life in the seafloor of vast abyssal regions along the Antarctic Polar Front.Deep Sea Research Part II Topical Studies in Oceanography 06/2014; 108. DOI:10.1016/j.dsr2.2014.05.011 · 2.76 Impact Factor
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ABSTRACT: A novel Gram-staining-negative, non-pigmented, rod-shaped, strictly aerobic, extremely halophilic bacterium, designated strain IA16T, was isolated from saline mud of the hypersaline lake Aran-Bidgol in Iran. Cells of strain IA16T were not motile. Growth occurred between 2.5 and 5.2 M NaCl and optimally at 3.4 M NaCl. The optimum pH and temperature for growth of strain IA16T were pH 7.0 and 40 °C, respectively, while it was able to grow at pH and temperature ranges of 6.0-8.0 and 30-50 °C, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IA16T is a member of the family Rhodospirillaceae; however its similarity was as low as 91.6 %, 88.9 % and 88.7 % to the most closely related taxa including Rhodovibrio, Pelagibius and Fodinicurvata type species, respectively. The major cellular fatty acids of the isolate were C19:0 cyclo ω7c and C18:0. The polar lipid pattern of strain IA16T consisted of phosphatidylglycerol, diphosphatidylglycerol, four phospholipids, three aminolipids and two unknown lipid components. The cells of strain IA16T contained the ubiquinone Q-10. The G+C content of the genomic DNA of this strain was 67.0 mol%. The physiological, biochemical and phylogenetic differences between strain IA16T and other previously described taxa suggest that this strain represents a novel species in a new genus within the family Rhodospirillaceae, for which the name Limimonas halophila gen. nov., sp. nov. is proposed. The type strain of Limimonas halophila is strain IA16T (= IBRC-M 10018T= DSM 25584T).International Journal of Systematic and Evolutionary Microbiology 08/2012; DOI:10.1099/ijs.0.041236-0 · 2.80 Impact Factor
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ABSTRACT: Tistlia consotensis is a halotolerant Rhodospirillaceae that was isolated from a saline spring located in the Colombian Andes with a salt concentration close to seawater (4.5%w/vol). We cultivated this microorganism in three NaCl concentrations, i.e. optimal (0.5%), without (0.0%) and high (4.0%) salt concentration, and analyzed its cellular proteome. For assigning tandem mass spectrometry data, we first sequenced its genome and constructed a six reading frame ORF database from the draft sequence. We annotated only the genes whose products (872) were detected. We compared the quantitative proteome data sets recorded for the three different growth conditions. At low salinity general stress proteins (chaperons, proteases and proteins associated with oxidative stress protection), were detected in higher amounts, probably linked to difficulties for proper protein folding and metabolism. Proteogenomics and comparative genomics pointed at the CrgA transcriptional regulator as a key-factor for the proteome remodeling upon low osmolarity. In hyper-osmotic condition, T. consotensis produced in larger amounts proteins involved in the sensing of changes in salt concentration, as well as a wide panel of transport systems for the transport of organic compatible solutes such as glutamate. We have described here a straightforward procedure making a new environmental isolate quickly amenable to proteomics. BIOLOGICAL SIGNIFICANCE: The bacterium Tistlia consotensis was isolated from a saline spring in the Colombian Andes and represents an interesting environmental model to be compared with extremophiles or other moderate organisms. To explore the halotolerance molecular mechanisms of the bacterium Tistlia consotensis, we developed an innovative proteogenomic strategy consisting in i) genome sequencing, ii) quick annotation of the genes whose products were detected by mass spectrometry, and iii) comparative proteomics of cells grown in three salt conditions. We highlighted in this manuscript how efficient can be such approach compared to time-consuming genome annotation when pointing at the key proteins of a given biological question. We documented a large number of proteins found more produced when cells are cultivated in either hypo-osmotic or hyper-osmotic conditions.Journal of proteomics 05/2013; 97. DOI:10.1016/j.jprot.2013.05.020 · 3.93 Impact Factor