(25/80) Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm.

A rod-shaped marine bacterium, CL-TA03(T), isolated from a biofilm in a coastal fish farm in Tongyeong, Korea, was characterized for physiological and biochemical features, fatty acid profile and phylogenetic position based on 16S rRNA gene sequences. Analysis of the 16S rRNA gene sequence revealed a clear affiliation with the family Rhodobacteraceae. Phylogenetic analysis of the 16S rRNA gene sequence showed that the closest relatives of CL-TA03(T) were Thalassobius gelatinovorus and Thalassobius mediterraneus (95.6 % similarity). The sequence similarities between CL-TA03(T) and other type species of the Roseobacter lineage ranged from 92.4 to 95.4 %. Strain CL-TA03(T) is motile and grows on marine agar as colourless or beige colonies. The strain is able to grow optimally in the range of 3-5 % sea salts. It grows within a temperature range of 15-35 degrees C and at pH 6-10. The fatty acids are dominated by 18 : 1omega7c (64.1 %) and 11-methyl 18 : 1omega7c (10.6 %). The DNA G+C content is 57.2 mol%. According to physiological data, fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence, CL-TA03(T) is considered to represent a new genus in the family Rhodobacteraceae and the name Shimia marina gen. nov., sp. nov. is proposed. The type strain of Shimia marina is CL-TA03(T) (=KCCM 42117(T)=JCM 13038(T)).  (+info)

(26/80) The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism.

Purple aerobic anoxygenic phototrophs (AAPs) are the only organisms known to capture light energy to enhance growth only in the presence of oxygen but do not produce oxygen. The highly adaptive AAPs compose more than 10% of the microbial community in some euphotic upper ocean waters and are potentially major contributors to the fixation of the greenhouse gas CO2. We present the complete genomic sequence and feature analysis of the AAP Roseobacter denitrificans, which reveal clues to its physiology. The genome lacks genes that code for known photosynthetic carbon fixation pathways, and most notably missing are genes for the Calvin cycle enzymes ribulose bisphosphate carboxylase (RuBisCO) and phosphoribulokinase. Phylogenetic evidence implies that this absence could be due to a gene loss from a RuBisCO-containing alpha-proteobacterial ancestor. We describe the potential importance of mixotrophic rather than autotrophic CO2 fixation pathways in these organisms and suggest that these pathways function to fix CO2 for the formation of cellular components but do not permit autotrophic growth. While some genes that code for the redox-dependent regulation of photosynthetic machinery are present, many light sensors and transcriptional regulatory motifs found in purple photosynthetic bacteria are absent.  (+info)

(27/80) Production of antibacterial compounds and biofilm formation by Roseobacter species are influenced by culture conditions.

Bacterial communities associated with marine algae are often dominated by members of the Roseobacter clade, and in the present study, we describe Roseobacter phenotypes that may provide this group of bacteria with selective advantages when colonizing this niche. Nine of 14 members of the Roseobacter clade, of which half were isolated from cultures of the dinoflagellate Pfiesteria piscicida, produced antibacterial compounds. Many non-Roseobacter marine bacteria were inhibited by sterile filtered supernatants of Silicibacter sp. TM1040 and Phaeobacter (formerly Roseobacter) strain 27-4, which had the highest production of antibacterial compound. In contrast, Roseobacter strains were susceptible only when exposed to concentrated compound. The production of antibacterial compound was influenced by the growth conditions, as production was most pronounced when bacteria were grown in liquid medium under static conditions. Under these conditions, Silicibacter sp. TM1040 cells attached to one another, forming rosettes, as has previously been reported for Phaeobacter 27-4. A spontaneous Phaeobacter 27-4 mutant unable to form rosettes was also defective in biofilm formation and the production of antibacterial compound, indicating a possible link between these phenotypes. Rosette formation was observed in 8 of 14 Roseobacter clade strains examined and was very pronounced under static growth in 5 of these strains. Attachment to surfaces and biofilm formation at the air-liquid interface by these five strains was greatly facilitated by growth conditions that favored rosette formation, and rosette-forming strains were 13 to 30 times more efficient in attaching to glass compared to strains under conditions where rosette formation was not pronounced. We hypothesize that the ability to produce antibacterial compounds that principally inhibit non-Roseobacter species, combined with an enhancement in biofilm formation, may give members of the Roseobacter clade a selective advantage and help to explain the dominance of members of this clade in association with marine algal microbiota.  (+info)

(28/80) Citreimonas salinaria gen. nov., sp. nov., a member of the Roseobacter clade isolated from a solar saltern.

A lemon-shaped marine bacterium, strain CL-SP20(T), isolated from hypersaline water from a solar saltern in Korea, was characterized in terms of its physiological and biochemical features, its fatty acid profile and its phylogenetic position based on 16S rRNA gene sequences. Analysis of the 16S rRNA gene sequence revealed a clear affiliation with the Roseobacter lineage (91.0-96.3 % similarity) of the family Rhodobacteraceae. However, strain CL-SP20(T) did not form a robust clade with any species of the Roseobacter clade, forming a distinct subline. Strain CL-SP20(T) is non-motile and forms beige colonies on marine agar. The strain is able to grow with sea salts at concentrations in the range 1-10 %, with optimal growth between 5 and 6 %. It grows at temperatures in the range 15-40 degrees C and at pH 6-10. The strain cannot oxidize thiosulfate. The fatty acids are dominated by 18 : 1omega7c (54.3 %) and 19 : 0 cyclo omega8c (20.4 %). The DNA G+C content is 67.3 mol%. According to the physiological data, fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence, strain CL-SP20(T) represents a novel species in a novel genus of the family Rhodobacteraceae, for which the name Citreimonas salinaria gen. nov., sp. nov. is proposed. The type strain of Citreimonas salinaria is CL-SP20(T) (=KCCM 42116(T)=JCM 13036(T)).  (+info)

(29/80) Maribius salinus gen. nov., sp. nov., isolated from a solar saltern and Maribius pelagius sp. nov., cultured from the Sargasso Sea, belonging to the Roseobacter clade.

Two strictly aerobic, Gram-negative bacteria, designated strains CL-SP27T and B5-6T, were isolated from the hypersaline water of a solar saltern in Korea and from the surface water of the Sargasso Sea, respectively. The two strains were rod-shaped, non-motile and grew on marine agar 2216 as beige colonies. Phylogenetic analyses of 16S rRNA gene sequences revealed a clear affiliation of the novel strains to the family Rhodobacteraceae. However, the novel strains were only distantly related to members of the Roseobacter clade, forming a distinct lineage. Although the 16S rRNA gene sequence similarity between strains CL-SP27T and B5-6T was very high (99.6 %), DNA-DNA relatedness between the strains was 48.4 %, suggesting that the strains be categorized as two genospecies. Additionally, the two novel strains could be differentiated by DNA G+C contents, fatty acid profiles, carbon source utilization patterns, antibiotic susceptibilities and biochemical characteristics. Based on taxonomic data obtained in this study, strains CL-SP27T and B5-6T represent separate species within a novel genus of the family Rhodobacteraceae, for which the names Maribius salinus gen. nov., sp. nov. (type species) and Maribius pelagius sp. nov. are proposed. The type strains of Maribius salinus and Maribius pelagius are CL-SP27T (=KCCM 42113T=JCM 13037T) and B5-6T (=KCCM 42336T=JCM 14009T), respectively.  (+info)

(30/80) Seasonal variations in the contributions of different bacterial groups to the uptake of low-molecular-weight compounds in northwestern Mediterranean coastal waters.

We analyzed the contributions of different heterotrophic bacterial groups to the uptake of several low-molecular weight compounds during a seasonal cycle on the northwestern Mediterranean coast (Blanes Bay Microbial Observatory). The bacterial assemblage structure had been shown to change substantially year-round for this site, but whether changes in the activities of the different bacterial groups also occurred on the seasonal scale was unknown. Microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization was used to analyze the patterns of glucose, amino acid, and ATP uptake by different bacterial groups. Gammaproteobacteria and Bacteroidetes were not very active in the uptake of glucose at any time of the year (<10% of cells were active) compared to Alphaproteobacteria (generally >20% of cells were active). Dissolved free amino acids were taken up considerably by Alphaproteobacteria and Gammaproteobacteria but not by Bacteroidetes. Relatively high percentages of cells of the three broad phylogenetic groups actively took up ATP, which could be related to the important phosphorous limitation of bacterial production during most of the year in Blanes Bay. The contribution of SAR11 to the uptake of the monomers was variable year-round, generally with fewer than 30% of the cells being active. By contrast, Roseobacter were highly overrepresented in the uptake of all the substrates throughout all the year, with more than 50% of cells being active in all the samples and for all substrates. Our results suggest that substantial changes in the activity of some phylogenetic groups of bacteria occur throughout the year.  (+info)

(31/80) Ecological genomics of marine Roseobacters.

Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.  (+info)

(32/80) Maritimibacter alkaliphilus gen. nov., sp. nov., a genome-sequenced marine bacterium of the Roseobacter clade in the order Rhodobacterales.

A Gram-negative, chemoheterotrophic, strictly aerobic, alkaliphilic, rod-shaped marine bacterium, designated HTCC2654(T), was isolated from the western Sargasso Sea by using a dilution-to-extinction culturing method. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HTCC2654(T) belonged to the Roseobacter clade of the order Rhodobacterales. The 16S rRNA gene sequence similarity of the strain with respect to other members of the Roseobacter clade ranged from 90.4 to 95.1 %. In the phylogenetic analyses, the strain formed an independent phyletic line and could not be assigned to any other known genera of the Rhodobacterales. The DNA G+C content of strain HTCC2654(T) was 61.7 mol% by HPLC and 64.1 mol% from genome sequences. The predominant constituents of the cellular fatty acids were C(16 : 0) 2-OH (27.3 %), 11-methyl C(18 : 1) omega 7c (19.6 %) and C(18 : 1) omega 7c (17.3 %), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine, which served to differentiate the strain from other members of the Roseobacter clade. On the basis of the taxonomic data obtained in this study, strain HTCC2654(T) represents a novel genus and species, for which the name Maritimibacter alkaliphilus gen. nov., sp. nov. is proposed. The type strain is HTCC2654(T) (=KCCM 42376(T)=NBRC 102057(T)).  (+info)