Roseovarius sp. 217
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA13576 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Seawater exposure to the gram negative marine bacterium Vibrio diazotrophicus induces a robust cellular response in sea urchin larvae that includes the migration of pigment cells to the gut epithelium, changes in cell behavior and altered gut morphology (Ho et al., 2016; PMID 27192936). To investigate the transcriptional underpinnings of this response, whole transcriptome sequencing was performed on mRNA isolated from larval samples collected at 0, 6, 12 and 24 hr of exposure to V. diazotrophicus. The morphological simplicity of the sea urchin larva provides a systems-level model for identifying biologically relevant transcriptional state changes in response to dysbiosis in the gut lumen.
2017-03-24 | GSE96940 | GEO
Project description:Dimethylsulfoniopropionate degrading marine bacterium
| PRJNA13464 | ENA
Project description:Polyamines, such as putrescine and spermidine, are aliphatic organic compounds with multiple amino groups. They are found ubiquitously in marine systems. However, compared with the extensive studies on the concentration and fate of other dissolved organic nitrogen compounds in seawater, such as dissolved free amino acids (DFAA), investigations of bacterially-mediated polyamine transformations have been rare. Bioinformatic analysis identified genes encoding polyamine transporters in 74 of 109 marine bacterial genomes surveyed, a surprising frequency for a class of organic nitrogen compounds not generally recognized as an important source of carbon and nitrogen for marine bacterioplankton. The genome sequence of marine model bacterium Silicibacter pomeroyi DSS-3 contains a number of genes putatively involved in polyamine use, including six four-gene ATP-binding cassette transport systems. In the present study, polyamine uptake and metabolism by S. pomeroyi was examined to confirm the role of putative polyamine-related genes, and to investigate how well current gene annotations reflect function. A comparative whole-genome microarray approach (Bürgmann et al., 2007) allowed us to identify key genes for transport and metabolism of spermidine in this bacterium, and specify candidate genes for in situ monitoring of polyamine transformations in marine bacterioplankton communities.
2008-12-31 | GSE13781 | GEO
Project description:Dunaliella tertiolecta is an extremophilic, green alga from the Chlorophyte lineage. It is found in coastal marine environments around the world. D. tertiolecta can tolerate extremes of heat, light, pH, and salinity. D. tertiolecta is under development for the production biofuels and other bioproducts because it can produce large quantities of neutral lipids, and it can be grown in open raceway ponds using only the inputs of seawater and sunlight. This isolate of D. tertiolecta (UTEX LB 999) was found in Oslofjord, Norway in 1938. This accession includes an RNA-Seq analysis of D. tertiolecta cultures grown in iron-replete (1.5 µM) or iron-deficient (0 µM) media.
2023-06-30 | GSE222141 | GEO
Project description:In estuaries and coastal areas, salinity regimes vary with river discharge, seawater evaporation, morphology of the coastal waterways, and dynamics of marine water mixing. Therefore, microalgae have to respond to salinity variations at various time scales, from daily to annual cycling. They might also adapt to physical alteration that might induce loss of connectivity and enclosure of water bodies. Here we integrate physiological-based assays, morphological plasticity with functional genomics approach to examine the regulatory change that occur during the acclimation to salinity in an estuary diatom, Thalassiosira weissflogii. We found that this diatom respond to salinity (i.e. 21, 28 and 35 psu) with minute adjustments of its physiology (i.e., carbon and silicon metabolisms, pigments concentration and photosynthetic parameters). In contrast after short- (~ 5 generations) or long-term (~ 700 generations) culture at the different salinity we found a large transcriptome reprogramming. With most of the genes being down-regulated in long-term, and only a few genes in common between short and long term experiments.
2018-10-02 | GSE73987 | GEO
Project description:Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock. Global transcriptional response to two levels of copper shock was assayed in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus. The two strains additionally showed a reduction in photosynthetic gene transcripts. Contrastingly, the open ocean strain showed a typical stress response whereas the coastal strain exhibited a more specific oxidative or heavy metal type response. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus may in part be a result of an increased ability to sense and respond in a more specialized manner.
2009-07-01 | GSE13910 | GEO
Project description:The marine bacterium Vibrio fischeri requires flagellar motility to undergo symbiotic initiation with its host, the Hawaiian bobtail squid Euprymna scolopes. We sought to identify the genes activated by the sigma54-dependent flagellar master regulator, FlrA, in V. fischeri, thereby determining the flagellar regulon in this model symbiont. We performed microarray analysis on wild-type Vibrio fischeri ES114 and a flrA deletion mutant, DM159, grown to mid-log phase in seawater tryptone, a condition in which cells are highly motile (two biological replicates per condition).
2013-04-05 | E-GEOD-45772 | biostudies-arrayexpress
Project description:Two Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacteria, designated as strains S88T and W115T, exhibiting catalase- and oxidase-positive reactions, were isolated from marine red algae in South Korea. Strain S88T exhibited growth at 20-30 °C, pH 6.0-9.0 and 2.0-5.0% (w/v) NaCl, while strain W115T grew at 20-30 °C, pH 7.0-9.0 and 2.0-5.0% (w/v) NaCl. Strain S88T contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C16 : 0 2-OH as major fatty acids (>5%), with major polar lipids being phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. Strain W115T contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0 as major fatty acids (>5%), with major polar lipids including phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and unidentified lipids. Ubiquinone-10 was the sole respiratory quinone in both strains, and the genomic DNA G+C contents were 57.0% for strain S88T and 56.5% for strain W115T. Despite 99.86% 16S rRNA gene sequence similarity, strains S88T and W115T shared 88.8% average nucleotide identity (ANI) and 36.8% digital DNA-DNA hybridization (dDDH) value, indicating different species. Phylogenetic and phylogenomic analyses based on 16S rRNA gene and genome sequences, respectively, revealed that strains S88T and W115T formed a phylogenetic lineage within the genus Roseovarius. ANI and dDDH values of both strains with other type strains were less than 73.7 and 20.3%, respectively, confirming that they represent novel species. Based on phenotypic, chemotaxonomic and molecular characteristics, strains S88T and W115T represent two novel species of the genus Roseovarius, for which the names Roseovarius phycicola sp. nov. (S88T =KACC 23423T =JCM 36647T) and Roseovarius rhodophyticola sp. nov. (W115T =KACC 23690T =JCM 36651T) are proposed, respectively.
| S-EPMC11554077 | biostudies-literature