Alteromonas sp. 76-1
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ABSTRACT:
PROVIDER: PRJEB28726 | ENA |
REPOSITORIES: ENA
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Project description:Polysaccharides from macroalgae are important bacterial nutrient source and central biogeochemical component in the oceans. To illuminate the cellular mechanisms of polysaccharide degradation by marine bacteria, growth of Alteromonas macleodii 83-1 on a mix of laminarin, alginate and pectin was characterized using transcriptomics, proteomics and exometabolomics. A. macleodii 83-1 showed two distinct growth stages, with exponential growth during laminarin utilization followed by maintenance during simultaneous alginate/pectin utilization. The biphasic growth coincided with major temporal shifts in gene expression and metabolite secretion, enabling to define major/accessory polysaccharide utilization loci, reconstruct the complete degradation pathways for each polysaccharide, as well as identify temporal phenotypes in other relevant traits. FT-ICR-MS revealed a distinct suite of secreted metabolites for each growth phase, with pyrroloquinoline quinone exclusively produced with alginate/pectin. The finding of substrate-unique phenotypes indicates an exquisite adaptation to polysaccharide utilization with probable relevance for the degradation of macroalgal biomass, which comprises a complex mix of polysaccharides. Moreover, substrate-unique exometabolomes possibly influence metabolic interactions with other community members. Overall, the presence of fine-tuned genetic machineries for polysaccharide degradation and the widespread detection of related CAZymes in global locations indicate an ecological relevance of A. macleodii in marine polysaccharide cycling and bacteria-algae interactions.
2018-08-01 | GSE107306 | GEO
Project description:Polysaccharides from macroalgae are important bacterial nutrient source and central biogeochemical component in the oceans. To illuminate the cellular mechanisms of polysaccharide degradation by marine bacteria, growth of Alteromonas macleodii 83-1 on a mix of laminarin, alginate and pectin was characterized using transcriptomics, proteomics and exometabolomics. A. macleodii 83-1 showed two distinct growth stages, with exponential growth during laminarin utilization followed by maintenance during simultaneous alginate/pectin utilization. The biphasic growth coincided with major temporal shifts in gene expression and metabolite secretion, enabling to define major/accessory polysaccharide utilization loci, reconstruct the complete degradation pathways for each polysaccharide, as well as identify temporal phenotypes in other relevant traits. FT-ICR-MS revealed a distinct suite of secreted metabolites for each growth phase, with pyrroloquinoline quinone exclusively produced with alginate/pectin. The finding of substrate-unique phenotypes indicates an exquisite adaptation to polysaccharide utilization with probable relevance for the degradation of macroalgal biomass, which comprises a complex mix of polysaccharides. Moreover, substrate-unique exometabolomes possibly influence metabolic interactions with other community members. Overall, the presence of fine-tuned genetic machineries for polysaccharide degradation and the widespread detection of related CAZymes in global locations indicate an ecological relevance of A. macleodii in marine polysaccharide cycling and bacteria-algae interactions.
2018-08-22 | PXD008280 | Pride
Project description:Alteromonas macleodii DE1 plasmid transcriptome
| PRJNA215067 | ENA
Project description:Prochlorococcus is found throughout the euphotic zone in the oligotrophic open ocean. Deep mixing and sinking in aggregates or while attached to particles can, however, transport cells below this sunlit zone, depriving them of light for extended periods of time and influencing their circulation via ocean currents. Viability of these cells over extended periods of darkness could shape the ecology and evolution of the Prochlorococcus collective. We have shown that when co-cultured with a heterotrophic microbe and subjected to repeated periods of extended darkness, Prochlorococcus cells develop a heritable dark-tolerant phenotype – through an apparent epigenetic mechanism – such that they survive longer periods of darkness. Here we examine this adaptation at the level of physiology and metabolism in co-cultures of dark-tolerant and parent strains of Prochlorococcus, each grown with the heterotroph Alteromonas under diel light:dark conditions. The relative abundance of Alteromonas is higher in dark-tolerant than parental co-cultures, while dark tolerant Prochlorococcus cells are also larger, contain less chlorophyll, and are less synchronized to the light:dark cycle. Meta-transcriptome analysis of the cultures further suggests that dark-tolerant co-cultures undergo a coupled shift in which Prochlorococcus uses more organic carbon and less photosynthesis, and Alteromonas uses more organic acids and fewer sugars. Collectively, the data suggest that dark adaptation involves a loosening of the coupling between Prochlorococcus metabolism and the light:dark cycle and a strengthening of the coupling between the carbon metabolism of Prochlorococcus and Alteromonas.
2024-04-23 | GSE264347 | GEO
Project description:Streptomyces sp. 76 strain:76 Genome sequencing
| PRJNA402581 | ENA
Project description:Acidovorax sp. 76 strain:76 Genome sequencing
| PRJNA442010 | ENA
Project description:In this study we characterized MV production by six different strains of Alteromonas macleodii, a cosmopolitan marine bacterium.
2023-07-20 | PXD037008 | Pride
Project description:modENCODE_submission_2944 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP203(official name : OP203 genotype : unc-119(ed3); wgIs203(nhr-76::TY1 EGFP FLAG; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-76::EGFP fusion protein is expressed in the correct nhr-76 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-76 transcription factor. made_by : R. Waterston ); Developmental Stage: L3; Genotype: unc-119(ed3); wgIs203(nhr-76::TY1 EGFP FLAG; unc-119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene nhr-76; Strain OP203(official name : OP203 genotype : unc-119(ed3); wgIs203(nhr-76::TY1 EGFP FLAG; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NHR-76::EGFP fusion protein is expressed in the correct nhr-76 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-76 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48689 | biostudies-arrayexpress