Photoperiodic spectral tuning of carbon metabolism in heterotrophic marine flavobacteria
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ABSTRACT:
PROVIDER: PRJNA532887 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Influence of the constant full-spectrum light and short-to-long wavelengths of the visible spectrum (red, green and blue lights) and the significance of 12 h photoperiod was tested on heterotrophic marine flavobacteria Siansivirga zeaxanthinifaciens CC-SAMT-1T. RNA-seq analysis revealed remarkable qualitative and quantitative variations in terms of gene expression in CC-SAMT-1T with respect to incident lights. While blue light illumination stimulated expression of genes involved in inorganic carbon metabolism, green˗red lights largely upregulated the genes participating in high-molecular-weight (HMW) organic carbon metabolism. Constant full-spectrum light also displayed the upregulation of genes involved in the metabolism of HMW organic carbon. Thus, the short-to-long wavelengths of visible light and the 12 h photoperiod most likely to play a key role in the marine carbon cycle by tuning heterotrophic bacterial metabolism.
2020-04-15 | GSE129810 | GEO
Project description:Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. However, the high complexity of in situ ecosystems renders it difficult to study these interactions. Two-member co-culture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of co-cultivation. The associated heterotrophic bacterial assembly mostly constituted five classes including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria. The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes from the co-culture system were reconstructed inclusive of Synechococcus and the five dominant heterotrophic bacterial populations. The only primary producer of the co-culture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TBDT, glycoside hydrolase, and peptidases proteins. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low molecular weight DOM, including Flavobacteria metabolism byproducts, through ABC, TRAP, and TTT transport systems. Polysaccharide-utilization loci present in the flavobacterial genomes encoded similar trans-membrane protein complexes as Sus/cellulosome and may influence their lifestyle preferences and close associations with phytoplankton. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking also contributed to the maintenance of the Synechococcus / heterotroph co-culture system and the interactions shaping the system.
2020-05-27 | PXD015067 | Pride
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Project description:Carbon limitation of heterotrophic dinitrogen fixation in the coastal Eastern Mediterranean Sea
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Project description:Photoperiodic control of smoltification
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Project description:Plants respond to seasonal cues such as the photoperiod, to adapt to current conditions and to prepare for environmental changes in the season to come. To assess photoperiodic responses at the protein level, we quantified the proteome of the model plant Arabidopsis thaliana by mass spectrometry across four photoperiods. This revealed coordinated changes of abundance in the proteins of photosynthesis, primary metabolism and secondary metabolic processes such as pigment biosynthesis, consistent with higher metabolic activity in long photoperiods. Higher translation rates during the day than during the night likely contribute to these changes, but rhythmic RNA profiles will alter their effects. Photoperiodic control of protein levels might be greatest if high translation rates only coincide with high transcript levels in some photoperiods. We term this mechanism ‘translational coincidence’, mathematically model its components, and demonstrate its effect on the Arabidopsis proteome. Datasets from a green alga and a cyanobacterium suggest that this mechanism is general, contributing to the seasonal control of the proteome in many phototrophic organisms, and favouring RNA rhythms even for stable proteins.
2018-02-27 | PXD006848 | Pride