Polaribacter sp. MED152
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ABSTRACT:
PROVIDER: PRJNA13543 | ENA |
REPOSITORIES: ENA
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Project description:Background: Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. Results: Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions. Conclusions: This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and may be used for acclimation to environmental conditions. RNA-seq study of sRNA populations in two species of diatoms using Illumina GAII high-throughput sequencing
2015-03-06 | E-GEOD-57987 | biostudies-arrayexpress
Project description:Background: Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. Results: Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions. Conclusions: This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and may be used for acclimation to environmental conditions.
2015-03-06 | GSE57987 | GEO
Project description:Phytoplankton and bacteria form the base of marine ecosystems and their interactions drive global biogeochemical cycles. The effect of bacteria and bacteria-produced compounds on diatoms range from synergistic to pathogenic and can affect the physiology and transcriptional patterns of the interacting diatom. Here, we investigate physiological and transcriptional changes in the marine diatom Thalassiosira pseudonana induced by extracellular metabolites of a known antagonistic bacterium Croceibacter atlanticus. Mono-cultures of C. atlanticus released compounds that inhibited diatom cell division and elicited a distinctive phenotype of enlarged cells with multiple plastids and nuclei, similar to what was observed when the diatom was co-cultured with the live bacteria. The extracellular C. atlanticus metabolites induced transcriptional changes in diatom pathways that include recognition and signaling pathways, cell cycle regulation, carbohydrate and amino acid production, as well as cell wall stability. Phenotypic analysis showed a disruption in the diatom cell cycle progression and an increase in both intra- and extracellular carbohydrates in diatom cultures after bacterial exudate treatment. The transcriptional changes and corresponding phenotypes suggest that extracellular bacterial metabolites, produced independently of direct bacterial-diatom interaction, may modulate diatom metabolism in ways that support bacterial growth.
2022-06-24 | GSE197934 | GEO
Project description:The polysaccharide β-mannan, which is common in terrestrial plants but unknown in microalgae, was recently detected during diatom blooms. We identified a β-mannan polysaccharide utilization locus (PUL) in the genome of the marine Flavobacterium Muricauda sp. MAR_2010_75 which resembles PULs in bacteria from diverse ecosystems. Proteomics showed the β-mannan induced translation of 22 proteins encoded within the PUL.
2022-11-24 | PXD033586 | Pride
Project description:We isolate the cultivable microbiome of a diatom and show that different bacteria have commensal, antagonistic, or synergistic effects on the diatom. One synergistic bacterium enhances growth of the diatom by production of auxin, a phytohormone. The diatom and its synergistic bacterium appear to use auxin and tryptophan as signaling molecules that drive nutrient exchange. Detection of auxin molecules and biosynthesis gene transcripts in the Pacific Ocean suggests that these interactions are widespread in marine ecosystems.
2015-05-29 | GSE65189 | GEO
Project description:Phytoplankton-bacteria interactions are pivotal in marine ecosystems, influencing primary production and biogeochemical cycles. Diatoms engage in diverse relationships with bacteria, ranging from mutualism to pathogenicity. This study explores the interaction between a novel Alteromonas macleodii strain from the Equatorial Pacific and the model Thalassiosira pseudonana across the diatom different growth phases. We demonstrate that A. macleodii’s algicidal activity depends on the diatom’s growth phase, defensive capacity, and nutrient availability. The algicidal effect manifests during the diatom’s stationary phase or with external nutrient supplementation, implicating organic matter availability as a key driver. Transcriptomic analysis reveals that A. macleodii shifts from motility-associated to growth-associated gene expression based on the diatom’s physiology and coculture duration. Filtrate assays and fluorescence microscopy suggest a two-stage infection model: initial bacterial motility and exudate secretion induce diatom death, followed by bacterial aggregation around debris. Comparative transcriptomics with other algal hosts highlights host-specific bacterial responses, underscoring the context-dependent nature of these interactions. Our findings provide a deeper understanding of the molecular mechanisms driving diatom-bacteria interactions, shedding light on their role in marine microbial ecology and ecosystem functioning.
2026-02-10 | GSE291849 | GEO
Project description:The marine diatom Guinardia delicatula is a cosmopolitan species that dominates seasonal blooms in the English Channel and the North Sea. Several eukaryotic parasites are known to induce the mortality of this key-stone species. Here, we report the isolation and the characterization of the first viruses that infect G. delicatula. Viruses were isolated from the Western English Channel (SOMLIT-ASTAN station) during the late summer bloom decline of G. delicatula. A combination of laboratory approaches revealed that these lytic viruses (GdelRNAV) are small untailed particles of 35-38 nm in diameter that replicated in the host cytoplasm where both unordered particles and crystalline arrays were formed. GdelRNAV displayed a linear single-stranded RNA genome of ~9 kb, including two open reading frames encoding for replication and structural polyproteins. Phylogenetic relationships based on the RNA-dependent-RNA-polymerase gene marker showed that GdelRNAV were new members of the Bacillarnavirus, a monophyletic genus belonging to the order Picornavirales. GdelRNAV were specific to several strains of G. delicatula, they were produced rapidly (< 12h) and in numbers (9.34 x 104 virions per host cell). We recorded a substantial delay (72 h) between virions release and host cell lysis. Our analysis points to variable viral susceptibilities of the host during the early exponential growth phase. Interestingly, we consistently failed to isolate viruses during spring and early summer while G. delicatula developed rapid and massive blooms. While our study suggests that viruses do contribute to the decline of G. delicatula late summer bloom, they may not be the primary mortality agents during the remaining blooms at SOMLIT-ASTAN. Future studies should focus on the relative contribution of the viral and eukaryotic pathogens to the control of Guinardia blooms to understand the fate of these prominent organisms in marine systems.
2019-01-30 | PXD010967 | Pride
Project description:Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curated reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. The model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications.
2023-03-10 | MODEL2204200002 | BioModels
Project description:Organism-specific depletion of highly abundant RNA species from bacterial total RNA
| PRJNA616314 | ENA
Project description:Background: Ocean temperatures are projected to increase over the coming century, with dramatic consequences for the marine biosphere. Diatoms are important contributors to marine primary production and the ocean carbon cycle, yet the molecular mechanisms that regulate their acclimation and adaptation to temperature are poorly understood. Method: Here we use a transcriptomic approach to identify the molecular mechanisms associated with temperature acclimation and adaptation in closely related colder- and warmer-adapted diatom species. Results: We find contrasting patterns of differential expression at sub- and supra-optimal temperatures across the two species, which may be due to adaptive changes in baseline expression. Frontloaded and divested pathways indicate protein processing machinery, membrane structure, and the balance between temperature-independent photosynthesis and temperature-dependent metabolism are key elements of adaptation to temperature changes. Conclusions: Our findings suggest that transcriptional frontloading and divestment may provide a framework to interpret diatom acclimation and adaptation to temperature and success under future warming.
2019-07-31 | GSE125205 | GEO