Biofilm metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA417492 | ENA |
REPOSITORIES: ENA
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Project description:Nanoscale zero valent iron (nZVI) is used to remediate aquifers polluted by organochlorines or heavy metals has been also considered for elimination of harmful algal blooms. Highly reactive nZVI then affects microorganisms in the application area. To date, various nZVI toxicity endpoints have been studied on different organisms. However, the underlying mechanistic related to iron defense pathways have not been explained sufficiently. Here we aim to describe the physiological and transcriptomic response of the microalga, Raphidocelis subcapitata ATCC 22662, to 100 mg/L of non-reactive nFe3O4, and reactive nZVI. The combined effect of shading by nanoparticles and release of Fe2+ from nZVI posed a stronger inhibition leading to deformed cells and cytosol leakage in 15% of cells. Transcriptomic analysis confirmed the stronger physiological effect of nZVI (7,380 differentially expressed genes [DEGs]) than nFe3O4 (4,601 DEGs) after 1 h. nZVI (but not nFe3O4) caused increased DNA repair and replication, while deactivated carbohydrate-energy metabolisms, mitochondria signaling, and transmembrane ion transport. The defense response of algal cells was immediate to successfully face oxidative stress.
2023-06-06 | GSE234088 | GEO
Project description:Harmful algal blooms are induced largely by nutrient enrichment common in warm waters. An increasingly frequent phenomenon is the “red tide”: blooms of dinoflagellate microalgae that accumulate toxins lethal to other organisms in high doses. Here, we present the de novo assembled genome (~4.75 Gbp) of Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate, and the associated transcriptome, proteome, and metabolome data from axenic cultures to elucidate the microalgal molecular responses to heat stress. We discovered, in a high-G+C genome with long introns and extensive genetic duplication, a complementary mechanism between RNA editing and exon usage that regulates dynamic expression and functional diversity of genes and proteins, and metabolic profiles that reflect reduced capacities in photosynthesis, central metabolism, and protein synthesis. These results based on multi-omics evidence demonstrate the genomic hallmark of a bloom-forming dinoflagellate, and how the complex gene structures combined with multi-level transcriptional regulation underpin concerted heat-stress responses.
2023-10-18 | PXD046193 | Pride
Project description:Prymnesium parvum is regarded as one of the most notorious harmful algal bloom (HAB) species worldwide. In recent years, it has frequently formed toxic blooms in coastal and brackish waters of America, Europe, Australia, Africa and Asia, causing large-scale mortalities of wild and cultured fish and other gill-breathing animals. In the last decade, blooms of P. parvum have expanded to inland fresh waters in the USA, presumably due to changes in environmental conditions. The aim of the experiment was to establish the gill transcriptomic responses to P. parvum in rainbow trout. We used 2 different concentrations of P. parvum and identified fish with low and moderate responses to the algae. Based on the dose of and the fish response, fish were classified into 4 groups with high exposure/moderate response (HM), high exposure/low response (HL), low exposure/low response (LL) and control group (C) with no exposure/no response. Gene expression profiling of the gill tissue was performed using a microarray platform developed and validated for rainbow trout.
2021-11-10 | E-MTAB-10541 | biostudies-arrayexpress
Project description:The inhibition of Harmful algal blooms (HABs) or red tides
| PRJNA706502 | ENA
Project description:<p>In annually reoccurring patterns, microalgae form blooms that persist and decline thereby contributing massively to global biogeochemical cycles. The decline of blooms is mainly caused by nutrient limitation and goes ahead with the aging of individual algal cells. Nutrient intake can re-initiate proliferation, but the processes involved are poorly understood. By investigating the bloom-forming diatom Coscinodiscus radiatus, we demonstrate how algae recover after nutrient influx. The rejuvenation physiology of the algae is characterized by metabolomic re-organization and the formation of extracellular vesicles. Regulated pathways mediating aging are centered around the methionine cycle in C. radiatus. Vesicles shuttle reactive oxygen species, oxylipins and other harmful metabolites out of the old cells, thereby re-enabling their proliferation. Metabolic processes involved in aging and vesicle production are modulated by bacteria. Using chemical signaling bacteria can trigger vesicle production thereby releasing organic nutrients for their growth and supporting algal growth as well.</p><p><br></p><p><strong>Metabolomics profiling of FACS purified EVs</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS5401' rel='noopener noreferrer' target='_blank'><strong>MTBLS5401</strong></a>.</p><p><strong>Metabolomics analysis</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS5368' rel='noopener noreferrer' target='_blank'><strong>MTBLS5368</strong></a>.</p>
2024-05-07 | MTBLS5401 | MetaboLights
Project description:<p>In annually reoccurring patterns, microalgae form blooms that persist and decline thereby contributing massively to global biogeochemical cycles. The decline of blooms is mainly caused by nutrient limitation and goes ahead with the aging of individual algal cells. Nutrient intake can re-initiate proliferation, but the processes involved are poorly understood. By investigating the bloom-forming diatom Coscinodiscus radiatus, we demonstrate how algae recover after nutrient influx. The rejuvenation physiology of the algae is characterized by metabolomic re-organization and the formation of extracellular vesicles. Regulated pathways mediating aging are centered around the methionine cycle in C. radiatus. Vesicles shuttle reactive oxygen species, oxylipins and other harmful metabolites out of the old cells, thereby re-enabling their proliferation. Metabolic processes involved in aging and vesicle production are modulated by bacteria. Using chemical signaling bacteria can trigger vesicle production thereby releasing organic nutrients for their growth and supporting algal growth as well.</p><p><br></p><p><strong>Metabolomics analysis</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS5368' rel='noopener noreferrer' target='_blank'><strong>MTBLS5368</strong></a>.</p><p><strong>Metabolomics profiling of FACS purified EVs</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS5401' rel='noopener noreferrer' target='_blank'><strong>MTBLS5401</strong></a>.</p>
2024-05-07 | MTBLS5368 | MetaboLights
Project description:Tursiops truncatus RAD sequencing for study of adaptation to harmful algal blooms
| PRJNA241352 | ENA
Project description:Dinoflagellates are phytoplanktonic organisms found in both freshwater and marine habitats. They are often studied because related to harmful algal blooms responsible for impacts on ecosystem functioning, economic damages for aquaculture and fishery industries and/or deleterious impacts for human health. In addition they are also known to produce bioactive compounds, such as for the treatment of cancer or beneficial effects for the treatment of Alzheimer’s disease. The dinoflagellate Amphidinium sp. is a cosmopolitan dinoflagellate species known to produce both cytotoxic and beneficial compounds. However, several studies reported that environmental changes (e.g. nutrient starvation, UV radiation and ocean acidification) may alter this production. The aim of this study was to sequence the full transcriptome of the dinoflagellate Amphidinium carterae in both nitrogen- starved and -repleted culturing conditions (1) to evaluated its response to nitrogen starvation, (2) to look for possible polyketide synthases (PKSs), involved in the synthesis of various compounds, in this studied clone, (3) if present, to evaluate if nutrient starvation can influence PKS activity, (4) to test strain cytotoxicity on human cells and (5) to look for other possible enzymes/proteins of biotechnological interest.
2017-12-01 | GSE94355 | GEO