Ontology highlight
ABSTRACT:
PROVIDER: PRJNA680010 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13122800_1.fastq.gz | Fastqsanger.gz | |||
| SRR13122800_2.fastq.gz | Fastqsanger.gz | |||
| SRR13122900_1.fastq.gz | Fastqsanger.gz | |||
| SRR13122900_2.fastq.gz | Fastqsanger.gz | |||
| SRR13122801_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 430 |
Similar Datasets
Project description:Divergent functions of two clades of flavodoxin in diatoms mitigate oxidative stress and iron limitation Thalassiosira pseudonana and 4 open-ocean diatoms were subjected to iron limitation or short-term oxidative stress (hydrogen peroxide). mRNA profiles of T. pseudonana (CCMP1335), Thalassiosira oceanica (CCMP1005), Amphora coffeaeformis (CCMP1405), Chaetoceros sp. (CCMP199), and Cylindrotheca closterium (CCMP340).
2022-11-07 | GSE217467 | GEO
Project description:Increasing atmospheric CO2 concentrations are causing decreased pH over vast expanses of the ocean. This decreasing pH may alter biogeochemical cycling of carbon and nitrogen via the microbial process of nitrification, a key process that couples these cycles in the ocean, but which is often sensitive to acidic conditions. Recent reports indicate a decrease in oceanic nitrification rates under experimentally lowered pH. How composition and abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) assemblages respond to decreasing oceanic pH, however, is unknown. We sampled microbes from two different acidification experiments and used a combination of qPCR and functional gene microarrays for the ammonia monooxygenase gene (amoA) to assess how acidification alters the structure of ammonia oxidizer assemblages. We show that despite widely different experimental conditions, acidification consistently altered the community composition of AOB by increasing the relative abundance of taxa related to the Nitrosomonas ureae clade. In one experiment this increase was sufficient to cause an increase in the overall abundance of AOB. There were no systematic shifts in the community structure or abundance of AOA in either experiment. These different responses to acidification underscore the important role of microbial community structure in the resiliency of marine ecosystems. amoA gene diversity from two ocean acidification experiments, Monterey Bay experiment (two time points, ambient and acidified) and Vineyard Sound experiment (ambient and acifidied, with and without nutrients) examined with 2 two-color arrays (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5.
2013-08-27 | E-GEOD-49956 | biostudies-arrayexpress
Project description:Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3,839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling.
2014-03-25 | GSE56132 | GEO
Project description:Increasing atmospheric CO2 concentrations are causing decreased pH over vast expanses of the ocean. This decreasing pH may alter biogeochemical cycling of carbon and nitrogen via the microbial process of nitrification, a key process that couples these cycles in the ocean, but which is often sensitive to acidic conditions. Recent reports indicate a decrease in oceanic nitrification rates under experimentally lowered pH. How composition and abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) assemblages respond to decreasing oceanic pH, however, is unknown. We sampled microbes from two different acidification experiments and used a combination of qPCR and functional gene microarrays for the ammonia monooxygenase gene (amoA) to assess how acidification alters the structure of ammonia oxidizer assemblages. We show that despite widely different experimental conditions, acidification consistently altered the community composition of AOB by increasing the relative abundance of taxa related to the Nitrosomonas ureae clade. In one experiment this increase was sufficient to cause an increase in the overall abundance of AOB. There were no systematic shifts in the community structure or abundance of AOA in either experiment. These different responses to acidification underscore the important role of microbial community structure in the resiliency of marine ecosystems. SUBMITTER_CITATION: Title: Acidification alters the composition of ammonia oxidizing microbial assemblages in marine mesocosms Journal: Marine Ecology Progress Series Issue: 492 Pages: 1-8 DOI: 10.3354/meps 10526 Authors: Jennifer L Bowen Patrick J Kearns Michael Holcomb Bess B Ward
2013-08-27 | GSE49956 | GEO
Project description:In this study we characterize microbial community features on the surface of Indian Ocean. 11 samples were collected from Indian Ocean and subjected for quantitative metaproteomics analysis for taxonomic and functional analysis. Our results suggested that metabolic tuning at metaproteomics levels enabled microbial community to sustain stable when subjected to environmental perturbations in the oligotrophic ocean.
2023-05-10 | PXD016285 | Pride
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
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification
2008-02-08 | GSE10119 | GEO
Project description:The physiological adaptations of diatoms to cope with Cu limitation are largely unknown. In the present study we investigated the response to Cu limitation in two strains of the model open ocean diatom T. oceanica (CCMP 1003 and CCMP 1005), focusing on physiological and proteomic changes in the photosynthetic apparatus. Our results show remarkable differences between the adaptations of TO05 and TO03 to low Cu, highlighting significant intra specific variations.
2017-08-15 | PXD006237 | Pride