Ontology highlight
ABSTRACT:
PROVIDER: PRJNA736025 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14766467_1.fastq.gz | Fastqsanger.gz | |||
| SRR14766467_2.fastq.gz | Fastqsanger.gz | |||
| SRR14766468_1.fastq.gz | Fastqsanger.gz | |||
| SRR14766468_2.fastq.gz | Fastqsanger.gz | |||
| SRR14766469_1.fastq.gz | Fastqsanger.gz |
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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 This experiment is part of a much larger experiment. We have produced 4 454 metatranscriptomic datasets and 6 454 metagenomic datasets. These were derived from 4 samples. The experiment is an ocean acidification mesocosm set up in a Norwegian Fjord in 2006. We suspended 6 bags containing 11,000 L of sea water in a Coastal Fjord and then we bubbled CO2 through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. We then induced a phytoplankton bloom in all six bags and took measurements and performed analyses of phytoplankton, bacterioplankton and physiochemical characteristics over a 22 day period. We took water samples from the peak of the phytoplankton bloom and following the decline of the phytoplankton bloom to analyses using 454 metagenomics and 454 metatranscriptomics. Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom. Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. Obviously High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm. Raw data for both the metagenomic and metatranscriptomic components are available at NCBI's Short Read Archive at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000101
2008-02-08 | E-GEOD-10119 | biostudies-arrayexpress
Project description:Rising atmospheric CO2 concentrations are leading to ocean acidification, altering the inorganic carbon buffer system with consequences for marine organisms. Here we applied RNA-seq and iTRAQ quantification to investigate the potential impacts of ocean acidification on the temperate coastal marine diatom Skeletonema marinoi.
2020-12-09 | PXD021416 | Pride
Project description:Coastal upwelling regions are among the most productive marine ecosystems but may be threatened by amplified ocean acidification. Increased acidification is hypothesized to reduce iron bioavailability for phytoplankton thereby expanding iron limitation and impacting primary production. Here we show from community to molecular levels that phytoplankton in an upwelling region respond to short-term acidification exposure with iron uptake pathways and strategies that reduce cellular iron demand. A combined physiological and multi-omics approach was applied to trace metal clean incubations that introduced 1200 ppm CO2 for up to four days. Although variable, molecular-level responses indicate a prioritization of iron uptake pathways that are less hindered by acidification and reductions in iron utilization. Growth, nutrient uptake, and community compositions remained largely unaffected suggesting that these mechanisms may confer short-term resistance to acidification; however, we speculate that cellular iron demand is only temporarily satisfied, and longer-term acidification exposure without increased iron inputs may result in increased iron stress.
2023-11-14 | PXD038549 | Pride
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:A high-density oligonucleotide microarray that targets functional genes in marine microbial community was designed as a result of a multi-institutional effort. The design is based on nucleotide sequence data obtained with metagenomics and metatranscriptomics. The chip targets ~20000 gene sequences represented by 145 gene categories relevant to microbial metabolism in the open ocean and coastal environments. The three domains of life and also viruses are represented on the chip. Using this microarray we were able to compare the functional responses of microbial communities to iron and phosphate enrichments in samples from the North Pacific Subtropical Gyre. The response was attributed to individual lineages of microorganisms including uncharacterized strains. Transcription of 68% of the gene probes was detected from a variety of microorganisms, and the patterns of gene transcription indicated a relief from iron limitation and transition into nitrogen limitation. When combined with physicochemical descriptions of each system, the use of microarrays can help to develop a comprehensive understanding of the changes in microbially-driven processes. We analyzed three samples amended with phosphate and two sample amended with iron (III) after 48h of incubation
2013-03-07 | E-GEOD-44448 | biostudies-arrayexpress
Project description:The comparision between gradual ocean acidification (GC) and one way ocean acidification (HC) of physiological and molecular responses on diatom Skeletonema costatum
2025-01-01 | GSE253819 | 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:Although N2 fixation can occur in free-living cyanobacteria, the unicellular endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is considered to be a dominant N2-fixing species in marine ecosystems. Four UCYN-A sublineages are known from partial nitrogenase (nifH) gene sequences. However, few studies have investigated their habitat preferences and regulation by their respective hosts in open-ocean versus coastal environments. Here, we compared UCYN-A transcriptomes from oligotrophic open-ocean versus nutrient-rich coastal waters. UCYN-A1 metabolism was more impacted by habitat changes than UCYN-A2. However, across habitats and sublineages genes for nitrogen fixation and energy production were highly transcribed. Curiously these genes, critical to the symbiosis for the exchange of fixed nitrogen for fixed carbon, maintained the same schedule of diel expression across habitats and UCYN-A sublineages, including UCYN-A3 in the open-ocean transcriptomes. Our results undersore the importance of nitrogen fixation in UCYN-A symbioses across habitats, with consequences for community interaction and global biogeochemical cycles.
2023-02-23 | GSE206403 | 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:Coastal Antarctic marine ecosystems play an important role in carbon cycling due to their highly productive seasonal phytoplankton blooms. Southern Ocean microbes are primarily limited by light and iron (Fe) and can be co-limited by cobalamin (vitamin B12 ). Micronutrient limitation is a key driver of ecosystem dynamics and influences the composition of blooms, which are often dominated by either diatoms or the haptophyte Phaeocystis antarctica, each with varied impacts on carbon cycling. However, the vitamin requirements and ecophysiology of the keystone species P. antarctica remains poorly characterized. Using cultures, physiological analysis, and comparative ’omics we examined the response of P. antarctica to a matrix of Fe-B12 conditions. We show that P. antarctica is not auxotrophic for B12 , as previously suggested, and report new mechanistic insights of its B12 response in cultures of predominantly solitary and colonial cells. Proteomics coupled with proteogenomics detected a B12 -independent methionine synthase fusion protein (MetE-fusion) that is expressed under vitamin limitation and is interreplaced with the B12 -dependent isoform (MetH) in replete conditions. Database searches returned homologs of the MetE-fusion protein in multiple Phaeocystis species and in a wide range of marine microbes, including other photosynthetic eukaryotes with polymorphic life cycles and also bacterioplankton. Furthermore, MetE-fusion homologs were found to be expressed in metaproteomic and metatranscriptomic field samples in polar and more geographically widespread regions. As climate change impacts micronutrient availability in the coastal Southern Ocean, our finding that P. antarctica has a flexible B12 metabolism has implications for its relative fitness compared to B12 -auxotrophic diatoms.
2023-02-27 | PXD031524 | Pride