Ontology highlight
ABSTRACT:
PROVIDER: PRJEB14793 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1530730.fastq.gz | Fastqsanger.gz | |||
| ERR1530740.fastq.gz | Fastqsanger.gz | |||
| ERR1530750.fastq.gz | Fastqsanger.gz | |||
| ERR1530760.fastq.gz | Fastqsanger.gz | |||
| ERR1530770.fastq.gz | Fastqsanger.gz |
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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:To test whether elevated CO2 , which drives seawater below pH 7.9, would shift the dynamical expression patterns diatoms in a more natural environment, we designed a controlled mesocosm study at Friday Harbor Laboratories (FHL) Ocean Acidification Environmental Laboratory (OAEL). Briefly, four independent mesocosm tanks were set up with continuous flow (10-12 mL/min) of filtered seawater from the Puget Sound to simulate mid-century (pH 7.9) and acidified oceanic conditions (pH 7.6) in duplicate. Mesocosm reservoirs were supplemented with nutrients and inoculated with T. pseudonana acclimated in FHL seawater. Mesocosms were outfitted with custom enclosures to simulate a 12:12 light:dark diel cycle. Cells for RNA extraction were sampled in the middle of the light and dark cycle and sequenced on Illumina NextSeq 500 platform.
2021-03-13 | GSE168812 | GEO
Project description:The filamentous diazotrophic cyanobacteria Trichodesmium spp. supply fixed nitrogen (N) to the N-depleted oligotrophic oceans where their growth is often limited by the low availability of phosphorus(P) and/or iron. Previous studies have mostly been focused on the effects of ocean acidification on Trichodesmium under nutrient sufficient or iron-limited conditions. Only a few studies have examined the impacts of ocean acidification on Trichodesmium grown at low P concentrations using non-steady-state batch cultures. Here we cultured Trichodesmium using P-limited continuous cultures (chemostat) to mimic steady-state oceanic low P condition, and used comparative NGS-derived Trichodesmium transcriptome profiling (RNA-seq) analysis to find differentially expressed genes and cellular pathways in response to acidification.
2022-10-13 | GSE181428 | 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 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:Mesocosms (600 L) were deployed at the Southern Ocean Time Series (SOTS) in Austral late summer during a high nutrient, low chlorophyll period. One mesocosm represented control, present-day conditions (high nutrients/low temperature/low pCO2/low Fe/low irradiance), while the other was amended to represent a projected 2100 scenario (low nutrients/high temperature/high pCO2/high Fe/high irradiance). Approximately 2 L were filtered from the mesocosms onto 5 µm filters at Days 0, 2, 4, and 7 of the incubation.
2022-10-26 | PXD021185 | Pride
Project description:In this research we present a transcriptomics analysis of the physiological response of a marine calcifier, Strongylocentrotus purpuratus, to ocean acidification, a decline in ocean pH that results from the absorption of anthropogenic carbon dioxide (CO2). Larvae were raised from fertilization to prism stage in seawater with elevated CO2 conditions based upon IPCC emissions scenario B1 (540ppm CO2) and A1FI (1020ppm CO2).
2009-08-14 | GSE13777 | 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: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:In recent years, increasing levels of dissolved carbon dioxide in seawater have led to an increase of ocean acidification (OA), which constitutes a major threat to marine ecosystems. As an important economically marine bivalve, Mactra veneriformis is highly susceptible to ocean acidification. In this study, we recorded and observed the mortality rate, oxygen consumption rate and ammonia excretion rate of different shell colour groups of M. veneriformis under the stress of ocean acidification (pH=7.6), and conducted transcriptome analysis of the mantle tissues of M. veneriformis with white and purple shell colours in the acidified group (pH=7.6) and the control group (pH=8.1) under the two conditions, which showed that there was a significant difference in mortality rate between the acidified group and the control group at day 30, but there was a significant difference in mortality rate between the white colors group and the purple colors group at day 30, which was not significant. The results showed that there was a significant difference in mortality between the acidified and control groups at day 30, but the difference in mortality between the white and purple shell colour groups at day 30 was not significant. In the transcriptome analysis, fatty acid synthase gene was up-regulated in two shell colours of M. veneriformis under acidification stress, which may be a molecular compensatory mechanism to reduce the susceptibility of organisms to oxidative damage of lipids; tyrosinase gene was up-regulated, which may be a compensatory mechanism of Tyr's regulatory mechanism to the formation of shell damages under acidification; carbonic anhydrase gene was up-regulated in the purple group of M. veneriformis under acidification stress, which may be a compensatory mechanism for the acidity of M. veneriformis to cope with environmental stress; the white group of M. veneriformis under acidification stress was up-regulated. The carbonic anhydrase gene was up-regulated in the purple group under acidification stress, which may be an acidity compensation mechanism of M. veneriformis in response to the environmental stress.
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Project description:Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS), RNA-Seq (i.e. transcriptomics), high-CO2 physiology experiments, and spatiotemporally separated samples isolated in situ (i.e. directly from the ocean) to examine the metabolic potential of genome-wide cytosine (5mC) methylation (i.e. epigenomics), its potential impacts to transcriptional dynamics under both present-day and future ocean acidification conditions, and its biogeographic conservation in the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.
2018-03-01 | GSE86991 | GEO