Ocean acidification alters skeleton formation in larvae of the sea urchin Lytechinus pictus
Ontology highlight
ABSTRACT:
ORGANISM(S): Strongylocentrotus purpuratus Lytechinus pictus
PROVIDER: GSE13655 | GEO | 2010/01/01
SECONDARY ACCESSION(S): PRJNA110205
REPOSITORIES: GEO
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Project description:Using standard morphometric methods and gene expression profiling with a DNA microarray, we explored the impacts of high CO2 conditions on development of the sea urchin, Lytechinus pictus, a pelagic larvae that forms a calcium carbonate endoskeleton. Larvae were raised from fertilization to pluteus stage in seawater with elevated CO2 conditions based upon IPCC emissions scenarios B1 (540ppm CO2) and A1FI (970ppm CO2). Larval L. pictus were cultured in seawater treated with three different concentrations of CO2. We aerated water in culture chambers with air that had been mixed to different CO2 concentrations chosen from IPCC predictions of future atmospheric CO2 levels (28). The B1 scenario, one of the most optimistic, predicts a stabilization of atmospheric CO2 levels at ~540 ppm by 2100, and the A1F1 scenario, which, reflecting a more âbusiness as usualâ scenario, predicts atmospheric CO2 levels of ~970 ppm by 2100. Compressed air (~380 ppm CO2) was used as a control condition. The culture chambers were 20 L buckets medified to allow aeration bubbles of the experimental gas to mix with and gently stir the culture water without contacting the larvae. Replacement seawater (0.35 μm filtered) was added at a constant rate of 0.5 L hr-1. Water pH of each chamber was monitored daily using a Radiometer Analytical PHM240 pH meter. Adult L. pictus were maintained in flowing seawater at ambient temperature (~15-18 ºC) and fed kelp until use. Spawning was induced by coelomic injection of 0.5 M KCl, and eggs were collected in 0.35 μm-filtered seawater. Eggs from 5 females were combined in approximately equal concentrations. Sperm from a single male was collected in the same way, diluted with filtered seawater and added to the egg mixture; thus, all the larvae are half-siblings. Immediately following fertilization, embryos were split into 12 culture chambers providing four replicates of the three CO2 treatments. At the 48 hour time point, a sample of 40,000 larvae was removed from each of the 8 cultures in the 380 and 970 ppm treatments and stored in1 mL Trizol at -80 ºC for later RNA analysis. The larval cDNA samples from each treatment were competitively hybridized on each microarray following a balanced incomplete block design (BIBD) with respect to the assignment of treatments to arrays. In this way, differential expression between all pairs of treatments is estimated with equal precision. Although dye swaps of technical replicates were not used, treatment and dye effects are orthogonal to one another, i.e. treatment effects can be estimated independently of dye effects.
2010-05-16 | E-GEOD-13655 | biostudies-arrayexpress
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: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). Adult S. purpuratus were collected using SCUBA from Goleta Pier (Goleta,CA, USA) and maintained in flowing seawater tables at 15-16°C. Spawning was induced by coelomic injection of 0.5M KCl following standard methods (Strathmann 1987). Eggs were collected from 3 females and separately fertilized by sperm from a single male (i.e. all larvae were full or half-siblings). Each of the three replicate cultures were divided in three (nine cultures total) and held in 10L flow-through containers filled with seawater aerated through a side arm with commercially manufactured air containing three different pCO2: 380ppm CO2 (present day atmospheric CO2 level, pH 8.01 ± 0.01), 540ppm CO2, an optimistic atmospheric CO2 concentration predicted by the Intergovernmental Panel on Climate Change for 2100 (B1 scenario, pH 7.96 ± 0.01) and 1020ppm CO2 (A1FI scenario, pH 7.88 ± 0.01). Larvae were cultured at 15°C until prism stage (40h post-fertilization). At the 40 hour time point, a sample of 60,000 larvae was removed from each of the 9 cultures in the 380, 540 and 1020 ppm treatments and stored in 1 mL Trizol at -80 ºC for later RNA analysis. The larval cDNA sample from each replicate 540ppm CO2 culture was competitively hybridized against the 380ppm CO2 control culture from the same replicate female. Similarly, the larval cDNA sample from each replicate 1020ppm CO2 culture was competitively hybridized against the 380ppm CO2 control culture from the same replicate female. Using dye swaps of technical replicates, treatment effects could be estimated independently of dye effects.
2009-08-14 | E-GEOD-13777 | biostudies-arrayexpress
Project description:In this study we investigated how changes in pH and ocean chemistry consistent with the scenarios of the Intergovernmental Panel on Climate Change (IPCC) drive major changes in gene expression, respiration, photosynthesis and symbiosis of the coral, Acropora millepora, long before they affect biomineralization. Changes in gene expression were consistent with metabolic suppression, an increase in oxidative stress, apoptosis and symbiont loss. Other expression patterns demonstrated up-regulation of membrane transporters, as well as the regulation of genes involved in membrane cytoskeletal interactions and cytoskeletal remodeling. These widespread changes in gene expression emphasize the need to expand future studies of ocean acidification to include a wider spectrum of cellular processes, many of which may occur well before impacts on calcification.
2012-07-30 | GSE28697 | GEO
Project description:We experimentally manipulate CO2 levels and investigate the effects of high-CO2/low pH on seagrass metabolism and underlying molecular mechanisms. Cymodocea nodosa plants were collected in Cadiz Bay at the end of January 2014 and transported to the mesocosm facility. After a one week acclimation period, C. nodosa were either kept under normal (400 ppm) or elevated (1200 ppm) CO2 concentration for 12 days. RNA extraction and sequencing was performed in all phases to test differential expression of genes in different conditions.
2017-05-31 | E-MTAB-4232 | biostudies-arrayexpress
Project description:The effects of ocean acidification (OA) on nitrous oxide (N2O) production and on the community composition of ammonium oxidising archaea (AOA) were examined in the northern and southern sub-polar and polar Atlantic Ocean. Two research cruises were performed during June 2012 between the North Sea and Arctic Greenland and Barent Seas, and in January-February 2013 to the Antarctic Scotia Sea. Seven stations were occupied in all during which shipboard experimental manipulations of the carbonate chemistry were performed through additions of NaHCO3- + HCl in order to examine the impact of short- term (48 hour for N2O and between 96 and 168 hour for AOA) exposure to control and elevated conditions of OA. During each experiment, triplicate incubations were performed at ambient conditions and at 3 lowered levels of pH which varied between 0.06 and 0.4 units according to the total scale and which were targeted at CO2 partial pressures of ~500, 750 and 1000 μatm. The AOA assemblage in both Arctic and Antarctic regions was dominated by two major archetypes that represent the marine AOA clades most often detected in seawater. There were no significant changes in AOA assemblage composition between the beginning and end of the incubation experiments. N2O production was sensitive to decreasing pHT at all stations and decreased by between 2.4 and 44% with reduced pHT values of between 0.06 and 0.4. The reduction in N2O yield from nitrification was directly related to a decrease of between 28 and 67% in available NH3 as a result of the pH driven shift in the NH3:NH4+ equilibrium. The maximum reduction in N2O production at conditions projected for the end of the 21st century was estimated to be 0.82 Tg N y-1.
2015-08-15 | GSE72072 | 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:In this study we investigated how changes in pH and ocean chemistry consistent with the scenarios of the Intergovernmental Panel on Climate Change (IPCC) drive major changes in gene expression, respiration, photosynthesis and symbiosis of the coral, Acropora millepora, long before they affect biomineralization. Changes in gene expression were consistent with metabolic suppression, an increase in oxidative stress, apoptosis and symbiont loss. Other expression patterns demonstrated up-regulation of membrane transporters, as well as the regulation of genes involved in membrane cytoskeletal interactions and cytoskeletal remodeling. These widespread changes in gene expression emphasize the need to expand future studies of ocean acidification to include a wider spectrum of cellular processes, many of which may occur well before impacts on calcification. We applied a reference microarray design for the experiment outlined in the study, which was a three condition experiment of ocean acidification: control pH 8.0-8.2, medium pH 7.8-7.9 and high pH 7.6-7.7, and across three time points: time zero, day 1 and day 28. Samples from time zero and control treatments were used to generate the reference sample for the microarray hybridization experiments. A total of 27 microarrays were used in the entire experiment, 3 biological replicates per treatment and timepoint. Reference samples in each array was labeled with Cy3, and the actual experimental samples with Cy5.
2012-07-29 | E-GEOD-28697 | biostudies-arrayexpress
Project description:Ocean acidification is recognized as one of the most pervasive anthropogenic impact on marine life. A variety of responses have been highlighted in different marine organisms ranging from physiology to gene and protein expression. However, most of these studies have been performed in laboratory exposing adults or developmental stages to CO2 enriched seawater. To what extend the information obtained from these in vitro experiments may be extrapolated to a natural environment is questionable. Here, we utilized the Castello volcanic CO2 vents at Ischia as natural laboratory to study the P. lividus population living at the low pH zone (pH~7.8) compared to those of sea urchins living at control sites. Wide-ranging analyses were performed in animals collected at the acidified site, including the monitoring of their position, the determination of the physico-chemical parameters of the coelomic fluid and an in depth characterization of coelomocytes regarding the number and type of cells, Hsp70 expression, redox status and protein expression through de-novo sequencing analyses. In addition, the respiration, nitrogen metabolism, and skeletal mineralogy of urchins from the vent were examined in comparison with those from control animals. Overall these analyses allowed to understand how the sea urchins can thrive in low pH/high CO2.
2022-02-28 | PXD009395 | Pride
Project description: Not available
| S-EPMC6603003 | biostudies-literature