GNPS Montastraea annularis coral community extract
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ FT
ORGANISM(S): Montastraea Annularis
SUBMITTER: Dorrestein
PROVIDER: MSV000078686 | GNPS | Wed May 28 15:53:00 BST 2014
REPOSITORIES: GNPS
Similar Datasets
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from blood samples from yellow-bellied marmots (Marmota flaviventris). DNA methylation data from n=159 blood samples. All samples were collected as part of a long-term study of a free-living population of yellow-bellied marmots in the Gunnison National Forest, Colorado (USA), where marmots were captured and blood samples collected biweekly during the their active season (May to August). Genomic DNA was extracted with Qiagen DNeasy blood and tissue kit.
2022-04-13 | GSE174544 | GEO
Project description:Soil microbial community is a complex blackbox that requires a multi-conceptual approach (Hultman et al., 2015; Bastida et al., 2016). Most methods focus on evaluating total microbial community and fail to determine its active fraction (Blagodatskaya & Kuzyakov 2013). This issue has ecological consequences since the behavior of the active community is more important (or even essential) and can be different to that of the total community. The sensitivity of the active microbial community can be considered as a biological mechanism that regulates the functional responses of soil against direct (i.e. forest management) and indirect (i.e. climate change) human-induced alterations. Indeed, it has been highglihted that the diversity of the active community (analyzed by metaproteomics) is more connected to soil functionality than the that of the total community (analyzed by 16S rRNA gene and ITS sequencing) (Bastida et al., 2016). Recently, the increasing application of soil metaproteomics is providing unprecedented, in-depth characterisation of the composition and functionality of active microbial communities and overall, allowing deeper insights into terrestrial microbial ecology (Chourey et al., 2012; Bastida et al., 2015, 2016; Keiblinger et al., 2016). Here, we predict the responsiveness of the soil microbial community to forest management in a climate change scenario. Particularly, we aim: i) to evaluate the impacts of 6-years of induced drought on the diversity, biomass and activity of the microbial community in a semiarid forest ecocosystem; and ii) to discriminate if forest management (thinning) influences the resistance of the microbial community against induced drought. Furthermore, we aim to ascertain if the functional diversity of each phylum is a trait that can be used to predict changes in microbial abundance and ecosystem functioning.
2021-02-02 | PXD005447 | Pride
Project description:2 uncultured phage metagenomes collected from Acropora millepora
| PRJNA52303 | ENA
Project description:Ocean acidification (OA) is negatively affecting calcification in a wide variety of marine organisms. These effects are acute for many tropical scleractinian corals under short-term experimental conditions, but it is unclear how these effects interact with ecological processes, such as competition for space, to impact coral communities over multiple years. This study sought to test the use of individual-based models (IBMs) as a tool to scale up the effects of OA recorded in short-term studies to community-scale impacts, combining data from field surveys and mesocosm experiments to parameterize an IBM of coral community recovery on the fore reef of Moorea, French Polynesia. Focusing on the dominant coral genera from the fore reef, Pocillopora, Acropora, Montipora and Porites, model efficacy first was evaluated through the comparison of simulated and empirical dynamics from 2010-2016, when the reef was recovering from sequential acute disturbances (a crown-of-thorns seastar outbreak followed by a cyclone) that reduced coral cover to ~0% by 2010. The model then was used to evaluate how the effects of OA (1,100-1,200 µatm pCO2) on coral growth and competition among corals affected recovery rates (as assessed by changes in % cover y-1) of each coral population between 2010-2016. The model indicated that recovery rates for the fore reef community was halved by OA over 7 years, with cover increasing at 11% y-1 under ambient conditions and 4.8% y-1 under OA conditions. However, when OA was implemented to affect coral growth and not competition among corals, coral community recovery increased to 7.2% y-1, highlighting mechanisms other than growth suppression (i.e., competition), through which OA can impact recovery. Our study reveals the potential for IBMs to assess the impacts of OA on coral communities at temporal and spatial scales beyond the capabilities of experimental studies, but this potential will not be realized unless empirical analyses address a wider variety of response variables representing ecological, physiological and functional domains.
| S-EPMC8284307 | biostudies-literature
Project description:Twelve coral colonies of Montipora capitata were collected from patch reefs located in Kāne’ohe Bay, O’ahu, Hawai’i. Colonies were brought to shore where they were immediately split into two equally sized pieces, which were acclimated before bleaching. Half of each colony went to an increased water temperature treatment (30°C, bleaching treatment) and the other stayed at ambient temperature (25°C, nonbleached treatment) for three weeks. For the bleaching treatment, experimental tank temperatures were increased 2°C per day ( 1°C every 12 hours) for four days to a final temperature of 30°C. Samples were collected before bleaching (T1) and 24 hours after bleached colonies were returned to ambient temperature (T2), through 3 months post-bleaching (T6).
2024-11-08 | PXD021262 | Pride
Project description:Twelve inshore and six offshore colonies were reciprocally transplanted during 1 year (July 2017- July 2018) at Florida Keys (location). After this period samples were collected from the field and brought to the Experimental Reef Laboratory facilities (RSMAS, Miami) to be acclimated to 30C during 7 days in six aquaria. Three aquaria were keep under initial conditions for the duration of the experiment (30C) and three aquaria had the temperature increased everyday during 7 days to a final temperature of 32C. A total of 56 samples were collected for RNAseq after 6 days of the temperature treatment and stored at -80C.
2024-05-01 | GSE233773 | GEO
Project description:Metagenomic sequencing of Tara Pacific coral samples.
| PRJEB52368 | ENA
Project description:The emergence of genomic tools for reef-building corals and symbiotic anemones comes at a time when alarming losses in coral cover are being observed worldwide. These tools hold great promise in elucidating novel and unforeseen cellular processes underlying the successful mutualism between corals and their algal endosymbionts (Symbiodinium spp.). Since thermal stress triggers a breakdown in the symbiosis (coral bleaching), measuring the transcriptomic response to thermal stress-induced bleaching offers an extraordinary view of the cellular processes specific to coral-algal symbioses. In the present study, we utilized a cDNA microarray containing 2,059 genes of the Caribbean Elkhorn coral Acropora palmata to identify genes differentially expressed upon thermal stress. Fragments from four separate colonies were exposed to elevated temperature (3˚C increase) for two days, and samples were frozen for microarray analysis after 24 and 48 hours. Fragments experienced a 60% reduction in algal cell density after two days. 204 genes were differentially expressed in samples collected one day after thermal stress; in samples collected after two days, 104 genes. Annotations of the differentially expressed genes indicate a conserved cellular stress response in A. palmata involving: 1) growth arrest; 2) chaperone activity; 3) nucleic acid stabilization and repair; and 4) the removal of damaged macromolecules. Other differentially expressed processes include sensory perception, metabolite transfer between host and symbiont, nitric oxide signaling, and modifications to the actin cytoskeleton and extracellular matrix. The results are also compared to those from a previous coral microarray study of thermal stress in Montastraea faveolata.
2009-10-31 | GSE16151 | GEO
Project description:Use CEN quechers method to extract 2.5g honey and use PSA to clean up matrix. Using ACN-water-0.01%HCOOH for compound separation and HRMS analysis with Thermo Orbitrap Exploris 120. Data was acquired in Full scan-ddms2 mode. This included a full scan over the m/z range 100- 1000 at full width at half maximum (FWHM) resolution of 60,000, and a data-dependent-MS2 scan at FWHM resolution of 15,000 on the top 4 ions. The ionization was performed in positive ESI with an inlusion list collated from OPPIN website, and to gain more information about fragment ions in the QC sample, we use an Automated Exclusion List Generation workflow, so one QC sample finally gave 3 injections.
| MSV000092860 | MassIVE
Project description:Raw metagenomic sequences from water samples collected around an Acropora pulchra colony (Tema’e Beach reef, Mo’orea)
| PRJEB54597 | ENA