Coral Microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA544686 | ENA |
REPOSITORIES: ENA
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Project description:Florida’s coral reefs are currently experiencing a multi-year disease-related mortality event, that has resulted in massive die-offs in multiple coral species. Approximately 21 species of coral, including both Endangered Species Act-listed and the primary reef-building species, have displayed tissue loss lesions which often result in whole colony mortality [Stony Coral Tissue Loss Disease (SCTLD)]. Determining the causative agent(s) of coral disease relies on a multidisciplinary approach since the causation may be a combination of abiotic, microbial or viral agents. Metaproteomics was used to survey changes in the molecular landscape in the coral holobiont with the goal of providing useful information not only in diagnosis, but for prediction and prognosis. Specifically, in the case of SCTLD, defining molecular changes in the coral holobiont will help define disease progression and aid in identifying the causative agent by clearly defining traits of disease progression shared across affected species. Using samples from nine coral species (46 samples total; those appearing healthy, n = 23, and diseased, n = 23), analysis of the coral and its associated microbiome were performed using bottom-up proteomics. Ongoing analysis (including improving coral holobiont genome-based search space) will demonstrate the utility of this approach and help define improved future experiments.
2021-05-21 | PXD026192 | Pride
Project description:microbiome from coral tissue Metagenome
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Project description:Stony corals generate their calcium carbonate exoskeleton in a highly controlled biomineralization process mediated by a variety of macromolecules including proteins. Fully identifying and classifying these proteins is crucial to understanding their role in exoskeleton formation, yet no optimal method to extract and isolate and characterize coral skeletal proteins has been established and their complete composition remains obscure. Here, we tested four skeletal protein extraction protocols using acetone precipitation and ultrafiltration dialysis filters to present a comprehensive scleractinian coral skeletal proteome. We identified a total of 60 proteins in the coral skeleton, 44 of which were not present in previously published stony coral skeletal proteomes. Extracted protein treatment protocols carried out in this study revealed that there is no “one optimal method” and each protocol revealed a unique set of method-exclusive proteins. To better understand the general mechanism of skeletal protein transportation, we further examined the proteins’ gene ontology, transmembrane domains, and signal peptides. We found that transmembrane domain proteins and signal peptide secretion pathways, by themselves, could not explain the transportation of proteins to the skeleton . We therefore propose that proteins are transported to the skeletal via vesicles and possibly non-traditional secretion pathways.
2020-06-16 | PXD017891 | Pride
Project description:The field of metabolomics generally lacks standardized methods for the preparation of samples prior to analysis. This is especially true for metabolomics of reef-building corals, where the handful of studies that have been published employ a range of sample preparation protocols. The utilization of metabolomics may prove essential in understanding coral biology in the face of increasing environmental threats, and an optimized method for preparing coral samples for metabolomics analysis would aid this cause. The current study evaluates three important steps during samples processing of stony corals: (i) metabolite extraction, (ii) metabolism preservation and (iii) subsampling. Results indicate that a modified Bligh and Dyer extraction is more reproducible across multiple coral species compared to methyl tert-butyl ether and methanol extractions, while a methanol extraction is superior for feature detection. Additionally, few differences are detected between spectra from frozen or lyophilized coral samples. Finally, extraction of entire coral nubbins increases feature detection, but decreases throughput and is more susceptible to subsampling error compared to a novel tissue powder subsampling method. Overall, we recommend the use of a modified Bligh and Dyer extraction, lyophilized samples, and analysis of brushed tissue powder for the preparation of reef-building coral samples for 1H NMR metabolomics.
2019-03-20 | MTBLS862 | MetaboLights