Accessing BCO-DMO data
Brought to you by BCO-DMO
|
|
BCO-DMO ERDDAP
Accessing BCO-DMO data |
log in
Brought to you by BCO-DMO |
| Dataset Title: | Fv/Fm for cultured Clade A & B Symbiodinium with 2 treatments measured over a range of temperatures 
|
| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_732890) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Files
| Make a graph
|
Attributes {
s {
Strain {
String bcodmo_name "taxon";
String description "Symbiodinium strain";
String long_name "Strain";
String units "unitless";
}
Species {
String bcodmo_name "species";
String description "Symbiodinium species";
String long_name "Species";
String units "unitless";
}
Treatment {
Byte _FillValue 127;
Byte actual_range 26, 31;
String bcodmo_name "treatment";
String description "relevant treatment (see methods): 26 = control temperature; 31 = high temperature treatment";
String long_name "Treatment";
String units "unitless";
}
Replicate {
String bcodmo_name "replicate";
String description "experimental repetition identifier";
String long_name "Replicate";
String units "unitless";
}
Temperature {
Float32 _FillValue NaN;
Float32 actual_range 26.0, 46.2;
String bcodmo_name "temperature";
String description "measurement temperature";
String long_name "Temperature";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
String units "degrees Celsius";
}
Fv_Fm {
Float32 _FillValue NaN;
Float32 actual_range -0.9, 0.397;
String bcodmo_name "Fv2Fm";
String description "Max photochemical quantum efficiency";
String long_name "FV FM";
String units "dimensionless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Symbiodinium culture preparation: Cultures were obtained from the LaJeunesse
algal collection at Penn State University. Phylogenetic relationships of these
strains are described in Parkinson et al., (2015). Symbiodinium cultures were
grown and maintained in liquid media (ASPA-8A, Blank, 1987) at 26 \\u02daC with
fluorescent lights delivering 80-100 \\u03bcmol quanta m-2 s-1 (measured using
a DIVING-PAM equipped with a flat cosine-corrected Fiber Quantum Sensor, Walz,
Germany) on a 12:12 hours Light:Dark photoperiod in Innovator 44 incubators
(New Brunswick, USA). Symbiodinium cultures of equal starting concentration (3
x 104 cells 126 mL-1) for each strain were grown for 7.5 days at 26 \\u02daC at
logarithmic growth phase prior to experimentation. After 7.5 days of
incubation at 26 \\u02daC, one culture of each strain was subjected to a high
temperature treatment of 31 \\u02daC for two light cycles and one dark cycle
(i.e., 1.5 d), whilst another was maintained at 26 \\u02daC.
Data collection:\\u00a0100 \\u03bcL aliquots (8.33 x 104 cells mL-1, calculated
as the average of twelve independent hemocytometer measurements) of dark-
adapted cultures were then subjected to 5 minutes of elevated temperatures in
a thermocycler (Eppendorf Mastercycler Pro S).
Chlorophyll fluorescence parameters were measured immediately after the 5 min
temperature exposure using a Fluorometer (see below). Measurements were
performed at 25 temperatures (i.e. 26, 30.3, 30.5, 31, 31.7, 32.6, 33.7, 34.8,
35.9, 36.8, 37.6, 38.1, 38.3, 38.8, 38.9, 39.4, 40.1, 41,42, 43, 44, 44.9,
45.6, 46.1, 46.2 \\u02daC) and replicated three times per Symbiodinium strain
per treatment. A modified protocol by D\\u00edaz-Almeyda et al., 2011 was used.
Fv/Fm was automatically calculated/determined by fitting each fluorescence
transient to the bio-physical model of Kolber et al. (1998) using the FIREPRO
software (Satlantic, Version 1.4.3) integrated with the FIRe system.
Reference excitation profile used by FIReView to normalize the variable
fluorescence profile: [EXCFOP.TXT](\\\\\"https://datadocs.bco-
dmo.org/docs/medina/Varadero_Reef/data_docs/732890/1/EXCFOP.TXT\\\\\")
Column 1: incremental sample counter
Column 2: elapsed time measured in microSeconds (uS)
Column 3: reference excitation profile
Column 4: relative fluorescence profile normalized to the reference
excitation, or the fluorescence yield
Calibration date: 1/ 1/2002
Time (in seconds) of day reading was taken =\\u00a079931
Methodology Reference:
D\\u00edaz-Almeyda, E., Thom\\u00e9, P. E., Hafidi, M. El, and Iglesias-
Prieto, R. (2011). Differential stability of photosynthetic membranes and
fatty acid composition at elevated temperature in Symbiodinium. Coral Reefs,
30(1), 217\\u2013225.
[https://doi.org/10.1007/s00338-010-0691-5](\\\\\"https://doi.org/10.1007/s00338-010-0691-5\\\\\").";
String awards_0_award_nid "551036";
String awards_0_award_number "OCE-1442206";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1442206";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "Michael E. Sieracki";
String awards_0_program_manager_nid "50446";
String awards_1_award_nid "717027";
String awards_1_award_number "OCE-1642311";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1642311";
String awards_1_funder_name "NSF Division of Ocean Sciences";
String awards_1_funding_acronym "NSF OCE";
String awards_1_funding_source_nid "355";
String awards_1_program_manager "Michael E. Sieracki";
String awards_1_program_manager_nid "50446";
String cdm_data_type "Other";
String comment
"Symbiodinium Fv/Fm over a temperature gradient
Fv/Fm for Clade A & B Symbiodinium with 2 temperature treatments measured over a range of temperatures
PI: M. Medina (PSU)
version: 2018-03-26";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2018-04-04T19:41:57Z";
String date_modified "2019-12-11T16:16:16Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.732890.1";
String history
"2024-04-23T18:37:42Z (local files)
2024-04-23T18:37:42Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_732890.html";
String infoUrl "https://www.bco-dmo.org/dataset/732890";
String institution "BCO-DMO";
String instruments_0_acronym "Fluorometer";
String instruments_0_dataset_instrument_description
"Used to measure fluorescence. Settings: default settings of the manufacturer with the following changes: Gain: 800; # of samples: 4; STF: 60 μs. See Exc profile,the reference excitation profile used by FIReView to normalize the variable fluorescence profile.
See also: http://www.seabird.com/FIRe-System";
String instruments_0_dataset_instrument_nid "732902";
String instruments_0_description "A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/113/";
String instruments_0_instrument_name "Fluorometer";
String instruments_0_instrument_nid "484";
String instruments_0_supplied_name "Fluorescence Induction and Relaxation (FIRe) Fluorometer system and fibre optic probe (Satlantic, Halifax, Nova Scotia, Canada)";
String keywords "bco, bco-dmo, biological, chemical, data, dataset, dmo, erddap, Fv_Fm, management, oceanography, office, preliminary, replicate, species, strain, temperature, treatment";
String license "https://www.bco-dmo.org/dataset/732890/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/732890";
String param_mapping "{'732890': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/732890/parameters";
String people_0_affiliation "Pennsylvania State University";
String people_0_affiliation_acronym "PSU";
String people_0_person_name "Mónica Medina";
String people_0_person_nid "472486";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Pennsylvania State University";
String people_1_affiliation_acronym "PSU";
String people_1_person_name "Roberto Iglesias-Prieto";
String people_1_person_nid "717031";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Emory University";
String people_2_person_name "Erika Díaz-Almeyda";
String people_2_person_nid "733106";
String people_2_role "Scientist";
String people_2_role_type "originator";
String people_3_affiliation "Pennsylvania State University";
String people_3_affiliation_acronym "PSU";
String people_3_person_name "Frederic Joseph Pollock";
String people_3_person_nid "733104";
String people_3_role "Scientist";
String people_3_role_type "originator";
String people_4_affiliation "Pennsylvania State University";
String people_4_affiliation_acronym "PSU";
String people_4_person_name "Joost Samir Mansour";
String people_4_person_nid "733100";
String people_4_role "Contact";
String people_4_role_type "related";
String people_5_affiliation "Woods Hole Oceanographic Institution";
String people_5_affiliation_acronym "WHOI BCO-DMO";
String people_5_person_name "Nancy Copley";
String people_5_person_nid "50396";
String people_5_role "BCO-DMO Data Manager";
String people_5_role_type "related";
String project "GCMB,Varadero Reef";
String projects_0_acronym "GCMB";
String projects_0_description
"Description from NSF award abstract:
Coral reefs are among the most biologically diverse marine ecosystems on the planet, and provide substantial economic and ecological benefits to coastal communities. Corals are composed of both the Cnidarian animal host and complex communities of unique and underexplored microbial organisms. Today these natural wonders are in global decline, threatened by the intersecting effects of multiple stressors including overfishing, pollution, and climate change. These stressors can alter coral microbial communities in ways that may contribute to the susceptibility of corals to disease or overgrowth by algae. Therefore, understanding the relationships between corals and their microbiota may be useful for efforts to understand coral disease and preserve reef ecosystems. The microbial diversity of coral species in many diverse and ancient groups of corals remains unexplored, but understanding these communities will help to extend the knowledge gained in well-studied corals to diverse reefs worldwide. This project aims to describe microbial diversity across all major groups of reef-building corals in each of several distinct ecosystems across the globe, to determine the genome sequences and metabolic capabilities of key coral bacteria, and to test whether the composition of coral microbial communities helps to explain the overall vulnerability or resistance of different coral species to stress or disease.
Coral species differ in their susceptibility to bleaching and disease, but these differences are only partially explained by coral phylogeny. Therefore this project will test the extent to which incorporating the microbiota (or their contributed genes) better predicts these and other traits. Recent technological advances have broadened understanding of how complex microbiomes shape the life history, physiology, and evolution of their multicellular hosts (e.g., the human microbiome). The use of newly developed DNA sequencing techniques will allow a more complete exploration of microbial diversity in corals than has previously been feasible, while advanced computational methods will help to maximize the value of sequenced bacterial genomes. Improved predictive models that incorporate both coral phylogeny and microbial function will help inform conservation strategies and yield predictive biomarkers for coral vulnerability to disease or bleaching. Relating the diversity of corals to the diversity of their microbes will also provide important insights into how intimate symbiotic associations with microorganisms arose and are maintained in diverse animals.";
String projects_0_end_date "2018-08";
String projects_0_geolocation "Circumtropical";
String projects_0_name "Coevolution of scleractinian corals and their associated microorganisms";
String projects_0_project_nid "551037";
String projects_0_project_website "http://oregonstate.edu/microbiology/vegathurberlab/global-coral-microbiome-project";
String projects_0_start_date "2014-09";
String projects_1_acronym "Varadero Reef";
String projects_1_description
"NSF Award Abstract:
Coral reefs provide invaluable services to coastal communities, but coral populations worldwide are in a state of unprecedented decline. Studying resilient reefs is of primary importance for coral conservation and restoration efforts. A unique natural experiment in coral resilience to stress has been playing out in Cartagena Bay, Colombia since the Spanish conquistadors diverted the Magadalena River into the Bay in 1582. Varadero Reef at the southern mouth of the Bay has survived centuries of environmental insults and changing conditions with up to 80% coral cover. This reef provides an ideal system to test biological robustness theory. Given that Varadero is a highly perturbed system, we hypothesize that while likely more robust to perturbation than nearby pristine reefs, it will be less physiologically efficient. Some of the large star coral colonies (Orbicella faveolata) at this site have existed since before the construction of the Canal del Dique. These coral specimens contain invaluable information regarding the conditions of the Magdalena River wathershed and its construction in the XIV century. Changes in turbidity of the plume associated with the urban industrial and agricultural development of Colombia can be documented as variations in calcification rates and changes in the microstructure of the skeleton. The Colombian government has announced the approval for the construction of a shipping channel that will go right over this reef, with the goal to start dredging as early as Fall 2016 or early 2017. The RAPID funding mechanism would enable immediate collection of data and information of why this reef has survived centuries of environmental stress that can shed light on what genotype combinations of coral and its microbial constituents will fare better in similar conditions at other reef locations around the world. Coral reef conservation biology will benefit from this study by generating data for the development of stress diagnostic tools to identify resilient corals. This project will help broaden participation in science by training a diverse cohort of students to work effectively in the global arena while fostering productive collaborations with several Colombian researchers and educational institutions. Students will also gain cultural empathy and sensitivity through direct engagement with the members of society who are most directly impacted by coral reef degradation (e.g. fishermen). Student researchers from Penn State University will work alongside their Colombian counterparts to develop a series of bilingual blog posts to record the cultural and scientific aspects of this project's research expeditions. The blog postings will be submitted for wide dissemination to the Smithsonian's Ocean Portal where Penn State students have published in the past. An educational coral kit developed by the Medina Lab and extensively tested in schools in the US has been translated into Spanish and will be used in local schools in Cartagena and vicinities. All expedition data and metadata will be incorporated into the Global Coral Microbiome Project's interactive web portal, a responsive outreach tool allows researchers, students and/or teachers to access a wealth of information about every coral colony we sample and to virtually explore coral reefs around the world from any internet-enabled device.
This research will generate information to understand functional traits related to symbioses stability under different perturbation regimes. Comparative analyses of microbiome modifications generated during the reciprocal transplantation will allow us to document possible differential responses of the holobionts to acute and chronic stressors relative to corals not exposed to significant levels of perturbation. The development of local bio-optical models of coral calcification and the characterization of the coral holobiont will permit the distinction between the effects in calcification attributed to local turbidity from those that can be ;attributed to differences in host genotype and/or microbial community composition and function. The information recorded in coral skeletons can be used to reconstruct the rates of agricultural, industrial and urban development of Colombia through the last 5 centuries as changes in the turbidity of the effluent of the Magdalena River.";
String projects_1_end_date "2018-06";
String projects_1_geolocation "Caribbean Sea (10°18’10”N, 75°34’ 55”W)";
String projects_1_name "RAPID: Coral robustness: lessons from an \"improbable\" reef";
String projects_1_project_nid "717028";
String projects_1_start_date "2016-07";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Coral photosynthetic endosymbionts (Symbiodinium) are phylogenetically very diverse, yet the extent of inter- and intraspecific functional variation within clades remains largely underexplored. Understanding this variability will be critical for future research on climate change mediated responses. A properly functioning thylakoid membrane is essential for optimal photosynthetic performance both in free-living and in hospite conditions. Here we analyze the thylakoid membrane melting points of 13 Symbiodinium strains from species in Clades B and A, grown at both control (26 \\u00b0C) and high temperature (31 \\u00b0C). We observed a broad range of responses to thermal stress regardless of taxonomic rank. Our results support and augment a growing body of literature demonstrating that functional differences among Symbiodinium spp. are as distinct at lower taxonomic levels (i.e. interspecific) as they are among major clades. These findings highlight the importance of assessing the variability of plastid traits across the Symbiodinium tree.";
String title "Fv/Fm for cultured Clade A & B Symbiodinium with 2 treatments measured over a range of temperatures";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.