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Dataset Title:  Concentrations of colored dissolved organic matter, dissolved organic carbon,
and total phosphorous from experiments conducted at the University of Hawaii,
Manoa in 2015 (Coral DOM2)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_723868)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
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Things You Can Do With Your Graphs

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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Major_Benthic_Constituent {
    String bcodmo_name "site_descrip";
    String description "Type of organism|substrate in aquaria (coral|macroalgae|sand|rubble)";
    String long_name "Major Benthic Constituent";
    String units "unitless";
  Nutrient_Addition {
    String bcodmo_name "treatment";
    String description "Nominal Level of nutrient addition (ambient|low|high)";
    String long_name "Nutrient Addition";
    String units "unitless";
  Water_Bath {
    Byte _FillValue 127;
    Byte actual_range 1, 3;
    String bcodmo_name "treatment";
    String description "Experimental Replicate water bath tank (1|2|3)";
    String long_name "Water Bath";
    String units "unitless";
  Week {
    Byte _FillValue 127;
    Byte actual_range 0, 4;
    String bcodmo_name "time_elapsed";
    String description "Week of continuous nutrient addition (0|2|4)";
    String long_name "Week";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
    String units "unitless";
  Ultra_Violet_Humic_like {
    Float64 _FillValue NaN;
    Float64 actual_range 0.006100374, 0.105203946;
    String bcodmo_name "unknown";
    String description "Coble Peak A (Ultra Violet Humic-like)";
    String long_name "Ultra Violet Humic Like";
    String units "Raman units of water (RU)";
  Marine_Humic_like {
    Float64 _FillValue NaN;
    Float64 actual_range 6.18318e-4, 0.175470203;
    String bcodmo_name "unknown";
    String description "Coble Peak M (Marine Humic-like)";
    String long_name "Marine Humic Like";
    String units "Raman units of water (RU)";
  Visible_Humic_like {
    Float64 _FillValue NaN;
    Float64 actual_range 0.008174298, 0.109941957;
    String bcodmo_name "unknown";
    String description "Coble Peak C (Visible Humic-like)";
    String long_name "Visible Humic Like";
    String units "Raman units of water (RU)";
  Tryptophan_like {
    Float64 _FillValue NaN;
    Float64 actual_range 0.006615842, 0.436893496;
    String bcodmo_name "unknown";
    String description "Coble Beak T (Tryptophan-like)";
    String long_name "Tryptophan Like";
    String units "Raman units of water (RU)";
  Tyrosine_like {
    Float64 _FillValue NaN;
    Float64 actual_range 0.0, 0.487962641;
    String bcodmo_name "unknown";
    String description "Coble Peak B (Tyrosine-like)";
    String long_name "Tyrosine Like";
    String units "Raman units of water (RU)";
  Phenylalanine_like {
    Float64 _FillValue NaN;
    Float64 actual_range 0.0, 1.710984446;
    String bcodmo_name "unknown";
    String description "Coble Peak F (Phenylalanine-like)";
    String long_name "Phenylalanine Like";
    String units "Raman units of water (RU)";
  Proteinaceous_fDOM {
    Float64 _FillValue NaN;
    Float64 actual_range 0.006615842, 2.631633106;
    String bcodmo_name "unknown";
    String description "Sum of peaks A,M, and C (Proteinaceous fDOM)";
    String long_name "Proteinaceous F DOM";
    String units "Raman units of water (RU)";
  Humic_like_fDOM {
    Float64 _FillValue NaN;
    Float64 actual_range 0.014892989, 0.348826997;
    String bcodmo_name "unknown";
    String description "Sum of peaks T,B,and F (Humic-like fDOM)";
    String long_name "Humic Like F DOM";
    String units "Raman units of water (RU)";
  TP_avg {
    Float32 _FillValue NaN;
    Float32 actual_range 0.08, 2.34;
    String bcodmo_name "P";
    String description "Average Total Phosphorous (TP)";
    String long_name "TP Avg";
    String units "micromoles per liter (µmol L-1)";
  DOC {
    Float32 _FillValue NaN;
    Float32 actual_range 63.73, 124.13;
    String bcodmo_name "DOC";
    String description "Dissolved Organic Carbon (DOC)";
    String long_name "DOC";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/";
    String units "micromoles per liter (µmol L-1)";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"The experiments were conducted at the Research Field Station Marine Lab (FSML)
Kaneohe Bay, Hawaii, (HIMB; 21.4326 \\u02da, -157.7866\\u02da).
The following sections contain methodology excerpts from Quinlain et al.
(2018) relevant to this dataset.
Collection of major reef constituents:
Three visibly healthy colonies each of Porites compressa and Montipora
capitata, two locally abundant hermatypic corals, were collected between 4 and
7 meters depth from fringing reef immediately adjacent to the Hawai'i
Institute of Marine Biology in K\\u0101ne'ohe Bay, Hawai'i (HIMB; 21.435
\\u02da, -157.787\\u02da) between 12 and 16 October 2015. Each colony was
fragmented into 36 nubbins and one nubbin from each colony was mounted onto
each of 36 polystyrene frames (roughly 10 cm2) using epoxy putty. Each frame
had 6 nubbins (3 Porites, 3 Montipora); one nubbin from each colony per frame;
24.8 \\u00b1 5.23 g dry weight P. compressa, 21.9 \\u00b1 5.05 g dry weight of
M. capitata. Corals were allowed to acclimate 10 days before the start of the
experiment. Rubble of dead skeleton from P. compressa skeleton was haphazardly
collected in conjunction with the coral collections, separated into 36 equal
portions (78.9 \\u00b1 3.42 g dry weight) and contained within polyethylene
mesh netting containers. The macroalga Gracilaria sp. (Rhodophyta) was
collected from the north point of HIMB (21.4360\\u02da, -157.7881\\u02da); any
visible invertebrates and epiphytes within the macroalgae were removed, fronds
were separated into 36 equal portions (11.0 \\u00b1 0.55 g wet weight) and
contained within polyethylene mesh netting mesh containers. Sand was collected
from the top 3 cm of aerobic reef sand on the eastern edge of HIMB
(21.4350\\u02da, -157.7871\\u02da) using a 7.5 cm diameter core and was left
undisturbed in each of the 36 petri dishes in which it was collected.
Aquaria and nutrient enrichment systems:
Square polycarbonate aquaria (n = 36) were affixed with an upper spigot drain
to hold water level constant at 6 L, acid washed and soaked for 72 hours in
flowing seawater to leach plasticizers prior to the experiment, scrubbed
clean, rinsed with freshwater and dried. Each aquarium was filled with 4
benthic constituent units (either four coral frames, four algal or rubble mesh
portion containers or four sand dishes) and placed into one of three 1300L
flow-through seawater tanks (12 aquaria per tank) as water baths to maintain
stable temperature. Each tank thus contained one replicate aquarium of each
benthic group maintained at each nutrient level (Figure 1, Quinlain et al.
2018). Source water from K\\u0101ne'ohe Bay was filtered through a sand filter
followed by a 20 \\u00b5m polyethylene cartridge pre-filter to exclude large
plankton. A concentrated nutrient mix (2 mmol L-1 sodium nitrate and 0.67 mmol
L-1 monosodium phosphate, 20L) was prepared every other day by amending
seawater with a frozen concentrated stock in a pre-cleaned polycarbonate
carboy stored at ambient temperatures in the dark. Both the source water and
nutrient mixture were pumped by continuous peristalsis through platinum cured
silicone tubes into nutrient mixing aquaria with 90 minute residence times
maintained at three concentrations (ambient, low and high; mean and time
series concentrations in Figure 1 and Figure S2, respectively, Quinlain et
al., 2018) then distributed by peristalsis to the experimental aquaria
maintained at a 5-hour residence time. Each week all aquaria were replaced
with cleaned and dried aquaria and randomly rearranged spatially within
incubation tanks, but maintained in three replicate experimental blocks cycled
among 1300 L tanks to account for light and temperature variation; means of
288 \\u00b1 354 \\u00b5mol photon m-2 s-1 and 25.9 \\u00b11.9 \\u02daC did not
differ significantly among water baths and are detailed in a companion
manuscript (Silbiger et al., 2018).
Dissolved Organic Matter (DOM) sample collection and analysis:
DOM samples were collected biweekly over a period of four weeks from each
aquaria using acid washed and seawater leached treatment-specific, rubber free
polyethylene syringes and filtered through a 0.2 \\u00b5m polyethersulfone
filter (25 mm; Sterlitech) in a polypropylene filter holder (Swin-lok;
Whatman). Filtrate was collected in acid washed, combusted, triple sample-
rinsed amber borosilicate vials with teflon septa lids and stored dark at
4\\u02daC until analysis within 1 month of collection. Dissolved organic carbon
(DOC) was measured as non-purgeable organic carbon via acidification, sparging
and high temperature platinum catalytic oxidation on a Shimadzu TOC-V (Carlson
et al. 2010). Nutrient samples were collected identically, but frozen (-20
\\u00b0C) in polyethylene centrifuge tubes, thawed to room temperature, mixed
thoroughly and analyzed on a Seal Analytical Segmented Flow Injection
AutoAnalyzer AA3HR for simultaneous determination of soluble reactive
phosphate (PO43-), ammonium (NH4+), nitrate + nitrite (N + N; NO3- + NO2-),
silicate (SiO4) and total dissolved nitrogen and phosphorus (TDN, TDP; via in-
line persulfate/ultraviolet oxidation). Dissolved organic nitrogen (DON) was
calculated as the difference between TDN and the sum of ammonium, nitrate and
Samples for fluorescence spectroscopy were measured using an Horiba Aqualog
scanning fluorometer following the methods of Nelson et al. (2015) and
processed using a Matlab (v2007b) script (see processing section below). Six
PARAFAC components were validated using split half validation and outlier
analysis (Figure S1, Quinlain et al., 2018). All PARAFAC components had
similar excitation-emission maxima and strong covariation among samples with
previously identified fluorophores; thus for subsequent analyses, we examined
established fluorescence maxima from the literature (Table S1, Quinlain et
al., 2018; Coble ,1996; Stedmon et al., 2003; Lakowicz, 2010).";
    String awards_0_award_nid "675030";
    String awards_0_award_number "OCE-1538393";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1538393";
    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 cdm_data_type "Other";
    String comment 
"CRANE: fDOM, DOC, and TP 
  PI: Craig Nelson 
  data version 1: 2018-01-17";
    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 "2018-01-17T16:48:28Z";
    String date_modified "2019-06-27T14:48:52Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.723868.1";
    String history 
"2024-04-24T23:01:06Z (local files)
2024-04-24T23:01:06Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_723868.das";
    String infoUrl "https://www.bco-dmo.org/dataset/723868";
    String institution "BCO-DMO";
    String instruments_0_acronym "Fluorometer";
    String instruments_0_dataset_instrument_nid "726350";
    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 "Horiba Aqualog scanning fluorometer";
    String instruments_1_acronym "Shimadzu TOC-V";
    String instruments_1_dataset_instrument_nid "726351";
    String instruments_1_description "A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method.";
    String instruments_1_instrument_external_identifier "http://onto.nerc.ac.uk/CAST/124";
    String instruments_1_instrument_name "Shimadzu TOC-V Analyzer";
    String instruments_1_instrument_nid "603";
    String instruments_2_acronym "FIA";
    String instruments_2_dataset_instrument_nid "726352";
    String instruments_2_description "An instrument that performs flow injection analysis. Flow injection analysis (FIA) is an approach to chemical analysis that is accomplished by injecting a plug of sample into a flowing carrier stream. FIA is an automated method in which a sample is injected into a continuous flow of a carrier solution that mixes with other continuously flowing solutions before reaching a detector. Precision is dramatically increased when FIA is used instead of manual injections and as a result very specific FIA systems have been developed for a wide array of analytical techniques.";
    String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB36/";
    String instruments_2_instrument_name "Flow Injection Analyzer";
    String instruments_2_instrument_nid "657";
    String instruments_2_supplied_name "Seal Analytical Segmented Flow Injection AutoAnalyzer AA3HR";
    String keywords "addition, average, bath, bco, bco-dmo, benthic, biological, chemical, commerce, constituent, data, dataset, department, dmo, doc, dom, erddap, humic, Humic_like_fDOM, like, major, Major_Benthic_Constituent, management, marine, Marine_Humic_like, nutrient, Nutrient_Addition, oceanography, office, phenylalanine, Phenylalanine_like, preliminary, proteinaceous, Proteinaceous_fDOM, TP_avg, tryptophan, Tryptophan_like, tyrosine, Tyrosine_like, ultra, Ultra_Violet_Humic_like, violet, visible, Visible_Humic_like, water, Water_Bath, week";
    String license "https://www.bco-dmo.org/dataset/723868/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/723868";
    String param_mapping "{'723868': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/723868/parameters";
    String people_0_affiliation "University of Hawaii at Manoa";
    String people_0_affiliation_acronym "HIMB";
    String people_0_person_name "Craig E. Nelson";
    String people_0_person_nid "51538";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "University of Hawaii at Manoa";
    String people_1_affiliation_acronym "HIMB";
    String people_1_person_name "Craig E. Nelson";
    String people_1_person_nid "51538";
    String people_1_role "Contact";
    String people_1_role_type "related";
    String people_2_affiliation "University of Hawaii at Manoa";
    String people_2_affiliation_acronym "HIMB";
    String people_2_person_name "Zachary A. Quinlan";
    String people_2_person_nid "726344";
    String people_2_role "Contact";
    String people_2_role_type "related";
    String people_3_affiliation "Woods Hole Oceanographic Institution";
    String people_3_affiliation_acronym "WHOI BCO-DMO";
    String people_3_person_name "Amber York";
    String people_3_person_nid "643627";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Coral DOM2";
    String projects_0_acronym "Coral DOM2";
    String projects_0_description 
"NSF award abstract:
Coral reef degradation, whether driven by overfishing, nutrient pollution, declining water quality, or other anthropogenic factors, is associated with a phase shift towards a reefs dominated by fleshy algae. In many cases managing and ameliorating these stressors does not lead to a return to coral dominance, and reefs languish in an algal-dominated state for years. Nearly a decade of research has demonstrated that trajectories toward increasing algal dominance are restructuring microbial community composition and metabolism; the investigators hypothesize that microbial processes facilitate the maintenance of algal dominance by metabolizing organic compounds released by algae thereby stressing corals through hypoxia and disease. The resilience of reefs to these phase shifts is a critical question in coral reef ecology, and managing reefs undergoing these community shifts requires developing an understanding of the role of microbial interactions in facilitating algal overgrowth and altering reef ecosystem function. The research proposed here will investigate the organics produced by algae, the microbes that metabolize the organics, and the impacts of these processes on coral health and growth. This research has implications for managing reef resilience to algal phase shifts by testing the differential resistance of coral-associated microbial communities to algae and defining thresholds of algal species cover which alter ecosystem biogeochemistry. This project provides mentoring across multiple career levels, linking underrepresented undergraduates, two graduate students, a postdoctoral researcher, and a beginning and established investigators.
This project will integrate dissolved organic matter (DOM) geochemistry, microbial genomics and ecosystem process measurements at ecologically-relevant spatial and temporal scales to test hypothetical mechanisms by which microbially-mediated feedbacks may facilitate the spread of fleshy algae on Pacific reef ecosystems. A key product of this research will be understanding how the composition of corals and algae on reefs interact synergistically with complex microbial communities to influence reef ecosystem resilience to algal phase shifts. Emerging molecular and biogeochemical methods will be use to investigate mechanisms of microbial-DOM interactions at multiple spatial and temporal scales. This project will leverage the background environmental data, laboratory facilities and field logistical resources of the Mo'orea Coral Reef Long Term Ecological Research Project in French Polynesia and contribute to the mission of that program of investigating coral reef resilience in the face of global change. The investigators will quantify bulk diel patterns of DOM production and characterize the composition of chromophoric components and both free and acid-hydrolyzable neutral monosaccharides and amino acids from varying benthic algae sources. The team will also characterize planktonic and coral-associated microbial community changes in taxonomic composition and gene expression caused by algal DOM amendments in on-site controlled environmental chambers using phylogenetics and metatranscriptomics, including tracking algal exudate utilization by specific microbial lineages. Field-deployed 100 liter tent mesocosms will be used to examine in situ diel patterns of coupled DOM production and consumption, microbial community genomics and ecosystem metabolism over representative benthic communities comprising combinations of algal and coral species. Together these experimental results will guide interpretation of field surveys of centimeter-scale spatial dynamics of planktonic and coral-associated microbial genomics and metabolism at zones of coral-algal interaction, including boundary layer dynamics of oxygen, bacteria and DOM using planar optodes, high-throughput flow cytometry and fluorescence spectroscopy.";
    String projects_0_end_date "2018-11";
    String projects_0_geolocation "Pacific Coral Reefs";
    String projects_0_name "Collaborative Research: Dissolved organic matter feedbacks in coral reef resilience: The genomic & geochemical basis for microbial modulation of algal phase shifts";
    String projects_0_project_nid "675025";
    String projects_0_start_date "2015-12";
    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 "Concentrations of colored dissolved organic matter, dissolved organic carbon, and total phosphorous from experiments conducted at the University of Hawaii, Manoa in 2015.";
    String title "Concentrations of colored dissolved organic matter, dissolved organic carbon, and total phosphorous from experiments conducted at the University of Hawaii, Manoa in 2015 (Coral DOM2)";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";


Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

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
For example,
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.

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