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Title Sum-
Institution Dataset ID
     data   graph     files  public 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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The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String 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).
attribute NC_GLOBAL awards_0_award_nid String 675030
attribute NC_GLOBAL awards_0_award_number String OCE-1538393
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1538393 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Michael E. Sieracki
attribute NC_GLOBAL awards_0_program_manager_nid String 50446
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String CRANE: fDOM, DOC, and TP
PI: Craig Nelson
data version 1: 2018-01-17
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2018-01-17T16:48:28Z
attribute NC_GLOBAL date_modified String 2019-06-27T14:48:52Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.723868.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/723868 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Fluorometer
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 726350
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/113/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Fluorometer
attribute NC_GLOBAL instruments_0_instrument_nid String 484
attribute NC_GLOBAL instruments_0_supplied_name String Horiba Aqualog scanning fluorometer
attribute NC_GLOBAL instruments_1_acronym String Shimadzu TOC-V
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 726351
attribute NC_GLOBAL instruments_1_description String A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String http://onto.nerc.ac.uk/CAST/124 (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Shimadzu TOC-V Analyzer
attribute NC_GLOBAL instruments_1_instrument_nid String 603
attribute NC_GLOBAL instruments_2_acronym String FIA
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 726352
attribute NC_GLOBAL instruments_2_description String 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.
attribute NC_GLOBAL instruments_2_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB36/ (external link)
attribute NC_GLOBAL instruments_2_instrument_name String Flow Injection Analyzer
attribute NC_GLOBAL instruments_2_instrument_nid String 657
attribute NC_GLOBAL instruments_2_supplied_name String Seal Analytical Segmented Flow Injection AutoAnalyzer AA3HR
attribute NC_GLOBAL keywords String 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
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/723868/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/723868 (external link)
attribute NC_GLOBAL param_mapping String {'723868': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/723868/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of Hawaii at Manoa
attribute NC_GLOBAL people_0_affiliation_acronym String HIMB
attribute NC_GLOBAL people_0_person_name String Craig E. Nelson
attribute NC_GLOBAL people_0_person_nid String 51538
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String University of Hawaii at Manoa
attribute NC_GLOBAL people_1_affiliation_acronym String HIMB
attribute NC_GLOBAL people_1_person_name String Craig E. Nelson
attribute NC_GLOBAL people_1_person_nid String 51538
attribute NC_GLOBAL people_1_role String Contact
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String University of Hawaii at Manoa
attribute NC_GLOBAL people_2_affiliation_acronym String HIMB
attribute NC_GLOBAL people_2_person_name String Zachary A. Quinlan
attribute NC_GLOBAL people_2_person_nid String 726344
attribute NC_GLOBAL people_2_role String Contact
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL people_3_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_3_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_3_person_name String Amber York
attribute NC_GLOBAL people_3_person_nid String 643627
attribute NC_GLOBAL people_3_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_3_role_type String related
attribute NC_GLOBAL project String Coral DOM2
attribute NC_GLOBAL projects_0_acronym String Coral DOM2
attribute NC_GLOBAL projects_0_description String 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.
attribute NC_GLOBAL projects_0_end_date String 2018-11
attribute NC_GLOBAL projects_0_geolocation String Pacific Coral Reefs
attribute NC_GLOBAL projects_0_name String Collaborative Research: Dissolved organic matter feedbacks in coral reef resilience: The genomic & geochemical basis for microbial modulation of algal phase shifts
attribute NC_GLOBAL projects_0_project_nid String 675025
attribute NC_GLOBAL projects_0_start_date String 2015-12
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Concentrations of colored dissolved organic matter, dissolved organic carbon, and total phosphorous from experiments conducted at the University of Hawaii, Manoa in 2015.
attribute NC_GLOBAL title String 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)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Major_Benthic_Constituent   String  
attribute Major_Benthic_Constituent bcodmo_name String site_descrip
attribute Major_Benthic_Constituent description String Type of organism|substrate in aquaria (coral|macroalgae|sand|rubble)
attribute Major_Benthic_Constituent long_name String Major Benthic Constituent
attribute Major_Benthic_Constituent units String unitless
variable Nutrient_Addition   String  
attribute Nutrient_Addition bcodmo_name String treatment
attribute Nutrient_Addition description String Nominal Level of nutrient addition (ambient|low|high)
attribute Nutrient_Addition long_name String Nutrient Addition
attribute Nutrient_Addition units String unitless
variable Water_Bath   byte  
attribute Water_Bath _FillValue byte 127
attribute Water_Bath actual_range byte 1, 3
attribute Water_Bath bcodmo_name String treatment
attribute Water_Bath description String Experimental Replicate water bath tank (1|2|3)
attribute Water_Bath long_name String Water Bath
attribute Water_Bath units String unitless
variable Week   byte  
attribute Week _FillValue byte 127
attribute Week actual_range byte 0, 4
attribute Week bcodmo_name String time_elapsed
attribute Week description String Week of continuous nutrient addition (0|2|4)
attribute Week long_name String Week
attribute Week nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/ (external link)
attribute Week units String unitless
variable Ultra_Violet_Humic_like   double  
attribute Ultra_Violet_Humic_like _FillValue double NaN
attribute Ultra_Violet_Humic_like actual_range double 0.006100374, 0.105203946
attribute Ultra_Violet_Humic_like bcodmo_name String unknown
attribute Ultra_Violet_Humic_like description String Coble Peak A (Ultra Violet Humic-like)
attribute Ultra_Violet_Humic_like long_name String Ultra Violet Humic Like
attribute Ultra_Violet_Humic_like units String Raman units of water (RU)
variable Marine_Humic_like   double  
attribute Marine_Humic_like _FillValue double NaN
attribute Marine_Humic_like actual_range double 6.18318E-4, 0.175470203
attribute Marine_Humic_like bcodmo_name String unknown
attribute Marine_Humic_like description String Coble Peak M (Marine Humic-like)
attribute Marine_Humic_like long_name String Marine Humic Like
attribute Marine_Humic_like units String Raman units of water (RU)
variable Visible_Humic_like   double  
attribute Visible_Humic_like _FillValue double NaN
attribute Visible_Humic_like actual_range double 0.008174298, 0.109941957
attribute Visible_Humic_like bcodmo_name String unknown
attribute Visible_Humic_like description String Coble Peak C (Visible Humic-like)
attribute Visible_Humic_like long_name String Visible Humic Like
attribute Visible_Humic_like units String Raman units of water (RU)
variable Tryptophan_like   double  
attribute Tryptophan_like _FillValue double NaN
attribute Tryptophan_like actual_range double 0.006615842, 0.436893496
attribute Tryptophan_like bcodmo_name String unknown
attribute Tryptophan_like description String Coble Beak T (Tryptophan-like)
attribute Tryptophan_like long_name String Tryptophan Like
attribute Tryptophan_like units String Raman units of water (RU)
variable Tyrosine_like   double  
attribute Tyrosine_like _FillValue double NaN
attribute Tyrosine_like actual_range double 0.0, 0.487962641
attribute Tyrosine_like bcodmo_name String unknown
attribute Tyrosine_like description String Coble Peak B (Tyrosine-like)
attribute Tyrosine_like long_name String Tyrosine Like
attribute Tyrosine_like units String Raman units of water (RU)
variable Phenylalanine_like   double  
attribute Phenylalanine_like _FillValue double NaN
attribute Phenylalanine_like actual_range double 0.0, 1.710984446
attribute Phenylalanine_like bcodmo_name String unknown
attribute Phenylalanine_like description String Coble Peak F (Phenylalanine-like)
attribute Phenylalanine_like long_name String Phenylalanine Like
attribute Phenylalanine_like units String Raman units of water (RU)
variable Proteinaceous_fDOM   double  
attribute Proteinaceous_fDOM _FillValue double NaN
attribute Proteinaceous_fDOM actual_range double 0.006615842, 2.631633106
attribute Proteinaceous_fDOM bcodmo_name String unknown
attribute Proteinaceous_fDOM description String Sum of peaks A,M, and C (Proteinaceous fDOM)
attribute Proteinaceous_fDOM long_name String Proteinaceous F DOM
attribute Proteinaceous_fDOM units String Raman units of water (RU)
variable Humic_like_fDOM   double  
attribute Humic_like_fDOM _FillValue double NaN
attribute Humic_like_fDOM actual_range double 0.014892989, 0.348826997
attribute Humic_like_fDOM bcodmo_name String unknown
attribute Humic_like_fDOM description String Sum of peaks T,B,and F (Humic-like fDOM)
attribute Humic_like_fDOM long_name String Humic Like F DOM
attribute Humic_like_fDOM units String Raman units of water (RU)
variable TP_avg   float  
attribute TP_avg _FillValue float NaN
attribute TP_avg actual_range float 0.08, 2.34
attribute TP_avg bcodmo_name String P
attribute TP_avg description String Average Total Phosphorous (TP)
attribute TP_avg long_name String TP Avg
attribute TP_avg units String micromoles per liter (µmol L-1)
variable DOC   float  
attribute DOC _FillValue float NaN
attribute DOC actual_range float 63.73, 124.13
attribute DOC bcodmo_name String DOC
attribute DOC description String Dissolved Organic Carbon (DOC)
attribute DOC long_name String DOC
attribute DOC nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/CORGZZZX/ (external link)
attribute DOC units String micromoles per liter (µmol L-1)

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

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