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     data   graph     files  public Fluorescent characteristics of the dissolved organic exudates of two species of crustose
coralline algae in two water treatments and their effect on the microbial community cell count
   ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_783581

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 following sections contain methodology excerpts from Quinlain et al.
(2019) relevant to this dataset.

Crustose Coraline Algae Collection and Identification
Both Hydrolithon reinboldii and Porolithon onkodes were collected from Patch
Reef 42 (21.4785\u02da, -157.8281\u02da) in K\u0101ne'ohe Bay, O'ahu, Hawai'i
on 4 May 2017. Porolithon onkodes is a common CCA species in the Pacific Ocean
that is often used for larval settlement experiments with coral species in
Australia (Heyward and Negri 1999). It is typically found in high light and
high flow environments, such as at the top of the patch reefs in
K\u0101ne\u2018ohe Bay. This species is characterized by its smooth surface
texture, and diagnostic depressions of trichosite fields. While there is a
recent paper showing that this species is a species complex globally
(Gabrielson et al., 2018), we retain the use of the name P. onkodes here to be
consistent with the published taxonomic monograph for CCA in Hawai\u02bbi
(Adey et al., 1982). Hydrolithon reinboldii is also a common CCA species that
is found throughout the Pacific Ocean. It is known to facilitate coral larval
settlement (Harrington et al., 2004). This species often lives cryptically in
cracks in the reef or on the bottom of small pieces of calcium carbonate
rubble. It is characterized by slightly raised hemispherical single pore
conceptacles (400-600 \u00b5m in diameter), and a patchy surface texture
referred to as tessellate (Adey et al., 1982).

Fragments of both species of CCA were trimmed using bone cutters to ensure
only a single plant was on each fragment. Each fragment still retained bare
calcium carbonate along with the individual species of CCA. To control for the
bare calcium carbonate, encrusted fragments of calcium carbonate were
similarly trimmed to remove any small CCA plants and epiphytes leaving only
the calcium carbonate rubble and endophytes. After fragmentation the specimens
were haphazardly placed into six containers and randomized within a 1300 L
flow through seawater bath to maintain all treatments at a stable temperature,
which was the same as those found in K\u0101ne\u2018ohe Bay. As there are
currently no studies on the effect of fragmentation on exudate production we
allowed the fragmented algae to recover for five days before starting the
exudation experiment. Flow through seawater baths were covered by shade cloth
to reduce natural irradiance to levels similar to those found at depth in
K\u0101ne\u2018ohe Bay where both species are naturally found. Both species
were exposed to the same light levels as to not bias by variation of abiotic
parameters.

Incubations and sample collection
Twenty-four 250 mL glass beakers were washed with 10% volumetric HCl, rinsed
with milliq-water and air-dried. At 07:30 on 9 May, 3 L of seawater (sand
filtered and collected from the Hawai\u2018i Institute of Marine Biology flow-
through seawater system in K\u0101ne'ohe Bay) was vacuum pre-filtered through
0.2\u00b5m polyethersulfone filters (47 mm; Sterlitech) in a 500 mL
polysulfone graduated filter holder. Before water was aliquoted into the
beakers, samples for fluorescent DOM (fDOM), dissolved organic carbon (DOC),
and flow cytometry (FCM) were collected from the 500 mL polysulfone graduated
filter holder. Each beaker was filled and randomized within a 1300L flow
through seawater bath to maintain stable temperature between the treatments.
Each organism treatment beaker (water control, calcium carbonate control,
Hydrolithon reinboldii, or Porolithon onkodes) was filled with seawater
(filtered or unfiltered) and replicated (n = 3) for a total of 24 beakers (4
organismal treatments * 2 water treatments * 3 replicates). Filtered and
unfiltered treatments were designed to capture differences in sloughing
behavior between species. A Multiple trimmed fragments of each organism were
placed within their respective beakers so that the total surface area within
each replicate beaker was standardized to 20-30 square cm (25.57 \u00b1 4.13
cm2). The incubation began at 9:00 and was halted at 17:00 to maintain only
exudates produced during the daylight hours. Surface area was digitally
determined at the end of the experiment by analyzing images to scale with
image-J (Schindelin, Arganda-Carreras, & Frise et al, 2012).

DOM samples were collected at the beginning of the experiment before
aliquoting the water at 9:00 and from each beaker at 17:00. DOM samples were
immediately filtered through a 0.2 \u00b5m polyethersulfone filter (47 mm;
Sterlitech) in a 500 mL polysulfone graduated filter holder. Filtrate was
poured directly from polysulfone graduated filter holder into its respective
sample vial, Filtrate for fDOM samples were collected in acid washed,
combusted, triple sample-rinsed amber borosilicate vials with Teflon septa
caps and stored dark at 4\u02daC until analysis for fDOM within 24 hours. DOC
was collected in acid washed, combusted, triple sample rinsed clear
borosilicate vials with Teflon septa caps and measured as non-purgeable
organic carbon via acidification, sparging and high temperature platinum
catalytic oxidation on a Shimadzu TOC-V at the UCSB DOM Analytical Lab
following the methods outlined by Carlson et al. (2010). Samples for flow
cytometry were collected by pipet (1 ml amended to a final concentration of
0.5% paraformaldehyde, mixed by inversion, snap frozen -80\u00baC) at 9:00,
13:00, and 17:00.

Sample analysis
Flow Cytometry: Flow cytometry was used to measure total nucleic acid-stained
cell concentrations. Samples were thawed and 200 \u00b5L were aliquoted into
u-bottomed 96-well autosampler plates and stained with 2 \u00b5L of 100X SYBR
Green I stain (final concentration of 0.5X). Samples were analyzed on an
Attune Acoustic Focusing Cytometer with Autosampler Attachment (Life
Technologies, Eugene, OR, USA). Samples were run at a flow rate of 100 \u00b5L
min-1 on standard sensitivity; 150 \u03bcL of sample was aspirated, 75 \u03bcL
was counted and data was collected only from the last 50 \u03bcL (event rates
were empirically determined to be steady only after 25 \u03bcL of continuous
sample injection per Nelson et al., 2015).

Fluorescence spectroscopy: Samples for fluorescence spectroscopy were measured
using an Horiba Aqualog scanning fluorometer following the methods of Nelson
et al. (2015), including scan time and resolution, spectral data processing,
inner filter correction, Raman unit standardization, blank subtraction and
PARAFAC modeling (Stedmon and Bro 2008; Lawaetz and Stedmon 2009; Kothawala et
al. 2013). Scans were processed using a Matlab (v2007b) script written and
specified by Nelson et al. (2015) and Quinlan et al., (2018; most recent
version available at DOI: 10.5281/zenodo/3479841), modified to additionally
capture the peak present at Excitation 240 nm and Emission 300 nm
(phenylalanine-like: Lakowicz 2010). Six modeled components were validated
using split half validation and outlier analysis (Quinlan et. al., 2018). All
PARAFAC components had similar excitation-emission maxima and strong
covariation among samples with previously identified fluorophores (Quinlan,
et. al., 2018); for subsequent analyses we examined established fluorescence
maxima from the literature (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 Hawaiian crustose coralline algae dissolved organic matter
PI: Craig E. Nelson (University of Hawaii)
Version date: 2019-12-06
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 2019-12-05T20:02:09Z
attribute NC_GLOBAL date_modified String 2019-12-06T20:31:52Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.783581.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/783581 (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 783589
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 783590
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_1_supplied_name String Shimadzu TOC-V Analyzer
attribute NC_GLOBAL instruments_2_acronym String FIA
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 783588
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 acid, area, bco, bco-dmo, biological, cells, chemical, commerce, data, dataset, delta, delta_Cells, department, dmo, doc, erddap, fulvic, Fulvic_Acid_like, hours, humic, inhabitant, like, management, marine, Marine_Humic_like, oceanography, office, phenylalanine, Phenylalanine_like, preliminary, replicate, surface, Surface_Area, timepoint, tryptophan, Tryptophan_like, tyrosine, Tyrosine_like, ultra, Ultra_Violet_Humic_like, violet, visible, Visible_Humic_like, water
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/783581/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/783581 (external link)
attribute NC_GLOBAL param_mapping String {'783581': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/783581/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of Hawaii at Manoa
attribute NC_GLOBAL people_0_affiliation_acronym String SOEST
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 SOEST
attribute NC_GLOBAL people_1_person_name String Zachary A. Quinlan
attribute NC_GLOBAL people_1_person_nid String 726344
attribute NC_GLOBAL people_1_role String Contact
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Shannon Rauch
attribute NC_GLOBAL people_2_person_nid String 51498
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_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 Fluorescent characteristics of the dissolved organic exudates of two species of crustose coralline algae (Hydrolithon reinboldii and Porolithon onkodes) in two water treatments (pre-filtered and unfiltered) and their effect on the microbial community cell count.
attribute NC_GLOBAL title String Fluorescent characteristics of the dissolved organic exudates of two species of crustose coralline algae in two water treatments and their effect on the microbial community cell count
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Water   String  
attribute Water bcodmo_name String treatment
attribute Water description String Water treatment
attribute Water long_name String Water
attribute Water units String unitless
variable Inhabitant   String  
attribute Inhabitant bcodmo_name String sample
attribute Inhabitant description String Organism or control treatment
attribute Inhabitant long_name String Inhabitant
attribute Inhabitant nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Inhabitant units String unitless
variable Replicate   byte  
attribute Replicate _FillValue byte 127
attribute Replicate actual_range byte 1, 3
attribute Replicate bcodmo_name String replicate
attribute Replicate description String Replicate beaker
attribute Replicate long_name String Replicate
attribute Replicate units String unitless
variable Timepoint   byte  
attribute Timepoint _FillValue byte 127
attribute Timepoint actual_range byte 1, 3
attribute Timepoint bcodmo_name String time_point
attribute Timepoint description String Time-lapse of data collection
attribute Timepoint long_name String Timepoint
attribute Timepoint units String unitless
variable Hours   byte  
attribute Hours _FillValue byte 127
attribute Hours actual_range byte 1, 8
attribute Hours bcodmo_name String time_elapsed
attribute Hours description String Hours of incubation
attribute Hours long_name String Hours
attribute Hours nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/ (external link)
attribute Hours units String hours
variable Cells   double  
attribute Cells _FillValue double NaN
attribute Cells actual_range double 13.64, 1141.92
attribute Cells bcodmo_name String abundance
attribute Cells description String number of cells measure by FCM
attribute Cells long_name String Cells
attribute Cells nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute Cells units String cells per microliter (cells uL-1)
variable delta_Cells   double  
attribute delta_Cells _FillValue double NaN
attribute delta_Cells actual_range double -94.86, 479.061225
attribute delta_Cells bcodmo_name String abundance
attribute delta_Cells description String change in cells from T0:TF
attribute delta_Cells long_name String Delta Cells
attribute delta_Cells nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute delta_Cells units String cells per microliter (cells uL-1)
variable Surface_Area   float  
attribute Surface_Area _FillValue float NaN
attribute Surface_Area actual_range float 16.603, 36.147
attribute Surface_Area bcodmo_name String surface_area
attribute Surface_Area description String sum surface area of cca in treatment
attribute Surface_Area long_name String Surface Area
attribute Surface_Area units String square centimeters (cm^2)
variable Ultra_Violet_Humic_like   double  
attribute Ultra_Violet_Humic_like _FillValue double NaN
attribute Ultra_Violet_Humic_like actual_range double 0.0198831163049, 0.0545693486016
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 0.0222084940491, 0.056609340363
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 0.0199823279068, 0.0593025147738
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 0.0166615440204, 0.0844118245414
attribute Tryptophan_like bcodmo_name String unknown
attribute Tryptophan_like description String Coble Peak 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 0.0197481729303, 0.06007038535
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, 0.0417268191721
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 Fulvic_Acid_like   double  
attribute Fulvic_Acid_like _FillValue double NaN
attribute Fulvic_Acid_like actual_range double 0.0096660756124, 0.0284126318272
attribute Fulvic_Acid_like bcodmo_name String unknown
attribute Fulvic_Acid_like description String Stedmon peak D (Fulvic acid like)
attribute Fulvic_Acid_like long_name String Fulvic Acid Like
attribute Fulvic_Acid_like units String Raman units of water (RU)
variable DOC   float  
attribute DOC _FillValue float NaN
attribute DOC actual_range float 131.47, 232.59
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 (umol 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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