http://lod.bco-dmo.org/id/dataset/884537
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2022-11-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Photosynthetic irradiance capacity of coral fragments measured during a heatwave experiment done September to November 2018 using reef building corals collected in Kāne'ohe Bay, O'ahu, Hawai'i
2023-01-31
publication
2023-01-31
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-01-31
publication
https://doi.org/10.26008/1912/bco-dmo.884537.1
Hollie Putnam
University of Rhode Island
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Strand, E., Putnam, H. (2023) Photosynthetic irradiance capacity of coral fragments measured during a heatwave experiment done September to November 2018 using reef building corals collected in Kāne'ohe Bay, O'ahu, Hawai'i. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-01-31 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.884537.1 [access date]
Heatwave Experiment: Photosynthetic Irradiance Dataset Description: Methods and Sampling: <p><em><strong>Photosynthetic Irradiance Curves: </strong></em>Prior to experimental exposures, 10 coral fragments (5 per species) were used to generate a photosynthesis-irradiance curve to determine saturating irradiance for assessing rates of photosynthesis. Fragments were exposed to 10 light levels: 0, 15, 30, 60, 91, 136, 227, 416, 529, and 756 µmol m-2 s-1 generated by two LED lights (Aqua Illumination Hydra FiftyTwo) hung above the incubation chambers (described below). Rates of oxygen consumption or evolution were extracted using curve fitting of a non-linear least squares fit for a non-rectangular hyperbola (NLLS; Marshall &amp; Biscoe 1980, Heberling 2013) was used to identify PI curve characteristics of each species. This model is as follows: = фPAR+√(φPPFD + Pmax)2-4ΘφPAR Pmax2Θ-Rd . Theta was set at 0.6 for <em>M. capitata </em>and 0.64 for <em>P. acuta</em>. Photosynthesis-irradiance curves were performed four times throughout the experiment on fragments of both species in the HTHC treatment to determine that there were no significant changes in Ik that occured during bleaching, and thus no need to change light settings used to measure respiration and photosynthetic rates.</p>
<p>Fragments were placed in individual respiration chambers (~610mL), with individual temperature (Pt1000 temperature sensor, PreSens) and fiber-optic oxygen probes (Oxygen Dipping Probes DP-PSt7, accuracy = ± 0.05% O2, PreSens) connected to a 10-channel oxygen meter (OXY-10 ST, accuracy = ± 1.0 °C, resolution = 0.1 °C, PreSens), to evaluate photosynthesis under saturating light conditions, as determined by PI curves described above, and light enhanced dark respiration (LEDR; Edmunds and Davies 1988). The respirometry setup consisted of 10 chambers with stirbars. Samples were measured in a series of runs that consisted of eight fragments (n=4 per species and n=2 blank chambers) per run, and exposed to PAR irradiance of 590 ± 7.16 µmol photons m-2 s-1 for 15 minutes to assess photosynthetic rates. Immediately afterwards, these fragments were exposed to dark conditions (0 µmol photons m-2 s-1) for 20 minutes to assess LEDR. Following respirometry, fragments were set back in their respective tanks.</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756623 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756623
completed
Hollie Putnam
University of Rhode Island
808-554-1462
120 Flagg Rd.
Kingston
RI
02881
USA
hputnam@uri.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sampling_point
Light_Level
Fragment_ID
Intercept
Aumol_L_sec
Temp
Date
Sample_ID
Plug_Number
Chamber_Channel
Position
Bin_ID
Run
Species
Fragment_Number
Sample_Type
Temp_Cat
Chamber_Vol_L
Surf_Area_cm2
Start_time
Stop_Time
Light_Dark
Light_Value
Notes
QC
sample_micromol_s
blank_micromol_s
corr_micromol_s
micromol_cm2_s
micromol_cm2_h
source_file
Apex cosine corrected PAR Sensor
Fiber-optic oxygen probes Oxygen Dipping Probes DP-PSt7 PreSens
Pt1000 temperature sensor, PreSens
theme
None, User defined
number
sample description
sample identification
dissolved Oxygen
water temperature at measurement depth
date
species scientific name (binomial)
volume
surface_area
time_start
time_end
PAR
comments
irradiance
file_name
featureType
BCO-DMO Standard Parameters
Biospherical PAR sensor
LI-COR LI-192 PAR Sensor
Oxygen Microelectrode Sensor
PreSens OXY-10 Mini oxygen meter
Water Temperature Sensor
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
NSFOCE-BSF: COLLABORATIVE RESEARCH: Elucidating adaptive potential through coral holobiont functional integration
https://sites.rutgers.edu/coralbase/
NSFOCE-BSF: COLLABORATIVE RESEARCH: Elucidating adaptive potential through coral holobiont functional integration
<p>NSF Abstract:</p>
<p>The remarkable success of coral reefs is explained by interactions of the coral animal with its symbiotic microbiome that is comprised of photosynthetic algae and bacteria. This total organism, or "holobiont", enables high ecosystem biodiversity and productivity in coral reefs. These ecosystems are, however, under threat from a rapidly changing environment. This project aims to integrate information from the cellular to organismal level to identify key mechanisms of adaptation and acclimatization to environmental stress. Specific areas to be investigated include the role of symbionts and of epigenetics (molecular "marks" on coral DNA that regulate gene expression). These aspects will be studied in Hawaiian corals to determine whether they explain why some individuals are sensitive or resistant to environmental perturbation. Results from the proposed project will also provide significant genomic resources that will contribute to fundamental understanding of how complex biological systems generate emergent (i.e., unexpected) properties when faced with fluctuating environments. Broader impacts will extend beyond scientific advancements to include postdoctoral and student training in Science, Technology, Engineering and Mathematics (STEM). Data generated in the project will be used to train university students and do public outreach through live videos of experimental work, and short stop-action animations for topics such as symbiosis, genomics, epigenetics, inheritance, and adaptation. The research approaches and results will be shared with the public in Hawaii through the Hawaii Institute of Marine Biology education department and presentations at Hawaiian hotels, as well as at Rutgers University through its 4-H Rutgerscience Saturdays and 4-H Rutgers Summer Science Programs.</p>
<p>Symbiosis is a complex and ecologically integrated interaction between organisms that provides emergent properties key to their survival. Such is the case for the relationship between reef-building corals and their microbiome, a meta-organism, where nutritional and biogeochemical recycling provide the necessary benefits that fuel high reef productivity and calcification. The rapid warming and acidification of our oceans threatens this symbiosis. This project addresses how relatively stress resistant and stress sensitive corals react to the environmental perturbations of increased temperature and reduced pH. It utilizes transcriptomic, epigenetic, and microbial profiling approaches, to elucidate how corals respond to environmental challenges. In addition to this profiling, work by the BSF Israeli partner will implement powerful analytical techniques such as network theory to detect key transcriptional hubs in meta-organisms and quantify biological integration. This work will generate a stress gene inventory for two ecologically important coral species and a (epi)genome and microbiome level of understanding of how they respond to the physical environment. Acknowledgment of a role for epigenetic mechanisms in corals overturns the paradigm of hardwired genetic control and highlights the interplay of genetic and epigenetic variation that may result in emergent evolutionary and ecologically relevant properties with implications for the future of reefs. Furthermore, clarifying the joint contribution of the microbiome and host in response to abiotic change will provide an important model in metazoan host-microbiome biotic interactions.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Holobiont Integration
largerWorkCitation
project
eng; USA
oceans
2018-09-22
2018-11-17
Hawaii, Rhode Island, New Jersey, Israel
0
BCO-DMO catalogue of parameters from Photosynthetic irradiance capacity of coral fragments measured during a heatwave experiment done September to November 2018 using reef building corals collected in Kāne'ohe Bay, O'ahu, Hawai'i
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/885739.rdf
Name: sampling_point
Units: unitless
Description: <p>Record number</p>
http://lod.bco-dmo.org/id/dataset-parameter/885740.rdf
Name: Light_Level
Units: unitless
Description: <p>Light level number on scale of 1-10</p>
http://lod.bco-dmo.org/id/dataset-parameter/885741.rdf
Name: Fragment_ID
Units: unitless
Description: <p>Fragment replicate ID number with species initials (PA, MC) indicated</p>
http://lod.bco-dmo.org/id/dataset-parameter/885742.rdf
Name: Intercept
Units: umol/L/second (micromol per liter per second)
Description: <p>Intercept value from PreSens </p>
http://lod.bco-dmo.org/id/dataset-parameter/885743.rdf
Name: Aumol_L_sec
Units: umol per liter per second
Description: <p>change in dissolved oxygen value</p>
http://lod.bco-dmo.org/id/dataset-parameter/885744.rdf
Name: Temp
Units: degrees Celsius (°C)
Description: <p>Temperature at that time of umol.L.sec data point</p>
http://lod.bco-dmo.org/id/dataset-parameter/885745.rdf
Name: Date
Units: units
Description: <p>Date of PI curve</p>
http://lod.bco-dmo.org/id/dataset-parameter/885746.rdf
Name: Sample_ID
Units: unitless
Description: <p>Fragment.ID and Date </p>
http://lod.bco-dmo.org/id/dataset-parameter/885747.rdf
Name: Plug_Number
Units: unitless
Description: <p>The individual coral fragment ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/885748.rdf
Name: Chamber_Channel
Units: unitless
Description: <p>The chamber and channel ID number that was associated with that coral fragment during PI curve</p>
http://lod.bco-dmo.org/id/dataset-parameter/885749.rdf
Name: Position
Units: unitless
Description: <p>Position in the PI curve set up associated with that chamber during that run</p>
http://lod.bco-dmo.org/id/dataset-parameter/885750.rdf
Name: Bin_ID
Units: unitless
Description: <p>The bin in the PI curve set up associated with that chamber during that run</p>
http://lod.bco-dmo.org/id/dataset-parameter/885751.rdf
Name: Run
Units: unitless
Description: <p>PI curve run number for that sampling date </p>
http://lod.bco-dmo.org/id/dataset-parameter/885752.rdf
Name: Species
Units: unitless
Description: <p>Coral host species: Montipora capitata or Pocillopora acuta </p>
http://lod.bco-dmo.org/id/dataset-parameter/885753.rdf
Name: Fragment_Number
Units: unitless
Description: <p>Fragment replicate ID number </p>
http://lod.bco-dmo.org/id/dataset-parameter/885754.rdf
Name: Sample_Type
Units: unitless
Description: <p>Sample or Blank indication</p>
http://lod.bco-dmo.org/id/dataset-parameter/885755.rdf
Name: Temp_Cat
Units: degrees Celsius (°C)
Description: <p>Temperature of calibration from PreSens</p>
http://lod.bco-dmo.org/id/dataset-parameter/885756.rdf
Name: Chamber_Vol_L
Units: liters (L)
Description: <p>Volume in liters of the chamber that coral fragment was in</p>
http://lod.bco-dmo.org/id/dataset-parameter/885757.rdf
Name: Surf_Area_cm2
Units: cm2
Description: <p>Estimated surface area of that coral fragment</p>
http://lod.bco-dmo.org/id/dataset-parameter/885758.rdf
Name: Start_time
Units: unitless
Description: <p>Time that PI curve light level was started</p>
http://lod.bco-dmo.org/id/dataset-parameter/885759.rdf
Name: Stop_Time
Units: unitless
Description: <p>Time that PI curve light level ended</p>
http://lod.bco-dmo.org/id/dataset-parameter/885760.rdf
Name: Light_Dark
Units: unitless
Description: <p>Light or Dark indication</p>
http://lod.bco-dmo.org/id/dataset-parameter/885761.rdf
Name: Light_Value
Units: nm (nanometers)
Description: <p>PAR value for that light level </p>
http://lod.bco-dmo.org/id/dataset-parameter/885762.rdf
Name: Notes
Units: unitless
Description: <p>Notes taken during PI curve in the field</p>
http://lod.bco-dmo.org/id/dataset-parameter/885763.rdf
Name: QC
Units: unitless
Description: <p>Notes taken during quality control </p>
http://lod.bco-dmo.org/id/dataset-parameter/885764.rdf
Name: sample_micromol_s
Units: umol per liter per second
Description: <p>Calculated coral fragment's PI curve rate for that light level</p>
http://lod.bco-dmo.org/id/dataset-parameter/885765.rdf
Name: blank_micromol_s
Units: umol per liter per second
Description: <p>The calculated blank chamber's PI curve rate for that light level</p>
http://lod.bco-dmo.org/id/dataset-parameter/885766.rdf
Name: corr_micromol_s
Units: umol per liter per second
Description: <p>Calculated corrected value (sample value - blank value; sample.micromol.s - blank.micromol.s)</p>
http://lod.bco-dmo.org/id/dataset-parameter/885767.rdf
Name: micromol_cm2_s
Units: umol per liter per second
Description: <p>Calculated corrected value normalized to surface area (corr.micromol.s/Surf.Area.cm2)</p>
http://lod.bco-dmo.org/id/dataset-parameter/885768.rdf
Name: micromol_cm2_h
Units: umol per liter per hour
Description: <p>Calculated corrected value</p>
http://lod.bco-dmo.org/id/dataset-parameter/885769.rdf
Name: source_file
Units: unitless
Description: <p>The name of the source ifle</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
30838
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/7d46e111-dd62-4ad1-8265-6af8df9783df/content
download
97041
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/3ca39720-ff6a-510a-9b5e-d3f4b0e4e13f/content
download
https://doi.org/10.26008/1912/bco-dmo.884537.1
download
onLine
dataset
<p><em><strong>Photosynthetic Irradiance Curves: </strong></em>Prior to experimental exposures, 10 coral fragments (5 per species) were used to generate a photosynthesis-irradiance curve to determine saturating irradiance for assessing rates of photosynthesis. Fragments were exposed to 10 light levels: 0, 15, 30, 60, 91, 136, 227, 416, 529, and 756 µmol m-2 s-1 generated by two LED lights (Aqua Illumination Hydra FiftyTwo) hung above the incubation chambers (described below). Rates of oxygen consumption or evolution were extracted using curve fitting of a non-linear least squares fit for a non-rectangular hyperbola (NLLS; Marshall &amp; Biscoe 1980, Heberling 2013) was used to identify PI curve characteristics of each species. This model is as follows: = фPAR+√(φPPFD + Pmax)2-4ΘφPAR Pmax2Θ-Rd . Theta was set at 0.6 for <em>M. capitata </em>and 0.64 for <em>P. acuta</em>. Photosynthesis-irradiance curves were performed four times throughout the experiment on fragments of both species in the HTHC treatment to determine that there were no significant changes in Ik that occured during bleaching, and thus no need to change light settings used to measure respiration and photosynthetic rates.</p>
<p>Fragments were placed in individual respiration chambers (~610mL), with individual temperature (Pt1000 temperature sensor, PreSens) and fiber-optic oxygen probes (Oxygen Dipping Probes DP-PSt7, accuracy = ± 0.05% O2, PreSens) connected to a 10-channel oxygen meter (OXY-10 ST, accuracy = ± 1.0 °C, resolution = 0.1 °C, PreSens), to evaluate photosynthesis under saturating light conditions, as determined by PI curves described above, and light enhanced dark respiration (LEDR; Edmunds and Davies 1988). The respirometry setup consisted of 10 chambers with stirbars. Samples were measured in a series of runs that consisted of eight fragments (n=4 per species and n=2 blank chambers) per run, and exposed to PAR irradiance of 590 ± 7.16 µmol photons m-2 s-1 for 15 minutes to assess photosynthetic rates. Immediately afterwards, these fragments were exposed to dark conditions (0 µmol photons m-2 s-1) for 20 minutes to assess LEDR. Following respirometry, fragments were set back in their respective tanks.</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Raw photosynthetic (temperature corrected) data was thinned every 40 seconds and rates of oxygen flux were calculated by local linear regressions in LoLinR package (Olito et al. 2017) in µmol L-1 s-1. Rates were corrected to chamber volume including coral displacement. Rates of the blank chambers were subtracted from the rates of the coral fragments within each run to account for background photosynthesis or respiration due to phytoplankton, zooplankton, and bacteria.&nbsp; Rates of oxygen flux were normalized to surface area by the wax dipping technique (Veal et al. 2010) for final units of µmol cm-2 h-1. Net photosynthesis was calculated by subtracting the respiration rates of the dark runs from the gross photosynthetic rates of the light runs, to isolate photosynthetic rates of the symbionts from the light enhanced dark respiration (LEDR) of the coral holobiont.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Apex cosine corrected PAR Sensor
Apex cosine corrected PAR Sensor
PI Supplied Instrument Name: Apex cosine corrected PAR Sensor PI Supplied Instrument Description:Apex cosine corrected PAR Sensor to measure light Instrument Name: Biospherical PAR sensor Instrument Short Name: Instrument Description: An irradiance sensor designed to measure Photosynthetically Active Radiation (PAR), manufactured by Biospherical Instruments Inc.
PI Supplied Instrument Name: PI Supplied Instrument Description:Li-Cor cosine corrected PAR sensor (LI-192) to measure light Instrument Name: LI-COR LI-192 PAR Sensor Instrument Short Name:LI-COR LI-192 PAR Instrument Description: The LI-192 Underwater Quantum Sensor (UWQ) measures underwater or atmospheric Photon Flux Density (PPFD) (Photosynthetically Available Radiation from 360 degrees) using a Silicon Photodiode and glass filters encased in a waterproof housing. The LI-192 is cosine corrected and features corrosion resistant, rugged construction for use in freshwater or saltwater and pressures up to 800 psi (5500 kPa, 560 meters depth). Typical output is in um s-1 m-2. The LI-192 uses computer-tailored filter glass to achieve the desired quantum response. Calibration is traceable to NIST. The LI-192 serial numbers begin with UWQ-XXXXX. LI-COR has been producing Underwater Quantum Sensors since 1973.
These LI-192 sensors are typically listed as LI-192SA to designate the 2-pin connector on the base of the housing and require an Underwater Cable (LI-COR part number 2222UWB) to connect to the pins on the Sensor and connect to a data recording device.
The LI-192 differs from the LI-193 primarily in sensitivity and angular response.
193: Sensitivity: Typically 7 uA per 1000 umol s-1 m-2 in water. Azimuth: < ± 3% error over 360° at 90° from normal axis. Angular Response: < ± 4% error up to ± 90° from normal axis.
192: Sensitivity: Typically 4 uA per 1000 umol s-1 m-2 in water. Azimuth: < ± 1% error over 360° at 45° elevation. Cosine Correction: Optimized for underwater and atmospheric use.
(www.licor.com) Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0120/
Fiber-optic oxygen probes Oxygen Dipping Probes DP-PSt7 PreSens
Fiber-optic oxygen probes Oxygen Dipping Probes DP-PSt7 PreSens
PI Supplied Instrument Name: Fiber-optic oxygen probes Oxygen Dipping Probes DP-PSt7 PreSens Instrument Name: Oxygen Microelectrode Sensor Instrument Short Name:O2 Microelectrode Instrument Description: Any microelectrode sensor that measures oxygen. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/351/
PI Supplied Instrument Name: Instrument Name: PreSens OXY-10 Mini oxygen meter Instrument Short Name: Instrument Description: The OXY-10 mini is a precise multi-channel oxygen meter for up to 10 'in-house' sensors, simultaneously controlling and reading them. The meter is used with oxygen sensors based on a 2mm optical fibre. The meter is compatible with sensors that are type PSt3 which has a detection limit 15 ppb, 0 - 100% oxygen.
Pt1000 temperature sensor, PreSens
Pt1000 temperature sensor, PreSens
PI Supplied Instrument Name: Pt1000 temperature sensor, PreSens Instrument Name: Water Temperature Sensor Instrument Short Name:Water Temp Sensor Instrument Description: General term for an instrument that measures the temperature of the water with which it is in contact (thermometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/134/