http://lod.bco-dmo.org/id/dataset/884544
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)
Coral physiology parameters acquired 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.884544.1
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) Coral physiology parameters acquired 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.884544.1 [access date]
Heatwave Experiment: Multivariate Physiology Dataset Description: Methods and Sampling: <p>Corals sampled at six reefs within Kāne'ohe Bay, O'ahu, Hawai'i:</p>
<p>1.) USA: Hawaii HIMB: 21.436056, -157.786861<br />
2.) USA: Hawaii Reef.11.13: 21.450806, -157.794944<br />
3.) USA: Hawaii Reef.35.36: 21.473889, -157.833667<br />
4.) USA: Hawaii Reef.18: 21.450806, -157.811139<br />
5.) USA: Hawaii Lilipuna.Fringe: 21.429417, -157.791111<br />
6.) USA: Hawaii Reef.42.43: 21.477194, -157.826889</p>
<p>Experiment conducted at the Hawai'i Institute of Marine Biology.</p>
<p dir="ltr"><em><strong>Photosynthesis and Respiration Rates: </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><br />
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 immediately snap-frozen in liquid nitrogen and stored at -80°C.</p>
<p><strong><em>Sample Collection and Endosymbiont Density: </em></strong>Coral tissue was removed from the coral skeletons by airbrushing (Iwata Eclipse HP-BCS) with ice-cold 1X Phosphate Buffer Saline (PBS) solution, separating the soft tissue from the calcium carbonate skeleton and the total volume was recorded. The tissue slurry was then homogenized for 15 seconds at high speed (PRO Scientific Bio-Gen PRO200 Homogenizer). Of the total tissue slurry, 500 µL was taken for endosymbiont density, 500 µL for host soluble protein and host total antioxidant capacity, 1 mL for chlorophyll concentration assays, and 5 mL for ash-free dry weight. The skeleton was rinsed in freshwater and soaked in 20% bleach for 24 hours and dried at room temperature for 24 hours. The single dip wax-dipping technique <a href="https://paperpile.com/c/TUbZMv/9cRs">(Veal et al. 2010)</a> was used to determine surface area of each dried fragment skeleton.<em> </em>Symbiodiniaeceae cell concentration was quantified with 6 technical replicate counts on a haemocytometer (Hausser Scientific Bright-Line Counting Chamber) after homogenizing the tissue slurry for 1 minute. The average count (cells mL-1) was standardized to homogenate volume and surface area to produce cell density values in cells cm-2.</p>
<p><em><strong>Host soluble protein and total antioxidant capacity: </strong></em>To quantify host soluble protein and host total antioxidant capacity the host tissue was isolated from symbionts by centrifugation at 10,000g for 10 minutes at 4°C. Soluble host protein of the supernatant was measured using the Pierce BCA Protein Assay Kit (Pierce Biotechnology, Waltham, Massachusetts, Catalog #23225) with two duplicates per sample measured by a 96 well microplate reader (BioTek Synergy HTX Multi-Mode Reader) at a wavelength of 562 nm. Resulting values were compared to a bovine serum albumin standard curve and standardized to homogenate volume and surface area to obtain host soluble protein values (mg cm-2). Host total antioxidant capacity was quantified in duplicates per sample with the Cell BioLabs OxiSelect Total Antioxidant Capacity (TAC) Assay Kit (Catalog #STA-360) manufacturer’s instructions and compared to a uric acid standard curve to obtain Copper Reducing Equivalents (CRE) in mmol L-1. CRE values were standardized to total soluble protein for final values in units of CRE μmol mg-1.</p>
<p><strong><em>Chlorophyll concentration: </em></strong>To isolate symbiont cells for chlorophyll concentration measurements, a 1 mL aliquot of tissue homogenate was centrifuged at 13,000 g for 3 min and the supernatant was discarded. 1 mL of acetone was added to the symbiont pellet and incubated in the dark at 4°C for 24 hours. Samples and acetone blanks were read in duplicate (200 μL each) on a 96-well microplate reader at λ = 630 and 663 nanometers. Chlorophyll pigments a and c2 were calculated with the following dinoflagellate equations, respectively: 11.43E663 - 0.64E630 and 27.09E630 - 3.63E663 (Jeffrey and Humphrey 1975). Concentration values were multiplied by 0.584 to correct for the path length of the plate, and standardized by both surface area (μg cm-2) and cell density (μg cells-1).</p>
<p><em><strong>Tissue Biomass: </strong></em>To quantify biomass as ash-free dry weight (AFDW), 5 mL of tissue slurry was centrifuged at 13,000 g for 3 minutes. 4 mL of the supernatant host tissue was removed and placed in pre-weighed burned aluminum pan and the symbiont pellet was resuspended in 1 mL PBS solution and added to separate pre-weighed burned aluminum pans. The samples were placed in a drying oven for 24 hours at 60°C (Thermo Scientific Heratherm General Protocol Oven, Catalog #51028112), weighed, and then placed in a muffle furnace for 4 hours at 500°C (Thermo Scientific Lindberg Blue M Muffle Furnace, Catalog #BF51728C-1). AFDW (mg cm-2) of the host and symbiont fractions were calculated as the post-drying oven weight (dry weight) - post-muffle furnace weight and final values were normalized to surface area. Symbiont to host (S:H) AFDW ratios were calculated by dividing the symbiont AFDW by the host AFDW.</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
Site_Name
Site_Latitude
Site_Longitude
Plug_ID
Species
ANALYSIS
Timepoint
Treatment
Tank
Temperature
CO2
Pgross_umol_cm2_hr
Pnet_umol_cm2_hr
PR
Rdark_umol_cm2_hr
Pnet_cell
chla_ug_cm2
chla_ug_cells
AFDW_mg_cm2_Sym
AFDW_mg_cm2_Host
AFDW_mg_cells_Sym
Ratio_S_H
prot_mg_cm2
cre_umol_mgprot
haemo_cells_cm2
vol_mL
surface_area_cm2
Thermo Scientific Heratherm General Protocol Oven, Catalog #51028112
Hausser Scientific Bright-Line Counting Chamber
PRO Scientific Bio-Gen PRO200 Homogenizer
Thermo Scientific Lindberg Blue M Muffle Furnace, Catalog #BF51728C-1
BioTek Synergy HTX Multi-Mode Reader
theme
None, User defined
site
latitude
longitude
sample identification
species scientific name (binomial)
sample description
sample time
treatment
tank
photosynthetic rate
respiration rate
chlorophyll a
wet_weight_biomass
protein concentration
Copper
density
volume
surface_area
featureType
BCO-DMO Standard Parameters
Centrifuge
Drying Oven
Hemocytometer
Homogenizer
muffle furnace
plate reader
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
biota
oceans
-157.833667
-157.786861
21.429417
21.477194
2018-09-22
2018-11-17
Hawaii, Rhode Island, New Jersey, Israel
0
BCO-DMO catalogue of parameters from Coral physiology parameters acquired 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/885995.rdf
Name: Site_Name
Units: unitless
Description: <p>The reef location where that sample was collected (6 options total)</p>
http://lod.bco-dmo.org/id/dataset-parameter/885996.rdf
Name: Site_Latitude
Units: decimal degrees
Description: <p>Latitude of coral sampling site, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/885997.rdf
Name: Site_Longitude
Units: decimal degrees
Description: <p>Longitude of coral sampling site, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/885998.rdf
Name: Plug_ID
Units: unitless
Description: <p>The individual coral fragment ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/885999.rdf
Name: Species
Units: unitless
Description: <p>Coral host species: Montipora capitata or Pocillopora acuta</p>
http://lod.bco-dmo.org/id/dataset-parameter/886000.rdf
Name: ANALYSIS
Units: unitless
Description: <p>Physiology for all entries indicating that fragment was sampled for physiology</p>
http://lod.bco-dmo.org/id/dataset-parameter/886001.rdf
Name: Timepoint
Units: unitless
Description: <p>The sampling time point; at what point during the experiment was that fragment sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/886002.rdf
Name: Treatment
Units: unitless
Description: <p>Temperature and pCO2 treatment exposure indication. Ambient Temperature Ambient pCO2 (ATAC), Ambient Temperature High pCO2 (ATHC), High Temperature Ambient pCO2 (HTAC), or High Temperature High pCO2 (HTHC).</p>
http://lod.bco-dmo.org/id/dataset-parameter/886003.rdf
Name: Tank
Units: unitless
Description: <p>The tank number that coral fragment was sampled from (12 options; 3 tanks per treatment)</p>
http://lod.bco-dmo.org/id/dataset-parameter/886004.rdf
Name: Temperature
Units: unitless
Description: <p>Temperature treatment indication: high or ambient</p>
http://lod.bco-dmo.org/id/dataset-parameter/886005.rdf
Name: CO2
Units: unitless
Description: <p>pCO2 treatment indication: high or ambient</p>
http://lod.bco-dmo.org/id/dataset-parameter/886006.rdf
Name: Pgross_umol_cm2_hr
Units: umol/cm2/hr
Description: <p>Gross photosynthesis measurement normalized to host surface area. Units are change in oxygen levels</p>
http://lod.bco-dmo.org/id/dataset-parameter/886007.rdf
Name: Pnet_umol_cm2_hr
Units: umol/cm2/hr
Description: <p>Net photosynthesis measurement normalized to host surface area. Units are change in oxygen levels</p>
http://lod.bco-dmo.org/id/dataset-parameter/886008.rdf
Name: PR
Units: umol/cm2/hr
Description: <p>Ratio of Net photosynthetic rates (Pnet_umol.cm2.hr; u mol cm-2 h-1) to Respiration rates (Rdark_umol.cm2.hr; u mol cm-2 h-1)</p>
http://lod.bco-dmo.org/id/dataset-parameter/886009.rdf
Name: Rdark_umol_cm2_hr
Units: umol/cm2/hr
Description: <p>Respiration rates measurement normalized to host surface area. Units are change in oxygen levels</p>
http://lod.bco-dmo.org/id/dataset-parameter/886010.rdf
Name: Pnet_cell
Units: umol/cm2/hr
Description: <p>Net photosynthesis measurement normalized to endosymbiont density. Units are change in oxygen levels</p>
http://lod.bco-dmo.org/id/dataset-parameter/886011.rdf
Name: chla_ug_cm2
Units: ug cm-2
Description: <p>Chlorophyll-a concentration measurement normalized to host surface area</p>
http://lod.bco-dmo.org/id/dataset-parameter/886012.rdf
Name: chla_ug_cells
Units: ug cell-1
Description: <p>Chlorophyll-a concentration measurement normalized to endosymbiont density</p>
http://lod.bco-dmo.org/id/dataset-parameter/886013.rdf
Name: AFDW_mg_cm2_Sym
Units: mg cm-2
Description: <p>Symbiont Tissue Biomass Ash-Free Dry Weight (AFDW) measurement normalized to host surface area (AFDW)</p>
http://lod.bco-dmo.org/id/dataset-parameter/886014.rdf
Name: AFDW_mg_cm2_Host
Units: mg cm-
Description: <p>Host Tissue Biomass Ash-Free Dry Weight (AFDW) measurement normalized to host surface area (AFDW)</p>
http://lod.bco-dmo.org/id/dataset-parameter/886015.rdf
Name: AFDW_mg_cells_Sym
Units: mg cell-1
Description: <p>Symbiont Tissue Biomass Ash-Free Dry Weight (AFDW) measurement normalized to endosymbiont density (AFDW)</p>
http://lod.bco-dmo.org/id/dataset-parameter/886016.rdf
Name: Ratio_S_H
Units: mg cm-2
Description: <p>Ratio of Symbiont Tissue Biomass : Host Tissue Biomass</p>
http://lod.bco-dmo.org/id/dataset-parameter/886017.rdf
Name: prot_mg_cm2
Units: mg cm-2
Description: <p>Host soluble protein normalized to host surface area</p>
http://lod.bco-dmo.org/id/dataset-parameter/886018.rdf
Name: cre_umol_mgprot
Units: umol mg protein-1
Description: <p>Host total antioxidant capacity in Copper Reducing Equivalents normalized to host soluble protein</p>
http://lod.bco-dmo.org/id/dataset-parameter/886019.rdf
Name: haemo_cells_cm2
Units: cells cm-2
Description: <p>Endosymbiont density normalized to host surface area</p>
http://lod.bco-dmo.org/id/dataset-parameter/886020.rdf
Name: vol_mL
Units: milliliters (ml)
Description: <p>Volume of homogenate collected </p>
http://lod.bco-dmo.org/id/dataset-parameter/886021.rdf
Name: surface_area_cm2
Units: units
Description: <p>The calculated surface area based on the standard curve used </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
129944
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/dec0b4af-1eb6-5586-990e-ad97bd297fd0/content
download
https://doi.org/10.26008/1912/bco-dmo.884544.1
download
onLine
dataset
<p>Corals sampled at six reefs within Kāne'ohe Bay, O'ahu, Hawai'i:</p>
<p>1.) USA: Hawaii HIMB: 21.436056, -157.786861<br />
2.) USA: Hawaii Reef.11.13: 21.450806, -157.794944<br />
3.) USA: Hawaii Reef.35.36: 21.473889, -157.833667<br />
4.) USA: Hawaii Reef.18: 21.450806, -157.811139<br />
5.) USA: Hawaii Lilipuna.Fringe: 21.429417, -157.791111<br />
6.) USA: Hawaii Reef.42.43: 21.477194, -157.826889</p>
<p>Experiment conducted at the Hawai'i Institute of Marine Biology.</p>
<p dir="ltr"><em><strong>Photosynthesis and Respiration Rates: </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><br />
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 immediately snap-frozen in liquid nitrogen and stored at -80°C.</p>
<p><strong><em>Sample Collection and Endosymbiont Density: </em></strong>Coral tissue was removed from the coral skeletons by airbrushing (Iwata Eclipse HP-BCS) with ice-cold 1X Phosphate Buffer Saline (PBS) solution, separating the soft tissue from the calcium carbonate skeleton and the total volume was recorded. The tissue slurry was then homogenized for 15 seconds at high speed (PRO Scientific Bio-Gen PRO200 Homogenizer). Of the total tissue slurry, 500 µL was taken for endosymbiont density, 500 µL for host soluble protein and host total antioxidant capacity, 1 mL for chlorophyll concentration assays, and 5 mL for ash-free dry weight. The skeleton was rinsed in freshwater and soaked in 20% bleach for 24 hours and dried at room temperature for 24 hours. The single dip wax-dipping technique <a href="https://paperpile.com/c/TUbZMv/9cRs">(Veal et al. 2010)</a> was used to determine surface area of each dried fragment skeleton.<em> </em>Symbiodiniaeceae cell concentration was quantified with 6 technical replicate counts on a haemocytometer (Hausser Scientific Bright-Line Counting Chamber) after homogenizing the tissue slurry for 1 minute. The average count (cells mL-1) was standardized to homogenate volume and surface area to produce cell density values in cells cm-2.</p>
<p><em><strong>Host soluble protein and total antioxidant capacity: </strong></em>To quantify host soluble protein and host total antioxidant capacity the host tissue was isolated from symbionts by centrifugation at 10,000g for 10 minutes at 4°C. Soluble host protein of the supernatant was measured using the Pierce BCA Protein Assay Kit (Pierce Biotechnology, Waltham, Massachusetts, Catalog #23225) with two duplicates per sample measured by a 96 well microplate reader (BioTek Synergy HTX Multi-Mode Reader) at a wavelength of 562 nm. Resulting values were compared to a bovine serum albumin standard curve and standardized to homogenate volume and surface area to obtain host soluble protein values (mg cm-2). Host total antioxidant capacity was quantified in duplicates per sample with the Cell BioLabs OxiSelect Total Antioxidant Capacity (TAC) Assay Kit (Catalog #STA-360) manufacturer’s instructions and compared to a uric acid standard curve to obtain Copper Reducing Equivalents (CRE) in mmol L-1. CRE values were standardized to total soluble protein for final values in units of CRE μmol mg-1.</p>
<p><strong><em>Chlorophyll concentration: </em></strong>To isolate symbiont cells for chlorophyll concentration measurements, a 1 mL aliquot of tissue homogenate was centrifuged at 13,000 g for 3 min and the supernatant was discarded. 1 mL of acetone was added to the symbiont pellet and incubated in the dark at 4°C for 24 hours. Samples and acetone blanks were read in duplicate (200 μL each) on a 96-well microplate reader at λ = 630 and 663 nanometers. Chlorophyll pigments a and c2 were calculated with the following dinoflagellate equations, respectively: 11.43E663 - 0.64E630 and 27.09E630 - 3.63E663 (Jeffrey and Humphrey 1975). Concentration values were multiplied by 0.584 to correct for the path length of the plate, and standardized by both surface area (μg cm-2) and cell density (μg cells-1).</p>
<p><em><strong>Tissue Biomass: </strong></em>To quantify biomass as ash-free dry weight (AFDW), 5 mL of tissue slurry was centrifuged at 13,000 g for 3 minutes. 4 mL of the supernatant host tissue was removed and placed in pre-weighed burned aluminum pan and the symbiont pellet was resuspended in 1 mL PBS solution and added to separate pre-weighed burned aluminum pans. The samples were placed in a drying oven for 24 hours at 60°C (Thermo Scientific Heratherm General Protocol Oven, Catalog #51028112), weighed, and then placed in a muffle furnace for 4 hours at 500°C (Thermo Scientific Lindberg Blue M Muffle Furnace, Catalog #BF51728C-1). AFDW (mg cm-2) of the host and symbiont fractions were calculated as the post-drying oven weight (dry weight) - post-muffle furnace weight and final values were normalized to surface area. Symbiont to host (S:H) AFDW ratios were calculated by dividing the symbiont AFDW by the host AFDW.</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
2023-09-08 [D.Gerlach]
- Corrected parameter mapping to be 'proteins' for amounts, rather than 'protein' name.
- Added NODC topic of 'biota'
Specified by BCO-DMO Data Managers
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
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PI Supplied Instrument Name: Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.
Thermo Scientific Heratherm General Protocol Oven, Catalog #51028112
Thermo Scientific Heratherm General Protocol Oven, Catalog #51028112
PI Supplied Instrument Name: Thermo Scientific Heratherm General Protocol Oven, Catalog #51028112 Instrument Name: Drying Oven Instrument Short Name: Instrument Description: a heated chamber for drying
Hausser Scientific Bright-Line Counting Chamber
Hausser Scientific Bright-Line Counting Chamber
PI Supplied Instrument Name: Hausser Scientific Bright-Line Counting Chamber Instrument Name: Hemocytometer Instrument Short Name:Hemocytometer Instrument Description: A hemocytometer is a small glass chamber, resembling a thick microscope slide, used for determining the number of cells per unit volume of a suspension. Originally used for performing blood cell counts, a hemocytometer can be used to count a variety of cell types in the laboratory. Also spelled as "haemocytometer". Description from:
http://hlsweb.dmu.ac.uk/ahs/elearning/RITA/Haem1/Haem1.html.
PRO Scientific Bio-Gen PRO200 Homogenizer
PRO Scientific Bio-Gen PRO200 Homogenizer
PI Supplied Instrument Name: PRO Scientific Bio-Gen PRO200 Homogenizer Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
Thermo Scientific Lindberg Blue M Muffle Furnace, Catalog #BF51728C-1
Thermo Scientific Lindberg Blue M Muffle Furnace, Catalog #BF51728C-1
PI Supplied Instrument Name: Thermo Scientific Lindberg Blue M Muffle Furnace, Catalog #BF51728C-1 Instrument Name: muffle furnace Instrument Short Name: Instrument Description: A muffle furnace or muffle oven (sometimes retort furnace in historical usage) is a furnace in which the subject material is isolated from the fuel and all of the products of combustion, including gases and flying ash. A type of jacketed enclosure that is used to heat a material to significantly high temperatures while keeping it contained and fully isolated from external contaminants, chemicals or substances. Muffle furnaces are usually lined with stainless steel, making them largely corrosion-resistant.
BioTek Synergy HTX Multi-Mode Reader
BioTek Synergy HTX Multi-Mode Reader
PI Supplied Instrument Name: BioTek Synergy HTX Multi-Mode Reader PI Supplied Instrument Description:96 well microplate reader (BioTek Synergy HTX Multi-Mode Reader) Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.