http://lod.bco-dmo.org/id/dataset/865193
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
2021-11-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Incubation experiments were conducted in St. John, US Virgin Islands to investigate the macronutrient drawdown response of reef seawater microbial communities to exudates released from the coral species Porites astreoides and Gorgonia ventalina.
2022-11-10
publication
2022-11-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-11-10
publication
https://doi.org/10.26008/1912/bco-dmo.865193.1
Amy Apprill
Woods Hole Oceanographic Institution
principalInvestigator
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
principalInvestigator
Laura Gray
Woods Hole Oceanographic Institution
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: Weber, L., Apprill, A., Kujawinski, E. (2022) Incubation experiments were conducted in St. John, US Virgin Islands to investigate the macronutrient drawdown response of reef seawater microbial communities to exudates released from the coral species Porites astreoides and Gorgonia ventalina. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-11-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.865193.1 [access date]
Exudate Uptake Incubations - Macronutrient Data Dataset Description: <p>Note:
The macronutrient concentrations in this dataset reflect the raw data and have not been normalized (as is presented in the manuscript Weber et al., 2022)</p>
<p>Other relevant files and publications:</p>
<p>The targeted and untargeted metabolomics data and metadata associated with this study are located on the MetaboLights database under accession numbers MTBLS2855 and MTBLS3286.</p>
<p>The 16S rRNA gene sequencing data and metadata associated with this study are located on the NCBI Sequence Read Archive (SRA) under BioProject PRJNA739882. BioSample accession numbers are not linked with the data submitted to BCO-DMO because samples for flow cytometry and macronutrients were not always collected at the same time as samples collected for microbial community analyses, meaning that only some of the samples collected for microbial community analyses have affiliated microbial abundances and nutrient concentrations.</p> Methods and Sampling: <p>Experiments were conducted to monitor responses of reef seawater microbial communities to concentrated exudates from <em>P. astreoides</em> and <em>G. ventalina</em>. After the organism incubations were conducted, excess filtrate (2 l) from 3 of the 6 colony/fragment incubations (selected randomly) were pooled into an acid-washed, 10 l carboy and mixed. Excess filtrate (~2 l) from the three control incubations were also pooled into a second, acid-washed, 10 l carboy and mixed.</p>
<p>For the <em>P. astreoides</em> experiment, surface seawater was collected from the offshore site and coarsely filtered through a GF/A filter (1.6 µm nominal pore size) using peristalsis to remove larger cells and minimize heterotrophic grazing, but retain bacteria and archaea. Approximately 2.4 l of this inoculum was added separately to each of the 10 l carboys (pooled coral and control filtrate) to create a 5:2 ratio of filtrate: inoculum. After this addition, each carboy was mixed and a suite of samples were collected for different analyses including cell counts, inorganic and organic macronutrient quantification, and 16S rRNA gene sequencing. This collection marked the first timepoint (0 hours [hrs]) for the exudate uptake experiment. For the <em>G. ventalina</em> experiment, reef seawater inoculum was collected from Tektite reef (Table S1).</p>
<p>For each experiment, coral metabolite or control filtrate seawater were transferred into separate 1 l acid-washed polycarbonate bottles (6 bottles per treatment). Within each treatment (coral and control), 3 of the 6 bottles were blackened to block light. The bottles were placed into a flow-through seawater table. PAR readings in the seawater table for the <em>P. astreoides</em> and <em>G. ventalina</em> experiments ranged from 250 – 1000 and 164 - 530 µmol quanta m -2s -1, respectively, with variation caused by shading and cloud cover. Over the course of 48 hours, samples were collected for cell counts (1 ml) at all timepoints (0, 12, 24, 36, and 48 hrs), macronutrient analyses (30 – 40 ml) at 0 and 48 hrs, and microbial community analyses (60 – 300 ml) at 0, 24, and 48 hrs.&nbsp;</p>
<p>Samples (40 ml) collected for total organic carbon (TOC) and total nitrogen (TN) analyses were aliquoted into combusted, borosilicate EPA vials and acidified using 75 µl of phosphoric acid. Samples were stored at room temperature for two weeks and then refrigerated at 4 °C until analysis.</p>
<p>For inorganic nutrient analyses, seawater (30 ml) was allocated into acid-washed, polypropylene bottles (Nalgene) and frozen at -20 °C.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1736288 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736288
completed
Amy Apprill
Woods Hole Oceanographic Institution
508-289-2649
Marine Chemistry and Geochemistry Department 266 Woods Hole Road, MS# 4
Woods Hole
MA
02543
USA
aapprill@whoi.edu
pointOfContact
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
508-289-3493
266 Woods Hole Rd. MS #4
Woods Hole
MA
02543
USA
ekujawinski@whoi.edu
pointOfContact
Laura Gray
Woods Hole Oceanographic Institution
508-289-2981; 301-602-1540
Marine Chemistry and Geochemistry Department 266 Woods Hole Road, Mailstop 4
Woods Hole
MA
02543
USA
laura.gray@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_ID
sample_type
LD
Incubation
Time
Total_Organic_Carbon
Total_Nitrogen
Total_Organic_Nitrogen
Phosphate
Nitrite_Nitrat
Silicate
Nitrite
Ammonium
Nitrate
theme
None, User defined
sample identification
sample description
incubation time or duration
total organic Carbon
Nitrogen
total organic Nitrogen
phosphate
nitrate plus nitrite
Silicate (reactive silica)
Nitrite
Ammonium
Nitrate
featureType
BCO-DMO Standard Parameters
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.
Signature exometabolomes of Caribbean corals and influences on reef picoplankton
https://osprey.bco-dmo.org/project/746196
Signature exometabolomes of Caribbean corals and influences on reef picoplankton
<p><em>NSF Award Abstract:</em><br />
Coral reefs are some of the most diverse and productive ecosystems in the ocean. Globally, reefs have declined in stony (reef-building) coral abundance due to environmental variations, and in the Caribbean this decline has coincided with an increase in octocoral (soft coral) abundance. This phase shift occurring on Caribbean reefs may be impacting the interactions between the sea floor and water column and particularly between corals and picoplankton. Picoplankton are the microorganisms in the water column that utilize organic matter released from corals to support their growth. These coral-picoplankton interactions are relatively unstudied, but could have major implications for reef ecology and coral health. This project will take place in the U.S. territory of the Virgin Islands (USVI) and will produce the first detailed knowledge about the chemical diversity and composition of organic matter released from diverse stony coral and octocoral species. This project will advance our understanding of coral reef microbial ecology by allowing us to understand how different coral metabolites impact picoplankton growth and dynamics over time. The results from this project will be made publically accessible in a freely available online magazine, and USVI minority middle and high school students will be exposed to a lesson about chemical-biological interactions on coral reefs through established summer camps. This project will also contribute to the training of USVI minority undergraduates as well as a graduate student.</p>
<p>Coral exometabolomes, which are the sum of metabolic products of the coral together with its microbiome, are thought to structure picoplankton communities in a species-specific manner. However, a detailed understanding of coral exometabolomes, and their influences on reef picoplankton, has not yet been obtained. This project will utilize controlled aquaria-based experiments with stony corals and octocorals, foundational species of Caribbean reef ecosystems, to examine how the exometabolomes of diverse coral species differentially influence the reef picoplankton community. Specifically, this project will capitalize on recent developments in mass spectrometry-based metabolomics to define the signature exometabolomes of ecologically important and diverse stony corals and octocorals. Secondly, this project will determine how the exometabolomes of these corals vary with factors linked to coral taxonomy as well as the coral-associated microbiome (Symbiodinium algae, bacteria and archaea). With this new understanding of coral exometabolomes, the project will then apply a stable isotope probe labeling approach to the coral exometabolome and will examine if and how (through changes in growth and activity) the seawater picoplankton community incorporates coral exometabolomes from different coral species over time. This project will advance our ability to evaluate the role that coral exometabolomes play in contributing to benthic-picoplankton interactions on changing Caribbean reefs.</p>
Coral Exometabolomes
largerWorkCitation
project
eng; USA
oceans
-64.727413483487
-64.727413483487
18.315773476842
18.315773476842
2022-11-10
U.S. Virgin Islands
0
BCO-DMO catalogue of parameters from Incubation experiments were conducted in St. John, US Virgin Islands to investigate the macronutrient drawdown response of reef seawater microbial communities to exudates released from the coral species Porites astreoides and Gorgonia ventalina.
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/865202.rdf
Name: Sample_ID
Units: unitless
Description: <p>Sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/865203.rdf
Name: sample_type
Units: unitless
Description: <p>Sample Type</p>
http://lod.bco-dmo.org/id/dataset-parameter/865204.rdf
Name: LD
Units: unitless
Description: <p>Samples were either incubated in the presence or absence of light.</p>
http://lod.bco-dmo.org/id/dataset-parameter/865205.rdf
Name: Incubation
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/865206.rdf
Name: Time
Units: unitless
Description: <p>This metadata category reflects the timepoints when each sample was collected. The timepoints include na (before the beginning of the experiment), T0 (at 0 hr after the experiment was started) and so on.</p>
http://lod.bco-dmo.org/id/dataset-parameter/865207.rdf
Name: Total_Organic_Carbon
Units: micrometers (um)
Description: <p>Total organic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/865208.rdf
Name: Total_Nitrogen
Units: micrometers (um)
Description: <p>Total nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/865209.rdf
Name: Total_Organic_Nitrogen
Units: micrometers (um)
Description: <p>Total organic nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/865210.rdf
Name: Phosphate
Units: micrometers (um)
Description: <p>Phosphate</p>
http://lod.bco-dmo.org/id/dataset-parameter/865211.rdf
Name: Nitrite_Nitrat
Units: micrometers (um)
Description: <p>Nitrite and Nitrate</p>
http://lod.bco-dmo.org/id/dataset-parameter/865212.rdf
Name: Silicate
Units: micrometers (um)
Description: <p>Silicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/865213.rdf
Name: Nitrite
Units: micrometers (um)
Description: <p>Nitrite and Nitrate</p>
http://lod.bco-dmo.org/id/dataset-parameter/865214.rdf
Name: Ammonium
Units: micrometers (um)
Description: <p>Ammonium</p>
http://lod.bco-dmo.org/id/dataset-parameter/865215.rdf
Name: Nitrate
Units: micrometers (um)
Description: <p>Nitrate</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
3798
https://darchive.mblwhoilibrary.org/bitstream/1912/29494/1/dataset-865193_exudate-uptake-incubations-macronutrient-data__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.865193.1
download
onLine
dataset
<p>Experiments were conducted to monitor responses of reef seawater microbial communities to concentrated exudates from <em>P. astreoides</em> and <em>G. ventalina</em>. After the organism incubations were conducted, excess filtrate (2 l) from 3 of the 6 colony/fragment incubations (selected randomly) were pooled into an acid-washed, 10 l carboy and mixed. Excess filtrate (~2 l) from the three control incubations were also pooled into a second, acid-washed, 10 l carboy and mixed.</p>
<p>For the <em>P. astreoides</em> experiment, surface seawater was collected from the offshore site and coarsely filtered through a GF/A filter (1.6 µm nominal pore size) using peristalsis to remove larger cells and minimize heterotrophic grazing, but retain bacteria and archaea. Approximately 2.4 l of this inoculum was added separately to each of the 10 l carboys (pooled coral and control filtrate) to create a 5:2 ratio of filtrate: inoculum. After this addition, each carboy was mixed and a suite of samples were collected for different analyses including cell counts, inorganic and organic macronutrient quantification, and 16S rRNA gene sequencing. This collection marked the first timepoint (0 hours [hrs]) for the exudate uptake experiment. For the <em>G. ventalina</em> experiment, reef seawater inoculum was collected from Tektite reef (Table S1).</p>
<p>For each experiment, coral metabolite or control filtrate seawater were transferred into separate 1 l acid-washed polycarbonate bottles (6 bottles per treatment). Within each treatment (coral and control), 3 of the 6 bottles were blackened to block light. The bottles were placed into a flow-through seawater table. PAR readings in the seawater table for the <em>P. astreoides</em> and <em>G. ventalina</em> experiments ranged from 250 – 1000 and 164 - 530 µmol quanta m -2s -1, respectively, with variation caused by shading and cloud cover. Over the course of 48 hours, samples were collected for cell counts (1 ml) at all timepoints (0, 12, 24, 36, and 48 hrs), macronutrient analyses (30 – 40 ml) at 0 and 48 hrs, and microbial community analyses (60 – 300 ml) at 0, 24, and 48 hrs.&nbsp;</p>
<p>Samples (40 ml) collected for total organic carbon (TOC) and total nitrogen (TN) analyses were aliquoted into combusted, borosilicate EPA vials and acidified using 75 µl of phosphoric acid. Samples were stored at room temperature for two weeks and then refrigerated at 4 °C until analysis.</p>
<p>For inorganic nutrient analyses, seawater (30 ml) was allocated into acid-washed, polypropylene bottles (Nalgene) and frozen at -20 °C.</p>
Specified by the Principal Investigator(s)
<p>Samples collected for total organic carbon (TOC) and total nitrogen (TN) analyses were investigated at the Woods Hole Oceanographic Institution using a Shimadzu TOC-VCSH total organic carbon analyzer with a TNM-1 module [4].</p>
<p>Samples collected for inorganic nutrient analyses were shipped to Oregon State University and the concentrations of nitrite, nitrite + nitrate, ammonium, silicate, and phosphate were obtained using a continuous segmented flow system (described in 18). Total organic nitrogen concentrations were obtained by subtracting the sum of the inorganic nitrogen species (nitrite and nitrate + ammonium) from the total nitrogen concentrations. Values measured below the detection limits of the instruments (ammonium= 0.02 M, phosphate = 0.01 M, nitrite + nitrate = 0.07 M, nitrite = 0.01 M) were reported as zero.</p>
<p>&nbsp;</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