http://lod.bco-dmo.org/id/dataset/874724
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
2022-05-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Dissolved oxygen and temperature data from loggers deployed in Bahia Almirante (Coral microbiome resilience project)
2026-03-17
publication
2026-03-17
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-10-10
publication
https://doi.org/10.26008/1912/bco-dmo.874724.1
Rachel Collin
Smithsonian Tropical Research Institute
principalInvestigator
Andrew Altieri
Smithsonian Tropical Research Institute
principalInvestigator
Carolina Cesar
Smithsonian Tropical Research Institute
principalInvestigator
Noelle Lucey
Smithsonian Tropical Research Institute
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: Lucey, N., Cesar, C., Altieri, A., Collin, R. (2022) Dissolved oxygen and temperature data from loggers deployed in Bahia Almirante (Coral microbiome resilience project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-05-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.874724.1 [access date]
Dissolved oxygen and temperature data from loggers deployed in Bahia Almirante Dataset Description: Methods and Sampling: <p><strong>Methodology&nbsp;</strong></p>
<p>OnSET HOBO Dissolved Oxygen Loggers (Model U26-001) were calibrated with new optical caps using HOBOware Software. Calibration included a 100% saturation point and 0% saturation point, using 0% Onset’s zero-calibration solution, following the manufacturer instructions.</p>
<p>Loggers were deployed using Hobo Onset Shuttle and programmed to record hourly measurements. A copper antifouling cover was installed on each logger to reduce fouling. Loggers were then brought to the field sites and secured to concrete blocks on the seafloor. The face of the optical sensor was oriented to be perpendicular to the seafloor, so sediment was unable to collect on the surface.</p>
<p>Data were collected every 3-6 months. Sensor caps were replaced every 6 months with new, calibrated sensors.&nbsp;&nbsp;</p>
<p><strong>Sampling and Analytical Procedures</strong></p>
<p>Loggers measured temperature (C) and dissolved oxygen (mg/L) hourly at their deployment location.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2048955 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2048955
onGoing
Rachel Collin
Smithsonian Tropical Research Institute
202-633-4700 ext 28766
collinr@si.edu
pointOfContact
Andrew Altieri
Smithsonian Tropical Research Institute
305-250-8840
365 Weil Hall PO Box 116580
Gainesville
FL
32611-6580
USA
andrew.altieri@essie.ufl.edu
pointOfContact
Carolina Cesar
Smithsonian Tropical Research Institute
pointOfContact
Noelle Lucey
Smithsonian Tropical Research Institute
1781531984
Smithsonian Tropical Research Institute STRI Unit 9100, Box 0948
Naos Island
Calzada de Amador
DPO AA 34002
Panama
luceynm@si.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
site
depth_m
logger
serial_number
datetime
DO_mgL_raw
tempC
DO_mgL
DO_percent_sat
Site_Latitude
Site_Longitude
OnSET HOBO Dissolved Oxygen Loggers Model U26-001
theme
None, User defined
No BCO-DMO term
depth
instrument
inst_serial_numb
ISO_DateTime_Local
dissolved Oxygen
water temperature at measurement depth
latitude
longitude
featureType
BCO-DMO Standard Parameters
Oxygen 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.
Collaborative Research: Biodiversity and resilience of corals and their microbiomes in response to ocean deoxygenation
https://osprey.bco-dmo.org/project/838054
Collaborative Research: Biodiversity and resilience of corals and their microbiomes in response to ocean deoxygenation
<p><em>NSF Award Abstract:</em><br />
The world's oceans are facing the threat of deoxygenation - events of low dissolved oxygen insufficient for marine life and healthy ecosystems - which is accelerating along with other global crises including climate change and ocean acidification. The pace of these changes can lead to rapid shifts in the structure of marine communities due to changes in the distribution, abundance, and diversity of species. This collaborative project is among the first to examine the consequences of deoxygenation on coral reefs, which are sentinel ecosystems for studying ecological responses to global change because of their importance to human society, sensitivity to stress, and intricate relationships among their inhabitants. Specifically, the research team investigates why and how some coral species are more tolerant than others and the role that bacteria associated with the corals have in such tolerance. This predictive understanding is important to support conservation and management efforts by identifying stress-tolerant coral species and establishing indicators for assessment of hypoxia stress. The project provides training for multiple undergraduate and graduate students and postdoctoral researchers. Findings from this project are disseminated through undergraduate and graduate courses taught at the University of Florida, a teacher training program at the Bocas del Toro Research Station at STRI in Panama, a workshop in Panama to build a community of scientists and informed practitioners, and webinars, toolkits, and other resources communicated through established networks of coral conservation and management practitioners.</p>
<p>Understanding the responses of coral reefs to ocean deoxygenation is limited to a few post hoc assessments of how unanticipated hypoxic events have impacted macrofauna. This project employs a predictive approach to examine the resilience of coral reef communities to ocean deoxygenation by examining both corals and their associated microbiomes. Complimentary manipulative laboratory and field experiments and surveys along natural gradients of hypoxic stress are being used to answer the following three fundamental questions about how variation in the tolerance of corals and their microbiomes predicts the resilience of reefs to deoxygenation: (1) How does the physiological response of the coral to hypoxia predict community shifts in the microbiome with deoxygenation? (2) To what degree do corals and their microbiomes show evidence of acclimatization to reduced oxygen, and how do these functional shifts confer increased resistance to subsequent hypoxic stress? (3) How are the feedbacks between coral hosts and their microbiomes apparent in the recovery of coral communities from hypoxia and patterns of community structure at the seascape scale? This project aims at developing a mechanistic and predictive understanding of coral reef community responses to ocean deoxygenation by examining stability and resilience at two levels of ecological organization: the assemblage of coral species at the reef scale, and the assemblage of microbes at the holobiont scale. Moreover, this study examines how those responses are coupled by feedbacks at the colony scale through coral physiological responses and microbial functional shifts.</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>
Coral microbiome resilience
largerWorkCitation
project
eng; USA
oceans
-82.35242
-82.21741
9.21416
9.3484
2021-09-07
2024-11-27
Caribbean Coast of Panama 9 N 82 W
0
BCO-DMO catalogue of parameters from Dissolved oxygen and temperature data from loggers deployed in Bahia Almirante (Coral microbiome resilience 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
http://lod.bco-dmo.org/id/dataset-parameter/874874.rdf
Name: site
Units: units
Description: <p>Site where the reef that the loggers were deployed on. Site locations include: Cayo Hermanas (SIS), Cayo Roldan (ROL), Seagal (SGL), Punta STRI (PST), and Hostpital Point (HOS).</p>
http://lod.bco-dmo.org/id/dataset-parameter/874875.rdf
Name: depth_m
Units: meters (m)
Description: <p>Depth of logger deployment.</p>
http://lod.bco-dmo.org/id/dataset-parameter/874876.rdf
Name: logger
Units: unitless
Description: <p>Short name (ID) used for the logger associated with the collected measurement.</p>
http://lod.bco-dmo.org/id/dataset-parameter/874877.rdf
Name: serial_number
Units: unitless
Description: <p>Serial number of the logger used for data collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/874878.rdf
Name: datetime
Units: unitless
Description: <p>Datetime associted with measurement in UTC. </p>
http://lod.bco-dmo.org/id/dataset-parameter/874879.rdf
Name: DO_mgL_raw
Units: mg/L
Description: <p>Raw dissolved oxygen measurement. </p>
http://lod.bco-dmo.org/id/dataset-parameter/874880.rdf
Name: tempC
Units: degrees Celsius
Description: <p>Water temperature at time of measurement.</p>
http://lod.bco-dmo.org/id/dataset-parameter/874881.rdf
Name: DO_mgL
Units: mg/L
Description: <p>Dissolved oxygen adjusted to account for salinity.</p>
http://lod.bco-dmo.org/id/dataset-parameter/874882.rdf
Name: DO_percent_sat
Units: unitless
Description: <p>Dissolved oxygen adjusted to account for salinity via percent saturation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/995023.rdf
Name: Site_Latitude
Units: decimal degrees
Description: <p>Latitude of the site associated with data collection in decimal degrees. A positive value indicates a northern latitude coordinate. </p>
http://lod.bco-dmo.org/id/dataset-parameter/995024.rdf
Name: Site_Longitude
Units: decimal degrees
Description: <p>Longitude of the site associated with data collection in decimal degrees. A negative value indicates a western longitude coordinate. </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
4203056
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/e980c6b9-01cb-5c0f-9404-9dab4035500b/content
download
https://doi.org/10.26008/1912/bco-dmo.874724.1
download
onLine
dataset
<p><strong>Methodology&nbsp;</strong></p>
<p>OnSET HOBO Dissolved Oxygen Loggers (Model U26-001) were calibrated with new optical caps using HOBOware Software. Calibration included a 100% saturation point and 0% saturation point, using 0% Onset’s zero-calibration solution, following the manufacturer instructions.</p>
<p>Loggers were deployed using Hobo Onset Shuttle and programmed to record hourly measurements. A copper antifouling cover was installed on each logger to reduce fouling. Loggers were then brought to the field sites and secured to concrete blocks on the seafloor. The face of the optical sensor was oriented to be perpendicular to the seafloor, so sediment was unable to collect on the surface.</p>
<p>Data were collected every 3-6 months. Sensor caps were replaced every 6 months with new, calibrated sensors.&nbsp;&nbsp;</p>
<p><strong>Sampling and Analytical Procedures</strong></p>
<p>Loggers measured temperature (C) and dissolved oxygen (mg/L) hourly at their deployment location.&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>Research Data Processing Steps:</strong></p>
<p>1. Record salinity at each site during the deployment of each logger.</p>
<p>2. To download the data</p>
<ul>
<li>Connect Logger to HOBOware software, then select Readout data. To adjust the dissolved oxygen with the current salinity, on the readout data window, click “Process,” then add salinity value previously recorded at the site that is being readout, and then click on&nbsp; “Create a new series”. DO Adj Conc and DO Percent Sat series appear on Plot Setup. Data are visualized with the “Plot” function.</li>
</ul>
<p>3. Export to .csv file using File &gt; “Export Data Table”.</p>
<ul>
<li>Clean .csv file according to deployment time of each logger.</li>
</ul>
Specified by the Principal Investigator(s)
Version 1:
- Loaded calibration site log from "Phyical_Monitoring_Calibration_Site_Log.csv" (CSV format, using filename as resource name; missing values: "", "nd", "NA")
- Loaded physical monitoring data from "Bocas_DO_Temp_LoggerData.xlsx" (Excel format, sheet 1, named "874724_v1_physical_monitoring_data"; missing values: "", "nd")
- Applied uppercase transformation to the "site" field in the physical monitoring data to standardize site name case for joining
- Joined calibration site log to physical monitoring data in half-outer mode on site name (source key: "Site", target key: "site"), bringing in "Latitude" (mapped to "Site_Latitude") and "Longitude" (mapped to "Site_Longitude") using first-value aggregation
- Replaced literal "NA" strings with empty values in fields: "site", "depth", "logger", "serial_number", "datetime", "DO_mgL_raw", "tempC", "DO_mgL", "DO_percent_sat", "Site_Latitude", "Site_Longitude"
- Converted "datetime" field from "%m/%d/%y %H:%M" (UTC) to ISO 8601 format "%Y-%m-%dT%H:%MZ" (UTC), output type datetime
- Set field types: "depth_m" as integer; "serial_number" as integer; "DO_mgL", "DO_mgL_raw", "DO_percent_sat", "Site_Latitude", "Site_Longitude", "tempC" as number; "datetime" as datetime with format "%Y-%m-%dT%H:%MZ"; "site" and "logger" as string
- Output written to "874724_v1_physical_monitoring_data.csv"
- The temporal range of Version 1 is 2021-09-07 to 2022-03-22.
Version 2:
- Version 2 contains depth measurements in meters, where Version 1 contained depth values in feet.
- Version 2 of this dataset contains additional years of data, which are now represented in the data file along with the original years represented in Version 1. The temporal range of Version 2 is 2021-09-07 to 2024-11-27.
- Loaded calibration site log from "Phyical_Monitoring_Calibration_Site_Log.csv" (CSV format, using filename as resource name; missing values: "", "nd", "NA")
- Loaded physical monitoring data from "Bocas_DO_Temp_LoggerData.xlsx" (Excel format, sheet 1, named "874724_v2_physical_monitoring_data"; missing values: "", "nd")
- Applied uppercase transformation to the "site" field in the physical monitoring data to standardize site name case for joining
- Joined calibration site log to physical monitoring data in half-outer mode on site name (source key: "Site", target key: "site"), bringing in "Latitude" (mapped to "Site_Latitude") and "Longitude" (mapped to "Site_Longitude") using first-value aggregation
- Replaced literal "NA" strings with empty values in fields: "site", "depth_m", "logger", "serial_number", "datetime", "DO_mgL_raw", "tempC", "DO_mgL", "DO_percent_sat", "Site_Latitude", "Site_Longitude"
- Converted "datetime" field from "%m/%d/%y %H:%M" (UTC) to ISO 8601 format "%Y-%m-%dT%H:%MZ" (UTC), output type datetime
- Set field types: "depth_m" as integer; "serial_number" as integer; "DO_mgL", "DO_mgL_raw", "DO_percent_sat", "Site_Latitude", "Site_Longitude", "tempC" as number; "datetime" as datetime with format "%Y-%m-%dT%H:%MZ"; "site" and "logger" as string
- Output written to "874724_v2_physical_monitoring_data.csv"
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
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
OnSET HOBO Dissolved Oxygen Loggers Model U26-001
OnSET HOBO Dissolved Oxygen Loggers Model U26-001
PI Supplied Instrument Name: OnSET HOBO Dissolved Oxygen Loggers Model U26-001 PI Supplied Instrument Description:Loggers were deployed using Hobo Onset Shuttle and programmed to record hourly measurements.
Instrument Name: Oxygen Sensor Instrument Short Name:Dissolved Oxygen Sensor Instrument Description: An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed