http://lod.bco-dmo.org/id/dataset/958181
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
2025-04-07
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Benthic community data from surveys of reefs in southwestern Puerto Rico during 2018 and 2020
2025-05-22
publication
2025-05-22
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-05-22
publication
https://doi.org/10.26008/1912/bco-dmo.958181.1
Ernesto F. Weil
University of Puerto Rico - Mayaguez
principalInvestigator
Juan Jose Cruz Motta
University of Puerto Rico - Mayaguez
principalInvestigator
Nikolaos V. Schizas
University of Puerto Rico - Mayaguez
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: Weil, E. F., Schizas, N. V., Cruz Motta, J. J. (2025) Benthic community data from surveys of reefs in southwestern Puerto Rico during 2018 and 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-05-22 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.958181.1 [access date]
Reef surveys before SCTLD (2018 and 2020) Dataset Description: Methods and Sampling: <p>The surveys were conducted at various shallow depths (3-, 4-, 10-, 15-meters (m)) in the reefs Turrumote 2, Romero, Guilligan Is, Guanica Bay, Cayo Coral, and Punta Guanica. These reefs are located in southwestern Puerto Rico (approx. lat. 17.8849, long. -67.01546, depth 3-15 m).</p>
<p>The methodology used in the field was the line transect method. The length of each line was 10 m.</p>
<p>Five haphazardly placed, 10-m long permanent, linear/band transects were set up in each of at least three depth intervals (0-5, 7-12, and &gt; 15 m) in several localities prior to the arrival of the disease. They were surveyed before the epizootic event started, to estimate initial live coral cover, during the peak of the event to estimate disease prevalence and species impacted, and again after the disease arrested to estimate impact at the population and community levels.</p>
<p>The linear distance (in centimeters (cm)) of each different substrate (live coral colonies, sponges, zoanthids, crustose coralline algae, etc.) under the tape was measured along each ten-meter-long transect. Relative cover (as a percent (%)) for each substrate in each transect was calculated and added up for each transect. The overall and average percent cover for each biological group and substrate was then estimated for each depth and each locality. Variability in live coral cover across depth intervals in each reef and locality, and among localities will be compared before, during, and after the SCTLD epizootic event.</p>
<p>All coral colonies were checked for health status (healthy, SCTLD infected, other diseases, and bleaching) along a band transect (10 x 2 m (20 sqm) marked by the linear tape. Proportions of colonies in each health category will be calculated for each depth, locality, and over time. Variability in the temporal dynamics of SCTLD prevalence for each foundational, susceptible species impacted will be assessed across depth intervals within each locality, across localities, and over time.</p>
<p><strong>Instrumentation:</strong><br />
Besides the individual diving equipment and an underwater camera, no special instruments were needed to collect the live coral cover. A fiberglass graduated 30-m long tape, a PVC pipe (1-m long), a slate, underwater paper, and pencils were the materials used. Additionally, we had HOBO temp loggers (ONSET Corp.) in several localities, which will provide seasonal/annual variability and the number of days/weeks with higher-than-normal water temperatures.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2000863 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2000863
completed
Ernesto F. Weil
University of Puerto Rico - Mayaguez
787-899-2048 ext. 241
Department of Marine Sciences P.O. Box 9000
Mayaguez
PR
00681-9000
Puerto Rico
reefpal@gmail.com
pointOfContact
Juan Jose Cruz Motta
University of Puerto Rico - Mayaguez
787-899-2048 ext. 228
Department of Marine Sciences Call Box 9000
Mayagüez
00681
Puerto Rico
juan.cruz13@upr.edu
pointOfContact
Nikolaos V. Schizas
University of Puerto Rico - Mayaguez
787-248-0057
Department of Marine Sciences Call Box 9000
Mayagüez
PR
00681
US
nikolaos.schizas@upr.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Year
Date
Locality
Latitude
Longitude
Reef_Number
Transect
Depth
Depth_code
Group
Genera
Species_code
Species_name
Raw_data
linear_cover
percent_cover
30-m long tape
underwater camera
underwater paper and pencils
HOBO temp loggers (ONSET Corp.)
theme
None, User defined
year
date
site
latitude
longitude
transect
depth
site description
taxon
taxon_code
species scientific name (binomial)
length
percent coverage
featureType
BCO-DMO Standard Parameters
Measuring Tape
Underwater Camera
Underwater Writing Slate
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.
RAPID: MICROBIOME AND POPULATION DYNAMICS IN SCLERACTINIAN CORAL TISSUE LOSS DISEASE INFECTED CORALS IN PUERTO RICO
https://osprey.bco-dmo.org/project/831183
RAPID: MICROBIOME AND POPULATION DYNAMICS IN SCLERACTINIAN CORAL TISSUE LOSS DISEASE INFECTED CORALS IN PUERTO RICO
<p><em>Location:</em> The study will be carried out in reefs off La Parguera Natural Reserve, on the south-west coast of Puerto Rico. Facilities are located within the Reserve, so we have quick and easy access to the reefs for collections and surveys. Caribbean Sea, Southwest Puerto Rico, Lat. 17.8849 Long. -67.01546</p>
<p><em>NSF Award Abstract:</em><br />
Modern coral reefs are the result of thousands of years of growth and development, but their demise is occurring at alarming rates around the World. In the Caribbean alone, over 60% of live coral cover has been lost in many reefs in just 30-40 years. Consequently, their ecological and economic benefits to coastal communities are also declining. Disease outbreaks and more intense and frequent bleaching (loss of the microalgae in coral tissues) events associated with increasing water temperatures are some of the main factors for coral reef mass mortalities. The highly infectious and deadly Scleractinian Coral Tissue Loss Disease (SCTLD), first identified in 2014 in Florida, is quickly moving through the Caribbean causing extensive mortalities across important reef-building corals. Current research is focused in after-infection events to identify the pathogen and characterize the signs, patterns and consequences of SCTLD transmission. This study investigates coral tissues and the coral-associated bacteria communities before, during and after the infection has occurred in reefs in Puerto Rico. The societal broader impact of the project relates to the significant ecosystem services provided by coral reefs, which are threatened by SCTLD. The project will also support training of a graduate student.</p>
<p>Questions about etiological variability and the temporal dynamics of the microbiome in SCTLD-affected coral species remain unanswered. Specifically, this proposal addresses the following questions: (1) What are the changes in the microbiome composition and abundances of the susceptible coral species when infected with SCTLD? (2) What is the variability in virulence, prevalence and mortality within and amongst species in different phases of the infection and in different habitats? The research site is in La Parguera Natural Reserve, southwest Puerto Rico, where the research team has characterized and monitored several reefs and environmental conditions from the shore to the shelf edge since 2003. This project includes surveys of permanent transects and molecular characterization of tissue/mucus samples, and microbial communities within those, collected from healthy colonies of two to three of the most susceptible coral species (i.e., Meandrina meandrites, M. jacksoni and Orbicella faveolata) and colonies of two resistant species (i.e., Montastraea cavernosa, Porites astreoides) at the long-term monitoring site. The expected arrival of SCTLD to Puerto Rico in Fall 2019, offers the team of researchers a unique window of opportunity to capture reef biological conditions before, during and after infection to complement other research efforts to better understand the ecological dynamics, prevalence and consequences of this new deadly coral disease.</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>
RAPID-SCTLD-PR
largerWorkCitation
project
eng; USA
oceans
-67.97467
-66.75667
17.92155
17.96783
2018-01-18
2020-10-11
Southwest Puerto Rico, Caribbean Sea
0
BCO-DMO catalogue of parameters from Benthic community data from surveys of reefs in southwestern Puerto Rico during 2018 and 2020
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/958284.rdf
Name: Year
Units: unitless
Description: <p>Year of the transect work</p>
http://lod.bco-dmo.org/id/dataset-parameter/958285.rdf
Name: Date
Units: unitless
Description: <p>Date of the transect work</p>
http://lod.bco-dmo.org/id/dataset-parameter/958286.rdf
Name: Locality
Units: unitless
Description: <p>Name of the reef location of the transect work</p>
http://lod.bco-dmo.org/id/dataset-parameter/958287.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of the transect work</p>
http://lod.bco-dmo.org/id/dataset-parameter/958288.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of the transect work</p>
http://lod.bco-dmo.org/id/dataset-parameter/958289.rdf
Name: Reef_Number
Units: unitless
Description: <p>Numerical coding of the reef</p>
http://lod.bco-dmo.org/id/dataset-parameter/958290.rdf
Name: Transect
Units: unitless
Description: <p>Replicate number of transect</p>
http://lod.bco-dmo.org/id/dataset-parameter/958291.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth of the transect</p>
http://lod.bco-dmo.org/id/dataset-parameter/958292.rdf
Name: Depth_code
Units: unitless
Description: <p>Depth code: SHA = shallow, INT = intermediate, DEEP = Deep.</p>
http://lod.bco-dmo.org/id/dataset-parameter/958293.rdf
Name: Group
Units: unitless
Description: <p>Code used to indicate the group:<br />
ACT = ACTINARIA,<br />
ALG = Algae,<br />
CYA = CYANOBACTERIA,<br />
HYD = Hydrozoan,<br />
OCT = Octocoral,<br />
PSE = PEYSSONNELIA,<br />
RUB = RUBBLE,<br />
SPO =Sponge,<br />
SCL = Scleractinian,<br />
SAN = Sand,<br />
T+S = TURF + SAND,<br />
ZOA = ZOANTHID.</p>
http://lod.bco-dmo.org/id/dataset-parameter/958294.rdf
Name: Genera
Units: unitless
Description: <p>Genera of organisms encountered in the transect</p>
http://lod.bco-dmo.org/id/dataset-parameter/958295.rdf
Name: Species_code
Units: unitless
Description: <p>Species (code) of organisms encountered in the transect</p>
http://lod.bco-dmo.org/id/dataset-parameter/958296.rdf
Name: Species_name
Units: unitless
Description: <p>Species (name) of organisms encountered in the transect</p>
http://lod.bco-dmo.org/id/dataset-parameter/958297.rdf
Name: Raw_data
Units: centimeters (cm)
Description: <p>Distance from the beginning of the line transect</p>
http://lod.bco-dmo.org/id/dataset-parameter/958298.rdf
Name: linear_cover
Units: centimeters (cm)
Description: <p>Distance from the beginning of each 20 cm interval of the transect</p>
http://lod.bco-dmo.org/id/dataset-parameter/958299.rdf
Name: percent_cover
Units: percentage (%)
Description: <p>Percent cover of the transect by each organism</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
646080
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/59a994cc-2370-43cc-829c-1e840fbf5f26/content
download
https://doi.org/10.26008/1912/bco-dmo.958181.1
download
onLine
dataset
<p>The surveys were conducted at various shallow depths (3-, 4-, 10-, 15-meters (m)) in the reefs Turrumote 2, Romero, Guilligan Is, Guanica Bay, Cayo Coral, and Punta Guanica. These reefs are located in southwestern Puerto Rico (approx. lat. 17.8849, long. -67.01546, depth 3-15 m).</p>
<p>The methodology used in the field was the line transect method. The length of each line was 10 m.</p>
<p>Five haphazardly placed, 10-m long permanent, linear/band transects were set up in each of at least three depth intervals (0-5, 7-12, and &gt; 15 m) in several localities prior to the arrival of the disease. They were surveyed before the epizootic event started, to estimate initial live coral cover, during the peak of the event to estimate disease prevalence and species impacted, and again after the disease arrested to estimate impact at the population and community levels.</p>
<p>The linear distance (in centimeters (cm)) of each different substrate (live coral colonies, sponges, zoanthids, crustose coralline algae, etc.) under the tape was measured along each ten-meter-long transect. Relative cover (as a percent (%)) for each substrate in each transect was calculated and added up for each transect. The overall and average percent cover for each biological group and substrate was then estimated for each depth and each locality. Variability in live coral cover across depth intervals in each reef and locality, and among localities will be compared before, during, and after the SCTLD epizootic event.</p>
<p>All coral colonies were checked for health status (healthy, SCTLD infected, other diseases, and bleaching) along a band transect (10 x 2 m (20 sqm) marked by the linear tape. Proportions of colonies in each health category will be calculated for each depth, locality, and over time. Variability in the temporal dynamics of SCTLD prevalence for each foundational, susceptible species impacted will be assessed across depth intervals within each locality, across localities, and over time.</p>
<p><strong>Instrumentation:</strong><br />
Besides the individual diving equipment and an underwater camera, no special instruments were needed to collect the live coral cover. A fiberglass graduated 30-m long tape, a PVC pipe (1-m long), a slate, underwater paper, and pencils were the materials used. Additionally, we had HOBO temp loggers (ONSET Corp.) in several localities, which will provide seasonal/annual variability and the number of days/weeks with higher-than-normal water temperatures.</p>
Specified by the Principal Investigator(s)
<p>Identification of benthic species was done by the diver <em>in situ</em>. Most of the survey data has been entered into Excel spreadsheets and edited for errors. We still have to finish a couple of localities to then run the analyses with parametric and multivariate analyses to assess significant variability and changes in live coral cover, disease prevalence, biodiversity, and the impact of the disease at the population and community levels.</p>
Specified by the Principal Investigator(s)
- Converted the species code list to CSV format and imported the file into the BCO-DMO system.
- Imported original file "RAW-DATA-GUANICA-REEFS-2018-2020-EW-REV-jan25.xlsx" into the BCO-DMO system.
- Removed rows 75 and 76 of the original Excel file (as instructed by the submitter to correct for duplicate rows of data).
- Converted dates to YYYY-MM-DD format.
- Converted latitude and longitude values from degrees and decimal minutes to decimal degrees; rounded values to 5 decimal places.
- Renamed fields to comply with BCO-DMO naming conventions.
- Made the following changes for consistent formatting/use of codes:
-- Replaced "Turf" with "TUR" in the "Group" column.
-- Replaced "OCT" and "Oct" with "Octocoral" in the "Genera" column.
-- Replaced "SPO" and "Spo" with "Sponge" in the "Genera" column.
-- Replaced "Turf+Sand" with "Turf and sand" in the "Genera" column.
-- Replaced "OCT" and "oct" with "Oct" in the "Species" column.
-- Replaced "Romero2" with "Romero 2" in the "Locality" column.
- For rows where "Genera" = "Palythoa", and "Species" = "Pame", changed "Pame" to "Pcar".
- Corrected the species code list so "Pcar" = "Palythoa caribaeorum".
- Joined the species code list to the primary data file, creating a new column "Species_name".
- Renamed the original "Species" column to "Species_code".
- Saved the final file as "958181_v1_reef_surveys_2018_2020.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
30-m long tape
30-m long tape
PI Supplied Instrument Name: 30-m long tape PI Supplied Instrument Description:A fiberglass graduated 30-m long tape, a PVC pipe (1-m long), a slate, underwater paper and pencils were the materials used. Instrument Name: Measuring Tape Instrument Short Name: Instrument Description: A tape measure or measuring tape is a flexible ruler. It consists of a ribbon of cloth, plastic, fibre glass, or metal strip with linear-measurement markings. It is a common tool for measuring distance or length.
underwater camera
underwater camera
PI Supplied Instrument Name: underwater camera Instrument Name: Underwater Camera Instrument Short Name: Instrument Description: All types of photographic equipment that may be deployed underwater including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/180/
underwater paper and pencils
underwater paper and pencils
PI Supplied Instrument Name: underwater paper and pencils PI Supplied Instrument Description:A fiberglass graduated 30-m long tape, a PVC pipe (1-m long), a slate, underwater paper and pencils were the materials used. Instrument Name: Underwater Writing Slate Instrument Short Name: Instrument Description: Underwater writing slates and pencils are used to transport pre-dive plans underwater, to record facts whilst underwater and to aid communication with other divers.
HOBO temp loggers (ONSET Corp.)
HOBO temp loggers (ONSET Corp.)
PI Supplied Instrument Name: HOBO temp loggers (ONSET Corp.) PI Supplied Instrument Description:We had HOBO temp loggers (ONSET Corp.) in several localities, which will provide seasonal/annual variability and the number of days/weeks with higher-than-normal water temperatures. 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/