Dataset: Emerald Reef Seasonal Monitoring, 2014-2015

Name: Coral species sample collection log from the Emerald Reef during 2014-2015 (Reef coral symbioses project)
Published: 2016-02-04
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:25.67878 E:-80.09747 S:25.67563 W:-80.09765

Project:

New insights into the response of reef corals to climate change using the symbiont to host cell ratio as a metric of bleaching susceptibility (Reef coral symbioses)

Principal Investigator:

Andrew Baker (University of Miami Rosenstiel School of Marine and Atmospheric Science, UM-RSMAS)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2016-02-04

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Coral species sample collection log from the Emerald Reef during 2014-2015 (Reef coral symbioses project)

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Description

Data are organized in columns containing the unique tissue sample ID, coral species, colony ID (tag number in the field) and information regarding the collection (date, location, collector). The survey took place at Emerald Reef, off Key Biscayne, northern Florida Keys, between 15 and 30 feet of depth

Access to the DNA sample data themselves will be restricted until analysis is completed, typically within 2 years of collection.

Methods & Sampling

Coral tissue biopsies were taken from replicate, one-inch cores of Montastraea cavernosa as small scrapings along a polyp’s calyx wall using a razor blade. The samples were immediately placed into 300uL of 1% SDS in DNA Buffer in 1.5mL Eppendorf tubes and heated to 65°C for one hour, where they are now stable at room temperature. Small aliquots of this lysate are then removed for DNA extraction on as as-needed basis.

We retain archived lysates (consisting of SDS-lysed tissue and a small piece of skeleton) that are stable long-term (>18 years) at room temperature.

Data for this project will ultimately include symbiont:host cell ratios for these samples using a variety of Symbiodinium clade-specific probes. In addition, data may also include the results of ITS2 genotyping using Denaturing Gradient Gel Electrophoresis (DGGE). Additional data, such as environmental data collected by dataloggers during experiments or field deployments, may also be contributed.

Data Processing Description

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard
- reformatted dates from m/d/y to yyyy-mm-dd
- replaced spaces with underscores
- replaced empty cells with nd
- replaced '?' with 'maybe'
- replaced commas with other suitable punctation (; - :)

Version 2 (2021-06-10) replaces version 1 (2016-02-04).
* There was an unsupported character in the source file. Converted to utf-8. Comment in line now reads
"no_tag_–_By_buoy" after converting to UTF-8.
* Added parameter information for lat and lon columns.

Data Files

File
monitor_EmeraldReef.csv (Comma Separated Values (.csv), 83.26 KB) MD5:1d496aafee9dc892eabde21ea198f7a6 Primary data file for dataset ID 616042

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1358699

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Baker_lab_2015		2015-04-04	UM-RSMAS		data info

Instruments

None available yet

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
collector	person who collected coral	unitless	investigator
comments	comments; often pertaining to condition	unitless	comment
comments_new_tags	comments pertaining to tags	unitless	comment
date_collected	date specimen collected	yyyy-mm-dd	date
depth_ft	depth	feet	depth
lat	Latitude	decimal degrees	lat
location	location of coral	unitless	site
lon	Longitude	decimal degrees	lon
photo	either yes if photo taken or photo id number	unitless	no_bcodmo_term
sample	coral sample identification	unitless	sample
species	taxonomic genus+species	unitless	species
tag	specimen tag number	unitless	sample

Status message

Database

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Dataset: Emerald Reef Seasonal Monitoring, 2014-2015