http://lod.bco-dmo.org/id/dataset/924394
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
2024-04-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Information about sequences of coral, Acropora cervicornis, collected from host colonies at the Mote Marine Laboratory in situ coral nursery in Looe Key, Lower Florida Keys in November and December 2019
2024-04-04
publication
2024-04-04
revision
BCO-DMO Linked Data URI
2024-04-04
creation
http://lod.bco-dmo.org/id/dataset/924394
Erinn M. Muller
Mote Marine Laboratory
principalInvestigator
Grace J. Klinges
Oregon State University
principalInvestigator
Sara D. Williams
Mote Marine Laboratory
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: Muller, E. M., Williams, S. D., Klinges, G. J. (2024) Information about sequences of coral, Acropora cervicornis, collected from host colonies at the Mote Marine Laboratory in situ coral nursery in Looe Key, Lower Florida Keys in November and December 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-04-04 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/924394 [access date]
Acropora cervicornis 16S Sequences Metadata and NCBI SRA accessions associated with Williams et al., 2022 Dataset Description: Methods and Sampling: <p>Complete methods are published in Williams, et al. (2022) and summarized here. 74 genotypes of <em>Acropora cervicornis</em> in Mote Marine Laboratory's in situ nursery in the Lower Florida Keys were fragmented and collected between November and December 2018. The fragments were flash-frozen using liquid nitrogen and were then immediately stored at -80 degrees Celsius (°C) until further processing. DNA was isolated from the frozen coral fragments (sub-sampled for 4-5 polyps first) using DNeasy PowerSoil Kits (QIAGEN, Germantown, MD, USA) with modifications to the manufacturer's protocol. Sample bacterial communities were determined using 16S rRNA Illumina sequencing on the MiSeq platform. DNA was sent to MR DNA (<a href="http://www.mrdnalab.com" target="_blank">http://www.mrdnalab.com</a>, Shallowater, TX, USA) for barcoding, amplification, and sequencing. Amplification of the 16S rRNA gene variable region (V4) was conducted using primers 515F and 806R. A polymerase chain reaction was performed using the HotStarTaq Plus Master Mix Kit (QIAGEN, Germantown, MD, USA) and products were checked on a 2% agarose gel to determine the success of amplification and the relative intensity of bands. Samples were pooled and then purified using calibrated Agencourt Ampure XP beads (Beckman Coulter, CA, USA). The pooled DNA library was made using the Illumina TruSeq DNA library preparation protocol. Paired-end sequencing (sequencing read length of 300 base pairs) was performed at MR DNA using a single flow cell on a MiSeq following the manufacturer's guidelines.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1452538 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1452538
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1923836 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1923836
Funding provided by National Fish and Wildlife Foundation (NFWF) Award Number: 62145
onGoing
Erinn M. Muller
Mote Marine Laboratory
941-388-4441 x 310
1600 Ken Thompson Parkway
Sarasota
FL
34241
USA
emuller@mote.org
pointOfContact
Grace J. Klinges
Oregon State University
Center for Global Discovery and Conservation Science
Tempe
AZ
USA
gklinges@asu.edu
pointOfContact
Sara D. Williams
Mote Marine Laboratory
1600 Ken Thompson Parkway
Sarasota
FL
34236
USA
swilliams@mote.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioProject
SRA_Study
BioSample
Sample_Name
SRA_Run
SRA_Sample
SRA_Experiment
Experiment_Title
SRA_title
Library_Strategy
Library_Source
Library_Selection
Library_Layout
Platform
Instrument_Model
Design
DataStore_FileType
Site
Collection_Date
Latitude
Longitude
Host_Organism
Genotype_MoteID
Origin
Illumina MiSeq platform
PCR
theme
None, User defined
NCBI BioProject accession
NCBI SRA study accession (SRP)
NCBI BioSample accession
sample identification
NCBI SRA run accession (SRR)
NCBI SRA Sample accession (SRS)
NCBI SRA experiment accession (SRX)
brief description
sampling_method
sample description
instrument
instrument model
site
date
latitude
longitude
species scientific name (binomial)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
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.
CAREER: Applying phenotypic variability to identify resilient Acropora cervicornis genotypes in the Florida Keys
https://osprey.bco-dmo.org/project/642850
CAREER: Applying phenotypic variability to identify resilient Acropora cervicornis genotypes in the Florida Keys
<p><em>NSF Award Abstract:</em><br />
Caribbean staghorn coral was one of the most common corals within reefs of the Florida Keys several decades ago. Over the last 40 years disease, bleaching, overfishing and habitat degradation caused a 95% reduction of the population. Staghorn coral is now listed as threatened under the U.S. Endangered Species Act of 1973. Within the past few years, millions of dollars have been invested for the purpose of restoring the population of staghorn coral within Florida and the U.S. Virgin Islands. Significant effort has been placed on maintaining and propagating corals of known genotypes within coral nurseries for the purpose of outplanting. However, little is known about the individual genotypes that are currently being outplanted from nurseries onto coral reefs. Are the genotypes being used for outplanting resilient enough to survive the three major stressors affecting the population in the Florida Keys: disease, high water temperatures, and ocean acidification? The research within the present study will be the first step in answering this critically important question. The funded project will additionally develop a research-based afterschool program with K-12 students in the Florida Keys and U.S. Virgin Islands that emphasizes an inquiry-based curriculum, STEM research activities, and peer-to-peer mentoring. The information from the present study will help scientists predict the likelihood of species persistence within the lower Florida Keys under future climate-change and ocean-acidification scenarios. Results of this research will also help guide restoration efforts throughout Florida and the Caribbean, and lead to more informative, science-based restoration activities.</p>
<p><em>Acropora cervicornis</em> dominated shallow-water reefs within the Florida Keys for at least the last half a million years, but the population has recently declined due to multiple stressors. Understanding the current population level of resilience to three major threats - disease outbreaks, high water temperatures, and ocean acidification conditions - is critical for the preservation of this threatened species. Results from the present study will answer the primary research question: will representative genotypes from the lower Florida Keys provide enough phenotypic variation for this threatened species to survive in the future? The present proposal will couple controlled laboratory challenge experiments with field data and modeling applications, and collaborate with local educators to fulfill five objectives: 1) identify <em>A. cervicornis</em> genotypes resistant to disease, 2) identify <em>A. cervicornis</em> genotypes resilient to high water temperature and ocean acidification conditions, 3) quantify how high water temperature and ocean acidification conditions impact disease dynamics on <em>A. cervicornis</em>; 4) determine tradeoffs in life-history traits because of resilience factors; and 5) apply a trait-based model, which will predict genotypic structure of a population under different environmental scenarios.</p>
Resilient Acerv
largerWorkCitation
project
Collaborative Research: Tracking the interacting roles of the environment, host genotype, and a novel Rickettsiales in coral disease susceptibility
https://osprey.bco-dmo.org/project/820022
Collaborative Research: Tracking the interacting roles of the environment, host genotype, and a novel Rickettsiales in coral disease susceptibility
<p><em>NSF Award Abstract:</em><br />
Historically one of the most abundant reef-building corals in Florida and the wider Caribbean, the staghorn coral, <em>Acropora cervicornis</em>, is now listed as critically endangered primarily because of previous and reoccurring disease events. Understanding the holistic mechanisms of disease susceptibility in this coral is a top concern of practitioners engaged in conservation and restoration. The investigators recently discovered a group of parasitic bacteria common within the microbial community of <em>A. cervicornis</em> that can reduce the growth and health of corals when reefs are exposed to nutrient polluted waters. Determining how interactions among the coral host, this parasitic microbe, and the environment are linked to disease susceptibility provides critical insight and greater success of future restoration efforts. Yet the complexity of animal microbiomes and the contextual nature of disease make it difficult to identify the specific cause of many disease outbreaks. In this project, the investigators conduct experiments to explore the interactions among different genetic strains of coral and these bacteria in various nutrient scenarios to better understand how this bacterium affects the susceptibility of staghorn coral to diseases. This project also characterizes the genomics, host range, and local and global distribution of this bacterial coral parasite to determine how its evolutionary history and physiology drive disease susceptibility in this important coral species. The project trains two postdocs, one technician, and seven students (one graduate, six undergraduates) in integrative sciences that span marine science, physiology, genetics, microbiology, omics, and statistical modeling. A research-based after school program in Florida is expanded to include microbiology and create a new program module called Microbial warriors, with a focus on women in science. The investigators produce documentary style films and outreach materials to broadly communicate the project science and conservation efforts to local and national communities via presentations at Mote Marine Lab and the Oregon Museum of Science and Industry. This project is co-funded by the Biological Oceanography Program in the Division of Ocean Sciences and the Symbiosis, Defense, and Self-recognition Program in the Division of Integrative Organismal Systems.</p>
<p>The investigators recently identified a marine <em>Rickettsiales</em> bacterium that, in corals, can be stimulated to grow in the presence of elevated nitrogen and phosphorous species. Based on genomic reconstruction and phylogeography, this bacteria is classified as a novel bacterial genus, <em>Candidatus Aquarickettsia</em>, and showed that it is broadly associated with scleractinian corals worldwide. Importantly, using a model system, the endangered <em>Acropora cervicornis</em> coral, the team has also shown that the growth of this bacterium in vivo is associated with reduced host growth and increased disease susceptibility. This project aims to more completely evaluate the mechanisms behind and impacts of these inducible infections on coral physiology and host-bacterial symbiosis. The investigators conduct nutrient dosing experiments on different coral genotypes with various <em>Rickettsiales</em> abundances. Using a range of omics and microscopy techniques, the team quantifies the resulting effects on holobiont phenotypes. The investigators are also comparing the genomes of these bacteria in the different Acroporid hosts and other coral genera to evaluate facets of the bacterium's evolutionary history, as well as to identify possible mechanisms of its proliferation, virulence, and host specificity. This interdisciplinary project mechanistically links nutrients to temporal changes in host, algal symbiont, and bacterial parasite physiology and also explain why there is natural variation in these responses by exploring how host and parasite genotypes and growth dynamics combined with environmental contextuality alter holobiont phenotypes.</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 Rickettsiales
largerWorkCitation
project
eng; USA
oceans
-81.4005
-81.4005
24.5627
24.5627
2019-11-01
2019-12-31
From projects that focused on the following 2 locations: 1. Florida Keys, Summerland Key, FL 24.563595°, -81.278572° 2. at Oregon State University and in the Florida Keys at Mote Marine Laboratory
0
BCO-DMO catalogue of parameters from Information about sequences of coral, Acropora cervicornis, collected from host colonies at the Mote Marine Laboratory in situ coral nursery in Looe Key, Lower Florida Keys in November and December 2019
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/924441.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/924442.rdf
Name: SRA_Study
Units: unitless
Description: <p>SRA study identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/924443.rdf
Name: BioSample
Units: unitless
Description: <p>SRA BioSample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/924444.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample Name</p>
http://lod.bco-dmo.org/id/dataset-parameter/924445.rdf
Name: SRA_Run
Units: unitless
Description: <p>SRA run identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/924446.rdf
Name: SRA_Sample
Units: unitless
Description: <p>SRA sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/924447.rdf
Name: SRA_Experiment
Units: unitless
Description: <p>SRA experiment identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/924448.rdf
Name: Experiment_Title
Units: unitless
Description: <p>SRA experiment title</p>
http://lod.bco-dmo.org/id/dataset-parameter/924449.rdf
Name: SRA_title
Units: unitless
Description: <p>Descriptive title of SRA study</p>
http://lod.bco-dmo.org/id/dataset-parameter/924450.rdf
Name: Library_Strategy
Units: unitless
Description: <p>Type of library prep ("AMPLICON")</p>
http://lod.bco-dmo.org/id/dataset-parameter/924451.rdf
Name: Library_Source
Units: unitless
Description: <p>Source of genetic material ("METAGENOMIC")</p>
http://lod.bco-dmo.org/id/dataset-parameter/924452.rdf
Name: Library_Selection
Units: unitless
Description: <p>Library selection method ("PCR")</p>
http://lod.bco-dmo.org/id/dataset-parameter/924453.rdf
Name: Library_Layout
Units: unitless
Description: <p>Library layout ("PAIRED")</p>
http://lod.bco-dmo.org/id/dataset-parameter/924454.rdf
Name: Platform
Units: unitless
Description: <p>Sequencing platform ("ILLUMINA")</p>
http://lod.bco-dmo.org/id/dataset-parameter/924455.rdf
Name: Instrument_Model
Units: unitless
Description: <p>Sequencing instrument model ("Illumina MiSeq")</p>
http://lod.bco-dmo.org/id/dataset-parameter/924456.rdf
Name: Design
Units: unitless
Description: <p>Sequencing design description</p>
http://lod.bco-dmo.org/id/dataset-parameter/924457.rdf
Name: DataStore_FileType
Units: unitless
Description: <p>File type of data stored on SRA ("fastq")</p>
http://lod.bco-dmo.org/id/dataset-parameter/924458.rdf
Name: Site
Units: unitless
Description: <p>Sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/924459.rdf
Name: Collection_Date
Units: unitless
Description: <p>Date of sampling as year-month-day (YYYY-MM-DD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/924460.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Sampling latitude; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/924461.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Sampling longitude; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/924462.rdf
Name: Host_Organism
Units: unitless
Description: <p>Host from which microbiome samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/924463.rdf
Name: Genotype_MoteID
Units: unitless
Description: <p>Microsatellite genotype identifier used by Mote Marine Laboratory</p>
http://lod.bco-dmo.org/id/dataset-parameter/924464.rdf
Name: Origin
Units: unitless
Description: <p>Original collection location of host organism prior to moving to Mote's in situ coral nursery. Locations are within the Florida Keys, USA.</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
https://osprey.bco-dmo.org/dataset/924394/data/download
download
onLine
dataset
<p>Complete methods are published in Williams, et al. (2022) and summarized here. 74 genotypes of <em>Acropora cervicornis</em> in Mote Marine Laboratory's in situ nursery in the Lower Florida Keys were fragmented and collected between November and December 2018. The fragments were flash-frozen using liquid nitrogen and were then immediately stored at -80 degrees Celsius (°C) until further processing. DNA was isolated from the frozen coral fragments (sub-sampled for 4-5 polyps first) using DNeasy PowerSoil Kits (QIAGEN, Germantown, MD, USA) with modifications to the manufacturer's protocol. Sample bacterial communities were determined using 16S rRNA Illumina sequencing on the MiSeq platform. DNA was sent to MR DNA (<a href="http://www.mrdnalab.com" target="_blank">http://www.mrdnalab.com</a>, Shallowater, TX, USA) for barcoding, amplification, and sequencing. Amplification of the 16S rRNA gene variable region (V4) was conducted using primers 515F and 806R. A polymerase chain reaction was performed using the HotStarTaq Plus Master Mix Kit (QIAGEN, Germantown, MD, USA) and products were checked on a 2% agarose gel to determine the success of amplification and the relative intensity of bands. Samples were pooled and then purified using calibrated Agencourt Ampure XP beads (Beckman Coulter, CA, USA). The pooled DNA library was made using the Illumina TruSeq DNA library preparation protocol. Paired-end sequencing (sequencing read length of 300 base pairs) was performed at MR DNA using a single flow cell on a MiSeq following the manufacturer's guidelines.</p>
Specified by the Principal Investigator(s)
- Imported original file "BCODMO_Sample_MetaData_ACER16S_Williams_etal.csv" into the BCO-DMO system.
- Converted "Collection_Date" from Excel format to YYYY-MM-DD.
- Reordered columns.
- Removed "N" and "W" from "Latitude" and "Longitude" columns.
- Made longitude values negative to indicate West direction.
- Saved the final file as "924394_v1_a_cerv_sequence_metadata_williams_et_al_2022.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
Illumina MiSeq platform
Illumina MiSeq platform
PI Supplied Instrument Name: Illumina MiSeq platform Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PCR
PCR
PI Supplied Instrument Name: PCR Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)