http://lod.bco-dmo.org/id/dataset/924465
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)
Acropora cervicornis 16S rRNA sequence metadata: nutrient- and disease-exposed from samples collected at Mote Marine Laboratory in situ nursery from June to July 2022
2025-07-24
publication
2025-07-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-07-25
publication
https://doi.org/10.26008/1912/bco-dmo.924465.1
Rebecca Vega Thurber
Oregon State University
principalInvestigator
Erinn M. Muller
Mote Marine Laboratory
principalInvestigator
Grace J. Klinges
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: Klinges, G. J., Muller, E. M., Vega Thurber, R. (2025) Acropora cervicornis 16S rRNA sequence metadata: nutrient- and disease-exposed from samples collected at Mote Marine Laboratory in situ nursery from June to July 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-07-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.924465.1 [access date]
Acropora cervicornis 16S rRNA sequence metadata: nutrient- and disease-exposed Dataset Description: Methods and Sampling: <p>Samples of coral tissue, skeleton, and mucus were taken from two genotypes of <em>Acropora cervicornis </em>prior to nutrient enrichment (n = 20 per genotype), prior to disease exposure (n = 18 per genotype), and at various stages during disease development. All surviving ramets at one week after disease exposure were sampled. To sample each coral, 6-8 polyps&nbsp;were excised using a flame-sterilized blade and placed in a 1.5mL microcentrifuge tube containing 1mL of DNA/RNA shield (Zymo Research, R1100-250, Irvine, CA, USA). Samples were transferred to a -80℃ freezer for long-term storage. In preparation for DNA extractions, the samples were removed from the -80℃ freezer and thawed on ice. With flame-sterilized tweezers, half of the biomass was transferred to a Disruptor Tube (Omega Bio-Tek, Norcross, GA, USA), the other half was kept as a bioarchive and returned to -80℃. DNA from each sample was isolated utilizing the E.Z.N.A. DNA/RNA Isolation Kit (Omega Bio-Tek, Norcross, GA, USA) with slight modifications to the manufacturer’s protocol to increase yield. DNA isolates were stored at -80℃. DNA quantity and quality was assessed utilizing a NanoDrop spectrophotometer (Thermo Fisher Scientific™, Waltham, MA, USA). Samples were submitted to MR DNA for 16S rRNA PCR amplification and sequencing (www.mrdnalab.com, Shallowater, TX, USA). Amplification of the 16S rRNA gene was conducted using the 515F-806R primer set, which targets the V4 region of the 16S rRNA, with barcodes on the forward primer (Apprill et al., 2015). The 16S rRNA gene V4 variable region was amplified via a 30-cycle PCR using the HotStarTaq Plus Master Mix Kit (Qiagen, Germantown, MD) under the following conditions: 95°C for 5 minutes, followed by 30 cycles of 95°C for 30 seconds, 53°C for 40 seconds and 72°C for 1 minute, after which a final elongation step at 72°C for 10 minutes was performed. After amplification, PCR products were checked in 2% agarose gel to determine the success of amplification and the relative intensity of bands. Samples were multiplexed using unique dual indices and are pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples were purified using calibrated Ampure XP beads (Beckman Coutler, CA, USA). Then the pooled and purified PCR product was used to prepare an Illumina DNA library. A PCR negative control was included in library preparation but did not produce a viable library. Paired-end sequencing was performed at MR DNA on an Illumina MiSeq following the manufacturer's guidelines.</p>
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 NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1923926 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1923926
completed
Rebecca Vega Thurber
Oregon State University
rvegathurber@gmail.com
pointOfContact
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
Mote Marine Laboratory
Center for Global Discovery and Conservation Science
Tempe
AZ
USA
gklinges@asu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
NCBI_Project
sample_name
Latitude
Longitude
collection_date
accession
organism
env_broad_scale
env_local_scale
env_medium
geo_loc_name
host
replicate
coral_id
treatment
timepoint
exposure
group
status
tank
library_ID
title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
filename
filename2
theme
None, User defined
NCBI BioProject accession
sample description
latitude
longitude
date
NCBI BioSample accession
animal group (category)
region
replicate
No BCO-DMO term
treatment
time_point
sample identification
seq_descrip
instrument
instrument model
datatype
file_name
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.
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
-81.454384
-81.454384
24.661552
24.661552
2022-06-29
2022-07-27
at Oregon State University and in the Florida Keys at Mote Marine Laboratory
0
BCO-DMO catalogue of parameters from Acropora cervicornis 16S rRNA sequence metadata: nutrient- and disease-exposed from samples collected at Mote Marine Laboratory in situ nursery from June to July 2022
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/969790.rdf
Name: NCBI_Project
Units: unitless
Description: <p>NCBI Bioproject accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/969791.rdf
Name: sample_name
Units: unitless
Description: <p>Sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/969792.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sampling location, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/969793.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sampling location, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/969794.rdf
Name: collection_date
Units: unitless
Description: <p>Sampling date</p>
http://lod.bco-dmo.org/id/dataset-parameter/969795.rdf
Name: accession
Units: unitless
Description: <p>SRA sample identifier, NCBI Biosample accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/969796.rdf
Name: organism
Units: unitless
Description: <p>SRA organism identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/969797.rdf
Name: env_broad_scale
Units: unitless
Description: <p>sampling location, broad-scale environmental context (EMBL-EBI ENVO ontology)</p>
http://lod.bco-dmo.org/id/dataset-parameter/969798.rdf
Name: env_local_scale
Units: unitless
Description: <p>sampling location, local-scale environmental context (EMBL-EBI ENVO ontology)</p>
http://lod.bco-dmo.org/id/dataset-parameter/969799.rdf
Name: env_medium
Units: unitless
Description: <p>sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/969800.rdf
Name: geo_loc_name
Units: unitless
Description: <p>sampling location, geographic location of the origin of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/969801.rdf
Name: host
Units: unitless
Description: <p>animal host</p>
http://lod.bco-dmo.org/id/dataset-parameter/969802.rdf
Name: replicate
Units: unitless
Description: <p>replicate number within genotype (range 1-20)</p>
http://lod.bco-dmo.org/id/dataset-parameter/969803.rdf
Name: coral_id
Units: unitless
Description: <p>genotype and replicate number</p>
http://lod.bco-dmo.org/id/dataset-parameter/969804.rdf
Name: treatment
Units: unitless
Description: <p>nutrient exposed or not</p>
http://lod.bco-dmo.org/id/dataset-parameter/969805.rdf
Name: timepoint
Units: unitless
Description: <p>NT0 = prior to nutrient exposure, NT3/DT0 = after nutrient exposure and prior to disease exposure, DT0 = prior to diease exposure (not nutrient exposed), DT1 = first signs of disease, DT2 = secondary signs of disease, DT1 H = healthy coral sampled contemporaneously with disease timepoint 1, H = healthy, ND = disease exposed but no diease signs, Mortality = non-disease-related mortality</p>
http://lod.bco-dmo.org/id/dataset-parameter/969806.rdf
Name: exposure
Units: unitless
Description: <p>Baseline (before nutrient exposure), Nutrients 3 weeks, or Reef - July Baseline</p>
http://lod.bco-dmo.org/id/dataset-parameter/969807.rdf
Name: group
Units: unitless
Description: <p>Disease or Unexposed</p>
http://lod.bco-dmo.org/id/dataset-parameter/969808.rdf
Name: status
Units: unitless
Description: <p>health status at time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/969809.rdf
Name: tank
Units: unitless
Description: <p>aquarium identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/969810.rdf
Name: library_ID
Units: unitless
Description: <p>Unique identifier for the sequencing library (can be the sample name repeated).</p>
http://lod.bco-dmo.org/id/dataset-parameter/969811.rdf
Name: title
Units: unitless
Description: <p>Library title</p>
http://lod.bco-dmo.org/id/dataset-parameter/969812.rdf
Name: library_strategy
Units: unitless
Description: <p>Sequencing library strategy</p>
http://lod.bco-dmo.org/id/dataset-parameter/969813.rdf
Name: library_source
Units: unitless
Description: <p>Source of sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/969814.rdf
Name: library_selection
Units: unitless
Description: <p>Selection used for sequencing library</p>
http://lod.bco-dmo.org/id/dataset-parameter/969815.rdf
Name: library_layout
Units: unitless
Description: <p>single or paired end sequencing reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/969816.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform manufacturer</p>
http://lod.bco-dmo.org/id/dataset-parameter/969817.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencer model</p>
http://lod.bco-dmo.org/id/dataset-parameter/969818.rdf
Name: design_description
Units: unitless
Description: <p>Description explaining how this library was prepared and sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/969819.rdf
Name: filetype
Units: unitless
Description: <p>File type</p>
http://lod.bco-dmo.org/id/dataset-parameter/969820.rdf
Name: filename
Units: unitless
Description: <p>Forward reads file name</p>
http://lod.bco-dmo.org/id/dataset-parameter/969821.rdf
Name: filename2
Units: unitless
Description: <p>Reverse reads file name</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
121466
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/50a4d619-9ee5-42d4-b422-bc06ca4f9ffa/content
download
https://doi.org/10.26008/1912/bco-dmo.924465.1
download
onLine
dataset
<p>Samples of coral tissue, skeleton, and mucus were taken from two genotypes of <em>Acropora cervicornis </em>prior to nutrient enrichment (n = 20 per genotype), prior to disease exposure (n = 18 per genotype), and at various stages during disease development. All surviving ramets at one week after disease exposure were sampled. To sample each coral, 6-8 polyps&nbsp;were excised using a flame-sterilized blade and placed in a 1.5mL microcentrifuge tube containing 1mL of DNA/RNA shield (Zymo Research, R1100-250, Irvine, CA, USA). Samples were transferred to a -80℃ freezer for long-term storage. In preparation for DNA extractions, the samples were removed from the -80℃ freezer and thawed on ice. With flame-sterilized tweezers, half of the biomass was transferred to a Disruptor Tube (Omega Bio-Tek, Norcross, GA, USA), the other half was kept as a bioarchive and returned to -80℃. DNA from each sample was isolated utilizing the E.Z.N.A. DNA/RNA Isolation Kit (Omega Bio-Tek, Norcross, GA, USA) with slight modifications to the manufacturer’s protocol to increase yield. DNA isolates were stored at -80℃. DNA quantity and quality was assessed utilizing a NanoDrop spectrophotometer (Thermo Fisher Scientific™, Waltham, MA, USA). Samples were submitted to MR DNA for 16S rRNA PCR amplification and sequencing (www.mrdnalab.com, Shallowater, TX, USA). Amplification of the 16S rRNA gene was conducted using the 515F-806R primer set, which targets the V4 region of the 16S rRNA, with barcodes on the forward primer (Apprill et al., 2015). The 16S rRNA gene V4 variable region was amplified via a 30-cycle PCR using the HotStarTaq Plus Master Mix Kit (Qiagen, Germantown, MD) under the following conditions: 95°C for 5 minutes, followed by 30 cycles of 95°C for 30 seconds, 53°C for 40 seconds and 72°C for 1 minute, after which a final elongation step at 72°C for 10 minutes was performed. After amplification, PCR products were checked in 2% agarose gel to determine the success of amplification and the relative intensity of bands. Samples were multiplexed using unique dual indices and are pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples were purified using calibrated Ampure XP beads (Beckman Coutler, CA, USA). Then the pooled and purified PCR product was used to prepare an Illumina DNA library. A PCR negative control was included in library preparation but did not produce a viable library. Paired-end sequencing was performed at MR DNA on an Illumina MiSeq following the manufacturer's guidelines.</p>
Specified by the Principal Investigator(s)
<p>No processing was performed post-sequencing on reads submitted to SRA.&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