http://lod.bco-dmo.org/id/dataset/928636
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
2024-05-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sampling and experimental metadata related to 'Candidatus' Aquarickettsia rohweri transcriptome data from host Acropora cervicornis colonies collected at Looe Key, Lower Florida Keys from Apr to Jun of 2019
2024-05-24
publication
2024-05-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-03-20
publication
https://doi.org/10.26008/1912/bco-dmo.928636.1
Rebecca Vega Thurber
Oregon State University
principalInvestigator
Erinn M. Muller
Mote Marine Laboratory
principalInvestigator
Grace J. Klinges
Mote Marine Laboratory
principalInvestigator
Lauren Speare
Oregon State University
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: Vega Thurber, R., Muller, E. M., Klinges, G. J., Speare, L. (2025) Sampling and experimental metadata related to 'Candidatus' Aquarickettsia rohweri transcriptome data from host Acropora cervicornis colonies collected at Looe Key, Lower Florida Keys from Apr to Jun of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.928636.1 [access date]
Dataset Description: <p>These Ca. Aquarickettsia rohweri transcriptome data were published in Speare et al, (2023, doi: 10.1101/2023.06.08.544262) and are part of NCBI BioProject PRJNA1048415.&nbsp;<br />
<br />
Closely related data also part of the same NCBI BioProject were published in Klinges et al. (2023, doi: 10.1093/femsec/fiac013) which published the experiment and accompanying data (16S, coral health status, coral growth rate) from the same samples.</p> Methods and Sampling: <p>Fragments (~5cm) of <em>Acropora cervicornis</em> genotype ML-50 (Coral Sample Registry (Moura et al., 2021) accession: fa13971c-ea34-459e-2f13-7bfddbafd327) were collected from the Mote Marine Laboratory in situ coral nursery in Looe Key (24.5627,-81.4005) between April and June of 2019.&nbsp;&nbsp;<br />
<br />
Prior to experimental manipulation, fragments were allowed to acclimate to aquarium conditions for seven days. Nutrient enrichment was performed four times a day for 42 days (six weeks). Coral fragments were sacrificed for sampling: prior to nutrient exposure (T0), and after six weeks. Using sterile bone cutters, tissue was scraped from each fragment (avoiding the apical tip) and added directly to 2 mL tubes containing 0.5ml DNA/RNA shield (Zymo Research) and Lysing Matrix A (MP Biomedicals, 0.5 g garnet matrix and one 1/4" ceramic sphere). Tubes were immediately preserved at -80°C until further processing. Total RNA was extracted from 500 μl of tissue slurry using the E.Z.N.A.® DNA/RNA Isolation Kit (Omega Bio-Tek) and then stored at -80°C until further processing. Residual DNA contamination was removed from RNA isolates using the RQ1 RNase-Free DNase (Promega). Ribosomal RNA was removed using equal parts ‘plant leaf’, ‘human/mouse’ and ‘bacteria’ Ribo-Zero kits (Illumina). RNA quality and concentration were verified by BioAnalyzer (Agilent Technologies, Santa Clara, CA) and quantitative PCR, respectively. cDNA library prep and sequencing was performed at Oregon State University’s Center for Quantitative Life Sciences (CQLS) Core Laboratories with the HiSeq 3000 platform. Three biological replicates for each treatment were sequenced (n=9).&nbsp;<br />
<br />
Instruments:</p>
<p>Mote Marine Lab flow-through seawater raceways and 4.7L tanks: held corals during experiment&nbsp;<br />
boiler and chiller: controlled aquarium temperature<br />
Sterile bone cutters: used to collect coral tissue from each fragment<br />
-80°C Freezer: used to keep samples at a low temp prior to processing<br />
BioAnalyzer (Agilent Technologies, Santa Clara, CA): used to verify RNA quality and concentration<br />
Oregon State University’s Center for Quantitative Life Sciences (CQLS) Core Laboratories with the HiSeq 3000 platform: used for sample sequencing<br />
<br />
Organism identifiers (ScientificName, NCBI Taxonomy ID, Life Science Identifier (LSID):<br />
Acropora cervicornis, NCBI:txid6130,&nbsp;urn:lsid:marinespecies.org:taxname:206989<br />
'Candidatus' Aquarickettsia rohweri, NCBI:txid2602574, N/A</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
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
Lauren Speare
Oregon State University
262-844-0179
laurenspeare@gatech.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_name
BioSample_Accession
SRA
BioProject
Data_Type
Scope
Organism
Collected_Host_Organism
Strain
isolation_source
Collection_Year
Collection_date_note
Treatment
Illumina HiSeq 3000 platform
BioAnalyzer (Agilent Technologies, Santa Clara, CA)
theme
None, User defined
sample identification
NCBI BioSample accession
NCBI SRA Sample accession (SRS)
NCBI BioProject accession
sample description
year
treatment
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Bioanalyzer
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: 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
-81.4543
-81.4005
24.5627
24.66164
2019-05-01
2019-05-01
at Oregon State University and in the Florida Keys at Mote Marine Laboratory
0
BCO-DMO catalogue of parameters from Sampling and experimental metadata related to 'Candidatus' Aquarickettsia rohweri transcriptome data from host Acropora cervicornis colonies collected at Looe Key, Lower Florida Keys from Apr to Jun of 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/928644.rdf
Name: Sample_name
Units: unitless
Description: <p>description</p>
http://lod.bco-dmo.org/id/dataset-parameter/928645.rdf
Name: BioSample_Accession
Units: unitless
Description: <p>BioSample accession number in the National Center for Biotechnology Information (NCBI) BioSample database</p>
http://lod.bco-dmo.org/id/dataset-parameter/928646.rdf
Name: SRA
Units: unitless
Description: <p>Sample accession number in the NCBI Sequence Read Archive (SRA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/928647.rdf
Name: BioProject
Units: unitless
Description: <p>BioProject identifier at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/928648.rdf
Name: Data_Type
Units: unitless
Description: <p>Date type description (e.g. Raw sequence reads)</p>
http://lod.bco-dmo.org/id/dataset-parameter/928649.rdf
Name: Scope
Units: unitless
Description: <p>Sample scope description</p>
http://lod.bco-dmo.org/id/dataset-parameter/928650.rdf
Name: Organism
Units: unitless
Description: <p>Organism description for the sequence accessions</p>
http://lod.bco-dmo.org/id/dataset-parameter/928651.rdf
Name: Collected_Host_Organism
Units: unitless
Description: <p>Host organism collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/928652.rdf
Name: Strain
Units: unitless
Description: <p>strain (as shown with NCBI BioSample)</p>
http://lod.bco-dmo.org/id/dataset-parameter/928653.rdf
Name: isolation_source
Units: unitless
Description: <p>Isolation source (from the host organism)</p>
http://lod.bco-dmo.org/id/dataset-parameter/928657.rdf
Name: Collection_Year
Units: unitless
Description: <p>Collection year (of host)</p>
http://lod.bco-dmo.org/id/dataset-parameter/928658.rdf
Name: Collection_date_note
Units: unitless
Description: <p>Description of month and year range during which sampling took place</p>
http://lod.bco-dmo.org/id/dataset-parameter/956580.rdf
Name: Treatment
Units: unitless
Description: <p>Treatment description (see "Methods & Sampling" for full explanation of treatments).</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
2242
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a5ef5cac-2fce-4e12-9c61-258480e1cbe1/content
download
https://doi.org/10.26008/1912/bco-dmo.928636.1
download
onLine
dataset
<p>Fragments (~5cm) of <em>Acropora cervicornis</em> genotype ML-50 (Coral Sample Registry (Moura et al., 2021) accession: fa13971c-ea34-459e-2f13-7bfddbafd327) were collected from the Mote Marine Laboratory in situ coral nursery in Looe Key (24.5627,-81.4005) between April and June of 2019.&nbsp;&nbsp;<br />
<br />
Prior to experimental manipulation, fragments were allowed to acclimate to aquarium conditions for seven days. Nutrient enrichment was performed four times a day for 42 days (six weeks). Coral fragments were sacrificed for sampling: prior to nutrient exposure (T0), and after six weeks. Using sterile bone cutters, tissue was scraped from each fragment (avoiding the apical tip) and added directly to 2 mL tubes containing 0.5ml DNA/RNA shield (Zymo Research) and Lysing Matrix A (MP Biomedicals, 0.5 g garnet matrix and one 1/4" ceramic sphere). Tubes were immediately preserved at -80°C until further processing. Total RNA was extracted from 500 μl of tissue slurry using the E.Z.N.A.® DNA/RNA Isolation Kit (Omega Bio-Tek) and then stored at -80°C until further processing. Residual DNA contamination was removed from RNA isolates using the RQ1 RNase-Free DNase (Promega). Ribosomal RNA was removed using equal parts ‘plant leaf’, ‘human/mouse’ and ‘bacteria’ Ribo-Zero kits (Illumina). RNA quality and concentration were verified by BioAnalyzer (Agilent Technologies, Santa Clara, CA) and quantitative PCR, respectively. cDNA library prep and sequencing was performed at Oregon State University’s Center for Quantitative Life Sciences (CQLS) Core Laboratories with the HiSeq 3000 platform. Three biological replicates for each treatment were sequenced (n=9).&nbsp;<br />
<br />
Instruments:</p>
<p>Mote Marine Lab flow-through seawater raceways and 4.7L tanks: held corals during experiment&nbsp;<br />
boiler and chiller: controlled aquarium temperature<br />
Sterile bone cutters: used to collect coral tissue from each fragment<br />
-80°C Freezer: used to keep samples at a low temp prior to processing<br />
BioAnalyzer (Agilent Technologies, Santa Clara, CA): used to verify RNA quality and concentration<br />
Oregon State University’s Center for Quantitative Life Sciences (CQLS) Core Laboratories with the HiSeq 3000 platform: used for sample sequencing<br />
<br />
Organism identifiers (ScientificName, NCBI Taxonomy ID, Life Science Identifier (LSID):<br />
Acropora cervicornis, NCBI:txid6130,&nbsp;urn:lsid:marinespecies.org:taxname:206989<br />
'Candidatus' Aquarickettsia rohweri, NCBI:txid2602574, N/A</p>
Specified by the Principal Investigator(s)
<p>This section describes how the related sequence data&nbsp; (raw data deposited at NCBI) were processed and analyzed for the results publication Speare et al. (2023).<br />
<br />
Quality scores were calculated for each sequence using FastQC and MultiQC; low-quality scores (average score &lt;20 across 5bp) were removed. Adapters were trimmed using bbduck (BBTools User Guide); successful trimming was confirmed using FastQC/MultiQC. Forward and reverse reads were then interleaved using reformat (BBTools User Guide), mapped to the ‘Ca.’ A. rohweri genome using BowTie2, and counted using HTSeq-count. The limit of detection for each gene was one read per gene. The vegan package in R was used to perform principal coordinates analysis (PCoA) using the Bray-Curtis dissimilarity index, PerMANOVA using the Adonis function, and beta-diversity using the permutest.betadisper function. Differential expression analysis was performed through DeSeq2. Data were graphed in Graphpad Prism and edited for publication using Inkscape 1.0.</p>
Specified by the Principal Investigator(s)
* Sheet 1 of submitted file "NCBI_data_A_rohweri_transcriptomes_2024.xlsx" was imported into the BCO-DMO data system for this dataset. Metadata lines above the data table were incorporated as additional data columns.
* Data were then revised by the original data submitter to add treatment information to the data table. The revised file 928636_v1_ca-aquarickettsia-rohweri-transcriptomes_withTreatment.csv was imported into the BCO-DMO data system. This table will appear as Data File: "928636_v1_ca-aquarickettsia-rohweri-transcriptomes.csv" on this dataset page.
* Additional columns added from NCBI Biosample information for organism and host.
* Additional collection information columns added from metadata provided in email correspondence (collection year and month range description).
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
* Coordinates for coral nursery on Looe Key were added to metadata from information provided in email correspondence.
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 HiSeq 3000 platform
Illumina HiSeq 3000 platform
PI Supplied Instrument Name: Illumina HiSeq 3000 platform PI Supplied Instrument Description:Oregon State University’s Center for Quantitative Life Sciences (CQLS) Core Laboratories with the HiSeq 3000 platform: used for sample sequencing 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.
BioAnalyzer (Agilent Technologies, Santa Clara, CA)
BioAnalyzer (Agilent Technologies, Santa Clara, CA)
PI Supplied Instrument Name: BioAnalyzer (Agilent Technologies, Santa Clara, CA) PI Supplied Instrument Description:Used to verify RNA quality and concentration Instrument Name: Bioanalyzer Instrument Short Name:Bioanalyzer Instrument Description: A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.