http://lod.bco-dmo.org/id/dataset/847425
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
2021-04-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sequences from the coral Acropora cervicornis determined before and after bleaching at the Mote Marine Laboratory in August and September 2015
2023-10-27
publication
2023-10-27
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-11-01
publication
https://doi.org/10.26008/1912/bco-dmo.847425.1
Rebecca Vega Thurber
Oregon State University
principalInvestigator
Erinn M. Muller
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., Vega Thurber, R., Muller, E. (2023) Sequences from the coral Acropora cervicornis determined before and after bleaching at the Mote Marine Laboratory in August and September 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-10-27 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.847425.1 [access date]
Acropora cervicornis bleaching sequences Dataset Description: <p>Sequence data can be found in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under accession number SRP267474 with the associated BioProject PRJNA639601. Additional metadata related to the NCBI submission are provided in Supplemental File "MIMARKS.specimen.host-associated.5.0.xlsx".</p> Methods and Sampling: <p>A total of two replicate fragments (ramets) from 16 genotypically distinct host colonies (genets) were collected from the Mote Marine Laboratory in situ coral nursery in August 2015. In September 2015, another set of two ramets from 15 of the same genets of <em>Acropora cervicornis</em> were collected from the Mote Marine Laboratory in situ coral nursery (one genotype, G20, was not available due to high mortality rates). By this time the nursery corals had been experiencing anomalously high water temperatures reaching approximately ~2° Celsius (C) above historical averages, represented by 8 degree heating weeks (DHWs) under NOAA's Coral Reef Watch products (<a href="http://www.coralreefwatch.noaa.gov" target="_blank">http://www.coralreefwatch.noaa.gov</a>). These ramets were the same individuals utilized in Muller et al. (2018) to assess changes in disease susceptibility prior to and after bleaching. Genotypes were delineated in that study via microsatellite genotyping (Baums et al., 2005). When corals appeared healthy (i.e., no visual signs of bleaching) genotype 3 was completely resistant to white band disease, and genotype 7 had only 1 out of 5 replicates succumb to disease after exposure. Genotypes 3 and 7 both were resistant to white band disease even after bleaching. All ramets hosted <em>Symbiodinium fitti</em>, the main species of <em>Symbiodiniaceae</em> found in the Mote <em>A. cervicornis</em> nursery corals (Muller et al. 2018, Parkinson et al., 2018). All corals sampled in September were visibly bleached and showed a significant reduction in photochemical efficiency using Pulse Amplitude Modulator fluorometry (see Muller et al., 2018). Upon returning to the lab, all samples were flash-frozen in liquid nitrogen and stored in at -80°C until processing. A total of two polyps were scraped from each replicate using a sterile razor blade, and total DNA was extracted from polyp tissue using the MoBio Powersoil kit.</p>
<p>The bacterial community dynamics of each sample was analyzed using 16S rRNA Illumina sequencing on the MiSeq platform. 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). A polymerase chain reaction (PCR) was performed using the HotStarTaq Plus Master Mix Kit (Qiagen, USA) under the following conditions: 94°C for 3 minutes, followed by 28 cycles of 94°C for 30 seconds, 53°C for 40 seconds and 72°C for 1 minute, followed by a final elongation step at 72°C for 5 minutes. PCR products were checked on a 2% agarose gel to determine the success of amplification and the relative intensity of bands. Multiple samples were pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples were purified using calibrated Angencourt Ampure XP beads (Beckman Coutler, CA, USA). Then the pooled DNA library was generated using the Illumina TruSeq DNA library preparation protocol. A PCR negative control was included in library preparation but did not produce a viable library. Paired-end sequencing was performed at MR DNA (<a href="http://www.mrdnalab.com" target="_blank">http://www.mrdnalab.com</a>, Shallowater, TX, USA) using a single flow cell on a MiSeq following the manufacturer’s guidelines.</p>
<p><strong>Known problems/issues:</strong><br />
Genotype 20 was not sampled after bleaching due to mortality.</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
asNeeded
Dataset Version: 1
Unknown
bioproject_accession
sample_name
SRA_run_ID
SRA_study_ID
SRA_title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design
filetype
filename
filetype2
filename2
site
collection_date
lat
lon
Host_organism
genotype
bleach_status
Illumina MiSeq
Pulse Amplitude Modulator fluorometry
polymerase chain reaction (PCR)
theme
None, User defined
NCBI BioProject accession
sample identification
NCBI SRA run accession (SRR)
NCBI SRA study accession (SRP)
sample description
sampling_method
instrument
file_name
site
date
latitude
longitude
taxon
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Fluorometer
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.
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
biota
oceans
-81.4005
-81.4005
24.5627
24.5627
2015-08-01
2015-09-30
at Oregon State University and in the Florida Keys at Mote Marine Laboratory
0
BCO-DMO catalogue of parameters from Sequences from the coral Acropora cervicornis determined before and after bleaching at the Mote Marine Laboratory in August and September 2015
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/914159.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/914160.rdf
Name: sample_name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/914161.rdf
Name: SRA_run_ID
Units: unitless
Description: <p>SRA run identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/914162.rdf
Name: SRA_study_ID
Units: unitless
Description: <p>SRA study identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/914163.rdf
Name: SRA_title
Units: unitless
Description: <p>Descriptive title of SRA study</p>
http://lod.bco-dmo.org/id/dataset-parameter/914164.rdf
Name: library_strategy
Units: unitless
Description: <p>Type of library prep ("AMPLICON")</p>
http://lod.bco-dmo.org/id/dataset-parameter/914165.rdf
Name: library_source
Units: unitless
Description: <p>Source of genetic material ("GENOMIC")</p>
http://lod.bco-dmo.org/id/dataset-parameter/914166.rdf
Name: library_selection
Units: unitless
Description: <p>Library selection method ("PCR")</p>
http://lod.bco-dmo.org/id/dataset-parameter/914167.rdf
Name: library_layout
Units: unitless
Description: <p>Library layout ("PAIRED")</p>
http://lod.bco-dmo.org/id/dataset-parameter/914168.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform ("ILLUMINA")</p>
http://lod.bco-dmo.org/id/dataset-parameter/914169.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencing instrument model ("Illumina MiSeq")</p>
http://lod.bco-dmo.org/id/dataset-parameter/914170.rdf
Name: design
Units: unitless
Description: <p>Sequencing design description</p>
http://lod.bco-dmo.org/id/dataset-parameter/914171.rdf
Name: filetype
Units: unitless
Description: <p>Type of file, read 1 ("fastq")</p>
http://lod.bco-dmo.org/id/dataset-parameter/914172.rdf
Name: filename
Units: unitless
Description: <p>Name of file, read 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/914173.rdf
Name: filetype2
Units: unitless
Description: <p>Type of file, read 2 ("fastq")</p>
http://lod.bco-dmo.org/id/dataset-parameter/914174.rdf
Name: filename2
Units: unitless
Description: <p>Name of file, read 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/914175.rdf
Name: site
Units: unitless
Description: <p>Sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/914176.rdf
Name: collection_date
Units: unitless
Description: <p>Date of sampling as year and month (YYYY-MM)</p>
http://lod.bco-dmo.org/id/dataset-parameter/914177.rdf
Name: lat
Units: decimal degrees
Description: <p>Sampling latitude; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/914178.rdf
Name: lon
Units: decimal degrees
Description: <p>Sampling longitude; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/914179.rdf
Name: Host_organism
Units: unitless
Description: <p>Host from which microbiome samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/914180.rdf
Name: genotype
Units: unitless
Description: <p>Microsatellite genotype ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/914181.rdf
Name: bleach_status
Units: unitless
Description: <p>Bleach status. Either Bleached or Apparently Healthy</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
34221
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/080c933f-1bc7-4efc-b584-dad92c1fc640/content
download
https://doi.org/10.26008/1912/bco-dmo.847425.1
download
onLine
dataset
<p>A total of two replicate fragments (ramets) from 16 genotypically distinct host colonies (genets) were collected from the Mote Marine Laboratory in situ coral nursery in August 2015. In September 2015, another set of two ramets from 15 of the same genets of <em>Acropora cervicornis</em> were collected from the Mote Marine Laboratory in situ coral nursery (one genotype, G20, was not available due to high mortality rates). By this time the nursery corals had been experiencing anomalously high water temperatures reaching approximately ~2° Celsius (C) above historical averages, represented by 8 degree heating weeks (DHWs) under NOAA's Coral Reef Watch products (<a href="http://www.coralreefwatch.noaa.gov" target="_blank">http://www.coralreefwatch.noaa.gov</a>). These ramets were the same individuals utilized in Muller et al. (2018) to assess changes in disease susceptibility prior to and after bleaching. Genotypes were delineated in that study via microsatellite genotyping (Baums et al., 2005). When corals appeared healthy (i.e., no visual signs of bleaching) genotype 3 was completely resistant to white band disease, and genotype 7 had only 1 out of 5 replicates succumb to disease after exposure. Genotypes 3 and 7 both were resistant to white band disease even after bleaching. All ramets hosted <em>Symbiodinium fitti</em>, the main species of <em>Symbiodiniaceae</em> found in the Mote <em>A. cervicornis</em> nursery corals (Muller et al. 2018, Parkinson et al., 2018). All corals sampled in September were visibly bleached and showed a significant reduction in photochemical efficiency using Pulse Amplitude Modulator fluorometry (see Muller et al., 2018). Upon returning to the lab, all samples were flash-frozen in liquid nitrogen and stored in at -80°C until processing. A total of two polyps were scraped from each replicate using a sterile razor blade, and total DNA was extracted from polyp tissue using the MoBio Powersoil kit.</p>
<p>The bacterial community dynamics of each sample was analyzed using 16S rRNA Illumina sequencing on the MiSeq platform. 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). A polymerase chain reaction (PCR) was performed using the HotStarTaq Plus Master Mix Kit (Qiagen, USA) under the following conditions: 94°C for 3 minutes, followed by 28 cycles of 94°C for 30 seconds, 53°C for 40 seconds and 72°C for 1 minute, followed by a final elongation step at 72°C for 5 minutes. PCR products were checked on a 2% agarose gel to determine the success of amplification and the relative intensity of bands. Multiple samples were pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples were purified using calibrated Angencourt Ampure XP beads (Beckman Coutler, CA, USA). Then the pooled DNA library was generated using the Illumina TruSeq DNA library preparation protocol. A PCR negative control was included in library preparation but did not produce a viable library. Paired-end sequencing was performed at MR DNA (<a href="http://www.mrdnalab.com" target="_blank">http://www.mrdnalab.com</a>, Shallowater, TX, USA) using a single flow cell on a MiSeq following the manufacturer’s guidelines.</p>
<p><strong>Known problems/issues:</strong><br />
Genotype 20 was not sampled after bleaching due to mortality.</p>
Specified by the Principal Investigator(s)
<p>Demultiplexing and barcode removal was performed using sabre (v1.0) (Copyright © Nikhil Joshi, UC Davis), during which a total of 7,499,952 reads with no barcode match were discarded from the initial pool of 15,577,446 reads. A total of 8,077,494 reads across 62 samples were subsequently processed using DADA2 (v1.16) (Callahan et al., 2016) in R (v1.1.383) (R Development Core Team, 2008). DADA2 identifies unique 16S rRNA sequences at single-nucleotide resolution (amplicon sequence variants, ASVs) using a core denoising algorithm that models substitution errors in Illumina reads. Based on quality plots, forward and reverse reads were truncated at their 3′ end at 260 and 210 base pairs, respectively. Sequences were truncated at the first position having a quality score less than or equal to 10, and reads with a total expected error of &gt;1 or with the presence of Ns were discarded, resulting in a total of 6,178,780 reads. Amplicon sequence variants (ASVs) were inferred from unique reads and paired-end reads were subsequently merged to equal 3,089,390 reads. ASVs that did not match a target length of 292 ± 2 (77 ASVs) were discarded. Two-parent chimeras (bimeras) were removed and taxonomy was assigned at 100% sequence identity using the Silva reference database (v132) in order to preserve the high resolution of ASV data (Quast et al., 2012). The Silva taxonomic classifications for the genera MD3-55 and HIMB11 were changed to Ca. Aquarickettsia and Roseobacter, respectively, in accordance with current literature identifications (Klinges et al., 2019, Durham et al., 2014). The resulting ASV table contained 2,979 unique ASVs across 62 samples and was imported into phyloseq (v1.30.0) (McMurdie &amp; Holmes, 2013). A total of 102 ASVs were then removed from the dataset that were annotated as mitochondrial or chloroplast sequences, corresponding to 613 and 25,100 reads, respectively. Although there were no singletons in the dataset, 2,052 unique ASVs were present in only one sample each. Next, ASVs with a total count across the dataset in the bottom first-quartile (count = 29) were removed resulting in a total of 2,618,743 total reads, 2,133 unique ASVs, and a median sample depth of 36,970 reads.</p>
Specified by the Principal Investigator(s)
- Imported original file named "BCO-DMO Data_acropora_cervicornis_bleaching.xlsx" into the BCO-DMO system.
- Added a column for "collection_date" in YYYY-MM format.
- Saved the final file as "847425_v1_bleaching_sequences.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
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq 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.
Pulse Amplitude Modulator fluorometry
Pulse Amplitude Modulator fluorometry
PI Supplied Instrument Name: Pulse Amplitude Modulator fluorometry Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
polymerase chain reaction (PCR)
polymerase chain reaction (PCR)
PI Supplied Instrument Name: polymerase chain reaction (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)