http://lod.bco-dmo.org/id/dataset/935908
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
2024-08-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial communities and relative abundances of the pathogen Vibrio coralliilyticus in feces of coral reef fish collected on the north shore of Mo’orea, French Polynesia, Oct 2020
2024-11-13
publication
2024-11-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-11-20
publication
https://doi.org/10.26008/1912/bco-dmo.935908.1
Adrienne M.S. Correa
Rice University
principalInvestigator
Carsten G.B. Grupstra
Rice 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: Correa, A. M., Grupstra, C. (2024) Bacterial communities and relative abundances of the pathogen Vibrio coralliilyticus in feces of coral reef fish collected on the north shore of Mo’orea, French Polynesia, Oct 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-11-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.935908.1 [access date]
Bacterial communities and relative abundances of the pathogen Vibrio coralliilyticus in feces of coral reef fish Dataset Description: Methods and Sampling: <p>All collections were conducted in October 2020 from the back reef (1-2 m depth) and fore reef (5-10 m depth) in Moorea, between LTER sites 1 and 2 of the Moorea Coral Reef (MCR) Long Term Ecological Research (LTER) site. Obligate corallivores were defined as fish that eat corals nearly exclusively (&gt;90% of stomach content or number of bites; Harmelin-Vivien and Bouchon-Navaro, 1983; Rotjan and Lewis, 2008), and facultative corallivores were defined as fish that were observed to feed on coral for a minor to major part of their diet, while also feeding on algae or other invertebrates (~5-80% of bites from corals; Harmelin-Vivien and Bouchon-Navaro, 1983; Rotjan and Lewis, 2008; Viviani et al., 2019; Ezzat et al., 2020). The selected species included four obligate corallivore species (butterflyfishes <em>Chaetodon ornatissimus</em>, "CHOR"; <em>Chaetodon lunulatus</em>, “CHLU”; <em>Chaetodon reticulatus</em>, “CHRE”; and the filefish <em>Amanses scopas</em>, “AMSC”), three facultative corallivore species (butterflyfishes <em>Chaetodon citrinellus</em>, “CHCI”; and <em>Chaetodon pelewensis</em>, “CHPE”; and the parrotfish <em>Chlorurus spilurus</em>, “CHSP”), and three grazer/detritivore species (surgeonfishes <em>Ctenochaetus flavicauda</em>, “CTFL”; <em>Ctenochaetus striatus</em>, "CTST"; and <em>Zebrasoma scopas</em>, “ZESC”). Coral and algal samples were collected from locally abundant coral and algae genera (Pratchett, 2014; Burkepile et al., 2020), including the corals <em>Acropora hyacinthus</em> (“ACR”), <em>Pocillopora</em> species complex (“POC”, Gélin et al., 2017; Johnston et al., 2018), and <em>Porites lobata</em> species complex (“POR”, Forsman et al., 2009; Forsman et al., 2015); and mixed communities of turf algae (“Turf”) as well as macroalgae in the general <em>Asparagopsis </em>(“Asp”), <em>Dictyota</em> (“Dict”), <em>Lobophora</em> (“Lob”), <em>Sargassum</em>(“Sarg”), and <em>Turbinaria</em> sp. (“Turb”). Sediment (“SED”; 250 ml) and water (“WAT”; 1.9 L) were collected concomitantly with fish and environmental samples using sterilized containers. Following collection, all samples (fish, coral, algae, sediments and water) were immediately transported on ice to the lab, where they were processed using sterile methods as described in Grupstra et al. (2021) and preserved in DNA/RNA Shield (Zymo Research, CA).</p>
<p>&nbsp;</p>
<p><strong>Sequencing and analysis of 16S rRNA gene amplicons from&nbsp;<em>in situ </em>samples</strong></p>
<p>DNA was extracted from all samples using the ZymoBIOMICS DNA/RNA Miniprep kit (Zymo Research, CA) according to the manufacturer’s instructions, but with a 1hr proteinase K incubation (35°C) before the lysis buffer step. Library preparation and sequencing was conducted at the Genomics Core Lab at the Institute of Arctic Biology of the University of Alaska Fairbanks. All samples were sequenced using the 16S rRNA gene V4 primers 515f (GTGYCAGCMGCCGCGGTAA) and 806rB (GGACTACNVGGGTWTCTAAT) on Illumina MiSeq using v3 2x300bp chemistry (Apprill et al., 2015; Parada et al., 2016; Walters et al., 2016). Mock communities (HM-782D, BEI Resources, VA), extraction negatives, and plate negatives were included to facilitate the identification and removal of potential contaminants <em>in silico</em> (Davis et al., 2018).</p>
<p>&nbsp;</p>
<p><strong>Quantitative PCR of&nbsp;<em>Vibrio coralliilyticus</em>&nbsp;genes in fish feces</strong></p>
<p>Quantitative PCR (qPCR) was conducted using vcpARTF and vcpARTR qPCR primers developed for the bacterial coral pathogen <em>Vibrio coralliilyticus</em> (Wilson et al., 2013) and results were standardized using primers for general bacteria 967F and 1046R (Sogin et al., 2006; Chen et al., 2011; Shiu et al., 2020). Standard curves (for <em>V. coralliilyticus</em> and general bacteria) were made from a <em>Vibrio coralliilyticus</em>culture (AS008) isolated from corals collected in the Flower Garden Banks National Marine Sanctuary (northwest Gulf of Mexico). Sequencing of the full-length 16S gene region of bacterial DNA with primers 8F and 1513R resulted in 97.5% percent identity with <em>V. coralliilyticus</em> strain U2 (accession MK999891.1) with 100% query cover. The primers vcpARTR and vcpARTF were used to amplify metalloprotease genes and the amplicon was then cleaned using a genejet PCR purification kit (Thermo Fisher, MA); resultant DNA concentrations were acquired using Qubit (Thermo Fisher, MA). A standard curve was made using serial dilutions from 109 to 100 gene copies per µl template; the standard curve for <em>V. coralliiyticus</em> primers vcpARTR and vcpARTF had an efficiency of 106.2%; the standard curve for general bacteria primers 967F and 1046R had an efficiency of 92.3%. Sanger sequencing of gene fragments amplified using vcpARTF and vcpARTR primers from DNA extracted from <em>C. striatus</em> feces resulted in a top hit against a <em>V. coralliilyticus</em> strain P4 metalloprotease gene (accession JQ345042.1) with an e-value of 3x10-12 (query cover 58%, percent identity 85%).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2145472 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2145472
completed
Adrienne M.S. Correa
Rice University
amsc@berkeley.edu
pointOfContact
Carsten G.B. Grupstra
Rice University
777 Glades Road
Boca Raton
FL
33431
USA
cgrupstra@fau.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_name
SRA
BioSample
organism
strain
isolation_source
collection_date
geo_loc_name
depth
env_broad_scale
host_description
host_tissue_sampled
host_diet
host_feces_dCT
host_AphiaID
host_ScientificName
host_LSID
Illumina MiSeq
Qubit (Thermo Fisher, MA)
theme
None, User defined
sample identification
NCBI SRA Sample accession (SRS)
NCBI BioSample accession
sample description
site description
date
region
depth range
count
taxon_code
taxon
Life Science Identifier (LSID)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Fluorometer
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: Testing the effects of predator-derived feces on host symbiont acquisition and health
https://osprey.bco-dmo.org/project/868967
CAREER: Testing the effects of predator-derived feces on host symbiont acquisition and health
<p><em>NSF Award Abstract:</em></p>
<p>Climate change and local-scale anthropogenic stressors are degrading coral reefs across the globe. When conditions become too stressful on reefs, corals can lose beneficial microbial symbionts (e.g., dinoflagellates in the family Symbiodiniaceae) that live in their tissues via a process called ?bleaching?. Although Symbiodiniaceae play key roles in the health of coral colonies, we know little about the processes that make symbionts available in the environment to prospective host corals. This research tests the extent to which the feces of coral-eating fish, which contain live Symbiodiniaceae, facilitate symbiont acquisition by corals in their early life stages. It will generate seminal knowledge on how corallivore feces impact coral symbioses and health, and will assess the ecological importance of corallivorous fishes as drivers of coral symbiont assemblages. This research also test the extent to which corallivore feces are a source of food and nutrients that impact coral health; this has particular relevance to the survival and recovery of bleached adult corals. This research can ultimately inform intervention strategies to support reef resilience and mitigate reef degradation. Results from this project will be communicated widely in scientific arenas, in undergraduate education programs, and to the public via multimedia content and outreach. The Houston Independent School District (HISD, Houston, TX) is the nation?s 7th largest public school system. This work will also support economically disadvantaged and first-generation undergraduate students in pursuing STEM majors and careers through multi-year research experiences.</p>
<p>Symbioses between foundation species (e.g., corals, sponges, trees) and microbiota (e.g., microeukaryotes, bacteria) underpin the biodiversity, productivity, and stability of ecosystems. Consumers, such as predators and herbivores, shape communities of these foundation species through trophic interactions. For instance, grazers contribute to the maintenance of coral dominance on reefs via consumption of macroalgal competitors. However, the indirect effects of other consumers on foundation species are rarely examined. Few studies have tested how consumers affect microbiota assembly in corals, even though coral symbionts (e.g., dinoflagellates in the family Symbiodiniaceae) play key roles in reef function and persistence. Corallivorous (coral-eating) fishes were recently demonstrated to egest large quantities of live Symbiodiniaceae cells as they swim across reefs. This research is testing the hypothesis that corallivore feces promote coral dominance on reefs by supporting coral acquisition of key symbionts and nutrients. The following research objectives will be accomplished: (1) to quantify the contribution of corallivorous fish feces to coral symbiont acquisition; and (2) to test the extent to which corallivorous fish feces influence coral health and recovery from thermal stress. Reefs are being degraded globally due to climate-change induced bleaching and associated mortality. This project is teasing apart the extent to which nutrients and/or live symbionts associated with corallivore feces contribute to the resilience of bleached corals under ambient and heat stress conditions. The research is tightly integrated with two education objectives: (1) to organize a Research Experience for Teachers (RET) program in which rigorous learning modules that high school teachers can incorporate into their Environmental Systems course offerings are developed and tested; and (2) to provide undergraduate students with a multi-year research experience through a partnership with the Rice Emerging Scholars Program (RESP).</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>
Fish transmit microbes
largerWorkCitation
project
eng; USA
biota
oceans
-149.849444
-149.827222
-17.483056
-17.474444
2020-10-01
2020-10-31
0
BCO-DMO catalogue of parameters from Bacterial communities and relative abundances of the pathogen Vibrio coralliilyticus in feces of coral reef fish collected on the north shore of Mo’orea, French Polynesia, Oct 2020
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/938719.rdf
Name: sample_name
Units: unitless
Description: <p>Biological sample name, contains year ("20"), species abbreviation, and sample number; abbreviations represent species or medium from which sample was derived; Obligate corallivores: Chaetodon ornatissimus, "CHOR"; Chaetodon lunulatus, “CHLU”; Chaetodon reticulatus, “CHRE”; Amanses scopas, “AMSC”. Facultative corallivores: Chaetodon citrinellus, “CHCI”; Chaetodon pelewensis, “CHPE”; Chlorurus spilurus, “CHSP”. Grazer/detritivores: Ctenochaetus flavicauda, “CTFL”; Ctenochaetus striatus, "CTST"; Zebrasoma scopas, “ZESC”. Corals: Acropora hyacinthus “ACR”; Pocillopora species complex, “POC”; Porites lobata species complex, “POR”. Algae: mixed communities of turf algae, “Turf”; Asparagopsis, “Asp”; Dictyota, “Dict”; Lobophora, “Lob”; Sargassum, “Sarg”; Turbinaria, “Turb". Environmental: Sediment, “SED”' water, “WAT”</p>
http://lod.bco-dmo.org/id/dataset-parameter/938720.rdf
Name: SRA
Units: unitless
Description: <p>NCBI SRA sample accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/938721.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI Biosample accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/938722.rdf
Name: organism
Units: unitless
Description: <p>Organism type</p>
http://lod.bco-dmo.org/id/dataset-parameter/938723.rdf
Name: strain
Units: unitless
Description: <p>Type of strains in community; mixed community, mock community</p>
http://lod.bco-dmo.org/id/dataset-parameter/938724.rdf
Name: isolation_source
Units: unitless
Description: <p>General description of isolation location type</p>
http://lod.bco-dmo.org/id/dataset-parameter/938727.rdf
Name: collection_date
Units: unitless
Description: <p>Year and month of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/938728.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Geographic location of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/938729.rdf
Name: depth
Units: meters (m)
Description: <p>Sampling depth range</p>
http://lod.bco-dmo.org/id/dataset-parameter/938730.rdf
Name: env_broad_scale
Units: unitless
Description: <p>Broad-scale environmental context</p>
http://lod.bco-dmo.org/id/dataset-parameter/938732.rdf
Name: host_description
Units: unitless
Description: <p>Host organism or medium description; water, sediment, coral species, fish species</p>
http://lod.bco-dmo.org/id/dataset-parameter/938733.rdf
Name: host_tissue_sampled
Units: unitless
Description: <p>Sample type; feces, coral, algae, water, or sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/938734.rdf
Name: host_diet
Units: unitless
Description: <p>Diet of the host organism; Obligate corallivore, Facultative corallivore, or Grazer/detritivore</p>
http://lod.bco-dmo.org/id/dataset-parameter/938735.rdf
Name: host_feces_dCT
Units: cycles
Description: <p>Delta cycle threshold; calculated by subtracting the cycle threshold at which the general bacteria assay amplified from the cycle threshold at which the Vibrio coralliilyticus assay amplified</p>
http://lod.bco-dmo.org/id/dataset-parameter/938736.rdf
Name: host_AphiaID
Units: unitless
Description: <p>ID in the World Register of Marine Species that pairs to the scientificName</p>
http://lod.bco-dmo.org/id/dataset-parameter/938737.rdf
Name: host_ScientificName
Units: unitless
Description: <p>Scientific name matched to the World Register of Marine Species</p>
http://lod.bco-dmo.org/id/dataset-parameter/938738.rdf
Name: host_LSID
Units: unitless
Description: <p>Identifier for the scientific name in lowest level taxonomic rank matched to the World Register of Marine Species</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
41523
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/96874fcf-5b0b-4db7-b18c-6202a64e1569/content
download
https://doi.org/10.26008/1912/bco-dmo.935908.1
download
onLine
dataset
<p>All collections were conducted in October 2020 from the back reef (1-2 m depth) and fore reef (5-10 m depth) in Moorea, between LTER sites 1 and 2 of the Moorea Coral Reef (MCR) Long Term Ecological Research (LTER) site. Obligate corallivores were defined as fish that eat corals nearly exclusively (&gt;90% of stomach content or number of bites; Harmelin-Vivien and Bouchon-Navaro, 1983; Rotjan and Lewis, 2008), and facultative corallivores were defined as fish that were observed to feed on coral for a minor to major part of their diet, while also feeding on algae or other invertebrates (~5-80% of bites from corals; Harmelin-Vivien and Bouchon-Navaro, 1983; Rotjan and Lewis, 2008; Viviani et al., 2019; Ezzat et al., 2020). The selected species included four obligate corallivore species (butterflyfishes <em>Chaetodon ornatissimus</em>, "CHOR"; <em>Chaetodon lunulatus</em>, “CHLU”; <em>Chaetodon reticulatus</em>, “CHRE”; and the filefish <em>Amanses scopas</em>, “AMSC”), three facultative corallivore species (butterflyfishes <em>Chaetodon citrinellus</em>, “CHCI”; and <em>Chaetodon pelewensis</em>, “CHPE”; and the parrotfish <em>Chlorurus spilurus</em>, “CHSP”), and three grazer/detritivore species (surgeonfishes <em>Ctenochaetus flavicauda</em>, “CTFL”; <em>Ctenochaetus striatus</em>, "CTST"; and <em>Zebrasoma scopas</em>, “ZESC”). Coral and algal samples were collected from locally abundant coral and algae genera (Pratchett, 2014; Burkepile et al., 2020), including the corals <em>Acropora hyacinthus</em> (“ACR”), <em>Pocillopora</em> species complex (“POC”, Gélin et al., 2017; Johnston et al., 2018), and <em>Porites lobata</em> species complex (“POR”, Forsman et al., 2009; Forsman et al., 2015); and mixed communities of turf algae (“Turf”) as well as macroalgae in the general <em>Asparagopsis </em>(“Asp”), <em>Dictyota</em> (“Dict”), <em>Lobophora</em> (“Lob”), <em>Sargassum</em>(“Sarg”), and <em>Turbinaria</em> sp. (“Turb”). Sediment (“SED”; 250 ml) and water (“WAT”; 1.9 L) were collected concomitantly with fish and environmental samples using sterilized containers. Following collection, all samples (fish, coral, algae, sediments and water) were immediately transported on ice to the lab, where they were processed using sterile methods as described in Grupstra et al. (2021) and preserved in DNA/RNA Shield (Zymo Research, CA).</p>
<p>&nbsp;</p>
<p><strong>Sequencing and analysis of 16S rRNA gene amplicons from&nbsp;<em>in situ </em>samples</strong></p>
<p>DNA was extracted from all samples using the ZymoBIOMICS DNA/RNA Miniprep kit (Zymo Research, CA) according to the manufacturer’s instructions, but with a 1hr proteinase K incubation (35°C) before the lysis buffer step. Library preparation and sequencing was conducted at the Genomics Core Lab at the Institute of Arctic Biology of the University of Alaska Fairbanks. All samples were sequenced using the 16S rRNA gene V4 primers 515f (GTGYCAGCMGCCGCGGTAA) and 806rB (GGACTACNVGGGTWTCTAAT) on Illumina MiSeq using v3 2x300bp chemistry (Apprill et al., 2015; Parada et al., 2016; Walters et al., 2016). Mock communities (HM-782D, BEI Resources, VA), extraction negatives, and plate negatives were included to facilitate the identification and removal of potential contaminants <em>in silico</em> (Davis et al., 2018).</p>
<p>&nbsp;</p>
<p><strong>Quantitative PCR of&nbsp;<em>Vibrio coralliilyticus</em>&nbsp;genes in fish feces</strong></p>
<p>Quantitative PCR (qPCR) was conducted using vcpARTF and vcpARTR qPCR primers developed for the bacterial coral pathogen <em>Vibrio coralliilyticus</em> (Wilson et al., 2013) and results were standardized using primers for general bacteria 967F and 1046R (Sogin et al., 2006; Chen et al., 2011; Shiu et al., 2020). Standard curves (for <em>V. coralliilyticus</em> and general bacteria) were made from a <em>Vibrio coralliilyticus</em>culture (AS008) isolated from corals collected in the Flower Garden Banks National Marine Sanctuary (northwest Gulf of Mexico). Sequencing of the full-length 16S gene region of bacterial DNA with primers 8F and 1513R resulted in 97.5% percent identity with <em>V. coralliilyticus</em> strain U2 (accession MK999891.1) with 100% query cover. The primers vcpARTR and vcpARTF were used to amplify metalloprotease genes and the amplicon was then cleaned using a genejet PCR purification kit (Thermo Fisher, MA); resultant DNA concentrations were acquired using Qubit (Thermo Fisher, MA). A standard curve was made using serial dilutions from 109 to 100 gene copies per µl template; the standard curve for <em>V. coralliiyticus</em> primers vcpARTR and vcpARTF had an efficiency of 106.2%; the standard curve for general bacteria primers 967F and 1046R had an efficiency of 92.3%. Sanger sequencing of gene fragments amplified using vcpARTF and vcpARTR primers from DNA extracted from <em>C. striatus</em> feces resulted in a top hit against a <em>V. coralliilyticus</em> strain P4 metalloprotease gene (accession JQ345042.1) with an e-value of 3x10-12 (query cover 58%, percent identity 85%).</p>
Specified by the Principal Investigator(s)
<p><strong>Analysis of 16S rRNA gene amplicons</strong></p>
<p>Bacterial 16-S reads were processed in RStudio (version 1.1.456) through the DADA2 pipeline (version 1.11.0, Callahan et al., 2016) and using phyloseq (v1.38). The DADA2 pipeline generated a table of amplicon sequence variants (ASVs), and bacteria taxonomy was assigned using the SILVA rRNA database (version 132, Quast et al., 2012). Non-target (<em>e.g.</em>, mitochondrial, chloroplast) reads and singletons were removed. A total of 865 potential contaminant ASVs were identified and removed with the decontam package (v. 1.10.0) using the prevalence method (Davis et al., 2018). A total of 160 samples with &gt;1,000 reads remained after these initial quality control and filtering steps (excluding negatives and mock communities), with a mean of 15,263 reads per sample. All analyses outlined below were conducted based on this dataset, but additional ASV and sample filtering steps were included for several of the approaches. Raw sequencing data are deposited on the SRA (BioProject PRJNA935035).</p>
<p>&nbsp;</p>
<p><strong>Quantitative PCR of <em>Vibrio coralliilyticus</em> genes in fish feces</strong></p>
<p>Amplification of the <em>V. coralliilyticus</em> target gene at &lt;30 cycles was counted as a positive detection, which roughly corresponded to amplification of the 102 gene copies µl-1 standard (Ct=30.4). Delta cycle threshold (dCT) values were calculated by subtracting the cycle threshold at which the signal from general bacteria primers was detected from the cycle threshold at which <em>V. coralliilyticus</em> was detected. Higher dCT values indicate lower relative abundances of <em>V. coralliilyticus</em>.</p>
Specified by the Principal Investigator(s)
- Imported "qPCR data.CSV", "taxon_identifiers.csv", and "BCODMO_List_SRA.xlsx" into the BCO-DMO system
- Worked with submitter to determine corrections to identifiers, changing "Sample.Name" values in "qPCR data.CSV" from "CTSI1" to "CTST9" and from "ZESC8" (where the "dCT" value was "17.473") to "ZESC9"
- Joined "qPCR data.CSV" and "BCODMO_List_SRA.xlsx" on the sample identifiers by creating a temporary column that removed the "20" from the beginning of "Sample Name", adding all columns from "BCODMO_List_SRA.xlsx" and "dCT" from "qPCR data.CSV"
- Included "diet" field information from "qPCR data.CSV" where the isolated "species" column matched the species indicated in the "Sample Name" of "BCODMO_List_SRA.xlsx"
- Added month of collection to the "*collection_date" column in "BCODMO_List_SRA.xlsx" as it was referenced in the methods section
- Added a lat and lon for all rows to indicate the subject reef's general location by creating the fields "isolation_lat" and "isolation_lon"
- Checked all scientific names referenced in methods section and the methods section of related dataset using World Register of Marine Species (WoRMS) Taxon Match. All scientific names referenced are valid and accepted names as of 2024-09-23. Included the complete list in taxon_identifiers.csv as a supplemental file.
- Included "Identification_in_methods", "matched_AphiaID", "LSID", "AphiaID_accepted", and "ScientificName_accepted" in "taxon_identifiers.csv" supplemental file
- Removed "sp." and spp." from "host" field values in "BCODMO_List_SRA.xlsx"
- Joined "taxon_identifiers.csv" and "BCODMO_List_SRA.xlsx", using "host" field values from "BCODMO_List_SRA.xlsx" and "ScientificName_accepted" from "taxon_identifiers.csv"
- Renamed fields to comply with system requirements by removing special characters and spaces and to indicate which fields specifically applied to the host organism or medium by adding "host_" to the field names
- Saved final file as "935908_v1_bact_vibrio_coralliilyticus_rdna_accessions.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 PI Supplied Instrument Description:DNA was extracted from all samples using the ZymoBIOMICS DNA/RNA Miniprep kit (Zymo Research, CA) according to the manufacturer’s instructions, but with a 1hr proteinase K incubation (35°C) before the lysis buffer step. Library preparation and sequencing was conducted at the Genomics Core Lab at the Institute of Arctic Biology of the University of Alaska Fairbanks. All samples were sequenced using the 16S rRNA gene V4 primers 515f (GTGYCAGCMGCCGCGGTAA) and 806rB (GGACTACNVGGGTWTCTAAT) on Illumina MiSeq using v3 2x300bp chemistry. 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.
Qubit (Thermo Fisher, MA)
Qubit (Thermo Fisher, MA)
PI Supplied Instrument Name: Qubit (Thermo Fisher, MA) PI Supplied Instrument Description:The primers vcpARTR and vcpARTF were used to amplify metalloprotease genes and the amplicon was then cleaned using a genejet PCR purification kit (Thermo Fisher, MA); resultant DNA concentrations were acquired using Qubit (Thermo Fisher, MA). A standard curve was made using serial dilutions from 109 to 100 gene copies per µl template; the standard curve for V. coralliiyticus primers vcpARTR and vcpARTF had an efficiency of 106.2%; the standard curve for general bacteria primers 967F and 1046R had an efficiency of 92.3%. 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/