http://lod.bco-dmo.org/id/dataset/553168
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
2015-03-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Illumina sequenced 16S rRNA genes amplified from the different life stages of 2 corals in Kaneohe Bay, Oahu, Hawaii during 2010 (MiCoDe project)
2015-03-04
publication
2015-03-04
revision
BCO-DMO Linked Data URI
2015-03-04
creation
http://lod.bco-dmo.org/id/dataset/553168
Michael S. Rappé
University of Hawaiʻi at Mānoa
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: Rappé, M. S. (2015) Illumina sequenced 16S rRNA genes amplified from the different life stages of 2 corals in Kaneohe Bay, Oahu, Hawaii during 2010 (MiCoDe project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-03-04) Version Date 2015-03-04 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/553168 [access date]
Illumina sequenced 16S rRNA genes amplified from different life stages of 2 corals Dataset Description: <p>Illumina sequenced 16S rRNA genes amplified from different life stages of the corals&nbsp;<em>Fungia scutaria</em>&nbsp;and&nbsp;<em>Montipora capitata</em>&nbsp;from central Kaneohe Bay off of the island of Oahu, Hawaii.</p> Methods and Sampling: <p><strong><em>Fungia scutaria</em>&nbsp;sample collection</strong></p>
<p>Adult specimens of the solitary coral&nbsp;<em>F. scutaria</em>&nbsp;were collected from Kaneohe Bay on the northeastern shore of Oahu, Hawaii in the Pacific Ocean in June 2010 and kept in open-system tanks (sea tables) at the Hawaii Institute of Marine Biology in anticipation of spawning events. Following spawning, eggs and sperm were collected for fertilization in Petri dishes, and replicate batches of larvae were raised in 0.1 µm-filtered (sterile), 1.6 µm-filtered (excludes&nbsp;<em>Symbiodinium</em>&nbsp;and zooplankton), 20 µm-filtered (excludes zooplankton) or raw seawater. Samples from each life history stage (eggs, larvae, juveniles, and adults) were frozen for DNA analysis in DNA lysis buffer. Eggs and embryos were rinsed in sterilized seawater upon sampling. Each adult sample consists of three small pieces of an individual coral combined in one tube. Ca. 1 L of seawater was sampled from the sea tables one hour prior to the final spawning event, filtered, and frozen for DNA analysis in DNA lysis buffer. 50 mL of the culture water was sampled from the Petri dish treatments (originally 0.1 µm-filtered, 1.6 µm-filtered, or 20 µm-filtered seawater) after approximately 72 hours of exposure to the developing coral larvae during the final experiment.</p>
<p><strong><em>Montipora capitata</em>&nbsp;sample collection</strong></p>
<p>Fragments of adult specimens of the colonial coral&nbsp;<em>M. capitata</em>&nbsp;were collected from Kaneohe Bay in June 2010 and July 2011 and kept in sea tables at HIMB in anticipation of spawning events. Following spawning, egg-sperm bundles were collected from the sea tables for fertilization in Petri dishes, and replicate batches of larvae were raised in 0.1 µm-filtered, 1.6 µm-filtered, or 20 µm-filtered seawater. Samples from each life history stage (egg-sperm bundles, larvae, juveniles, and adults) were frozen for DNA analysis in DNA lysis buffer. Egg-sperm bundles were rinsed in TFF sterilized seawater upon sampling. Each adult sample consists of three small pieces of an individual coral combined in one tube. Ca. 1 L of seawater was sampled from the sea tables approximately one hour prior to the final spawning event, filtered, and frozen for DNA analysis in DNA lysis buffer. 35 mL of the culture water was sampled from the Petri dish treatments (originally 0.1 µm-filtered, 1.6 µm-filtered, or 20 µm-filtered seawater) after approximately 72 hours of exposure to the developing coral larvae during the final experiment in 2010, filtered, and frozen for DNA analysis in DNA lysis buffer. Additionally, throughout summer 2010, field-spawned egg-sperm bundles and field-fertilized larvae were collected from Kaneohe Bay and raised under the same treatments (0.1 µm-filtered, 1.6 µm-filtered, 20 µm-filtered, or raw seawater), and sampled in the same manner and at the same life-history stages (egg-sperm bundles, larvae, juveniles, and adults) as the corals spawned in sea tables. Ca. 1 L of seawater was sampled from the Kaneohe Bay lagoon 1 hour prior to the August 2010 field-spawning event and 1 hour after the June and July 2010 field-spawning events, filtered, and filters were frozen for DNA analysis in DNA lysis buffer.</p>
<p><strong>DNA extraction and Illumina amplicon sequencing of bacterial SSU rRNA genes&nbsp;</strong></p>
<p>Nucleic acids were extracted from&nbsp;<em>F. scutaria</em>&nbsp;corals and filters using the NucleoSpin Soil Kit (Macherey-Nagel, Duren, Germany) following the manufacturer’s protocol, modified as follows: lysis buffer SL1 and Enhancer SX were used, lysis time was increased to 20 min and two subsequent elution steps were performed with 50 µl fresh elution buffer each. DNA quality and yield were checked by agarose gel electrophoresis.</p>
<p>Nucleic acids were extracted from&nbsp;<em>M. capitata</em>&nbsp;samples and filters using the PowerSoil DNA Isolation Kit (MO BIO, Carlsbad, CA) following the manufacturer’s protocol, modified as follows: initial physical disruption time (via vortex) was increased to 30 min, and two subsequent elution steps were performed with 100 µl fresh DNA-Free PCR Grade water each. DNA quality and yield were checked by agarose gel electrophoresis.</p>
<p>The V4 region of the 16S rRNA gene was amplified with the primer pair F515/R806, which include Illumina flowcell adapter sequences and a sample-specific barcode on the reverse primer. The MasterTaq Kit (5 PRIME, Hamburg, Germany) was used for all PCR reactions. Amplification was performed using a touchdown protocol as in as follows: initial denaturation at 95°C for 3 min, and 30 cycles at 95°C for 30 sec, 65°C for 1 min (decreasing by 0.5°C per cycle), and 72°C for 2 min. After these 30 cycles, a further 5 – 7 cycles were performed using an annealing temperature of 50°C, and concluding with a final extension at 72°C for 20 min. Resulting PCR amplicons were quantified using the PicoGreen dsDNA assay (Invitrogen, Carlsbad, CA), pooled at equimolar concentrations and subsequently cleaned using the UltraClean PCR Clean-Up Kit (MO BIO Laboratories, Carlsbad, CA). Sequencing of the&nbsp;<em>F. scutaria</em>&nbsp;PCR products was performed on an Illumina MiSeq at the University of Colorado BioFrontiers Institute (Boulder, CO), while sequencing of the&nbsp;<em>M. capitata</em>&nbsp;PCR products was performed on an Illumina MiSeq at the University of Hawaii HIMB Genetics Core Facility (Kaneohe, HI).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0928806 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0928806
completed
Michael S. Rappé
University of Hawaiʻi at Mānoa
808-372-2394
University of Hawaii at Manoa - Hawaii Institute of Marine Biology 46-007 Lilipuna Rd
Kaneohe
HI
96744
USA
rappe@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 2015-03-04
Unknown
species
sample_type
treatment
sample_id
date_coll
lat
lon
BioSample
SRA_accession
Thermal Cycler
theme
None, User defined
species scientific name (binomial)
sample type
treatment
sample identification
date
latitude
longitude
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Rappe_2010
service
Deployment Activity
Kaneohe Bay, Oahu, Hawaii
place
Locations
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.
The Development of Microbial Associations in Major Reef Building Corals of the Pacific Ocean
http://www.soest.hawaii.edu/oceanography/faculty/rappe/RappeLab/CAM.html
The Development of Microbial Associations in Major Reef Building Corals of the Pacific Ocean
<p><em>Description from NSF award abstract:</em><br />
Fundamental to the study of coral-microbial associations is an understanding of when and how the relationships are established, and their specificity. Recently, the investigators provided the first evidence of a specific association between an early life history stage of a coral (<em>Pocillopora meandrina</em>) and a particular group of bacteria (Jannaschia lineage of the Roseobacter clade of Alphaproteobacteria). They will be expanding this work by examining the onset of microbial associations in key reef building corals from Hawaii in the North Pacific Ocean and Moorea, French Polynesia, in the South Pacific Ocean. Understanding the onset, specificity and function of the microbial community associated with these coral species is necessary to understand and predict the coral holobiont response to a changing environment.</p>
<p>The main objectives of this proposal are to:<br />
1. Use cultivation independent techniques to identify and quantify microorganisms associated with several major reef building corals of Hawaii in the North Pacific Ocean that represent a variety of reproductive strategies (brooding and broadcast spawning) and differing modes of zooxanthellae symbiont transmission (vertical vs. horizontal), throughout the reproductive cycle, early developmental stages, and post-settlement stages of each.<br />
2. Collect and analyze similar samples from the same (or similar) species of coral found in the South Pacific Ocean in Moorea, French Polynesia, in order to assess whether the associations documented in objective 1 are localized to Hawaii, or broadly distributed across the Pacific and likely to represent common features of coral development.<br />
3. Use fluorescence in situ hybridization to enumerate cells of the Jannaschia lineage of the Roseobacter clade throughout the development cycle of P. meandrina collected in Hawaii. The PIs will expand this objective to include other coral species, target bacteria, and/or geographic location as they identify additional associations.<br />
4. Isolate microorganisms prevalent in cultivation-independent surveys of P. meandrina-associated microbial communities (e.g. Jannaschia sp.) by the application of novel culturing techniques, in order to develop model systems for the investigation of coral-microbe interactions.</p>
<p>Coral reefs are in decline as a result of increasing environmental stress due to anthropogenic activity, and there is now considerable evidence indicating that they are under threat from the effects of rising sea surface temperature and ocean acidification. Microorganisms associated with corals are thought to play a variety of potentially important roles in maintaining the health and resiliency of the coral host, and advances in methodology primarily driven by developments in the field of molecular biology are facilitating growing insight into this association. Much of coral-microbial research is focused on the contribution of microorganisms to disease and bleaching, and is focused almost exclusively on adult coral colonies. This study will provide unique information on the manner in which microorganisms interact with healthy corals throughout their developmental cycle, the specificity of these relationships, how they are initiated, and their distribution and frequency in nature.</p>
MiCoDe
largerWorkCitation
project
eng; USA
biota
oceans
Kaneohe Bay, Oahu, Hawaii
2015-03-04
Kaneohe Bay, HI, USA; and Cook’s Bay, Moorea, French Polynesia
0
BCO-DMO catalogue of parameters from Illumina sequenced 16S rRNA genes amplified from the different life stages of 2 corals in Kaneohe Bay, Oahu, Hawaii during 2010 (MiCoDe 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
http://lod.bco-dmo.org/id/dataset-parameter/553189.rdf
Name: species
Units: unitless
Description: <p>species of coral</p>
http://lod.bco-dmo.org/id/dataset-parameter/553190.rdf
Name: sample_type
Units: unitless
Description: <p>developmental stage</p>
http://lod.bco-dmo.org/id/dataset-parameter/553191.rdf
Name: treatment
Units: unitless
Description: <p>conditions including filtration size of seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/553192.rdf
Name: sample_id
Units: unitless
Description: <p>sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/553193.rdf
Name: date_coll
Units: yyyy-mm-dd
Description: <p>date collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/553194.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/553195.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/553196.rdf
Name: BioSample
Units: unitless
Description: <p>GenBank BioSample id</p>
http://lod.bco-dmo.org/id/dataset-parameter/553197.rdf
Name: SRA_accession
Units: unitless
Description: <p>GenBank SRA_accession id</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
88708
https://datadocs.bco-dmo.org/file/P66Gw04s4Jw1J6/illumina_2015_sort.csv
illumina_2015_sort.csv
Primary data file for dataset ID 553168
download
https://osprey.bco-dmo.org/dataset/553168/data/download
download
onLine
dataset
<p><strong><em>Fungia scutaria</em>&nbsp;sample collection</strong></p>
<p>Adult specimens of the solitary coral&nbsp;<em>F. scutaria</em>&nbsp;were collected from Kaneohe Bay on the northeastern shore of Oahu, Hawaii in the Pacific Ocean in June 2010 and kept in open-system tanks (sea tables) at the Hawaii Institute of Marine Biology in anticipation of spawning events. Following spawning, eggs and sperm were collected for fertilization in Petri dishes, and replicate batches of larvae were raised in 0.1 µm-filtered (sterile), 1.6 µm-filtered (excludes&nbsp;<em>Symbiodinium</em>&nbsp;and zooplankton), 20 µm-filtered (excludes zooplankton) or raw seawater. Samples from each life history stage (eggs, larvae, juveniles, and adults) were frozen for DNA analysis in DNA lysis buffer. Eggs and embryos were rinsed in sterilized seawater upon sampling. Each adult sample consists of three small pieces of an individual coral combined in one tube. Ca. 1 L of seawater was sampled from the sea tables one hour prior to the final spawning event, filtered, and frozen for DNA analysis in DNA lysis buffer. 50 mL of the culture water was sampled from the Petri dish treatments (originally 0.1 µm-filtered, 1.6 µm-filtered, or 20 µm-filtered seawater) after approximately 72 hours of exposure to the developing coral larvae during the final experiment.</p>
<p><strong><em>Montipora capitata</em>&nbsp;sample collection</strong></p>
<p>Fragments of adult specimens of the colonial coral&nbsp;<em>M. capitata</em>&nbsp;were collected from Kaneohe Bay in June 2010 and July 2011 and kept in sea tables at HIMB in anticipation of spawning events. Following spawning, egg-sperm bundles were collected from the sea tables for fertilization in Petri dishes, and replicate batches of larvae were raised in 0.1 µm-filtered, 1.6 µm-filtered, or 20 µm-filtered seawater. Samples from each life history stage (egg-sperm bundles, larvae, juveniles, and adults) were frozen for DNA analysis in DNA lysis buffer. Egg-sperm bundles were rinsed in TFF sterilized seawater upon sampling. Each adult sample consists of three small pieces of an individual coral combined in one tube. Ca. 1 L of seawater was sampled from the sea tables approximately one hour prior to the final spawning event, filtered, and frozen for DNA analysis in DNA lysis buffer. 35 mL of the culture water was sampled from the Petri dish treatments (originally 0.1 µm-filtered, 1.6 µm-filtered, or 20 µm-filtered seawater) after approximately 72 hours of exposure to the developing coral larvae during the final experiment in 2010, filtered, and frozen for DNA analysis in DNA lysis buffer. Additionally, throughout summer 2010, field-spawned egg-sperm bundles and field-fertilized larvae were collected from Kaneohe Bay and raised under the same treatments (0.1 µm-filtered, 1.6 µm-filtered, 20 µm-filtered, or raw seawater), and sampled in the same manner and at the same life-history stages (egg-sperm bundles, larvae, juveniles, and adults) as the corals spawned in sea tables. Ca. 1 L of seawater was sampled from the Kaneohe Bay lagoon 1 hour prior to the August 2010 field-spawning event and 1 hour after the June and July 2010 field-spawning events, filtered, and filters were frozen for DNA analysis in DNA lysis buffer.</p>
<p><strong>DNA extraction and Illumina amplicon sequencing of bacterial SSU rRNA genes&nbsp;</strong></p>
<p>Nucleic acids were extracted from&nbsp;<em>F. scutaria</em>&nbsp;corals and filters using the NucleoSpin Soil Kit (Macherey-Nagel, Duren, Germany) following the manufacturer’s protocol, modified as follows: lysis buffer SL1 and Enhancer SX were used, lysis time was increased to 20 min and two subsequent elution steps were performed with 50 µl fresh elution buffer each. DNA quality and yield were checked by agarose gel electrophoresis.</p>
<p>Nucleic acids were extracted from&nbsp;<em>M. capitata</em>&nbsp;samples and filters using the PowerSoil DNA Isolation Kit (MO BIO, Carlsbad, CA) following the manufacturer’s protocol, modified as follows: initial physical disruption time (via vortex) was increased to 30 min, and two subsequent elution steps were performed with 100 µl fresh DNA-Free PCR Grade water each. DNA quality and yield were checked by agarose gel electrophoresis.</p>
<p>The V4 region of the 16S rRNA gene was amplified with the primer pair F515/R806, which include Illumina flowcell adapter sequences and a sample-specific barcode on the reverse primer. The MasterTaq Kit (5 PRIME, Hamburg, Germany) was used for all PCR reactions. Amplification was performed using a touchdown protocol as in as follows: initial denaturation at 95°C for 3 min, and 30 cycles at 95°C for 30 sec, 65°C for 1 min (decreasing by 0.5°C per cycle), and 72°C for 2 min. After these 30 cycles, a further 5 – 7 cycles were performed using an annealing temperature of 50°C, and concluding with a final extension at 72°C for 20 min. Resulting PCR amplicons were quantified using the PicoGreen dsDNA assay (Invitrogen, Carlsbad, CA), pooled at equimolar concentrations and subsequently cleaned using the UltraClean PCR Clean-Up Kit (MO BIO Laboratories, Carlsbad, CA). Sequencing of the&nbsp;<em>F. scutaria</em>&nbsp;PCR products was performed on an Illumina MiSeq at the University of Colorado BioFrontiers Institute (Boulder, CO), while sequencing of the&nbsp;<em>M. capitata</em>&nbsp;PCR products was performed on an Illumina MiSeq at the University of Hawaii HIMB Genetics Core Facility (Kaneohe, HI).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong></p>
<p>original file:&nbsp;Shulse_Illumina_2015_metadata_V2.xls<br />
- added conventional header with dataset name, PI name<br />
- renamed parameters to BCO-DMO standard<br />
- reformatted date from d-Mon-yy to yyyy-mm-dd<br />
- replaced NA with nd<br />
- replaced spaces with underscores<br />
- replaced special characters: = lteq<br />
- reordered columns<br />
- sorted date by species, sample_type, sample_id</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
PI Supplied Instrument Name: PI Supplied Instrument Description:Illumina MiSeq desktop sequencer 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.
Thermal Cycler
Thermal Cycler
PI Supplied Instrument Name: Thermal Cycler PI Supplied Instrument Description:MyCycler thermal cycler (Bio-Rad Laboratories, Hercules, CA, USA) 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)
Deployment: Rappe_2010
Rappe_2010
Hawaii_reef
shoreside
Rappe_2010
Michael S. Rappé
University of Hawaiʻi at Mānoa
Hawaii_reef
shoreside