http://lod.bco-dmo.org/id/dataset/552349
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
2015-03-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Population analysis and metagenomics of Japanese tsunami marine debris mussels along the Hawaii, Washington and Oregon coasts in 2012 (JTMD-BF project)
2015-02-27
publication
2015-02-27
revision
BCO-DMO Linked Data URI
2015-02-27
creation
http://lod.bco-dmo.org/id/dataset/552349
Dr Jonathan Geller
Moss Landing Marine Laboratories
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: Geller, J. (2015) Population analysis and metagenomics of Japanese tsunami marine debris mussels along the Hawaii, Washington and Oregon coasts in 2012 (JTMD-BF project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-02-27) Version Date 2015-02-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/552349 [access date]
Population analysis and metagenomics of Japanese tsunami marine debris mussels Dataset Description: <p>A major objective of the JTMD project was to characterize the biodiversity of the arriving and landed JTMD fauna and flora. One constituent of the landed biota were mussels in the genus <em>Mytilus</em>, known to be member of a species complex (including species native to western North America). We therefore undertook genetic analysis of <em>Mytilus</em> contained on JTMD for purposes of species identification. To augment morphological assessment of diversity of JTMD fouling organisms, we performed metabarcoding, in which bulk samples were extracted for DNA and DNA barcoding markers sequenced in parallel.</p>
<p>Access to this dataset is temporarily RESTRICTED until publication. Please contact the PI for further information</p> Methods and Sampling: <p>Mytilus specimens were collected from Japanese tsunami marine debris (JTMD) from 2012-2014 at coastal sites in Washington, Oregon and Hawaii.</p>
<p><strong>Population level analysis of focal JTMD species.</strong> Mytilus spp. were one of the most common organisms on JTMD. Cytochrome c oxidase subunit III was chosen for species identification of mussels because available female-specific primers allowed a simpler approach to species discrimination than the standard COI primers, which amplify both male and female sequences and complicate analyses. The proposed method of pooling tissues for bulk DNA extraction and post-sequencing analysis of haplotype variation was set aside due to presumed sequence error observed when sequencing individual mussel amplicons. Instead, 695 mussels were extracted for DNA and sequenced individually on the Ion Torrent platform. Addition of index nucleotides to PCR products allowed post-sequencing separation of sequences by source mussel. Bins of reads from individual mussels were mapped to reference sequences of female M. galloprovincialis, M. trossulus, and M. coruscus. Known distribution of Mytilus suggested that mussels in Japan would be M. galloprovincialis. A sample of mussels for which Ion Torrent sequencing resulted in identification as M. trossulus or M. coruscus were reanalyzed by preparation of new PCR product and Sanger sequencing.</p>
<p><strong>Metagenomic analysis of JTMD assemblages.</strong> Four 15 cm2 samples were scraped from the sides and top of the floating dock "Misawa 1" that beached near Newport Oregon in June 2012. Samples were preserved in ethanol and shipped to Moss Landing Marine Laboratories. Entire samples were decanted of ethanol and homogenized in an IKE Basic Mill. Ten grams of each sample were extracted with the Mo Bio Powersoil Mega DNA extraction kit (Mo Bio, Carlsbad, CA). Cytochrome c oxidase subunit I was PCR amplified, and prepared for sequencing on the Ion Torrent PGM. Resulting reads were pooled, quality and size filtered, and assembled into operational taxonomic units (OTUs) using the Velvet assembler. Gene OTUs were compared to eukaryotic COI sequences culled from Genbank by using variants of the search term for COI (COI, COX1, Cytochrome oxidase subunit I, Cytochrome c oxidase subunit I, etc...) and excluding prokaryota. We also specifically searched for COI sequences associated with of morphologically identified JTMD specie and congeners, as well as con-familials when morphological identification was limited to the family level.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1266234 Award URL: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1266234
onGoing
Dr Jonathan Geller
Moss Landing Marine Laboratories
geller@mlml.calstate.edu
pointOfContact
asNeeded
Dataset Version: 2015-02-27
Unknown
taxon
species
accession_number
pairwise_id
DNA sequencer
Thermal Cycler
Homogenizer
theme
None, User defined
taxon
species
accession number
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
Homogenizer
instrument
BCO-DMO Standard Instruments
JTMD_2012
service
Deployment Activity
Hawaii, Washington and Oregon coast
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.
Testing the Invasion Process: Survival, Dispersal, Genetic Characterization and Attenuation of Marine Biota on the 2011 Japanese Tsunami Marine Debris Field.
https://www.bco-dmo.org/project/471584
Testing the Invasion Process: Survival, Dispersal, Genetic Characterization and Attenuation of Marine Biota on the 2011 Japanese Tsunami Marine Debris Field.
<p><strong>I. Biodiversity; Population and Food Web Analysis; Viability and Reproductive Condition; Dispersal Track and Growth History; Shellfish Pathogens/Parasites</strong></p>
<p>This project seeks to document the biodiversity of Japanese species on arriving tsunami-generated debris, through morphological and genetic identification (including massively parallel DNA sequencing of whole community samples) andthrough quantitative replicate samples to determine numerical abundance, density, frequency, and biomass. In addition, species accumulation and rarefaction curves will be determinded to estimate total inbound diversity.</p>
<p><em>Focuses include</em>:</p>
<p>- Population structure of selected taxa, based on size/age class distributions.<br />
- Viability and reproductive condition of selected taxa, based on fecundity, gonadal indices, and/or spore production, upon arrival.<br />
- Food web analyses based upon tissue stable isotope ratios <em>(</em>δ13C and δ15N<em>).</em><br />
- Dispersal track and growth history of selected taxa based on oxygen isotopic and elemental composition of shell calcite.<br />
- Identity and prevalence of parasites and pathogens in oysters (<em>Crassostrea gigas</em>) and mussels (<em>Mytilus galloprovincialis</em>).</p>
<p><strong>II. Biotic Attrition Over Time</strong></p>
<p>Comparison of dead species assemblages on JTMD to live assemblages to assess the fate and alteration of debris communities over time.</p>
<p><strong>III. Genetic Matching of Novel Invasions With JTMD Biota</strong></p>
<p>Genetically characterize populations of target species so that if and when new invasions are detected, or when previously established invasions appear to be newly expanding or appearing in new locations, genetic studies can be undertaken to determine if these events are related to the JTMD phenomenon.</p>
<p>This is a Rapid Response Grant.</p>
<p>2020-09-30: Final data was not submitted for this project. The data for this research are available at the Dryad data depository (<a href="https://dx.doi.org/10.5061/dryad.rh01m">http://dx.doi.org/10.5061/dryad.rh01m</a>). Contact Dr. Carlton for more information.</p>
JTMD-BF
largerWorkCitation
project
eng; USA
biota
oceans
Hawaii, Washington and Oregon coast
2015-02-27
North Pacific Ocean (W and E)
0
BCO-DMO catalogue of parameters from Population analysis and metagenomics of Japanese tsunami marine debris mussels along the Hawaii, Washington and Oregon coasts in 2012 (JTMD-BF 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/552360.rdf
Name: taxon
Units: unitless
Description: phylum and more specific taxonomic group
http://lod.bco-dmo.org/id/dataset-parameter/552361.rdf
Name: species
Units: unitless
Description: genus and species name
http://lod.bco-dmo.org/id/dataset-parameter/552362.rdf
Name: accession_number
Units: unitless
Description: Genbank record that matched the recovered seqeunce
http://lod.bco-dmo.org/id/dataset-parameter/552363.rdf
Name: pairwise_id
Units: unitless
Description: Pairwise Identity is the percent similarity between recovered sequence and the Genbank record
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
https://www.bco-dmo.org/dataset/552349/data/download
download
onLine
dataset
<p>Mytilus specimens were collected from Japanese tsunami marine debris (JTMD) from 2012-2014 at coastal sites in Washington, Oregon and Hawaii.</p>
<p><strong>Population level analysis of focal JTMD species.</strong> Mytilus spp. were one of the most common organisms on JTMD. Cytochrome c oxidase subunit III was chosen for species identification of mussels because available female-specific primers allowed a simpler approach to species discrimination than the standard COI primers, which amplify both male and female sequences and complicate analyses. The proposed method of pooling tissues for bulk DNA extraction and post-sequencing analysis of haplotype variation was set aside due to presumed sequence error observed when sequencing individual mussel amplicons. Instead, 695 mussels were extracted for DNA and sequenced individually on the Ion Torrent platform. Addition of index nucleotides to PCR products allowed post-sequencing separation of sequences by source mussel. Bins of reads from individual mussels were mapped to reference sequences of female M. galloprovincialis, M. trossulus, and M. coruscus. Known distribution of Mytilus suggested that mussels in Japan would be M. galloprovincialis. A sample of mussels for which Ion Torrent sequencing resulted in identification as M. trossulus or M. coruscus were reanalyzed by preparation of new PCR product and Sanger sequencing.</p>
<p><strong>Metagenomic analysis of JTMD assemblages.</strong> Four 15 cm2 samples were scraped from the sides and top of the floating dock "Misawa 1" that beached near Newport Oregon in June 2012. Samples were preserved in ethanol and shipped to Moss Landing Marine Laboratories. Entire samples were decanted of ethanol and homogenized in an IKE Basic Mill. Ten grams of each sample were extracted with the Mo Bio Powersoil Mega DNA extraction kit (Mo Bio, Carlsbad, CA). Cytochrome c oxidase subunit I was PCR amplified, and prepared for sequencing on the Ion Torrent PGM. Resulting reads were pooled, quality and size filtered, and assembled into operational taxonomic units (OTUs) using the Velvet assembler. Gene OTUs were compared to eukaryotic COI sequences culled from Genbank by using variants of the search term for COI (COI, COX1, Cytochrome oxidase subunit I, Cytochrome c oxidase subunit I, etc...) and excluding prokaryota. We also specifically searched for COI sequences associated with of morphologically identified JTMD specie and congeners, as well as con-familials when morphological identification was limited to the family level.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:</p>
<p>- added conventional header with dataset name, PI name, version date<br />
- renamed parameters to BCO-DMO standard<br />
- replaced blanks with underscores</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
DNA sequencer
DNA sequencer
PI Supplied Instrument Name: DNA sequencer PI Supplied Instrument Description:Ion Torrent platform Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
Thermal Cycler
Thermal Cycler
PI Supplied Instrument Name: Thermal Cycler 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)
Homogenizer
Homogenizer
PI Supplied Instrument Name: Homogenizer PI Supplied Instrument Description:IKA Basic Mill Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
Deployment: JTMD_2012
JTMD_2012
Carlton_shore
shoreside
JTMD_2012
Dr James T. Carlton
Williams College
Carlton_shore
shoreside