http://lod.bco-dmo.org/id/dataset/728146
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
2018-02-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Genetic accession numbers for viral and bacterial metagenomes from Asteroid sea stars including sea star wasting disease state and collection information from sites worldwide between 2013 and 2016 (Sea Star Microbiology project)
2018-03-02
publication
2018-03-02
revision
BCO-DMO Linked Data URI
2018-03-02
creation
http://lod.bco-dmo.org/id/dataset/728146
Ian Hewson
Cornell 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: Hewson, I. (2018) Genetic accession numbers for viral and bacterial metagenomes from Asteroid sea stars including sea star wasting disease state and collection information from sites worldwide between 2013 and 2016 (Sea Star Microbiology project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2018-03-02 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/728146 [access date]
Dataset Description: <p>This dataset contains Asteroid sea star genetic accession numbers at the National Center for Biotechnology Information (NCBI) in addition to information about the sea stars sampled including collection date, location, and notation of sea star wasting disease (SSWD) symptoms.&nbsp; Sea star sampling took place at sites worldwide between 2013 and 2016.</p>
<p>These data were utilized in the following publication (Hewson et al., 2018)</p> Methods and Sampling: <p><strong>For viral metagenomes: </strong></p>
<p>1 g of preserved or frozen tissue was homogenized in 25 mL of 0.02um filtered PBS in a NutriBullet blender. The homogenate was centrifuged briefly at 3,000 x g to remove large tissue debris and ossicles, and the supernatant filtered through 0.2um Durapore filters to remove cellular debris. The filtrate was precipitated with PEG-8000 (1 g/ml) overnight. The filtrate was then centrifuged at 22,000 x g for 30 min, the supernatant decanted, and the pellet resuspended in 1 ml 0.02 um filtered PBS. The resuspension was filtered through a 0.2 µm Acrodisc PES filter. Samples were then treated with DNAseI, RNAse One and Benzonase for 3 h. Nuclease activity was stopped by the addition of x vol ETDA (25 mM). Viral DNA in the purified suspension was extracted using the Zymo Viral DNA kit. The DNA was amplified prior to sequencing using the WGA2 kit V2 (GE Biosciences) before submission to the Cornell Biotechnology Resource Center (BRC) for library preparation and sequencing.</p>
<p><strong>For bacterial metagenomes: </strong></p>
<p>Samples of asymptomatic asteroid tissues (~ 1cm2) were excised from dorsal surfaces and lesioned tissues were excised from symptomatic asteroids, and then homogenized in 10mL of 0.02 µm filtered phosphate buffered saline using the NutriBullet for 1 minute. Homogenates were allowed to settle for 5 min before 1 mL supernatant was removed and placed into sterile microcentrifuge tubes. The homogenate (400 µL) was purified on PERCOLL step gradients (800 µL each step at 70% and 30%) to remove host cells. Gradients were centrifuged at 12,000 x g for 90 min (4oC). The interface between 30% and 70% was determined with reference to a dense E. coli culture run on an identical gradient. The interface was removed and DNA extracted using the ZR Bacterial &amp; Fungal DNA kit (Zymo Research) following manufacturer’s recommendations. The interface fraction was then targeted for metagenomic library preparation. DNA was extracted from the cell fraction and amplified using the GenomePLEX kit (Sigma Aldrich).</p>
<p>Collection note:&nbsp;The sea star samples were collected by collaborators (samples other than P.&nbsp;ochraceus&nbsp;or P.&nbsp;helianthoides&nbsp;- these were collected by Ian Hewson) intertidally by hand.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1537111 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1537111
completed
Ian Hewson
Cornell University
1-607-255-0151
Department of Microbiology Wing Hall 403
Ithaca
NY
14853
USA
hewson@cornell.edu
pointOfContact
asNeeded
Unknown
Accession_number
Library_Name
Library_Description
Host_Species
Disease_State
Date_of_Collection
Location_Description
Latitude
Longitude
Illumina MiSeq Sequencer
theme
None, User defined
accession number
sample description
taxon
date
site
latitude
longitude
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
SeaStarMicrobiology_Hewson
service
Deployment Activity
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.
Microbial ecology of sea star wasting disease
http://seastarwastingdisease.wordpress.com
Microbial ecology of sea star wasting disease
<p>Beginning in June 2013 and continuing to present (May 2015), over 20 species of sea stars (Asteroidea, Echinodermata) have been affected by sea star wasting disease (SSWD), affecting populations from central Alaska to Baja California. The disease has lead to greatly reduced abundance or disappearance of these keystone predators, which may result in profound alteration to benthic community structure. Recent work has identified the sea star associated densovirus (SSaDV) as the most likely causative agent of the disease. SSaDV is related to densoviruses inhabiting other echinoderms worldwide, and has been present in West Coast asteroid populations for at least 72 years. Hence, there remain significant knowledge gaps in our understanding of how SSaDV actually elicits SSWD symptoms, especially how the echinoderm host, densovirus and microbiome constituents interact. This project will address three major questions: 1) does viral infection change the composition of the sea star microbiome?, 2) what is the variation of viral genomes and their associated virulence?, and 3) does larval dispersal spread the disease between habitats? This project will address these hypotheses through time-course measurements of host, pathogen and associated microorganisms, genome-genome comparisons between historical and contemporary viral strains, and through experiments targeting larvae and juvenile asteroids in aquaria and in nature. </p>
<p>This project will address three fundamental questions relating to Sea Star Wasting Disease (SSWD): 1) How does SSaDV causes SSWD symptoms and how does the disease progress from primary infection through animal mortality; 2) How do current genotypes of SSaDV vary from those present historically, and is virulence related to genome polymorphisms; and 3) Are larvae and juvenile asteroids differentially affected by SSaDV, and are broadcast-spawned bipinarria a viable mechanism for SSaDV dispersal between distant habitats. The first question will be addressed by experimental inoculation of naïve sea stars with SSaDV, then time-course monitoring of host transcription (i.e. transcriptomics via RNAseq), microbiome composition via 16S rRNA sequencing and quantitative PCR, and viral load and prevalence using quantitatice PCR. The second question will be addressed by amplifying the entire genome of SSaDV and related densoviruses, then perform genome-genome comparisons to identify polymorphic DNA in key protein-encoding regions. The third question will be addressed by collecting bipinarria from plankton at field locations adjacent to spawning asteroid populations, and by performing time-course observations of captive juvenile sea stars and monitoring their bacterial and viral loads using quantitative PCR. This work will be performed primarily in the Salish Sea region, with SSaDV - naïve asteroids collected from Alaskan waters.</p>
Sea Star Microbiology
largerWorkCitation
project
eng; USA
oceans
-124.713444
151.758016
-34.11126
55.762037
2013-09-20
2016-02-16
Salish Sea and Alaskan Waters
0
BCO-DMO catalogue of parameters from Genetic accession numbers for viral and bacterial metagenomes from Asteroid sea stars including sea star wasting disease state and collection information from sites worldwide between 2013 and 2016 (Sea Star Microbiology 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/728157.rdf
Name: Accession_number
Units: unitless
Description: <p>Link to accession at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/728158.rdf
Name: Library_Name
Units: unitless
Description: <p>Name of library</p>
http://lod.bco-dmo.org/id/dataset-parameter/728159.rdf
Name: Library_Description
Units: unitless
Description: <p>Description of the library</p>
http://lod.bco-dmo.org/id/dataset-parameter/728160.rdf
Name: Host_Species
Units: unitless
Description: <p>Species from which viral/bacterial sequences were obtained</p>
http://lod.bco-dmo.org/id/dataset-parameter/728161.rdf
Name: Disease_State
Units: unitless
Description: <p>Sea star wasting disease (SSWD) state (Asymptomatic|SSWD-affected)</p>
http://lod.bco-dmo.org/id/dataset-parameter/728162.rdf
Name: Date_of_Collection
Units: unitless
Description: <p>Date of host collection in format dd-mmm-yy</p>
http://lod.bco-dmo.org/id/dataset-parameter/728163.rdf
Name: Location_Description
Units: unitless
Description: <p>Site location (Country; Site) of host collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/728164.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of host collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/728165.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of host collection</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
10893
https://datadocs.bco-dmo.org/file/R88XmlEcvJNr7E/SeaStarGenbankAccessions.csv
SeaStarGenbankAccessions.csv
Primary data file for dataset ID 728146
download
https://osprey.bco-dmo.org/dataset/728146/data/download
download
onLine
dataset
<p><strong>For viral metagenomes: </strong></p>
<p>1 g of preserved or frozen tissue was homogenized in 25 mL of 0.02um filtered PBS in a NutriBullet blender. The homogenate was centrifuged briefly at 3,000 x g to remove large tissue debris and ossicles, and the supernatant filtered through 0.2um Durapore filters to remove cellular debris. The filtrate was precipitated with PEG-8000 (1 g/ml) overnight. The filtrate was then centrifuged at 22,000 x g for 30 min, the supernatant decanted, and the pellet resuspended in 1 ml 0.02 um filtered PBS. The resuspension was filtered through a 0.2 µm Acrodisc PES filter. Samples were then treated with DNAseI, RNAse One and Benzonase for 3 h. Nuclease activity was stopped by the addition of x vol ETDA (25 mM). Viral DNA in the purified suspension was extracted using the Zymo Viral DNA kit. The DNA was amplified prior to sequencing using the WGA2 kit V2 (GE Biosciences) before submission to the Cornell Biotechnology Resource Center (BRC) for library preparation and sequencing.</p>
<p><strong>For bacterial metagenomes: </strong></p>
<p>Samples of asymptomatic asteroid tissues (~ 1cm2) were excised from dorsal surfaces and lesioned tissues were excised from symptomatic asteroids, and then homogenized in 10mL of 0.02 µm filtered phosphate buffered saline using the NutriBullet for 1 minute. Homogenates were allowed to settle for 5 min before 1 mL supernatant was removed and placed into sterile microcentrifuge tubes. The homogenate (400 µL) was purified on PERCOLL step gradients (800 µL each step at 70% and 30%) to remove host cells. Gradients were centrifuged at 12,000 x g for 90 min (4oC). The interface between 30% and 70% was determined with reference to a dense E. coli culture run on an identical gradient. The interface was removed and DNA extracted using the ZR Bacterial &amp; Fungal DNA kit (Zymo Research) following manufacturer’s recommendations. The interface fraction was then targeted for metagenomic library preparation. DNA was extracted from the cell fraction and amplified using the GenomePLEX kit (Sigma Aldrich).</p>
<p>Collection note:&nbsp;The sea star samples were collected by collaborators (samples other than P.&nbsp;ochraceus&nbsp;or P.&nbsp;helianthoides&nbsp;- these were collected by Ian Hewson) intertidally by hand.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Data Manager Processing Notes:<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* converted latitude/longtitude in decmal degrees with directional to decimal degrees with South and West as negative values<br />
* commas in data changed to semicolons to support csv output*&nbsp;<br />
* added links to NCBI accessions<br />
* species name&nbsp; Parvalusta exigua&nbsp;changed to&nbsp;Prvulastra exigua&nbsp; (accepted name http://www.marinespecies.org/aphia.php?p=taxdetails&amp;id=459556) after communication with PI<br />
* species name&nbsp; Mathasterias muizenberg&nbsp;changed to&nbsp;Marthasterias glacialis&nbsp;(accepted name http://www.marinespecies.org/aphia.php?p=taxdetails&amp;id=123803) after communication with PI.&nbsp; This may become&nbsp;Marthasterias&nbsp;glacialis (subsp. muizenberg) in future.</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
Illumina MiSeq Sequencer
Illumina MiSeq Sequencer
PI Supplied Instrument Name: Illumina MiSeq 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.
Deployment: SeaStarMicrobiology_Hewson
SeaStarMicrobiology_Hewson
shoreside Alaska
shoreside
SeaStarMicrobiology_Hewson
Ian Hewson
shoreside Alaska
shoreside