http://lod.bco-dmo.org/id/dataset/3974
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
2013-06-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Accession numbers with links to GenBank sequences of labyrinthulomycete 18S rRNA genes from sediment and water column samples collected around Long Island, NY from 2005-2008 (LabyLI project)
2013-06-25
publication
2013-06-25
revision
BCO-DMO Linked Data URI
2013-06-25
creation
http://lod.bco-dmo.org/id/dataset/3974
Jackie L. Collier
Stony Brook University - SoMAS
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: Collier, J. L. (2013) Accession numbers with links to GenBank sequences of labyrinthulomycete 18S rRNA genes from sediment and water column samples collected around Long Island, NY from 2005-2008 (LabyLI project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 06/25/2013) Version Date 2013-06-25 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3974 [access date]
samples around Long Island, NY for Labyrinthulomycete PCR and sequences Dataset Description: <p>Accession numbers with links to GenBank sequences of labyrinthulomycete 18S rRNA genes from sediment and water column samples collected around Long Island, NY.</p>
<p>Collado Mercado et al, 2010 ABSTRACT: Labyrinthulomycetes (Labyrinthulea) are ubiquitous marine osmoheterotrophic protists that appear to be important in decomposition of both allochthonous and autochthonous organic matter. We used a cultivation-independent method based on the labyrinthulomycete-specific primer LABY-Y to PCR amplify, clone, and sequence 68 nearly full-length 18S rDNA amplicons from 4 sediment and 3 seawater samples collected in estuarine habitats around Long Island, New York, USA. Phylogenetic analyses revealed that all 68 amplicons belonged to the Labyrinthulea. Only 15 of the 68 amplicons belonged to the thraustochytrid phylogenetic group (Thraustochytriidae). None of these 15 were similar to cultivated strains, and 11 formed a novel group. The remaining 53 amplicons belonged either to the labyrinthulid phylogenetic group (Labyrinthulidae) or to other families of Labyrinthulea that have not yet been described. Of these amplicons, 37 were closely related to previously cultivated Aplanochytrium spp. and Oblongichytrium spp. Members of these 2 genera were also cultivated from 1 of the sediment samples. The 16 other amplicons were not closely related to cultivated strains, and 15 belonged to 5 groups of apparently novel labyrinthulomycetes. Most of the novel groups of amplicons also contained environmental sequences from surveys of protist diversity using universal 18S rDNA primers. Because the primer LABY-Y is biased against several groups of labyrinthulomycetes, particularly among the thraustochytrids, these results may underestimate the undiscovered diversity of labyrinthulomycetes.</p> Methods and Sampling: <p>Approximate sampling positions (latitude and longitude) were determined from navigational maps.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0726702 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0726702
completed
Jackie L. Collier
Stony Brook University - SoMAS
Jackie.Collier@stonybrook.edu
pointOfContact
asNeeded
Dataset Version: 06/25/2013
Unknown
sample
sample_type
date
site
lat
lon
depth_w
size_fraction
sediment_description
clone_number
accession_number
theme
None, User defined
sample identification
sample type
date_local
site
latitude
longitude
depth_w
No BCO-DMO term
sample description
accession number
featureType
BCO-DMO Standard Parameters
lab_SBU_Collier
service
Deployment Activity
Long Island, NY
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.
Labyrinthulomycete diversity and abundance
https://osprey.bco-dmo.org/project/2259
Labyrinthulomycete diversity and abundance
<p><i>The following description is an excerpt from the NSF award abstract:</i> <br />
The Labyrinthulomycetes (labyrinthulids, thraustochytrids, and aplanochytrids) are ubiquitous, diverse, and abundant marine protists. They are thought to live mainly as saprobes, obtaining their nutrition from non-living particulate organic matter (POM) of algal, higher plant, or animal origin. Thus, while Labyrinthulomycetes are not "fungi" in a taxonomic sense, they may function as "fungi" in an ecological sense, playing similar roles in the decomposition of POM. Because of their high content of essential polyunsaturated fatty acids (PUFAs), Labyrinthulomycetes may also play a role in the nutrition of marine metazoans by improving the food quality of detritus ("trophic upgrading"). However, evidence of their role decomposing marine POM is somewhat circumstantial, and thus does not support quantitative conclusions about their function or importance. The long-term goal of this project is to gather the evidence about Labyrinthulomycete abundance and diversity that will be needed to better understand their role in marine ecosystems.</p>
<p>This project aims to develop molecular genetic methods based on the polymerase chain reaction (PCR) to investigate the diversity and abundance of Labyrinthulomycetes. The existing Labyrinthulomycete-specific PCR primers for 18S ribosomal DNA (rDNA) cannot recognize a potentially important component of Labyrinthulomycete diversity (some groups of thraustochytrids). The investigators will develop new 18S rDNA primers that will allow better estimation of the diversity of the Labyrinthulomycetes, and then use these primers to gather 18S rDNA sequence data from a variety of habitats. The resulting sequence data will diversity of these organisms to be quantified in the field relative to the representatives currently in culture. These primers (or others designed in the course of the project) will be used to develop quantitative real-time PCR assays to determine the abundance of Labyrinthulomycetes (and subgroups of Labyrinthulomycetes) in environmental samples. Methods will also be developed to cultivate novel Labyrinthulomycetes detected in local sediments during the preliminary sequencing efforts.</p>
LabyLI
largerWorkCitation
project
eng; USA
oceans
Long Island, NY
2013-06-25
Long Island, NY, USA
0
BCO-DMO catalogue of parameters from Accession numbers with links to GenBank sequences of labyrinthulomycete 18S rRNA genes from sediment and water column samples collected around Long Island, NY from 2005-2008 (LabyLI 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/35307.rdf
Name: sample
Units: unitless
Description: <p>sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/35308.rdf
Name: sample_type
Units: unitless
Description: <p>type of sample: water or sediment</p>
http://lod.bco-dmo.org/id/dataset-parameter/35309.rdf
Name: date
Units: dd-mmm-yyyy
Description: <p>collection data: local time</p>
http://lod.bco-dmo.org/id/dataset-parameter/35310.rdf
Name: site
Units: unitless
Description: <p>collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/35311.rdf
Name: lat
Units: decimal degrees
Description: <p>approximate latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/35312.rdf
Name: lon
Units: decimal degrees
Description: <p>approximate longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/35313.rdf
Name: depth_w
Units: meters
Description: <p>bottom depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/35314.rdf
Name: size_fraction
Units: microns
Description: <p>size fraction of water samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/35315.rdf
Name: sediment_description
Units: unitless
Description: <p>sediment description</p>
http://lod.bco-dmo.org/id/dataset-parameter/35316.rdf
Name: clone_number
Units: unitless
Description: <p>clone identification number</p>
http://lod.bco-dmo.org/id/dataset-parameter/35317.rdf
Name: accession_number
Units: unitless
Description: <p>GenBank accession number</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
13152
https://datadocs.bco-dmo.org/file/qAAoEzwH8wpA65/labyLI.csv
labyLI.csv
Primary data file for dataset ID 3974
download
https://osprey.bco-dmo.org/dataset/3974/data/download
download
onLine
dataset
<p>Approximate sampling positions (latitude and longitude) were determined from navigational maps.</p>
Specified by the Principal Investigator(s)
<p>See:<br />
Collado Mercado, E., J. C. Radway, and J. L. Collier. 2010. Novel uncultivated labyrinthulomycetes revealed by 18S rDNA sequences from seawater and sediment samples. Aquatic Microbial Ecology 58: 215-228. <a href="http://www.int-res.com/articles/ame2010/58/a058p215.pdf" target="_blank">[pdf]</a></p>
<p>Sequence accession numbers deposited in GenBank are indicated in the data file via hyperlinks.</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
Deployment: lab_SBU_Collier
lab_SBU_Collier
Long_Island_shore
shoreside
lab_SBU_Collier
Jackie L. Collier
Stony Brook University - SoMAS
Long_Island_shore
shoreside