http://lod.bco-dmo.org/id/dataset/3652
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
2012-05-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Accession numbers for planktonic ciliate haplotypes collected on R/V Lowell Weicker in the Long Island Sound in 2008
2012-05-11
publication
2012-05-11
revision
BCO-DMO Linked Data URI
2012-05-11
creation
http://lod.bco-dmo.org/id/dataset/3652
George McManus
University of Connecticut
principalInvestigator
Laura A. Katz
Smith College
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: McManus, G., Katz, L. A. (2012) Accession numbers for planktonic ciliate haplotypes collected on R/V Lowell Weicker in the Long Island Sound in 2008. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 11 May 2012) Version Date 2012-05-11 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3652 [access date]
Accession numbers for planktonic ciliate haplotypes Dataset Description: <p>Accession numbers are given for planktonic ciliate haplotypes found in Long Island Sound.</p> Methods and Sampling: <p>Six stations were sampled in Long Island Sound on 13 August 2008. DNA was extracted and amplified. Two rDNA primers were used (OCSP-A and OCSP-B), resulting in the generation of two separate clone libraries.</p>
<p>More information on sample locations, methodology, and results can be found in the following publication and its <a target="_blank" href="http://www.int-res.com/articles/suppl/a064p051_supp.pdf">supplement</a>:<br />
Tamura, M, LA Katz, and GB McManus. 2011. Distribution and diversity of Oligotrich and Choreotrich ciliates in a large temperate estuary. Aquat. Microb. Ecol. 64:51-67. doi:10.3354/ame01509 (<a href="http://www.science.smith.edu/departments/Biology/lkatz/documents/Tamura_et_al_2011.pdf" target="_blank">PDF</a>)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0648711 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0648711
completed
George McManus
University of Connecticut
860-405-8602
Department of Marine Sciences, University of Connecticut 1080 Shennecossett Rd.
Groton
CT
06340
USA
george.mcmanus@uconn.edu
pointOfContact
Laura A. Katz
Smith College
413-585-3825
Department of Biological Sciences Smith College Burton Hall 201
Northampton
MA
01063
USA
lkatz@smith.edu
pointOfContact
asNeeded
Dataset Version: 11 May 2012
Unknown
primer_set
sequence_name
accession_number
Automated Sequencer
Niskin bottle
theme
None, User defined
No BCO-DMO term
accession number
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Niskin bottle
instrument
BCO-DMO Standard Instruments
LW_LIS08
service
Deployment Activity
Long Island Sound
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 hypotheses about diversity, gene flow, and effective population size in marine planktonic ciliates
http://microzooplankton.uconn.edu
Testing hypotheses about diversity, gene flow, and effective population size in marine planktonic ciliates
<p>The microbial ecologist Tom Fenchel recently said, “The decoupling of molecular and classical (including experimental) approaches to environmental microbiology has not been fruitful and it represents one of the most important challenges for the field in the coming years.” (Fenchel 2005). Classical approaches center on the centuries-old tradition of describing individual species via meticulous observation and analysis to generate monographs, such as is done for plants and animals. Unfortunately, the rush to new molecular techniques has sometimes ignored this tradition, with claims about new lineages never seen before and reports of staggering diversity of microbial eukaryotes based on environmental DNA samples not backed up by even the most elementary microscopic observations.</p>
<p>In the face of this disconnect between the traditional and the molecular, we propose a marriage of the two approaches in the study of marine ciliate diversity and gene flow. Our own data show that in some clades of planktonic ciliates (Strombidiidae) there is indeed a high level of molecular diversity underlying a relatively small number of morphospecies. In other clades (some choreotrichs), the opposite appears to be true, with morphological heterogeneity underlain by apparently clonal lines, based on molecular data. Currently, we do not understand what sustains diversity in some clades; nor do we know why other clades show low diversity. But this problem is amenable to both experimental and observational approaches.</p>
<p>This proposal uses a two-pronged approach, combining molecular (clone libraries, DGGE,FISH) and traditional (light microscopy) techniques to address three broad questions:<br />
<b>i.</b> What are the most important physical and biological factors that affect distribution and diversity of planktonic marine ciliates?<br />
<b>ii.</b> What is the effective population size for marine ciliate populations, and how does this compare to census population sizes?<br />
<b>iii.</b> How well do traditional morphological descriptions of ciliate species fare when compared with molecular characterizations?</p>
<p>Using a combination of molecular and microscopy methods, we will address these questions in coastal planktonic ciliates. Analyses of the resulting data will yield insights into the nature of ciliate species and patterns of gene flow within the North Atlantic.</p>
CiliateDivGenePop
largerWorkCitation
project
eng; USA
oceans
Long Island Sound
2012-05-11
Coastal Northwest Atlantic, from Long Island Sound to Maine
0
BCO-DMO catalogue of parameters from Accession numbers for planktonic ciliate haplotypes collected on R/V Lowell Weicker in the Long Island Sound in 2008
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/27541.rdf
Name: primer_set
Units: dimensionless
Description: <p>Name of the primer and resulting clone library.</p>
http://lod.bco-dmo.org/id/dataset-parameter/27542.rdf
Name: sequence_name
Units: dimensionless
Description: <p>Haplotype name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/27543.rdf
Name: accession_number
Units: dimensionless
Description: <p>Accession number and link to GenBank.</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
8884
https://datadocs.bco-dmo.org/file/2GGXpV4hZPKwOO/accession_numbers.csv
accession_numbers.csv
Primary data file for dataset ID 3652
download
https://osprey.bco-dmo.org/dataset/3652/data/download
download
onLine
dataset
<p>Six stations were sampled in Long Island Sound on 13 August 2008. DNA was extracted and amplified. Two rDNA primers were used (OCSP-A and OCSP-B), resulting in the generation of two separate clone libraries.</p>
<p>More information on sample locations, methodology, and results can be found in the following publication and its <a target="_blank" href="http://www.int-res.com/articles/suppl/a064p051_supp.pdf">supplement</a>:<br />
Tamura, M, LA Katz, and GB McManus. 2011. Distribution and diversity of Oligotrich and Choreotrich ciliates in a large temperate estuary. Aquat. Microb. Ecol. 64:51-67. doi:10.3354/ame01509 (<a href="http://www.science.smith.edu/departments/Biology/lkatz/documents/Tamura_et_al_2011.pdf" target="_blank">PDF</a>)</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
Automated Sequencer
Automated Sequencer
PI Supplied Instrument Name: Automated Sequencer PI Supplied Instrument Description:Samples were sequenced in either an ABI 3000 automated sequencer or in an ABI 377 automated 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.
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:Suface samples were taken with a bucket; Niskin bottles were used to take samples below the pycnocline. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: LW_LIS08
LW_LIS08
R/V Lowell Weicker
R/V Lowell Weicker
vessel
LW_LIS08
George McManus
University of Connecticut
R/V Lowell Weicker
R/V Lowell Weicker
vessel