http://lod.bco-dmo.org/id/dataset/626679
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
2015-11-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Physical meta associated with marine metagenome samples collected collected on the R/V Cape Hatteras (CH0112) cruise in the NW Atlantic Continental Shelf during 2015 (CiliateSequencing project)
2015-11-23
publication
2015-11-23
revision
BCO-DMO Linked Data URI
2015-11-23
creation
http://lod.bco-dmo.org/id/dataset/626679
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. (2015) Physical meta associated with marine metagenome samples collected collected on the R/V Cape Hatteras (CH0112) cruise in the NW Atlantic Continental Shelf during 2015 (CiliateSequencing project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-11-23) Version Date 2015-11-23 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/626679 [access date]
Physical meta associated with marine metagenome samples collected along the New England Shelf, USA Dataset Description: <p>Physical data associated with samples from NCBI BioProject SRA######,&nbsp;PRJNA297691 (not yet public, 2015-11-18)</p>
<p><strong>References:</strong></p>
<p>Santoferrara L.F., Grattepanche J-D., Katz L.A., McManus G.B. (submitted) Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?</p>
<p>Grattepanche J-D., Santoferrara L.F., McManus G.B., Katz L.A. (submitted) Unexpected biodiversity of ciliates in marine samples.</p> Methods and Sampling: <p>Seawater samples were screened through a 80 um mesh, then sequentially filtered through 10 um and 2 um polycarbonate filters; DNA was extracted from half-filters.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1130033 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1130033
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: 2015-11-23
Unknown
cruise_id
geo_loc_name
isolation_source
organism
samp_collect_device
depth_w
date_collected
lat
lon
sample_name
layer_sampled
depth
temp
sal
O2
fluor
theme
None, User defined
Cruise identfier
site
No BCO-DMO term
instrument
depth_w
date
latitude
longitude
sample identification
depth
water temperature at measurement depth
salinity
dissolved Oxygen
fluorescence
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird 9
instrument
BCO-DMO Standard Instruments
CH0112
service
Deployment Activity
NW Atlantic Continental Shelf
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.
Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us?
http://microzooplankton.uconn.edu
Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us?
<p>The Ocean's biomass and diversity are predominantly microbial, yet this aspect of diversity remains underexplored. Efforts in recent years have begun to document microbial diversity in marine systems, and to elucidate the processes that structure assemblages across space and time. This project focuses on two important sister clades of microbial eukaryotes, the oligotrich and choreotrich ciliates. These organisms comprise a major component of planktonic food webs as they graze on phytoplankton, and are in turn eaten by zooplankton and larval fish.</p>
<p>Earlier molecular work on ciliate diversity relied on light microscopy, construction of clone libraries and Sanger sequencing. This revealed a high degree of cryptic diversity (similar species that are genetically distinct), which is surprising, given the long-held idea that all microbes are globally distributed and that few species exist, at least as compared to animals and plants. This past work also showed that ciliate assemblages contain a few highly abundant forms and many rare ones, consistent with the concept of a "rare biosphere". However, these methods are limited by high costs of both labor and materials, so that efforts to sample any local assemblage comprehensively usually resulted in undersaturation (repeated sampling continued to uncover new species). Next generation approaches are needed to truly assess the depths of biodiversity in planktonic ciliates.</p>
<p>This project brings together investigators with strengths in ecology, taxonomy and oceanography (PI McManus) and in molecular evolution, systematics and bioinformatics (PI Katz). Pyrosequencing will be used to sample the oligotrich and choreotrich ciliates ’to exhaustion’ in coastal environments. Denaturing gradient gel electrophoresis (DGGE), a technique that generates a fingerprint of the diversity in a sample, will be used to pre-select samples for pyrosequencing based on where strong gradients are observed in the composition of assemblages in relation to environmental factors (density fronts, thermolclines, etc.). Using these approaches, combined with the informatics pipeline already in place, this project will address three specific objectives:</p>
<p><strong>Objective 1.</strong> Determine the spatial scale of variability in ciliate diversity by measuring how ciliate assemblages change over meter, kilometer, 100 km, and basin scales.</p>
<p><strong>Objective 2.</strong> Assess the contributions of different size classes of ciliates to overall assemblage diversity.</p>
<p><strong>Objective 3.</strong> Experimentally evaluate factors that control the temporal shift of individual species from rarity to commonness in a natural assemblage, and vice versa.</p>
<p>Note: See the related collaborative project, "<a href="http://www.bco-dmo.org/project/560529">Patterns of diversity in planktonic ciliates: spatio-temporal scales and community assembly in the coastal ocean</a>", funded by awards OCE-1435515 and OCE-1436003.</p>
CiliateSequencing
largerWorkCitation
project
eng; USA
biota
oceans
NW Atlantic Continental Shelf
2015-11-23
NW Atlantic Continental Shelf
0
BCO-DMO catalogue of parameters from Physical meta associated with marine metagenome samples collected collected on the R/V Cape Hatteras (CH0112) cruise in the NW Atlantic Continental Shelf during 2015 (CiliateSequencing 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/626725.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/626726.rdf
Name: geo_loc_name
Units: unitless
Description: <p>The geolocation of the collection: Atlantic Ocean</p>
http://lod.bco-dmo.org/id/dataset-parameter/626727.rdf
Name: isolation_source
Units: unitless
Description: <p>Source of the sample: seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/626728.rdf
Name: organism
Units: unitless
Description: <p>In this case the organism is a sample of marine seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/626729.rdf
Name: samp_collect_device
Units: unitless
Description: <p>sample collection device</p>
http://lod.bco-dmo.org/id/dataset-parameter/626730.rdf
Name: depth_w
Units: meters
Description: <p>depth of water at sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/626731.rdf
Name: date_collected
Units: dd-Mon-yyyy
Description: <p>date sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/626732.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/626733.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/626734.rdf
Name: sample_name
Units: unitless
Description: <p>sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/626735.rdf
Name: layer_sampled
Units: unitless
Description: <p>layer of water sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/626736.rdf
Name: depth
Units: meters
Description: <p>depth of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/626737.rdf
Name: temp
Units: degrees Celsius
Description: <p>temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/626738.rdf
Name: sal
Units: PSU
Description: <p>salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/626739.rdf
Name: O2
Units: mg L-1
Description: <p>dissolved oxygen</p>
http://lod.bco-dmo.org/id/dataset-parameter/626740.rdf
Name: fluor
Units: arbitrary units
Description: <p>chlorophyll fluorescence</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
4487
https://datadocs.bco-dmo.org/file/p99nDGnCA2JGjZ/SRA_Hatteras.csv
SRA_Hatteras.csv
Primary data file for dataset ID 626679
download
https://osprey.bco-dmo.org/dataset/626679/data/download
download
onLine
dataset
<p>Seawater samples were screened through a 80 um mesh, then sequentially filtered through 10 um and 2 um polycarbonate filters; DNA was extracted from half-filters.</p>
Specified by the Principal Investigator(s)
<p>Data were processed in SeaBird Seasave software, version 7.21a using instrument configuration files provided by RV Hatteras ship operations.&nbsp; Raw hexadecimal data files were converted to base 10.&nbsp; Processed data were imported into Excel.</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: Instrument Name: CTD Sea-Bird 9 Instrument Short Name:CTD SBE 9 Instrument Description: The Sea-Bird SBE 9 is a type of CTD instrument package. The SBE 9 is the Underwater Unit and is most often combined with the SBE 11 Deck Unit (for real-time readout using conductive wire) when deployed from a research vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorometer, altimeter, etc.). Note that in most cases, it is more accurate to specify SBE 911 than SBE 9 since it is likely a SBE 11 deck unit was used. more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Cruise: CH0112
CH0112
R/V Cape Hatteras
Community Standard Description
International Council for the Exploration of the Sea
R/V Cape Hatteras
vessel
CH0112
George McManus
University of Connecticut
R/V Cape Hatteras
Community Standard Description
International Council for the Exploration of the Sea
R/V Cape Hatteras
vessel