http://lod.bco-dmo.org/id/dataset/3959
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
2013-06-07
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
CTD data from 39 stations from R/V Cape Hatteras cruise CH0112 in the Northwest Atlantic Continental Shelf in 2012 (CiliateSequencing project)
2013-06-07
publication
2013-06-07
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-11-06
publication
https://doi.org/10.1575/1912/bco-dmo.3959.1
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. (2013) CTD data from 39 stations from R/V Cape Hatteras cruise CH0112 in the Northwest Atlantic Continental Shelf in 2012 (CiliateSequencing project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2013-06-07 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.3959.1 [access date]
CTD data from 39 stations from CH0112 cruise. Dataset Description: <p>Temperature, conductivity, fluorescence, and oxygen measured by CTD are reported for 39 stations sampled during July 2012 on the CH0112 cruise (R/V Cape Hatteras).</p> Methods and Sampling: <p>23 stations were sampled along a transect from Narragansett, RI to the shelf break. 16 stations were sampled on the way back.</p>
<p>---------------------------------------------<br />
<strong>Header information from CTD files:</strong><br />
Sea-Bird SBE 9 Data File:<br />
Software Version Seasave V 7.20a<br />
Temperature SN = 0967<br />
Conductivity SN = 0626<br />
Number of Bytes Per Scan = 41<br />
Number of Voltage Words = 4<br />
Number of Scans Averaged by the Deck Unit = 1<br />
Append System Time to Every Scan<br />
---------------------------------------------</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1129734 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1129734
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: 1
Unknown
sta
lat_start
lon_start
month_start
day_start
year
time_start
ISO_DateTime_UTC
press
depth
cond
temp
temp2
fluor
O2
scan
CTD Sea-Bird 9
theme
None, User defined
station number
latitude at start time of measurement
longitude at start time of measurement
month_start
day_start
year
time_start
ISO_DateTime_UTC
water pressure
depth
conductivity
water temperature at measurement depth
temperature (temp2) from secondary sensor
fluorescence
Dissolved_Oxygen
scan
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
oceans
NW Atlantic Continental Shelf
-71.4673
-71.4587
39.7763
41.2477
2012-07-06
2012-07-09
NW Atlantic Continental Shelf
0
BCO-DMO catalogue of parameters from CTD data from 39 stations from R/V Cape Hatteras cruise CH0112 in the Northwest Atlantic Continental Shelf in 2012 (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/35109.rdf
Name: sta
Units: unitless
Description: <p>Station ID number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35110.rdf
Name: lat_start
Units: decimal degrees
Description: <p>Latitude at start of CTD cast. North = positive.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35111.rdf
Name: lon_start
Units: decimal degrees
Description: <p>Longitude at start of CTD cast. West = negative.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35112.rdf
Name: month_start
Units: mm (01 to 12)
Description: <p>2-digit month at start of cast.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35113.rdf
Name: day_start
Units: dd (01 to 31)
Description: <p>2-digit day of month at start of cast.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35114.rdf
Name: year
Units: unitless
Description: <p>4-digit year in YYYY format.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35115.rdf
Name: time_start
Units: HHMM.mm
Description: <p>Time at start of cast (UTC).</p>
http://lod.bco-dmo.org/id/dataset-parameter/35116.rdf
Name: ISO_DateTime_UTC
Units: YYYY-MM-DDTHH:MM:SS[.xx]Z
Description: <p>Date/time (UTC) at start of cast formatted to ISO 8601 standard.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35117.rdf
Name: press
Units: decibars
Description: <p>Pressure</p>
http://lod.bco-dmo.org/id/dataset-parameter/35118.rdf
Name: depth
Units: meters
Description: <p>Depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/35119.rdf
Name: cond
Units: S/m
Description: <p>Conductivity in Siemens per meter.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35120.rdf
Name: temp
Units: degrees C
Description: <p>Temperature (degrees Celsius) from primary sensor.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35121.rdf
Name: temp2
Units: degrees C
Description: <p>Temperature (degrees Celsius) from secondary sensor.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35122.rdf
Name: fluor
Units: ug/L
Description: <p>Chlorophyll fluorescence (micrograms per liter) measured by Chelsea Aqua 3 sensor. Fluorescence values should be interpreted as "arbitrary units" <br />because calibrations have not been applied.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35123.rdf
Name: O2
Units: mg/L
Description: <p>Oxygen (milligrams per liter) measured by SBE 43 sensor.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35124.rdf
Name: scan
Units: integer
Description: <p>CTD scan 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
26570671
https://darchive.mblwhoilibrary.org/bitstream/1912/24790/1/dataset-3959_ctdch0112__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.3959.1
download
onLine
dataset
<p>23 stations were sampled along a transect from Narragansett, RI to the shelf break. 16 stations were sampled on the way back.</p>
<p>---------------------------------------------<br />
<strong>Header information from CTD files:</strong><br />
Sea-Bird SBE 9 Data File:<br />
Software Version Seasave V 7.20a<br />
Temperature SN = 0967<br />
Conductivity SN = 0626<br />
Number of Bytes Per Scan = 41<br />
Number of Voltage Words = 4<br />
Number of Scans Averaged by the Deck Unit = 1<br />
Append System Time to Every Scan<br />
---------------------------------------------</p>
Specified by the Principal Investigator(s)
<p>CTD processing:&nbsp; SeaSoft (V 7.20a) was used to convert from hexadecimal raw data, then a low pass filter was made on T and C data, using SeaSoft to synchronize instrument time constants. loopedit was used in SeaSoft to smooth out loops in the CTD path as it went down.</p>
<p>NOTE: Fluorescence values should be interpreted as "arbitrary units" because calibrations have not been applied.</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
CTD Sea-Bird 9
CTD Sea-Bird 9
PI Supplied Instrument Name: CTD Sea-Bird 9 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