http://lod.bco-dmo.org/id/dataset/712344
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
2017-08-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Initial field conditions at Kane‘ohe Bay, Oahu, Hawaii and abundances of Parvocalanus crassirostris and Bestilina similis nauplii, May/June 2013 (EAGER: Copepod nauplii project)
2017-08-07
publication
2017-08-07
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-01-20
publication
https://doi.org/10.26008/1912/bco-dmo.712344.1
Erica Goetze
University of Hawaiʻi at Mānoa
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: Goetze, E. (2021) Initial field conditions at Kane‘ohe Bay, Oahu, Hawaii and abundances of Parvocalanus crassirostris and Bestilina similis nauplii, May/June 2013 (EAGER: Copepod nauplii project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-08-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.712344.1 [access date]
Initial conditions and naupliar abundances of Parvocalanus crassirostris and Bestilina similis: MEPS 2017 Dataset Description: Methods and Sampling: <p>From Jungbluth et al. 2017 – MEPS:</p>
<p><strong>Estimates of in situ naupliar abundance</strong></p>
<p>Naupliar abundances of the 2 target species in situ were estimated using a quantitative polymerase chain reaction (qPCR)-based method (Jungbluth et al. 2013), as well as microscopic counts of calanoid and cyclopoid nauplii. The qPCR-based method allows application of individual species grazing rates to in situ abundances to estimate the total potential grazing impact of each species. Samples were collected by duplicate vertical microplankton net tows (0.5 m diameter ring net, 63 µm mesh) from near bottom (10 m depth) to the surface with a low speed flow meter (General Oceanics). The contents of each net were split quantitatively. One half was size-fractionated through a series of 5 Nitex sieves (63, 75, 80, 100, and 123 µm) to separate size groups of nauplii from later developmental stages, and each was preserved in 95% non-denatured ethyl alcohol (EtOH). The second half of the sample was preserved immediately in 95% EtOH for counts of total calanoid and total cyclopoid nauplii, which were used for comparison to the qPCR-based results of the abundance of each calanoid species. All samples were stored on ice in the field until being transferred to a -20°C freezer in the laboratory. EtOH in the sample bottles was replaced with fresh EtOH within 12 to 24 h of collection to ensure high-quality DNA for analysis (Bucklin 2000).</p>
<p>The 3 smallest plankton size fractions from the net collection were analyzed with qPCR to enumerate <em>P. crassirostris </em>and <em>B. similis</em> nauplius abundances (Jungbluth et al. 2013). In brief, DNA was extracted from 3 plankton size fractions (63, 75, and 80 µm) using a modified QIAamp Mini Kit procedure (Qiagen). The total number of DNA copies in each sample was then measured using species-specific DNA primers and qPCR protocols (Jungbluth et al. 2013). On each qPCR plate, 4 to 5 standards spanning 4 to 5 orders of magnitude in DNA copy number were run along with the 2 biological replicates of a size fraction for each sampling date along with a no template control (NTC), all in triplicate. A range of 0.04 to 1 ng µl-1 of total DNA per sample was measured on each plate ensuring that the range of standards encompassed the amplification range of samples, with equal total DNA concentrations run in each well on individual plates. In all cases, amplification efficiencies ranged from 92 to 102%, and melt-curves indicated amplification of only the target species. The qPCR estimate of each species' mitochondrial cytochrome oxidase c subunit I (COI) DNA copy number was converted to an estimate of nauplius abundance using methods described in Jungbluth et al. (2013).</p>
<p><strong>Conditions</strong></p>
<p>Salinity and temperature in the field were measured using a YSI 6600V2 sonde prior to collecting water for bottle incubations. For chl a, triplicate 305 ml samples were filtered onto GF/Fs (Whatman), flash-frozen (LN2), and kept at -80°C freezer until measurements were made 4 mo later. Chl a (and phaeopigment) was measured using a Turner Designs (model 10AU) fluorometer, using the standard extraction and acidification technique (Yentsch &amp; Menzel 1963, Strickland &amp; Parsons 1972).</p>
<p>For complete methodology, see the Supplemental Files section.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1255697 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1255697
completed
Erica Goetze
University of Hawaiʻi at Mānoa
808-956-7156
Department of Oceanography, University of Hawaii at Manoa 1000 Pope Road
Honolulu
HI
96822
United States
egoetze@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
experiment
date_local
lat
lon
sal
temp
chl_a
chl_std_err
counted_total_nauplii
counted_total_nauplii_se
qPCR_Parvocalanus
qPCR_Parvocalanus_se
qPCR_Bestiolina
qPCR_Bestiolina_se
General Oceanics Digital Flowmeter
microplankton net
Roche LC96 thermalcycler
theme
None, User defined
experiment id
No BCO-DMO term
latitude
longitude
salinity
water temperature at measurement depth
chlorophyll a
abundance
featureType
BCO-DMO Standard Parameters
Flow Meter
Microscope - Optical
Plankton Net
qPCR Thermal Cycler
instrument
BCO-DMO Standard Instruments
Goetze_2012-2013
service
Deployment Activity
Kaneohe Bay, HI
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.
EAGER: New molecular methods for studying copepod nauplii in the field
https://osprey.bco-dmo.org/project/473049
EAGER: New molecular methods for studying copepod nauplii in the field
<p><em>Description from NSF Award Abstract:</em><br />
The most abundant metazoans in the open sea are often the earliest developmental stages of copepods, their nauplii. Nauplii remain under-studied due to the limitations of conventional techniques and an historical emphasis on studying the larger mesozooplankton. However, there is increasing recognition that nauplii play important roles in food web dynamics, and considerable evidence that nauplii may be important trophic intermediaries between microbial and classical food webs due to their high abundance, high weight-specific ingestion rates, and ability to feed on relatively small particles. This team of investigators is developing a novel molecular approach to studying diverse populations of nauplii in mixed field samples based on quantitative Polymerase Chain Reaction (qPCR). They propose to complete development and validation of this qPCR-based technique for enumeration of nauplii, and evaluate its utility in the field. The specific objectives of this research are to identify and reduce technical and biological sources of error in the methodology, determine the accuracy of the method across a range of environmental conditions, and complete one paired field experiment that compares the grazing impact of naupliar and protozoan micro-grazers in a model subtropical coastal ecosystem.</p>
<p><strong>Note:</strong> This project is funded by an NSF EAGER award.</p>
<p><em>Related publications:</em><br />
Jungbluth, M.J., Goetze, E., and Lenz, P.H. 2013. Measuring copepod naupliar abundance in a subtropical bay using quantitative PCR. Marine Biology, 160: 3125-3141. doi: <a href="http://dx.doi.org/10.1007/s00227-013-2300-y" target="_blank">10.1007/s00227-013-2300-y</a></p>
<p>Jungbluth, M.J., and Lenz, P.H. 2013. Copepod diversity in a subtropical bay based on a fragment of the mitochondrial COI gene. Journal of Plankton Research, 35(3): 630-643. doi: <a href="http://dx.doi.org/10.1093/plankt/fbt015" target="_blank">10.1093/plankt/fbt015</a></p>
EAGER: Copepod nauplii
largerWorkCitation
project
eng; USA
oceans
Kaneohe Bay, HI
-157.78
-157.78
21.432
21.432
2013-05-27
2013-06-05
Kaneohe Bay, Oahu, Hawaii
0
BCO-DMO catalogue of parameters from Initial field conditions at Kane‘ohe Bay, Oahu, Hawaii and abundances of Parvocalanus crassirostris and Bestilina similis nauplii, May/June 2013 (EAGER: Copepod nauplii 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/714215.rdf
Name: experiment
Units: unitless
Description: <p>experiment number</p>
http://lod.bco-dmo.org/id/dataset-parameter/714216.rdf
Name: date_local
Units: unitless
Description: <p>local date formatted as yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/714217.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/714218.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/714219.rdf
Name: sal
Units: ppt
Description: <p>seawater salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/714220.rdf
Name: temp
Units: degrees celcius
Description: <p>seawater temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/714221.rdf
Name: chl_a
Units: micrograms/liter
Description: <p>chlorophyll-a concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/714222.rdf
Name: chl_std_err
Units: micrograms/liter
Description: <p>standard error of chl_a concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/714223.rdf
Name: counted_total_nauplii
Units: nauplii/liter
Description: <p>counted abundance of total nauplius population</p>
http://lod.bco-dmo.org/id/dataset-parameter/714224.rdf
Name: counted_total_nauplii_se
Units: nauplii/liter
Description: <p>standard error of counted_total_nauplii</p>
http://lod.bco-dmo.org/id/dataset-parameter/714225.rdf
Name: qPCR_Parvocalanus
Units: nauplii/liter
Description: <p>abundance of Parvocalanus crassirostris nauplii based on qPCR</p>
http://lod.bco-dmo.org/id/dataset-parameter/714226.rdf
Name: qPCR_Parvocalanus_se
Units: nauplii/liter
Description: <p>standard error of qPCR_Parvocalanus</p>
http://lod.bco-dmo.org/id/dataset-parameter/714227.rdf
Name: qPCR_Bestiolina
Units: nauplii/liter
Description: <p>abundance of Bestiolina similis nauplii based on qPCR</p>
http://lod.bco-dmo.org/id/dataset-parameter/714228.rdf
Name: qPCR_Bestiolina_se
Units: nauplii/liter
Description: <p>standard error fo qPCR_Bestiolina</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
592
https://darchive.mblwhoilibrary.org/bitstream/1912/26596/1/dataset-712344_initial-conditions-and-naupliar-abundances-meps-2017__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.712344.1
download
onLine
dataset
<p>From Jungbluth et al. 2017 – MEPS:</p>
<p><strong>Estimates of in situ naupliar abundance</strong></p>
<p>Naupliar abundances of the 2 target species in situ were estimated using a quantitative polymerase chain reaction (qPCR)-based method (Jungbluth et al. 2013), as well as microscopic counts of calanoid and cyclopoid nauplii. The qPCR-based method allows application of individual species grazing rates to in situ abundances to estimate the total potential grazing impact of each species. Samples were collected by duplicate vertical microplankton net tows (0.5 m diameter ring net, 63 µm mesh) from near bottom (10 m depth) to the surface with a low speed flow meter (General Oceanics). The contents of each net were split quantitatively. One half was size-fractionated through a series of 5 Nitex sieves (63, 75, 80, 100, and 123 µm) to separate size groups of nauplii from later developmental stages, and each was preserved in 95% non-denatured ethyl alcohol (EtOH). The second half of the sample was preserved immediately in 95% EtOH for counts of total calanoid and total cyclopoid nauplii, which were used for comparison to the qPCR-based results of the abundance of each calanoid species. All samples were stored on ice in the field until being transferred to a -20°C freezer in the laboratory. EtOH in the sample bottles was replaced with fresh EtOH within 12 to 24 h of collection to ensure high-quality DNA for analysis (Bucklin 2000).</p>
<p>The 3 smallest plankton size fractions from the net collection were analyzed with qPCR to enumerate <em>P. crassirostris </em>and <em>B. similis</em> nauplius abundances (Jungbluth et al. 2013). In brief, DNA was extracted from 3 plankton size fractions (63, 75, and 80 µm) using a modified QIAamp Mini Kit procedure (Qiagen). The total number of DNA copies in each sample was then measured using species-specific DNA primers and qPCR protocols (Jungbluth et al. 2013). On each qPCR plate, 4 to 5 standards spanning 4 to 5 orders of magnitude in DNA copy number were run along with the 2 biological replicates of a size fraction for each sampling date along with a no template control (NTC), all in triplicate. A range of 0.04 to 1 ng µl-1 of total DNA per sample was measured on each plate ensuring that the range of standards encompassed the amplification range of samples, with equal total DNA concentrations run in each well on individual plates. In all cases, amplification efficiencies ranged from 92 to 102%, and melt-curves indicated amplification of only the target species. The qPCR estimate of each species' mitochondrial cytochrome oxidase c subunit I (COI) DNA copy number was converted to an estimate of nauplius abundance using methods described in Jungbluth et al. (2013).</p>
<p><strong>Conditions</strong></p>
<p>Salinity and temperature in the field were measured using a YSI 6600V2 sonde prior to collecting water for bottle incubations. For chl a, triplicate 305 ml samples were filtered onto GF/Fs (Whatman), flash-frozen (LN2), and kept at -80°C freezer until measurements were made 4 mo later. Chl a (and phaeopigment) was measured using a Turner Designs (model 10AU) fluorometer, using the standard extraction and acidification technique (Yentsch &amp; Menzel 1963, Strickland &amp; Parsons 1972).</p>
<p>For complete methodology, see the Supplemental Files section.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- reformatted date from d-Mon-yy to yyyy-mm-dd</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
General Oceanics Digital Flowmeter
General Oceanics Digital Flowmeter
PI Supplied Instrument Name: General Oceanics Digital Flowmeter PI Supplied Instrument Description:Low velocity rotor Instrument Name: Flow Meter Instrument Short Name:Flow Meter Instrument Description: General term for a sensor that quantifies the rate at which fluids (e.g. water or air) pass through sensor packages, instruments, or sampling devices. A flow meter may be mechanical, optical, electromagnetic, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/388/
PI Supplied Instrument Name: Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
microplankton net
microplankton net
PI Supplied Instrument Name: microplankton net PI Supplied Instrument Description:0.5 m diameter ring net, 63 µm mesh Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
Roche LC96 thermalcycler
Roche LC96 thermalcycler
PI Supplied Instrument Name: Roche LC96 thermalcycler Instrument Name: qPCR Thermal Cycler Instrument Short Name:qPCR Instrument Description: An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).
Deployment: Goetze_2012-2013
Goetze_2012-2013
lab UHawaii_SOEST
laboratory
Goetze_2012-2013
Erica Goetze
University of Hawaiʻi at Mānoa
lab UHawaii_SOEST
laboratory