http://lod.bco-dmo.org/id/dataset/714300
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
2017-09-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Copepods Parvocalanus crassirostris naupliar ingestion and clearance rates on natural prey assemblages from Kaneohe Bay, Oahu, 2015 (JEMBE 2017) (EAGER: Copepod nauplii project)
2017-09-06
publication
2017-09-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-01-20
publication
https://doi.org/10.26008/1912/bco-dmo.714300.1
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) Copepods Parvocalanus crassirostris naupliar ingestion and clearance rates on natural prey assemblages from Kaneohe Bay, Oahu, 2015 (JEMBE 2017) (EAGER: Copepod nauplii project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-09-06 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.714300.1 [access date]
Naupliar ingestion and clearance rates: JEMBE 2017 Dataset Description: Methods and Sampling: <p>From Jungbluth et al. 2017 – JEMBE:<br />
Naupliar grazing rates were measured on field-collected prey assemblages in bottle incubation experiments in the laboratory.&nbsp;Nauplii&nbsp;used in these experiments were derived from laboratory culture populations of&nbsp;Parvocalanus crassirostris, originally established from animals collected in Kaneʻohe Bay.&nbsp;At 18-h prior to the start of each experiment, adults were isolated and fed&nbsp;Tisochrysis lutea&nbsp;(formerly&nbsp;Isochrysis galbana&nbsp;Tahitian strain [Bendif et al., 2013]) at a concentration of 105–106&nbsp;cells&nbsp;mL−&nbsp;1&nbsp;After 6-h, adults were removed, and eggs and nauplii were allowed to develop for 12-h in order to produce a cohort of mid-stage nauplii (N3-N4) with a narrow age-range at the beginning of each experiment. Sets of approximately 50 nauplii were isolated into small volumes (&lt;&nbsp;10&nbsp;mL) of 0.2&nbsp;μm filtered&nbsp;seawater&nbsp;1–2&nbsp;h prior to the start of each grazing experiment.</p>
<p>Seawater for the prey assemblage was collected from the central basin of the southern semi-enclosed region of Kane'ohe Bay, Oahu, Hawai'i (21°25'56"N, 157°46'47"W) on two dates: 10 March 2015 (Experiment: E1) and 22 April 2015 (Experiment: E2). Seawater was collected from ~ 2 m depth using a 5 L General Oceanics Niskin bottle deployed by hand line, and gently transferred using acid-washed silicon tubing directly from the Niskin bottle into 20 L covered (dark) polycarbonate carboys. The seawater was transported to the laboratory within 2-h of collection. The collected water was gently pre-screened (35 µm Nitex mesh), which was intended to remove all in situ nauplii and other large grazers, so that the only metazoan grazers in the bottles were the added nauplii. The &lt; 35 µm incubation water was added to pre-washed (10% HCL rinse, followed by 3 rinses with experimental seawater) 1 L polycarbonate bottles (total volume: 1120 mL).</p>
<p>Nutrients were not amended in control or treatment bottles due to the expected low rates of excretion by these small biomass nauplii over the incubation duration as compared with baseline levels in Kane'ohe Bay, and also in order to minimize development of artificially high nutrients given prevailing oligotrophic conditions in the study area. Excretion rates of copepods are a function of biomass (Vidal and Whitledge, 1982, Mauchline, 1998), with excretion by nauplii roughly an order of magnitude lower than conspecific adults. At a nauplius grazer concentration of 50 nauplii in a 1 L volume, excretion rates result in values 2 to 3 orders of magnitude below the average nitrogen concentrations of 0.2–1.0 µM in Kane?ohe Bay (Drupp et al., 2011). Therefore, excretion rates in bottle incubations were expected to have negligible impacts on prey growth rates in experimental bottles, and nutrient amendment would have only altered the prey community further away from in situ conditions.</p>
<p>The isolated N3-N4 nauplii were transferred into triplicate &lt; 35 µm incubation water bottles (grazing treatments) and placed on a bottle roller (4–6 rpm) to maintain prey in suspension for the duration of the incubation period. Parallel triplicate control treatments (incubation water without added nauplii) were also placed on the bottle roller. Grazing rates were measured using two densities of naupliar grazers: high (N = 92–97 nauplii L- 1) and moderate (N = 45–50 nauplii L- 1) densities. All incubations were run for a total of 24-h in the dark, with subsamples taken every six hours to examine changes in ingestion rates over time. Experiments were run at 21 °C, which is at the low end of the range of annual temperature fluctuations for this region of Kane'ohe Bay (20–29 °C in prior 5 years [Franklin et al., 2015]).</p>
<p>During the course of the incubation, triplicate 2-mL volumes of each subsample were measured with a Coulter Counter (Beckman-Coulter Multisizer III) with a 100 µm orifice tube, yielding a spectrum of particle sizes from 2 to 35 µm ESD, as well as quantitative abundance data. In a diverse environment with a variety of autotrophic and heterotrophic pico- to microplankton, standard cell quantification methods (e.g. epifluorescence microscopy, inverted microscopy) do not reliably preserve some components of the community (Omori and Ikeda, 1984, Sherr and Sherr, 1993), requiring a patchwork of methods to quantify the full potential suite of prey items. In the absence of large cells or of abiotic particles that may result in unreliable quantification (e.g. Harbison and McAlister, 1980), the Coulter Counter is an appropriate and more reliable means of describing how the abundance of different sized cells change over the duration of grazing incubations (Paffenhöfer, 1984), with results comparable to methods based on gut fluorescence and egg production (Kiørboe et al., 1985). Water subsamples for Coulter Counter measurements were taken directly from experimental bottles upon addition of nauplii at the start of each experiment (time 0) and at each six-hour time point, being careful to retain nauplii as experimental grazers by recovery of animals on a 35 µm cap filter and washing them back into bottles during sub-sampling with a small volume of filtered seawater.</p>
<p>Data on prey size (ESD) and abundance from the Coulter Counter were further processed using R (Core Team, 2013). Prey ESD was converted to biovolume (BV, µm3), then to carbon (C, pg C cell- 1) using the relationship C = 0.216 × BV0.939 (Menden-Deuer and Lessard, 2000). Averages (triplicate Coulter Counter measurements) were binned into 5 functionally relevant prey size groupings (2–5, 5–10, 10–15, 15–20, and 20–35 µm), chosen to ensure comparable data to a prior study of adult copepod grazing in Kane'ohe Bay (Calbet et al., 2000). The binned data for initial and final time points for each control and treatment bottle were used to calculate carbon ingestion (I, ng C grazer- 1 h-1) and clearance (F, mL grazer- 1 h-1) rates on each prey size group using the equations of Frost (1972), and are reported here only where F or I &gt; 0.</p>
<p>Linear regressions were used to evaluate whether there was a relationship between control bottle prey biomass and incubation duration, and between measured ingestion rates (I) and incubation time. An analysis of covariance (ANCOVA) was used to test for significant (p &lt; 0.05) effects of incubation time, predator treatment (Plow, Phigh), and experiment (E1, E2) on carbon ingestion rates (I), and for interactions between variables, accounting for random error due to differences between replicate bottles. The ANCOVAs were performed for each prey size group or total prey using the aov function in the package stat with time, predator treatment, and experiment as potentially interacting factors, and incorporating bottle replicate error as a random effect. The coefficient of variation (CV, %) was calculated for cell abundance estimates and followed by a two-way ANOVA and post-hoc Tukey test to evaluate for the effects of prey size group and incubation time on variation in cell abundance. In many studies of zooplankton grazing (e.g., Atienza et al., 2006, Calbet et al., 2009, Almeda et al., 2011), significant differences in prey growth rates between control and treatment bottles were tested, and then only significantly different conditions were considered in further interpretations of I. Here, significant differences (t-test, p &lt; 0.05) between treatment and control prey growth rates were used to evaluate whether the significance of this test was affected by the duration of incubation. All statistical analyses were conducted using the program R (stats package) (R core team, 2016).</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
species
experiment
treatment
incubation_time
expt_type
prey_type_size_range
biomass_grazing_rate
biomass_grazing_rate_se
clearance_rate
clearance_rate_se
grazing_rate
grazing_rate_se
Beckman Coulter Multisizer III Coulter Counter
theme
None, User defined
taxon
experiment id
treatment
incubation time or duration
experiment type
length_range
Zooplankton feeding
featureType
BCO-DMO Standard Parameters
Coulter Counter
instrument
BCO-DMO Standard Instruments
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
biota
oceans
-157.78
-157.78
21.432
21.432
2015-03-10
2015-03-10
Kaneohe Bay, Oahu, Hawaii
0
BCO-DMO catalogue of parameters from Copepods Parvocalanus crassirostris naupliar ingestion and clearance rates on natural prey assemblages from Kaneohe Bay, Oahu, 2015 (JEMBE 2017) (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/837047.rdf
Name: species
Units: unitless
Description: <p>copepod species used in grazing experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/837048.rdf
Name: experiment
Units: unitless
Description: <p>experiment number: E1 or E2</p>
http://lod.bco-dmo.org/id/dataset-parameter/837049.rdf
Name: treatment
Units: unitless
Description: <p>experimental treatment. PLOW = low predator treatment (50 nauplii L-1); PHIGH = high predator treatment (100 nauplii L-1)</p>
http://lod.bco-dmo.org/id/dataset-parameter/837050.rdf
Name: incubation_time
Units: hours
Description: <p>duration of incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/837051.rdf
Name: expt_type
Units: unitless
Description: <p>whether control or treatment</p>
http://lod.bco-dmo.org/id/dataset-parameter/837052.rdf
Name: prey_type_size_range
Units: micrometers
Description: <p>size range of prey items</p>
http://lod.bco-dmo.org/id/dataset-parameter/837053.rdf
Name: biomass_grazing_rate
Units: nanograms Carbon/nauplius/hour (ng C nauplius-1 h-1)
Description: <p>ingestion rates; biomass grazing rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/837054.rdf
Name: biomass_grazing_rate_se
Units: nanograms Carbon/nauplius/hour (ng C nauplius-1 h-1)
Description: <p>standard error of biomass grazing rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/837055.rdf
Name: clearance_rate
Units: milliliters/nauplius/hour (mL nauplius-1 hour-1)
Description: <p>clearance rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/837056.rdf
Name: clearance_rate_se
Units: milliliters/nauplius/hour (mL nauplius-1 hour-1)
Description: <p>standard error of clearance rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/837057.rdf
Name: grazing_rate
Units: nanograms Carbon/nauplius/hour (ng C nauplius-1 h-1)
Description: <p>grazing rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/837058.rdf
Name: grazing_rate_se
Units: nanograms Carbon/nauplius/hour (ng C nauplius-1 h-1)
Description: <p>standard error of grazing rate</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
7614
https://darchive.mblwhoilibrary.org/bitstream/1912/26593/1/dataset-714300_naupliar-ingestion-jembe-2017__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.714300.1
download
onLine
dataset
<p>From Jungbluth et al. 2017 – JEMBE:<br />
Naupliar grazing rates were measured on field-collected prey assemblages in bottle incubation experiments in the laboratory.&nbsp;Nauplii&nbsp;used in these experiments were derived from laboratory culture populations of&nbsp;Parvocalanus crassirostris, originally established from animals collected in Kaneʻohe Bay.&nbsp;At 18-h prior to the start of each experiment, adults were isolated and fed&nbsp;Tisochrysis lutea&nbsp;(formerly&nbsp;Isochrysis galbana&nbsp;Tahitian strain [Bendif et al., 2013]) at a concentration of 105–106&nbsp;cells&nbsp;mL−&nbsp;1&nbsp;After 6-h, adults were removed, and eggs and nauplii were allowed to develop for 12-h in order to produce a cohort of mid-stage nauplii (N3-N4) with a narrow age-range at the beginning of each experiment. Sets of approximately 50 nauplii were isolated into small volumes (&lt;&nbsp;10&nbsp;mL) of 0.2&nbsp;μm filtered&nbsp;seawater&nbsp;1–2&nbsp;h prior to the start of each grazing experiment.</p>
<p>Seawater for the prey assemblage was collected from the central basin of the southern semi-enclosed region of Kane'ohe Bay, Oahu, Hawai'i (21°25'56"N, 157°46'47"W) on two dates: 10 March 2015 (Experiment: E1) and 22 April 2015 (Experiment: E2). Seawater was collected from ~ 2 m depth using a 5 L General Oceanics Niskin bottle deployed by hand line, and gently transferred using acid-washed silicon tubing directly from the Niskin bottle into 20 L covered (dark) polycarbonate carboys. The seawater was transported to the laboratory within 2-h of collection. The collected water was gently pre-screened (35 µm Nitex mesh), which was intended to remove all in situ nauplii and other large grazers, so that the only metazoan grazers in the bottles were the added nauplii. The &lt; 35 µm incubation water was added to pre-washed (10% HCL rinse, followed by 3 rinses with experimental seawater) 1 L polycarbonate bottles (total volume: 1120 mL).</p>
<p>Nutrients were not amended in control or treatment bottles due to the expected low rates of excretion by these small biomass nauplii over the incubation duration as compared with baseline levels in Kane'ohe Bay, and also in order to minimize development of artificially high nutrients given prevailing oligotrophic conditions in the study area. Excretion rates of copepods are a function of biomass (Vidal and Whitledge, 1982, Mauchline, 1998), with excretion by nauplii roughly an order of magnitude lower than conspecific adults. At a nauplius grazer concentration of 50 nauplii in a 1 L volume, excretion rates result in values 2 to 3 orders of magnitude below the average nitrogen concentrations of 0.2–1.0 µM in Kane?ohe Bay (Drupp et al., 2011). Therefore, excretion rates in bottle incubations were expected to have negligible impacts on prey growth rates in experimental bottles, and nutrient amendment would have only altered the prey community further away from in situ conditions.</p>
<p>The isolated N3-N4 nauplii were transferred into triplicate &lt; 35 µm incubation water bottles (grazing treatments) and placed on a bottle roller (4–6 rpm) to maintain prey in suspension for the duration of the incubation period. Parallel triplicate control treatments (incubation water without added nauplii) were also placed on the bottle roller. Grazing rates were measured using two densities of naupliar grazers: high (N = 92–97 nauplii L- 1) and moderate (N = 45–50 nauplii L- 1) densities. All incubations were run for a total of 24-h in the dark, with subsamples taken every six hours to examine changes in ingestion rates over time. Experiments were run at 21 °C, which is at the low end of the range of annual temperature fluctuations for this region of Kane'ohe Bay (20–29 °C in prior 5 years [Franklin et al., 2015]).</p>
<p>During the course of the incubation, triplicate 2-mL volumes of each subsample were measured with a Coulter Counter (Beckman-Coulter Multisizer III) with a 100 µm orifice tube, yielding a spectrum of particle sizes from 2 to 35 µm ESD, as well as quantitative abundance data. In a diverse environment with a variety of autotrophic and heterotrophic pico- to microplankton, standard cell quantification methods (e.g. epifluorescence microscopy, inverted microscopy) do not reliably preserve some components of the community (Omori and Ikeda, 1984, Sherr and Sherr, 1993), requiring a patchwork of methods to quantify the full potential suite of prey items. In the absence of large cells or of abiotic particles that may result in unreliable quantification (e.g. Harbison and McAlister, 1980), the Coulter Counter is an appropriate and more reliable means of describing how the abundance of different sized cells change over the duration of grazing incubations (Paffenhöfer, 1984), with results comparable to methods based on gut fluorescence and egg production (Kiørboe et al., 1985). Water subsamples for Coulter Counter measurements were taken directly from experimental bottles upon addition of nauplii at the start of each experiment (time 0) and at each six-hour time point, being careful to retain nauplii as experimental grazers by recovery of animals on a 35 µm cap filter and washing them back into bottles during sub-sampling with a small volume of filtered seawater.</p>
<p>Data on prey size (ESD) and abundance from the Coulter Counter were further processed using R (Core Team, 2013). Prey ESD was converted to biovolume (BV, µm3), then to carbon (C, pg C cell- 1) using the relationship C = 0.216 × BV0.939 (Menden-Deuer and Lessard, 2000). Averages (triplicate Coulter Counter measurements) were binned into 5 functionally relevant prey size groupings (2–5, 5–10, 10–15, 15–20, and 20–35 µm), chosen to ensure comparable data to a prior study of adult copepod grazing in Kane'ohe Bay (Calbet et al., 2000). The binned data for initial and final time points for each control and treatment bottle were used to calculate carbon ingestion (I, ng C grazer- 1 h-1) and clearance (F, mL grazer- 1 h-1) rates on each prey size group using the equations of Frost (1972), and are reported here only where F or I &gt; 0.</p>
<p>Linear regressions were used to evaluate whether there was a relationship between control bottle prey biomass and incubation duration, and between measured ingestion rates (I) and incubation time. An analysis of covariance (ANCOVA) was used to test for significant (p &lt; 0.05) effects of incubation time, predator treatment (Plow, Phigh), and experiment (E1, E2) on carbon ingestion rates (I), and for interactions between variables, accounting for random error due to differences between replicate bottles. The ANCOVAs were performed for each prey size group or total prey using the aov function in the package stat with time, predator treatment, and experiment as potentially interacting factors, and incorporating bottle replicate error as a random effect. The coefficient of variation (CV, %) was calculated for cell abundance estimates and followed by a two-way ANOVA and post-hoc Tukey test to evaluate for the effects of prey size group and incubation time on variation in cell abundance. In many studies of zooplankton grazing (e.g., Atienza et al., 2006, Calbet et al., 2009, Almeda et al., 2011), significant differences in prey growth rates between control and treatment bottles were tested, and then only significantly different conditions were considered in further interpretations of I. Here, significant differences (t-test, p &lt; 0.05) between treatment and control prey growth rates were used to evaluate whether the significance of this test was affected by the duration of incubation. All statistical analyses were conducted using the program R (stats package) (R core team, 2016).</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong></p>
<p>- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions</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
Beckman Coulter Multisizer III Coulter Counter
Beckman Coulter Multisizer III Coulter Counter
PI Supplied Instrument Name: Beckman Coulter Multisizer III Coulter Counter PI Supplied Instrument Description:100 µm orifice tube Instrument Name: Coulter Counter Instrument Short Name: Instrument Description: An apparatus for counting and sizing particles suspended in electrolytes. It is used for cells, bacteria, prokaryotic cells and virus particles. A typical Coulter counter has one or more microchannels that separate two chambers containing electrolyte solutions.
from https://en.wikipedia.org/wiki/Coulter_counter