http://lod.bco-dmo.org/id/dataset/779368
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
2019-10-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Continuous culture studies of possible climate change effects: Thalassiosira pseudonana CCMP1335 growth in nitrate-limited and nutrient-replete cultures
2020-05-07
publication
2020-05-07
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-09-30
publication
https://doi.org/10.26008/1912/bco-dmo.779368.1
Edward Laws
Louisiana State University College of the Coast and Environment
principalInvestigator
Uta Passow
University of California-Santa Barbara
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: Laws, E., Passow, U. (2020) Continuous culture studies of possible climate change effects: Thalassiosira pseudonana CCMP1335 growth in nitrate-limited and nutrient-replete cultures. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-05-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.779368.1 [access date]
Thalassiosira pseudonana: NO3-limited and nutrient-replete cultures Dataset Description: <p>The marine diatom <em>Thalassiosira pseudonana</em> clone CCMP 1335 was grown in a continuous culture system on a 14:10 light-dark cycle under either nitrate-limited or nutrient-replete conditions, a photoperiod irradiance of either 50 or 300 micro-mol photons per square meter per second, partial pressures of either 400 or 1000 ppm CO2, and temperatures ranging from 5 to 32 degrees Celsius. Growth rates, photosynthetic rates, respiration rates, C:N ratios, C:Chlorophyll-a ratios, productivity indices, Fv/Fm ratios, and the initial slope and light-saturated asymptote of short-term photosynthesis-irradiance curves are reported.</p> Methods and Sampling: <p>The culture was grown in either a nitrate-limited or nutrient-replete continuous culture system on a 14:10 L:D cycle of illumination at temperatures of 5, 10, 15, 20, 25, 30, 31, and 32°C. The irradiance during the photoperiod was either 50 or 300 micro-mol photons m–2&nbsp;s–1. Photosynthetically active radiation (400–700 nm) was measured with a Biospherical Instruments model QSL 2100 quantum sensor. Temperature was controlled to within 0.1°C by circulating water from a Haake model DC10 temperature-controlled water bath through the outer jacket of the reaction chamber. The dilution rate of the growth chamber was controlled with a peristaltic pump (Masterflex Model 77200-60) to within ± 0.002 per day. The CO2 concentration in the laboratory was monitored with a CO2METER model AZ-004 meter calibrated at 0 and 400 ppm CO2&nbsp;with a standard gas mixture.</p>
<p>The system was judged to be in steady state when cell counts, measured with a Beckman Coulter model Z1 particle counter, had been reproducible to within ± 2% for at least 4 doubling times. Chlorophyll&nbsp;a&nbsp;concentrations were determined from samples collected on glass fiber filters and extracted in methanol. The absorbances were measured at 664 and 750 nm with a Cary Model 50 spectrophotometer. Concentrations of particulate carbon (PC) and particulate nitrogen (PN) were determined by filtering replicate 50-mL samples from the growth chamber onto GF/F glass fiber filters followed by analysis with an Exeter Analytical model CE-440 elemental analyzer. pH was measured with a Thermo Spectronic Heios spectrophotometer, as described in SOP 6B by&nbsp;Dickson, et al 2007&nbsp;with minor modifications, and with a Hach SensION model PH31 pH meter calibrated with standards on the total pH scale, prepared as per Millero, F.J., et al. "The use of buffers to measure the pH of seawater."&nbsp;Marine Chemistry&nbsp;44.2 (1993): 143-152, with minor modifications.</p>
<p>The growth medium consisted of artificial seawater with a total alkalinity of 2365 meq per liter. Nutrient concentrations corresponded to f/2 medium, with the exception of trace metals, which were added at the concentrations specified by Sunda and Hardison (Limnology &amp; Oceanography 52[6]:&nbsp; 2496–2506 [2007]). The nitrate concentration in the nitrate-limited experiments was 20 micromolar. The medium was sterile filtered (0.2 micron) into a 40-liter glass carboy that had been previously autoclaved. The growth chamber was an autoclaved glass reaction flask with a working volume of 2183 mL. In the first few experiments, the cells in the growth chamber were uniformly labeled with C-14 by adding 20 microcuries of C-14 bicarbonate to the nutrient reservoir to facilitate monitoring the concentration of organic carbon in the growth chamber. In those first few experiments, five-milliliter samples for C-14 activity in the organic carbon were withdrawn in triplicate from the growth chamber at two-hour intervals during the photoperiod. The samples were acidified with 1 mL of 1 N HCl to drive off inorganic carbon. The activity of C-14 in the samples was then determined by counting on a Packard Tri-Carb model 3100 TR liquid scintillation counter. During those first few studies, we determined that addition of C-14 in this way was unnecessary because we could adequately monitor the concentrations of PC by withdrawing samples for CHN analysis. Subsequent experiments relied entirely on CHN analyses for determination of particulate carbon and nitrogen concentrations.</p>
<p>Short-term (5-minute) photosynthesis-versus-irradiance curves (P-E curves) were measured at the start, middle, and end of the photoperiod. For these experiments, triplicate 5-mL aliquots from the growth chamber were added to liquid scintillation vials pre-inoculated with 0.85 microcuries of C-14 bicarbonate. The vials were incubated at irradiances of 5, 10, 20, 30, 55, 80, 120, 150, 200, 250, 300, and 350 micro-mol photons per square meter per second&nbsp;for 5 minutes. Fixation was stopped by adding 0.5 mL of 1 N HCl to the vials. Total alkalinity was determined using the open cell titration method described as SOP 3B by&nbsp;Dickson, et al 2007. DIC concentrations were then calculated from temperature, salinity, total alkalinity, and pH using the equations in Zeebe and Wolf-Gladrow, CO2&nbsp;in Seawater: Equilibrium, Kinetics, Isotopes.</p>
<p>Photosynthetic rates in these short-term experiments were found to be best described by a hyperbolic tangent function of the form P = Pm*tanh(E*alpha/Pm), where E is the irradiance, alpha is the initial slope of the photosynthesis-irradiance curve, and Pm is the asymptotic light-saturated photosynthetic rate. The values of Pm with units of grams carbon per gram chlorophyll&nbsp;a&nbsp;per hour and the value of alpha with units of meters squared (carbons/photon) per gram chlorophyll a were determined by least squares.&nbsp;</p>
<p>Measurements of Fv/Fm ratios (the ratio of variable fluorescence to maximal fluorescence after dark adaptation) were made within 30 minutes of each P-E assay, using a Z985 AquaPen fluorometer (Qubit Systems). Briefly, a 4-mL aliquot of culture from the growth chamber was added to each of three plastic 1-cm cuvettes, and each cuvette was immediately wrapped in aluminum foil. The cuvettes were incubated at the growth chamber temperature for 30–40 minutes, after which the foil was removed and a single Fv/Fm measurement was made on each cuvette in a darkened room. The background-corrected Fv/Fm ratio was automatically calculated by the AquaPen software. The light intensities of the saturating pulse and measurement pulse were 2100 and 0.03 micro-mol photons per square meter per second, respectively, both at a wavelength of 450 nm.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1536581 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1536581
completed
Edward Laws
Louisiana State University College of the Coast and Environment
225 578-3334
Louisiana State University School of the Coast and Environment 1002R Energy, Coast and Environment Building
Baton Rouge
LA
70803
USA
edlaws@lsu.edu
pointOfContact
Uta Passow
University of California-Santa Barbara
709-864-8010
Ocean Sciences Centre, Memorial University Marine Lab Road, Logy Bay
St. John's
Newfoundland
A1C 5S7
Canada
uta.passow@mun.ca
pointOfContact
asNeeded
Dataset Version: 1
Unknown
date
temp
limiting_factor
irradiance
pCO2
irrad_CO2
growth_day
growth_relative
PI_mean
dark_resp_day
dark_resp_growth
Fv_FM
PM_lights_on
PM_midday
PM_lights_off
PM_mean
PM_stderr
alpha_lights_on
alpha_midday
alpha_lights_off
alpha_mean
alpha_stderr
C_to_N
C_to_chl
N_to_chl
P_PM
growth_stdev_n
Hach SensION model PH31 pH meter
Cary Model 50 spectrophotometer
an Exeter Analytical model CE-440 elemental analyzer
Beckman Coulter model Z1 particle counter
PSI AquaPen C100
Z985 Cuvette Aquapen (Qubit Systems)
Packard Tri-Carb model 3100 TR liquid scintillation counter
CO2METER model AZ-004
Masterflex Model 77200-60 peristaltic pump
Biospherical Instruments model QSL 2100 quantum sensor
Thermo Spectronic Heios spectrophotometer
theme
None, User defined
date_local
water temperature at measurement depth
treatment
irradiance
Partial pressure of CO2
growth
production
respiration rate
No BCO-DMO term
Fv to Fm ratio
max photosynthesis
alpha
Carbon to Nitrogen ratio (C:N)
featureType
BCO-DMO Standard Parameters
Benchtop pH Meter
Cary 50 spectrophotometer
Chemostat
CHN Elemental Analyzer
Coulter Counter
Fluorometer
Fluorometer
Liquid Scintillation Counter
pCO2 Sensor
Pump
Radiometer
Spectrophotometer
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.
Collaborative Research: Effects of multiple stressors on Marine Phytoplankton
https://osprey.bco-dmo.org/project/654347
Collaborative Research: Effects of multiple stressors on Marine Phytoplankton
<p>The overarching goal of this project is to develop a framework for understanding the response of phytoplankton to multiple environmental stresses. Marine phytoplankton, which are tiny algae, produce as much oxygen as terrestrial plants and provide food, directly or indirectly, to all marine animals. Their productivity is thus important both for global elemental cycles of oxygen and carbon, as well as for the productivity of the ocean. Globally the productivity of marine phytoplankton appears to be changing, but while we have some understanding of the response of phytoplankton to shifts in one environmental parameter at a time, like temperature, there is very little knowledge of their response to simultaneous changes in several parameters. Increased atmospheric carbon dioxide concentrations result in both ocean acidification and increased surface water temperatures. The latter in turn leads to greater ocean stratification and associated changes in light exposure and nutrient availability for the plankton. Recently it has become apparent that the response of phytoplankton to simultaneous changes in these growth parameters is not additive. For example, the effect of ocean acidification may be severe at one temperature-light combination and negligible at another. The researchers of this project will carry out experiments that will provide a theoretical understanding of the relevant interactions so that the impact of climate change on marine phytoplankton can be predicted in an informed way. This project will engage high schools students through training of a teacher and the development of a teaching unit. Undergraduate and graduate students will work directly on the research. A cartoon journalist will create a cartoon story on the research results to translate the findings to a broader general public audience.</p>
<p>Each phytoplankton species has the capability to acclimatize to changes in temperature, light, pCO2, and nutrient availability - at least within a finite range. However, the response of phytoplankton to multiple simultaneous stressors is frequently complex, because the effects on physiological responses are interactive. To date, no datasets exist for even a single species that could fully test the assumptions and implications of existing models of phytoplankton acclimation to multiple environmental stressors. The investigators will combine modeling analysis with laboratory experiments to investigate the combined influences of changes in pCO2, temperature, light, and nitrate availability on phytoplankton growth using cultures of open ocean and coastal diatom strains (Thalassiosira pseudonana) and an open ocean cyanobacteria species (Synechococcus sp.). The planned experiments represent ideal case studies of the complex and interactive effects of environmental conditions on organisms, and results will provide the basis for predictive modeling of the response of phytoplankton taxa to multiple environmental stresses.</p>
Stressors on Marine Phytoplankton
largerWorkCitation
project
eng; USA
biota
oceans
-91.18412
-91.18412
30.4089
30.4089
2016-01-25
2019-10-01
0
BCO-DMO catalogue of parameters from Continuous culture studies of possible climate change effects: Thalassiosira pseudonana CCMP1335 growth in nitrate-limited and nutrient-replete cultures
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/779391.rdf
Name: date
Units: unitless
Description: <p>sampling date formatted as yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/779392.rdf
Name: temp
Units: degrees Celsius
Description: <p>temperature of culture</p>
http://lod.bco-dmo.org/id/dataset-parameter/779393.rdf
Name: limiting_factor
Units: unitless
Description: <p>limiting factor</p>
http://lod.bco-dmo.org/id/dataset-parameter/779394.rdf
Name: irradiance
Units: micromole photons/meter^2/second
Description: <p>irradiance during photoperiod</p>
http://lod.bco-dmo.org/id/dataset-parameter/779395.rdf
Name: pCO2
Units: parts per million by volume
Description: <p>partial pressure of carbon dioxide</p>
http://lod.bco-dmo.org/id/dataset-parameter/779396.rdf
Name: irrad_CO2
Units: unitless
Description: <p>Irradiance-CO2 combination: H = high; L = low</p>
http://lod.bco-dmo.org/id/dataset-parameter/779397.rdf
Name: growth_day
Units: per day
Description: <p>growth rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/779398.rdf
Name: growth_relative
Units: per day
Description: <p>relative growth rate: the ratio of the nutrient-limited growth rate to the nutrient-replete growth rate under otherwise identical conditions. Therefore the relative growth rates of nutrient-replete cultures are automatically 1.</p>
http://lod.bco-dmo.org/id/dataset-parameter/779399.rdf
Name: PI_mean
Units: grams Carbon/gram chl/hour
Description: <p>mean of the Productivity-Irradiance curve</p>
http://lod.bco-dmo.org/id/dataset-parameter/779400.rdf
Name: dark_resp_day
Units: per day
Description: <p>dark respiration rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/779401.rdf
Name: dark_resp_growth
Units: unitless
Description: <p>dark respiration/growth rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/779402.rdf
Name: Fv_FM
Units: unitless
Description: <p>maximum quantum yield (QY=Fv/Fm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/779403.rdf
Name: PM_lights_on
Units: grams Carbon/gram chl/hour
Description: <p>maximum photosynthetic rate at lights on</p>
http://lod.bco-dmo.org/id/dataset-parameter/779404.rdf
Name: PM_midday
Units: grams Carbon/gram chl/hour
Description: <p>maximum photosynthetic rate at midday</p>
http://lod.bco-dmo.org/id/dataset-parameter/779405.rdf
Name: PM_lights_off
Units: grams Carbon/gram chl/hour
Description: <p>maximum photosynthetic rate at lights off</p>
http://lod.bco-dmo.org/id/dataset-parameter/779406.rdf
Name: PM_mean
Units: grams Carbon/gram chl/hour
Description: <p>mean maximum photosynthetic rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/779407.rdf
Name: PM_stderr
Units: grams Carbon/gram chl/hour
Description: <p>standard error of mean maximum photosynthetic rate</p>
http://lod.bco-dmo.org/id/dataset-parameter/779408.rdf
Name: alpha_lights_on
Units: meters^2(moles Carbon/moles photons)/gram chla
Description: <p>alpha at lights on</p>
http://lod.bco-dmo.org/id/dataset-parameter/779409.rdf
Name: alpha_midday
Units: meters^2(moles Carbon/moles photons)/gram chla
Description: <p>alpha at midday</p>
http://lod.bco-dmo.org/id/dataset-parameter/779410.rdf
Name: alpha_lights_off
Units: meters^2(moles Carbon/moles photons)/gram chla
Description: <p>alpha at lights off</p>
http://lod.bco-dmo.org/id/dataset-parameter/779411.rdf
Name: alpha_mean
Units: meters^2(moles Carbon/moles photons)/gram chla
Description: <p>mean alpha</p>
http://lod.bco-dmo.org/id/dataset-parameter/779412.rdf
Name: alpha_stderr
Units: meters^2(moles Carbon/moles photons)/gram chla
Description: <p>standard error of mean alpha</p>
http://lod.bco-dmo.org/id/dataset-parameter/779413.rdf
Name: C_to_N
Units: unitless (grams/grams)
Description: <p>Carbon:Nitrogen ratio</p>
http://lod.bco-dmo.org/id/dataset-parameter/779414.rdf
Name: C_to_chl
Units: unitless (grams/grams)
Description: <p>Carbon:chlorophyll ratio</p>
http://lod.bco-dmo.org/id/dataset-parameter/779415.rdf
Name: N_to_chl
Units: unitless (grams/grams)
Description: <p>Nitrogen:chlorophyll ratio</p>
http://lod.bco-dmo.org/id/dataset-parameter/779416.rdf
Name: P_PM
Units: unitless
Description: <p>Ratio of mean photosynthesis to maximum photosynthetic production (P/PM)</p>
http://lod.bco-dmo.org/id/dataset-parameter/810854.rdf
Name: growth_stdev_n
Units: per day
Description: <p>This column contains both the standard deviation of the daily growth, plus the number of values used in the calculation.</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
6710
https://darchive.mblwhoilibrary.org/bitstream/1912/26245/1/dataset-779368_thalassiosira-pseudonana-ccmp1335-nitrate-limited-and-nutrient-replete-cultures__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.779368.1
download
onLine
dataset
<p>The culture was grown in either a nitrate-limited or nutrient-replete continuous culture system on a 14:10 L:D cycle of illumination at temperatures of 5, 10, 15, 20, 25, 30, 31, and 32°C. The irradiance during the photoperiod was either 50 or 300 micro-mol photons m–2&nbsp;s–1. Photosynthetically active radiation (400–700 nm) was measured with a Biospherical Instruments model QSL 2100 quantum sensor. Temperature was controlled to within 0.1°C by circulating water from a Haake model DC10 temperature-controlled water bath through the outer jacket of the reaction chamber. The dilution rate of the growth chamber was controlled with a peristaltic pump (Masterflex Model 77200-60) to within ± 0.002 per day. The CO2 concentration in the laboratory was monitored with a CO2METER model AZ-004 meter calibrated at 0 and 400 ppm CO2&nbsp;with a standard gas mixture.</p>
<p>The system was judged to be in steady state when cell counts, measured with a Beckman Coulter model Z1 particle counter, had been reproducible to within ± 2% for at least 4 doubling times. Chlorophyll&nbsp;a&nbsp;concentrations were determined from samples collected on glass fiber filters and extracted in methanol. The absorbances were measured at 664 and 750 nm with a Cary Model 50 spectrophotometer. Concentrations of particulate carbon (PC) and particulate nitrogen (PN) were determined by filtering replicate 50-mL samples from the growth chamber onto GF/F glass fiber filters followed by analysis with an Exeter Analytical model CE-440 elemental analyzer. pH was measured with a Thermo Spectronic Heios spectrophotometer, as described in SOP 6B by&nbsp;Dickson, et al 2007&nbsp;with minor modifications, and with a Hach SensION model PH31 pH meter calibrated with standards on the total pH scale, prepared as per Millero, F.J., et al. "The use of buffers to measure the pH of seawater."&nbsp;Marine Chemistry&nbsp;44.2 (1993): 143-152, with minor modifications.</p>
<p>The growth medium consisted of artificial seawater with a total alkalinity of 2365 meq per liter. Nutrient concentrations corresponded to f/2 medium, with the exception of trace metals, which were added at the concentrations specified by Sunda and Hardison (Limnology &amp; Oceanography 52[6]:&nbsp; 2496–2506 [2007]). The nitrate concentration in the nitrate-limited experiments was 20 micromolar. The medium was sterile filtered (0.2 micron) into a 40-liter glass carboy that had been previously autoclaved. The growth chamber was an autoclaved glass reaction flask with a working volume of 2183 mL. In the first few experiments, the cells in the growth chamber were uniformly labeled with C-14 by adding 20 microcuries of C-14 bicarbonate to the nutrient reservoir to facilitate monitoring the concentration of organic carbon in the growth chamber. In those first few experiments, five-milliliter samples for C-14 activity in the organic carbon were withdrawn in triplicate from the growth chamber at two-hour intervals during the photoperiod. The samples were acidified with 1 mL of 1 N HCl to drive off inorganic carbon. The activity of C-14 in the samples was then determined by counting on a Packard Tri-Carb model 3100 TR liquid scintillation counter. During those first few studies, we determined that addition of C-14 in this way was unnecessary because we could adequately monitor the concentrations of PC by withdrawing samples for CHN analysis. Subsequent experiments relied entirely on CHN analyses for determination of particulate carbon and nitrogen concentrations.</p>
<p>Short-term (5-minute) photosynthesis-versus-irradiance curves (P-E curves) were measured at the start, middle, and end of the photoperiod. For these experiments, triplicate 5-mL aliquots from the growth chamber were added to liquid scintillation vials pre-inoculated with 0.85 microcuries of C-14 bicarbonate. The vials were incubated at irradiances of 5, 10, 20, 30, 55, 80, 120, 150, 200, 250, 300, and 350 micro-mol photons per square meter per second&nbsp;for 5 minutes. Fixation was stopped by adding 0.5 mL of 1 N HCl to the vials. Total alkalinity was determined using the open cell titration method described as SOP 3B by&nbsp;Dickson, et al 2007. DIC concentrations were then calculated from temperature, salinity, total alkalinity, and pH using the equations in Zeebe and Wolf-Gladrow, CO2&nbsp;in Seawater: Equilibrium, Kinetics, Isotopes.</p>
<p>Photosynthetic rates in these short-term experiments were found to be best described by a hyperbolic tangent function of the form P = Pm*tanh(E*alpha/Pm), where E is the irradiance, alpha is the initial slope of the photosynthesis-irradiance curve, and Pm is the asymptotic light-saturated photosynthetic rate. The values of Pm with units of grams carbon per gram chlorophyll&nbsp;a&nbsp;per hour and the value of alpha with units of meters squared (carbons/photon) per gram chlorophyll a were determined by least squares.&nbsp;</p>
<p>Measurements of Fv/Fm ratios (the ratio of variable fluorescence to maximal fluorescence after dark adaptation) were made within 30 minutes of each P-E assay, using a Z985 AquaPen fluorometer (Qubit Systems). Briefly, a 4-mL aliquot of culture from the growth chamber was added to each of three plastic 1-cm cuvettes, and each cuvette was immediately wrapped in aluminum foil. The cuvettes were incubated at the growth chamber temperature for 30–40 minutes, after which the foil was removed and a single Fv/Fm measurement was made on each cuvette in a darkened room. The background-corrected Fv/Fm ratio was automatically calculated by the AquaPen software. The light intensities of the saturating pulse and measurement pulse were 2100 and 0.03 micro-mol photons per square meter per second, respectively, both at a wavelength of 450 nm.</p>
Specified by the Principal Investigator(s)
<p>Photosynthetic rates during two-hour intervals during the photoperiod were calculated by solving the differential equation</p>
<p>d(<em>PC</em>)/dt =&nbsp;<em>P</em>&nbsp;– D&nbsp;x&nbsp;<em>PC</em>&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;(1)</p>
<p>where&nbsp;<em>P</em>&nbsp;is the rate of production of&nbsp;<em>PC</em>&nbsp;in the growth chamber, D is the dilution rate of the growth chamber and d(<em>PC</em>)/dt is the rate of change of&nbsp;<em>PC</em>&nbsp;in the growth chamber. The solution of equation (1) between two points in time is</p>
<p><em>P</em>&nbsp;= D(<em>PC</em><sub>t</sub>&nbsp;–&nbsp;<em>PC</em><sub>0</sub>&nbsp;exp(–Dt))&nbsp;/(1 – exp(–Dt)&nbsp;)&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;(2)</p>
<p>where&nbsp;<em>PC</em><sub>0</sub>&nbsp; and&nbsp;<em>PC</em><sub>t</sub>&nbsp;are the concentrations of PC at the beginning and end of the time interval, respectively, and&nbsp;<em>t </em>is the duration of the time interval, which in this experiment was 2 hours. Values of&nbsp;<em>P</em>&nbsp;were calculated for each two-hour time interval during the photoperiod, normalized to the chlorophyll&nbsp;<em>a</em>&nbsp;concentration during each time interval, and then averaged to determine the photosynthetic rate per unit chlorophyll (productivity index or PI) during the photoperiod. Results are reported as grams of carbon per gram of chlorophyll&nbsp;<em>a</em>&nbsp;per hour&nbsp;averaged over the 14-h photoperiod.</p>
<p>Dark respiration rates were calculated from the natural logarithm of the ratio of the PC concentration at the end of the photoperiod and the beginning of the subsequent photoperiod. The natural logarithm of the ratio of the&nbsp;<em>PC concentrations</em> was equated to (D + D<sub>r</sub>)10/24, where D<sub>r</sub>&nbsp;is the dark respiration rate (with units of inverse days) and D is the dilution rate (with units of inverse days). Division by 24 converts these rates to hourly rates, and multiplication by 10 corrects for the fact that the duration of the dark period was 10 hours. Thus</p>
<p>&nbsp; D<sub>r</sub>&nbsp;= (24/10)ln (<em>PC</em><sub>e</sub>/&nbsp;<em>PC</em><sub>b</sub>) – D &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (3)</p>
<p>where&nbsp;<em>PC<sub>e</sub></em>&nbsp;and&nbsp;<em>PC<sub>b</sub></em>&nbsp;are the&nbsp;PC concentrations&nbsp;at the end of one photoperiod and the beginning of the next photoperiod, respectively.</p>
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- removed two rows that contained a mean and stdev for 'relative growth rate' (growth_relative)<br />
- moved the stdev and n (number of values in mean) for 'growth rate per day' (growth_day) to another column and called it 'growth_stdev_n'<br />
-&nbsp;reformatted date from yyyy.m.d to yyyy-mm-dd</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
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7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
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Woods Hole
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info@bco-dmo.org
http://www.bco-dmo.org
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For questions regarding this resource, please contact BCO-DMO via the email address provided.
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Hach SensION model PH31 pH meter
Hach SensION model PH31 pH meter
PI Supplied Instrument Name: Hach SensION model PH31 pH meter Instrument Name: Benchtop pH Meter Instrument Short Name:Benchtop pH Meter Instrument Description: An instrument consisting of an electronic voltmeter and pH-responsive electrode that gives a direct conversion of voltage differences to differences of pH at the measurement temperature. (McGraw-Hill Dictionary of Scientific and Technical Terms)
This instrument does not map to the NERC instrument vocabulary term for 'pH Sensor' which measures values in the water column. Benchtop models are typically employed for stationary lab applications.
Cary Model 50 spectrophotometer
Cary Model 50 spectrophotometer
PI Supplied Instrument Name: Cary Model 50 spectrophotometer PI Supplied Instrument Description:Used to measure absorbances were measured at 664 and 750 nm Instrument Name: Cary 50 spectrophotometer Instrument Short Name:Cary 50 Instrument Description: A Cary 50 spectrophotometer measures absorbance (200-800 nm). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0523/
PI Supplied Instrument Name: Instrument Name: Chemostat Instrument Short Name: Instrument Description: Devices in which controlled conditions are maintained for a chemical process to be carried out by organisms or biochemically active substances derived from such organisms.
an Exeter Analytical model CE-440 elemental analyzer
an Exeter Analytical model CE-440 elemental analyzer
PI Supplied Instrument Name: an Exeter Analytical model CE-440 elemental analyzer PI Supplied Instrument Description:Used to measure concentrations of particulate organic carbon (POC) and particulate nitrogen (PN) Instrument Name: CHN Elemental Analyzer Instrument Short Name:CHN_EA Instrument Description: A CHN Elemental Analyzer is used for the determination of carbon, hydrogen, and nitrogen content in organic and other types of materials, including solids, liquids, volatile, and viscous samples.
Beckman Coulter model Z1 particle counter
Beckman Coulter model Z1 particle counter
PI Supplied Instrument Name: Beckman Coulter model Z1 particle counter PI Supplied Instrument Description:Use to make cell counts 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
PSI AquaPen C100
PSI AquaPen C100
PI Supplied Instrument Name: PSI AquaPen C100 PI Supplied Instrument Description:Used to measure the maximum quantum yield, QY (Fv/Fm) with the manufacturer’s supplied plastic cuvettes containing 4 mL of culture each. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Z985 Cuvette Aquapen (Qubit Systems)
Z985 Cuvette Aquapen (Qubit Systems)
PI Supplied Instrument Name: Z985 Cuvette Aquapen (Qubit Systems) PI Supplied Instrument Description:Used to measure instantaneous chlorophyll fluorescence (F0). AquaPen settings: f = 30, F=71, A = 50. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Packard Tri-Carb model 3100 TR liquid scintillation counter
Packard Tri-Carb model 3100 TR liquid scintillation counter
PI Supplied Instrument Name: Packard Tri-Carb model 3100 TR liquid scintillation counter PI Supplied Instrument Description:Used to measure the activity of C-14 in the samples Instrument Name: Liquid Scintillation Counter Instrument Short Name:LSC Instrument Description: Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used to quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/
CO2METER model AZ-004
CO2METER model AZ-004
PI Supplied Instrument Name: CO2METER model AZ-004 PI Supplied Instrument Description:Used to monitor CO2 concentration in the laboratory. Calibrated at 0 and 400 ppm CO2 with a standard gas mixture Instrument Name: pCO2 Sensor Instrument Short Name:pCO2 Sensor Instrument Description: A sensor that measures the partial pressure of CO2 in water (pCO2)
Masterflex Model 77200-60 peristaltic pump
Masterflex Model 77200-60 peristaltic pump
PI Supplied Instrument Name: Masterflex Model 77200-60 peristaltic pump PI Supplied Instrument Description:Used to control the dilution rate of the growth chamber Instrument Name: Pump Instrument Short Name: Instrument Description: A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps
Biospherical Instruments model QSL 2100 quantum sensor
Biospherical Instruments model QSL 2100 quantum sensor
PI Supplied Instrument Name: Biospherical Instruments model QSL 2100 quantum sensor PI Supplied Instrument Description:Used to measure photosynthetically active radiation (400–700 nm) Instrument Name: Radiometer Instrument Short Name:Radiometer Instrument Description: Radiometer is a generic term for a range of instruments used to measure electromagnetic radiation (radiance and irradiance) in the atmosphere or the water column. For example, this instrument category includes free-fall spectral radiometer (SPMR/SMSR System, Satlantic, Inc), profiling or deck cosine PAR units (PUV-500 and 510, Biospherical Instruments, Inc). This is a generic term used when specific type, make and model were not specified. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/122/
Thermo Spectronic Heios spectrophotometer
Thermo Spectronic Heios spectrophotometer
PI Supplied Instrument Name: Thermo Spectronic Heios spectrophotometer PI Supplied Instrument Description:Used to measure pH Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/