Accessing BCO-DMO data
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| Dataset Title: | Results of laboratory experiment examining growth, CO2- and N2-fixation of Crocosphaera watsonii isolates in differing light intensities; conducted in the Hutchins Laboratory, USC 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_3962) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
isolate {
String bcodmo_name "taxon";
String description "Name of Crocosphaera watsonii isolate.";
String long_name "Isolate";
String units "text";
}
light {
Int16 _FillValue 32767;
Int16 actual_range 18, 300;
String bcodmo_name "irradiance";
String description "Light intensity. (For more about light measurement see: Australian National Algae Culture Collection and Plant Physiology Online.)";
String long_name "Light";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/VSRW/";
String units "micromoles quanta per square meter per second (umol quanta m-2 s-1)";
}
growth_rate {
Float32 _FillValue NaN;
Float32 actual_range 0.0762, 0.8141;
String bcodmo_name "unknown";
String description "Growth rate.";
String long_name "Growth Rate";
String units "per day";
}
growth_rate_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.00301, 0.0379;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of growth rate.";
String long_name "Growth Rate Sd";
String units "per day";
}
cell_diameter {
Float32 _FillValue NaN;
Float32 actual_range 2.28, 5.7317;
String bcodmo_name "unknown";
String description "Cell diamter in micrometers.";
String long_name "Cell Diameter";
String units "micrometers (um)";
}
cell_diameter_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.0438, 0.1932;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of cell diameter.";
String long_name "Cell Diameter Sd";
String units "micrometers (um)";
}
C_specific_CO2_fix {
Float32 _FillValue NaN;
Float32 actual_range 8.03e-4, 0.0242;
String bcodmo_name "unknown";
String description "C-specific CO2 fixation.";
String long_name "C Specific CO2 Fix";
String units "per hour";
}
C_specific_CO2_fix_sd {
Float32 _FillValue NaN;
Float32 actual_range 4.19e-5, 0.00344;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of C-specific CO2 fixation.";
String long_name "C Specific CO2 Fix Sd";
String units "per hour";
}
N_specific_gross_N2_fix {
Float32 _FillValue NaN;
Float32 actual_range 0.00973, 0.0451;
String bcodmo_name "unknown";
String description "N-specific gross N2 fixation.";
String long_name "N Specific Gross N2 Fix";
String units "per hour";
}
N_specific_gross_N2_fix_sd {
Float32 _FillValue NaN;
Float32 actual_range 8.61e-5, 0.00527;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of N-specific gross N2 fixation.";
String long_name "N Specific Gross N2 Fix Sd";
String units "per hour";
}
N_specific_net_15N2_fix {
Float32 _FillValue NaN;
Float32 actual_range 8.84e-6, 0.0169;
String bcodmo_name "unknown";
String description "N-specific net 15N2 fixation.";
String long_name "N Specific Net 15 N2 Fix";
String units "per hour";
}
N_specific_net_15N2_fix_sd {
Float32 _FillValue NaN;
Float32 actual_range 4.13e-6, 0.00219;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of N-specific net N2 fixation.";
String long_name "N Specific Net 15 N2 Fix Sd";
String units "per hour";
}
gross_to_net_N2fix {
Float32 _FillValue NaN;
Float32 actual_range 2.3955, 15.7753;
String bcodmo_name "unknown";
String description "Ratio of gross N2 fixation to net 15N2 fixation.";
String long_name "Gross To Net N2fix";
String units "ratio";
}
gross_to_net_N2fix_sd {
Float32 _FillValue NaN;
Float32 actual_range 0.075, 2.1655;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of the ratio of gross N2 fixation to net 15N2 fixation.";
String long_name "Gross To Net N2fix Sd";
String units "ratio";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"Culturing and experimental conditions
Stock cultures of the two Atlantic C. watsonii isolates were provided
courtesy of Dr. Eric Webb. Both isolates were collected in March 2002, WH0401
from 6\\u00ba 58.78' N, 49\\u00ba 19.70' W and WH0402 from 11\\u00ba 42.12S',
32\\u00ba 00.64'W. Triplicate cultures were grown using a semi-continuous
culturing technique (Garcia et al., 2011) at 28 degrees C in an artificial
seawater medium (Chen et al., 1996). Nutrients were added to autoclaved
seawater at the concentrations listed in the AQUIL recipe (Morel et al.,
1979), except for nitrate, which was omitted. The growth rates of cultures
were measured over 2\\u20133 day intervals and were used to determine the
dilution rate. Culture cell density was kept low (cells ml\\u20131 =
50\\u2013500 \\u00d7 103 for experiments with WH0401 and 5.0\\u201330 \\u00d7 103
for WH0402) to prevent light limitation of photosynthesis and deviation from
the expected pH values for respective pCO2 culture treatments. Light was
supplied with cool-white fluorescent lamps on a 12:12 h light:dark cycle and
measured with a LI-250A light meter (LiCor Biosciences, light sensor serial#
SPQA 4020). Because of large differences in cell size between WH0401 and
WH0402, WH0401 was cultured at higher cell densities to maintain relatively
equivalent levels of total culture biomass (0.1\\u20132.5 mM particulate C for
cultures of WH0401; 0.1\\u20131.3 mM particulate C for WH0402). Cells were
considered fully acclimated to treatment conditions after cultures had
remained at steady-state growth for seven generations or more (unless stated
otherwise). Fast growing cultures (i.e. high light cultures) were acclimated
for more than ten generations while slow growing cultures (i.e. low light and
low pCO2 cultures) were acclimated over two months but for fewer generations.
Cultures were sampled over the period between 24 and 48 h after the preceding
dilution to measure growth rates, gross and net 15N2-fixation rates,
CO2-fixation rates, and particulate elemental composition.
Light experiments
In order to quantify differences in growth and in the CO2- and N2-fixation
rate capacities of these two isolates of C. watsonii, the investigators
measured growth, CO2-fixation and gross and net N2-fixation rates, and
particulate carbon and nitrogen composition in response to a range of light
intensities.
Growth rate and cell density estimates
Growth rate was determined as an increase in culture cell density over time
with the equation NT=N0e\\u00b5T, where N0 and NT are the initial and final
culture cell densities, respectively, T is the time in days between culture
cell density estimates, and \\u00b5 is the specific growth rate. Culture cell
density was determined using a haemocytometer and an Olympus BX51 microscope.
Cell diameter was measured using an ocular micrometer calibrated with the same
microscope. Growth rates were fitted to a Monod linear hyperbolic function of
light (Monod, 1949) using Sigma Plot 10 software program. The hyperbola was
fit to the data without including the origin to yield the highest r2 value.
N2 fixation
The acetylene reduction assay described by Capone et al. (1993) was used to
estimate the gross N2-fixation rate. Rate measurements were initiated at the
beginning of the 12-h dark period, when C. watsonii is known to fix N2 (Mohr
et al., 2010a; Saito et al., 2011). Gross N2-fixation rates were calculated in
the same way as described in Garcia et al. (2011), using a Bunsen coefficient
for ethylene of 0.082 (Breitbarth et al., 2004) and an ethylene
production:N2-fixation ratio of 3:1.
Net N2-fixation rates were measured using the 15N2 isotope tracer method
(Mulholland & Bernhardt, 2005; Mulholland et al., 2004). Samples were prepared
the same way as described in Garcia et al. (2011). Briefly, 169 ml of each
experimental replicate was inoculated with 169 \\u00b5l of 99% doubly labelled
15N2 gas and incubated at 28 degrees C in complete darkness for 12 h during
the dark period. The incubation was then terminated by filtering the entire
volume onto precombusted (450 degree C, 4 h) GF/F filters for the analysis of
particulate 15N, total particulate N, and total particulate C. Filters were
dried at 80\\u201390 degrees C, pelleted, and combusted in a quartz column with
chromium oxide and silver wool at 1000 degrees C. For this analysis, ammonium
sulphate and sucrose were used as standards. At the time the experiments were
conducted, the investigators were not aware of the criticisms of the 15N2
uptake method that have been discussed by Mohr et al. (2010b). Thus, for
another independent estimate of net N2 fixation, the investigators calculated
a particulate N (PN) accumulation rate in cultures over time (deltaPN =
PNfinal - PNinitial). Particulate N was measured in subsamples of experimental
replicates that were incubated with 15N2 at the end of the dark period and
used as the end-period PN measurement (PNfinal). Because only one sample of PN
was collected, the investigators back-calculated an estimate of PNinitial
based on their measurements of cellular growth rate using the equation: growth
rate (d\\u20131) = [ln(PNfinal)\\u2013ln(PNinitial)]/(t2\\u2013t1), where t1 is
the initial time and t2 is the final time. Based on their measurements of
growth rates, the investigators assumed that PN per cell was in a daily steady
state. The gross N2-fixation rate:PN-accumulation rate ratio (hereafter the
gross:PN accumulation ratio) was then calculated and compared to the ratio of
gross N2-fixation rate:net 15N2-fixation rate ratio (gross:net), which is a
proxy for cellular N retention (Mulholland et al., 2004; Mulholland, 2007).
CO2 fixation
The rate of CO2 fixation was determined as described in Garcia et al. (2011)
using the H14CO3- incorporation method. CO2-fixation rates were determined by
first calculating the ratio of the radioactivity of 14C incorporated into
cells during 24 hours to the total radioactivity of H14CO3\\u2013. This ratio
was then multiplied by the total CO2 concentration (TCO2). TCO2 concentrations
were measured in the CO2-light experiments and were applied to all experiments
to calculate CO2-fixation rates for corresponding CO2 treatments. For the
light experiments, the investigators used a TCO2 value that was measured in
the present-day pCO2 treatments of the CO2-light experiments (2053 \\u00b5M
TCO2).
References:
BREITBARTH, E., MILLS, M.M., FRIEDRICHS, G. & LAROCHE, J. (2004). The Bunsen
gas solubility coefficient of ethylene as a function of temperature and
salinity and its importance for nitrogen fixation assays. Limnology and
Oceanography: Methods, 2: 282\\u2013288. DOI:
[10.4319/lom.2004.2.282](\\\\\"https://dx.doi.org/10.4319/lom.2004.2.282\\\\\")
CHEN, Y.B., ZEHR, J.P. & MELLON, M. (1996). Growth and nitrogen fixation of
the diazotrophic filamentous nonheterocystous cyanobacterium Trichodesmium sp.
IMS101 in defined media: Evidence for a circadian rhythm. Journal of
Phycology, 32: 916-923. DOI:
[10.1111/j.0022-3646.1996.00916.x](\\\\\"https://dx.doi.org/10.1111/j.0022-3646.1996.00916.x\\\\\")
Garcia, N. S., F.-X. Fu, , C. L. Breene, P. W. Bernhardt, M. R. Mulholland, J.
A. Sohm, and D. A. Hutchins. 2011. Interactive effects of irradiance and CO2
on CO2- and N2 fixation in the diazotroph Trichodesmium erythraeum
(Cyanobacteria). J. Phycol. 47: 1292-1303.
DOI:\\u00a0[10.1111/j.1529-8817.2011.01078.x](\\\\\"https://dx.doi.org/10.1111/j.1529-8817.2011.01078.x\\\\\")
MONOD, J. (1949). The growth of bacterial cultures. Annual Review of
Microbiology, 3: 371\\u2013394.
Morel, F. M. M., J. G. Rueter, D. M. Anderson, and Guillard, R. R. L. 1979.
Aquil: Chemically defined phytoplankton culture medium for trace metal
studies. J. Phycol. 15:135-141.
MULHOLLAND, M.R. (2007). The fate of nitrogen fixed by diazotrophs in the
ocean. Biogeosciences 4: 37\\u201351. DOI:
[10.5194/bg-4-37-2007](\\\\\"https://dx.doi.org/10.5194/bg-4-37-2007\\\\\")
MULHOLLAND, M.R. & BERNHARDT, P.W. (2005). The effect of growth rate,
phosphorus concentration and temperature on N2-fixation, carbon fixation, and
nitrogen release in continuous cultures of Trichodesmium IMS101. Limnology and
Oceanography, 50: 839\\u2013849. DOI:
[10.4319/lo.2005.50.3.0839](\\\\\"https://dx.doi.org/10.4319/lo.2005.50.3.0839\\\\\")
MULHOLLAND, M.R., BRONK, D.A. & CAPONE, D.G. (2004). N2 fixation and
regeneration of NH4+ and dissolved organic N by Trichodesmium IMS101. Aquatic
Microbial Ecology, 37: 85\\u201394. DOI:
[10.3354/ame037085](\\\\\"https://dx.doi.org/10.3354/ame037085\\\\\")";
String awards_0_award_nid "55189";
String awards_0_award_number "OCE-0722337";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0722337";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"C. watsonii light experiments
(Data published in Fig. 1 of Garcia et al. 2013 Eur. J. Phycology)
PI: David Hutchins (USC)
Contact: Fei-Xue Fu (USC)
Version: 11 June 2013";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2013-06-10T18:40:44Z";
String date_modified "2019-11-06T17:18:54Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.3962.1";
String history
"2024-04-24T14:45:33Z (local files)
2024-04-24T14:45:33Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_3962.html";
String infoUrl "https://www.bco-dmo.org/dataset/3962";
String institution "BCO-DMO";
String instruments_0_acronym "Light Meter";
String instruments_0_dataset_instrument_description "During culturing, light was measured with a LI-250A light meter (LI-COR Biosciences, light sensor serial # SPQA 4020).";
String instruments_0_dataset_instrument_nid "6180";
String instruments_0_description "Light meters are instruments that measure light intensity. Common units of measure for light intensity are umol/m2/s or uE/m2/s (micromoles per meter squared per second or microEinsteins per meter squared per second). (example: LI-COR 250A)";
String instruments_0_instrument_name "Light Meter";
String instruments_0_instrument_nid "703";
String instruments_0_supplied_name "Light Meter";
String instruments_1_acronym "Hemocytometer";
String instruments_1_dataset_instrument_description "Culture cell density was determined using a haemocytometer and an Olympus BX51 microscope.";
String instruments_1_dataset_instrument_nid "6181";
String instruments_1_description
"A hemocytometer is a small glass chamber, resembling a thick microscope slide, used for determining the number of cells per unit volume of a suspension. Originally used for performing blood cell counts, a hemocytometer can be used to count a variety of cell types in the laboratory. Also spelled as \"haemocytometer\". Description from:
http://hlsweb.dmu.ac.uk/ahs/elearning/RITA/Haem1/Haem1.html.";
String instruments_1_instrument_name "Hemocytometer";
String instruments_1_instrument_nid "704";
String instruments_1_supplied_name "Hemocytometer";
String keywords "bco, bco-dmo, biological, C_specific_CO2_fix, C_specific_CO2_fix_sd, carbon, carbon dioxide, cell, cell_diameter, cell_diameter_sd, chemical, co2, data, dataset, diameter, dioxide, dmo, erddap, fix, gross, gross_to_net_N2fix, gross_to_net_N2fix_sd, growth, growth_rate, growth_rate_sd, isolate, light, management, n2fix, N_specific_gross_N2_fix, N_specific_gross_N2_fix_sd, N_specific_net_15N2_fix, N_specific_net_15N2_fix_sd, net, oceanography, office, preliminary, rate, specific";
String license "https://www.bco-dmo.org/dataset/3962/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/3962";
String param_mapping "{'3962': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/3962/parameters";
String people_0_affiliation "University of Southern California";
String people_0_affiliation_acronym "USC";
String people_0_person_name "David A. Hutchins";
String people_0_person_nid "51048";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Southern California";
String people_1_affiliation_acronym "USC";
String people_1_person_name "Fei-Xue Fu";
String people_1_person_nid "51585";
String people_1_role "Contact";
String people_1_role_type "related";
String people_2_affiliation "University of Southern California";
String people_2_affiliation_acronym "USC";
String people_2_person_name "David A. Hutchins";
String people_2_person_nid "51048";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Shannon Rauch";
String people_3_person_nid "51498";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "Diaz N2-Fix in High CO2";
String projects_0_acronym "Diaz N2-Fix in High CO2";
String projects_0_description
"From NSF award abstract:
The importance of marine N2 fixation to present ocean productivity and global nutrient and carbon biogeochemistry is now universally recognized. Marine N2 fixation rates and oceanic N inventories are also thought to have varied over geological time due to climate variability and change. However, almost nothing is known about the responses of dominant N2 fixers in the ocean such as Trichodesmium and unicellular N2 fixing cyanobacteria to past, present and future global atmospheric CO2 regimes. Our preliminary data demonstrate that N2 and CO2 fixation rates, growth rates, and elemental ratios of Atlantic and Pacific Trichodesmium isolates are controlled by the ambient CO2 concentration at which they are grown. At projected year 2100 pCO2 (750 ppm), N2 fixation rates of both strains increased 35-100%, with simultaneous increases in C fixation rates and cellular N:P and C:P ratios. Surprisingly, these increases in N2 and C fixation due to elevated CO2 were of similar relative magnitude regardless of the growth temperature or P availability. Thus, the influence of CO2 appears to be independent of other common growth-limiting factors. Equally important, Trichodesmium growth and N2 fixation were completely halted at low pCO2 levels (150 ppm), suggesting that diazotrophy by this genus may have been marginal at best at last glacial maximum pCO2 levels of ~190 ppm. Genetic evidence indicates that Trichodesmium diazotrophy is subject to CO2 control because this cyanobacterium lacks high-affinity dissolved inorganic carbon transport capabilities. These findings may force a re-evaluation of the hypothesized role of past marine N2 fixation in glacial/interglacial climate changes, as well as consideration of the potential for increased ocean diazotrophy and altered nutrient and carbon cycling in the future high-CO2 ocean.
We propose an interdisciplinary project to examine the relationship between ocean N2 fixing cyanobacteria and changing pCO2. A combined field and laboratory approach will incorporate in situ measurements with experimental manipulations using natural and cultured populations of Trichodesmium and unicellular N2 fixers over range of pCO2 spanning glacial era to future concentrations (150-1500 ppm). We will also examine how effects of pCO2 on N2 and C fixation and elemental stoichiometry are moderated by the availability of other potentially growth-limiting variables such as Fe, P, temperature, and light. We plan to obtain a detailed picture of the full range of responses of important oceanic diazotrophs to changing pCO2, including growth rates, N2 and CO2 fixation, cellular elemental ratios, fixed N release, photosynthetic physiology, and expression of key genes involved in carbon and nitrogen acquisition at both the transcript and protein level.
This research has the potential to evolutionize our understanding of controls on N2 fixation in the ocean. Many of our current ideas about the interactions between oceanic N2 fixation, atmospheric CO2, nutrient biogeochemistry, ocean productivity, and global climate change may need revision to take into account previously unrecognized feedback mechanisms between atmospheric composition and diazotrophs. Our findings could thus have major implications for human society, and its increasing dependence on ocean resources in an uncertain future. This project will take the first vital steps towards understanding how a biogeochemically-critical process, the fixation of N2 in the ocean, may respond to our rapidly changing world during the century to come.";
String projects_0_end_date "2012-12";
String projects_0_geolocation "Laboratory";
String projects_0_name "CO2 control of oceanic nitrogen fixation and carbon flow through diazotrophs";
String projects_0_project_nid "2172";
String projects_0_start_date "2007-05";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Results of laboratory experiment examining growth, CO2- and N2-fixation of Crocosphaera watsonii isolates in differing light intensities; conducted in the Hutchins Laboratory, USC.";
String title "Results of laboratory experiment examining growth, CO2- and N2-fixation of Crocosphaera watsonii isolates in differing light intensities; conducted in the Hutchins Laboratory, USC";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.