http://lod.bco-dmo.org/id/dataset/883120
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
2022-11-01
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Carbonate chemistry data collected as part of a study of the "Community context and pCO2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria"
2022-12-27
publication
2022-12-27
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-01-03
publication
https://doi.org/10.26008/1912/bco-dmo.883120.1
James Morris
University of Alabama at Birmingham
principalInvestigator
Zhiying Lu
University of Alabama at Birmingham
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: Morris, J., Zhiying, L. (2023) Carbonate chemistry data collected as part of a study of the "Community context and pCO2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria". Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-12-27 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.883120.1 [access date]
Methods and Sampling: <p>&nbsp;&nbsp;&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown under similar conditions to those described in our previous experiment with&nbsp;<em>Prochlorococcus&nbsp;</em>(Hennon et al., 2017). Briefly, all cultures were prepared in acid-washed conical-bottom glass centrifuge tubes containing 13 mL of artificial seawater (ASW) amended with nutrient stocks&nbsp;(Hennon et al., 2017) and with acid and/or base to control pCO<sub>2</sub>. ASW (per L: 28.41 g NaCl, 0.79 g KCl, 1.58 g CaCl2*2H2O, 7.21 g MgSO4*7H2O, 5.18 g MgCl2*6H2O) was sterilized in acid-washed glass bottles, amended with 2.325 mM (final concentration) of filter-sterilized sodium bicarbonate, then bubbled with sterile air overnight.&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown in SEv (per L: 32&nbsp;μM NaNO<sub>3</sub>, 2&nbsp;μM NaH<sub>2</sub>PO<sub>4</sub>, 20&nbsp;μL SN trace metal stock, and 20&nbsp;μL F/2 vitamin stock). The primary differences between this medium and the PEv medium used in our earlier&nbsp;<em>Prochlorococcus</em>&nbsp;study are the nitrogen source (NO<sub>3</sub><sup>-</sup>&nbsp;vs. NH<sub>4</sub><sup>+</sup>, with molar concentration of N and N:P ratios identical to PEv) and the addition of F/2 vitamins (Hennon et al., 2017). Carbonate chemistry of each media batch was determined prior to pCO<sub>2</sub>&nbsp;manipulations by measuring alkalinity and pH by titration and colorimetry, respectively (Dickson et al., 2007)&nbsp;and then using the&nbsp;<em>oa&nbsp;</em>function in&nbsp;<em>seacarb</em>&nbsp;package in R to determine how much hydrochloric acid and bicarbonate (for 800 ppm pCO<sub>2</sub>) or sodium hydroxide (for 400 ppm pCO<sub>2</sub>) was needed to achieve desired experimental conditions (Gattuso and Lavigne, 2009).&nbsp; Acid and base amendments were introduced immediately prior to inoculation. Cultures were grown in a Percival growth chamber at 21º C under 150&nbsp;μmol photons m<sup>-2</sup>&nbsp;s<sup>-1</sup>&nbsp;on a 14:10 light:dark cycle.&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown on a rotating tissue culture wheel at approximately 60 rpm.&nbsp;After addition of amendments, absorbance values at 434, 578, and 730 nm were collected both before and after injection of m-cresol purple dye, and again after a second dye injection to correct for the impact of dye addition on solution pH.&nbsp; Equations from (Dickson et al., 2007) were used to compute the pH.&nbsp; The data are provided in the form of an Excel spreadsheet containing the necessary formulas for computing the pH from the absorbance data.&nbsp; pH assays were performed in microtiter plates using a BioTek H1 plate reader with an automated dye injection mechanism and temperature control.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851085 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851085
completed
James Morris
University of Alabama at Birmingham
Belle W. Baruch Institute for Marine and Coastal Sciences 715 Sumter Street
Columbia
SC
29208
USA
morris@inlet.geol.sc.edu
pointOfContact
Zhiying Lu
University of Alabama at Birmingham
1-252-773-2353
Campbell Hall, Office 474 1300 University Blvd
Birmingham
AL
35233
USA
luzy@uab.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample
Sample_Temp
Salinity
volume_dye
pH_sample_with_dye_corrections
pH_sample_without_dye_corrections
d730_1
d730_2
Sample_A_434
Sample_A_578
Sample_A_730
Sample_and_Dye_A_434
Sample_and_Dye_A_578
Sample_and_Dye_A_730
Sample_and_Dye_x2_A_434
Sample_and_Dye_x2_A_578
Sample_and_Dye_x2_A_730
A1_to_A2sub1
A1_to_A2sub2
pK2
delta_A1_to_A2
Constant_A
Constant_B
Constant_C
Dye_Correction_Incercept_a
Dye_Correction_slope_b
A1_to_A2_corrected
BioTek H1 plate reader
theme
None, User defined
sample identification
sample description
salinity
sample_volume
pH
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
plate reader
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: Ecology and Evolution of Microbial Interactions in a Changing Ocean
https://osprey.bco-dmo.org/project/752763
Collaborative Research: Ecology and Evolution of Microbial Interactions in a Changing Ocean
<p><em>NSF Award Abstract:</em><br />
Carbon dioxide released from fossil fuels is causing the ocean to become more acidic. Much attention has been given to how this will affect shelled animals like corals, but acidification also affects the algae that form the base of the ocean food chain. It is possible that future algal communities will look very different than they do today, with potentially negative consequences for fisheries, recreation, and climate. Alternatively, it is possible that these algae will be able to adapt rapidly enough to avoid the worst of it. This study looks at algae adapting to acidification in real time in the lab, focusing on "marketplace" interactions between the algae and the bacteria they live alongside. The researchers also go to sea to learn whether adaptations from the lab experiments are beneficial under real-world conditions. Ultimately, this project is helping scientists better understand how the ocean's most important and most overlooked organisms will respond to the changes humans are causing in their habitat. The researchers also use their scientific work to create fun educational opportunities from grade school to college, including agar art classes where students learn about microbial ecology by "painting" with freshly-isolated ocean bacteria.</p>
<p>The effect of ocean acidification on calcifying organisms has been well-studied, but less is known about how changing pH will affect phytoplankton. Previous work showed that the mutualistic interaction between the globally abundant cyanobacterium Prochlorococcus and its "helper" bacterium Alteromonas broke down under projected future CO2 conditions, leading to a strong decrease in the fitness of Prochlorococcus. It is possible that such interspecies interactions between microbes are important for many ecological processes, but a lack of understanding of how these interactions evolve makes it difficult to predict how important they are. This project is using laboratory evolution experiments to discover how evolution shapes the interactions between bacteria and algae like Prochlorococcus, and how these co-evolutionary dynamics might influence the biogeochemical processes that shape Earth's climate. Four research cruises to the Bermuda Atlantic Time Series are also planned to study how natural algal/bacterial communities respond to acidification, and whether evolved microbes from laboratory experiments have a competitive advantage in complex, natural communities exposed to elevated CO2. The ultimate goal of this project is to gain a mechanistic understanding of microbial interactions that can be used to inform models of Earth's oceans and biological feedbacks on global climate.</p>
LTPE
largerWorkCitation
project
eng; USA
oceans
2016-10-01
2022-06-01
Lab work: Birmingham, Alabama and New York, New York. Field Work: Bermuda Atlantic Time Series.
0
BCO-DMO catalogue of parameters from Carbonate chemistry data collected as part of a study of the "Community context and pCO2 impact the transcriptome of the "helper" bacterium Alteromonas in co-culture with picocyanobacteria"
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/885770.rdf
Name: Sample
Units: unitless
Description: <p>Sample Identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/885771.rdf
Name: Sample_Temp
Units: degrees Celsius
Description: <p>Temperature of the sample at the time of pH measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/885772.rdf
Name: Salinity
Units: PSU
Description: <p>Salinity of the medium</p>
http://lod.bco-dmo.org/id/dataset-parameter/885773.rdf
Name: volume_dye
Units: milliliters (mL)
Description: <p>Amount of dye injected at each injection point</p>
http://lod.bco-dmo.org/id/dataset-parameter/885774.rdf
Name: pH_sample_with_dye_corrections
Units: unitless
Description: <p>pH of the sample taking into account both dye injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/885775.rdf
Name: pH_sample_without_dye_corrections
Units: unitless
Description: <p>pH of the sample only considering the first dye injection</p>
http://lod.bco-dmo.org/id/dataset-parameter/885776.rdf
Name: d730_1
Units: unitless
Description: <p>Difference between initial and injection 1 A730 readings</p>
http://lod.bco-dmo.org/id/dataset-parameter/885777.rdf
Name: d730_2
Units: unitless
Description: <p>Difference between initial and injection 2 A730 readings</p>
http://lod.bco-dmo.org/id/dataset-parameter/885778.rdf
Name: Sample_A_434
Units: unitless
Description: <p>Absorbance at 434nm before dye injection</p>
http://lod.bco-dmo.org/id/dataset-parameter/885779.rdf
Name: Sample_A_578
Units: unitless
Description: <p>Absorbance at 578nm before dye injection</p>
http://lod.bco-dmo.org/id/dataset-parameter/885780.rdf
Name: Sample_A_730
Units: unitless
Description: <p>Absorbance at 730nm before dye injection</p>
http://lod.bco-dmo.org/id/dataset-parameter/885781.rdf
Name: Sample_and_Dye_A_434
Units: unitless
Description: <p>Absorbance at 434nm after 1 dye injection</p>
http://lod.bco-dmo.org/id/dataset-parameter/885782.rdf
Name: Sample_and_Dye_A_578
Units: unitless
Description: <p>Absorbance at 578nm after 1 dye injection</p>
http://lod.bco-dmo.org/id/dataset-parameter/885783.rdf
Name: Sample_and_Dye_A_730
Units: unitless
Description: <p>Absorbance at 730nm after 1 dye injection</p>
http://lod.bco-dmo.org/id/dataset-parameter/885784.rdf
Name: Sample_and_Dye_x2_A_434
Units: unitless
Description: <p>Absorbance at 434nm after 2 dye injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/885785.rdf
Name: Sample_and_Dye_x2_A_578
Units: unitless
Description: <p>Absorbance at 578nm after 2 dye injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/885786.rdf
Name: Sample_and_Dye_x2_A_730
Units: unitless
Description: <p>Absorbance at 730nm after 2 dye injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/885787.rdf
Name: A1_to_A2sub1
Units: unitless
Description: <p>Ratio of A578:A434 after 1 injection</p>
http://lod.bco-dmo.org/id/dataset-parameter/885788.rdf
Name: A1_to_A2sub2
Units: unitless
Description: <p>Ratio of A578:A434 after 2 injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/885789.rdf
Name: pK2
Units: unitless
Description: <p>pKa of the dye, corrected for salinity and temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/885790.rdf
Name: delta_A1_to_A2
Units: unitless
Description: <p>Difference in absorbance ratios between first and second dye injections</p>
http://lod.bco-dmo.org/id/dataset-parameter/885791.rdf
Name: Constant_A
Units: unitless
Description: <p>Constant A = E1(HI-)/E2(HI-); extinction coefficient from Dickson et al. 2007 SOP6b eq. 7</p>
http://lod.bco-dmo.org/id/dataset-parameter/885792.rdf
Name: Constant_B
Units: unitless
Description: <p>Constant B = E1(I-2)/E2(HI-); extinction coefficient from Dickson et al. 2007 SOP6b eq. 7</p>
http://lod.bco-dmo.org/id/dataset-parameter/885793.rdf
Name: Constant_C
Units: unitless
Description: <p>Constant C = E2(I-2)/E2(HI-); extinction coefficient from Dickson et al. 2007 SOP6b eq. 7</p>
http://lod.bco-dmo.org/id/dataset-parameter/885794.rdf
Name: Dye_Correction_Incercept_a
Units: unitless
Description: <p>Intercept of regression line for the two dye injections, for correcting for effect of dye addition</p>
http://lod.bco-dmo.org/id/dataset-parameter/885795.rdf
Name: Dye_Correction_slope_b
Units: unitless
Description: <p>Slope of regression line for the two dye injections, for correcting for effect of dye addition</p>
http://lod.bco-dmo.org/id/dataset-parameter/885796.rdf
Name: A1_to_A2_corrected
Units: unitless
Description: <p>Ratio of A578:A434 corrected for effect of dye addition</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
5883
https://darchive.mblwhoilibrary.org/bitstream/1912/29585/1/dataset-883120_carbonate-chemistry__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.883120.1
download
onLine
dataset
<p>&nbsp;&nbsp;&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown under similar conditions to those described in our previous experiment with&nbsp;<em>Prochlorococcus&nbsp;</em>(Hennon et al., 2017). Briefly, all cultures were prepared in acid-washed conical-bottom glass centrifuge tubes containing 13 mL of artificial seawater (ASW) amended with nutrient stocks&nbsp;(Hennon et al., 2017) and with acid and/or base to control pCO<sub>2</sub>. ASW (per L: 28.41 g NaCl, 0.79 g KCl, 1.58 g CaCl2*2H2O, 7.21 g MgSO4*7H2O, 5.18 g MgCl2*6H2O) was sterilized in acid-washed glass bottles, amended with 2.325 mM (final concentration) of filter-sterilized sodium bicarbonate, then bubbled with sterile air overnight.&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown in SEv (per L: 32&nbsp;μM NaNO<sub>3</sub>, 2&nbsp;μM NaH<sub>2</sub>PO<sub>4</sub>, 20&nbsp;μL SN trace metal stock, and 20&nbsp;μL F/2 vitamin stock). The primary differences between this medium and the PEv medium used in our earlier&nbsp;<em>Prochlorococcus</em>&nbsp;study are the nitrogen source (NO<sub>3</sub><sup>-</sup>&nbsp;vs. NH<sub>4</sub><sup>+</sup>, with molar concentration of N and N:P ratios identical to PEv) and the addition of F/2 vitamins (Hennon et al., 2017). Carbonate chemistry of each media batch was determined prior to pCO<sub>2</sub>&nbsp;manipulations by measuring alkalinity and pH by titration and colorimetry, respectively (Dickson et al., 2007)&nbsp;and then using the&nbsp;<em>oa&nbsp;</em>function in&nbsp;<em>seacarb</em>&nbsp;package in R to determine how much hydrochloric acid and bicarbonate (for 800 ppm pCO<sub>2</sub>) or sodium hydroxide (for 400 ppm pCO<sub>2</sub>) was needed to achieve desired experimental conditions (Gattuso and Lavigne, 2009).&nbsp; Acid and base amendments were introduced immediately prior to inoculation. Cultures were grown in a Percival growth chamber at 21º C under 150&nbsp;μmol photons m<sup>-2</sup>&nbsp;s<sup>-1</sup>&nbsp;on a 14:10 light:dark cycle.&nbsp;<em>Synechococcus</em>&nbsp;cultures were grown on a rotating tissue culture wheel at approximately 60 rpm.&nbsp;After addition of amendments, absorbance values at 434, 578, and 730 nm were collected both before and after injection of m-cresol purple dye, and again after a second dye injection to correct for the impact of dye addition on solution pH.&nbsp; Equations from (Dickson et al., 2007) were used to compute the pH.&nbsp; The data are provided in the form of an Excel spreadsheet containing the necessary formulas for computing the pH from the absorbance data.&nbsp; pH assays were performed in microtiter plates using a BioTek H1 plate reader with an automated dye injection mechanism and temperature control.</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
BioTek H1 plate reader
BioTek H1 plate reader
PI Supplied Instrument Name: BioTek H1 plate reader Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.