Dataset: Carbonate chemistry

Name: 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"
Published: 2022-12-27
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.883120.1

Temporal Extent: 2016-10-01 - 2022-06-01

Project:

Collaborative Research: Ecology and Evolution of Microbial Interactions in a Changing Ocean (LTPE)

Principal Investigator:

James Morris (University of Alabama at Birmingham, UA/Birmingham)

Scientist:

Zhiying Lu (University of Alabama at Birmingham, UA/Birmingham)

Student:

Marcelo Malisano Barreto Filho (University of Alabama at Birmingham, UA/Birmingham)

Melissa Walker (University of Alabama at Birmingham, UA/Birmingham)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-12-27

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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"

Abstract:

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" (Barreto Filho et al., 2022). The following results abstract describes these data along with related datasets which can be accessed from the "Related Datasets" section of this page. Many microbial photoautotrophs depend on heterotrophic bacteria for accomplishing essential functions. Environmental changes, however, could alter or eliminate such interactions. We investigated the effects of changing pCO2 on gene expression in co-cultures of 3 strains of picocyanobacteria (Synechococcus strains CC9311 and WH8102 and Prochlorococcus strain MIT9312) paired with the ‘helper’ bacterium Alteromonas macleodii EZ55. Co-culture with cyanobacteria resulted in a much higher number of up- and down-regulated genes in EZ55 than pCO2 by itself. Pathway analysis revealed significantly different expression of genes involved in carbohydrate metabolism, stress response, and chemotaxis, with different patterns of up- or down-regulation in co-culture with different cyanobacterial strains. Gene expression patterns of organic and inorganic nutrient transporter and catabolism genes in EZ55 suggested resources available in the culture media were altered under elevated (800 ppm) pCO2 conditions. Altogether, changing expression patterns were consistent with the possibility that the composition of cyanobacterial excretions changed under the two pCO2 regimes, causing extensive ecophysiological changes in both members of the co-cultures. Additionally, significant downregulation of oxidative stress genes inMIT9312/EZ55 cocultures at 800 ppm pCO2 were consistent with a link between the predicted reduced availability of photorespiratory byproducts (i.e., glycolate/2PG) under this condition and observed reductions in internal oxidative stress loads for EZ55, providing a possible explanation for the previously observed lack of “help” provided by EZ55 to MIT9312 under elevated pCO2. The data stored in this archive permit the recalculation of the pH measurements shown in Table 1 of the results publication Barreto Filho et al. (2022).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date PID Issued
2022-12-27	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.883120.1	2023-01-03

Methods & Sampling

Synechococcus cultures were grown under similar conditions to those described in our previous experiment with Prochlorococcus (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 (Hennon et al., 2017) and with acid and/or base to control pCO2. 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. Synechococcus cultures were grown in SEv (per L: 32 μM NaNO3, 2 μM NaH2PO4, 20 μL SN trace metal stock, and 20 μL F/2 vitamin stock). The primary differences between this medium and the PEv medium used in our earlier Prochlorococcus study are the nitrogen source (NO3- vs. NH4+, 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 pCO2 manipulations by measuring alkalinity and pH by titration and colorimetry, respectively (Dickson et al., 2007) and then using the oa function in seacarb package in R to determine how much hydrochloric acid and bicarbonate (for 800 ppm pCO2) or sodium hydroxide (for 400 ppm pCO2) was needed to achieve desired experimental conditions (Gattuso and Lavigne, 2009). Acid and base amendments were introduced immediately prior to inoculation. Cultures were grown in a Percival growth chamber at 21º C under 150 μmol photons m-2 s-1 on a 14:10 light:dark cycle. Synechococcus cultures were grown on a rotating tissue culture wheel at approximately 60 rpm. 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. Equations from (Dickson et al., 2007) were used to compute the pH. The data are provided in the form of an Excel spreadsheet containing the necessary formulas for computing the pH from the absorbance data. pH assays were performed in microtiter plates using a BioTek H1 plate reader with an automated dye injection mechanism and temperature control.

Data Files

File
carb_chem.csv (Comma Separated Values (.csv), 5.75 KB) MD5:fb8861fc038cf4322d40644bab2c7684 Primary data file for dataset ID 883120

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851085

Deployments

None available yet

Instruments

plate reader

Supplied Name: BioTek H1 plate reader

Supplied Description:

Instrument Type

Generic Name: plate reader

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample	Sample Identifier	unitless	sample
Sample_Temp	Temperature of the sample at the time of pH measurement	degrees Celsius	sample_descrip
Salinity	Salinity of the medium	PSU	sal
volume_dye	Amount of dye injected at each injection point	milliliters (mL)	sample_volume
pH_sample_with_dye_corrections	pH of the sample taking into account both dye injections	unitless	pH
pH_sample_without_dye_corrections	pH of the sample only considering the first dye injection	unitless	pH
d730_1	Difference between initial and injection 1 A730 readings	unitless	no_bcodmo_term
d730_2	Difference between initial and injection 2 A730 readings	unitless	no_bcodmo_term
Sample_A_434	Absorbance at 434nm before dye injection	unitless	no_bcodmo_term
Sample_A_578	Absorbance at 578nm before dye injection	unitless	no_bcodmo_term
Sample_A_730	Absorbance at 730nm before dye injection	unitless	no_bcodmo_term
Sample_and_Dye_A_434	Absorbance at 434nm after 1 dye injection	unitless	no_bcodmo_term
Sample_and_Dye_A_578	Absorbance at 578nm after 1 dye injection	unitless	no_bcodmo_term
Sample_and_Dye_A_730	Absorbance at 730nm after 1 dye injection	unitless	no_bcodmo_term
Sample_and_Dye_x2_A_434	Absorbance at 434nm after 2 dye injections	unitless	no_bcodmo_term
Sample_and_Dye_x2_A_578	Absorbance at 578nm after 2 dye injections	unitless	no_bcodmo_term
Sample_and_Dye_x2_A_730	Absorbance at 730nm after 2 dye injections	unitless	no_bcodmo_term
A1_to_A2sub1	Ratio of A578:A434 after 1 injection	unitless	no_bcodmo_term
A1_to_A2sub2	Ratio of A578:A434 after 2 injections	unitless	no_bcodmo_term
pK2	pKa of the dye, corrected for salinity and temperature	unitless	no_bcodmo_term
delta_A1_to_A2	Difference in absorbance ratios between first and second dye injections	unitless	no_bcodmo_term
Constant_A	Constant A = E1(HI-)/E2(HI-); extinction coefficient from Dickson et al. 2007 SOP6b eq. 7	unitless	no_bcodmo_term
Constant_B	Constant B = E1(I-2)/E2(HI-); extinction coefficient from Dickson et al. 2007 SOP6b eq. 7	unitless	no_bcodmo_term
Constant_C	Constant C = E2(I-2)/E2(HI-); extinction coefficient from Dickson et al. 2007 SOP6b eq. 7	unitless	no_bcodmo_term
Dye_Correction_Incercept_a	Intercept of regression line for the two dye injections, for correcting for effect of dye addition	unitless	no_bcodmo_term
Dye_Correction_slope_b	Slope of regression line for the two dye injections, for correcting for effect of dye addition	unitless	no_bcodmo_term
A1_to_A2_corrected	Ratio of A578:A434 corrected for effect of dye addition	unitless	no_bcodmo_term

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Dataset: Carbonate chemistry