Dataset: OA Lit Review

Name: Literature review of Ocean Acidification (OA) effects on phytoplankton (P-ExpEv project)
Published: 2015-07-07
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.554221.2

Project:

Impacts of Evolution on the Response of Phytoplankton Populations to Rising CO2 (P-ExpEv)

Program:

Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) (SEES-OA)

Principal Investigator:

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

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2015-07-07

Restricted:

Validated:

Yes

Current State:

Final with updates expected

Literature review of Ocean Acidification (OA) effects on phytoplankton (P-ExpEv project)

Abstract:

Literature review of Ocean Acidification (OA) effects on phytoplankton (P-ExpEv project)

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2015-07-07	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.554221.2	2022-05-18

Description

Literature review of Ocean Acidification (OA) effects on phytoplankton, focusing on growth rate effects.

Details of literature review are contained in Dutkiewicz et al. 2015 (10.1038/NCLIMATE2722). Any use or re-analysis of this data should cite this paper.

Methods & Sampling

Compilation of Acidification Experiments
(modified from supplemental material associated with Dutkiewicz et al., submitted 2015)

In order to develop a baseline understanding of the responses of phytoplankton groups to ocean acidification, we conducted a comprehensive literature search of laboratory studies (current as of December 2014). We focused on growth rate effects, but additional data were recorded as well. A search of the Web of Science was conducted using the search phrase "(coccolith* OR diatom* OR prochloroc* OR synechoc* OR trichodes* OR crocosphae* OR diazotroph*) AND (CO₂ OR "carbon dioxide" OR "ocean acidification") AND ("growth rate")". Each abstract was read and any paper that mentioned a comparison between ambient and elevated CO₂ conditions was downloaded. Additional papers were selected based on reference lists from the above papers and personal communications with researchers. We further curated these papers by excluding any that i) did not actually compare growth rates at different CO₂ concentrations, ii) did not specify the CO₂ levels examined, iii) used CO₂ concentrations outside the range 250 – 1100 ppmv, iv) attempted to separately manipulate CO₂ concentration and pH using organic buffers, v) manipulated CO₂/pH in such a way as to radically change alkalinity, and/or vi) presented data in such a way that it was impossible to calculate a ratio of elevated:ambient growth rates. One additional paper was removed because it had been retracted. We also did not consider comparisons of growth rates for organisms in mixed communities or for freshwater species.

Table 1 (PDF) shows the papers that were used for the meta-analysis, and Table 2 (PDF)shows the papers that were rejected along with the reasons for rejection. Values were collected from tabulated data in papers where possible; otherwise values were estimated visually from figures. No attempt was made to extract information about replication level, variance, or significance level of data; only experimental means were collected. Many papers examined the response to CO₂ enrichment under a variety of environmental conditions (e.g., different light or nutrient levels). Each environment was considered as a unique experiment, and no attempt was made to examine covariance or synergy between any other parameter and response to CO₂.

All data points in the dataset represent ratios of the value in a high CO₂ experiment to the value in an ambient CO₂ environment.

Data Processing Description

BCO-DMO Processing Notes:
- Replaced spaces with underscores in the reference, organism, and class columns.
- Removed commas and parentheses from the reference column.
- Replaced commas with semi-colons throughout the dataset.
- Replaced blanks 'nd', meaning 'no data'.
- Modified parameter names to conform with BCO-DMO naming conventions.
- Created new column, 'measurement_type', and sorted data accordingly.

Version history:
Version 2 (current): published 2015-07-07 (spreadsheet submitted by J.J. Morris on 0215-07-03; significant changes made in the organization of data, including the creation of separate columns for different CO₂ conditions). Version 2 is available from the "Get Data" button on this page.

Version 1: published 2015-03-26 (spreadsheet submitted by J.J. Morris on 19 March 2015). Version 1 is attached as a Supplemental File (OA_Lit_Review_03262015.csv)

Data Files

File
OA_Lit_Review.csv (Comma Separated Values (.csv), 228.60 KB) MD5:6f4fe8b519c9b8cf2cf6dad3b11e2ce9 Primary data file for dataset ID 554221

Supplemental Files

File
OA_Lit_Review_03262015.csv (Comma Separated Values (.csv), 109.86 KB) MD5:0cf2b33d5e91fb3b697504cd0ae827b9 Version 1 of dataset "OA Lit Review" (datset ID 554221; PI Morris)
Table_1_Morris.pdf (Portable Document Format (.pdf), 325.32 KB) MD5:59a70d3a6dade0b40922e1f1d34fb28f Citations of the papers that were used for the meta-analysis. Supplemental File for dataset "OA Lit Review" (dataset ID 554221; PI: Morris).
Table_2_Morris.pdf (Portable Document Format (.pdf), 226.37 KB) MD5:c06fe89d9305bf8027ea2821c10ae050 List of papers that were rejected along with the reasons for rejection. Supplemental File for dataset "OA Lit Review" (dataset ID 554221; PI: Morris).

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1316101

Deployments

None available yet

Instruments

None available yet

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
reference	Source for the row's data.	text	reference_paper
organism	Species/strain analyzed.	text	taxon
class	Functional group of organism: Coccolithophore, diatom, other large, diazotroph, Prochlorococcus, or other small.	text	class
CO2_low	CO2 concentration of "Low CO2" value examined.	refer to "CO2_units"	no_bcodmo_term
CO2_high	CO2 concentration of "High CO2" value examined.	refer to "CO2_units"	no_bcodmo_term
CO2_units	Units in which CO2 concentration was expressed: ppm, parts per million; pH, pH as a proxy for CO2; M, moles CO2 per L of solution.	text	no_bcodmo_term
temp	Temperature of the observation in C.	degrees Celsius	temp
light	Light level in micromoles photons m-2 s-1.	micromoles photons per square meter per second (m-2 s-1)	no_bcodmo_term
notes	Other important variables OR reason that the paper was excluded from consideration.	text	no_bcodmo_term
measurement_type	Whether the given data points are from a high CO2 treatment (High_CO2), a low CO2 treatment (Low_CO2), or are the ratio of high:low CO2 (Ratio_high_to_low_CO2) for the indicated parameter.	text	no_bcodmo_term
growth_rate	Calculated from exponential growth rates.	cell # or proxy thereof and d^-1 unless otherwise stated	growth
yield	Maximum cell concentration.	cells (or filaments)	no_bcodmo_term
cell_vol	Cell volume, absolute measurement.	cubic micrometers (um^3) per cell	no_bcodmo_term
cell_vol_FC	Cell volume, approximation from flow cytometer light scattering.	Flow cytometer estimate	no_bcodmo_term
cell_diam	Cell diameter.	micrometers (um)	no_bcodmo_term
cells_per_fil_len	Cells/filament length.	micrometers (um)	no_bcodmo_term
surf_area	Surface area.	square micrometers per cell (um^2 cell^-1)	no_bcodmo_term
surf_area_to_vol	Surface area:volume ratio.	Ratio	no_bcodmo_term
POC	Amount of organic carbon per cell.	micromoles per cell (umol cell^-1) or per chlorophyll (chl^-1) where cell densities not given	POC
PON	Amount of nitrogen per cell.	micromoles per cell (umol cell^-1)	PON
POP	Amount of phosphorus per cell.	micromoles per cell (umol cell^-1)	POP
PIC	Amount of inorganic carbon per cell.	micromoles per cell (umol cell^-1) or per chlorophyll (chl^-1) where cell densities not given	PIC
PIC_to_POC	Ratio of inorganic to organic carbon.	ratio	no_bcodmo_term
C_to_N	Carbon:nitrogen ratio.	M/M	C_to_N
C_to_P	Carbon:phosphorus ratio.	M/M	no_bcodmo_term
N_to_P	Nitrogen:phosphorus ratio.	M/M	no_bcodmo_term
chla_pg_per_cell	Concentration of chl A per cell.	picograms per cell (pg cell^-1)	no_bcodmo_term
chla_ug_per_umolC	Concentration of chl A per mole of carbon.	micrograms per micromoles Carbon (ug umolC^-1)	no_bcodmo_term
chla	Cell-normalized fluorescence; Amount of chlorophyll estimated from in vivo chlorophyll fluorescence.	cell-normalized fluorescence	no_bcodmo_term
acc_pig_pg_per_cell	Accessory pigments; concentration of pigments such as carotenoids per cell.	picograms per cell (pg cell^-1)	no_bcodmo_term
acc_pig_ug_per_umolC	Concentrations of pigments such as carotenoids per mole of carbon.	micrograms per micromoles Carbon (ug umolC^-1)	no_bcodmo_term
tot_carb	Total carbohydrates per cell.	picograms per cell (pg cell^-1)	no_bcodmo_term
tot_protein	Total proteins per cell.	picograms per cell (pg cell^-1)	no_bcodmo_term
RUBISCO_activity	RUBISCO activity; from cell extracts, normalized to total protein.	mAb340 mgprotein^-1	no_bcodmo_term
RUBISCO_exp	RUBISCO expression: transcripts per cell.	arbitrary units	no_bcodmo_term
alpha_init_slope	Alpha: initial slope of the PE curve measured from O2 evolution.	initial slope	no_bcodmo_term
alpha	Alpha: initial slope of the PE curve measured based on CO2 fixation.	micromoles C per milligram chlorophyll per hour per microeinstein (umolC mgchl^-1 h^-1 uein^-1)	alpha
Pmax_for_PE_curve	Pmax: inferred asymptote of the PE curve measured from O2 evolution.	millimoles O2 per milligram chlorophyll per hour (mmolO2 mgchl^-1 h^-1)	no_bcodmo_term
Pbmax	Pbmax: inferred asymptote of the PE curve measured from CO2 fixation.	micromoles C per milligram chlorophyll per hour (umolC mgChl^-1 h^-1)	no_bcodmo_term
Ek	Ek: light saturation constant for the PE curve.	microEinsteins (uEin)	no_bcodmo_term
Ec	Ec: irradiance necessary to yield sufficient energy for growth via photosynthesis.	compensation light; microEinsteins (uEin)	no_bcodmo_term
beta	Beta: initial slope of photosynthesis vs. DIC curve.	micromoles O2 per milligram chlorophyll per hour per micromole DIC (umolO2 mgchl^-1 h^-1 umolDIC^-1)	beta
Km	Km: light saturation constant for the photosynthesis vs. DIC curve.	CO2 affinity; milliMolar DIC (mM DIC)	no_bcodmo_term
Pmax_for_DIC_curve	Pmax for DIC curve: inferred asymptote of the photosynthesis vs. DIC curve.	micromoles O2 per milligram chlorophyll per hour (umolO2 mgchl^-1 h^-1)	no_bcodmo_term
Phi_max	Phi-max: moles of CO2 fixed per mole of photons.	moles C per moles quanta (molC molquanta^-1)	no_bcodmo_term
abar	Abar*. Chlorophyll absorption coefficient.	Chl abs coefficient; m^2 mgChl^-1	no_bcodmo_term
rETRmax	rETRmax: maximum rate of photosynthetic electron transfer.	umol m^-2 s^-1	no_bcodmo_term
C_fix_nmol_per_cell_hr	C fixation: rate of CO2 fixed per cell.	nmol cell^-1 h^-1	no_bcodmo_term
C_fix_nmol_per_mgChl_hr	C fixation: rate of CO2 fixed per mg Chl A.	nmolC mgChl^-1 h^-1	no_bcodmo_term
C_spec_CO2_fix	Carbon specific CO2 fixation: rate of CO2 fixed per mole of carbon.	h^-1	no_bcodmo_term
net_photosyn_uM	Net photosynthesis: moles O2 produced per mg chl A.	uMO2 mgchla^-1 h^-1	no_bcodmo_term
net_drk_resp_umol	Net dark respiration: moles O2 consumed per mg chl A.	umolO2 mg chla^-1 h^-1	no_bcodmo_term
net_photosyn_pmol	Net photosynthesis: moles O2 produced per cell.	pmolO2 cell^-1 d^-1	no_bcodmo_term
net_drk_resp_pmol	Net dark respiration: moles O2 consumed per cell.	pmolO2 cell^-1 d^-1	no_bcodmo_term
N_cost_photosyn	N cost of photosynthesis: Amount of nitrogen assimilated per mole of CO2 fixed.	mmolN molCfixed^-1 d^-1	no_bcodmo_term
PIC_prod	PIC Production: rate of PIC production per cell.	pmol cell^-1 d^-1	no_bcodmo_term
POC_prod	POC production: rate of POC production per cell.	pmol cell^-1 d^-1	no_bcodmo_term
PIC_to_POC_prod	PIC/POC Productivity ratio.	Ratio	no_bcodmo_term
PON_prod_uptake	PON prod/uptake: rate of nitrogen uptake per cell.	pmolN cell^-1 d^-1	no_bcodmo_term
NO3_uptake	NO3 uptake: rate of nitrate uptake per cell.	femtomoles per cell per hour (fmol cell^-1 h^-1)	no_bcodmo_term
NH4_uptake	NH4 uptake: rate of ammonium uptake per cell.	femtomoles per cell per hour (fmol cell^-1 h^-1)	no_bcodmo_term
P_prod_uptake	P prod/uptake: rate of phosphorus assimilation per cell.	picomoles P per cell per day (pmolP cell^-1 d^-1)	no_bcodmo_term
Si_prod_uptake	Si prod/uptake: rate of silicate uptake per cell.	picomoles per cell per day (pmol cell^-1 d^-1)	no_bcodmo_term
CO2_to_HCO3_uptake	Ratio of CO2 uptake to HCO3 uptake.	Ratio	no_bcodmo_term
CO2_leakage	CO2 leakage: rate of CO2 loss to gross uptake of DIC.	efflux:gross uptake	no_bcodmo_term
abb_cocco	% aberrant coccoliths: Proportion of cells showing microscopic evidence of malformed coccoliths.	%	no_bcodmo_term
detach_cocco	# detached coccoliths/coccospheres: abundance of coccoliths without coccolithophores.	count	no_bcodmo_term
Fv_to_Fm	Fv/Fm: Variable fluorescence (a measure of photosynthetic efficiency/health).	Ratio of arbitrary fluorescence units	no_bcodmo_term
N_fix_nmol	N fixation: rate of fixation of N2 gas per mole of carbon.	nanomoles N per micromoles C per hour (nmolN umolC^-1 h^-1)	no_bcodmo_term
N_fix_fmol	N fixation: rate of fixation of N2 gas per cell.	femtomoles N per cell per hour (fmolN cell^-1 h^-1)	no_bcodmo_term
N_fix_umol	N fixation: rate of fixation of N2 gas per mg Chl a.	micromoles N per milligram chlorophyll per hour (umolN mgChl^-1 h^-1)	no_bcodmo_term
Nspec_N_fix	N specific N fixation: rate of N fixation per mole of cellular nitrogen.	h^-1	no_bcodmo_term
DOC_umol_per_chl	DOC: dissolved organic carbon per mg chl A.	umol chl^-1	no_bcodmo_term
DOC_umol_per_L	DOC: dissolved organic carbon per liter of culture media.	umol L^-1	no_bcodmo_term
DON_umol_per_chl	DON: dissolved organic nitrogen per mg chl A.	umol chl^-1	no_bcodmo_term
DMSP_prod	DMSP production: rate of production of dimethylsulfoniopropionate normalized to cell volume.	uM h^-1 cell volume^-1	no_bcodmo_term
DMSP	DMSP: amount of DMSP per cell.	fmol cell^-1	DMSP
membr_perm	Membrane permeability: a measure of viability based on uptake of a fluorescent dye.	viability; arbitrary fluorescence units	no_bcodmo_term
Fe_to_C	Fe:C: iron to carbon ratio.	umol mol^-1	no_bcodmo_term
Mo_to_C	Mo:C: molybdenum to carbon ratio.	umol mol^-1	no_bcodmo_term
Fe_use_eff	Fe use Efficiency: amount of CO2 fixed per mole of Fe assimilated.	molC molFe^-1 d^-1	no_bcodmo_term
Mo_use_eff	Mo use efficiency: amount of CO2 fixed per mold of Mo assimilated.	molC molMo^-1 d^-1	no_bcodmo_term
UV_inhib	UV inhibition: growth rate inhibition by ultraviolet light, %.	%	no_bcodmo_term
TEP_exudates	TEP exudates: moles of carbon in the form of transparent extracellular polymers per mL of culture media.	fmolC um^-3	no_bcodmo_term
domoic_acid_quota	Domoic acid quota: amount of domoic acid per cell.	picomoles per cell (pmol cell^-1)	no_bcodmo_term
domoic_acid_prod	Domoic acid production: rate of domoic acid production per cell.	picomoles per cell per day (pmol cell^-1 d^-1)	no_bcodmo_term
Si	Si: moles of silicon per cell.	picomoles per cell (pmol cell^-1)	Si
Si_to_C	Si:C ratio: silicon to carbon ratio.	M/M	no_bcodmo_term
HCO3_uptake	HCO3 uptake: rate of bicarbonate attack per mg chlA.	micromoles per milligram chlorophyll per hour (umol mgchl^-1 h^-1)	no_bcodmo_term
CO2_uptake	CO2 uptake: rate of CO2 uptake per mg chlA.	micromoles per milligram chlorophyll per hour (umol mgchl^-1 h^-1)	no_bcodmo_term
K1_2_CO2_uptake	K1/2 CO2: half-saturation constant for CO2 uptake.	umol L^-1	no_bcodmo_term
K1_2_HCO3_uptake	K1/2 HCO3: half-saturation constant for HCO3 uptake.	umol L^-1	no_bcodmo_term
ecarbonic_anydr_act	eCarbonic Anhydrase activity: units of extracellular carbonic anhydrase active per mg chl A.	U ugchla^-1	no_bcodmo_term
icarbonic_anhydr_act	iCarbonic anhydrase activity: units of intracellular carbonic anhydrase activity per mg chl A.	U ugchla^-1	no_bcodmo_term
DIC_uptake	DIC uptake: rate of uptake of dissolved inorganic carbon per liter of culture media.	umol L^-1 d^-1	no_bcodmo_term
DIC_leakage	DIC leakage: rate of dissolved inorganic carbon leaker per liter of culture media.	umol L^-1 d^-1	no_bcodmo_term
saxitoxin	Saxitoxin: moles per cell.	fmol cell^-1	no_bcodmo_term

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Dataset: OA Lit Review