Dataset: Syn-Pro Co-cultures

Name: Data on laboratory cultures and statistical analysis code associated with the paper "Co-culture with Synechococcus facilitates the growth of Prochlorococcus under ocean acidification conditions" published in Environmental Microbiology
Published: 2021-02-05
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.839925.1

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:

2021-02-05

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Data on laboratory cultures and statistical analysis code associated with the paper "Co-culture with Synechococcus facilitates the growth of Prochlorococcus under ocean acidification conditions" published in Environmental Microbiology

Abstract:

Data on laboratory cultures and statistical analysis code pertaining to the paper "Co-culture with Synechococcus facilitates the growth of Prochlorococcus under ocean acidification conditions" published in Environmental Microbiology (doi:10.1111/1462-2920.15277). The data and code in this package allow one to re-run all the analyses performed in the paper.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2021-02-05	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.839925.1	2021-02-09

Description

The data and code in this package allow one to re-run all the analyses performed in the paper "Co-culture with Synechococcus facilitates Prochlorococcus growth under ocean acidification conditions", published in Environmental Microbiology (doi:10.1111/1462-2920.15277). Each file is provided separately and all files are packaged into the file Syn-Pro_Co-cultures.zip.

To re-run the analyses, place all the files in one directory, set that directory to the working directory in R, and copy-and-paste the entire contents of the file KnightDataAnalysis.txt into the R window and hit "enter". You may need to install the plyr, lme4, and emmeans packages beforehand. A description of each file is in the ReadMe.txt file.

Methods & Sampling

All data from this study are based on growth rate measurements from laboratory cultures of cyanobacteria acclimated to either 400 ppm or 800 ppm pCO2. Full details are included in Knight & Morris (2020). Brief summaries of the two experiments and their analyses are reported below.

1. Survey of Prochlorococcus and Synechococcus culture responses to year 2100 pCO2. We tested the growth rate response of several different strains of each genus, representing the most globally abundant ecotype varieties, to 800 ppm pCO2, similar to what is expected to exist by the end of the century. Cultures were acclimated for 3 cycles of semi-continuous culture at the target pCO2, and then growth curves were collected by flow cytometry for 3 further transfer cycles. Cultures were diluted into fresh media while still in exponential growth phase. Both exponential growth rates (slope of cell density vs. time during logarithmic growth) and Malthusian growth rates (based only on starting and ending cell densities, and the elapsed time of the culture) were calculated. Growth rate responses were expressed as the ratio of growth rate at 800 ppm over 400 ppm, and were compared to values reported previously in the literature for other marine cyanobacteria.

2. Head-to-head Prochlorococcus vs. Synechococcus experiments. We chose one strain of each genus from Experiment 1 to compete in co-culture with each other. Strains were chosen to have opposite growth rate responses, such that Prochlorococcus was predicted to be outcompeted at 800 ppm pCO2. Growth of each competitor was measured by flow cytometry, where the two genera have easily distinguishable fluorescence signatures. Relative fitness of Prochlorococcus was expressed as the difference in growth rate between Prochlorococcus and Synechococcus. Linear models were used to analyze the effects of cell density and relative frequency on competition outcomes.

Media preparation: All experiments were conducted in media with an artificial seawater base. Carbonate parameters were carefully measured using titration to determine alkalinity and either potentiometric or colorimetric assays to determine pH. pCO2 was manipulated by addition of calibrated doses of HCl or NaOH, along with NaHCO3 to preserve alkalinity if necessary, in hermetically sealed test tubes with approximately no headspace. Culture growth was assessed every two days by removing a 100 uL aliquot for flow cytometric analysis.

Data Processing Description

Data Processing:All data were analyzed in R v 3.6.1. Linear models were used for most analyses, with post-hoc comparisons conducted using the emmeans package Full code necessary to re-run our analyses is contained in the file KnightDataAnalysis.txt included with this package.

Data Files

File
CompDataProcessed.csv (Comma Separated Values (.csv), 11.50 KB) MD5:53b2154909a12fdc7e275597971f3d8e CompDataProcessed.csv and CompDataProcess.outlierremoved.csv These are the co-culture competition experiments summarized in manuscript Figures 3 and 4. Experiment: Two experimental blocks were performed, one by author Knight (Maggie) and one by author Morris (Jeff). Culture: Each competition paired one of 6 Prochlorococcus clones, designated as LTPE 26-31, with one of 6 Synechococcus clones, designated LTPE 45-50. CO2: Either 400 ppm (0) or 800 ppm (1) pCO2. Replicate: In some cases multiple replicates of a particular clone pairing were performed, this column indicates which replicate a given row corresponds to. Transfer: Each culture was transferred into fresh media at least 2 times, giving at least 3 separate cultures in sequence. This column indicates which sequential transfer each row represents. Time: Time (days) between inoculation and transfer. InitPro, InitSyn, FinalPro, FinalSyn: densities in cells/mL of Prochlorococcus or Synechococcus at the beginning and end of the transfer. ProGR, SynGR: malthusian growth rate of Prochlorococcus and Synechococcus respectively, calculated as described in the manuscript. InitProFreq: Initial frequency (0-1) of Prochlorococcus. Wpro: Fitness calculated as the ratio of the Prochlorococcus malthusian growth rate vs. the Synechococcus malthusian growth rate. Dimensionless. Spro: Fitness calculated as the difference of the Prochlorococcus and Synechococcus malthusian growth rates. Units d^-1. InitDens, LogInitDens: Total cyanobacterial cell density at the beginning of the experiment. ProExGR, SynEXGR: as ProGR/SynGR, but using the exponential growth rate. WproEX, SproEx: as Wpro and Spro, but calculated using the exponential growth rates. LagPro, LagSyn: lag time in days, calculated as described in the manuscript.
CompDataProcessed.outlierremoved.csv (Comma Separated Values (.csv), 23.93 KB) MD5:deadf46e9bc4a963c2dfde0d1cce7549 CompDataProcessed.csv and CompDataProcess.outlierremoved.csv These are the co-culture competition experiments summarized in manuscript Figures 3 and 4. Experiment: Two experimental blocks were performed, one by author Knight (Maggie) and one by author Morris (Jeff). Culture: Each competition paired one of 6 Prochlorococcus clones, designated as LTPE 26-31, with one of 6 Synechococcus clones, designated LTPE 45-50. CO2: Either 400 ppm (0) or 800 ppm (1) pCO2. Replicate: In some cases multiple replicates of a particular clone pairing were performed, this column indicates which replicate a given row corresponds to. Transfer: Each culture was transferred into fresh media at least 2 times, giving at least 3 separate cultures in sequence. This column indicates which sequential transfer each row represents. Time: Time (days) between inoculation and transfer. InitPro, InitSyn, FinalPro, FinalSyn: densities in cells/mL of Prochlorococcus or Synechococcus at the beginning and end of the transfer. ProGR, SynGR: malthusian growth rate of Prochlorococcus and Synechococcus respectively, calculated as described in the manuscript. InitProFreq: Initial frequency (0-1) of Prochlorococcus. Wpro: Fitness calculated as the ratio of the Prochlorococcus malthusian growth rate vs. the Synechococcus malthusian growth rate. Dimensionless. Spro: Fitness calculated as the difference of the Prochlorococcus and Synechococcus malthusian growth rates. Units d^-1. InitDens, LogInitDens: Total cyanobacterial cell density at the beginning of the experiment. ProExGR, SynEXGR: as ProGR/SynGR, but using the exponential growth rate. WproEX, SproEx: as Wpro and Spro, but calculated using the exponential growth rates. LagPro, LagSyn: lag time in days, calculated as described in the manuscript.
GrowthRates.csv (Comma Separated Values (.csv), 28.03 KB) MD5:dd9a96af6cd1501a5509be2d1f1951dc GrowthRates.csv: These represent the data summarized in manuscript Figure 1. Strain: Cyanobacterial strain. Genus: either Prochlorococcus or Synechococcus. CO2: Either 400 ppm (CO2-) or 800 ppm (CO2+) pCO2. Time: The number of days between culture inoculation and transfer into fresh media. DensInit: Culture density at inoculation, in cells/mL. DensFinal: Culture density at transfer, in cells/mL. RealizedGR, ExponentialGR: malthusian and exponential growth rates in d^-1, calculated as described in the text. Lag: lag time in days, calculated as described in the text.
GRR.csv (Comma Separated Values (.csv), 2.82 KB) MD5:7ba9d168a3412d4b3c91f0bf2e8f2e8b GRR.csv These represent the data summarized in manuscript Figure 2. Strain: Cyanobacterial strain. Dataset: Either this study (Morris) or our previous meta-analysis (Dutkiewicz). Genus: Either Prochlorococcus, Synechococcus, or "Diazotroph". Flag: Either Prochlorococcus (Pro) or not (NotPro). CO2-r, CO2+r: malthusian growth rate at 400ppm or 800ppm pCO2 respectively. Only available for experiments from this study; previous reports summarized in Dutkiewicz et al 2015 only included exponential growth rates. CO2-x, CO2+x: as above, but exponential growth rates. rgrr, xgrr: "growth rate response" for malthusian and exponential growth rates, calculated as described in the manuscript.
KnightDataAnalysis.txt (Octet Stream, 54.49 KB) MD5:430c5412eada34f56aafa946a4870393 To re-run the analyses, place all the files in one directory, set that directory to the working directory in R, and copy-and-paste the entire contents of the file KnightDataAnalysis.txt into the R window and hit "enter". You may need to install the plyr, lme4, and emmeans packages beforehand.
ReadMe.txt (Octet Stream, 4.25 KB) MD5:8e292e82fd8e4f63f6ea72ea1bcabdd9 ReadMe file describing all the other files and how to use them.
Syn-Pro_Co-cultures.zip (ZIP Archive (ZIP), 42.19 KB) MD5:90ad67d8f6207b485578c60fcf624d3e .zip package containing all the files needed to re-run the analyses performed in the paper "Co-culture with Synechococcus facilitates Prochlorococcus growth under ocean acidification conditions".
Together.csv (Comma Separated Values (.csv), 24.26 KB) MD5:28c83887dfd3bc1e80c7b23ae94a3d4b Together.csv This is the data summarized in manuscript Figure 5. It includes all the cultures from CompDataProcessed.outlierremoved.csv as well as comparison cultures with only one of the two cyanobacterial strains. Strain: Either Prochlorococcus or Synechococcus. Together: Row either corresponds to data collected from unialgal cultures (No) or co-cultures of both strains (Yes). Time: The number of days between culture inoculation and transfer into fresh media. DensInit: Culture density at inoculation, in cells/mL. DensFinal: Culture density at transfer, in cells/mL. RealizedGR, ExponentialGR: malthusian and exponential growth rates in d^-1, calculated as described in the text. Lag: lag time in days, calculated as described in the text.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1540158

Deployments

None available yet

Instruments

Algal Growth Chamber

Supplied Name: Percival algal growth chambers

Supplied Description:

Cultures were incubated in Percival algal growth chambers.

Instrument Type

Generic Name: Algal Growth Chamber

Generic Description:

A chamber specifically designed for the growth of algae in flasks. The chamber typically provides controlled temperature, humidity, and light conditions.

Automatic titrator

Supplied Name: Mettler-Toledo titrator

Supplied Description:

Alkalinity was measured using a Mettler-Toledo titrator.

Instrument Type

Generic Name: Automatic titrator

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB12/

Generic Description:

Instruments that incrementally add quantified aliquots of a reagent to a sample until the end-point of a chemical reaction is reached.

Flow Cytometer

Supplied Name: Luminex Guava HT-1 flow cytometer

Supplied Description:

Most data in this study were collected using a Luminex Guava HT-1 flow cytometer.

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

pH Sensor

Supplied Name: custom-calibrated pH probe

Supplied Description:

pH was measured using either a custom-calibrated pH probe or colorimetrically using m-cresol purple administered by sequential injection in a BioTek Synergy H1 spectrophotometer plate reader.

Instrument Type

Generic Name: pH Sensor

Generic Description:

An instrument that measures the hydrogen ion activity in solutions.

The overall concentration of hydrogen ions is inversely related to its pH. The pH scale ranges from 0 to 14 and indicates whether acidic (more H+) or basic (less H+).

plate reader

Supplied Name: BioTek Synergy H1 spectrophotometer plate reader

Supplied Description:

pH was measured using either a custom-calibrated pH probe or colorimetrically using m-cresol purple administered by sequential injection in a BioTek Synergy H1 spectrophotometer plate reader.

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

None available yet

Database

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Dataset: Syn-Pro Co-cultures