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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.
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.
Explanations of column headings:
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
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.
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.
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