Prochlorococcus marinus responses to light and oxygen
Prochlorococcus marinus, the smallest picocyanobacterium, comprises multiple clades occupying distinct niches, currently across tropical and sub-tropical oligotrophic ocean regions, including Oxygen Minimum Zones. Ocean warming may open growth-permissive temperatures in new, poleward photic regimes, along with expanded Oxygen Minimum Zones. We used ocean metaproteomic data on current Prochlorococcus marinus niches, to guide testing of Prochlorococcus marinus growth across a matrix of peak irradiances, photoperiods, spectral bands and dissolved oxygen. MED4 from Clade HLI requires greater than 4 h photoperiod, grows at 25 µmol O~2~ L^-1^ and above, and exploits high cumulative diel photon doses. MED4, however, relies upon an alternative oxidase to balance electron transport, which may exclude it from growth under our lowest, 2.5 µmol O~2~ L^-1^, condition. SS120 from clade LLII/III is restricted to low light under full 250 µmol O~2~ L^-1^, shows expanded light exploitation under 25 µmol O~2~ L^-1^, but is excluded from growth under 2.5 µmol O~2~ L^-1^. Intermediate oxygen suppresses the cost of PSII photoinactivation, and possibly the enzymatic production of H~2~O~2~ in SS120, which has limitations on genomic capacity for PSII and DNA repair. MIT9313 from Clade LLIV is restricted to low blue irradiance under 250 µmol O~2~ L^-1^, but exploits much higher irradiance under red light, or under lower O~2~ concentrations, conditions which slow photoinactivation of PSII and production of reactive oxygen species. In warming oceans, range expansions and competition among clades will be governed not only by light levels. Short photoperiods governed by latitude, temperate winter, and depth attenuation of light, will exclude clade HLI (including MED4) from some habitats. In contrast, clade LLII/III (including SS120), and particularly clade LLIV (including MIT9313), may exploit higher light niches nearer the surface, under expanding OMZ conditions, where low O~2~ relieves the stresses of oxidation stress and PSII photoinhibition.
Prochlorococcus, Oxygen, Photoperiod
Data was imported and tidied into R (v4.1.3), running under R-studio (Posit Team, v2023.06.0), using the 'tidyverse' [@R-tidyverse], 'glue' [@R-glue], 'ggh4x' [@R-ggh4x], 'ggtext' [@R-ggtext], 'ggpubr' [@R-ggpubr], 'minpack.lm' [@R-minpack.lm], [@R-data.table], [@R-zoo], [@R-mgcv], [@R-kable] and 'nlstools' [@R-nlstools] packages. Formatted outputs were generated from Rmarkdown files using the 'knitr' [@R-knitr] and 'bookdown' [@R-bookdown] packages. The 'MultiCultiCatalog' googlesheet containing metadata was read using the [@R-googlesheets4] package.
All data and annotated code for data import, transformations and analyses are available at are available on the figshare data repository (DOI: 10.6084/m9.figshare.25959061).
All data and annotated code are also available at https://github.com/FundyPhytoPhys/prochlorococcus_o2
The metadata for Multicultivator runs is generated from "Code/Import_MetaData.Rmd" which calls in the googlesheet: https://docs.google.com/spreadsheets/d/1ZXpwR7Gfto-uRzVdXzMpQF4frbrvMLH_IyLqonFZRSw/edit#gid=0
Data Dictionary can be found in "Docs/prochlorococcus_O2_DataDictionary.csv"
Imports metadata for Multicultivator experiments. Metadata URL location: https://docs.google.com/spreadsheets/d/1ZXpwR7Gfto-uRzVdXzMpQF4frbrvMLH_IyLqonFZRSw/edit#gid=0 and outputs "CultureCatalog.Rds"
This script imports and tidies Muticultivator data in simple .csv long form (Data/RawData/MultiCultiData.zip/"yyyymmdd_PICO_MCXXXXXX_RUNXXX.csv") based upon project specific values for variables set by the user. Multicultivator data files are too large to upload in a single .zip folder therefore 3 .zipped folders ("MultiCultiData1.zip", "MultiCultiData2.zip" and "MultiCultiData3.zip") are uploaded. Uncomment the 'DataIn' line with the folder name containing the intended files for import. Individual multicultivator runs are imported and tidied one at a time. A metadata catalog (Data/RawData/"CultureCatalog.Rds") is imported and merges with the imported data based upon shared values for the variables 'MC', 'Tube', and 'Filename' which unambiguously identify a given growth trajectory measured at OD680 or OD720. Each individually imported and tidied multicultivator run is saved as a .Rds in the "Data/ImportedData/ImportedMCData" folder as "yyyymmdd_PICO_MCXXXXXX_RUNXXX_TargetDataMetaFilter.Rds" for further processing in "Code/Process_MCData.Rmd".
This script reads in individually tidied Muticultivator runs from "Data/ImportedData/ImportedMCData" folder and implements logistic and other growth curve fits to the MultiCultivator growth trajectories. The processed .Rds are saved in the "Data/ProcessedData/ProcessedMCData" folder as "yyyymmdd_PICO_MCXXXXXX_RUNXXX_ProcessDataNestGrowth.Rds" for further processing in "Code/Merge_MCGrowthData.Rmd".
This script reads in all individually processed Muticultivator runs containing growth fits from the "/Data/ProcessedData/ProcessedMCData" folder and merges the data into 1 data frame. This single data frame is saved as a .Rds called "PICO_Processed_MCGrowthFits.Rds" in the "/Data/CleanData/CleanedMCData" folder to be merged later with PUR data using the "Merge_GrowthPURData.Rmd" script.
This script imports and tidies all Jaz spectrometer emission files (.txt) from "Data/RawData/JazEmData.zip". The tidied data of all the emission spectra is saved as one .Rds named "PICO_Imported_JazEmData.Rds" in the "Data/ImportedData/ImportedJazEmData" folder for further analysis in "Process_OlisJazEmData.Rmd".
This script imports and tidies all OLIS 14 UV/VIS Clarity spectrophotometer whole cell absorbance files (.asc) from "Data/RawData/OlisData.zip". The tidied data of all the absorbance spectra is saved as one .Rds named "PICO_Imported_OlisData.Rds" in the "Data/ImportedData/ImportedOlisData" folder for further analysis in "Process_OlisJazEmData.Rmd".
This script imports, merges and calculates the Photosynthetically Usuable Radiation (PUR) from the "PICO_Imported_JazEmData.Rds" and the "PICO_Imported_OlisData.Rds" files. The tidied data of all the PUR, absorbance and emission spectra is saved as one .Rds named "PICO_Processed_OlisJazMetaPUR.Rds" in the "Data/ImportedData/ImportedJazEmData" folder to be merged with growth data using the "Merge_GrowthPURData.Rmd" script.
This script imports and merges the "PICO_Processed_MCGrowthFits.Rds" and "PICO_Processed_OlisJazMetaPUR.Rds" and assigns Photosynthetically Usuable Radiation (PUR) from the calculated PUR results in "PICO_Processed_OlisJazMetaPUR.Rds" to the appropriate matching PAR and WL for each strain in the "PICO_Processed_MCGrowthFits.Rds". The tidied data of all the growth rate estimates, PUR, PAR and nested data frames containing whole cell absorbance and emission spectra and Multicultivator OD measurements for every combination of the growth matrix experiments is saved as "PICO_Merged_GrowthFitsPURPAR.Rds" in the "Data/CleanData" folder and used to generate statistics and figures using "Plots_GAM.Rmd" and "Plots_PURFits.Rmd" and figures using "Plots_Growth.Rmd".
This .Rmd reads in "PICO_Merged_GrowthFitsPURPAR.Rds" from the "Data/CleanData" folder and produces a Generalized Additive Model (GAM) to examine the relationship between the chlorophyll proxy (ΔOD) growth rate across the blue and red spectral wavebands, photoperiod and PAR levels for each P.marinus ecotype in this study. The GAM function from the R package mgcv (Wood, 2022) was used to model the growth rate with smoothing terms to indicate the 90, 50 and 10% quantiles. The generated GAM plots ("MED4PARGAM.png", "SS120PARGAM.png" and "MIT9313PARGAM.png") are saved in the "Output/Figures" folder and later read into "Manuscript_O2.Rmd".
This .Rmd reads in "PICO_Merged_GrowthFitsPURPAR.Rds" from the "Data/CleanData" folder and generates figures that are later called into "Manuscript_O2.Rmd". The generated plots ("PurParPlot.png","OverlayPlots.png" and "deltaODLogGrowthPlot.png") are saved in the "Output/Figures" folder.
This .Rmd reads in "PICO_Merged_GrowthFitsPURPAR.Rds" from the "Data/CleanData" folder and generates a one-way ANOVA to examine statistical differences between Harrison and Platt four parameter model fit to 660 nm (red light) and 450 nm (blue light) growth data for each combination of strain and [O~2~]. Additionally, a one-way ANOVA was used to examine statistical differences between Harrison and Platt four parameter model fit to each photoperiod (4 h, 8 h, 12 h, 16 h) and pooled photoperiod growth data for each combination of strain and [O~2~]. Photoperiod growth data that showed complete growth inhibition for each combination of strain, [O~2~] and imposed spectral waveband were omitted from the pooled photoperiod model. Statistical differences were determined at P value < 0.05. Dummy values of no growth (µ = 0) for dark conditions at PAR of 0 µE were assigned for each combination of [O~2~], photoperiod and spectral waveband for each strain to anchor the starting point of the model. The generated PUR fit plots ("BluevsRedPurFitsPlots.png" and "PhotoperiodPurFitsPlots.png") are saved in the "Output/Figures" folder and later read into "Manuscript_O2.Rmd".
This .Rmd reads in "ProchlorococcusGenomeData.Rds" from the "Data/CleanData" folder. The generated plots ("ProchlorococcusEnzymeKms.png", "DNARepairFig.png" and "ProchlorococcusLightEnzymesFig.png") are saved in the "Output/Figures" folder and later read into "Manuscript_O2.Rmd".
This .Rmd reads in "poi.RDS" from the "Data/ProcessedData/ProcessedOceanProtein" folder and generates figures that are later called into "Manuscript_O2.Rmd". The generated plots ("CladeProchloroPhotosynthDepthO2.png" and "CladeProchloroProteinMetabDepthO2.png") are saved in the "Output/Figures" folder.
This .Rmd reads in "DepthPhotoperiodTableFilter.Rds" from the "Data/ProcessedData" folder and generates figure 'Output/Figures/NicheMap.png' that is later called into "Manuscript_O2.Rmd".
This .Rmd uses R Markdown and knits to .docx and html to produce a manuscript style document formatted for PLOS ONE publication. The .Rmd reads in "PICO_Merged_GrowthFitsPURPAR.Rds" from the "Data/CleanData" folder and generates a table of maximum growth rate for each strain grown under each [O~2~] condition. Figures are read in from the "Output/Figures" folder. The Word and html documents are saved as "Manuscript_O2.docx" and "Manuscript_O2.html" in the "Code" folder.
This is the template used to format the knitted WORD document.
These are required files to format the authorship and affiliations properly when knitting to html and Word.
This file overwrites the bookdown default settings in the yaml and allows the knitted .docx and html to be saved in the "Output" folder.
Figures generated using "Code/Plots_Growth.Rmd":
Figures generated using "Code/Plots_GAM.Rmd":
Figures generated using "Code/Plots_PURfits.Rmd":
Figures generated using "Code/Plots_Genome.Rmd":
Figures generated using "Code/Plots_OceanProtein.Rmd":
Figure generated using "Code/Plots_ProNicheMap.Rmd":
The editable Powerpoint file named "LabeledMC.pptx" was used to generated the labeled Multicultivator picture named "LabeledMC.png".
Contains all .tiff figures renamed to match the order in which they appear in the manuscript (Fig1 to Fig12) and "Manuscript_O2_PLOS1.docx" is the manuscript formatted as per PLOS ONE guideline for submission.
Contains all .tiff figures renamed to match the order in which they appear in the manuscript and "Manuscript_O2_PLOS2.docx" is the manuscript formatted as per PLOS ONE guideline for submission.