Datasets from "Optimal growth conditions of the haptophyte Chrysochromulina leadbeateri causing massive fish mortality in Northern Norway"

Clone repository (UNIX-like systems and macOS)

git clone https://github.com/Mr-Mathias-F/Chrysochromulina-leadbeateri-growth-rates

Experimental design

The study used a high-throughput experimental design to screen the growth rates of the fish-killing haptophyte Chrysochromulina leadbeateri, which caused massive fish mortality in Northern Norway in 1991 and 2019. The figure below shows a schematic depiction of the experimental design.

Data analysis

All files used for data processing, analysis and Arduino light panel programming are in the Analysis folder using R (version 4.2.1).

Datasets used in high-throughput Chrysochromulina leadbeateri (HTCL) growth rate experiments

HTCL_dataset_metadata.csv / HTCL_dataset_metadata.xlsx

Dataset with Chrysochromulina leadbeateri chlorophyll-a measurement with full metadata.

Column description:

• Date_Time – Date (in YYYY-MM-DD format) and time (in HH:MM:SS format) for each in vivo chlorophyll-a measurement
• Date – Date (in YYYY-MM-DD format) for each in vivo chlorophyll-a measurement
• Time – Time (in HHMM format) for each in vivo chlorophyll-a measurement
• Experiment.x – Experimental name
• ID_unique – Unique well identifier for each plate (concatenation of well ID (Row and Col) with Plate.x)
• Plate.x – Plate number in the experiment
• ID – Well identifier
• Row – Well row
• Col – Well column
• Chl – Measured in vivo chlorophyll-a measurement in Chrysochromulina leadbeateri
• Well – Well identifier (identical to ID)
• Plate.y – Plate number in the experiment (identical to Plate.x)
• Light_panel – Identification of which light panel used
• Group – Taxonomic clade of species
• Genus – Taxonomic genus of species
• Species – Taxonomic species name
• Strain_Experiment_Replicate – Description of strain from which experiment and replicate (concatenation of Strain, Experiment.x and replicate)
• Strain_Experiment – Description of strain from which experiment (concatenation of Strain and Experiment.x)
• Strain – Strain of Chrysochromulina leadbeateri used
• Species_Strain – Description of species and which strain (concatenation of Species and Strain)
• Medium – Medium used in the experiment
• Replicate – Identification of technical replicate within experiment for combination of culture condition
• Salinity – Salinity treatment of the medium
• Temperature – Temperature treatment (°C)
• Light_period – Number of hours (h) with light on in a given day
• Light_intensity – Irradiance treatment (µmol m^-2 s^-1)
• Experiment.y – Identification of experiment
• Timepassed – Time passed since starting experiment (based on the time of the first measurement)
• Day – Time passed in number of days (rounded from Timepassed to integer)

metaPR2_Chrysochromulina_leadbeateri.csv / metaPR2_Chrysochromulina_leadbeateri.xlsx

Extracted data from the metaPR2 dataset for species Chrysochromulina leadbeateri.

Column description:

• depth – Depth level (m) of the metabarcode sample
• salinity – Salinity at sampling site
• temperature – Temperature (°C) at sampling site
• asv_code – Assigned amplicon sequence variant (ASV) code of Chrysochromulina leadbeateri
• n_reads_pct – Percentage (%) read of ASV out of total reads
• longitude – Coordinate indicating the north-south position of the sample (°N / °S)
• latitude – Coordinate indicating the east-west position of the sample (°E / °W)

HTCL_dataset_validation.csv / HTCL_dataset_validation.xlsx

Dataset with Chrysochromulina leadbeateri strain UIO394 in vivo chlorophyll-a measurements and cell concentations (cells mL^-1).

Column description:

• Replicate – Identification of replicate
• Day – Time passed (d) since experiment start
• IVF_mean – Mean in vivo chlorophyll-a measurements of Chrysochromulina leadbeateri
• IVF_sd – Standard deviation of mean in vivo chlorophyll-a measurements for technical replicates
• Cell_conc – Cell concentration of Chrysochromulina leadbeateri determined by manual cell counting (cells mL^-1)
• Species – Taxonomic Species name
• Temp – Temperature (°C)
• Salintiy – Salinity of the medium
• Date – Date (in DD-MM-YYYY format)

HTCL_mumax.xlsx

Dataset with Chrysochromulina leadbeateri maximum specific growth rates obtained from the spline models.

Column description:

• Strain – Strain of Chrysochromulina leadbeateri used
• Salinity – Salinity treatment of the medium
• Temperature – Temperature treatment (°C)
• Irradiance – Irradiance treatment (µmol m^-2 s^-1)
• Experiment ID – Identification of experiment
• Maximum specific growth rate – The maximum specific growth rate (d^-1) estimated for given combination of Strain, Salinity, Temperature, Irradiance and Experiment ID
• Standard deviation – Standard deviation of the maximum specific growth rates of all technical replicates for given combination of Strain, Salinity, Temperature, Irradiance and Experiment ID