Phytoplankton Photophysiology Utilities: A Python Toolbox for the Standardization of Processing Active Chlorophyll-a Fluorescence Data

• Published in: Frontiers in Marine Science Vol. 8
• Main Authors: Ryan-Keogh, Thomas J., Robinson, Charlotte M.
• Format: Journal Article
• Language: English
• Published: Lausanne Frontiers Research Foundation 05.07.2021; Frontiers Media S.A
• Subjects: Biogeochemistry; Chlorophyll; Chlorophyll a; chlorophyll fluorescence; Community involvement; Cruises; Data; Data collection; Data processing; Exports; fast repetition and relaxation chlorophyll fluorescence induction; fast repetition fluorometry; Fluorescence; Fluorimeters; Instruments; Open source software; Parameters; photophysiology; Photosynthesis; Phytoplankton; Protocol; python; Quality control; Seawater; Standardization; Uptake
• ISSN: 2296-7745; 2296-7745
• DOI: 10.3389/fmars.2021.525414

The uptake and application of single turnover chlorophyll fluorometers to the study of phytoplankton ecosystem status and microbial functions has grown considerably in the last two decades. However, standardization of measurement protocols, processing of fluorescence transients and quality control of derived photosynthetic parameters is still lacking and makes community goals of large global databases of high-quality data unrealistic. We introduce the Python package Phytoplankton Photophysiology Utilities (PPU), an adaptable and open-source interface between Fast Repetition Rate and Fluorescence Induction and Relaxation instruments and python. The PPU package includes a variety of functions for the loading, processing and quality control of single turnover fluorescence transients from many commercially available instruments. PPU provides the user with greater flexibility in the application of the Kolber-Prasil-Falkowski model; tools for plotting, quality control, correcting instrument biases and high-throughput processing with ease; and a greater appreciation for the uncertainties in derived photosynthetic parameters. Using data from three research cruises across different biogeochemical regimes, we provide example applications of PPU to fit raw active chlorophyll-a fluorescence data from three commercial instruments and demonstrate tools which help to reduce uncertainties in the final fitted parameters.