Abstract
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.
Highlights
The first uses of in-vivo chlorophyll-a fluorescence measurements were as a proxy for chlorophylla concentration of photosynthetic organisms (Lorenzen, 1966)
In this paper we present an open-source tool, Phytoplankton Photophysiology Utilities (PPU), that can be used to process raw chlorophyll-a fluorescence data from a variety of commercial instruments, where we focused on the Chelsea Technologies Group FASTTracka I and FASTOcean and Sea-Bird Scientific Fluorescence Induction and Relaxation (FIRe)
This paper presents the detailed methods of PPU using example datasets from the three instruments that were deployed in flow-through mode across different biogeochemical regions, demonstrating the versatility and robustness of the optimization routines whilst providing the necessary statistical metrics to perform quality control
Summary
The first uses of in-vivo chlorophyll-a fluorescence measurements were as a proxy for chlorophylla concentration of photosynthetic organisms (Lorenzen, 1966). More recent advances in active chlorophyll-a in-vivo fluorescence enable measurements of photosynthetic efficiency (Kolber and Falkowski, 1993). One of the most prevalent approaches is fast repetition rate fluorometry (FRRf; Kolber et al, 1998) and its variant fluorescence induction relaxation fluorometry (FIRe; Gorbunov and Falkowski, 2004). This is predominantly due to the versatility of these instruments. Commercial fast repetition rate or fluorescence induction relaxation instruments exhibit large dynamic ranges in detection sensitivity suitable for application to eutrophic and oligotrophic systems (Röttgers, 2007). The ability to measure multiple parameters such as the functional absorption cross section and electron transport kinetics (Kolber et al, 1998; Gorbunov and Falkowski, 2004; Röttgers, 2007); as well as the capacity to collect measurements in the laboratory (Fujiki et al, 2007; Mckew et al, 2013; Schuback et al, 2015), connected to a flow-through aquatic water system (Behrenfeld et al, 2006; Houliez et al, 2017) or in-situ (Moore et al, 2003; Suggett et al, 2006b; Fujiki et al, 2008, 2011), including on autonomous platforms (Carvalho et al, 2020), are advantageous features of this type of instrumentation
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
