![]() ![]() 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). This is predominantly due to the versatility of these instruments. 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). A variety of instrumentation types have been utilized by the community, from the early models of pump and probe fluorometers ( Falkowski et al., 1986), to the more recent PicoF Lifetime Fluorometry ( Lin et al., 2016). Active chlorophyll- a fluorescence has been widely adopted by the oceanographic community as a rapid, non-destructive technique to assess ecosystem status and microbial function across large temporal ( Suggett et al., 2006a) and spatial scales ( Behrenfeld et al., 1996 Suzuki et al., 2002 Moore et al., 2005, 2006a, b) approaching those of entire oceanic ecosystems ( Behrenfeld and Kolber, 1999 Behrenfeld et al., 2006 Suggett et al., 2006b). More recent advances in active chlorophyll- a in- vivo fluorescence enable measurements of photosynthetic efficiency ( Kolber and Falkowski, 1993). The first uses of in-vivo chlorophyll- a fluorescence measurements were as a proxy for chlorophyll- a concentration of photosynthetic organisms ( Lorenzen, 1966). ![]() ![]() 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. 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. 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. 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. 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. 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. 2Remote Sensing and Satellite Research Group, Earth and Planetary Sciences, Curtin University, Perth, WA, Australia.1Southern Ocean Carbon and Climate Observatory, Smart Places, CSIR, Cape Town, South Africa. ![]()
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