Application of Single Turnover Active Chlorophyll Fluorescence for Phytoplankton Productivity Measurements. Version 2.0, June, 26, 2023.

Abstract

This document represents the collective efforts of SCOR Working Group 156, ‘Active Chlorophyll Fluorescence for Autonomous Measurements of Global Marine Primary Productivity’. The group was established in 2019, bringing together researchers and instrument manufacturers from 10 countries and 6 continents to develop standards of best practice in the application of single turnover active chlorophyll fluorescence (ST-ChlF) for phytoplankton photo-physiology and productivity measurements. We focused our efforts on single turnover ChlF methods, which are most prevalent in phytoplankton research, while recognizing that other approaches, including Pulse Amplitude Modulation (PAM) fluorescence, are also commonly employed with macro-algae, corals and terrestrial plants. Some of the material in this document will apply to those related measurement techniques. During the period between 2019-2022, our group worked to build consensus around best practice for the collection, analysis, interpretation and archiving of ST-ChlF data from a variety of aquatic environments. This work was aimed at facilitating wide-spread use of ST-ChlF methods by the international research community, focussing on two key objectives outlined in the Working Group’s terms of reference: 1. To develop, implement and document internationally-agreed best practice for the acquisition and analysis of ST-ChlF data to retrieve photosynthetic parameters and primary productivity estimates. 2. To develop, implement and document standardised ST-ChlF data output formats and archiving approaches. As a first step towards these objectives, we published a review article (Schuback et al. 2021), outlining applications, opportunities and current limitations of ST-ChlF measurements. This highlevel review was aimed at readers wishing to apply ST-ChlF methods and interpret the resulting data in the most robust manner possible. Journal length restrictions precluded in-depth treatment of many important topics, including instrument calibration, data fitting and spectral correction. In this User Guide, we expand on the material presented by Schuback et al. (2021), providing handson guidance for both experts and new users alike. With this document, we aim to provide both a strong theoretical background for ST-ChlF methods, and a practical handbook to inform the application of these methods across a wide range of aquatic environments. We assume that readers of have a basic understanding of aquatic photosynthesis, as outlined, for example, by Falkowski and Raven (2013). This document represents the first complete version of the SCOR ST-ChlF user guide. It is being released to the international research community for a period of open consultation. We encourage comments and suggestions, which can be addressed to the working group co-chairs, Philippe Tortell and David Suggett. We expect the contents of this User Guide to evolve significantly over time, through our own efforts and with input from other experts and end-users. Revised versions of the User Guide will be posted on the Ocean Best Practices site (https://www.oceanbestpractices.org/), and interested readers are encouraged to check periodically for updates. In follow up work, we aim to further develop existing open-source software (e.g. Ryan-Keogh and Robinson, 2021) to facilitate ST-ChlF data analysis from a range of different instruments and formats. This document is intended to serve the needs of a wide range of users, from novices (first year graduate students, for example) to expert researchers with decades of experience using ST-ChlF methods. We anticipate that some readers will require only high-level information on key operational parameters needed for successful ST-ChlF measurements, while others will be interested in further exploring the underlying ideas and concepts. For this reason, the document includes appendices that provide greater detail on some topics presented in the main document. In subsequent versions of this User Guide, we aim to include linked Jupyter notebooks, with handson tutorials and data processing tools. These software tools will help facilitate the inter-comparison of measurements collected by different users and instruments, supporting the development of globally-coherent ST-ChlF data compilations.