A practical guide to long-term field PAM chlorophyll fluorescence measurements: setup, installation, data processing with R package 'LongTermPAM' and interpretation.

Pulse-amplitude modulated (PAM) chlorophyll fluorescence (ChlF) measurements provide a non-invasive method to study the regulation of the light reactions of photosynthesis in situ. PAM ChlF contributes also to the advancement of the interpretation of long-term observations of remotely sensed solar induced fluorescence by revealing the mechanistic connection between ChlF and photosynthetic function. However, long-term field PAM ChlF measurements remain uncommon due to challenges associated with the outdoor environment, instrument installation and maintenance, or data processing and interpretation. We here provide guidelines and recommendations to support long-term field installation of PAM ChlF systems, including the design of specialized field installation supports. We also introduce a dedicated R-package (LongTermPAM) to help users filter and analyse long-term data. Methods are demonstrated using two long-term datasets obtained with a MONI-PAM system (Monitoring PAM, Walz GmbH, Germany) on Scots pine and Norway spruce in a boreal forest. The LongTermPAM R-package helped filter spurious observations caused by dew, ice or snow, permitting calculation of photochemical (PQ) and non-photochemical quenching (NPQ) parameters and their associated yields. Finally, we illustrate how PQ and NPQ regulate the relationship between ChlF and photochemical yields, and discuss how variations in leaf PAR absorption, energy partitioning between photosystems II and I, and the contribution of photosystem I to the total ChlF signal can influence the interpretation of PAM ChlF, emphasizing the value of complementary measurements to capture variability in these factors. Although based on our experience with the MONI-PAM system in a boreal environment, most issues hereby addressed can be broadly applied to other long-term PAM monitoring systems and environments.