DOI: 10.5061/dryad.mgqnk990r
title: Data for: The photosynthetic response of spectral chlorophyll fluorescence differs across species and light environments in a boreal forest ecosystem

description: Chlorophyll fluorescence can serve as a proxy of photosynthesis in boreal
 forests. When sustained non-photochemical quenching (NPQS) relaxes towards
 summer, leaf chlorophyll fluorescence (ChlF) emission increases along with
 photosynthesis. Yet, other physical and physiological factors can also
 leave a measurable imprint on the fluorescence emission spectra, and
 disrupt this relationship. We measured leaf-level spectral ChlF of Scots
 pine, Norway spruce and lingonberry exposed to contrasting light
 environments throughout the spring recovery of photosynthesis,
 simultaneously with a series of photosynthetic, biochemical and
 morphological traits. Correlations between traits and ChlF spectral
 components were analyzed to identify the mechanisms underlying both the
 spatial variation found between species and light environments, and the
 temporal variation found across the study period. Spatially, we found
 evidence of baseline differences in leaf-level ChlF magnitude, which we
 attribute to species- and light environment-specific changes in leaf
 morphology. Temporally, ChlF magnitude followed the relaxation of
 NPQS  towards summer, but only in upper canopy foliage and
 lingonberry, suggesting a seasonal compensation effect between sustained
 photochemical quenching (PQS) and NPQS, potentially decoupling the
 seasonal relationship between ChlF and photosynthesis in shaded foliage.
 Finally, we show subtle changes in the shape of the ChlF spectra that took
 place independently of chlorophyll concentration dynamics, pointing to the
 complexity of NPQs which can involve structural rearrangements in the
 thylakoids and changes in the relative contribution of PSI to emitted
 ChlF. We conclude that the diversity of species and light environments
 found within an ecosystem generates a baseline level of variation in leaf
 spectral ChlF as well as contrasting seasonal photosynthetic acclimation
 patterns. These sources of variability should be taken into account when
 developing quantitative models for the interpretation of ChlF data, in
 particular for applications involving high resolution SIF imaging systems
 capable of resolving different plant individuals and their parts.
description: The dataset was collected during a measuring campaign carried out
 at Station for Measuring Ecosystem-Atmosphere Relation (SMEAR-II) in
 Hyytiälä, southern Finland (61⁰50’ N, 24⁰17’ E) from February
 to July 2017. The data available here are raw or pre-processed and if it
 concerns, the pre-processing procedure is described in the readme files
 available in each variable-dedicated folder. The chlorophyll fluorescence
 dataset (folder: spectral_fluorescence) has been collected
 with an Optical Chamber protocol as described in the methods section of
 the associated manuscript referenced above. From the dataset available
 in this depository, the chlorophyll fluorescence data was
 processed by a series of Singular Value Decomposition (SVD) analyses to
 evaluate the relative role of vectors in explaining the spatial and
 temporal variation of chlorophyll fluorescence spectra. The remaining
 datasets (folders: PAM fluorescence, gas exchange, pigments, light
 environment, and SMEAR, where environmental variables from the station are
 available) have been used to test their correlations with the SVD vectors
 in order to investigate the relative roles that different variables have
 in controlling the spatial and temporal variation of chlorophyll
 fluorescence spectra. Results of these analyses have been presented in the
 publication titled "The photosynthetic response of spectral
 chlorophyll fluorescence differs across species and light environments in
 a boreal forest ecosystem" in the Agricultural and Forest Meteorology
 Journal.
description: The dataset is divided into folders for each of the measured
 variables. In the SMEAR folder, three variables regarding environmental
 variables of the SMEAR-II measuring station are included. In the spectral
 fluorescence folder, separate files for each analyzed case (species and
 canopy position) are included. The readme file in each folder contains an
 explanation of each of the variables in the dataset, its measurement
 device, measurement units, file layout, and pre-processing (if concerns).
 Information on how the measurements were done can be found in the
 associated manuscript referenced above.