DOI: 10.5281/zenodo.18223267
title: Acclimation of young Silver fir (Abies alba Mill.) to stand light microclimate

description: These data were collected within the project SanSilva, supported by the National Agency for Agricultural Research (NAZV) under grant no. QL24010275, entitled “Silver fir as an important tree species for forest conversion in the Czech Republic, and the influence of regeneration fellings and site conditions on its growth, vitality, resilience to phytopathological agents, and mycorrhizal development.”

Current-year needles were collected from young (10–16-year-old) silver fir trees, from the upper (3rd whorl) canopy part. Fast chlorophyll fluorescence kinetics (OJIP) were measured by FluorPen immediately after branch cutting, and needle reflectance (350 – 2500 nm) was acquired in the laboratory using ASD Fieldspec 4 Wide-Res connected to the ASD Plant probe. 

Needle collection was performed during September 2025 at 12 forest stands in the Czech Republic. Study sites represented silver fir regeneration stands under different silvicultural practices forming a gradient of the incident light: shelter-wood cut, which means the highest degree of shading by mature trees, then natural regeneration under sparse canopy, small clear cut, and gap cut, which represent a moderate degree of shading by mature trees, and clear cut, which means no shading. Besides the light gradient, the study sites also differ in soil water availability, including non-enriched and water-enriched conditions

 

Metadata and Site Description:

Sampling and identificationSampling - Sampling campaign identifier in the format YYYYMMDD, indicating the date of field measurements.Locality - Name of the sampling locality where measurements were conducted.Tree - Numeric identifier of the sampled tree within a locality or plot.ID - Unique identifier of each measurement, combining plot and tree information.NAC - Needle Age Classes (Cohort).

Spatial informationCoord_N - Geographic latitude of the sampling location in decimal degrees (WGS84).Coord_E - Geographic longitude of the sampling location in decimal degrees (WGS84).

Temporal informationTime - Date and time of measurement in human-readable format (DD.MM.YYYY HH:MM).Cas - Time of measurement (HH:MM), representing the local time at which the measurement was performed.

Plot and regeneration characteristicsPlocha - Plot identifier within the locality.Obnovni_typ - Regeneration or silvicultural treatment type applied at the plot level.

Examples include:Holina (Clear cut)Nasek (Small Clear Cut)Clonna_sec (Shelter)Priroz_obn (Natural Regeneration)Kotlik (Gap Cut)

Light conditionsLight - Light environment classification corresponding to the regeneration or canopy opening type(e.g. Clear_Cut, Gap_Cut, Shelter, Natural_Reg, Small_Clear_Cut).Light_2 - Abbreviated categorical code describing light conditions(e.g. CC, GC, NR, SCC, Sh).

Forest typology and site conditionsSoub_Les_Typ - Forest site complex classification code describing soil and site characteristics.LesTyp - Forest type classification according to national forest typology.Situace - Position or situational category of the sampled tree within the stand or regeneration unit.

Water and microclimatic conditionsWater - Water availability or treatment category(e.g. En = enriched, Non_En = non-enriched).WaterEnrich - Water enrichment status code(e.g. W0 = no enrichment, W1 = enriched).Microclima - Combined microclimatic classification integrating light and water conditions(e.g. SCC_W0, CC_W1, NR_W0, GC_W1).

 

Raw fluorescence signal

Columns:ms11 – ms2001621 (columns starting with ms indicate milliseconds after the onset of actinic light )

Time-resolved chlorophyll a fluorescence intensity measured during fast fluorescence induction (OJIP curve)

Fluorescence parameters:

F₀ - Minimal fluorescence at 50 μs when all PSII reaction centers are open (dark-adapted state)Fⱼ - Fluorescence at J-stepFᵢ - Fluorescence at I-stepFₘ - Maximal fluorescence when all PSII reaction centers are closed by saturating pulseFᵥ - Variable fluorescence (Fₘ - F₀) - the capacity for photochemistryVⱼ - Relative variable fluorescence at J-step: (Fⱼ - F₀)/(Fₘ - F₀)

Fₘ/F₀ - Ratio indicating PSII performance capacityFᵥ/F₀ - Related to the quantum efficiency of PSIIFᵥ/Fₘ (Phi_P₀) - Maximum quantum yield of PSII photochemistry in dark-adapted state

Psi_₀ - Probability that trapped exciton moves electron into electron transport chain (1 - Vⱼ)Phi_E₀ - Quantum yield of electron transport: (1 - F₀/Fₘ) × Psi_₀Pi_Abs - Flux of photons absorbed by the antenna pigments Chl* ABS/RC - Absorption flux per reaction center DI₀/RC - Dissipated energy flux per RC (ABS/RC - TR₀/RC)

 

Hyperspectral needle reflectance values in %:Reflectance in %, range 350-2500 nm (VIS-SWIR)

Column names follow the convention X###, where:X350 corresponds to 350 nmX2500 corresponds to 834 nmSpectral resolution: 1 nm