DOI: 10.5061/dryad.qjq2bvqvb
title: The effect of light availability and spatio-temporal heterogeneity on the soil seed bank diversity in temperate forests

description: Light is a key driver of understory plant diversity, also important for
 seed germination, yet its effect on forests soil seed bank diversity
 remains underexplored. This study assessed the impact of both light
 availability and spatio-temporal heterogeneity on soil seed bank
 diversity. We hypothesized that increased light availability and
 heterogeneity at plot and landscape scale enhance soil seed bank species
 richness, particularly when accounting for historical canopy cover
 changes. Additionally, we expected that higher light availability
 increased similarity between the soil seed bank and understory vegetation.
 To test this, we established six subplots (25 m² each) within each of 30
 plots (1 ha), in the Southern Black Forest, Germany. Within each subplot,
 soil cores (10 cm diameter, 0–15 cm depth) were collected and subsequently
 pooled to produce one composite sample per plot (n = 30). Soil seed bank
 species were identified through a germination experiment. Light
 availability and understory composition were recorded in the field. To
 test the effect of both present versus past landscape structure on soil
 seed bank diversity, percentage canopy cover and patch density (for a 500
 m buffer) were calculated from contemporary and historical remote sensing
 data highlighting areas with continuous forest canopy cover since 1963. At
 the plot scale, light availability and heterogeneity did not have an
 effect on species richness but the dissimilarity between the soil seed
 bank and the understory significantly increased with light heterogeneity.
 Stands with more heterogeneous light conditions promoted the occurrence of
 different subsets of species in the soil seed bank or the understory. At
 the landscape scale, soil seed bank species richness increased
 significantly with increased patch density of continuous canopy cover,
 highlighting the role of past canopy openings. Overall this study
 highlights how light heterogeneity and historical disturbances shape soil
 seed bank diversity in managed forests.
description: # The effect of light availability and spatio-temporal heterogeneity on
 seed bank diversity in temperate forests This submission includes two
 datasets associated with the manuscript: 1. **Community matrix** –
 seed_and_composition.csv -Species abundance data for seed bank and
 understory vegetation. 2. **Diversity and environmental data** –
 seed_and_div_complete.csv - Seed bank diversity, environmental variables,
 and Ellenberg indicator values. #### (1) Community Matrix: Seed Bank and
 Understory **File:** `seed_and_composition.csv`\ **Dimensions:** 56 rows ×
 95 columns Rows: * Each row represents a vegetation survey at one of 28
 forest plots. * Plot names ending in `_s` refer to **seed bank** data;
 names without `_s` refer to **understory vegetation**. * Two plots were
 excluded due to insufficient germination (see manuscript). Columns: * Each
 column represents a plant species (in Latin binomial form, lowercase, with
 spaces). * Values indicate species abundance: * Seed bank: number of
 individuals germinated. * Understory: estimated species cover. * The data
 are untransformed and include both herbaceous and woody species. Exclusion
 of plots for analysis For the community composition analysis, two plots
 were excluded: One plot (CFB172) was removed because only Vaccinium
 myrtillus emerged in the seed bank, resulting in random placement in
 ordination analyses. A second plot (CFB118), from which only one Betula
 pendula seedling emerged, was excluded due to the unusually low soil
 volume collected (caused by shallow forest soil), making it incomparable
 with other samples. For all other analyses, only the second plot (CFB118)
 was excluded, as the low sampling volume was identified as a potential
 source of contamination and not representative of seed bank composition.
 #### (2) Diversity and Environmental Data **File:**
 `seed_and_div_complete.csv`\ **Dimensions:** 29 rows × 26 columns\ Each
 row represents a site, combining diversity metrics, canopy openness,
 forest landscape metrics, and Ellenberg indicator values. * Forest cover
 and patch density were calculated for a 500 m radius using EFDA
 (1985–2022) and aerial photos from 1968. * Ellenberg values were
 calculated as abundance-weighted medians for both vegetation layers. *
 Light-demanding species were defined by Ellenberg L values of 6–9. ####
 Column Descriptions (seed_and_div_complete) * Plot: Unique site identifier
 * species_richness: Number of seed bank species observed in the
 germination experiment * shannon_diversity: Shannon's diversity index
 of the seed bank * density_total: Total number of individuals germinated
 (per pot) * density_excl_juncus: As above, excluding Juncus effusus *
 Opn_mean: Mean canopy openness (%) based on six hemispherical photos per
 plot. * Opn_cv:Coefficient of variation of canopy openness *
 percent_forest_500_current: % forest cover within 500 m (based on 2022
 satellite data) * percent_forest_500_continuous: % forest cover within 500
 m that remained undisturbed from 1968 to 2022 * pd_500_current: Forest
 patch density (per 100 ha) based on 2022 forest cover *
 pd_500_continuous:Forest patch density (per 100 ha) based on continuous
 forest cover (1968–2022) * proportion_light_6_9_und: Proportion of
 understory species classified as light-demanding (Ellenberg L: 6–9) *
 proportion_light_6_9_seed_bank: Same as above for seed bank species *
 median_L_und: Median Ellenberg L value for understory vegetation *
 median_T_und: Median Ellenberg T (temperature) * median_K_und: Median
 Ellenberg K (continentality) * median_F_und: Median Ellenberg F (moisture)
 * median_R_und: Median Ellenberg R (soil pH) * median_N_und: Median
 Ellenberg N (nutrients) * median_L_seed_bank: Median Ellenberg L for seed
 bank species * median_T_seed_bank: Median Ellenberg T for seed bank
 species * median_K_seed_bank: Median Ellenberg K for seed bank species *
 median_F_seed_bank: Median Ellenberg F for seed bank species *
 median_R_seed_bank: Median Ellenberg R for seed bank species *
 median_N_seed_bank: Median Ellenberg N for seed bank species *
 species_richness_und: Number of understory species identified in the field
 References: Viana-Soto, A., & Senf, C. (2024). The European Forest
 Disturbance Atlas: A forest disturbance monitoring system using the
 Landsat archive. Earth Syst. Sci. Data Discuss., 2024, 1–42.\ Landesarchiv
 Baden-Württemberg. (2017, 2021). Landesvermessungsamt Baden-Württemberg:
 Landesbefliegung Baden-Württemberg 1968—Luftbilder und digitale
 Orthophoto. Retrieved from Landesarchiv-bw website:
 [https://www2.landesarchiv-bw.de/ofs21/olf/struktur.php?bestand=61797&klassi=001.001](https://www2.landesarchiv-bw.de/ofs21/olf/struktur.php?bestand=61797&klassi=001.001) Ellenberg, H., & Leuschner, C. (2010). Vegetation Mitteleuropas mit den Alpen: In ökologischer, dynamischer und historischer Sicht (Vol. 8104). Utb. #### (3) R analysis for the research questions and figures **File:** `code_for_analysis_figures.Rmd` The code aims to answer the following three questions and the associated figures of the manuscript: (Q1) How do light availability and heterogeneity impact seed bank diversity and seed bank community composition? (Q2) How does the dissimilarity between the seed bank and the understory aboveground layer community composition relate to light availability and spatial heterogeneity? (Q3) At the landscape scale, how do contemporary and continuous canopy cover and canopy cover heterogeneity (as proxies for changing light conditions) impact the soil seed bank diversity?