DOI: 10.5061/dryad.hmgqnk9pv
title: Data from: Contrasting impacts of short- and long-term large herbivore exclusion on understory net CO2 exchange in a boreal forest

description: Across boreal forests, trees are the main living biomass carbon (C) stock,
 but the understory vegetation can contribute significantly to the C
 cycling and net forest carbon dioxide (CO2) balance. The patchy understory
 vegetation which consists of sunlit (i.e., lichen-like) and shaded
 habitats (i.e., dwarf shrub-like) is often altered by ungulate grazers.
 Grazers may influence understory CO2 exchange, and consequently, the
 forest CO2 balance. Grazing affects differently the biomass of slow
 growing lichens compared to the faster growing mosses and dwarf shrubs,
 and therefore the effects of grazing on CO2 exchange in the patchy
 understory vegetation could vary temporally. We studied how excluding
 grazing for short- and long-term affects the CO2 exchange and vegetation
 biomass in the understory of an oligotrophic Scots pine forest. We
 measured growing season (2019, 2020) CO2 exchange across sunlit and shaded
 habitats inside fences that had excluded large grazers for 0–1 and 25–26
 years and in the adjacent grazed area. In addition, we measured the height
 of understory vegetation. We found that short-term grazer exclusion
 increased ecosystem CO2 source fluxes only in the shaded habitats.
 However, long-term exclusion of grazing decreased CO2 net release
 regardless of the habitat type. Furthermore, grazer exclusion increased
 moss depth immediately which coincided with an abrupt intensification of
 CO2 net release. Considering the impacts of grazing over both short- and
 long-term may help to forecast C fluxes more accurately which may be
 relevant for informed climate solutions regionally and even on a larger
 scale.
description: CO<sub>2</sub> fluxes were measured on two understory
 vegetation types in short- and long-term large herbivore exclosures and in
 an adjacent grazed area with manual and automated chamber over the growing
 seasons of 2019 and 2020. The manual CO<sub>2</sub>
 measurements were accompained with soil temperature measurements. In
 addition, vegetation height was measured across study plots in 2020. This
 data consist of four different data sets as follows: automated
 CO<sub>2</sub>, manual CO<sub>2</sub>, vegetation
 height, and soil temperature.  Automated
 CO<sub>2</sub> data The automated system
 measured CO<sub>2</sub> fluxes at an interval of 1h and
 continued for 24h day<sup>-1</sup> from June until October in
 2019 and 2020. Each measurement consisted of a 2-min pre-purge period, a
 3-min measurement period and a 60 sec post-purge period. The system (model
 LI-8100A, Li-Cor Inc., Lincoln, NE, USA) consisted of an analyzer control
 unit (LI-8100A), a multiplexer (LI-8150), and eight automated clear
 chambers (8100-104C). NEE was calculated from the exponential change of
 the CO<sub>2</sub> concentration during chamber closure
 excluding the 45-second ‘dead band’. Manual
 CO<sub>2</sub> data The manual measurements
 were taken 1-3 per week from May until October in 2019 and 2020. The
 measurement protocol consisted of two measurements at each study plot: net
 ecosystem exchange (NEE) under full light, then the chamber was vented,
 placed over the ground, and covered with an opaque chamber for measuring
 ecosystem respiration (ER). The system consisted of a custom-made chamber
 (2-mm thick transparent polycarbonate, diam. 30 cm × height 39 cm)
 equipped with a fan, a CO<sub>2</sub> sensor (model GMP343,
 Vaisala Inc., Vantaa, Finland), and air temperature and humidity sensor
 (model HMP75, Vaisala Inc.). CO<sub>2</sub> concentration
 (ppm), relative humidity (%), and temperature (℃) during each manual
 measurement were logged every 5 sec for 2 min with a handheld logger
 (model MI70, Vaisala Inc.). NEE and ER were calculated from the linear
 change of the CO<sub>2</sub> concentration in the chamber by
 the ideal gas equation, and gross ecosystem productivity (GEP) was
 obtained by subtracting ER from NEE. Vegetation
 height Vegetation heights were measured at two
 locations within each study plot: one in the CO<sub>2</sub>
 study plot and the other in an undisturbed monitoring plot. For
 undisturbed monitoring plots, the height of six dwarf shrubs, lichens, and
 mosses (if available) were measured and then average height for each
 vegetation group was calculated. In CO<sub>2</sub> study plot,
 the height of three dwarf shrubs, lichens, and mosses (if available) were
 measured and these values were used to calculate the average height for
 each vegetation group. Soil temperature
 Soil temperature was measured manually from three points in each
 short-term exclosure CO<sub>2</sub> study plot. The values
 were used to calculate the average soil temperature for each
 CO<sub>2</sub> study plot. Model: Lollipop™ Traceable
 Thermometer, Traceable® Products Inc., Webster, TX, USA.                 
                           
description: # Contrasting impacts of short- and long-term large herbivore exclusion on
 understory net CO<sub>2</sub> exchange in a boreal forest
 [https://doi.org/10.5061/dryad.hmgqnk9pv](https://doi.org/10.5061/dryad.hmgqnk9pv) This data was used to study the impacts of short- and long-term large herbivore exclusion on growing season CO<sub>2</sub> fluxes (net ecosystem exchange [NEE], ecosystem respiration [ER], and gross ecosystem production [GEP]) and vegetation height in a boreal pine forest. The experimental set up consisted of fences that have been excluding large ungulates for 0-1 year (i.e., short-term ungrazed, 'SUG') and 25-26 years (i.e., long-term ungrazed, 'LUG') compared with their adjacent grazed area ('GRZ'). CO<sub>2</sub> fluxes were measured on permanently marked study plots in the fenced and grazed areas across two understory habitat types: sunlit (i.e., lichen-like) and shaded (i.e., dwarf shrub/moss-like) habitats. The CO<sub>2</sub> data was collected during the growing seasons of 2019 and 2020 with automated and manual chamber methods. Vegetation heights (i.e., lichen, moss, and dwarf shrub height) were measured across each study plot in 2020. In addition, soil temperature of each study plot was measured automatically in LUG and GRZ and manually in SUG. This data showed that short-term grazer exclusion increased CO<sub>2</sub> source in the shaded habitats but long-term exclusion decreased CO<sub>2</sub> source regardless of the habitat type. Furthermore, grazer exclusion increased moss depth immediately which coincided with an abrupt intensification of CO<sub>2</sub> net release. ## Description of the data and file structure The data consists of separate files categorized as follows: Automated CO<sub>2</sub>, Manual CO<sub>2</sub>, Vegetation height, and Soil temperature. **Automated CO<sub>2</sub> data** The automated system measured CO<sub>2</sub> fluxes at an interval of 1 h and continued for 24 h day<sup>-1</sup> across two understory habitat types in long-term exclosure and in an adjacent grazed area (n=8). CO<sub>2</sub> fluxes were measured from June until October in 2019 and 2020. The system (model LI-8100A, Li-Cor Inc., Lincoln, NE, USA) consisted of an analyzer control unit (LI-8100A), a multiplexer (LI-8150), and eight automated clear chambers (8100-104C). Each measurement consisted of a 2-min pre-purge period, a 3-min measurement period and a 60 sec post-purge period. Net ecosystem exchange was calculated from the exponential change of the CO<sub>2</sub> concentration during chamber closure excluding the 45-second ‘dead band’. The data is organized into one .csv file consisting of the following variables: | Description of the variables | | ---------------------------- | | Plot_ID: study plot | | Grazing: grazed (GRZ), long-term ungrazed (LUG) | | Habitat: understory vegetation, shaded (i.e., dwarf shrub/moss-like) and sunlit (i.e., lichen-like) | | Year: Year of measurements | | Month: Month of measurements | | Week: Week of measurements | | DOY: Day of year | | Time: Time of measurements (24h, hh:mm) | | Date: Date of measurements (mm/dd/yy) | | R2: Correlation coefficient for exponential fit | | RH: Relative humidity inside the chamber | | Chamber_temp: Air temperature inside (°C) the chamber | | CO2: CO<sub>2</sub> flux computed from exponential fit (µmol/mol m<sup>-2</sup> s<sup>-1</sup>) | Missing values are indicated as 'NA'. This data can be used to investigate the impacts of large herbivores on seasonal variations in daily net ecosystem exchange across understory habitats of boreal pine forest. **Manual CO<sub>2</sub> data** The manual measurements were taken in short- and long-term large herbivore exclosures and in an adjacent grazed area (n=30) across two understory habitat types. CO<sub>2</sub> fluxes were measured 1-3 per week from May until October in 2019 and 2020. The system consisted of a custom-made chamber (2-mm thick transparent polycarbonate, diam. 30 cm × height 39 cm) equipped with a fan, a CO<sub>2</sub> sensor (model GMP343, Vaisala Inc., Vantaa, Finland), and air temperature and humidity sensor (model HMP75, Vaisala Inc.). CO<sub>2</sub> concentration (ppm), relative humidity (%), and temperature (℃) during each manual measurement were logged every 5 sec for 2 min with a handheld logger (model MI70, Vaisala Inc.). The measurement protocol consisted of two measurements at each study plot: net ecosystem exchange (NEE) under full light, then the chamber was vented, placed over the ground, and covered with an opaque chamber for measuring ecosystem respiration (ER). NEE and ER were calculated from the linear change of the CO<sub>2</sub> concentration in the chamber by the ideal gas equation, and gross ecosystem productivity (GEP) was obtained by subtracting ER from NEE. The data is organized into one .csv file consisting of the following variables: | Description of the variables: | | ----------------------------- | | Plot_ID: study plot | | Grazing: grazed (GRZ), long-term ungrazed (LUG), short-term ungrazed (SUG) | | Habitat: understory vegetation, shaded (i.e., dwarf shrub/moss-like) and sunlit (i.e., lichen-like) | | Block: Spatial block of study plots | | Year: Year of measurements | | Month: Month of measurements | | Week: Week of measurements | | DOY: Day of year | | Time: Time of measurements (24h, hh:mm) | | Date: Date of measurements (mm/dd/yy) | | R2: Correlation coefficient for linear fit | | RH: Relative humidity inside the chamber | | Chamber_temp: Air temperature inside (°C) the chamber | | NEE umol CO2: Net Ecosystem Exchange computed from linear fit (µmol m<sup>-2</sup> s<sup>-1</sup>) | | NEE mg CO2: Net Ecosystem Exchange computed from linear fit (mg m<sup>-2</sup> s<sup>-1</sup>) | | ER umol CO2: Ecosystem Respiration computed from linear fit (µmol m<sup>-2</sup> s<sup>-1</sup>) | | ER mg CO2: Ecosystem Respiration computed from linear fit (mg m<sup>-2</sup> s<sup>-1</sup>) | | GEP umol CO2: Gross Ecosystem Production computed from linear fit (µmol m<sup>-2</sup> s<sup>-1</sup>) | | GEP mg CO2: Gross Ecosystem Production computed from linear fit (mg m<sup>-2</sup> s<sup>-1</sup>) | Missing values are indicated as 'NA'. This data can be used to investigate the impacts of large herbivores on seasonal variations in daytime NEE, ER, and GEP across understory habitats of boreal pine forest over different temporal scales. **Vegetation height** Vegetation heights were measured on two understory habitat types in short-('SUG') and long-term ('LUG') large herbivore exclosures and in an adjacent grazed area ('GRZ'). The vegetation heights were measured at each CO<sub>2</sub> study plot (n=30) and at an undisturbed vegetation monitoring plots that in GRZ and LUG were located approximately 1 m away from each CO<sub>2</sub> study plot (n=12) and in each exclosure of SUG in central locations of both habitat types (n=6). In the CO<sub>2</sub> study plots, the height of three dwarf shrubs, lichens, and mosses (if available) were measured and these values were used to calculate the average height for each vegetation group. For the undisturbed monitoring plots, the height of six dwarf shrubs, lichens, and mosses (if available) were measured and then average height for each vegetation group was calculated. The data is organized into one .csv file consisting of the following variables: | Description of the variables: | | ----------------------------- | | Plot_ID: study plot | | Habitat: understory vegetation, shaded (i.e., dwarf shrub/moss-like) and sunlit (i.e., lichen-like) | | Grazing: grazed (GRZ), long-term ungrazed (LUG), short-term ungrazed (SUG) | | CO2/UDA: CO<sub>2</sub> measurement plot (CO2)/undisturbed monitoring plot (UD) within a study plot | | Moss mean: average height of mosses (cm) | | Lichen mean: average height of lichens (cm) | | Shrub mean: average height of dwarf shrubs (cm) | Missing values are indicated as '*NA*'. This data can be used to investigate the impacts of large herbivores on vegetation height across sunlit (i.e., lichen-like) and shaded (i.e., dwarf shrub/moss-like) habitats of boreal pine forest over different temporal scales. This data can be combined with Manual CO2 data to study the impacts of vegetation height to CO<sub>2</sub> fluxes. **Soil temperature** Soil temperature was measured across two understory habitat types in study plots of short-term exclosure (n=18) once a week from June until October in 2019 and 2020. Soil temperature was measured manually at 5 cm depth from three points and these values were used to calculate the average soil temperature for each CO<sub>2</sub> study plot. Model: Lollipop™ Traceable Thermometer, Traceable® Products Inc., Webster, TX, USA. The data is organized into one .csv file consisting of the following variables: | Description of the variables: | | ----------------------------- | | Plot_ ID: study plot | | Habitat: understory vegetation, shaded (i.e., dwarf shrub/moss-like) and sunlit (i.e., lichen-like) | | Grazing: short-term ungrazed (SUG) | | Date: Date of measurements (mm/dd/yy) | | Year: Year of measurements | | Month: Month of measurements | | Week: Week of measurements | | Soil temp: Mean soil temperature (°C) | This data can be used to investigate the impacts of short-term large herbivore exclosure on soil temperature across sunlit (i.e., lichen-like) and shaded (i.e., dwarf shrub/moss-like) habitats of boreal pine forest. ## Sharing/Access information The meteorological data (precipitation, temperature, snow depth) used for the description of the study area was derived from the open data base of Finnish Meteorological Institute (https://en.ilmatieteenlaitos.fi/download-observations). The automated soil temperature data for grazed and long-term ungrazed areas were obtained from Oulanka research station. ## Code/Software The data was analysed and visualized using R software (R Core Team, version 4.1.0). Linear mixed effect models were fitted with using the 'lme' function from the *nlme*-package (Pinheiro et al. 2021) followed by ANOVA and data visualizations were performed by *ggplot2*-package (Wickham 2016).