DOI: 10.5061/dryad.n02v6wxbj
title: Data from: Soil conditions mediate cucumber-root (<em>Medeola virginiana</em>) plant responses to white-tailed deer herbivory

description: In eastern North America, cucumber-root (Medeola virginiana) is a widely
 distributed perennial forest herb that has been used as an ecological
 indicator of white-tailed deer (Odocoileus virginiana) browsing due to its
 predictable responses to deer exclusion (i.e., increased height,
 abundance). However, cucumber-root is less likely to occupy sites with
 high concentrations of soil manganese (Mn), which may limit its utility as
 an indicator under limiting soil conditions. We examined responses of
 cucumber-root total counts and flowering abundance to deer exclusion,
 competitive release from surrounding vegetation, and soil application of
 dolomitic limestone to determine the relative effects of these treatments
 over 7 years (2014-2021). Prior to treatment, initial total and flowering
 abundance were best explained by soil extractable Mn concentration.
 Post-treatment, fencing best explained increases in total counts, but
 flowering abundance was most affected by soil extractable Mn and pH.
 Initial soil Mn concentrations determined the effectiveness of dolomitic
 limestone application; microplots with moderate to high soil Mn (&gt;
 6 cmolc kg-1) had increased flowering with increased pH, while flowering
 decreased on microplots with initially low soil Mn concentrations
 (&lt; 6 cmolc kg-1). We suspect changes to soil chemistry from liming
 affected plant stress, but that stress was either alleviated or
 intensified depending on initial soil Mn concentrations. Herbivory is an
 important driver of plant abundance across our study area but flowering
 response, a critical component of plant demography, seems to be driven by
 soil Mn. Cucumber-root may have limited utility as an indicator because
 soil chemistry mediates flowering responses to deer exclusion.
description: <em>Study Area and Study Design</em>
 The study area was in central Pennsylvania on the Rothrock and
 Bald Eagle State Forests in the Ridge and Valley Physiographic Province
 (Fig. 1a). Both state forests are primarily forested with contiguous,
 oak-dominated hardwood stands classified as red oak (<em>Q.
 rubra</em>) – mixed hardwood forest (Zimmerman et al. 2012).
 Overstory species composition varies by elevation, with red oak, chestnut
 oak (<em>Q. montana</em>), black oak (<em>Q.
 velutina</em>), and scarlet oak (<em>Q. coccinea</em>)
 being the dominant overstory trees on ridgetops and red maple
 (<em>Acer rubrum</em>) and yellow poplar
 (<em>Liriodendron tulipifera</em>) dominant at lower
 elevations. From 100 potential locations across both
 state forests that span 198 km<sup>2</sup>, 24 sites were
 randomly selected for plot establishment (Fig 1b). Plots consisted of a
 network of eleven 14.63 m diameter subplots (1/60<sup>th</sup>
 ha; 1/24<sup>th</sup> acre; 168 m<sup>2</sup>)
 oriented around a center subplot (subplot 1) at specified azimuths (Fig.
 1c). Each subplot contained a single nested circular 3.30 m diameter
 microplot (1/750<sup>th</sup> ha;
 1/300<sup>th</sup> acre; 13.5 m<sup>2</sup>) 3.66
 m due east of each subplot center (Fig 1c). Microplots were numbered the
 same as the subplots in which they were nested.
 <em>Treatment Applications</em>
 Microplots 5-11 at each location received one of seven potential
 treatment combinations (fence alone, herbicide alone, lime alone, a two
 way combination of lime + fence, lime + herbicide, fence + herbicide, or a
 three-way combination lime + fence + herbicide). The fence-only treatment
 was always at microplot 5, but the remaining treatments were randomly
 assigned to microplots 6-11. Microplots 1-4 served as controls and had no
 treatments applied. Following a vegetation inventory
 (described below), 1.8 m tall polyvinyl deer fences were installed around
 all microplots assigned a fence treatment in the summer of 2014 (27 May–14
 August) and they were maintained yearly. At the same time as fence
 installation, pelletized dolomitic limestone
 (CaMg(CO<sub>2</sub>)<sub>3</sub>) was applied by
 hand to each microplot assigned a lime treatment at a rate of 5 Mg
 ha<sup>-1</sup> (6.7 kg per microplot). A one-time 5 Mg
 ha<sup>-1</sup> application was chosen to raise soil pH and
 increase Ca and Mg cation concentrations to offset soil chemistry changes
 attributed to acid deposition (Drohan & Sharpe 1997) while
 remaining consistent with other studies (e.g., Moore et al. 2008; Long et
 al. 2012). Over an 11-day period from 17 to 28 August
 2015 (following the 2015 summer vegetation monitoring season), microplots
 assigned to an herbicide treatment were broadcast sprayed with 1.9L of a
 non-targeted herbicide, oil–water emulsification mix of 1.5% v
 v<sup>-1</sup> ester triclopyr and 3.0% v
 v<sup>-1</sup> amine glyphosate combined with a 1.5% v
 v<sup>-1</sup> emulsifier and 0.05% v
 v<sup>-1</sup> non-ionic surfactant. All understory vegetation
 in the microplot was sprayed to minimize the variation of the treatment
 application, and all sprayed vegetation was affected due to the
 non-selective nature of the herbicide. Our previous work showed that
 ericaceous vegetation was reduced in response to herbicide treatment
 (Begley-Miller et al. 2024). <em>Vegetation Data
 Collection</em> Cucumber-root counts in each
 microplot were recorded across all 24 locations in 2014 (pre-treatment),
 and again in 2021 (7 years after treatment). Despite their rhizomatous
 nature, we considered ramets as “individuals” and recorded total counts
 (flowering and non-flowering combined), and flowering counts (flowering or
 fruiting individuals only) accordingly. <em>Soil
 Sampling and Chemical Analysis</em> In 2014
 (pre-treatment) and 2016 (two years post-lime application), soil samples
 were collected by morphological soil horizon to a depth of 40cm from
 microplots 1, 5, 6, 7, 8, 9, 10, and 11 (plus microplots 2–4 when time
 allowed) at each location. We pooled the Oa and A horizons together for
 analysis because the A horizon was thin and indistinguishable from the Oa
 horizon. Soil pH values were measured from each sample using 0.01M
 CaCl<sub>2</sub> with a 1:5 soil-to-solution ratio (The
 Pennsylvania State University Agricultural Analytical Services Laboratory;
 Hendershot et al. 2008). For 2014 samples, the
 USDA-NRCS Kellogg Soil Survey Laboratory (KSSL) in Lincoln, NE extracted
 Ca (cmol<sub>c</sub> kg<sup>−1</sup>) at
 unbuffered soil pH using ammonium acetate (NH<sub>4</sub>OAc)
 and displacement with 2 M KCl (Hendershot et al. 2008; Soil Survey Staff
 2014). They extracted Mn (mg kg<sup>−1</sup>) separately using
 1 N KCl (Long et al. 1997; Long et al. 2011; Soon et al. 2008), and we
 converted Mn values to cmol<sub>c</sub>
 kg<sup>−1</sup> for consistency. For 2016 samples, Ca, Mg, K,
 Mn, and Al were extracted from 5g of soil for mineral horizons and 1.25g
 of soil for organic horizons using 1M NH<sub>4</sub>Cl with a
 6-hour manual vacuum. Detection of elements from the extraction was with
 ICP-OES with one blank and one standard soil run per 22
 samples.  To ensure consistency in our assessment of
 soil chemistry, we only included soil parameters from the uppermost
 organic horizon (the Oa/A horizon) in the analysis for both years (2014
 and 2016). Due to the different extraction methods for cations and metals
 used in 2014 and 2016, we only assessed changes to soil chemistry after
 application of dolomitic limestone using 2016 control v. treatment data.
 We report 2014 soil chemistry data in cmol<sub>c</sub>
 kg<sup>-1</sup> and 2016 soil chemistry data in mg
 L<sup>-1</sup>.
description: # Data from: Soil conditions mediate cucumber-root (*Medeola virginiana*)
 plant responses to white-tailed deer herbivory Dataset DOI:
 [10.5061/dryad.n02v6wxbj](https://doi.org/10.5061/dryad.n02v6wxbj) ##
 Description of the data and file structure ### Files and variables ####
 File: jpe_data.csv ##### Variables * UID: Unique ID is a combination of
 state forest, plot, and subplot ID that denotes where data are collected.
 The first digit is state forest (1=Rothrock, 2=Bald Eagle), the second two
 digits are plot ID (01-50), and the last two digits are subplot ID
 (01-11). * Fence: Yes or No whether the microplot received a fencing
 treatment * Lime: Yes or No whether the microplot received lime treatment
 * Herbicide: Yes or No whether the microplot received and herbicide
 treatment * Mevi14: Total count (vegetative and flowering) of *Medeola
 virginiana* in 2014.  * Mevi21: Total count (vegetative and flowering) of
 *Medeola virginiana* in 2021.  * Flower 14: Total count (flowering only)
 of *Medeola virginiana* in 2014.  * Flower21: Total count (flowering only)
 of *Medeola virginiana* in 2021.  * pH14: 2014 pH values at each microplot
 extracted via CaCl. * pH16: 2016 pH values at each microplot extracted via
 CaCl. * Mn14: 2014 KCl Extractable Mn (cmol(+)/kg) from soil analysis at
 each microplot. * Ca14: 2014 extracted Ca (cmolc kg−1) values at
 unbuffered soil pH using ammonium acetate (NH4OAc) and displacement with 2
 M KCl. * Mn16: 2016 extracted Mn values using 1M NH~4~Cl with a 6-hour
 manual vacuum and detection with ICP-OES.  * Ca16: 2016 extracted Ca
 values using 1M NH~4~Cl with a 6-hour manual vacuum and detection with
 ICP-OES.  ## Code/software R Core Team (2025). \_R: A Language and
 Environment for Statistical Computing_. R Foundation for Statistical
 Computing, Vienna, Austria.
 [https://www.R-project.org/](https://www.R-project.org/). ## Access
 information Other publicly accessible locations of the data: * None Data
 was derived from the following sources: * Field collected data.