DOI: 10.5061/dryad.gxd2547wd
title: Data from: Ectomycorrhizal fungal community succession and fragmentation across subalpine forest edges nearly 3 decades postharvest

description: Ectomycorrhizal fungi (EMF) are sensitive to stand-removing disturbances.
 The re-establishment of diverse EMF communities, including return of the
 rarer fungi typical of old-growth stands, may take longer than a century.
 Using smaller cutovers, with their high edge to area ratio, has the
 potential to accelerate postharvest EMF community recovery by increasing
 proximity to mature forests. By contrast, forest edges produce a
 fragmentation effect that could eventually inflict a negative influence on
 EMF taxa of the remaining forest. We compared both succession and
 fragmentation patterns across small openings at 27 years postharvest in a
 high-elevation coniferous forest. We sampled 90 m transects across forest
 edges of nine 1-ha openings, using long-read metabarcoding of EMF from
 mycorrhizal root tips, and Sanger sequencing of epigeous sporocarps to
 assess EMF community response. A timber harvesting effect on root tip EMF
 communities was still evident, with significant differences among
 species assemblages between the opening, edge and interior forest
 habitats. Furthermore, EMF richness of root tips in the openings
 declined by 27%, on average, beginning at 10 m from the
 forest edge, illustrating how the previously observed influence
 of overstory trees had not expanded into the openings during this
 time. An influx of multi-seral taxa into the young stands was instead
 likely driven by spore dispersal, which may have been facilitated
 in these small cutovers where regenerating saplings were never
 more than 50 m from mature trees. While EMF richness on tree roots was
 maintained in the interior forest, sporocarp fruiting was
 curtailed within forest edges, alongside some reductions in
 forest- dependent taxa, likely reflecting fragmentation stress.
 Overall, the potential benefits of small openings appeared constrained by
 environmental factors, such as open canopies and limited rooting density,
 that delay the re-establishment of late-seral EMF species. The negative
 effect of edges on EMF reproduction and abundance of some taxa in the
 forest adjacent to the openings should be considered when designing
 retention forestry systems as part of sustainable forest management. Our
 results suggest medium to large patches of retained trees may reduce
 fragmentation stress and better sustain an array of late-seral forest
 fungi.
description: We sampled 90 m transects across forest edges of nine 1-ha
 openings, using Pacific Bioscience (PacBio) sequencing of EMF from
 mycorrhizal root tips, and Sanger sequencing of epigeous sporocarps to
 assess EMF community response. PacBio sequences were analyzed using DADA2
 and fungal names were assigned using a combination version 8 of the full
 UNITE + INSD dataset for eukaryotes and a priori knowledge.
description: # Data from: Ectomycorrhizal fungal community succession and fragmentation
 across subalpine forest edges nearly 3 decades postharvest ## Description
 of the data and file structure We sampled 90 m transects across forest
 edges of nine 1-ha openings, using Pacific Bioscience (PacBio) sequencing
 of EMF from mycorrhizal root tips, and Sanger sequencing of epigeous
 sporocarps to assess EMF community response. PacBio sequences were
 analyzed using DADA2 and fungal names were assigned using a combination
 version 8 of the full UNITE + INSD dataset for eukaryotes and a priori
 knowledge. ### Files and variables #### File: Dryad_2_7Sept2025.zip
 **Description**: This folder includes all of the data and code used in the
 preparation of the manuscript. Code should be run in order of the folders
 (01-06) and the order given within folders when relevant. Each subfolder
 has its own README. Each subfolder (e.g., 01_Bioinformatics) should have
 the necessary files in “indata” to be run independently of the preceding
 folders. This way, you may run the scripts in any given folder even if
 issues are encountered with preceding code. Paths in code assume that this
 folder is named “Dryad”. If the folder name has changed once unzipped,
 change it back to “Dryad” or adjust file paths accordingly. #### File:
 EMF_Cutoff0_Environ_DRYAD.csv **Description:** Ectomycorrhizal fungal data
 and environmental data (stand structure, subalpine fir foliar nutrition,
 and soil chemistry) collected in nine 1-ha high elevation clearcuts in a
 spruce-fir forest at Sicamous Creek. Sequencing was done using PacBio
 sequencing. ##### Variables * Plot_Name: The name given to an individual
 experimental plot (81) * Block: The block (3) a sample was located in as
 determined by original maps of Sicamous Creek. Blocks increased in
 elevation as follows: A, B, C. * Transect: The transect (9) a sample was
 located in. Transects were established perpendicular to harvested edges,
 at the approximate center of the edge. Transects spanned 45 m into the
 forest and 45 m into the harvested area. Transect names were based on the
 block and the name assigned to that opening at the time of harvest *
 Distance: The distance from the harvested edge into the forest (4
 locations per transect, negative number) or into the opening (4 locations
 per transect, positive number). Distances were taken in meters. The
 harvested edge is distance 0. * Habitat: The habitat a sample was taken
 in. Habitats were either U (uncut forest: distances -45, -30, -20) , E
 (Edge: distances -10, 0, 10), or C (Clearcut: distances 20, 30, and 45) *
 Mature_S_100m2: The number of live *P. engelmannii* individuals greater
 than or equal to a meter tall within a 5.65 m radius circle *
 Mature_F_100m2: The number of live *A. lasiocarpa* individuals greater
 than or equal to a meter tall within a 5.65 m radius circle * Ca_mg_kg:
 Calcium content in milligrams per kilogram of current year *A. lasiocarpa
 foliage* * K_mg_kg: Potassium content in milligrams per kilogram of
 current year *A. lasiocarpa foliage* * Mg_mg_kg: Magnesium content in
 milligrams per kilogram of current year *A. lasiocarpa foliage* * P_mg_kg:
 Phosphorus content in milligrams per kilogram of current year *A.
 lasiocarpa foliage* * S_mg_kg: Sulfur content in milligrams per kilogram
 of current year *A. lasiocarpa foliage* * N_Perc: Percent nitrogen of
 current year *A. lasiocarpa foliage* * O_pH: pH of the soil organic layer
 * O_N_perc: Percent nitrogen of the soil organic layer * O_C_perc: Percent
 carbon of the soil organic layer * M_pH: pH of the mineral soil layer *
 M_N_perc: Percent nitrogen of the mineral soil layer * M_C_perc: Percent
 carbon of the mineral soil layer * Org_depth: The depth of the organic
 soil layer in cm (not including litter) * Latin binomials: The names
 assigned to all ectomycorrhizal fungi (EMF) found on root tips at the
 site. The data is displayed as number of reads per plot. All fungi
 considered to be ectomycorrhizal, regardless of read count are included.
 #### File: Sporocarp_Locations_Dryad.csv **Description:** Location of
 ectomycorrhizal fungal sporocarps collected in six 1-ha high elevation
 clearcuts in a spruce-fir forest at Sicamous Creek. Sequencing was done
 using Sanger sequencing. ##### Variables * Block: The block (3) a sample
 was located in as determined by original maps of Sicamous Creek. Blocks
 increased in elevation as follows: A, B, C. * Transect: The transect (6) a
 sample was located in. Transects were established perpendicular to
 harvested edges, at the approximate center of the edge. Transects spanned
 45 m into the forest and 45 m into the harvested area. Transect names were
 based on the block and the name assigned to that opening at the time of
 harvest * Distance: The distance in meters from the harvested edge into
 the forest (negative number) or into the opening (positive number). The
 harvested edge is distance 0. * Habitat: The habitat a sample was taken
 in. Habitats were either U (uncut forest) , E (Edge), or C (Clearcut) *
 Latin binomials: The names assigned to all ectomycorrhizal fungi (EMF)
 found as sporocarps at the site (excluding those gathered for the mock
 community). The data is displayed binomially. A '1' indicated
 that the fungus was found at that location. Blank cells indicated that the
 fungus was not found at that location. All fungi considered to be
 ectomycorrhizal, regardless of number of occurrences, are included.  ####
 File: Sporocarps_NameHistory_Dryad.csv **Description:** Sporocarp naming
 changed over time. This file is a key to trace names of sporocarps as they
 appear in the supplemental table to how they appear in GenBank submissions
 and location files.  ##### Variables * ID: Unique sequence identifier: *
 Other_old_names: Any taxon name that may have been used for this seqence
 that is no represented in the other columns.  * LP_gb_submission: Taxon
 name assigned to the sequence when submitted to GenBank * ref_id_UNITE08:
 Taxon name of the closest matching reference sequence from UNITE version
 08. * Final_name_supp\_tbl: Taxon name as it appears in the supplemental
 table * SH: Species hypothesis of the closest matching reference sequence
 from UNITE version 08. ## Code/software Fully annotated R codes will be
 included with this dataset.  ## Access information Other publicly
 accessible locations of the data: * Ectomycorrhizal fungal data from root
 tips: Accession PRJNA1006434 in the Sequence Read Archive
 (ncbi.nlm.nih.gov/sra) * Ectomycorrhizal fungal data from sporocarps:
 Accessions OR676968 - OR676997 (mock community) and
 submission [SUB14748481 (opens in new
 window)](https://submit.ncbi.nlm.nih.gov/subs/genbank/SUB14748481)in
 GenBank (ncbi.nlm.nih.gov/genbank)