Data from: Ectomycorrhizal fungal community succession and fragmentation across subalpine forest edges nearly 3 decades postharvest
Data files
Sep 09, 2025 version files 314.26 MB
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Dryad_2_7Sept2025.zip
314.17 MB
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EMF_Cutoff0_Environ_DRYAD.csv
52.72 KB
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README.md
6.78 KB
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Sporocarp_Locations_Dryad.csv
17.45 KB
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Sporocarps_NameHistory_Dryad.csv
6.71 KB
Abstract
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 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)in GenBank (ncbi.nlm.nih.gov/genbank)
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.
