DOI: 10.5061/dryad.3j9kd51s7
title: Data from: Fungal and beetle diversity in deciduous fine woody debris in spruce-dominated forests in relation to substrate quantity and quality

description: Deciduous fine woody debris (DFWD) is a common deadwood substrate type in
 boreal conifer-dominated forests, but it is usually present in low
 volumes, and its importance for deadwood-dependent biodiversity is poorly
 understood. In this study, we investigated how DFWD-associated fungal and
 beetle diversity depends on local substrate availability and quality, and
 how species diversity differs between DFWD and coarse deciduous deadwood
 (birch logs) in boreal mixed spruce-dominated forests in southern Finland.
 We studied 25 forest plots (each 0.16 ha), measuring and sampling all
 pieces of DFWD with a diameter of 2–5 cm and a minimum length of 50 cm.
 Wood-inhabiting fungi were surveyed from wood samples by DNA metabarcoding
 and saproxylic beetles were surveyed by bark sieving. Our results showed a
 clear positive relationship between DFWD abundance and the diversity of
 fungi and beetles. Tree species and decay class diversity were not
 important in explaining fungal and beetle diversity or community
 composition, possibly due to the low degree of variation in DFWD quality
 among the study plots. DFWD hosted more diverse fungal assemblages than
 birch logs, including species of conservation concern, while no red-listed
 beetle species were observed on DFWD. Overall, species assemblages
 associated with fine and coarse deciduous deadwood were non-nested. Thus,
 DFWD represents a non-redundant complementary deadwood resource type
 alongside coarse deciduous deadwood in boreal forests.
description: Study sites (n=25) were located in Norway spruce dominated
 forests in the cities of Espoo, Helsinki, Vantaa, Lahti and Tampere in
 southern Finland. At each site, we collected and measured all pieces of
 deciduous fine woody debris with basal diameter between 2 and 5 cm and
 minimum length of 50 cm within a 0.16 ha sample plot (20 m × 80 m). For
 every piece, we recorded tree species, decay class, basal diameter, and
 length. Fragments originating from the same branch or stem were recorded
 as individual pieces if they had been fragmented before collection. We
 applied the following decay stage classification: 1 = hard, undecayed; 2 =
 knife penetrates through softened wood near the surface; 3 = piece holds
 its shape, but knife penetrates deeper into the wood; 4 = piece decayed
 and soft throughout, starting to lose shape. In addition to fine woody
 debris, we sampled 20 naturally downed birch logs (mean basal diameter
 26.5 cm). From fine woody debris, we extracted wood
 samples for fungal metabarcoding analysis by drilling at a distance of ca.
 2-15 cm from the basal end of each piece. We removed bark and surface
 layer of the wood with a knife and drilled into the wood with a
 DNA-sterilized 6 mm drill head through the freshly exposed wood surface.
 We collected 7.5 ml portions of the resulting wood powder per piece and
 pooled them into composite plot-level samples. We then divided each pooled
 wood powder sample into two parallel subsamples. We extracted wood samples
 from birch logs (one per log) by drilling at five points with 1 m
 intervals starting at 50 cm from the basal end of each log. We drilled ca.
 5 cm deep into the wood from one of the vertical sides of the log after
 removing bark. We ground the wood powder samples from DFWD and birch logs
 further into fine powder in a bead beater. Samples were beaten in 30 ml
 aliquots in 50 ml capsules with 8 mm steel bead for 2 min in 30 Hz. Tools
 were DNA sterilized with bleach solution between samples. We made two DNA
 extractions from each parallel subsample from fine woody debris, resulting
 in total of four replicate extractions per one plot-level sample of fine
 woody debris, and one DNA extraction per one birch log sample. DNA was
 extracted from ca. 90 mg of wood powder and eluted into 50 µl final
 elution volume with DNeasy Plant Pro extraction kit (Qiagen, Hilden, DE)
 according to the manufacturer’s instructions. For fungal metabarcoding,
 the internal transcribed spacer 2 of the nrRNA coding region was amplified
 with primers ITS3-2024F (GCATCGATGAAGAACGCAGC) and ITS4-2409R
 (TCCTCCGCTTATTGATATGC). Indexed amplicons were sequenced with Illumina
 NovaSeq 6000 (paired-end 250 bp) at Novogene Co (Cambridge, GB). Sequence
 reads were demultiplexed, and index and primer sequences were removed from
 paired-end reads. Further sequence processing was done with vsearch
 (v2.18.0). R1 and R2 reads were quality filtered, and then assembled.
 Assembled reads were chimera filtered de novo. Remaining reads were
 clustered into operational taxonomic units (OTUs) with 98% similarity
 threshold. OTUs were taxonomically assigned with 80% confidence cutoff
 using Naïve Bayesian Classifier trained with UNITE (v9, dynamic, all
 eucaryotes) database in mothur v1.36.1. For the analyses of fungal OTU
 community composition and richness, we converted read abundances into
 presence-absence by applying 1‰ relative abundance threshold. We checked
 for spurious sequencing results by comparing replicate samples of fine
 woody debris based on Jaccard distances. We identified three instances
 where one of the four replicates was notably discordant with the other
 three (Jaccard distance &gt;0.7) and discarded those replicates from
 further analyses. For DFWD samples, OTU presence-absence data was then
 concatenated from individual replicates to sample level.
 We collected saproxylic beetles by peeling and sifting bark. From
 fine woody debris, collected samples by peeling off loose bark from all
 pieces collected within the sample plot. From birch logs, we sampled 1 m²
 of bark per log. After sifting, the resulting wood litter was placed in
 plastic bags and studied later indoors, by spreading the litter in small
 lots on a white tray and collecting all beetle adults and larvae. We
 identified extracted adult beetles to species morphologically and larvae
 by sequencing the cytochrome c oxidase subunit I barcode gene region with
 the primers LCO1490 (GGTCAACAAATCATAAAGATATTGG) and HCO2198
 (TAAACTTCAGGGTGACCAAAAAATCA). We used BOLD as the reference database for
 barcode sequence identification. In addition, a few species were recorded
 based on visual observations of characteristic exit holes and larval
 galleries in the wood.
description: # Data from: Fungal and beetle diversity in deciduous fine woody debris in
 spruce-dominated forests in relation to substrate quantity and quality
 [https://doi.org/10.5061/dryad.3j9kd51s7](https://doi.org/10.5061/dryad.3j9kd51s7) Data originate from a study on fungal and beetle diversity associated with deciduous fine woody debris and birch logs in spruce-dominated forests in southern Finland. DATA & FILE OVERVIEW 1\. Description of dataset File List: File 1 Name: 'Korhonen et al 2024 Fungi_presabs_DFWD_replicates.csv' File 1 Description: File contains presence-absence occurrence data of fungal OTUs (columns) across subsamples (rows) of deciduous fine woody debris. File 2 Name: 'Korhonen et al 2024 Fungi_presabs_DFWD_sites.csv' File 2 Description: File contains presence-absence occurrence data of fungal OTUs (columns) in deciduous fine woody debris across sites (rows). File 3 Name: 'Korhonen et al 2024 Fungi_presabs_BirchLog_samples.csv' File 3 Description: File contains presence-absence occurrence data of fungal OTUs (columns) across birch log samples (rows). File 4 Name: 'Korhonen et al 2024 Fungi_DFWD_SampleNo_SiteNo_table.csv' File 4 Description: Maps sample replicates (SampleNo; in File 1) onto site-level samples (SiteNo; in Files 2 and 10) of deciduous fine woody debris. In addition, sample replicates identified as outliers are indicated. File 5 Name: 'Korhonen et al 2024 Fungi_ITS2_OTU_taxonomy.csv' File 5 Description: File contains taxonomic annotations for fungal ITS2 OTUs. File 6 Name: 'Korhonen et al 2024 Beetles_presabs_DFWD_sites.csv' File 6 Description: File contains presence-absence occurrence data of beetle species (columns) on deciduous fine woody debris across sites (rows). File 7 Name: 'Korhonen et al 2024 Beetles_presabs_BirchLog_samples.csv' File 7 Description: File contains presence-absence occurrence data of beetle species (columns) on birch logs (rows). File 8 Name: 'Korhonen et al 2024 Beetle_species_metadata.csv' File 8 Description: File contains metadata related to beetle species. File 9 Name: 'Korhonen et al 2024 Site_and_DFWD_sample_metadata.csv' File 9 Description: File contains metadata related to sampling sites and site-level samples of deciduous fine woody debris. File 10 Name: 'Korhonen et al 2024 BirchLog_sample_metadata.csv' File 10 Description: File contains metadata related to sampled birch logs. DATA-SPECIFIC INFORMATION FOR FILE 1: 'Korhonen et al 2024 Fungi_presabs_DFWD_replicates.csv' 1\. Number of variables/columns: 913 data columns + 1 header column (SampleNo, corresponding to SampleNo in File 4) 2\. Number of cases/rows: 100 data rows + 1 header row (corresponding to OTU_name in File 5) 3\. Column separator: ; 4\. Column explanations ``` Columns represent fungal OTUs specified in the the header row. Values indicate whether OTU was detected (1) or not (0). ``` DATA-SPECIFIC INFORMATION FOR FILE 2: 'Korhonen et al 2024 Fungi_presabs_DFWD_sites.csv' 1\. Number of variables/columns: 913 data columns + 1 header column (SiteNo, corresponding to SiteNo in Files 4 and 9) 2\. Number of cases/rows: 25 data rows + 1 header row (corresponding to OTU_name in File 5) 3\. Column separator: ; 4\. Column explanations ``` Columns represent fungal OTUs specified in the the header row. Values indicate whether OTU was detected (1) or not (0). ``` DATA-SPECIFIC INFORMATION FOR FILE 3: 'Korhonen et al 2024 Fungi_presabs_BirchLog_samples.csv' 1\. Number of variables/columns: 376 data columns + 1 header column (BirchLogNo, corresponding to BirchLogNo in File 10) 2\. Number of cases/rows: 20 data rows + 1 header row (corresponding to OTU_name in File 5) 3\. Column separator: ; 4\. Column explanations ``` Columns represent fungal OTUs specified in the the header row. Values indicate whether OTU was detected (1) or not (0). ``` DATA-SPECIFIC INFORMATION FOR FILE 4: 'Korhonen et al 2024 Fungi_DFWD_SampleNo_SiteNo_table.csv' 1\. Number of variables/columns: 4 columns 2\. Number of cases/rows: 100 data rows + 1 header row 3\. Column separator: ; 4\. Column explanations Col 1: SampleNo Numeric identifier of a sample replicate Col 2: SiteNo Numeric identifier of site Col 3: SampleCode Laboratory code for sample (format: [SiteCode]-[Subsampling level 1: A or B][Subsampling level 2: 1 or 2]) Col 4: Valid/Outlier Indication of whether a sample replicate was deemed as valid or as an outlier. (values: 'valid' or 'outlier') DATA-SPECIFIC INFORMATION FOR FILE 5: 'Korhonen et al 2024 Fungi_ITS2_OTU_taxonomy.csv' 1\. Number of variables/columns: 17 columns 2\. Number of cases/rows: 5630 data rows + 1 header row 3\. Column separator: ; 4\. Column explanations ``` Col 1: OTU_name Unique identifier of OTU Col 2: OTU_ID Original unique identifier of OTU used in the bioinformatic pipeline Col 3: RepSeq Representative ITS2 sequence of OTU Col 4: k Taxonomic assignment to Domain (NA if not specified) Col 5: k% Support for taxonomic assignment to Kingdom (values: 80-100, NA when &lt;80) Col 6: p Taxonomic assignment to Phylum (NA if not specified) Col 7: p% Support for taxonomic assignment to Phylum (values: 80-100, NA when &lt;80) Col 8: c Taxonomic assignment to Class (NA if not specified) Col 9: c% Support for taxonomic assignment to Class (values: 80-100, NA when &lt;80) Col 10: o Taxonomic assignment to Order (NA if not specified) Col 11: o% Support for taxonomic assignment to Order (values: 80-100, NA when &lt;80) Col 12: f Taxonomic assignment to Family (NA if not specified) Col 13: f% Support for taxonomic assignment to Family (values: 80-100, NA when &lt;80) Col 14: g Taxonomic assignment to Genus (NA if not specified) Col 15: g% Support for taxonomic assignment to Genus (values: 80-100, NA when &lt;80) Col 16: s Taxonomic assignment to Species (NA if not specified) Col 17: s% Support for taxonomic assignment to Species (values: 80-100, NA when &lt;80) ``` DATA-SPECIFIC INFORMATION FOR FILE 6: 'Korhonen et al 2024 Beetles_presabs_DFWD_sites.csv' 1\. Number of variables/columns: 92 data columns + 1 header column (SiteNo, corresponding to SiteNo in File 9) 2\. Number of cases/rows: 25 data rows + 1 header row 3\. Column separator: ; 4\. Column explanations ``` Columns represent beetle species specified in the the header row. Values indicate whether species was detected (1) or not (0). ``` DATA-SPECIFIC INFORMATION FOR FILE 7: 'Korhonen et al 2024 Beetles_presabs_BirchLog_samples.csv' 1\. Number of variables/columns: 92 data columns + 1 header column (BirchLogNo, corresponding to BirchLogNo in File 10) 2\. Number of cases/rows: 20 data rows + 1 header row 3\. Column separator: ; 4\. Column explanations ``` Columns represent beetle species specified in the the header row. Values indicate whether species was detected (1) or not (0). ``` DATA-SPECIFIC INFORMATION FOR FILE 8: 'Korhonen et al 2024 Beetle_species_metadata.csv' 1\. Number of variables/columns: 5 columns 2\. Number of cases/rows: 92 data rows + 1 header row 3\. Column separator: ; 4\. Column explanations ``` Col 1: Species Beetle species name Col 2: Authority Taxonomic authority or the species name Col 3: Family Taxonomic family of the species Col 4: Finnish_Red_List_2019 Red-list status of the species according to the Finnish assessment from 2019 (values: "LC" or "NT") Col 5: Rarity Rarity of the species according to the Finnish Biodiversity Information Facility (2024) (values: "Common", "Rare" or "Very rare") ``` DATA-SPECIFIC INFORMATION FOR FILE 9: 'Korhonen et al 2024 Site_and_DFWD_sample_metadata.csv' 1\. Number of variables/columns: 27 columns 2\. Number of cases/rows: 25 + 1 header row 3\. Column separator: ; 4\. Decimal separator for numeric variables: \\, 5\. Column explanations Col 1: SiteNo Unique identifier of the sampling site Col 2: SiteCode Another unique identified of the sampling site (redundant) Col 3: Site Name of the sampling site Col 4: Region Region of the sampling site (values: "Helsinki region", "Lahti" or "Tampere") Col 5: WGS_84_X Longitudinal coordinate of the sampling site in WGS84 format Col 6: WGS_84_Y Latitudinal coordinate of the sampling site in WGS84 format Col 7: CollectionDate_fungi Day when deciduous fine woody debris was sampled for fungi (YYYY-MM-DD) Col 8: CollectionDate_insects Day when deciduous fine woody debris was sampled for beetles (YYYY-MM-DD) Col 9: BasALivTot Basal area of all living trees with DBH &gt;= 5 cm within the study plot (m²/ha) Col 10: BasALivSpru Basal area of living Norway spruce (Picea abies) trees with DBH &gt;= 5 cm within the study plot (m²/ha) Col 11: BasALivDec Basal area of living broad-leaved trees with DBH &gt;= 5 cm within the study plot (m²/ha) Col 12: N_DW_units Total number of deciduous fine woody debris pieces collected within the study plot Col 13: Betula Number of fine birch (Betula spp.) deadwood pieces collected within the study plot Col 14: Sorbus Number of fine rowan (Sorbus aucuparia) deadwood pieces collected within the study plot Col 15: Populus Number of fine aspen (Populus tremula) deadwood pieces collected within the study plot Col 16: Alnus Number of fine alder (Alnus spp.) deadwood pieces collected within the study plot Col 17: Salix Number of fine willow (Salix caprea) deadwood pieces collected within the study plot Col 18: Corylus Number of fine hazel (Corylus avellana) deadwood pieces collected within the study plot Col 19: Tilia Number of fine linden (Tilia cordata) deadwood pieces collected within the study plot Col 20: Quercus Number of fine oak (Quercus robus) deadwood pieces collected within the study plot Col 21: Prunus Number of fine Prunus padus deadwood pieces collected within the study plot Col 22: Unspecified Number of fine unidentified deadwood pieces collected within the study plot Col 23: DecayClass_1 Number of fine decay class 1 deciduous deadwood pieces collected within the study plot Col 24: DecayClass_2 Number of fine decay class 2 deciduous deadwood pieces collected within the study plot Col 25: DecayClass_3 Number of fine decay class 3 deciduous deadwood pieces collected within the study plot Col 26: DecayClass_4 Number of fine decay class 4 deciduous deadwood pieces collected within the study plot Col 27: ValidReplicates Number of valid fungal subsample replicated produced from the site-level sample (see File 4) (value: 3 or 4) DATA-SPECIFIC INFORMATION FOR FILE 10: 'Korhonen et al 2024 BirchLog_sample_metadata.csv' 1\. Number of variables/columns: 16 columns 2\. Number of cases/rows: 25 + 1 header row 3\. Column separator: ; 4\. Decimal separator for numeric variables: \\, 5\. Column explanations Col 1: BirchLogNo Unique identifier of the birch log Col 2: SampleCode Another unique identified of the birch log (redundant) Col 3: SiteNo Unique identifier of the sampling site Col 4: CollectionDate Day of sampling (YYYY-MM-DD) Col 5: Species Species of birch (Betula pendula, Betula pubescens or unknown) Col 6: FallType Description of how the tree has falled (broken, fallen top, felled, uprooted, unknown) Col 7: Diam-50cm Diameter of the log at 50 cm distance from the basal end (cm) Col 8: Diam-150cm Diameter of the log at 150 cm distance from the basal end (cm) Col 9: Diam-250cm Diameter of the log at 250 cm distance from the basal end (cm) Col 10: Diam-350cm Diameter of the log at 350 cm distance from the basal end (cm) Col 11: Diam-450cm Diameter of the log at 450 cm distance from the basal end (cm) Col 12: DecayClass-50cm Decay class of the log at 50 cm distance from the basal end (integer 1-4 or NA) Col 13: DecayClass-150cm Decay class of the log at 150 cm distance from the basal end (integer 1-4 or NA) Col 14: DecayClass-250cm Decay class of the log at 250 cm distance from the basal end (integer 1-4 or NA) Col 15: DecayClass-350cm Decay class of the log at 350 cm distance from the basal end (integer 1-4 or NA) Col 16: DecayClass-450cm Decay class of the log at 450 cm distance from the basal end (integer 1-4 or NA)