Data from: Fungal and beetle diversity in deciduous fine woody debris in spruce-dominated forests in relation to substrate quantity and quality
Data files
Oct 18, 2024 version files 3.05 MB
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Korhonen_et_al_2024_Beetle_species_metadata.csv
5.59 KB
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Korhonen_et_al_2024_Beetles_presabs_BirchLogs_samples.csv
5.59 KB
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Korhonen_et_al_2024_Beetles_presabs_DFWD_sites.csv
6.52 KB
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Korhonen_et_al_2024_BirchLog_sample_metadata.csv
1.83 KB
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Korhonen_et_al_2024_Fungi_DFWD_SampleNo_SiteNo_table.csv
1.90 KB
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Korhonen_et_al_2024_Fungi_ITS2_OTU_taxonomy.csv
2.74 MB
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Korhonen_et_al_2024_Fungi_presabs_BirchLog_samples.csv
18.88 KB
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Korhonen_et_al_2024_Fungi_presabs_DFWD_replicates.csv
192.13 KB
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Korhonen_et_al_2024_Fungi_presabs_DFWD_sites.csv
54.88 KB
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Korhonen_et_al_2024_Site_and_DFWD_sample_metadata.csv
3.91 KB
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README.md
12.04 KB
Abstract
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.
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 <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 <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 <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 <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 <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 <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 <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 >= 5 cm within the study plot (m²/ha)
Col 10: BasALivSpru Basal area of living Norway spruce (Picea abies) trees with DBH >= 5 cm within the study plot (m²/ha)
Col 11: BasALivDec Basal area of living broad-leaved trees with DBH >= 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)
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 >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.