DOI: 10.5061/dryad.44j0zpcng
title: Data from: How do attached crown parts and branches contribute to the diversity of saproxylic fungi and beetles in downed and decaying spruce trees?

description: A significant proportion of forest-dwelling species in boreal forests are
 saproxylic, i.e., dependent on deadwood. To safeguard deadwood-associated
 diversity in managed forest landscapes, it is important to understand how
 substrate preferences and specialization structure saproxylic species
 communities across different deadwood resource types. In this study, we
 investigated the diversity and associations of saproxylic fungi and
 beetles at the scale of entire trees to understand how different tree
 parts contribute to species diversity. To do this, we sampled species
 assemblages in trunks (d &gt; 15 cm), tops (d 5–10 cm) and branches
 (d &lt; 5 cm) of 31 fallen Norway spruce trees. Fungal assemblages
 were investigated with DNA metabarcoding from wood samples, and beetles
 were surveyed by bark peeling and sieving. Our results showed that, fungal
 and beetle assemblages were clearly differentiated between trunks and
 branches. In the tops, fungal community composition was intermediate
 between trunks and branches, whereas beetle species composition was more
 closely aligned with trunks. Trunks and branches both harbored specialized
 fungal and beetle species, but no species were identified as specialists
 of tops. Fungal and beetle richness were lowest in branches, and fungal
 richness peaked in tops. Substrate specialization of saproxylic species at
 the scale of individual trees imply that deadwood restoration in managed
 forests should prioritize whole-tree retention instead of partial
 retention such as artificial high stumps or pruned logs.
description: Study sites were located in Norway spruce (Picea abies) dominated
 forests in the cities of Espoo, Helsinki, Vantaa, Lahti and Tampere in
 southern Finland. At each site, we sampled wood-inhabiting fungi and
 saproxylic beetles in one or two fallen spruce trees. We selected tree
 trunks in early stages of decomposition. In all trees, fruiting-bodies of
 wood-decay fungi were visibly developing on the surface, but most of the
 stem surface was still covered by bark. Fungal and beetle sampling was
 conducted between August and November 2022. We
 collected wood samples for the analysis of wood-inhabiting fungi by
 drilling from the basal section of the downed trunk, from the top of the
 tree, and from the branches. The basal part was sampled at five
 equidistant points from 50 cm to 850 cm distance from the base on both
 vertical sides of the trunk. The top was sampled at five equidistant
 points on one side of the stem along a section where stem tapered from 10
 cm to 5 cm in thickness. Branch samples were collected from five branches
 randomly picked at roughly equidistant points along the trunk from the
 lowest branching point to 10 cm stem thickness. From each branch, we
 sampled a segment 20-35 cm outward from the trunk. At
 each drilling point, we exposed a fresh wood surface with a knife and
 extracted wood with a 6 mm drill head down to a maximum depth of 5 cm.
 Drill dust was collected directly into a sterilized polyethylene bags
 yielding one sample from each tree compartment per one tree. Samples were
 stored in -20 °C, and later ground into fine dust in a bead beater in 50
 ml capsules with 8 mm steel bead for 2 min in 30 Hz. We DNA sterilized
 tools with bleach solution between samples when extracting and processing
 the wood samples. DNA was extracted from ca. 90 mg of
 wood powder and eluted into 50 µl final elution volume with DNeasy Plant
 Pro extraction kit according to the manufacturer’s instructions. For the
 analysis of wood-inhabiting fugal communities by 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). Sequence reads were
 demultiplexed, and index and primer sequences were removed from paired-end
 reads. Subsequent sequence processing was done with vsearch v2.18.0. R1
 and R2 reads were quality filtered and 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) database in mothur v1.36.1. For further
 analyses, we converted OTU read abundances into presence-absence data by
 applying 1% relative abundance threshold. We sampled
 saproxylic beetles at the basal end of the trunk, at the middle part of
 the trunk, at the top of the tree, and from the branches. At each sampling
 point along the trunk and top, we sampled a fixed 1
 m<sup>2</sup> area of bark. For branch sampling, we picked
 five branches per tree randomly along the length of the tree and sampled
 from the total bark area available on those branches.
 Beetles were collected by peeling and sifting bark. We identified
 adult beetles to species morphologically and larvae and pupae 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, species were recorded based
 on visual observations of characteristic exit holes and larval galleries
 in the wood.
description: # Data from: How do tops and branches contribute to the saproxylic
 diversity in fallen spruce trees?
 [https://doi.org/10.5061/dryad.44j0zpcng](https://doi.org/10.5061/dryad.44j0zpcng) This dataset contains data collected from urban spruce-dominated forests in southern Finland where we have studied fungal and beetle assemblages associated with fallen and decaying spruce trees. Data files include (1) tables describing fungal and beetle community composition (presence-absence of fungal Operational Taxonomic Units and beetle species) across trees and tree compartments, (2) taxonomic metadata related to fungal OTUs and beetle species, and (3) metadata related to study sites and trees. ## Description of the data and file structure File List: File 1 Name: 'Korhonen et al 2024 Fungal_OTU_presabs.csv' File 1 Description: File contains presence-absence occurrence data of fungal OTUs (columns) in samples (rows). File 2 Name: 'Korhonen et al 2024 Fungal_OTU_taxonomy_and_metadata.csv' File 2 Description: File contains taxonomic annotations and other metadata related to fungal OTUs. File 3 Name: 'Korhonen et al 2024 Beetle_species_presabs.csv' File 3 Description: File contains presence-absence occurrence data of beetle species (columns) in samples (rows). File 4 Name: 'Korhonen et al 2024 Beetle_species_metadata.csv' File 4 Description: File contains metadata related to beetle species. File 5 Name: 'Korhonen et al 2024 Tree_metadata.csv' File 5 Description: File contains metadata related to sampled trees. File 6 Name: 'Korhonen et al 2024 Beetles_raw_data.csv' File 6 Description: File contains beetle observation data in long format. DATA-SPECIFIC INFORMATION FOR FILE 1: 'Korhonen et al 2024 Fungal_OTU_presabs.csv' 1. Number of variables/columns: 243 data columns + 1 header column (SampleID: values have the following format 'Fungi_[tree compartment]_[TreeNo]') 2. Number of cases/rows: 93 data rows + 1 header row (corresponding to OTU_ID in File 2) 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 Fungal_OTU_taxonomy_and_metadata.csv' 1. Number of variables/columns: 20 columns 2. Number of cases/rows: 243 data rows + 1 header row 3. Column separator: ; 4. Column explanations Col 1: OTU_ID Unique identifiers of OTUs Col 2: RepSeq Representative ITS2 sequences of OTUs Col 3: k Taxonomic assignment to Domain (NA if not specified) Col 4: k% Support for taxonomic assignment to Kingdom (values: 80-100, NA when &lt;80) Col 5: p Taxonomic assignment to Phylum (NA if not specified) Col 6: p% Support for taxonomic assignment to Phylum (values: 80-100, NA when &lt;80) Col 7: c Taxonomic assignment to Class (NA if not specified) Col 8: c% Support for taxonomic assignment to Class (values: 80-100, NA when &lt;80) Col 9: o Taxonomic assignment to Order (NA if not specified) Col 10: o% Support for taxonomic assignment to Order (values: 80-100, NA when &lt;80) Col 11: f Taxonomic assignment to Family (NA if not specified) Col 12: f% Support for taxonomic assignment to Family (values: 80-100, NA when &lt;80) Col 13: g Taxonomic assignment to Genus (NA if not specified) Col 14: g% Support for taxonomic assignment to Genus (values: 80-100, NA when &lt;80) Col 15: s Taxonomic assignment to Species (NA if not specified) Col 16: s% Support for taxonomic assignment to Species (values: 80-100, NA when &lt;80) Col 17: Comment Alternative taxonomic identification for the sequence suggested by the authors. NA if no comment was made. DATA-SPECIFIC INFORMATION FOR FILE 3: 'Korhonen et al 2024 Beetle_species_presabs.csv' 1. Number of variables/columns: 101 data columns + 1 header column (SampleID: values have the following format 'Beetles_[tree compartment]_[TreeNo]') 2. Number of cases/rows: 124 data rows + 1 header row (corresponding to Species_name in File 4) 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 4: 'Korhonen et al 2024 Beetle_species_metadata.csv' 1. Number of variables/columns: 3 columns 2. Number of cases/rows: 101 data rows + 1 header row 3. Column separator: ; 4. Column explanations Col 1: Species_name Scientific name of the species (text) Col 2: Authority Author suffix for the scientific name (text) Col 3: Rarity Rarity of the species according to the Finnish Biodiversity Information Facility (2024) (text; Common, Rare) DATA-SPECIFIC INFORMATION FOR FILE 5: 'Korhonen et al 2024 Tree_metadata.csv' 1. Number of variables/columns: 17 columns 2. Number of cases/rows: 31 data rows + 1 header row 3. Column separator: ; 4. Decimal separator for numeric variables: , 5. Column explanations Col 1: TreeNo Unique identifiers of trees (numeric; ascending from 01 to 32, excluding 19) Col 2: Latitude Latitude in WGS 84 (numeric) Col 3: Longitude Longitude in WGS 84 (numeric) Col 4: Elevation Elevation in meters above sea level (numeric; meters) Col 5: City Name of the city where tree was located (text) Col 6: SiteName Name of the site where tree was located (text) Col 7: Date_Fungi Day when fungi were sampled (YYYY-MM-DD) Col 8: Date_Beetles Day when beetles were sampled (YYYY-MM-DD) Col 9: Length Length of the fallen tree from the base to the top, excluding the stump for broken trees (numeric; meters) Col 10: FallType Type of the fallen tree (3 = uprooted tree, 4A = broken tree with &gt; 1.3 m high stumo, 4B = broken tree with &lt; 1.3 m high stump, 10B = felled tree) Col 11: Cut Whether the tree had be cut in two or more pieces: 0=No, 1=Yes Col 12: Trunk_diam_mean Average of diameter measurements at the wood sampling points along the trunk section of the tree (numeric; cm) Col 13: Trunk_decay_mean Average of decay classes (integer 1-5) measured at the wood sampling points along the trunk section of the tree (numeric) Col 14: Trunk_bark_mean Proportion of bark cover on the trunk section of the tree where wood samples were taken (numeric; 0-1) Col 15: Top_decay_mean Average of decay classes (integer 1-5) measured at the wood sampling points along the top section of the tree (numeric) Col 16: Top_bark_mean Proportion of bark cover on the top section of the tree (numeric; 0-1) Col 17: Branch_diam_mean Average diameter of the branches that were picked for wood sampling (numeric; cm) DATA-SPECIFIC INFORMATION FOR FILE 6: 'Korhonen et al 2024 Beetles_raw_data.csv' 1. Number of variables/columns: 12 columns 2. Number of cases/rows: 693 data rows + 1 header row 3. Column separator: ; 4. Column explanations Col 1: TreeNo Unique identifiers of trees (numeric; ascending from 01 to 32, excluding 19) Col 2: TreeCompartment Tree compartment (text; Trunk_base, Trunk_middle, Top, Branches) Col 3: Date Day when beetles were sampled (YYYY-MM-DD) Col 4: Diameter Diameter of the beetle sampling area (numeric; cm, NA if not specified) Col 5: Length Length of the beetle sampling area along the stem (numeric; cm, NA if not specified) Col 6: DecayClass Decay class of the wood in the beetle sampling area (integer 1-5, NA if not specified) Col 7: BarkCover Proportion of bark cover on the beetle sampling area (numeric; %, NA if not specified) Col 8: FungalFruitingBodies Fungal fruiting bodies observed on the beetle sampling area (text; list of fungal species, NA if not specified) Col 9: Species Scientific name of the observed beetle species (text; corresponding to Species_name in File 4) Col 10: SpAbb Abbreviation for the species name (text) Col 11: ObservationType Type of observation for the beetle species (text; adult individual, larva, pupa, tunnel) Col 12: Count The number of observed beetle individuals (integer) ## Sharing/Access information Fungal ITS2 sequence read data files associated with this study will be made available under BioProject ID PRJNA1012880 in the NCBI sequence read archive.