Data from: How do attached crown parts and branches contribute to the diversity of saproxylic fungi and beetles in downed and decaying spruce trees?
Data files
Dec 12, 2024 version files 297.14 KB
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Korhonen_et_al_2024_Beetle_species_metadata.csv
4.53 KB
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Korhonen_et_al_2024_Beetle_species_presabs.csv
29.62 KB
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Korhonen_et_al_2024_Beetles_raw_data.csv
65.68 KB
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Korhonen_et_al_2024_Fungal_OTU_presabs.csv
56.69 KB
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Korhonen_et_al_2024_Fungal_OTU_taxonomy_and_metadata.csv
129 KB
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Korhonen_et_al_2024_Tree_metadata.csv
3.56 KB
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README.md
8.07 KB
Abstract
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 > 15 cm), tops (d 5–10 cm) and branches (d < 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.
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'
- Number of variables/columns: 243 data columns + 1 header column (SampleID: values have the following format 'Fungi_[tree compartment]_[TreeNo]')
- Number of cases/rows: 93 data rows + 1 header row (corresponding to OTU_ID in File 2)
- Column separator: ;
- 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'
- Number of variables/columns: 20 columns
- Number of cases/rows: 243 data rows + 1 header row
- Column separator: ;
- 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 <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 <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 <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 <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 <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 <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 <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'
- Number of variables/columns: 101 data columns + 1 header column (SampleID: values have the following format 'Beetles_[tree compartment]_[TreeNo]')
- Number of cases/rows: 124 data rows + 1 header row (corresponding to Species_name in File 4)
- Column separator: ;
- 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'
- Number of variables/columns: 3 columns
- Number of cases/rows: 101 data rows + 1 header row
- Column separator: ;
- 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'
- Number of variables/columns: 17 columns
- Number of cases/rows: 31 data rows + 1 header row
- Column separator: ;
- Decimal separator for numeric variables: ,
- 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 > 1.3 m high stumo, 4B = broken tree with < 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'
- Number of variables/columns: 12 columns
- Number of cases/rows: 693 data rows + 1 header row
- Column separator: ;
- 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.
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 m2 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.
