DOI: 10.5061/dryad.9w0vt4bfr
title: Data from: Landscape context and substrate characteristics shape fungal communities of dead spruce in urban and semi-natural forests

description: Data from: Korhonen, A., Miettinen, O., Kotze, D.J., & Hamberg, L.
 (2022). Landscape context and substrate characteristics shape fungal
 communities of dead spruce in urban and semi-natural forests.
 Environmental Microbiology. DOI: 10.1111/1462-2920.15903 This
 dataset contains occurrence data of 475 fungal ITS2 sequence clusters
 (OTUs) across 360 sequenced samples originating from dead wood of
 Norway spruce (Picea abies). Wood samples were collected from 90 downed
 spruce trunks, at four points from each trunk. Trunks were
 at intermediate stages of decay and located in spruce-dominated
 stands in 24 urban forests (66 trunks) and in 8 rural
 semi-natural forests (24 trunks) in southern Finland. The data consists of
 an OTU table (sequence read counts in each sample) and
 sample metadata (locality information, trunk
 characteristics and environmental variables).
description: All study sites represented
 forest stands with natural herb-rich to mesic heathland forest vegetation,
 Norway spruce (<em>Picea abies</em>) as the dominant tree
 species, and the age of dominant trees at least 60 years. Urban study
 sites (24 sites, 66 trunks) were distributed across the Helsinki
 metropolitan area (combined population of ca. 1.2 million) in southern
 Finland, and semi-natural study sites (8 sites, 24 trunks) in the
 surrounding rural areas. Urban sites represented deadwood hotspots within
 the urban landscape where deadwood had accumulated in large volumes
 locally. Semi-natural sites represented unmanaged stands with large
 volumes of deadwood and minimal signs of logging history and other human
 disturbances, including recreational use. At each site, we searched for
 fallen Norway spruce trunks that were at intermediate stages of decay
 (predominantly decay class 3 according to Renvall’s (1995) five-stage
 classification) and had a diameter of 20–40 cm at 4–6 m from the base.
 Decay class 3 is defined as the stage in which the decaying trunk has
 already partly rotten (knife penetrates ca. 3–5 cm into the wood easily)
 but still retains its shape. At this decay stage, spruce trunks are mostly
 decorticated, and the wood surface is being colonized by epixylic lichens
 and bryophytes. In the urban area, 1–4 trunks were chosen per site
 depending on the availability of suitable tree trunks. In semi-natural
 areas, we chose three suitable trunks per site randomly. All trunks were situated inside a
 closed forest with mean canopy openness of 23% (SD = 5). Distance between
 the trunk and the nearest forest edge varied from 7 to 589 m
 (Supplementary Table C1). Trunks in urban forests were generally closer to
 forest edges (median 53 m) than trunks in semi-natural forests (median 216
 m). However, neither canopy openness nor distance to the forest edge had
 any significant associations with properties of the tree trunks.
 Wood samples were collected
 from spruce trunks in October 2018. Four wood samples were taken from each
 tree trunk at 2, 4, 6, and 8 m distance from the base. Samples were
 extracted from the shadier side of the trunk. Epiphytes, bark and loose
 rotten wood were removed with a flame-sterilized knife to expose a clean
 surface of solid wood on the side of the trunk. Wood shavings were
 extracted with a flame-sterilized 6 mm diameter drill and collected into
 paper bags and stored at -20°C until DNA extraction. DNA was extracted with a
 NucleoSpin Soil (Macherey-Nagel, Düren, DE) extraction kit from 112 ± 52
 mg of sample material. Extraction was done according to the manufacturer’s
 instructions with lysis buffer SL2 and final elution in 30 µl volume. The
 ITS2 region was amplified using PCR with primers gITS7 (Ihrmark
 <em>et al.</em>, 2012) and ITS4 (White <em>et
 al.</em>, 1990) with 6 bp dual index for 28 cycles. The resulting
 PCR fragments were sequenced with the MiSeq v3 (Illumina, San Diego,
 US-CA) 2 × 300 bp paired-end system yielding 20–25 M raw sequence
 reads. Quality
 filtering and the removal of artefacts, primer‐dimers and primers from raw
 sequence reads (NCBI BioSample accessions SAMN19307225-SAMN19307584 under
 BioProject PRJNA732060) were conducted with the PipeCraft 1.0 pipeline.
 Raw ITS sequence reads were processed according to the manual with the
 following specifications. Assembly of paired-end reads and initial quality
 ﬁltering was conducted with vsearch v1.11.1 with the following parameters:
 minimum overlap 20, max differences 99, minimum length 150 bp, e_max 1,
 max ambiguous 0, and trunc qual 20. Chimera ﬁltering was performed for the
 reoriented reads using reference-based ﬁltering with Unite ITS2 ref. v7.1
 as the database, also removing primers and primer artifacts from sequences
 at this step. In addition, the fungal ITS2 region was extracted from reads
 with ITSx. The
 remaining 7.876 M sequences were then clustered with Swarm v2 algorithm (d
 = 1, fastidious = TRUE). These raw operational taxonomic units (OTUs) were
 identified to taxonomic groups with the Naïve Bayesian classifier using
 UNITE database v8.2 as the reference database and matched to the closest
 representative species hypothesis in the database using BLASTn. Raw OTUs
 that were assigned to the same named species with at least 90% confidence
 were then aggregated to combined OTUs. Raw OTUs that were not assigned to
 any named species-level taxon were compared to others that had the same
 UNITE species hypothesis as their closest match; if the representative
 sequence of an OTU had at least 97.5% sequence similarity to any other OTU
 in the same group, they were merged. Raw OTUs with &lt; 97.5%
 similarity to any other OTU were retained as separate OTUs.
 The diversity of fungal communities was measured with the Simpson
 diversity index. Before calculating the index, relative species (or OTU)
 abundances (read count divided by sample sequencing depth) were averaged
 between the two middlemost samples for each trunk (segments 2 and 3) to
 aggregate the data to trunk-level and to focus on the data that were most
 closely connected to the temperature measurement point within the tree
 trunk. Averaged species (or OTU) abundances were then used for calculating
 the index with R package iNEXT v.2.0.20. To assess the value of tree
 trunks as habitat for WIF species of conservation concern, we recorded the
 number of red-listed species present in each individual trunk. We
 considered species included in the national or regional IUCN Red List
 assessments across the hemi- and southern boreal northeastern Europe,
 i.e., Estonia (see Runnel, Miettinen, and Lõhmus, 2021), Finland
 (Kotiranta et al., 2019), Norway (NBIC, 2019), Sweden (SLU Artdatabanken,
 2020) and the Leningrad Region of Russian Federation (Geltman et al.,
 2018). A species was recorded as present if it accounted for at least 5‰
 of the total sequence reads in at least one sample. Characteristics of the downed
 spruce trunks were measured in June 2019. Measurements were taken from
 four 2 m segments between 1 and 9 m from the base of the tree trunk. Trunk
 diameter and distance between the bottom of the trunk and the soil surface
 directly below it was measured at the midpoint of each segment. Decay
 class (1–5) was determined for each segment based on knife penetration
 into the wood. Epiphyte cover (%) was measured for the top surface of each
 segment. Epiphyte cover consisted primarily of bryophyte mats. Wood
 moisture content (%), based on electric resistance, was measured (Moisture
 Meter ET-928, Clas Ohlson, Insjön, SE) from the shadier vertical side of
 the tree trunk at the midpoint of each segment. Measurements were made on
 an intact wood surface exposed by removing epiphytes, remains of bark and
 the most decayed layer of wood from the surface. The month of June, when
 all measurements were made, is at the end of the driest period of the year
 when wood moisture was expected to be close to the annual
 minimum. Temperature inside each tree
 trunk was monitored between the spring and fall of 2019 with a datalogger
 (iButton Thermochron DS1921G-F5, Maxim Integrated, San Jose, US-CA)
 embedded in the middle of the trunk. Dataloggers were inserted into
 drilled holes that were sealed tightly with wooden plugs. Temperature
 measurements were recorded synchronously with 4 h intervals from 1 AM to 9
 PM. To get an indication of how sensitive temperature inside the tree
 trunk was to external temperature changes, we extracted the maximum 4 h
 temperature change for each day of the measurement period between 1 May
 and 29 September. These values were then averaged across the days to yield
 one value for each trunk, the mean of daily maximum 4 h temperature
 changes.
description: OTU sequence read counts in each sample are presented in an OTU
 table 'Korhonen et al OTU_table_Tab_Delimited.txt'). This file
 also contains information about OTUs: e.g. representative sequences,
 taxonomic assignments, and BLAST search match results against UNITE
 database. Metadata is provided separately for
 individual samples ('Korhonen et al
 OTU_table_sample_metadata_Tab_Delimited.txt') and tree trunks
 ('Korhonen et al
 OTU_table_trunk_metadata_Tab_Delimited.txt').
 Variable explanations are provided in separate files
 ('Korhonen et al OTU_table_explanations_Tab_Delimited.txt' and
 'Korhonen et al
 OTU_table_metadata_explanations_Tab_Delimited.txt').
   DATA-SPECIFIC INFORMATION FOR:
 'Korhonen et al OTU_table_Tab_Delimited.txt'
 1. Number of variables/columns: 387 (See file 'Korhonen et
 al OTU_table_explanations_Tab_Delimited.txt' for variable
 explanations.) 2. Number of cases/rows: 475 data rows +
 1 total sequencing depth row + 1 header row 3.
 Abbreviations used: N/A; not applicable 4. Column
 separator: Tab Delimited  
 DATA-SPECIFIC INFORMATION FOR: 'Korhonen et al
 OTU_table_sample_metadata_Tab_Delimited.txt' 1.
 Number of variables/columns: 18 (See file 'Korhonen et al
 OTU_table_metadata_explanations_Tab_Delimited.txt' for variable
 explanations.) 2. Number of cases/rows: 360 data rows +
 1 header row 3. Decimal separator for numeric data:
 , 4. Column separator: Tab Delimited
   DATA-SPECIFIC INFORMATION FOR:
 'Korhonen et al
 OTU_table_trunk_metadata_Tab_Delimited.txt' 1.
 Number of variables/columns: 18 (See file 'Korhonen et al
 OTU_table_metadata_explanations_Tab_Delimited.txt' for variable
 explanations.) 2. Number of cases/rows: 90 data rows +
 1 header row 3. Decimal separator for numeric data:
 , 4. Column separator: Tab Delimited
   DATA-SPECIFIC INFORMATION FOR:
 'Korhonen et al
 OTU_table_explanations_Tab_Delimited.txt' 1.
 Number of variables/columns: 2 2. Number of cases/rows:
 28 + 1 header row 3. Abbreviations used: N/A; not
 applicable 4. Column separator: Tab Delimited
   DATA-SPECIFIC INFORMATION FOR:
 'Korhonen et al
 OTU_table_metadata_explanations_Tab_Delimited.txt'
 1. Number of variables/columns: 2 2. Number of
 cases/rows: 26 + 1 header row 3. Column separator: Tab
 Delimited