Analysis of Ectomycorrhizal Fungal Diversity, Relative Abundance, and Community Data in Effaråsen Scots Pine Forests: Effects of Tree Retention Level, Tree Distance, and Size.
Data files
Data files
Citation and access
Citation and access
Data access level:
Creator/Principal investigator(s):
Research principal:
Principal's reference number:
- SLU.ess.2025.4.2.IÄ-2
Data contains personal data:
No
Citation:
Method and outcome
Method and outcome
Time period(s) investigated:
Species and taxons:
Data collection - Field/Intervention experiment
Data collection - Field/Intervention experiment
Mode of collection:
Field/Intervention experiment
Description of the mode of collection:
In autumn 2017, 4.5 years post-logging, 10 composite soil samples were systematically collected from each of the 25 stands along 90-meter transects. Each composite sample consisted of three soil cores (3 cm diameter) pooled together. Composite samples were taken at 10-meter intervals, and GPS coordinates were recorded for each location. Only the organic mor layer was retained, with living mosses and mineral soil removed. Tree distances were measured using tape, and tree crown area (>2m height within a 15m buffer) was calculated using 2022 Swedish laser scanning data and ArcGIS Pro. The molecular protocols for DNA extraction and sequencing followed standard methodologies to accurately assess fungal community composition. This was done in close collaboration with the Department of Forest Mycology and Plant Pathology (Uppsala). Soil samples were collected in plastic tubes, promptly frozen, and processed by freeze-drying and grinding. DNA was extracted using the NucleoSpin Soil Genomic DNA extraction kit (Macherey-Nagel), and the ITS2 region of the ribosome-coding operon was amplified with tagged primers (gITS7 and ITS4). Sequencing was conducted on the Sequel I platform (Pacific Biosciences) at the National Genomic Infrastructure (NGI), SciLifeLab, Uppsala. Sequence filtering, clustering, and taxonomic identification were performed using established pipelines and databases, including SCATA and UNITE. Detailed protocols and methodologies are available in Lindahl et al. (2021).
Time period(s) for data collection:
2017-10-17 - 2017-10-18
Data collector:
- Swedish University of Agricultural Sciences
Opens a new window at ror.org.
ROROpens in a new tab
Source of the data:
- Biological samples
Temporal resolution:
7 month
Spatial resolution:
3.5 kilometres scale 1:11 440
Sample
Sample
Name:
Description of sample:
A total of 250 soil samples were sent for fungal community analysis. Samples, collected in plastic tubes, were frozen within 10 hours, freeze-dried, and finely ground in a ball mill. DNA was extracted from 50 mg of organic soil using the NucleoSpin Soil Genomic DNA kit (Macherey-Nagel, Germany). The ITS2 region was PCR-amplified with gITS7 and ITS4 primers, tagged for sample identification, and sequenced on the Sequel I platform (Pacific Biosciences, USA) at the National Genomic Infrastructure (NGI), SciLifeLab, Uppsala, Sweden. Sequencing data were processed using the SCATA pipeline (Swedish University of Agricultural Sciences). Quality filtering removed sequences <100 bp, with low quality scores, or mismatching primer tags. Remaining sequences were clustered into species hypotheses at 99% similarity using USEARCH and single linkage clustering. Species were identified by BLAST against the UNITE and NCBI databases, and sequences accounting for >1% of any sample were manually verified for taxonomic identity and ectomycorrhizal status. In total, 245 samples were successfully analyzed, optimized for accurate representation of fungal community composition.
Name:
Description of sample:
The samples used in this study consist of genetic samples collected and processed for analysis using the Sequel I platform. These samples include DNA extracted from soil samples which are prepared according to standardized protocols to ensure quality and integrity. The Sequel I platform enables accurate sequencing and data acquisition from these samples, providing reliable genetic information for subsequent analysis.
Instrument
Instrument
Name:
Soil sampler
Description of the instrument:
A stainless steel soil corer (3 cm diameter, 40 cm long) with a sharp edge was used to extract intact soil cores. The sharp edge allowed precise penetration into the soil, enabling efficient collection of undisturbed samples.
Name:
Sequel I platform
Description of the instrument:
Sequel I supports automated data collection and processing, reducing the risk of human error and ensuring consistency across datasets. Its features include data filtering, tagging, and exporting capabilities, allowing the collected data to be organized into formats suitable for further analysis,
Geographic coverage
Geographic coverage
Geographic location:
Geographic description:
Effaråsen is a long-term and large-scale field experiment site established in 2012. The area is located close to Mora in the Dalarna province in the southern boreal vegetation zone of Sweden (14°1'1"E 60°58'21"N).
Administrative information
Administrative information
Responsible department/unit:
Southern Swedish Forest Research Centre
Commissioning organisation:
- Forestry Research Institute of Sweden
Opens a new window at ror.org.
ROROpens in a new tab
Registration number at commissioning organization:
- 23348
Funding
Funding
Funding agency:
- FRAS II
Funding information:
Funded within the FRAS programme, see https://www.slu.se/institutioner/sydsvensk-skogsvetenskap/samverkan/fras2/om-fras-ii/ for list of funders.
