eDNA-based occurrence dataset on fungi from forest monitoring plots in Northwestern Siberia

Citation

Description

During the monitoring of fungal communities at permanent plots in different types of forests in boreal taiga zone (https://doi.org/10.15468/ge1hkl ), soil and forest litter samples were collected for sequencing of nrITS region of fungal eDNA on NanoporeMinION platform.

A total of 46 samples were collected from 6 sites in different types of forest communities. At each site, 3 to 5 samples of each substrate (soil and litter) were collected. Sampling was conducted in August during the period of active fungal community development. The substrate were collected from several points located 10 meters apart. Within each point, a composite sample about 50 g was collected. Samples were frozen on the day of collection until subsequent total DNA extraction.

Prior to extraction, the substrate was dried in a drying oven at 40°C and ground to a powder using a homogenizer. Approximately 0.05 g of this sample was used for DNA extraction following the manufacturer's protocol (SileksMagNA). Subsequent sample preparation for sequencing on the Nanopore MinION platform was performed using the published protocol (dx.doi.org/10.17504/protocols.io.kxygx3jwkg8j/v1).

The obtained sequences were processed using QIIME2 (Quantitative Insights Into Microbial Ecology 2, version 2023.9) with the following parameters (blastn;2.6.0+;e-value cutoff: 0.001). Clustering was performed using the Blast+ algorithm with 99% similarity. For taxonomic assignment, the UNITE database (version 9.0 2022.10.16) was used.

Metabarcoding of the ITS region (Nanopore MinION) revealed about 2300 SHs and 730 Linnean species.

The dataset represents an occurrence table with the DNA-derived extension table based on guidelines (Abarenkov et al. 2023). The first table (Occurrence Core) has 29 fields to describe features of samples and observed taxonomic occurrences with their abundances (number of reads). The related DNA-derived data table contains sequences linked to each occurrence with their metadata.

Sampling Description

Taxonomic Coverages

Geographic Coverages

Bibliographic Citations

1. Filippova N, Bulyonkova T (2017) The communities of terrestrial macrofungi in different forest types in vicinities of Khanty-Mansiysk (middle taiga zone of West Siberia). Biodiversity Data Journal 5: e20732. https://doi.org/10.3897/BDJ.5.e20732 - https://doi.org/10.3897/BDJ.5.e20732
2. Abarenkov K, Andersson AF, Bissett A, Finstad AG, Fossøy F, Grosjean M, Hope M, Jeppesen TS, Kõljalg U, Lundin D, Nilsson RN, Prager M, Provoost D, Schigel D, Suominen S, Svenningsen C, Frøslev TG (2023) Publishing DNA-derived data through biodiversity data platforms, v1.3. Copenhagen: GBIF Secretariat. https://doi.org/10.35035/doc-vf1a-nr22. Accessed on: 2023-10-29. - https://doi.org/10.35035/doc-vf1a-nr22
3. Tedersoo L, Bahram M, Zinger L, Nilsson RH, Kennedy P, Yang T, Anslan S, Mikryukov V (2022) Best practices in metabarcoding of fungi: From experimental design to results. Molecular Ecology 31 (10): 2769‑2795. https://doi.org/10.1111/mec.16460 - https://doi.org/10.1111/mec.16460