Laboratory for the development of metagenomic analysis techniques for rapid environmental impacts in conditions of intensive subsurface use

The Molecular Laboratory enabled the start of DNA barcoding of the Fungarium. The laboratory is equipped with several zones, including extraction, PCR, electrophoresis, purification and Sanger sequencing zones. The laboratory is staffed by qualified technicians and researchers. The YSU Fungarium collection was created as part of the revision of the diversity of fleshy fungi of West Siberian middle taiga and contains about 10 thousand dried specimens. Special attention has been paid to the communities of raised bogs, which are widespread in the region. The barcoding roject is designed to run for three years and will include a revision of all taxonomic groups represented in the Fungarium using modern molecular genetic methods. During the two years of the project, over 1500 extractions from about 1000 specimens were performed. About a third was a part of the revision of the large genus Cortinarius. Another large part was within the effort of raised bog fungi barcoding. The remaining specimens were from revisions of minor groups, students projects and sequencing of noteworthy finds and taxa potentially new to region or to science in general. Ready sequences are uploaded to the YSU Fungarium database in Specify 7. Sequence metadata, the edited sequence and original files are saved. Each sample may correspond to one or several sequences (different regions). Each sequence may have one or several original files with their sequencing parameters. Primer parameters are filled in a separate table.

A program on metabarcoding of fungal communities in different types of ecosystems in the taiga zone of Western Siberia was initiated. The first part of the project focuses on metabarcoding various substrates in raised peatand ecosystems. Currently, we are expanding the diversity of habitats by sampling soil and litter from different types of forests, studying fungal communities in phylloplanes, and investigating changes in species composition under the influence of oil spills. Two different approaches to eDNA sequencig are used: Illumina MiSeq (based on outsourcing DNA-samples) and Nanopore MinION technologies. To supplement long-term monitoring of fungal communities of the raised peatland with an environmental DNA approach, we completed a series of samplings of common substrates in the same locality in the Mukhrino Bog. Four major substrates were subjected to metabarcoding analysis: peat (from the surface layer to a depth of about 3 m), leaf litter of six bog plants, wood (represented by standardised wooden dowels) and mycorrhizal roots of two bog-dwelling trees. Metabarcoding of the ITS2 region (Illumina MiSeq platform) revealed about 1200 OTUs and 800 Linnean taxa. The obtained sequences were processed using QIIME2 (Quantitative Insights Into Microbial Ecology 2, version 2023.9). The sequence analysis revealed a total of 1259 OTUs classified into 471 species, 423 genera, 223 families, 86 orders, 30 classes, seven phyla and one kingdom at a 99% similarity level. About 42% of taxa were identified at the species level, 21% at the genus level and the rest at higher taxonomic levels. The dataset representing DNA-based occurrences published in GBIF as an occurrence dataset with the DNA-derived extension table based on guidelines (Filippova et al. 2023b).

A series of permanent plots and routs was initiated in vicitinity of Khanty-Mansiysk (Shapsha village) in 2014 to describe the species composition, quantitative structure and dynamics of communities in different forest and bog types. The logging being the main factor of disturbance in the area, we chose several stages of after-cut succession to locate 10 plots. Another series of plots was built in a raised bog community, at the research polygon of Mukhrino Field Station. The methods of sampling follow recommended in (Mueller et al., 2004, Biodiversity of fungi ..). The plots and routes are visited regularly since 2014 once in 1-2 weeks covering the whole vegetation season and allowing to describe the phenology of fruiting. The monitoring data is published in GBIF as sampling-event datasets and could be accessed through the following links: Filippova N (2022). Plot-based observations of terrestrial macrofungi in different forest types of boreal zone in West Siberia (2015-2021). Version 1.18. Yugra State University Biological Collection (YSU BC). Sampling event dataset https://doi.org/10.15468/ge1hkl accessed via GBIF.org on 2024-02-28. Filippova N, Rudykina E, Dobrynina A, Zvyagina E (2023). Plot-based observations of macrofungi in raised bogs in Western Siberia (2014-2023). Version 1.40. Yugra State University Biological Collection (YSU BC). Sampling event dataset https://doi.org/10.15468/e9g5ri accessed via GBIF.org on 2024-02-28. Filippova N (2022). Route-based survey of terrestrial macrofungi nearby Khanty-Mansiysk, Western Siberia. Version 1.8. Yugra State University Biological Collection (YSU BC). Sampling event dataset https://doi.org/10.15468/7mzitk accessed via GBIF.org on 2024-02-28.

The mycological research in the West Siberia stems from isolated studies in the beginning of the 20th century, but regular and systematic research dates back to the 1970-80s. Over the following decades several dozens of researches have worked in the area and more than thousand scientific works have been published. Fungal records database of West Siberia (FunWS) was developed to mobilize the literature-based occurrence records of fungi and fungi-related organisms published in previous literature. FunWS project description in Russian at Siberian Mycological Society web page. Overview of Mycological research in Northern West Siberia Overview of Mycological research in Southern West Siberia Algorithm of digitization process of FunWS, in Russian (doc) Bibliography of mycological research in West Siberia on 25.01.2022 (doc, excel)) The FunWS database includes about 30 fields describing species name, publication source, herbarium number, date of sampling, locality information, vegetation, substrate, and others. The occurrences in the database were extracted from previously published works, no herbarium collections or other unpublished records were included in the database. The database expords data in two datasets published in GBIF for the Southern and Northern parts of the region. Each dataset was described in a corresponding Data paper published in Biodiversity Data Journal in 2019 and 2021. Related Data Papers, posters and abstracts: Filippova N, Ageev D, Bolshakov S, Davydov EA, Filippova A, Filippov I, Gashkov S, Gorbunova I, Kalinina L, Kudashova N, Palomozhnykh E, Shabanova N, Tomoshevich M, Vayshlya O, Vlasenko A, Vlasenko V, Vorobʼeva I, Yakovchenko L, Zvyagina E (2021) The fungal literature-based occurrence database for southern West Siberia (Russia). Biodiversity Data Journal 9: e76789. https://doi.org/10.3897/BDJ.9.e76789 Filippova N, Ageev D, Bolshakov S, Vayshlya O, Vlasenko A, Vlasenko V, Gashkov S, Gorbunova I, Davydov EA, Zvyagina E, Kudashova N, Tomoshevich M, Filippova A, Shabanova N, Yakovchenko L, Vorob’eva I, Kalinina L, Palomozhnykh E (2021) The Fungal Literature-based Occurrence Database in Southern West Siberia (Russia). Biodiversity Information Science and Standards 5: e74178. https://doi.org/10.3897/biss.5.74178 Filippova N, et al. (2021) The Fungal Literature-based Occurrence Database in Southern West Siberia (Russia) [Poster, presented at TDWG 2021] https://doi.org/10.13140/RG.2.2.30819.89125 Filippova N, Arefyev S, Zvyagina E, Kapitonov V, Makarova T, Mukhin V, Sedelnikova N, Stavishenko I, Shiryaev A, Tolpysheva T, Ryabitseva N, Paukov A (2020) Fungal literature records database of the Northern West Siberia (Russia). Biodiversity Data Journal 8: e52963. https://doi.org/10.3897/BDJ.8.e52963