DNA-based occurrence dataset on peatland fungal communities studied by metabarcoding in north-western Siberia.

Background: The paper represents the first DNA-based occurrence dataset on peatland fungal communities published for north-western Siberia, the first for Russia and complements several existing datasets on metabarcoding of peat soils globally. New information: The aim of the present publication is to describe the first DNA-based occurrence dataset on fungal communities in peat soils and other substrates studied by the eDNA approach in the Mukhrino raised bog, located in a large paludified area of north-western Siberia. A comparison of the species diversity of larger fungi identified by the conventional approach and by eDNA showed a high proportion of shared taxa. Other groups (mainly Ascomycota), described by metabarcoding, revealed high diversity compared with conventional observation. Overall, the species richness identified in one peatland locality (the Mukhrino Bog) was comparable in number of species to the global estimation of fungal diversity in peatlands, previously reported in literature.

The diversity of macromycetes in peatlands: nine years of plot-based monitoring and barcoding in the raised bog "Mukhrino", West Siberia.

Background: Peatland ecosystems are defined by soils with sufficient under-decomposed organic layer, called peat, formed under anoxic conditions. Peatlands are widespread around the world, with several highly paludified regions, one of which is the Western Siberian Plain. Peatlands store large amounts of carbon and are important in their intact state to counteract climate change, as well as for a variety of other ecosystem functions. From the practical aspect, these ecosystems are used as a source of peat for fuel, peat-based fertilisers and growing media, berries and Sphagnum plantations. Fungi are the key part of the decomposer community of peatlands, playing a critical role in the aerobic decomposition in the upper peat layer. The community of peatland fungi is adapted to decomposition of peat and dead parts of Sphagnum in wet acidic conditions; they form specific mycorrhizal associations with a variety of plants. Thus, the research of fungal diversity of peatlands is important for several reasons: 1) adding knowledge of peatland fungal diversity to local or global biodiversity databases; 2) studying carbon cycling in peatlands; 3) using peat and peatlands for different applications, such as cultivation of Sphagnum with regards to some parasitic species of fungi and 4) peatland restoration and conservation, to mention a few. New information: The community of macromycetes of the raised bog "Mukhrino" in Western Siberia was studied using plot-based monitoring throughout a 9-year observation period. The revealed species diversity is represented by approximately 500 specimens in the Fungarium of Yugra State University collection. Selected specimens were used for barcoding of the ITS region to reveal a total of 95 species from 33 genera and three classes. The barcoding effort confirmed morphological identifications for most specimens and identified a number of cryptic species and several potentially new taxa. Based on regular all-season observations, we describe the phenology of the community sporophore production. The quantitative community structure, based on sporophores, revealed a difference in abundance between species by four orders of magnitude, with rare species representing nearly half of the species list. The inter-annual fruiting abundance varied several times by the total number of sporophores per year. To make the comparisons with global studies, we created an open access database of literature-based observations of fungi in peatlands, based on about 120 published papers (comprising about 1300 species) and compared our species list with this database.As a result, the study created an accurate representation of taxonomic and quantitative structure of the community of macromycetes in raised bogs in the region. The raw data of plot-based counts was published as a sampling-event dataset and the sequenced specimens with the sequence information as an DNA-derived extension dataset in GBIF.

Complex fitness landscape shapes variation in a hyperpolymorphic species.

It is natural to assume that patterns of genetic variation in hyperpolymorphic species can reveal large-scale properties of the fitness landscape that are hard to detect by studying species with ordinary levels of genetic variation. Here, we study such patterns in a fungus Schizophyllum commune, the most polymorphic species known. Throughout the genome, short-range linkage disequilibrium (LD) caused by attraction of minor alleles is higher between pairs of nonsynonymous than of synonymous variants. This effect is especially pronounced for pairs of sites that are located within the same gene, especially if a large fraction of the gene is covered by haploblocks, genome segments where the gene pool consists of two highly divergent haplotypes, which is a signature of balancing selection. Haploblocks are usually shorter than 1000 nucleotides, and collectively cover about 10% of the S. commune genome. LD tends to be substantially higher for pairs of nonsynonymous variants encoding amino acids that interact within the protein. There is a substantial correlation between LDs at the same pairs of nonsynonymous mutations in the USA and the Russian populations. These patterns indicate that selection in S. commune involves positive epistasis due to compensatory interactions between nonsynonymous alleles. When less polymorphic species are studied, analogous patterns can be detected only through interspecific comparisons.

Changes to DNA known as mutations may alter how the proteins and other components of a cell work, and thus play an important role in allowing living things to evolve new traits and abilities over many generations. Whether a mutation is beneficial or harmful may differ depending on the genetic background of the individual ­ that is, depending on other mutations present in other positions within the same gene ­ due to a phenomenon called epistasis. Epistasis is known to affect how various species accumulate differences in their DNA compared to each other over time. For example, a mutation that is rare in humans and known to cause disease may be widespread in other primates because its negative effect is canceled out by another mutation that is standard for these species but absent in humans. However, it remains unclear whether epistasis plays a significant part in shaping genetic differences between individuals of the same species. A type of fungus known as Schizophyllum commune lives on rotting wood and is found across the world. It is one of the most genetically diverse species currently known, so there is a higher chance of pairs of compensatory mutations occurring and persisting for a long time in S. commune than in most other species, providing a unique opportunity to study epistasis. Here, Stolyarova et al. studied two distinct populations of S. commune, one from the USA and one from Russia. The team found that ­ unlike in humans, flies and other less genetically diverse species ­ epistasis maintains combinations of mutations in S. commune that individually would be harmful to the fungus but together compensate for each other. For example, pairs of mutations affecting specific molecules known as amino acids ­ the building blocks of proteins ­ that physically interact with each other tended to be found together in the same individuals. One potential downside of having pairs of compensatory mutations in the genome is that when the organism reproduces, the process of making sex cells may split up these pairs so that harmful mutations are inherited without their partner mutations. Thus, epistasis may have helped shape the way S. commune and other genetically diverse species have evolved.

The fungal literature-based occurrence database for southern West Siberia (Russia).

BACKGROUND: The paper presents the initiative on literature-based occurrence data mobilisation of fungi and fungi-related organisms (literature-based occurrences, Darwin Core MaterialCitation) to develop the Fungal literature-based occurrence database for the southern West Siberia (FuSWS). The initiative on mobilisation of literature-based occurrence data started in the northern part of West Siberia in 2016. The present project extends the initiative to the southern regions and includes ten administrative territories (Tyumen Region, Sverdlovsk Region, Chelyabinsk Region, Omsk Region, Kurgan Region, Tomsk Region, Novosibirsk Region, Kemerovo Region, Altai Territory and Republic of Altai). The area occupies the central to southern part of the West Siberian Plain and extends for about 1.5 K km from the west to the east from the eastern slopes of the Ural Mountains to Yenisey River and from north to south-about 1.3 K km. The total area equals about 1.4 million km2.The initiative is actively growing in spatial, collaboration and data accumulation terms. The working group of about 30 mycologists from eight organisations dedicated to the data mobilisation was created as part of the Siberian Mycological Society (informal organisation since 2019). They have compiled the almost complete bibliographic list of mycology-related papers for the southern West Siberia, including over 900 publications for the last two centuries (the earliest dated 1800). All literature sources were digitised and an online library was created to integrate bibliography metadata and digitised papers using Zotero bibliography manager. The analysis of published sources showed that about two-thirds of works contain occurrences of fungi for the scope of mobilisation.At the time of the paper submission, the database had been populated with a total of about 8 K records from 93 sources. The dataset is uploaded to GBIF, where it is available for online search of species occurrences and/or download. The project's page with the introduction, templates, bibliography list, video-presentations and written instructions is available (in Russian) at the web site of the Siberian Mycological Society. The initiative will be continued in the following years to extract the records from all published sources. NEW INFORMATION: The paper presents the first project with the aim of literature-based occurrence data mobilisation of fungi and fungi-related organisms in the southern West Siberia. The full bibliography and a digital library of all regional mycological publications created for the first time includes about 900 published works. By the time of paper submission, nearly 8 K occurrence records were extracted from about 90 literature sources and integrated into the FuSWS database published in GBIF.

Fungal literature records database of the Northern West Siberia (Russia).

BACKGROUND: Mycological research in the Northern part of West Siberia has now become sufficient for review and digitisation as over 460 scientific works have been completed mainly since the beginning of the 20th century. The history of research in the region started from isolated studies at the beginning of the 20th century, but regular and systematic research started from the 1970s. Over the following decades, several dozens of researchers have worked in the area, but the reported occurrences were scattered amongst a broad variety of publications, mainly hardly available. The great need in digitisation and accumulation of fungal records reported in published literature in a standardised regional database has now become evident. The «Fungal records database of the Northern West Siberia¼ (FuNWS) was initiated in 2016 according to contemporary biodiversity data standards (Darwin Core), to be compatible and accessible by the broad research community. The database has been supplemented ever since by the collective effort of specialists working in the area. According to the database summary report, there are 3358 fungal and fungus-like species revealed in the Northern West Siberia at present. The richest in species number classes are Agaricomycetes (60%) and Lecanoromycetes (33%) with a total of 25 classes represented. The FuNWS database was uploaded to Global Biodiversity Information Facility (GBIF) (Ygra State University Biological Collection publisher) on 11 November 2017 (earlier titled «Fungal Records Database of Yugra, FReDY¼) to provide open access to the data and its reusability (Filippova et al. 2020). NEW INFORMATION: This publication summarises the results of the digitisation of literature-based occurrence records of fungi and fungus-like organisms initiated in the Northern part of West Siberia for the first time in the history of mycological research. The bibliography of regional mycological publications was created to include about 460 published works (Suppl. material 2). In total, about 140 literature sources were digitised and about 22000 occurrence records were integrated into the FuNWS database (Filippova et al. 2020).

Rapid Accumulation of Mutations in Growing Mycelia of a Hypervariable Fungus Schizophyllum commune.

The basidiomycete Schizophyllum commune has the highest level of genetic polymorphism known among living organisms. In a previous study, it was also found to have a moderately high per-generation mutation rate of 2×10-8, likely contributing to its high polymorphism. However, this rate has been measured only in an experiment on Petri dishes, and it is unclear how it translates to natural populations. Here, we used an experimental design that measures the rate of accumulation of de novo mutations in a linearly growing mycelium. We show that S. commune accumulates mutations at a rate of 1.24×10-7 substitutions per nucleotide per meter of growth, or ∼2.04×10-11 per nucleotide per cell division. In contrast to what has been observed in a number of species with extensive vegetative growth, this rate does not decline in the course of propagation of a mycelium. As a result, even a moderate per-cell-division mutation rate in S. commune can translate into a very high per-generation mutation rate when the number of cell divisions between consecutive meiosis is large.