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

The abstract presents the initiative to develop the Fungal Literature-based Occurrence Database for Southern West Siberia (FuSWS), which mobilizes occurrences of fungi from published literature (literature-based occurrences, Darwin Core MaterialCitation). The FuSWS database includes 28 fields describing species name, publication source, herbarium number (if exists), date of sampling or observation, locality information, vegetation, substrate, and others. The initiative on digitization of literature-based occurrence data started in the northern part of Western Siberia two years ago (Filippova et al. 2021a). The present project extends the initiative to the south and includes eight administrative regions (Sverdlovsk, Omsk, Kurgan, Tomsk, Novosibirsk, Kemerovo, Altay, and Gorny Altay). The area occupies the central to southern part of the West Siberian Plain. It extends for about 1.5 thousand 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 thousand km. The total area equals about 1.2 million km2.Currently, the project is actively growing in spatial, collaboration and data accumulation terms. The working group of about 30 mycologists from 16 organizations dedicated to the digitization initiative was created as part of the Siberian Mycological Society (informal organization since 2019). They have created the most complete bibliographic list of mycology-related papers for the Southern West Siberia, including over 800 publications for the last two centuries (the earliest dated 1800). At abstract submission, the database had been populated with a total of about 10K records from about 100 sources. The dataset is uploaded to GBIF, where it is available for online search of species occurrences and/or download (Filippova et al. 2021b) Fig. 1. The project's page with the introduction, templates, bibliography list, video-presentations and written instructions is available at the website of the Siberian Mycological Society (https://sibmyco.org/literaturedatabase).The following protocol describes the digitization workflow in detail:The bibliography of related publications is compiled using Zotero bibliographic manager. Only published works (peer-reviewed papers, conference proceedings, PhD theses, monographs or book chapters) are selected. If possible, the sources are digitized and added to the library as PDF files. The template of the FuSWS database is made with Google Sheets, which allows simultaneous use by several specialists, in a common data format provided. The simple Microsoft Excel template is also available for the offline databasing. The Darwin Core standard is applied to the database field structure to accommodate the relevant information extracted from the publications.From the available bibliography of publications related to the region, only works with species occurrences are selected for the databasing purpose. The main source of occurrences is annotated species lists with exact localities of the records. However, different sorts of other species citations are also extracted, provided that they had the connection to any geography. All occurrences are georeferenced, either from the coordinates provided in the paper, or from the verbatim description of the field work locality. The georeferencing of the verbatim descriptions is made using Yandex or Google map services. Depending on the quality of georeference provided in publications, the uncertainty is estimated as follows: 1) the coordinate of a fruiting structure or a plot provided in the publication gives the uncertainty about 3-30 meters; 2) the coordinate of the field work locality provided in publication gives the uncertainty about 500 m to 5 km; 3) the report of the species presence in a particular region gives the centroid of the area with the uncertainty radius to include its borders.The locality names reported in Russian are translated to English and written in the «locality» field. Russian descriptions are reserved in the field «verbatimLocality» for accuracy.When possible, the «eventDate» is extracted from the annotation data. Whenever this information is absent, the date of the publication is used instead with the remarks in the «verbatimEventDate» field.The ecological features, habitat and substrate preferences are written in the «habitat» field and reserved in Russian.The original scientific names reported in publications are filled in the «originalNameUsage» field. Correction of spelling errors is made using the GBIF Species Matching tool. This tool is also used to create the additional fields of taxonomic hierarchy from species to kingdom, to fill in the «taxonRank» field and to synonymize according to the GBIF Backbone Taxonomy.To track the digitization process, a worksheet is maintained. Each bibliographic record has a series of fields to describe the digitization process and its results: the total number of extracted occurrence records, general description of the occurrence quality, presence of the observation date, details of georeferencing and the name of a person responsible for the digitization

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

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 km . 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

Crowdsourcing Fungal Biodiversity : Revision of Inaturalist Observations in Northwestern Siberia

The paper presents the first analysis of crowdsourcing data of all observations of fungi (including lichens) and myxomycetes in Northwestern Siberia uploaded to iNaturalist.org to date (24.02.2022). The Introduction presents an analysis of fungal diversity crowdsourcing globally, in Russia, and in the region of interest. Materials and methods describe the protocol of uploading data to iNaturalist.org, the structure of the crowdsourcing community. initiative to revise the accumulated data. procedures of data analysis, and compilation of a dataset of revised crowdsourced data. The Results present the analysis of accumulated data by several parameters: temporal, geographical and taxonomical scope, observation and identification efforts, identifiability of various taxa, species novelty and Red Data Book categories and the protection status of registered observations. The Discussion provides data on usability of crowdsourcing data for biodiversity research and conservation of fungi, including pros and contras. The Electronic Supplements to the paper include an annotated checklist of observations of protected species with information on Red Data Book categories and the protection status, and an annotated checklist of regional records of new taxa. The paper is supplemented with a dataset of about 15 000 revised and annotated records available through Global Biodiversity Information Facility (GBIF). The tradition of crowdsourcing is rooted in mycological societies around the world, including Russia. In Northwestern Siberia, a regional mycological club was established in 2018, encouraging its members to contribute observations of fungi on iNaturalist.org. A total of about 15 000 observations of fungi and myxomycetes were uploaded so far, by about 200 observers, from three administrative regions (Yamalo-Nenetsky Autonomous Okrug, Khanty-Mansi Autonomous Okrug, and Tyumen Region). The geographical coverage of crowdsourcing observations remains low. However. the observation activity has increased in the last four years. The goal of this study consisted of a collaborative effort of professional mycologists invited to help with the identification of these observations and analysis of the accumulated data. As a result, all observations were reviewed by at least one expert. About half of all the observations have been identified reliably to the species level and received Research Grade status. Of those, 90 species (195 records) represented records of taxa new to their respective regions: 876 records of 53 species of protected species provide important data for conservation programmes. The other half of the observations consists of records still under-identified for various reasons: poor quality photographs, complex taxa (impossible to identify without microscopic or molecular study). or lack of experts in a particular taxonomic group. The Discussion section summarises the pros and cons of the use of crowdsourcing for the study and conservation of regional fungal diversity, and summarises the dispute on this subject among mycologists. Further research initiatives involving crowdsourcing data must focus on an increase in the quality of observations and strive to introduce the habit of collecting voucher specimens among the community of amateurs. The timely feedback from experts is also important to provide quality and the increase of personal involvement.Peer reviewe

Design and baseline characteristics of the finerenone in reducing cardiovascular mortality and morbidity in diabetic kidney disease trial

Background: Among people with diabetes, those with kidney disease have exceptionally high rates of cardiovascular (CV) morbidity and mortality and progression of their underlying kidney disease. Finerenone is a novel, nonsteroidal, selective mineralocorticoid receptor antagonist that has shown to reduce albuminuria in type 2 diabetes (T2D) patients with chronic kidney disease (CKD) while revealing only a low risk of hyperkalemia. However, the effect of finerenone on CV and renal outcomes has not yet been investigated in long-term trials. Patients and Methods: The Finerenone in Reducing CV Mortality and Morbidity in Diabetic Kidney Disease (FIGARO-DKD) trial aims to assess the efficacy and safety of finerenone compared to placebo at reducing clinically important CV and renal outcomes in T2D patients with CKD. FIGARO-DKD is a randomized, double-blind, placebo-controlled, parallel-group, event-driven trial running in 47 countries with an expected duration of approximately 6 years. FIGARO-DKD randomized 7,437 patients with an estimated glomerular filtration rate >= 25 mL/min/1.73 m(2) and albuminuria (urinary albumin-to-creatinine ratio >= 30 to <= 5,000 mg/g). The study has at least 90% power to detect a 20% reduction in the risk of the primary outcome (overall two-sided significance level alpha = 0.05), the composite of time to first occurrence of CV death, nonfatal myocardial infarction, nonfatal stroke, or hospitalization for heart failure. Conclusions: FIGARO-DKD will determine whether an optimally treated cohort of T2D patients with CKD at high risk of CV and renal events will experience cardiorenal benefits with the addition of finerenone to their treatment regimen. Trial Registration: EudraCT number: 2015-000950-39; ClinicalTrials.gov identifier: NCT02545049

Antiviral activity of fungi of the Novosibirsk Region: Pleurotus ostreatus and P. pulmonarius (Review)

The article reviews of antiviral properties of two species of fungi from the Novosibirsk Region of the genus Pleurotus. Fruit bodies and cultivated mycelium of Pleurotus ostreatus and P. pulmonarius are a promising source of extracts with polysaccharides, possessing antiviral and anti-cancer properties

Leccinum anastasiae V. Vlasenko 2023, sp. nov.

&lt;i&gt;Leccinum anastasiae&lt;/i&gt; V. Vlasenko, &lt;i&gt;sp. nov.&lt;/i&gt; Fig. 1. &lt;p&gt;MycoBank: MB 844740.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Type:&lt;/b&gt; &mdash; RUSSIA. The Republic of Altai, near Dzhazator (Belyashi) village, a habitat with solitary &lt;i&gt;Larix&lt;/i&gt; Mill. and &lt;i&gt;Salix&lt;/i&gt; L. trees on the border with a steppe meadow and a bog in the river&rsquo;s oxbow, on soil under &lt;i&gt;Salix bebbiana&lt;/i&gt; Sarg., 49.6914&deg; N, 87.4344&deg; E, 1569 m., 21 August 2019, &lt;i&gt;V.A. Vlasenko&lt;/i&gt; and &lt;i&gt;A.V. Vlasenko&lt;/i&gt; (holotype NSK 1014999).&lt;/p&gt; &lt;p&gt; &lt;b&gt;Etymology:&lt;/b&gt; &mdash;Named after mycologist Anastasia Vlasenko.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Description:&lt;/b&gt; &mdash;Basidiomata is medium-sized. Pileus is up to 4 cm in diam., convex, up to 1.4 cm thick, lacking a sterile margin; surface is dry, glabrous, rugulose, dark cream with a light marble pattern; context is thin, 1 mm thick, in the center of the pileus is up to 1 cm thick, white, and does not change color when bruised but may darken slightly; bright colors absent. Hymenophore is poroid; pores are angular, 0.3&ndash;0.6 mm in diam., concolorous, light cream, staining cinnamon brown if bruised and with age; tubes adnexed to deeply depressed around the stipe, up to 1.3 cm in length, tube walls are 0.05 mm thick, white-greyish-cream when young to pale cinnamon-brown with age. Stipe is 5 cm long, 0.6&ndash;1.0 cm broad, central, cylindrical, slightly curved, dense, fragile; surface dry, white, scabrous, scales are white at first, becoming pale to pale-cream, staining fuscous if bruised; context is white, light cream with age; basal mycelium is white. No distinctive odour. Basidiospores are 5.4&ndash;6.90 &times; 14.2&ndash;23.60 &mu;m, Q min = 2.62, Q max = 3.42, Qm = 2.96, spindle-shaped to elongate-ellipsoid, creamy brown with greenish-brown protoplast in KOH, smooth. Basidia are 6.5&ndash;11 &times; 20&ndash;28.5 &mu;m, clavate, thin-walled, 2&ndash;4-spored, hyaline in KOH; sterigmata are 4&ndash;5 &mu;m in length. Hymenophoral trama is boletoid, hyphae are subcylindrical, 3&ndash;7 &mu;m wide, and hyaline. Cheilo- and pleurocystidia are 7&ndash;12 &times; 18&ndash;30 &mu;m, spindle-shaped to fusiform, thin-walled, hyaline. Pileipellis is a trichoderm composed of filamentous hyphae 3.5&ndash;10 &mu;m wide, thin-walled, hyaline. Pileus trama is composed of hyphae 2.5&ndash;11 &mu;m wide, thin-walled, hyaline. Stipitipellis is composed of hyphae 2&ndash;8 &mu;m wide, thin-walled, hyaline. Caulocystidia are 9&ndash;10 &times; 18&ndash;28 &mu;m, spindle-shaped to fusiform, thin-walled, hyaline. Stipe trama is composed of hyphae 3&ndash;10 &mu;m wide, thin-walled, hyaline. Clamp connections are absent in all tissues.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Additional specimen examined:&lt;/b&gt; &mdash; RUSSIA. The Republic of Altai, near Dzhazator (Belyashi) village, the right bank of the Argut River, swampy habitat with &lt;i&gt;Salix&lt;/i&gt; L. trees by the river, on soil, 49.7244&deg; N, 87.3941&deg; E, 1601 m., 23 August 2019, &lt;i&gt;A. V&lt;/i&gt; &lt;i&gt;.&lt;/i&gt; &lt;i&gt;Vlasenko&lt;/i&gt; (paratype NSK 1014981).&lt;/p&gt; &lt;p&gt; &lt;b&gt;Habitat:&lt;/b&gt; &mdash;Scattered on the ground under &lt;i&gt;Salix bebbiana&lt;/i&gt; Sarg., near bogs in the river valleys between mountain ranges.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Distribution:&lt;/b&gt; &mdash;Southeast Altai (Kosh-Agach district of the Republic of Altai).&lt;/p&gt; &lt;p&gt; &lt;b&gt;GenBank accession numbers:&lt;/b&gt; ITS: ON524838, LSU: ON514264; &lt;i&gt;EF-1&alpha;&lt;/i&gt;: OR758905; &lt;i&gt;RPB2&lt;/i&gt;: OR758904.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Comments:&lt;/b&gt; &mdash;The new species &lt;i&gt;Leccinum anastasiae&lt;/i&gt; does not have orange and red tints in the cap color. Based on this, it is easy to differentiate it from other species of the genus, which have brightly colored fruiting bodies. The cap surface of &lt;i&gt;Leccinum anastasiae&lt;/i&gt; is creamy brown, and the surface of its pores becomes tobacco-like over time. It differs from the closely related species, &lt;i&gt;Leccinum schistophilum&lt;/i&gt; and &lt;i&gt;L&lt;/i&gt;. &lt;i&gt;snellii&lt;/i&gt; A.H. Sm., Thiers et Watling (1967: 120), by the absence of pink coloration in the upper and blue-green coloration in the lower part of the stipe when bruised.&lt;/p&gt; &lt;p&gt; The ITS1 nrDNA region in &lt;i&gt;Leccinum&lt;/i&gt; species contains many tandem repeats (Den Bakker &lt;i&gt;et al.&lt;/i&gt; 2004). The analysis of our aligned dataset showed the presence of 19 regions with &ldquo;TATTGAAAA&rdquo; repeats. The maximum number of such repeats in some sequences is up to 11 in &lt;i&gt;Leccinum holopus&lt;/i&gt;. In addition, there were 15 regions with &ldquo;CTAATAGAAA&rdquo; repeats, with a maximum number of repeats up to eight, also in &lt;i&gt;Leccinum holopus&lt;/i&gt;. The presence of such mini satellites negatively affects the phylogenetic reconstruction for the genus. Therefore, we performed a phylogenetic analysis of the ITS1-5.8S-ITS2 nrDNA region, excluding mini satellites from the sequences. Introns were also excluded from the sequences of all genes.&lt;/p&gt; &lt;p&gt; The ML analysis based on the ITS1-5.8S-ITS2 nrDNA region showed that the new species is closest to &lt;i&gt;Leccinum schistophilum&lt;/i&gt; (Fig. 2). The genetic distance of the &ldquo; &lt;i&gt;Leccinum anastasiae&lt;/i&gt; &rdquo; branch on the ITS tree is 0.022, with 97% bootstrap support.&lt;/p&gt; &lt;p&gt; In addition, the ML analysis based on the 28S+ &lt;i&gt;EF-1&alpha;&lt;/i&gt; + &lt;i&gt;RPB2&lt;/i&gt; DNA regions confirmed that the new species is closest to &lt;i&gt;Leccinum schistophilum&lt;/i&gt; (Fig. 3). The genetic distance of the &ldquo; &lt;i&gt;Leccinum anastasiae&lt;/i&gt; &rdquo; branch on the tree is 0.007, with 87% bootstrap support.&lt;/p&gt; &lt;p&gt; Despite some inconsistency in the topology of our ITS1-5.8S-ITS2 and 28S+ &lt;i&gt;EF-1&alpha;&lt;/i&gt; + &lt;i&gt;RPB2&lt;/i&gt; trees, the new species of &lt;i&gt;Leccinum anastasiae&lt;/i&gt; had the most similarity with &lt;i&gt;L&lt;/i&gt;. &lt;i&gt;schistophilum&lt;/i&gt;. Based on that, we performed a separate comparison of the sequences of these two species. It turned out studied sequences ITS1-5.8S-ITS2 and parts of the 28S, &lt;i&gt;EF-1&alpha;&lt;/i&gt; and &lt;i&gt;RPB2&lt;/i&gt; regions was quite variable, which allows us to declare the independence of these species.&lt;/p&gt; &lt;p&gt; Substrate and geographic factors are also crucial for species diagnostics. &lt;i&gt;Leccinum holopus&lt;/i&gt;, &lt;i&gt;L&lt;/i&gt;. &lt;i&gt;schistophilum&lt;/i&gt; and &lt;i&gt;L&lt;/i&gt;. &lt;i&gt;snellii&lt;/i&gt; growing on swamps form symbiotic associations with &lt;i&gt;Betula&lt;/i&gt; L. (1753: 982) spp. The new species &lt;i&gt;Leccinum anastasiae&lt;/i&gt; is associated with a unique symbiont, &lt;i&gt;Salix bebbiana&lt;/i&gt;.&lt;/p&gt;Published as part of &lt;i&gt;Vlasenko, Vyacheslav A., 2023, A new Leccinum species from the Altai Mountains, pp. 191-200 in Phytotaxa 625 (2)&lt;/i&gt; on pages 194-197, DOI: 10.11646/phytotaxa.625.2.5, &lt;a href="http://zenodo.org/record/10150942"&gt;http://zenodo.org/record/10150942&lt;/a&gt

A new Leccinum species from the Altai Mountains

Vlasenko, Vyacheslav A. (2023): A new Leccinum species from the Altai Mountains. Phytotaxa 625 (2): 191-200, DOI: 10.11646/phytotaxa.625.2.5, URL: https://phytotaxa.mapress.com/pt/article/download/phytotaxa.625.2.5/5127

Various methods for isolating DNA from fruiting bodies on the example of Pleurotus pulmonarius (higher basidiomycetes) of the Novosibirsk Region for barcoding of edible and medicinal mushrooms

We conducted experiments to increase the concentration of extracted DNA from the fruiting bodies of this species using various lysis buffers and extraction time. In general, DNA isolation according to the protocol using SDS made it possible to obtain higher concentrations thereof, as in the case of increasing the extraction time from 1 to 24 hours and using additional purification with chloroform

Distribution and niche of

We defined the regularities in spatial distribution of Macrolepiota excoriata based on the occurrence data, as well as bioclimatic characteristics in order to control species status in the natural environment. Points of presence occurring in the steppe of Central Altai Mountains have the most optimal conditions for M. excoriata in Asia

Morphological feature of

Based on morphological research methods, the morphological characteristics of a rare species of polyporoid fungi – Polyporus rhizophilus, adapted to live as a parasite of grasses in steppe communities of subarid and arid regions, were evaluated. Morphological structures of fruiting bodies of fungi are subject to variability, which may be due to the influence of environmental factors and the specifics of the substrate on which the fruiting bodies of fungi develop. The appearance of identical morphological features in different phylogenetic groups is adaptive convergent. In this regard, molecular genetic research is a necessary condition for distinguishing taxa and clarifying their phylogenetic relationships