Vladimir S. Mikryukov

University of Tartu · Institute of Ecology and Earth Sciences

Arbuscular mycorrhizal (AM) fungi - Glomeromycota and Endogonomycetes - comprise multiple species and higher-level taxa that have remained undescribed. We propose a mixed morphology- and DNA-based classification framework to promote taxonomic communication and shed light into the phylogenetic structure of these ecologically essential fungi. Based o...

Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database E...

Background Understanding biodiversity patterns is a central topic in biogeography and ecology, and it is essential for conservation planning and policy development. Diversity estimates that consider the evolutionary relationships among species, such as phylogenetic diversity and phylogenetic endemicity indices, provide valuable insights into the fu...

Phylogenetic diversity (PD) represents a fundamental measure of biodiversity, encapsulating the extent of evolutionary history within species groups. This measure, pivotal for understanding biodiversity's full dimension, has gained recognition by major environmental and scientific organisations, including the Intergovernmental Science-Policy Platfo...

In recent decades, the rapid climate warming in polar and alpine regions has been accompanied by an expansion of shrub vegetation. However, little is known about how changes in shrub distribution will change as the distribution of tree species and snow cover changes as temperatures rise. In this work, we analyzed the main environmental factors infl...

Partner specificity is a well‐documented phenomenon in biotic interactions, yet the factors that determine specificity in plant‐fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations...

To help solve the actual problem of global climate warming, it is important to comprehensively study soil organic carbon (SOC), soil fungi, and other parameters at different depths in the soil. This study was aimed at investigating the chemical and microbiological parameters and their interactions at various soil depths (0–5 to 195–200 cm) in an Ar...

UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digit...

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different lev...

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different lev...

Studies of plant–microbe interactions, including mutualistic, antagonistic, parasitic, or commensal microbes, have greatly benefited our understanding of ecosystem functioning. New molecular identification tools have increasingly revealed the association patterns between microorganisms and plants. Here, we integrated long-read PacBio single-molecul...

What grows where? Knowledge about where to find particular species in nature must have been key to the survival of humans throughout our evolution. Over time, and as people colonised new land masses and habitats, interactions with the local biota led to a wealth of combined traditional and scientific wisdom about the distributions of species and th...

Fungi comprise approximately 20% of all eukaryotic species and are connected to virtually all life forms on Earth. Yet, their diversity remains contentious, their distribution elusive, and their conservation neglected. We aim to flip this situation by synthesizing current knowledge. We present a revised estimate of 2–3 million fungal species with a...

Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers h...

Factors driving microbial community composition and diversity are well established but the relationship with microbial functioning is poorly understood, especially at large scales. We analysed microbial biodiversity metrics and distribution of potential functional groups along a gradient of increasing land-use perturbation, detecting over 79,000 ba...

Nitrogen (N) deposition and soil acidification are environmental challenges affecting ecosystem functioning, health, and biodiversity, but their effects on functional genes are poorly understood. Here, we utilized metabarcoding and metagenomics to investigate the responses of soil functional genes to N deposition along a natural soil pH gradient. S...

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present stud...

Partner specificity is a well-known phenomenon in biotic interactions, but little is known about biotic and abiotic factors that determine specificity in plant-fungal associations. Using PacBio sequencing of soils from monospecific and mixed forest stands, we determined the predictors driving partner specificity in both ectomycorrhizal plants and f...

Fungal metabarcoding of substrates such as soil, wood, and water are uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside of the ambit of the International Code of Nomenclature for algae, fungi, and plants. The present...

Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers h...

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here we used high‐resolution sequencing to assess endemicity patterns, global change vulnerability and conservation priority areas...

Molecular methods are increasingly used to identify species that lack conspicuous macro‐ or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long‐read high throughput sequencing (HTS) as opposed to the traditionally used...

The development of high‐throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview of current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational ana...

Fungi play pivotal roles in ecosystem functioning, but little is known about their global patterns of diversity, endemicity, vulnerability to global change drivers and conservation priority areas. We applied the high-resolution PacBio sequencing technique to identify fungi based on a long DNA marker that revealed a high proportion of hitherto unkno...

Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The datase...

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview about current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational...

Coarse woody debris (CWD) provides food and shelter to a large proportion of forest biota and is considered vital for biodiversity during periods of harsh weather. However, its importance in long-term stressed ecosystems remains largely unknown. In this work, we explored the contribution of CWD to fungal diversity along the gradient of boreal fores...

With the developments in DNA nanoball sequencing technologies and the emergence of new platforms, there is an increasing interest in their performance in comparison with the widely used sequencing-by-synthesis methods. Here, we test the consistency of metabarcoding results from DNBSEQ-G400RS (DNA nanoball sequencing platform by MGI-Tech) and NovaSe...

Owing to the high resolving power and efficiency of DNA sequencing, researchers have discovered the extremely high diversity of bacterial, fungal, protist, and microinvertebrate communities in the soil, wood, phyllosphere, and other natural media. Studies on the properties of these communities require powerful tools for analyzing multicomponent sys...

There were errors in the name of author László G. Nagy and in affiliation no. 31 in the original publication. The original article has been corrected.

The cryptic lifestyle of most fungi necessitates molecular identiication of the guild in environmental studies. Over the past decades, rapid development and afordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about f...

Soil microbiome has a pivotal role in ecosystem functioning, yet little is known about its build-up from local to regional scales. In a multi-year regional-scale survey involving 1251 plots and long-read third-generation sequencing, we found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional gr...

We evaluate the applicability of the microsatellite multiplex assay of 11 short tandem repeat loci for individual identification of sable and pine marten, taxonomic identification of Martes species, and assessment of inter-population separation of sable populations isolated by distance. Based on the screening, we detected 50 and 80–82 alleles in pi...

Territories around industrial enterprises represent gradients of soil acidity and heavy metal excess. Exploration of soil fungal communities in pollution gradients serves the remediation interests and brings fundamental knowledge about biota response to environmental changes. In this work, using industrial pollution as a model of environmental filt...

Boreal forests store a large portion of the planet’s terrestrial carbon. A significant portion of this carbon is stored in coarse woody debris (CWD). Industrial pollution greatly inhibits organic matter decomposition and thus enhances carbon sequestration in the soil. However, little is known about the decomposition of CWD in polluted areas. In thi...

The vertical partitioning of fungi in forest soils regulates nutrient cycling. Chemical stress inhibits the organic matter turnover, and the role of fungal niche partitioning in this phenomenon needs exploration. Using next-generation sequencing, we studied fungal communities in organic and mineral soil horizons in control (unpolluted) and industri...

The effects of industrial pollution on bird diversity have been widely studied using traditional diversity measures, which assume all species to be equivalent. We compared species richness and Shannon index with distance-based measures of taxonomic, functional, and phylogenetic diversity (the abundance-weighted mean nearest taxon distances), which...

This study examines the diversity and community structure of Acidobacteria, Actinobacteria, Eumycota, and Glomeromycota, as well as the microbial catabolic profile of spruce-fir and birch forest litter from control and industrially contaminated sites in the Middle and Southern Urals. Rare and dominant operational taxonomic units’ (OTU) role in cont...

We studied nine populations of a meadow mixed-mating plant Lychnis flos-cuculi growing in a gradient of copper smelter emissions. We hypothesize that metal tolerant populations in the polluted areas have experienced a loss of genetic variation and are more selfing than the populations from the unpolluted areas. One hundred and thirty-five parental...

A comparative analysis has been performed on the informativity of characteristics of the state of lichen cover calculated by two methods for evaluating lichen abundance (frequency and projective cover). A close correlation of the indices obtained by the two different methods was shown, as well as their significant association with the degree of str...

Background and Aims: Interspecific differences have been clearly shown in the contribution of endogenous spatial autocorrelation (caused by dispersal) to the spatial structure of undisturbed vegetation. However, this phenomenon has not been studied in industrially polluted areas, where heavy metals’ excess is traditionally considered to be the main...

The diversity and spatial structure of soil fungi (SF) and arbuscular mycorrhizal fungi (AMF) communities in the southern taiga forest litter were studied in sites with two contrasting contamination levels with copper smelter emissions. The operational taxonomic unit richness and evenness in the communities of both target groups decreased under con...

Studying the influence of reduced biological diversity on functioning and stability of ecosystems is one of the priorities of modern ecology. Numerous approaches to quantitative estimation of diversity have been developed, which even used to be a hindrance to the progress of ecology for some time. Recently, however, researchers succeeded in present...

The response to copper pollution was studied in the vegetative progeny of tufted hair grass (Deschampsia caespitosa (L.) Beauv.) and ragged robin (Lychnis flos-cuculi L.) plants growing together in chronically polluted areas around the Middle Ural Copper Smelter or in background areas. The root elongation test was used, with copper sulfate (0.006–0...

Проведен анализ изменчивости генетически закрепленных морфологических параметров листьев Lychnis flos-cuculi L. в градиенте влияния промышленных выбросов. Обнаружена как дифференциация близко расположенных популяций (удаленных на 2,5 км друг от друга) в зонах со сравнимыми уровнями загрязнения, так и сходство растений из удаленных на 30 км и контра...

n lichen symbiosis, fungal and algal partners form close associations, often codi- spersed by vegetative propagules. Due to the particular interdependence, processes such as colonization, dispersal or genetic drift are expected to result in congruent patterns of genetic structure in the symbionts. To study the population structure of an obligate sy...

The capacity of species for expansion and colonization of new habitats is a key condition for the maintenance of their populations. In this study, specific features of the reproductive potential have been analyzed in Lobaria pulmonaria populations growing under contrasting climatic conditions. Certain ecological determinants governing the developme...