Tomas Vetrovsky

Tomas Vetrovsky
The Czech Academy of Sciences | AVCR · Laboratory of Environmental Microbiology

PhD

About

82
Publications
22,726
Reads
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3,995
Citations
Citations since 2016
54 Research Items
3519 Citations
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20162017201820192020202120220200400600
20162017201820192020202120220200400600
20162017201820192020202120220200400600

Publications

Publications (82)
Article
As the European Alps are experiencing a strong climate warming; this study analyzed the soil microbiome at different altitudes and among different vegetation types at the Stelvio Pass (Italian Alps), aiming to i) characterize the composition and functional potential of the microbiome of soils and their gene expression during the peak vegetative sta...
Article
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Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe...
Article
Full-text available
Fungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the metaproteome of fungal communities is still scarce. Here, we conducted a field survey including data on fungal biomass (by phospholipid fatty acids, PLFA), community composition (b...
Article
Full-text available
Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms-fungi and bacteria-who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, th...
Article
Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (E...
Article
Fungi are a highly diverse group of soil organisms greatly contributing to the functioning of forest ecosystems. Consequently, the understanding of factors affecting their productivity and distribution is needed for the understanding of litter and soil ecology. While several drivers of fungal community composition have been identified, it is less c...
Article
High-throughput DNA sequencing has dramatically transformed several areas of biodiversity research including mycology. Despite limitations, high-throughput sequencing is nowadays a predominant method to characterize the alpha and beta diversity of fungal communities. Across the papers utilizing high-throughput sequencing approaches to study natural...
Article
Temperate coniferous forests sustain the highest levels of biomass of all terrestrial ecosystems and belong to the major carbon sinks on Earth. However, the community composition and its functional diversity depending on the habitat have yet to be unveiled. Here, we analyzed the proteomes from litter, plant roots, rhizosphere, and bulk soil in a te...
Article
Full-text available
Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO 2 emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the mic...
Article
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Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns, and little...
Article
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Species of the Trichophyton benhamiae complex are predominantly zoophilic pathogens with a worldwide distribution. These pathogens have recently become important due to their epidemic spread in pets and pet owners. Considerable genetic and phenotypic variability has been revealed in these emerging pathogens, but the species limits and host spectra...
Article
All termites have established a wide range of associations with symbiotic microbes in their guts. Some termite species are also associated with microbes that grow in their nests, but the prevalence of these associations remains largely unknown. Here, we studied the bacterial communities associated with the termites and galleries of three wood-feedi...
Article
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
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Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a br...
Article
Full-text available
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. the high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that driv...
Article
Alien plants represent a potential threat to environment and society. Understanding the process of alien plants naturalization is therefore of primary importance. In alien plants, successful establishment can be constrained by the absence of suitable fungal partners. Here, we used 42 independent datasets of ectomycorrhizal fungal (EcMF) communities...
Article
Forest soils represent important terrestrial carbon (C) pools, where C is primarily fixed in plant biomass and then is incorporated in the biomass of fungi and bacteria. Although classical concepts assume that fungi are the main decomposers of the recalcitrant organic matter within plant and microbial biomass, whereas bacteria are considered to mos...
Preprint
Full-text available
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultural and wild plants and pathogenicity. The high importance of fungi in the ecosystem processes contrasts with the incompleteness of understanding of the patterns of fungal biogeography and the environmental factors that drive...
Article
Ectomycorrhizal fungi (EcMF) are the key symbionts of numerous woody plants in many ecosystems worldwide (Smith & Read, 2008; Tedersoo, 2017). They positively affect host plant nutrient uptake (Smith & Read, 2008) and take part in essential ecosystem processes such as carbon sequestration, nutrient cycling and decomposition of organic matter (Read...
Article
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The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with diffe...
Article
Bacteria belong to the key players in the carbon cycling in forest soils and thus affect the global C balance. Our understanding of bacterial contribution to ecosystem processes relies on the analysis of whole communities. Here we combined strain isolation, genome sequencing and metatranscriptomics to analyse the activity of individual bacterial sp...
Article
Full-text available
Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the pre...
Article
Factors shaping community structure of soil microbiota have been intensively studied; however, the pattern in community composition and structure of soil microbiota at large geographical scales and factors regulating its metabolic activity remains poorly understood. Here, we used a field transplantation experiments to investigate the effects of sub...
Article
Full-text available
Zoophilic dermatophytes are the most important agents of the superficial mycoses in domestic and farm animals, and are often transmitted to humans. This group includes approximately ten specialized parasitic fungi belonging to the genera Trichophyton and Microsporum. While infections in animals have often mild symptoms or are asymptomatic, human in...
Article
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Aims Study of the microbial expression profile in the rhizosphere of two contrasting maize lines, differing in the Nitrogen Use efficiency (NUE). Methods The Lo5 and T250 inbred maize characterized by high and low NUE, respectively, were grown in rhizoboxes allowing precise sampling of rhizosphere and bulk soils. We conducted metatranscriptomic of...
Article
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Background: The impacts of man-made chemicals, in particular of persistent organic pollutants, are multifactorial as they may affect the integrity of ecosystems, alter biodiversity and have undesirable effects on many organisms. We have previously demonstrated that the belowground mycobiota of forest soils acts as a buffer against the biocide pollu...
Article
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Two long-term contaminated soils differing in contents of Pb, Zn, As, Cd were compared in a microcosm experiment for changes in microbial community structure and respiration after various treatments. We observed that the extent of long-term contamination (over 200 years) by toxic elements did not change the total numbers and diversity of bacteria b...
Article
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The concept of operational taxonomic units (OTUs), which constructs “mathematically” defined taxa, is widely accepted and applied to describe bacterial communities using amplicon sequencing of 16S rRNA gene. OTUs are often used to infer functional traits since they are considered to fairly represent of community members. However, the link between m...
Data
Neighbor-joining phylogenetic tree based on concatenated partial gyrB, rpoB, rpoD and gene sequences of strain P. bohemica IA19T and closely related species of the genus Pseudomonas. Bootstrap values (expressed as percentages of 1,000 replications) are shown at the branching points. Scale bar = 2 nucleotides (nt) substitutions per 100 nt. Accession...
Data
Neighbor-joining phylogenetic tree based on nearly complete (1,400 bp) 16S rRNA gene sequences of all Pseudomonas species closely related to P. bohemica IA19T and the species Acinetobacter baumannii DSM30007 T, which was included as an outgroup. Bootstrap values (expressed as percentages of 1,000 replications) are shown at the branching points. Sca...
Article
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Antimicrobial resistance is a worldwide problem that threatens the effectiveness of treatments for microbial infection. Consequently, it is essential to study unexplored niches that can serve for the isolation of new microbial strains able to produce antimicrobial compounds to develop new drugs. Bark beetles live in phloem of host trees and establi...
Article
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Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this...
Article
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Background Evergreen coniferous forests contain high stocks of organic matter. Significant carbon transformations occur in litter and soil of these ecosystems, making them important for the global carbon cycle. Due to seasonal allocation of photosynthates to roots, carbon availability changes seasonally in the topsoil. The aim of this paper was to...
Poster
Agricultural, forestry, industrial and urban lignocellulosic wastes are promising sustainable resources. In recent years, increasing attention has been devoted to the production of bioethanol from low cost lignocellulose contained in agri-food residues. Although Fungi are known to be the main producers degraders of lignocellulose, Actinobacteria we...
Article
Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning - that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered...
Article
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Identification of bacteria that produce carbohydrolytic enzymes is extremely important given the increased demand for these enzymes in many industries. Twenty lignocellulose-degrading bacterial isolates from Algerian compost and different soils were screened for their potential to produce different enzymes involved in biomass deconstruction. Based...
Article
Cellulose is the most abundant polysaccharide in the dead plant biomass, and its degradation is an important part of global carbon cycle. b-Glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. Genetic potential and expression of b-glucosidase genes were studied in the topsoil of a Picea abies forest in t...
Article
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Fungi represent a group of soil microorganisms fulfilling important ecological functions. Although several studies have shown that yeasts represent a significant proportion of fungal communities, our current knowledge is based mainly on cultivation experiments. In this study, we used amplicon sequencing of environmental DNA to describe the composit...
Article
Heterogeneity within forest topsoils including litter has been described at different scales, but rarely at the small scale. Here we asked whether the spatial heterogeneity of enzymatic activity can be linked to fungal community composition at the scale of a single Quercus petraea leaf. The activity of cellobiohydrolase (exocellulase) was measured...
Article
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Background: The search for new enzymes and microbial strains to degrade plant biomass is one of the most important strategies for improving the conversion processes in the production of environment-friendly chemicals and biofuels. In this study, we report a new Paenibacillus isolate, O199, which showed the highest efficiency for cellulose deconstru...
Article
Full-text available
Coniferous forest soils have an indispensable ecological role in the global cycles of nutrients on Earth. Despite the fact that microbial communities in this ecosystem were subject of multiple studies, the involvement of individual taxa in the processes of organic matter transformation and the functional roles of dominant and active bacteria are la...
Chapter
Stable isotope probing (SIP) provides the opportunity to label decomposer microorganisms that build their biomass on a specific substrate. In combination with high-throughput sequencing, SIP allows for the identification of fungal community members involved in a particular decomposition process. Further information can be gained through gene-target...
Poster
Identification of bacteria for the production of carbohydrolytic enzymes is extremely important given the increased demand for these enzymes in many industries. ln recent years, increasing attention has been devoted to lignocellulose decomposing enzymes involved in many biotechnological processes that includes bioethanol production, pulp, paper ind...
Article
Several previous studies indicated that Actinobacteria may be enriched in soils with elevated content of heavy metals. In this study, we have developed a method for the in-depth analysis of actinobacterial communities in soil through phylum-targeted high-throughput sequencing and used it to address this question and examine the community compositio...
Article
Although the commonly used internal transcribed spacer region of rDNA (ITS) is well suited for taxonomic identification of fungi, the information on the relative abundance of taxa and diversity is negatively affected by the multicopy nature of rDNA and the existence of ITS paralogues. Moreover, due to high variability, ITS sequences cannot be used...
Article
Understanding the ecology of coniferous forests is very important because these environments represent globally largest carbon sinks. Metatranscriptomics, microbial community, and enzyme analyses were combined to describe the detailed role of microbial taxa in the functioning of the Picea abies-dominated coniferous forest soil in two contrasting se...
Article
Full-text available
The unresolved ecophysiological significance of Dark Septate Endophytes (DSE) may be in part due to existence of morphologically indistinguishable cryptic species in the most common Phialocephala fortinii s. l.-Acephala applanata species complex (PAC). We inoculated three middle European forest plants (European blueberry, Norway spruce and silver b...
Article
Full-text available
The aim of the study was to evaluate the spectrum of causative agents of the main clinical forms of dermatophytoses in the Czech Republic by molecular genetic methods (MGM). During two years (from July 2011 to June 2013), 3255 cultivation specimens were positive for dermatophytes. The highest number of specimens was isolated from tinea unguinum (55...
Article
Full-text available
Taxonomy of dermatophytes has changed significantly in the past and it has never been stable. Last extensive changes appeared after revision of the group by molecular genetic methods. This paper introduces the advances in taxonomy of dermatophytes and helps to unify the species names in use among the Czech laboratories to simplify their communicati...
Article
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While it is known that several Actinobacteria produce enzymes that decompose polysaccharides or phenolic compounds in dead plant biomass, the occurrence of these traits in the environment remains largely unclear. The aim of this work was to screen isolated actinobacterial strains to explore their ability to produce extracellular enzymes that partic...
Article
Full-text available
Molecular Epidemiology of Dermatophytoses in the Czech Republic – Two-Year-Study Results The aim of the study was to evaluate the spectrum of causative agents of the main clinical forms of dermatophytoses in the Czech Republic by molecular genetic methods (MGM). During two years (from July 2011 to June 2013), 3255 cultivation specimens were positiv...
Article
Fungi are important in soils as both decomposers and plant symbionts, and an understanding of the composition of their complex communities is thus indispensable to answer a variety of ecological questions. 454 Pyrosequencing is currently the method of choice for the in-depth analysis of fungal communities. However, the interpretation of its results...
Article
Full-text available
16S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. Here we use the information from sequenced bacter...
Data
Full-text available
Neighbor-joining tree of 16S rRNA sequences from bacterial genomes where the pairwise similarity of at least one 16S rRNA pair within a genome was lower than 97%. (PDF)
Data
Top ten most abundant bacterial OTUs in Picea abies forest soil according to the 16S rRNA amplicon sequence copy numbers and estimated genome counts. (XLS)
Data
Full-text available
Distribution of 16S rRNA copy numbers in bacterial genomes belonging to selected phyla (classes). The numbers in parentheses indicate numbers of genomes in the respective groups. (PDF)
Data
Overview of bacterial genome sequences used in this study. (XLS)
Data
Fasta file containing all identified 16S rRNA sequences from bacterial genomes used in this study. (FAS)
Data
Fasta file containing aligned 16S rRNA sequences from bacterial genomes used in this study. (FAS)
Article
The contents of fungal biomass markers were analysed in the fruit bodies of dominant basidiomycetes from an ectomycorrhiza-dominated coniferous forest, and used to estimate the fungal biomass content in the litter and soil. The content of ergosterol (3.8 ± 2.0 mg g−1 dry fungal biomass) and the phospholipid fatty acid 18:2ω6,9 (11.6 ± 4.3 mg g−1) s...
Article
Full-text available
Production of the lignocellulose-degrading enzymes endo-1,4-β-glucanase, 1,4-β-glucosidase, cellobiohydrolase, endo-1,4-β-xylanase, 1,4-β-xylosidase, Mn peroxidase, and laccase was characterized in a common wood-rotting fungus Fomes fomentarius, a species able to efficiently decompose dead wood, and compared to the production in eight other fungal...
Article
Full-text available
Although the commonly used internal transcribed spacer region of rDNA (ITS) is well suited for taxonomic identification of fungi, the information on the relative abundance of taxa and diversity is negatively affected by the multi-copy nature of rDNA and the existence of ITS paralogues. Moreover, due to high variability, ITS sequences cannot be used...
Article
Full-text available
Natural environments often show high levels of spatial heterogeneity. With a methodology based on the immobilization of fluorescent substrates, the distribution of extracellular enzymes can be studied at a 2.3-mm resolution with a detection limit of 1.8 nmol · h−1 · cm−2. The method is applicable to environmental samples such as wood, litter, soil,...
Article
Full-text available
Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil...
Article
Full-text available
Saprotrophic wood-inhabiting basidiomycetes are the most important decomposers of lignin and cellulose in dead wood and as such they attracted considerable attention. The aims of this work were to quantify the activity and spatial distribution of extracellular enzymes in coarse wood colonised by the white-rot basidiomycete Fomes fomentarius and in...