Vojtěch Tláskal
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View article: Transcriptome-guided discovery of novel plant-associated genes in a rhizosphere Pseudomonas
Transcriptome-guided discovery of novel plant-associated genes in a rhizosphere Pseudomonas Open
This study provides new insights into the genetic basis of bacterial adaptation to the plant root environment. By integrating transcriptomic and comparative genomic analyses, we identified numerous genes upregulated during root colonizatio…
View article: Fragile foundations: succession patterns of bacterial communities in fine woody debris and soil under long-term microclimate influence
Fragile foundations: succession patterns of bacterial communities in fine woody debris and soil under long-term microclimate influence Open
Background Fine woody debris (FWD; deadwood < 10 cm diameter) is a crucial but often overlooked component of forest ecosystems. It provides habitat for microbial communities and enhances soil fertility through nutrient cycling. This role i…
View article: Short- and mid-term temporal variability of the human urinary microbiota: a prospective observational cohort study
Short- and mid-term temporal variability of the human urinary microbiota: a prospective observational cohort study Open
Background Understanding the temporal variability of the microbiome is critical for translating associations of the microbiome with health and disease into clinical practice. The aim of this study is to assess the extent of temporal variab…
View article: Fragile foundations: Succession patterns of bacterial communities in fine woody debris and soil under long-term microclimate influence
Fragile foundations: Succession patterns of bacterial communities in fine woody debris and soil under long-term microclimate influence Open
Background Fine woody debris (FWD) is a crucial yet often overlooked component of forest ecosystems, providing a dynamic habitat for microbial communities and playing a key role in carbon and nutrient cycling. In managed forests with low d…
View article: Disentangling drivers behind fungal diversity gradients along altitude and latitude
Disentangling drivers behind fungal diversity gradients along altitude and latitude Open
Summary Gradients in species diversity across elevations and latitudes have fascinated biologists for decades. While these gradients have been well documented for macroorganisms, there is limited consensus about their universality, shape a…
View article: Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes
Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes Open
View article: Regulators of aerobic and anaerobic methane oxidation in two pristine temperate peatland types
Regulators of aerobic and anaerobic methane oxidation in two pristine temperate peatland types Open
Despite covering <5% of Earth's terrestrial area, peatlands are crucial for global carbon storage and are hot spots of methane cycling. This study examined the dynamics of aerobic and anaerobic methane oxidation in two undisturbed peatl…
View article: Short- and mid-term temporal variability of the human urinary microbiota: an observational cohort study
Short- and mid-term temporal variability of the human urinary microbiota: an observational cohort study Open
Understanding the temporal variability of the microbiome is critical for translating associations of the microbiome with health and disease into clinical practice. The aim of this study is to assess the extent of temporal variability of th…
View article: Pacbio HiFi sequencing sheds light on key bacteria contributing to deadwood decomposition processes
Pacbio HiFi sequencing sheds light on key bacteria contributing to deadwood decomposition processes Open
Background In forest ecosystems, biological decomposition of deadwood components plays a pivotal role in nutrient cycling and in carbon storage by enriching soils with organic matter. However, deciphering the functional features of deadwoo…
View article: Decomposition of <i>Fomes fomentarius</i> fruiting bodies – transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda
Decomposition of <i>Fomes fomentarius</i> fruiting bodies – transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda Open
Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant …
View article: Biosynthetic gene clusters from deadwood-inhabiting microorganisms (short-read shotgun metagenome)
Biosynthetic gene clusters from deadwood-inhabiting microorganisms (short-read shotgun metagenome) Open
Biosynthetic gene clusters identified in shotgun metagenome from Fagus sylvatica deadwood. The deadwood microbiome was shotgun sequenced with Illumina HiSeq and assembled with Megahit. Biosynthetic gene clusters were predicted with antiSMA…
View article: Biosynthetic gene clusters from deadwood-inhabiting microorganisms (short-read shotgun metagenome)
Biosynthetic gene clusters from deadwood-inhabiting microorganisms (short-read shotgun metagenome) Open
Biosynthetic gene clusters identified in shotgun metagenome from Fagus sylvatica deadwood. The deadwood microbiome was shotgun sequenced with Illumina HiSeq and assembled with Megahit. Biosynthetic gene clusters were predicted with antiSMA…
View article: Leveraging genome-scale metabolic models to understand aerobic methanotrophs
Leveraging genome-scale metabolic models to understand aerobic methanotrophs Open
Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteo…
View article: Data for Decomposing Fomes fomentarius fruiting bodies, unlike fresh ones, represent a bacteria-rich habitat primarily driven by Arthropoda
Data for Decomposing Fomes fomentarius fruiting bodies, unlike fresh ones, represent a bacteria-rich habitat primarily driven by Arthropoda Open
These files represent the data files necessary to run the R script analysis for the paper "Decomposing Fomes fomentarius fruiting bodies, unlike fresh ones, represent a bacteria-rich habitat primarily driven by Arthropoda." A link to the p…
View article: Data for Decomposing Fomes fomentarius fruiting bodies, unlike fresh ones, represent a bacteria-rich habitat primarily driven by Arthropoda
Data for Decomposing Fomes fomentarius fruiting bodies, unlike fresh ones, represent a bacteria-rich habitat primarily driven by Arthropoda Open
These files represent the data files necessary to run the R script analysis for the paper "Decomposing Fomes fomentarius fruiting bodies, unlike fresh ones, represent a bacteria-rich habitat primarily driven by Arthropoda." A link to the p…
View article: Revealing new bacterial functions in the plant rhizoplane
Revealing new bacterial functions in the plant rhizoplane Open
Background Microorganisms play important ecological roles during interactions with plants. Although some microorganisms promote plant performance and are applied as biofertilizers, the molecular cross-talk of bacteria and plants is not ful…
View article: Information regarding the particulate methane monooxygenase enzyme of known methanotrophs
Information regarding the particulate methane monooxygenase enzyme of known methanotrophs Open
A collection of information with regard to the particulate methane monooxygenase (pmmo) enzyme of known methanotrophs which was extracted from NCBI is published in this database.
View article: Information regarding the particulate methane monooxygenase enzyme of known methanotrophs
Information regarding the particulate methane monooxygenase enzyme of known methanotrophs Open
A collection of information with regard to the particulate methane monooxygenase (pmmo) enzyme of known methanotrophs which was extracted from NCBI is published in this database.
View article: Bacterial, but not fungal, communities show spatial heterogeneity in European beech (<i>Fagus sylvatica L</i>.) deadwood
Bacterial, but not fungal, communities show spatial heterogeneity in European beech (<i>Fagus sylvatica L</i>.) deadwood Open
Deadwood decomposition and other environmental processes mediated by microbial communities are generally studied with composite sampling strategies, where deadwood is collected from multiple locations in a large volume, that produce an ave…
View article: Global Distribution of Carbohydrate Utilization Potential in the Prokaryotic Tree of Life
Global Distribution of Carbohydrate Utilization Potential in the Prokaryotic Tree of Life Open
This study expanded our knowledge of the phylogenetic distribution of carbohydrate-active enzymes across prokaryotic tree of life, including new phyla where the carbohydrate-active enzymes composition have not been described until now and …
View article: Factors Controlling Dead Wood Decomposition in an Old-Growth Temperate Forest in Central Europe
Factors Controlling Dead Wood Decomposition in an Old-Growth Temperate Forest in Central Europe Open
Dead wood represents an important pool of carbon and nitrogen in forest ecosystems. This source of soil organic matter has diverse ecosystem functions that include, among others, carbon and nitrogen cycling. However, information is limited…
View article: Bladder Microbiota Are Associated with Clinical Conditions That Extend beyond the Urinary Tract
Bladder Microbiota Are Associated with Clinical Conditions That Extend beyond the Urinary Tract Open
Background. Since the discovery of the human urinary microbiota (UM), alterations in microbial community composition have been associated with various genitourinary conditions. The aim of this exploratory study was to examine possible asso…
View article: Fungal Community Development in Decomposing Fine Deadwood Is Largely Affected by Microclimate
Fungal Community Development in Decomposing Fine Deadwood Is Largely Affected by Microclimate Open
Fine woody debris (FWD) represents the majority of the deadwood stock in managed forests and serves as an important biodiversity hotspot and refuge for many organisms, including deadwood fungi. Wood decomposition in forests, representing a…
View article: Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood
Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood Open
View article: Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition
Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition Open
Deadwood decomposition is responsible for a significant amount of carbon (C) turnover in natural forests. While fresh deadwood contains mainly plant compounds and is extremely low in nitrogen (N), fungal biomass and N content increase duri…
View article: Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood
Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood Open
The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-liv…
View article: Successional Development of Fungal Communities Associated with Decomposing Deadwood in a Natural Mixed Temperate Forest
Successional Development of Fungal Communities Associated with Decomposing Deadwood in a Natural Mixed Temperate Forest Open
Deadwood represents an important carbon stock and contributes to climate change mitigation. Wood decomposition is mainly driven by fungal communities. Their composition is known to change during decomposition, but it is unclear how environ…
View article: Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition
Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition Open
Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of reca…
View article: Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood
Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood Open
Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the …
View article: 16S rRNA sequences from deadwood studies
16S rRNA sequences from deadwood studies Open
16S rRNA representative sequence of bacterial genus Sodalis extracted from deadwood amplicon studies. Selected as most abundant sequence within OTUs at 97% similarity threshold.