Petr Baldrian

Petr Baldrian
The Czech Academy of Sciences | AVCR · Institue of Microbiology, Laboratory of Environmental Microbiology

PhD

About

390
Publications
106,498
Reads
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19,899
Citations
Introduction
Petr Baldrian currently works at the Institue of Microbiology, Laboratory of Environmental Microbiology, The Czech Academy of Sciences. Petr does research in Mycology, Microbiology and Ecology. The main research interest is the role of microorganisms in ecosystem functioning.
Additional affiliations
February 2017 - present
Charles University in Prague
Position
  • Professor (Associate)
January 2008 - present
Charles University in Prague
Position
  • External lecturer
Description
  • Lectures in Microbial Ecology, Geomicrobiology and Microbial Processes in the Environment
January 2007 - present
University of Helsinki
Education
September 1996 - October 2000
Charles University in Prague
Field of study
  • Microbiology
September 1991 - June 1996
Charles University in Prague
Field of study
  • Microbiology

Publications

Publications (390)
Article
Piper aduncum, a tree species native to the Neotropics, has been introduced to other tropical regions and successfully invades secondary forest in fallow land after small scale slash-and-burn agriculture in Papua New Guinea (PNG). However, the effect of P. aduncum invasion on soil chemical properties as well as soil biota remains poorly understood....
Article
Full-text available
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 on how deadwood properties such as chemical composition, decomposer abundance, community composition, and age...
Article
Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enric...
Article
Full-text available
The reduction of deadwood due to forest management threatens saproxylic diversity. Therefore, deadwood needs to be preserved and enriched. While the importance of deadwood tree identity is well investigated, the value of different object types and microclimate for diversity is insufficiently understood. Conservation-oriented forest management, ther...
Article
Bacteria play critical roles in soil ecosystems when decomposing structural components of biomass. However, the ability of individual bacterial taxa to utilize various biopolymers is understudied, hampering our understanding of the role of bacteria in the soil carbon cycle. Here, we in situ incubated in forest litter various biopolymers of plant an...
Preprint
An estimated 8.7 million eukaryotic species exist on our planet. However, recent tools for taxonomic classification of eukaryotes only dispose of 734 reference genomes. As most Eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recover Pro...
Preprint
An estimated 8.7 million eukaryotic species exist on our planet. However, recent tools for taxonomic classification of eukaryotes only dispose of 734 reference genomes. As most Eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recover Pro...
Article
Full-text available
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 an important input of nutrients into forest soils, is mainly driven by fungal communities that undergo continuou...
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
Full-text available
Many soil Actinobacteria are potent producers of extracellular enzymes decomposing lignocellulose. Four strains of Actinobacteria with a high potential to hydrolyse cellulose and hemicellulose were identified among environmental isolates. The strains were grown on raw lignocellulosic substrates (olive pomace, oat flakes, sawdust, and wheat straw) u...
Article
The mechanisms underlying microbial community dynamics and co‐occurrence patterns along ecological succession are crucial for understanding ecosystem recovery but remain largely unexplored. Here, we investigated community dynamics and taxa co‐occurrence patterns in bacterial and fungal communities across a well‐established chronosequence of post‐mi...
Article
Protists, in particular bacterivores, are essential players in the rhizosphere; thus, how their interactions with bacteria and fungi affect plant productivity and soil nutrient cycles warrants more attention. Using next-generation sequencing of the 18 S rRNA gene, we investigated the distribution of two major protistan phyla, Cercozoa and Endomyxa,...
Article
Full-text available
Yeasts are ubiquitous in temperate forests. While this broad habitat is well‐defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitat...
Article
Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resour...
Article
Full-text available
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
Fungi play a crucial role in dead wood decay, being the major decomposers of wood and affecting microbiota associated with dead wood. We sampled dead wood from five deciduous tree species over more than forty years of decay in a natural European floodplain forest with high tree species diversity. While the assembly of dead wood fungal communities s...
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
The diverse chemical, biological, and microbial properties of litter and organic matter (OM) in forest soil along an altitudinal gradient are potentially important for nutrient cycling. In the present study, we sought to evaluate soil chemical, biological, microbial, and enzymatic characteristics at four altitude levels (0, 500, 1,000, and 1,500 m)...
Article
Full-text available
The amount of carbon stored in deadwood is equivalent to about 8 per cent of the global forest carbon stocks1. The decomposition of deadwood is largely governed by climate2–5 with decomposer groups—such as microorganisms and insects—contributing to variations in the decomposition rates2,6,7. At the global scale, the contribution of insects to the d...
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
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
Full-text available
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 during decomposition. Here, we examined 18 genome-sequenced bacterial strains representing the dominant deadwood ta...
Article
Full-text available
Elucidating dynamics of soil microbial communities after disturbance is crucial for understanding ecosystem restoration and sustainability. However, despite the widespread practice of swidden agriculture in tropical forests, knowledge about microbial community succession in this system is limited. Here, amplicon sequencing was used to investigate e...
Article
Full-text available
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-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni i...
Article
Full-text available
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 environmental factors such as wood chemistry affect these successional patterns through their effects on dominant fung...
Preprint
Full-text available
Development of soil microbial communities along ecological succession is crucial for ecosystem functioning and maintenance. However, ecological processes mediating microbial community assembly and microbial co-occurrence patterns along ecological succession remain unclear. Here, we explored community phylogenetic structures, ecological processes dr...
Article
Full-text available
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and a...
Article
Ferns represent the basal group of vascular plants and are known to have fungal interactions with arbuscular mycorrhizal fungi, but diversity of endophytic fungi from ferns is rarely studied. Moreover, fungal diversity associated with ferns is likely underestimated as most studies have been performed based on a microscopic or culture-dependent appr...
Article
Full-text available
A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.
Article
Soil enzymatic activity was assessed in the Stelvio Pass area (Italian Central Alps) aiming to define the possible effects of climate change on microbial functioning. Two sites at two different elevations were chosen, a subalpine (2239 m) and an alpine belt (2604-2624 m), with mean annual air temperature differing by almost 3 °C, coherent with the...
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
Full-text available
Revealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a meta-analysis of 417 completely annotated extant and...
Article
Full-text available
Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence in...
Article
Despite several efforts to unravel the microbial diversity of soil, most microbes are still unknown. A re- cent large-scale effort based on genome-resolved metagenomics by Nayfach et al. has demonstrated how this approach can expand our understanding of novel bacterial lineages, including those from soils. Genomic catalogs of soil microbiomes are n...
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
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.
Article
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Belowground litter derived from tree roots has been shown as a principal source of soil organic matter in coniferous forests. Fate of tree root necromass depends on fungal communities developing on the decaying roots. Local environmental conditions which affect composition of tree root mycobiome may also influence fungal communities developing on d...
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
Full-text available
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
Full-text available
Fungi are recognized as efficient decomposers of biopolymers contained in soil or litter, but not all saprotrophic taxa are equally efficient in accessing various C sources. While many fungi may be considered generalists that are able to utilize complex biomass of plant, bacterial, and fungal origin, it is less clear which of the individual biopoly...
Article
Fungi are key mediators of ecosystem processes in temperate forests. Hence, understanding of fungal community development is central to better understand the mechanisms driving shifts in ecosystem processes during forest succession. We studied fungal communities in soil, rhizosphere and roots in a Central European forest chronosequence (1–137 years...
Conference Paper
Full-text available
Some microbes are important players in plant fitness, contributing to their nutrient acquisition and protection against diverse biotic and abiotic stresses [...]
Article
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An extensive screening of saprotrophic Basidiomycetes causing white rot (WR), brown rot (BR), or litter decomposition (LD) for the production of laccase and Mn-peroxidase (MnP) and decolorization of the synthetic dyes Orange G and Remazol Brilliant Blue R (RBBR) was performed. The study considered in total 150 strains belonging to 77 species. The a...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
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...
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
Full-text available
Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucor-omycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present...
Article
Full-text available
The objective of the present study was to evaluate how altitudinal gradients shape the composition of soil bacterial and fungal communities, humus forms and soil properties across six altitude levels in Hyrcanian forests. Soil microbiomes were characterized by sequencing amplicons of selected molecular markers. Soil chemistry and plant mycorrhizal...
Article
Termites are important plant biomass decomposers. Their digestive activity typically relies on pro-karyotes and protozoa present in their guts. In some cases, such as in fungus-growing termites, digestion also relies on ectosymbiosis with specific fungal taxa. To date, the mycobiome of termites has yet to be investigated in detail. We evaluated the...
Article
Full-text available
In temperate forests, climate seasonality restricts the photosynthetic activity of primary producers to the warm season from spring to autumn, while the cold season with temperatures below the freezing point represents a period of strongly reduced plant activity. Although soil microorganisms are active all-year-round, their expressions show seasona...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Cistus ladanifer scrublands are one of the most characteristic Mediterranean ecosystems. However, these pyr-ophytic scrublands, are severely affected by wildfires. To reduce this threat, fire prevention management practices are needed to protect these ecosystems. The aim of this study was to determine the effects of management treatments on bacteri...
Preprint
Full-text available
Unveiling the relationship between taxonomy and function in microbiomes is crucial to determine their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi was reported, this is not the case for archaea. Here, we used a meta-analysis of completely annotated extant gen...
Article
Full-text available
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...
Chapter
Recent molecular studies of the composition and diversity of fungal communities associated with decomposing plant litter are chiefly based on the amplification of gene markers from DNA via polymerase chain reaction (PCR) and subsequent sequencing. However, RNA provides a better view of the composition and function of active communities at a given p...
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...
Article
Full-text available
The evolutionary split between gymnosperms and angiosperms has far‐reaching implications for the current communities colonizing trees. The inherent characteristics of dead wood include its role as a spatially scattered habitat of plant tissue, transient in time. Thus, local assemblages in deadwood forming a food web in a necrobiome should be affect...
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...