Petr Baldrian

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

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to differe...

Background Grasslands provide fundamental ecosystem services that are supported by their plant diversity. However, the importance of plant taxonomic diversity for the diversity of other taxa in grasslands remains an open question. Here, we studied the associations between plant communities, soil chemistry and soil microbiome in wooded meadow of Čer...

Aim How community composition varies in space and what governs the variation has been extensively investigated in macroorganisms. However, we have only limited knowledge of microorganisms, especially fungi, despite their ecological and economic significance. Based on previous research, we define and test a series of hypotheses regarding the composi...

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 fully understood. We aim to reveal which bacterial genes are tightly associated with the adaptation to the plant h...

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities 1,2 . Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyo...

Biodiversity drives ecosystem processes but its influence on deadwood decomposition is poorly understood. To test effects of insect diversity on wood decomposition, we conducted a mesocosm experiment manipulating species richness and functional diversity of beetles. We applied a novel approach using computed tomography scanning to quantify decompos...

Arbuscular mycorrhizal (AM) fungi are crucial mutualistic symbionts of the majority of plant species, with essential roles in plant nutrient uptake and stress mitigation. The importance of AM fungi in ecosystems contrasts with our limited understanding of the patterns of AM fungal biogeography and the environmental factors that drive those patterns...

Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a va...

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, and varied plant symbioses. Due to their cryptic lifestyle, it was difficult to assess their diversity until the advent of methods of high-throughput sequencing. Based on the papers utilizing high-throughput sequencing approaches to study fungi in natural hab...

Metagenomics provides a tool to assess the functional potential of environmental and host-associated microbiomes based on the analysis of environmental DNA: assembly, gene prediction and annotation. While gene prediction is straightforward for most bacterial and archaeal taxa, it has limited applicability in the majority of eukaryotic organisms, in...

Mulches are highly effective in mitigating the risk of erosion generated after wildfires in fire-prone ecosystems. Despite being a technique commonly used, it remains completely unexplored how mulches interact with the positive effects of the emergent moss biocrust on the recovery and resilience of soils and their microbial communities. For this pu...

Despite host‐fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life‐history studies. We assembled a spore morphology database covering over 26,000 species of free‐living...

Mutualistic interactions between plants and soil fungi, mycorrhizae, control carbon and nutrient fluxes in terrestrial ecosystems. Soil of ecosystems featuring a particular type of mycorrhiza exhibit specific properties across multiple dimensions of soil functioning. The knowledge about the impacts of mycorrhizal fungi on soil functioning accumulat...

The species-energy hypothesis predicts increasing biodiversity with increasing energy in ecosystems. Proxies for energy availability are often grouped into ambient energy (i.e., solar radiation) and substrate energy (i.e., non-structural carbohydrates or nutritional content). The relative importance of substrate energy is thought to decrease with i...

The decomposition of wood and detritus is challenging to most macroscopic organisms due to the recalcitrant nature of lignocellulose. Moreover, woody plants often protect themselves by synthesizing toxic or nocent compounds which infuse their tissues. Termites are essential wood decomposers in warmer terrestrial ecosystems and, as such, they have t...

Plant–soil feedbacks (PSFs) are one of the major drivers of species coexistence in highly dynamic and low‐diversity communities, such as early successional stands or agricultural systems. However, in stable and species‐rich communities, PSFs are much more complex because of numerous species interactions. In this study, we aimed to reveal if PSFs of...

Alpine tundra ecosystems suffer from ongoing warming-induced tree encroachment and vegetation shifts. While the effects of tree line expansion on the alpine ecosystem receive a lot of attention, there is also an urgent need for understanding the effect of climate change on shifts within alpine vegetation itself, and how these shifts will consequent...

Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially...

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 average microbial community. In this study, we used amplicon sequencing to compare fungal and bacterial communitie...

Cistus scrublands are pyrophytic ecosystems and occur widely across Mediterranean regions. Management of these scrublands is critical to prevent major disturbances, such as recurring wildfires. This is because management appears to compromise the synergies necessary for forest health and the provision of ecosystem services. Furthermore, it supports...

As most Eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recovering Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of Eukaryotic genomes from metagenomes. This study assessed the reconstru...

Across free-living organisms, the ecology and evolution of offspring morphology is shaped by interactions with biotic and abiotic environments during dispersal and early establishment in new habitats. However, the ecology and evolution of offspring morphology for symbiotic species has been largely ignored despite host-symbiont interactions being ub...

Knowledge about the effects of tree species on the soil environment is crucial for implementation of sustainable forest management. The aim of our study was thus to compare the effects of 14 tree species with contrasting traits and origin in Poland and/or Europe on fungal and bacterial diversity in soils. To reduce confounding factors such as diffe...

Intensification of land use by humans has led to a homogenization of landscapes and decreasing resilience of ecosystems globally due to a loss of biodiversity, including the majority of forests. Biodiversity-ecosystem functioning (BEF) research has provided compelling evidence for a positive effect of biodiversity on ecosystem functions and service...

Stable isotope probing (SIP)Stable isotope probing (SIP) provides the opportunity to label decomposer microorganisms that build their biomass on a specific substrate. In combination with high-throughput sequencingHigh-throughput sequencing, SIPStable isotope probing (SIP) allows for the identification of microbial communityMicrobial communities mem...

Soil fungi play indispensable roles in all ecosystems including the recycling of organic matter and interactions with plants, both as symbionts and pathogens. Past observations and experimental manipulations indicate that projected global change effects, including the increase of CO2 concentration, temperature, change of precipitation and nitrogen...

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 demonstrated the potential for carbohydrate utilization of numerous yet uncultured phyla. Profiles of carbohydr...

Clearcutting represents a standard management practice in temperate forests with dramatic consequences for the forest ecosystem. The removal of trees responsible for the bulk of primary production can result in a complex response of the soil microbiome. While studies have shown that tree root-symbiotic ectomycorrhizal fungi disappear from soil and...

Microbial life represents the majority of Earth’s biodiversity. Across disparate disciplines from medicine to forestry, scientists continue to discover how the microbiome drives essential, macro-scale processes in plants, animals and entire ecosystems. Yet, there is an emerging realization that Earth’s microbial biodiversity is under threat. Here w...

Wood decomposition is a central process contributing to global carbon and nutrient cycling. Quantifying the role of the major biotic agents of wood decomposition, i.e. insects and fungi, is thus important for a better understanding of this process. Methods to quantify wood decomposition, such as dry mass loss, suffer from several shortcomings, such...

Microbial diversity plays an important role in the decomposition of soil organic matter. However, the pattern and drivers of the relationship between microbial diversity and decomposition remain unclear. In this study, we followed the decomposition of organic matter in soils where microbial diversity was experimentally manipulated. To produce a gra...

High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis rev...

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....

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...

Forest soil processes carried out by microorganisms are critical for the global carbon (C) cycle and climate. Characterizing the utilization of differently recalcitrant C sources is an important step towards understanding the ecosystem-level function of microorganisms in temperate forest soils. Here, using stable-isotope probing (SIP), we tracked C...

After wildfires in Mediterranean ecosystems, ruderal mosses are pioneer species, stabilizing the soil surface previous to the establishment of vascular vegetation. However, little is known about the implication of pioneer moss biocrusts for the recovery and resilience of soils in early post-fire stages in semi-arid areas. Therefore, we studied the...

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...

Several frameworks that recover genomes from Prokaryotes, Eukaryotes, and viruses from metagenomes exist. For those with little bioinformatics experience, it is difficult to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage from genomes belonging to different domains. MuDoGeR is a user-frie...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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,...

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...

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...

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...

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...

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...

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...

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)...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.

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...

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...