Petr Baldrian

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

Introduction Revegetation of barren substrates is often determined by the composition and distance of the nearest plant community, serving as a source of colonizing propagules. Whether such dispersal effect can be observed during the development of soil microbial communities, is not clear. In this study, we aimed to elucidate which factors structur...

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 mil...

Forests play a crucial role in global carbon cycling by absorbing and storing significant amounts of atmospheric carbon dioxide. Although boreal forests contribute to approximately 45% of the total forest carbon sink, tree growth and soil carbon sequestration are constrained by nutrient availability. Here, we examine if long‐term nutrient input enh...

While the succession of terrestrial plant communities is well studied, less is known about succession on dead wood, especially how it is affected by environmental factors. While temperate forests face increasing canopy mortality, which causes considerable changes in microclimates, it remains unclear how canopy openness affects fungal succession. He...

Effective conservation strategies are needed to prevent further loss of biodiversity. This requires a comprehensive assessment of species' presence, distribution, and population sizes. Such assessments can be extremely challenging for species-rich taxa, like fungi, which are difficult to detect and identify. In recent years, metabarcoding applied t...

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previousl...

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 poorly understood. Here, we studied the associations between plant communities, soil chemistry and soil microbiome in a wooded meadow of...

Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specialization...

Fungi are an integral part of the nitrogen and phosphorus cycling in trophic networks, as they participate in biomass decomposition and facilitate plant nutrition through root symbioses. Nutrient content varies considerably between the main fungal habitats, such as soil, plant litter or decomposing dead wood, but there are also large differences wi...

An increasing number of studies of above‐belowground interactions provide a fundamental basis for our understanding of the coexistence between plant and soil communities. However, we lack empirical evidence to understand the directionality of drivers of plant and soil communities under natural conditions: ‘Are soil microorganisms driving plant comm...

Revegetation of barren substrates is often determined by the composition and distance of the nearest plant community, serving as a source of colonising propagules. Whether such dispersal effect can be observed during the development of soil microbial communities, is not clear. In this study, we aimed to elucidate which factors structure plant and s...

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 structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbia...

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 deadwood microbiomes is challenging due to their complexity and the limitations of traditional cultivation methods. Ou...

The field of mycology has grown from an underappreciated subset of botany, to a valuable, modern scientific discipline. As this field of study has grown, there have been significant contributions to science, technology, and industry, highlighting the value of fungi in the modern era. This paper looks at the current research, along with the existing...

Inoculation of common bean seed with diversified bacterial synthetic communities can induce deep modifications of both seed and seedling microbiota, even in living potting soil.

Fungi are an integral part of the nitrogen and phosphorus cycling in trophic networks, as they participate in biomass decomposition and facilitate plant nutrition through root symbioses. Nutrient content varies considerably between the main fungal habitats, such as soil, plant litter or decomposing dead wood, but there are also large differences wi...

Background Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining ecosystem stability. The structure of the belowground microbiome is largely determined by individual plants, but it is not clear how...

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...

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

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...

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...