Petr Kohout

• PhD
• Researcher at The Czech Academy of Sciences

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, relia...

Introduction of exotic plants change soil microbial communities which may have detrimental ecological consequences for ecosystems. In this study, we examined the community structure and species richness of ectomycorrhizal (EcM) fungi associated with exotic pine plantations in relation to adjacent native ectomycorrhizal trees in Iran to elucidate th...

Similarly to plants from terrestrial ecosystems, aquatic species harbour wide spectra of root-associated fungi (RAF). However, comparably less is known about fungal diversity in submerged roots. We assessed the incidence and diversity of RAF in submerged aquatic plants using microscopy, culture-dependent and culture-independent techniques. We studi...

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect...

This study aimed to elucidate the relationship between ericaceous understorey shrubs and the diversity and abundance of ectomycorrhizal fungi (EcMF) associated with the invasive Pinus strobus and native Pinus sylvestris. Seedlings of both pines were grown in mesocosms and subjected to three treatments simulating different forest microhabitats: (a)...

Mycorrhiza is a symbiotic association between plant root and fungus, contributing to plant mineral nutrition and defence against antagonists. The mycorrhizal collaboration niche characterizes the position of plant species along a gradient of reliance on mycorrhiza. In this Perspective, we introduce the plant mycorrhizal traits that describe these n...

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 and drivers for microorganisms, such as fungi, despite the importance of fungal diversity for ecosystem functions and se...

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...

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...

All plant populations fluctuate in time. Apart from the dynamics imposed by external forces such as climate, these fluctuations can be driven by endogenous processes taking place within the community. In this study, we aimed to identify potential role of soil‐borne microbial communities in driving endogenous fluctuations of plant populations. We co...

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...

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...

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.

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...

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different lev...

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different lev...

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...

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...

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...

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...

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...

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...

Background Although fertilization and crop rotation practices are commonly used worldwide in agriculture to maximize crop yields, their long-term effect on the structures of soil microorganisms is still poorly understood. This study investigated the long-term impact of fertilization and crop rotation on soil microbial diversity and the microbial co...

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...

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fu...

Arbuscular mycorrhiza (AM) and ectomycorrhiza (EcM) are the most abundant and widespread types of mycorrhizal symbiosis, but there is little and sometimes conflicting information regarding the interaction between AM fungi (AMF) and EcM fungi (EcMF) in soils. Their competition for resources can be particularly relevant in successional ecosystems, wh...

Anthropogenic activities have severely altered biogeochemical cycles with far-reaching consequences for biodiversity and ecosystem functioning. The use of artificial fertilizers, increased legume cultivation and fossil fuel combustion has resulted in a twofold increase of inorganic nitrogen input in natural ecosystems worldwide, often with consider...

Fungi play pivotal roles in ecosystem functioning, but little is known about their global patterns of diversity, endemicity, vulnerability to global change drivers and conservation priority areas. We applied the high-resolution PacBio sequencing technique to identify fungi based on a long DNA marker that revealed a high proportion of hitherto unkno...

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...

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...

There is no consensus barcoding region for determination of arbuscular mycorrhizal fungal (AMF) taxa. To overcome this obstacle, we have developed an approach to sequence an AMF marker within the ribosome‐encoding operon (rDNA) that covers all three widely applied variable molecular markers. Using a nested PCR approach specific to AMF, we amplified...

The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT;...

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...

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.

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...

Arbuscular mycorrhizal fungi (AMF) colonize the roots of numerous aquatic and wetland plants, but the establishment and functioning of mycorrhizal symbiosis in submerged habitats have received only little attention. Three pot experiments were conducted to study the interaction of isoetid plants with native AMF. In the first experiment, arbuscular m...

This article is a Commentary on Rodriguez‐Ramos et al. (2021), pp. 1105–1117.

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...

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...

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...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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...

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...

We examined fungi associated with roots of isoetid plants collected from six Norwegian lakes. The composition of the diverse fungal communities was shaped mainly by host identity, while abiotic factors had negligible effects. The communities associated with roots of Subularia aquatica, Isoëtes echinospora and Isoëtes lacustris were dominated by Asc...

Species‐rich seminatural grasslands in Central Europe have suffered a dramatic loss of biodiversity due to conversion to arable land, but vast areas are being restored. Population recovery of orchids, which depend on mycorrhizal fungi for germination, is however limited. We hypothesised that ploughing and fertilisation caused shifts in orchid mycor...

Evolution of terrestrial plants, the first vascular plants, the first trees, and then whole forest ecosystems had far reaching consequences for Earth system dynamics. These innovations are considered important moments in the evolution of the atmosphere, biosphere, and oceans, even if the effects might have lagged by hundreds of thousands or million...

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...

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...

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...

Premise of the study: Genome duplication is associated with multiple changes at different levels, including interactions with pollinators and herbivores. Yet little is known whether polyploidy may also shape belowground interactions. Methods: To elucidate potential ploidy-specific interactions with arbuscular mycorrhizal fungi (AMF), we compared...

Microbial communities in roots and shoots of plants and in soil are important for plant growth and health and take part in important ecosystem processes. Therefore, understanding the factors that affect their diversity is important. We have analysed fungal and bacterial communities associated with plant shoots, roots and soil over a 1 km2 area in a...

It has been well established that grazing by fungivorous soil fauna alters competitive relationships among fungal species in simplified microcosmal conditions. To which extent fungal grazers modify the composition of complex fungal communities, however, remains little explored. We therefore addressed the question how microarthropods influence rhizo...

Forest management practices often severely affect forest ecosystem functioning. Tree removal by clearcutting is one such practice, producing severe impacts due to the total reduction of primary productivity. Here, we assessed changes to fungal community structure and decomposition activity in the soil, roots and rhizosphere of a Picea abies stand f...

Our study aimed to identify significant predictors (spatial distance, elevation, host plant taxonomy) which shape the structure of endophytic fungal (ENDF) and putative ericoid mycorrhizal (ErMF) communities associated with roots of Ericaceae in Papua New Guinea. Roots of five Ericaceae together with one non-Ericaceae species were sampled at an exp...

Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant‐associated fungal interaction netw...

The arbuscular mycorrhizal (AM) grass Calamagrostis epigejos and predominantly ectomycorrhizal (EcM) tree Salix caprea co-occur at post-mining sites spontaneously colonized by vegetation. During succession, AM herbaceous vegetation is replaced by predominantly EcM woody species. To better understand the interaction of AM and EcM plants during veget...

The aim of the study was to explore fungal community assembly during spontaneous primary succession. Pyrosequencing was used to investigate the root-associated fungal communities of two dominant trees Salix caprea and Betula pendula along a primary successional chronosequence (12-, 20-, 30- and 50-year-old sites) on a mine spoil bank in the Czech R...

Together with plants, soil microbial communities play an essential role in the development of stable ecosystems on degraded lands, such as post-mining spoil heaps. Our study addressed concurrent development of the vegetation and soil fungal and bacterial communities in the course of primary succession in a brown coal mine spoil deposit area in the...

This article is a Commentary on Smith et al ., 215 : 747–755 .

Ericoid mycorrhiza is a mutualistic relationship between several lineages of plants in the family Ericaceae (Cassiopoideae, Ericoideae, Harrimanelloideae, Styphelioideae, and Vaccinioideae subfamilies) and a diverse group of soil fungi. Compared to the more common mycorrhizal types such as arbuscular mycorrhiza and ectomycorrhiza, ericoid mycorrhiz...

Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in specie...

Ericoid mycorrhiza represents a key adaptation of the Ericaceae plants to facilitate their establishment in harsh conditions. The Ericaceae are a large family of flowering plants, with global distribution. However, our current knowledge about the ericoid mycorrhizal fungal diversity and ecology largely relates to the Northern Hemisphere. Our study...

Arbuscular mycorrhizal fungal (AMF) community assembly during primary succession has so far received little attention. It remains therefore unclear, which of the factors, driving AMF community composition, are important during ecosystem development. We addressed this question on a large spoil heap, which provides a mosaic of sites in different succ...

Arbuscular mycorrhizal (AM) fungi are ubiquitous microbes in terrestrial habitats with important roles in ecosystem functioning, but knowledge of their large scale biogeography remains particularly limited in some regions and in association with woody host species. The objective of this study was to characterize diversity and community structure of...

An extensive field trial was established on a fly ash deposit (1) to evaluate whether the inoculation with arbuscular mycorrhizal fungi (AMF) and/or ectomycorrhizal fungi (EcMF) improves growth and survival of 13 planted tree species and (2) to trace the inoculated mycorrhizal fungi in tree roots after one growing season. Molecular methods were app...

A central challenge in ecology is to understand the relative importance of processes that shape diversity patterns. Compared with aboveground biota, little is known about spatial patterns and processes in soil organisms. Here we examine the spatial structure of communities of small soil eukaryotes to elucidate the underlying stochastic and determin...

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...

Arbuscular mycorrhizal fungi (AMF) represent an important soil microbial group playing a fundamental role in many terrestrial ecosystems. We explored the effects of deterministic (soil characteristics, host plant life stage, neighbouring plant communities) and stochastic processes on AMF colonisation, richness and community composition in roots of...

Orchid mycorrhizal (OrM) symbionts play a key role in the growth of orchids, but the temporal variation and habitat partitioning of these fungi in roots and soil remain unclear. Temporal changes in root and rhizosphere fungal communities of Cypripedium calceolus , Neottia ovata and Orchis militaris were studied in meadow and forest habitats over th...

Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially...