Ondřej Koukol

Ondřej Koukol
Charles University, Faculty of Science (Prague, Czech Republic) · Dept. Botany

PhD

About

66
Publications
30,657
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Introduction
My present research includes taxonomy of (mostly) anamorphic ascomycetes. I use combination of both molecular and phenotypic methods including studies of herbarium material. Currently, I work on evaluation of taxonomical position of a couple of overlooked or understudied microfungi.
Additional affiliations
January 2007 - present
Charles University in Prague
Description
  • Teaching and researach in biodiversity and taxonomy of fungi, teaching about ecology of fungi.
January 2003 - May 2007
February 2002 - May 2007
The Czech Academy of Sciences
Position
  • PhD Student

Publications

Publications (66)
Article
Full-text available
Rhizopogon salebrosus, a common species found in western North America, has been recently considered an invasive species in Europe, based on ITS rDNA sequence records from ectomycorrhizal root tips. We collected in montane and submontane coniferous forests (both plantations and unmanaged forests) in the Czech Republic and Slovakia basidiocarps of a...
Article
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p>Cadophora orchidicola, a root-associated asexual species, did not have a clear placement within the paraphyletic genus Cadophora because it was not represented by sequences derived from the type material. Based on four newly obtained molecular marker sequences from the ex-type strain, a new genus, Leptodophora, is proposed, typified with C. orchi...
Article
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Novel species of fungi described in this study include those from various countries as follows: Antartica, Cladosporium austrolitorale from coastal sea sand. Australia, Austroboletus yourkae on soil, Crepidotus innuopurpureus on dead wood, Curvularia stenotaphri from roots and leaves of Stenotaphrum secundatum and Thecaphora stajsicii from capsules...
Article
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Recent progress in the discovery of fungal diversity has been enabled by intensive mycological surveys in centres of global biodiversity. Descriptions of new fungal species have been almost routinely based on phenotypic studies coupled with single or multigene phylogenetic analyses of DNA sequence data. However, high accessibility of sequencing ser...
Article
We discovered that Sarcoleotia globosa (Geoglossomycetes) fruited on the soil of ornamental Erica pot cultures, and its ascospores can germinate on plain agar. These findings prompted us to collect isolates from horticultural and natural environments in Japan and analyze their phylogeny and root colonizing ability. Pure cultures were successfully o...
Article
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During the informal Spring Micromyco 2019 meeting, we tested how newly obtained molecular barcodes of common or poorly known saprotrophic microfungi from more or less targeted collections may be useful for identification and taxonomic studies. Our aim was to obtain DNA sequences of fungi enabling their phylogenetic placement and routine identificat...
Article
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A high number of fungal strains were isolated from roots of Brassicaceae species collected across western and southern Europe, resulting in an unexpectedly rich collection of Cadophora species. These isolates enable us to present a new and comprehensive view of the ecological, morphological, and phylogenetic traits of root-inhabiting members of thi...
Article
The interactions of fungal guilds have recently been proposed as drivers of organic matter transformation in forest soils. We conducted a pot experiment with Norway spruce seedlings planted in spruce needle litter inoculated with several fungal strains belonging to different ecological guilds (saprotrophic, mycorrhizal, and root endophytic) to asse...
Article
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The pleosporalean anamorph Hermatomyces amphisporus is recorded for the first time from the U.S.A. based on several specimens collected on Sabal minor (Arecaceae) duringmycological surveys carried out in the state of Texas. Phylogenetic analyses of novel DNA sequence data belonging to four nuclear regions (ITS rDNA, EF1-�, RBP2, �-TUB) revealed its...
Preprint
Full-text available
A high number of fungal strains were isolated from roots of Brassicaceae species all over Europe, resulting in an unexpectedly rich collection of Cadophora species. These isolates enable us to present a new and comprehensive view of the ecological, morphological, and phylogenetic traits of root-inhabiting members of this helotialean genus. We provi...
Preprint
Full-text available
A high number of fungal strains were isolated from roots of Brassicaceae species collected across western and southern Europe, resulting in an unexpectedly rich collection of Cadophora species. These isolates enable us to present a new and comprehensive view of the ecological, morphological, and phylogenetic traits of root-inhabiting members of thi...
Article
Litter input is an important source of C and nutrients in forest soils that are liberated and utilized during decomposition. We have investigated the long-term decomposition of Picea abies and Calamagrostis villosa litters in montane spruce forest and the litter-associated fungi. The two litter types differed in initial nutrient content and decompo...
Article
Species of the genus Hermatomyces (Hermatomycetaceae, Pleosporales) are saprotrophic anamorphic ascomycetes that have been intensively studied mostly in South-East Asia and Panama. Species concepts were recently revised based on specimens from these regions using both phenotypic and molecular data. However, other tropical areas have been mostly ove...
Article
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During independent surveys of microfungi associated with Pinus spp. in the United States and the Czech Republic, a distinct fungus matching the generic concept of Septonema Corda was collected. It is characterized by distinctly ornamented conidiophores, branches, conidia and hyphae, ranging from verruculose to strongly verrucose with prominent roun...
Article
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Fungi associated with roots of Pinus wallichiana A.B. Jackson were evaluated for the first time in the recently published study by Tyub et al. (2018, Can. J. For. Res. 48(8): 923–929, doi: 10.1139/cjfr-2018-0084 ). A culture-free approach using RFLP profiling and the sequencing analysis of DNA extracted from fine root tips was used to identify ecto...
Article
Five new species belonging to Hermatomyces (Hermatomycetaceae, Pleosporales) are described based on morphological investigations of specimens collected on rotten twigs and stems of various plants in Panama as well as phylogenetic analyses of sequence data of nuclear ribosomal and protein coding genes (EF1-α, RPB2, β-TUB). The new species are descri...
Article
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Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to am...
Article
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A new combination is provided for Zythia nepenthis, a fungus repeatedly recorded on various Nepenthes plants in a greenhouse in Prague and successfully isolated from stem rot and conidial ten-drils. Phenotypic data including host specificity matches the description of Z. nepenthis. Based on sequences of ITS rDNA and the gene for b-tubulin, this spe...
Article
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Nová kombinace je navržena pro druh Zythia nepenthis, opakovaně zaznamenaný na různých rostlinách rodu Nepenthes ve skleníku v Praze a úspěšně izolovaný jak z hniloby stonku, tak z konidiálních kupek. Fenotypická data spolu s vazbou na Nepenthes jsou v souladu s popisem druhu Z. nepenthis. Na základě sekvencí ITS rDNA a genu pro β-tubulin byl tento...
Article
Endophytic fungi have to cope with various secondary metabolites produced by their host plant. Rhododendron tomentosum is an evergreen shrub with a high content of essential oil showing antimicrobial effects. The first aim of our study was to reveal the diversity of culturable endophytic fungi colonizing leaves of R. tomentosum. We isolated and ide...
Article
The phylogenetic affinities of the anamorphic fungus Ernakulamia cochinensis are investigated based on a representative specimen recently collected on Astrocaryum standleyanum (Arecaceae) in Panama. Molecular phylogenetic analyses using nuclear ribosomal DNA sequence data of the large subunit and the internal transcribed spacer region together with...
Article
Coelomycetes with hyaline stauroconidia represent a rare and undersampled group of fungi with often unknown teleomorphs. In the unique savanna-like vegetation at the base of the Barú volcano in Chiriquí Province, Panama, we discovered an anamorphic ascomycete associated with living shoots and leaves of Buddleja nitida (Scrophulariaceae) that produc...
Article
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Aquatic ascomycetes occur in freshwater and marine environments where they facilitate nutrient cycling and energy flow through the water column, and are the foundations of aquatic food webs. This study investigates the diversity and abundance of aquatic ascomycetes on submerged wood in freshwater, estuarine and marine habitats in north-west Scotlan...
Article
The symptoms of ash dieback caused by the fungus Hymenoscyphus fraxineus include wilting of the foliage followed by dieback of shoots, twigs and branches. Necroses in shoots are assumed to develop after infection through leaf petioles; however, clear evidence of this infection pathway has not yet been provided. Considering the multiple pathogen gen...
Article
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The new species Ramariopsis robusta Matouš & Holec is described based on collections from the Czech Republic and Slovakia. The species is highly supported in a phylogenetic tree based on the 28S rDNA gene. Morphologically, it is distinguished by its robust and densely branched white to cream basidiomata often growing in fascicles, with wide, often...
Article
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The population of European ash (Fraxinus excelsior) in Europe is severely affected by ash dieback disease caused by Hymen-oscyphus fraxineus. Endophytic fungi are known to influence tree fitness and there are efforts to use them directly or indirectly in the biological control of tree pathogens. To assess possible variation in the fungal community...
Article
Sooty bark disease (SBD) caused by the pathogen Cryptostroma corticale is currently one of the risks to the population of Acer pseudoplatanus in Europe. After a number of records of symptomatic and dead trees in Prague, assessment of the latent non-symptomatic stage of SBD was questioned as a means to forecast the health risk of the A. pseudoplatan...
Article
Full-text available
Novel species of fungi described in this study include those from various countries as follows: Australia: Apiognomonia lasiopetali on Lasiopetalum sp., Blastacervulus eucalyptorum on Eucalyptus adesmophloia, Bullanockia australis (incl. Bullanockia gen. nov.) on Kingia australis, Caliciopsis eucalypti on Eucalyptus marginata, Celerioriella petroph...
Article
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The genus Myriococcum was described based on a sterile fungus producing sclerotia. Misinterpretation of these structures resulted in the later addition of several largely unrelated species to this genus and controversy about its phylogenetic placement. The purpose of the study was to revise these species and elucidate their phylogenetic affinities....
Article
A set of historical specimens collected by the American mycologist Charles Leonard Smith in southeastern Nicaragua during 1896 and currently deposited at the Herbarium of the Charles University in Prague (PRC) was examined for the presence of microfungi. Despite the age of the specimens, twenty-two taxa were identified, seventeen of them to species...
Article
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Clavaria atrofusca was described by Velenovský in 1939 based on a single small collection from the Czech Republic. The species is rather rare and until 2009 it had further only been recorded from Switzerland and Denmark. Since 2009 it has also been collected in Norway, Sweden and in 2014 in the Czech Republic. Because the type locality at Mnichovic...
Article
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The native European saprotrophic species Hymenoscyphus albidus seems to be replaced in the recent decade by a closely related but invasive parasite of ash trees, H. fraxineus. Both species colonize the same niche, fallen petioles of ash leaves. In our study, we aimed at current distribution of H. fraxineus and attempted to find also H. albidus in C...
Article
Full-text available
Bartheletia paradoxa is an enigmatic microscopic basidiomycete restricted to leaves of ginkgo (Ginkgo biloba) in litter. This species forms a basal lineage to Agaricomycotina and its life cycle and ultrastructure are unique among members of this subdivision. To date, it has been recorded mostly in the litter of ginkgos planted as ornamental trees i...
Data
Localisation of sampling sites and species recorded on petioles of F. excelsior in Czechia between 2013 and 2015. Codes represent herbarium collections deposited in PRC. Entries marked with an asterisk refer to localities with spore traps.
Article
Desmazierella acicola (anamorph Verticicladium trifidum, Chorioactidaceae) represents a frequent colonizer of pine needles in litter. Considering the global diversity and distribution of pine species, we expected different phylogenetic lineages to exist in different geographical and climatic areas inhabited by these hosts. We compared DNA sequence...
Article
A fungus tentatively identified as Lophodermium sp. was repeatedly isolated from living secondary needles of mountain pine (Pinus mugo) in the Giant Mountains of Po-land. Needles showed symptoms of yellow spots, gradual discolouration and premature falling in July. Thin black zone lines, subepidermal conidiomata and partially subepidermal ascomata...
Article
The population structure of Hymenoscyphus fraxineus, the causal agent of ash dieback, was assessed at four closely located sites in the Czech Republic. To analyse the genetic variation, one Swiss and one Norwegian population with known population structures were selected as reference points. The analysis was performed using 16 previously published...
Article
Precise knowledge of the fungal succession in the litter of coniferous forests will facilitate understanding litter decomposition, in which fungi play a major role. We investigated the development of a fungal community during 3 yr of Picea abies litter decomposition in three control forest sites and three sites where bark-beetle attacks had killed...
Article
The anamorphic fungus Cryptostroma corticale (Xylariaceae) causing sooty bark disease (SBD) of Acer pseudoplatanus has been reported within the past decade in several European countries. In the last decade, severe drought conditions during summer also resulted in an outbreak of SBD in park areas in Prague (Czech Republic). Trees with the typical sy...
Article
Soil and litter fungi can colonise and decompose many natural materials, including highly resilient proteinaceous compounds of animal origin. The shells of terrestrial gastropods are formed from such a compound (conchiolin) combined with inorganic calcium carbonate. In this study, we investigated fungal communities colonising empty shells of the co...
Article
Full-text available
2013. Choroby igieł kosodrzewiny (Pinus mugo) w piętrze subalpejskim Karkonoszy. Sylwan 157 (10): 761−768. Mycological analyses of infected mountain pine needles were conducted for years 2011−2012. Yellow spots on needles were found in subalpine zone of the Karkonosze National Park. The isolation of fungi was conducted at the end of July in both ye...
Article
Numerous oomycetes colonise the crayfish cuticle, the best known being the crayfish plague pathogen Aphanomyces astaci. Although other oomycetes associated with crayfish complicate the isolation and molecular detection of A. astaci, their diversity is little known. To improve this knowledge, we analysed 95 oomycete isolates obtained during attempts...
Article
Full-text available
Mycological analyses of infected mountain pine needles were conducted for years 2011-2012. Yellow spots on needles were found in subalpine zone of the Karkonosze National Park. The isolation of fungi was conducted at the end of July in both years when the intensity of disease symptoms on needles was the highest. Infected needles were sampled from K...
Article
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Pentaster cepaeophilus gen. et sp. nov. (Pezizomycotina inc. sed.) is proposed for a fungus colonizing surface of empty shells of the land snail Cepaea hortensis. The genus is characterised by melanised, multiseptate staurosporous conidia with five arms seceding rhexolytically. The conidia are unique in that two arms form a central axis and three a...
Article
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A new species of Infundichalara (anamorphic Helotiales), a hitherto monotypic genus, is described from pine needle litter. Infundichalara minuta sp. nov. forms two conidiophore types. Erect penicillate conidiophores producing catenulate non-septate hyaline conidia form more frequently than Chalara-like conidiophores with funnel-shaped collarettes p...
Article
Full-text available
Novel species of microfungi described in the present study include the following from Australia: Phytophthora amnicola from still water, Gnomoniopsis smithogilvyi from Castanea sp., Pseudoplagiostoma corymbiae from Corymbia sp., Diaporthe eucalyptorum from Eucalyptus sp., Sporisorium andrewmitchellii from Enneapogon aff. lindleyanus, Myrmecridium b...
Article
Twelve unrelated microfungi from Scots pine (Pinus sylvestris) needle litter were selected to represent supposedly different ecophysiological traits. In order to explore the differences in their involvement in decomposition, activities of their hydrolytic enzymes were compared. Most strains were able to degrade cellulose. The highest exocellulase,...
Article
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The unmanaged Norway spruce montane forests in the Bohemian Forest National Park (Czech Republic) suffered from repeated large-scale bark beetle outbreaks in last decade. In this study, the diversity of culturable foliar endophyte microfungi in needles originating from eleven recently wind-fallen trees in this area was surveyed. Our aims were to de...
Article
Decomposition of Picea abies needles and production of extracellular enzymes involved in decomposition of lignin, cellulose, hemicelluloses and other organic compounds were studied in fungal strains of interior needle colonizers isolated from needles in different stages of decomposition (attached to trees, and early and late decomposition stages in...
Article
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A. Kubátová, O. Koukol, A. Nováková (2011): Geomyces destructans, phenotypic features of some Czech isolates. – Czech Mycol. 63(1): 65–75. The microscopic fungus Geomyces destructans is a psychrophilic dermatophyte causing since 2006 a serious bat disease in North America called white-nose syndrome (WNS). In Europe, G. destruc-tans has also been re...
Article
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Chalara is a genus of anamorphic fungi with typical phialidic conidiogenous cells. Species of Chalara live mostly as litter saprotrophs, many of them on coniferous litter. In this study, the morphology and DNA sequences (ITS rDNA, 28S rDNA and EF-1α) of strains of various species of Chalara isolated from coniferous litter needles were compared with...
Article
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In all terrestrial ecosystems, testate amoebae (TA) encounter fungi. There are strong indications that both groups engage in multiple interactions, including mycophagy and decomposition of TA shells, processes which might be fundamental in nutrient cycling in certain ecosystems. Here, we present the results of an experiment focusing on interactions...
Article
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Survey of seven strains determined as Septonema ochraceum (Dothideomycetes, inc. sed.) isolated from pine litter or obtained from public collections revealed three new species, Fusicladium cordae, F. sicilianum (Venturiaceae), Cladophialophora matsushimae (Herpotrichiellaceae) and a cryptic species morphologically identical to Devriesia americana (...
Article
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Bactrodesmium gabretae is described as a new species of hyphomycetes, based on morphological and molecular data. Bactrodesmium gabretae was isolated from prematurely fallen needles of Picea abies in the Bohemian Forest National Park, Czech Republic. It is characterised by whitish colonies, black sporodochium-like structures formed by loosely fascic...
Article
Previous studies of oribatid mite feeding preferences for different saprotrophic fungi were limited to ubiquitous fungal species, whereas saprophytes specialized to decompose particular substrates have been neglected. We examined the preference of seven oribatid mite species (Adoristes ovatus, Eniochthonius minutissimus, Eueremaeus silvestris, Noth...
Article
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Koukol O. (2009): Geographical distribution of Scleroconidioma sphagnicola in coniferous forests in Europe and Canada. – Czech Mycol. 61(1): 117–124. The distribution of the dematiaceous microfungus Scleroconidioma sphagnicola in coniferous lit-ter in Europe and Canada was assessed using a culture-dependent approach. Needles of various conif-erous...
Article
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Various biotic and abiotic factors may change the quality of cast spruce needles or induce premature casting, subsequently altering the composition of needle litter. We tested the decomposition efficiency of Setulipes androsaceus, a key litter decomposer in spruce forests, on needles of the Norway spruce (Picea abies) that fell into three different...
Article
In our screening, we aimed to detect phosphonates and other forms of organic phosphorus in basidiocarps and vegetative mycelia of six common basidiomycetes. Organic phosphorus-containing compounds were extracted in alkali and analysed using 31P NMR. Monoesters, diesters, pyrophosphates and polyphosphates detected in high amounts reflected the high...
Article
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The anamorphic fungal species Scleroconidioma sphagnicola was repeatedly isolated from spruce and pine litter needles in Šumava National Park. The morphology of thirteen strains of this fungal spe-cies was compared; oxidative enzymes and possible parasitism on Sphagnum in vitro were tested. Our results showed that all of the strains differed from t...
Article
Fungal decomposition of and phosphorus transformation from spruce litter needles (Picea abies) were simulated in systems containing litter needles inoculated with individual saprotrophic fungal strains and their mixtures. Fungal strains of Setulipes androsaceus (L.) Antonín, Chalara longipes (Preus) Cooke, Ceuthospora pinastri (Fr.) Höhn., Mollisia...
Article
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This study addressed competition of Scleroconidioma sphagnicola Tsuneda, Currah & Thormann with saprotrophic ascomycetes and basidiomycetes. We isolated this fungus, previously considered as a preferentially necrotrophic parasite of moss, from spruce needle litter. Competition of Scleroconidioma sphagnicola was simulated with strains of the autocht...
Article
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The effect of the saprotrophic ascomyceteChalara longipes on the decomposition of humic acids was determined in a cultivation experiment. The fungus was incubated in liquid cultures in a full-strength (F system) and an organic nitrogen-free medium (F-N system), both amended with pure humic acids isolated from spruce forest litter. Fungal biomass pr...
Article
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Koukol O. (2011): Early spring mycobiota of pine litter needles. – Czech Mycol. 63(2): 153–161. Rise in air temperature accompanied by snow-melting in early spring may affect fungi colonising litter needles. This study dealt with the diversity of communities of culturable microfungi colonising Scots pine litter at localities still covered by snow a...

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Projects (3)
Project
In the forest ecosystems of all four Croatian biogeographic regions it is planned to perform: (1) Biodiversity research within priority groups of epigeous fungi from the phylum Basidiomycota, (2) Biodiversity research within priority groups of epigeous fungi from the phylum Ascomycota, (3) Biodiversity research of hypogeous fungi, (4) DNA barcoding of minimum 1500 fungal samples, (5) Analysis on the impact of fungal species on forest ecosystem services in Croatia.
Project
Panama belongs among the recognized biodiversity hot spots. Though the fungal diversity has been intensively studied in recent years, there are still microfungal groups that are under-explored here and also in the whole Neotropics. During three visits to Panama, Chiriquí region, I collected numerous specimens of microfungi. Some of them known, some of them rare, some probably new for science. My aim is to characterize them including study of available reference herbarium material, culturing, DNA extraction and multigene analysis.
Project
The project covers various groups of fungi (mostly ascomycetes) that colonize pine needles in the litter in temperate, boreal and tropical areas. Pines are the most diverse group of conifers with natural distribution at the northern hemisphere, though planted by human worldwide. Knowledge of the associated microfungi may help in understanding ecosystem changes following introduction (invasion) of exotic trees. The main questions underlying the project are - which fungi accompany pines in their non-native areas and which local fungi are able to colonize this exotic substrate?