The majority of Earths biodiversity is unknown. This is particularly true for the vast part of so... more The majority of Earths biodiversity is unknown. This is particularly true for the vast part of soil biodiversity, which rarely can be observed directly. Metabarcoding of DNA extracted from the environment (eDNA) has become state-of-the-art in assessing soil biodiversity. Also for fungal community profiling eDNA is seen as an attractive alternative to classical surveying based on fruitbodies. However, it is unknown whether eDNA-metabarcoding provides a representative sample of fungal diversity and census of threatened species. Therefore conservation planning and assessment are still based on fruitbody inventories. Based on a dataset of unprecedented width and depth, representing both soil eDNA-metabarcoding and expert inventorying of fungal fruitbodies, we document for the first time the validity of eDNA as practical inventory method and measure of conservation value for fungi. Fruitbody data identified fewer species in total and per site, and had larger variance in site richness. Fo...
DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity... more DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants paired with plant ITS2 metabarcoding data of DNA extracted from soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity metrics, and does not require a sequence reference database; thus, it represents a promising m...
Background: In light of the biodiversity crisis and our limited ability to explain variation in b... more Background: In light of the biodiversity crisis and our limited ability to explain variation in biodiversity, it is time to rethink the way we study biodiversity and its causes. Inspired by the recently published ecospace framework, we developed a protocol for environmental and biotic mapping that is scalable to habitats, ecosystems and biomes. We applied our protocol as part of a comprehensive biodiversity study in Denmark. We selected study sites (40 x 40 m) using stratified random sampling along the major environmental gradients underlying biotic variation. Using standard methods, we collected vascular plant, bryophyte, macrofungi, lichen, gastropod and arthropod species lists for each site. To evaluate sampling efficiency, we calculated regional coverage (relative to the number of species known from Denmark per taxonomic group), and project scale coverage (i.e., based on the sample coverage per taxonomic groups). To cover eukaryotic organisms that are less easily targeted by cla...
Woody plants host diverse communities of associated organisms, including wood-inhabiting fungi. I... more Woody plants host diverse communities of associated organisms, including wood-inhabiting fungi. In this group, host effects on species richness and interaction network structure are not well understood, especially not at large geographical scales. We investigated ecological, historical and evolutionary determinants of fungal species richness and network modularity, that is, subcommunity structure, across woody hosts in Denmark, using a citizen science data set comprising > 80 000 records of > 1000 fungal species on 91 genera of woody plants. Fungal species richness was positively related to host size, wood pH, and the number of species in the host genus, with limited influence of host frequency and host history, that is, time since host establishment in the area. Modularity patterns were unaffected by host history, but largely reflected host phylogeny. Notably, fungal communities differed substantially between angiosperm and gymnosperm hosts. Host traits and evolutionary history appear to be more important than host frequency and recent history in structuring interactions between hosts and wood-inhabiting fungi. High wood acidity appears to act as a stress factor reducing fungal species richness, while large host size, providing increased niche diversity, enhances it. In some fungal groups that are known to interact with live host cells in the establishment phase, host selectivity is common, causing a modular community structure.
Based on morphological and molecular phylogenetic studies we present three new species in Cortina... more Based on morphological and molecular phylogenetic studies we present three new species in Cortinarius. Species descriptions are provided, along with discussions of phylogenetic and morphological affinities to similar taxa. Cortinarius majoranae, Cortinarius aquilanus and Cortinarius lepistoides spp. nov. are described. The first taxon is placed in section Percomes, whereas the last two belong to section Caerulescentes.
Kärcher & Seibt is a rare European species of the subgenus , section , neglected in recen... more Kärcher & Seibt is a rare European species of the subgenus , section , neglected in recent molecular studies. New primers (CortF and CortR) designed for species in the section allowed to obtain ITS rDNA sequence data from the holotype collection of ; according to the results, this epithet has priority over Rob. Henry ex Rob. Henry, Reumaux, and Bidaud, Moënne-Locc. & Reumaux. Morphological and ecological observations on recent collections of from the Czech Republic in comparison with the co-occurring are discussed. Nomenclatural and taxonomic comments on Rob. Henry, Rob. Henry, and Reumaux are also provided. So far, is known with certainty from Germany, France, and the Czech Republic, where it grows in deciduous forests on acid to neutral soils. Arsenic and its compounds were determined in and related species of the section : , , and . Total arsenic concentrations were in the range 3.6-30.2 mg kg (dry matter) and arsenobetaine was the major arsenic compound.
The taxonomy and phylogeny of sect. Multiformes (Cortinarius, subgen. Phlegmacium) are presented.... more The taxonomy and phylogeny of sect. Multiformes (Cortinarius, subgen. Phlegmacium) are presented. The present circumscription of the section is supported by molecular data and morphological features. The taxonomy is complex and many taxa are quite new and little known. Two new species are described. Altogether ten European species are recognized: C. multiformis, C. talimultiformis, C. frondosomultiformis sp. nov., C. rufoallutus, C. talus, C. melleicarneus, C. caesiolamellatus, C. caesiophylloides, C. pallidirimosus and C. armenicorius sp. nov. The ten recognized species are (i) more or less well-supported phylogenetically, but (ii) with a fairly low morphological differentiation. The species differs by >1% in ITS DNA from sister taxa, and each species pair show a morphological differentiation, though in most cases with overlapping characters. For instance, most species have overlapping variation in size and shape of the spores, and less than half of the species have formerly been recognized in morphological studies.
Abstract Cortinarius is a species-rich and morphologically challenging genus with a cosmopolitan ... more Abstract Cortinarius is a species-rich and morphologically challenging genus with a cosmopolitan distribution. Many names have not been used consistently and in some instances the same species has been described two or more times under separate names. This study focuses on subg. Phlegmacium as traditionally defined and includes species from boreal and temperate areas of the northern hemisphere. Our goals for this project were to: i) study type material to determine which species already have been described; ii) stabilize the use of Friesian and other older names by choosing a neo- or epitype; iii) describe new species that were discovered during the process of studying specimens; and iv) establish an accurate ITS barcoding database for Phlegmacium species. A total of 236 types representing 154 species were studied. Of these 114 species are described only once whereas 40 species had one ore more synonyms. Of the names studied only 61 were currently represented in GenBank. Neotypes are proposed for 21 species, and epitypes are designated for three species. In addition, 20 new species are described and six new combinations made. As a consequence ITS barcodes for 175 Cortinarius species are released.
Using molecular genetic methods we present a fresh look at Cortinarius subgenus Phlegmacium secti... more Using molecular genetic methods we present a fresh look at Cortinarius subgenus Phlegmacium section Purpurascentes. A phylogram presents an overview of the species in the section. For a delimitation of the section, morphological characters (e.g. discolouration of the flesh) and chemical characters (e.g. colour reactions with Lugol) are employed. With current knowledge, the section Purpurascentes encompasses 5 European species, for which we present photos, descriptions and a determination key.
Cortinarius koldingensis is described as a new species based on several collections from a small ... more Cortinarius koldingensis is described as a new species based on several collections from a small area in Denmark. Sequence data from the ITS marker places it in the Sulfurini group of the large Calochroi clade of Cortinarius subgenus Phlegmacium, along with C. sulfurinus and two North American taxa. It is phylogenetically distinct from the other species in the Sulfurini and differs from C. sulfurinus by several deviating morphological characteristics. The species has been collected on several occasions over the last 15 years from only one Danish locality. Despite extensive molecular screening of numerous possible conspecific specimens, including holotype and comparison with all publicly available ITS sequence data from specimens and environmental DNA alike, no match with specimens from elsewhere has been encountered, and we hypothesize that the species is rare in Europe.
The majority of Earths biodiversity is unknown. This is particularly true for the vast part of so... more The majority of Earths biodiversity is unknown. This is particularly true for the vast part of soil biodiversity, which rarely can be observed directly. Metabarcoding of DNA extracted from the environment (eDNA) has become state-of-the-art in assessing soil biodiversity. Also for fungal community profiling eDNA is seen as an attractive alternative to classical surveying based on fruitbodies. However, it is unknown whether eDNA-metabarcoding provides a representative sample of fungal diversity and census of threatened species. Therefore conservation planning and assessment are still based on fruitbody inventories. Based on a dataset of unprecedented width and depth, representing both soil eDNA-metabarcoding and expert inventorying of fungal fruitbodies, we document for the first time the validity of eDNA as practical inventory method and measure of conservation value for fungi. Fruitbody data identified fewer species in total and per site, and had larger variance in site richness. Fo...
DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity... more DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants paired with plant ITS2 metabarcoding data of DNA extracted from soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity metrics, and does not require a sequence reference database; thus, it represents a promising m...
Background: In light of the biodiversity crisis and our limited ability to explain variation in b... more Background: In light of the biodiversity crisis and our limited ability to explain variation in biodiversity, it is time to rethink the way we study biodiversity and its causes. Inspired by the recently published ecospace framework, we developed a protocol for environmental and biotic mapping that is scalable to habitats, ecosystems and biomes. We applied our protocol as part of a comprehensive biodiversity study in Denmark. We selected study sites (40 x 40 m) using stratified random sampling along the major environmental gradients underlying biotic variation. Using standard methods, we collected vascular plant, bryophyte, macrofungi, lichen, gastropod and arthropod species lists for each site. To evaluate sampling efficiency, we calculated regional coverage (relative to the number of species known from Denmark per taxonomic group), and project scale coverage (i.e., based on the sample coverage per taxonomic groups). To cover eukaryotic organisms that are less easily targeted by cla...
Woody plants host diverse communities of associated organisms, including wood-inhabiting fungi. I... more Woody plants host diverse communities of associated organisms, including wood-inhabiting fungi. In this group, host effects on species richness and interaction network structure are not well understood, especially not at large geographical scales. We investigated ecological, historical and evolutionary determinants of fungal species richness and network modularity, that is, subcommunity structure, across woody hosts in Denmark, using a citizen science data set comprising > 80 000 records of > 1000 fungal species on 91 genera of woody plants. Fungal species richness was positively related to host size, wood pH, and the number of species in the host genus, with limited influence of host frequency and host history, that is, time since host establishment in the area. Modularity patterns were unaffected by host history, but largely reflected host phylogeny. Notably, fungal communities differed substantially between angiosperm and gymnosperm hosts. Host traits and evolutionary history appear to be more important than host frequency and recent history in structuring interactions between hosts and wood-inhabiting fungi. High wood acidity appears to act as a stress factor reducing fungal species richness, while large host size, providing increased niche diversity, enhances it. In some fungal groups that are known to interact with live host cells in the establishment phase, host selectivity is common, causing a modular community structure.
Based on morphological and molecular phylogenetic studies we present three new species in Cortina... more Based on morphological and molecular phylogenetic studies we present three new species in Cortinarius. Species descriptions are provided, along with discussions of phylogenetic and morphological affinities to similar taxa. Cortinarius majoranae, Cortinarius aquilanus and Cortinarius lepistoides spp. nov. are described. The first taxon is placed in section Percomes, whereas the last two belong to section Caerulescentes.
Kärcher & Seibt is a rare European species of the subgenus , section , neglected in recen... more Kärcher & Seibt is a rare European species of the subgenus , section , neglected in recent molecular studies. New primers (CortF and CortR) designed for species in the section allowed to obtain ITS rDNA sequence data from the holotype collection of ; according to the results, this epithet has priority over Rob. Henry ex Rob. Henry, Reumaux, and Bidaud, Moënne-Locc. & Reumaux. Morphological and ecological observations on recent collections of from the Czech Republic in comparison with the co-occurring are discussed. Nomenclatural and taxonomic comments on Rob. Henry, Rob. Henry, and Reumaux are also provided. So far, is known with certainty from Germany, France, and the Czech Republic, where it grows in deciduous forests on acid to neutral soils. Arsenic and its compounds were determined in and related species of the section : , , and . Total arsenic concentrations were in the range 3.6-30.2 mg kg (dry matter) and arsenobetaine was the major arsenic compound.
The taxonomy and phylogeny of sect. Multiformes (Cortinarius, subgen. Phlegmacium) are presented.... more The taxonomy and phylogeny of sect. Multiformes (Cortinarius, subgen. Phlegmacium) are presented. The present circumscription of the section is supported by molecular data and morphological features. The taxonomy is complex and many taxa are quite new and little known. Two new species are described. Altogether ten European species are recognized: C. multiformis, C. talimultiformis, C. frondosomultiformis sp. nov., C. rufoallutus, C. talus, C. melleicarneus, C. caesiolamellatus, C. caesiophylloides, C. pallidirimosus and C. armenicorius sp. nov. The ten recognized species are (i) more or less well-supported phylogenetically, but (ii) with a fairly low morphological differentiation. The species differs by >1% in ITS DNA from sister taxa, and each species pair show a morphological differentiation, though in most cases with overlapping characters. For instance, most species have overlapping variation in size and shape of the spores, and less than half of the species have formerly been recognized in morphological studies.
Abstract Cortinarius is a species-rich and morphologically challenging genus with a cosmopolitan ... more Abstract Cortinarius is a species-rich and morphologically challenging genus with a cosmopolitan distribution. Many names have not been used consistently and in some instances the same species has been described two or more times under separate names. This study focuses on subg. Phlegmacium as traditionally defined and includes species from boreal and temperate areas of the northern hemisphere. Our goals for this project were to: i) study type material to determine which species already have been described; ii) stabilize the use of Friesian and other older names by choosing a neo- or epitype; iii) describe new species that were discovered during the process of studying specimens; and iv) establish an accurate ITS barcoding database for Phlegmacium species. A total of 236 types representing 154 species were studied. Of these 114 species are described only once whereas 40 species had one ore more synonyms. Of the names studied only 61 were currently represented in GenBank. Neotypes are proposed for 21 species, and epitypes are designated for three species. In addition, 20 new species are described and six new combinations made. As a consequence ITS barcodes for 175 Cortinarius species are released.
Using molecular genetic methods we present a fresh look at Cortinarius subgenus Phlegmacium secti... more Using molecular genetic methods we present a fresh look at Cortinarius subgenus Phlegmacium section Purpurascentes. A phylogram presents an overview of the species in the section. For a delimitation of the section, morphological characters (e.g. discolouration of the flesh) and chemical characters (e.g. colour reactions with Lugol) are employed. With current knowledge, the section Purpurascentes encompasses 5 European species, for which we present photos, descriptions and a determination key.
Cortinarius koldingensis is described as a new species based on several collections from a small ... more Cortinarius koldingensis is described as a new species based on several collections from a small area in Denmark. Sequence data from the ITS marker places it in the Sulfurini group of the large Calochroi clade of Cortinarius subgenus Phlegmacium, along with C. sulfurinus and two North American taxa. It is phylogenetically distinct from the other species in the Sulfurini and differs from C. sulfurinus by several deviating morphological characteristics. The species has been collected on several occasions over the last 15 years from only one Danish locality. Despite extensive molecular screening of numerous possible conspecific specimens, including holotype and comparison with all publicly available ITS sequence data from specimens and environmental DNA alike, no match with specimens from elsewhere has been encountered, and we hypothesize that the species is rare in Europe.
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Papers by Tobias Frøslev