Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    “CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?
    Hane, James K. ; Paxman, Jonathan ; Jones, Darcy A.B. ; Oliver, Richard P. ; Wit, Pierre de - \ 2020
    Frontiers in Microbiology 10 (2020). - ISSN 1664-302X
    biotroph - CAZymes - fungi - hemibiotroph - metabolism - necrotroph - plant pathogen

    The traditional classification of fungal and oomycete phytopathogens into three classes – biotrophs, hemibiotrophs, or necrotrophs – is unsustainable. This study highlights multiple phytopathogen species for which these labels have been inappropriately applied. We propose a novel and reproducible classification based solely on genome-derived analysis of carbohydrate-active enzyme (CAZyme) gene content called CAZyme-Assisted Training And Sorting of -trophy (CATAStrophy). CATAStrophy defines four major divisions for species associated with living plants. These are monomertrophs (Mo) (corresponding to biotrophs), polymertrophs (P) (corresponding to necrotrophs), mesotrophs (Me) (corresponding to hemibiotrophs), and vasculartrophs (including species commonly described as wilts, rots, or anthracnoses). The Mo class encompasses symbiont, haustorial, and non-haustorial species. Me are divided into the subclasses intracellular and extracellular Me, and the P into broad and narrow host sub-classes. This gives a total of seven discrete plant-pathogenic classes. The classification provides insight into the properties of these species and offers a facile route to develop control measures for newly recognized diseases. Software for CATAStrophy is available online at https://github.com/ccdmb/catastrophy. We present the CATAStrophy method for the prediction of trophic phenotypes based on CAZyme gene content, as a complementary method to the traditional tripartite “biotroph–hemibiotroph–necrotroph” classifications that may encourage renewed investigation and revision within the fungal biology community.

    Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi : is the picture complete?
    Collemare, Jérôme ; Seidl, Michael F. - \ 2019
    FEMS Microbiology Reviews 43 (2019)6. - ISSN 0168-6445 - p. 591 - 607.
    chromatin - fungi - secondary metabolites - transcriptional regulation

    Fungal secondary metabolites are small molecules that exhibit diverse biological activities exploited in medicine, industry and agriculture. Their biosynthesis is governed by co-expressed genes that often co-localize in gene clusters. Most of these secondary metabolite gene clusters are inactive under laboratory conditions, which is due to a tight transcriptional regulation. Modifications of chromatin, the complex of DNA and histone proteins influencing DNA accessibility, play an important role in this regulation. However, tinkering with well-characterised chemical and genetic modifications that affect chromatin alters the expression of only few biosynthetic gene clusters, and thus the regulation of the vast majority of biosynthetic pathways remains enigmatic. In the past, attempts to activate silent gene clusters in fungi mainly focused on histone acetylation and methylation, while in other eukaryotes many other post-translational modifications are involved in transcription regulation. Thus, how chromatin regulates the expression of gene clusters remains a largely unexplored research field. In this review, we argue that focusing on only few well-characterised chromatin modifications is significantly hampering our understanding of the chromatin-based regulation of biosynthetic gene clusters. Research on underexplored chromatin modifications and on the interplay between different modifications is timely to fully explore the largely untapped reservoir of fungal secondary metabolites.

    Trophic Regulations of the Soil Microbiome
    Thakur, Madhav P. ; Geisen, Stefan - \ 2019
    Trends in Microbiology 27 (2019)9. - ISSN 0966-842X - p. 771 - 780.
    bacteria - climate change - food webs - fungi - predators - top-down control

    The soil microbiome regulates vital ecosystem functions ranging from primary production to soil carbon sequestration. Yet, we have only begun to understand the factors regulating the soil microbiome. While the importance of abiotic factors is increasingly recognized, the roles of trophic regulations in driving the structure and function of the soil microbiome remain less explored. Here, we review the current understanding of how and when microbial and top predators of the soil shape the community structure and function of the soil microbiome via both direct and indirect effects. We finally highlight that the structure and function of the soil microbiome depend on the interactive effects among predation, plant inputs, and abiotic variables present in the soil.

    Dataset for: Presence of seed-borne pest and pathogens on/in the seed produced by farmers in the province of Cotopaxi
    Navarrete Cueva, Israel ; Andrade, Jorge ; Almekinders, Conny ; Struik, Paul - \ 2019
    Kansas State University
    seed degeneration - nematodes - fungi - viruses - seed tubers - seed damaging insects - Potato - Rhizoctonia - Streptomyces scabies - Fusarium - Silver scurf - Powdery scabs - Andean potato weevil - Potato tuber moth - White grub - Wireworm - Flea beetle - PVS - PVY - PVX - PLRV - APMoV - Globodera pallida - Tylenchus spp. - Pratylenchus spp. - Aphelenchoides spp. - Heterodera spp. - Meloidogyne spp. - Paratylenchus Spp. - Saprophytes - Tylenchorhynchus spp.
    Seed degeneration (PSD) threats potato production in developing countries. PSD is defined as the accumulation of pest and pathogens in/on the seed tuber due to the successive cycles of vegetative propagation leading potentially to a yield and quality reduction (Thomas-Sharma et al., 2016; Pl. Path. [vol 65, issue 1]). However, the understanding of PSD in the Andes is deficient due to the limited comprehension of the spatial distribution of potato seed- and soil- borne pests and pathogens. For this reason, 260 farmers´ seed lots and fields were surveyed in the province of Cotopaxi-Ecuador from September to October 2018. The survey was implemented using a stratified sampling design (stratum = Cantons of Latacunga, Pujilí, Salcedo and Saquisilí). The sample size was defined based on the seed replacement rate reported by farmers in a pilot study previously implemented. In each place, farmers kindly provided a sample of (1 to 10) potato seed tubers depending on their willingness. In addition to it, a soil sample was collected from the closest field to the house after farmers provided oral consent. Symptoms and damages on the seed tubers caused by insects and fungi were visually inspected following the methodology suggested by James (1971, [Canadian pl. dis. survey {vol. 51}]) and the photography guide of the main pests and pathogens of the potato crop in Ecuador (Montesdeoca et al., 2013)(Reported in sheet coined "Insects and Fungi"). Virus identification was carried out on plantlets coming from the tubers assessed previously. This was performed by using the kits and the protocol for DAS-ELISA manufactured and suggested by CIP (2007). Six viruses were identified: PVX, PVS, PVY, APLV, PLRV, and APMoV (Reported in sheet coined "Virus"). Forty three soil samples out of the 260 were selected depending on the farmers’ field altitude and landscape location (Reported in sheet coined "nematodes"). These were sent to the laboratory of Plant Protection of the National Agriculture Research Center (INIAP) for nematodes identification. Nematodes were identified according to the methodologies of Oostenbrink (1960) and Fenwick (1940). It is expected that this database contributes to a deeper knowledge about the presence of seed-borne pests and pathogens in the tropical highlands of Ecuador and to design better seed system interventions.;The dataset contains data about presence of seed-borne pest and pathogens on/in the seed produced by farmers in the province of Cotopaxi.
    Open-source data reveal how collections-based fungal diversity is sensitive to global change
    Andrew, Carrie ; Büntgen, Ulf ; Egli, Simon ; Senn-Irlet, Beatrice ; Grytnes, John Arvid ; Heilmann-Clausen, Jacob ; Boddy, Lynne ; Bässler, Claus ; Gange, Alan C. ; Heegaard, Einar ; Høiland, Klaus ; Kirk, Paul M. ; Krisai-Greilhüber, Irmgard ; Kuyper, Thomas W. ; Kauserud, Håvard - \ 2019
    American Journal of Botany 7 (2019)3. - ISSN 2168-0450
    collections data - diversity - fungi - macroecology - open-source - phenology records

    Premise of the Study: Fungal diversity (richness) trends at large scales are in urgent need of investigation, especially through novel situations that combine long-term observational with environmental and remotely sensed open-source data. Methods: We modeled fungal richness, with collections-based records of saprotrophic (decaying) and ectomycorrhizal (plant mutualistic) fungi, using an array of environmental variables across geographical gradients from northern to central Europe. Temporal differences in covariables granted insight into the impacts of the shorter- versus longer-term environment on fungal richness. Results: Fungal richness varied significantly across different land-use types, with highest richness in forests and lowest in urban areas. Latitudinal trends supported a unimodal pattern in diversity across Europe. Temperature, both annual mean and range, was positively correlated with richness, indicating the importance of seasonality in increasing richness amounts. Precipitation seasonality notably affected saprotrophic fungal diversity (a unimodal relationship), as did daily precipitation of the collection day (negatively correlated). Ectomycorrhizal fungal richness differed from that of saprotrophs by being positively associated with tree species richness. Discussion: Our results demonstrate that fungal richness is strongly correlated with land use and climate conditions, especially concerning seasonality, and that ongoing global change processes will affect fungal richness patterns at large scales.

    Metatranscriptomics reveals mycoviral populations in the ovine rumen
    Hitch, Thomas C.A. ; Edwards, Joan E. ; Gilbert, Rosalind A. - \ 2019
    FEMS Microbiology Letters 366 (2019)13. - ISSN 0378-1097
    fungi - mycobiome - mycovirus - RNA - rumen

    The rumen is known to contain DNA-based viruses, although it is not known whether RNA-based viruses that infect fungi (mycoviruses) are also present. Analysis of publicly available rumen metatranscriptome sequence data from sheep rumen samples (n = 20) was used to assess whether RNA-based viruses exist within the ovine rumen. A total of 2466 unique RNA viral contigs were identified that had homology to nine viral families. The Partitiviridae was the most consistently observed mycoviral family. High variation in the abundance of each detected mycovirus suggests that rumen mycoviral populations vary greatly between individual sheep. Functional analysis of the genes within the assembled mycoviral contigs suggests that the mycoviruses detected had simple genomes, often only carrying the machinery required for replication. The fungal population of the ovine rumen was also assessed using metagenomics data from the same samples, and was consistently dominated by the phyla Ascomycota and Basidomycota. The strictly anaerobic phyla Neocallimastigomycota were also present in all samples but at a low abundance. This preliminary investigation has provided clear evidence that mycoviruses with RNA genomes exist in the rumen, with further in-depth studies now required to characterise this mycoviral community and determine its role in the rumen.

    Combinations of Spok genes create multiple meiotic drivers in Podospora
    Vogan, Aaron A. ; Ament-Velásquez, Lorena ; Granger-Farbos, Alexandra ; Svedberg, Jesper ; Bastiaans, Eric ; Debets, Alfons Jm ; Coustou, Virginie ; Yvanne, Hélène ; Clavé, Corinne ; Saupe, Sven J. ; Johannesson, Hanna - \ 2019
    eLife 8 (2019). - ISSN 2050-084X
    evolutionary biology - fungi - gene drive - genetics - genomic conflict - genomics - Podospora - selfish genetic element - spore killer

    Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within a population. We identify two novel Spok homologs located within a large (74-167 kbp) region (the Spok block) that resides in different chromosomal locations in different strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse through cross-species transfer, and evolve by duplication and diversification within lineages.

    Enrichment of G4DNA and a Large Inverted Repeat Coincide in the Mitochondrial Genomes of Termitomyces
    Nieuwenhuis, Mathijs ; Peppel, Lennart J.J. van de; Bakker, Freek T. ; Zwaan, Bas J. ; Aanen, Duur K. - \ 2019
    Genome Biology and Evolution 11 (2019)7. - ISSN 1759-6653 - p. 1857 - 1869.
    fungi - G-quadruplex - inverted repeat - Lyophyllaceae - mtDNA

    Mitochondria retain their own genome, a hallmark of their bacterial ancestry. Mitochondrial genomes (mtDNA) are highly diverse in size, shape, and structure, despite their conserved function across most eukaryotes. Exploring extreme cases of mtDNA architecture can yield important information on fundamental aspects of genome biology. We discovered that the mitochondrial genomes of a basidiomycete fungus (Termitomyces spp.) contain an inverted repeat (IR), a duplicated region half the size of the complete genome. In addition, we found an abundance of sequences capable of forming G-quadruplexes (G4DNA); structures that can disrupt the double helical formation of DNA. G4DNA is implicated in replication fork stalling, double-stranded breaks, altered gene expression, recombination, and other effects. To determine whether this occurrence of IR and G4DNA was correlated within the genus Termitomyces, we reconstructed the mitochondrial genomes of 11 additional species including representatives of several closely related genera. We show that the mtDNA of all sampled species of Termitomyces and its sister group, represented by the species Tephrocybe rancida and Blastosporella zonata, are characterized by a large IR and enrichment of G4DNA. To determine whether high mitochondrial G4DNA content is common in fungi, we conducted the first broad survey of G4DNA content in fungal mtDNA, revealing it to be a highly variable trait. The results of this study provide important direction for future research on the function and evolution of G4DNA and organellar IRs.

    Data from: Relationships between fungal community composition in decomposing leaf litter and home-field advantage effects
    Veen, G.F. ; Snoek, L.B. ; Bakx-Schotman, Tanja ; Wardle, David A. ; Putten, W.H. van der - \ 2019
    decomposition - microbial community - fungi - sequencing - ITS - home-field advantage
    Increasing evidence suggests that specific interactions between microbial decomposers and plant litter, named home field advantage (HFA), influence litter breakdown. However, we still have limited understanding of whether HFA relates to specific microbiota, and whether specialized microbes originate from the soil or from the leaf microbiome. Here, we disentangle the roles of soil origin, litter types, and the microbial community already present on the leaf litter in determining fungal community composition on decomposing leaf litter and HFA. We collected litters and associated soil samples from a secondary succession gradient ranging from herbaceous vegetation on recently abandoned ex‐arable fields to forest representing the end stage of succession. In a greenhouse, sterilized and unsterilized leaf litters were decomposed for 12 months in soils from early to late successional stages according to a full factorial design. At the end, we examined fungal community composition on the decomposing litter. Fungal communities on decomposed late‐successional litter in late‐successional soil differed from those in early‐ and mid‐successional stage litter and soil combinations. Soil source had the strongest impact on litter fungal composition when using sterilized litter, while the impact of litter type was strongest when using unsterilized litter. Overall, we observed HFA, as litter decomposition was accelerated in home soils. Increasing HFA did not relate to the dissimilarity in overall fungal composition, but there was increasing dissimilarity in the relative abundance of the most dominant fungal taxon between decomposing litter in home and away soils. We conclude that early, mid and late succession litter types did not exert strong selection effects on colonization by microorganisms from the soil species pool. Instead, fungal community composition on decomposing litter differed substantially between litter types for unsterilized litter, suggesting that the leaf microbiome, either directly or indirectly, is an important determinant of fungal community composition on decomposing leaves. HFA related most strongly to the abundance of the most dominant fungal taxa on the decomposing litter, suggesting that HFA may be attributed to some specific dominant fungi rather than to responses of the whole fungal community.
    In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae
    Shi-Kunne, Xiaoqian ; Pedro Jové, Roger de; Depotter, Jasper R.L. ; Ebert, Malaika K. ; Seidl, Michael F. ; Thomma, Bart P.H.J. - \ 2019
    FEMS Microbiology Letters 366 (2019)7. - ISSN 0378-1097
    fungi - genomics - natural product - pathogen - Verticillium

    Fungi are renowned producers of natural compounds, also known as secondary metabolites (SMs) that display a wide array of biological activities. Typically, the genes that are involved in the biosynthesis of SMs are located in close proximity to each other in so-called secondary metabolite clusters. Many plant-pathogenic fungi secrete SMs during infection in order to promote disease establishment, for instance as cytocoxic compounds. Verticillium dahliae is a notorious plant pathogen that can infect over 200 host plants worldwide. However, the SM repertoire of this vascular pathogen remains mostly uncharted. To unravel the potential of V. dahliae to produce SMs, we performed in silico predictions and in-depth analyses of its secondary metabolite clusters. Using distinctive traits of gene clusters and the conserved signatures of core genes 25 potential SM gene clusters were identified. Subsequently, phylogenetic and comparative genomics analyses were performed, revealing that two putative siderophores, ferricrocin and TAFC, DHN-melanin and fujikurin may belong to the SM repertoire of V. dahliae.

    Relationships between fungal community composition in decomposing leaf litter and home-field advantage effects
    Veen, G.F. ; Snoek, Basten L. ; Bakx-Schotman, Tanja ; Wardle, David A. ; Putten, Wim H. van der - \ 2019
    Functional Ecology 33 (2019)8. - ISSN 0269-8463 - p. 1524 - 1535.
    decomposition - fungi - ITS - microbial community - sequencing - succession

    Increasing evidence suggests that specific interactions between microbial decomposers and plant litter, named home-field advantage (HFA), influence litter breakdown. However, we still have limited understanding of whether HFA relates to specific microbiota, and whether specialized microbes originate from the soil or from the leaf microbiome. Here, we disentangle the roles of soil origin, litter types and the microbial community already present on the leaf litter in determining fungal community composition on decomposing leaf litter and HFA. We collected litters and associated soil samples from a secondary succession gradient ranging from herbaceous vegetation on recently abandoned ex-arable fields to forest representing the end stage of succession. In a greenhouse, sterilized and unsterilized leaf litters were decomposed for 12 months in soils from early- to late-successional stages according to a full-factorial design. At the end, we examined fungal community composition on the decomposing litter. Fungal communities on decomposed late-successional litter in late-successional soil differed from those in early- and mid-successional stage litter and soil combinations. Soil source had the strongest impact on litter fungal composition when using sterilized litter, while the impact of litter type was strongest when using unsterilized litter. Overall, we observed HFA, as litter decomposition was accelerated in home soils. Increasing HFA did not relate to the dissimilarity in overall fungal composition, but there was increasing dissimilarity in the relative abundance of the most dominant fungal taxon between decomposing litter in home and away soils. We conclude that early-, mid- and late-succession litter types did not exert strong selection effects on colonization by micro-organisms from the soil species pool. Instead, fungal community composition on decomposing litter differed substantially between litter types for unsterilized litter, suggesting that the leaf microbiome, either directly or indirectly, is an important determinant of fungal community composition on decomposing leaves. HFA related most strongly to the abundance of the most dominant fungal taxa on the decomposing litter, suggesting that HFA may be attributed to some specific dominant fungi rather than to responses of the whole fungal community. A plain language summary is available for this article.

    Schimmel zet stro om in veevoer
    Cone, J.W. ; Sonnenberg, A.S.M. ; Nayan, Nazri ; Mao, Lei ; Ratni, E. - \ 2018
    biobased economy - animal nutrition - biomass - agricultural wastes - cellulose - fungi
    Continental-scale macrofungal assemblage patterns correlate with climate, soil carbon and nitrogen deposition
    Andrew, Carrie ; Halvorsen, Rune ; Heegaard, Einar ; Kuijper, Thomas W. ; Heilmann-Clausen, Jacob ; Krisai-Greilhuber, Irmgard ; Bässler, Claus ; Egli, Simon ; Gange, Alan C. ; Høiland, Klaus ; Kirk, Paul M. ; Senn-Irlet, Beatrice ; Boddy, Lynne ; Büntgen, Ulf ; Kauserud, Håvard - \ 2018
    Journal of Biogeography 45 (2018)8. - ISSN 0305-0270 - p. 1942 - 1953.
    assemblage - biogeography - climate - ectomycorrhizal - Europe - fungi - macroecology - saprotrophic - temporal change

    Aim: Macroecological scales of species compositional trends are well documented for a variety of plant and animal groups, but remain sparse for fungi, despite their ecological importance in carbon and nutrient cycling. It is, thus, essential to understand the composition of fungal assemblages across broad geographical scales and the underlying drivers. Our overall aim was to describe these patterns for fungi across two nutritional modes (saprotrophic and ectomycorrhizal). Furthermore, we aimed to elucidate the temporal component of fruiting patterns and to relate these to soil carbon and nitrogen deposition. Location: Central and Northern Europe. Methods: A total of 4.9 million fungal fruit body observations throughout Europe, collected between 1970 and 2010, were analysed to determine the two main environmental and geographical gradients structuring fungal assemblages for two main nutritional modes, saprotrophic and ectomycorrhizal fungi. Results: Two main gradients explaining the geography of compositional patterns were identified, for each nutritional mode. Mean annual temperature (and related collinear, seasonal measures) correlated most strongly with the first gradient for both nutritional modes. Soil organic carbon was the highest correlate of the second compositional gradient for ectomycorrhizal fungi, suspected as an indicator of vegetation- and pH-related covariates. In contrast, nitrogen deposition constituted a second gradient for saprotrophic fungi, likely a proxy for anthropogenic pollution. Compositional gradients and environmental conditions correlated similarly when the data were divided into two time intervals of 1970–1990 and 1991–2010. Evidence of compositional temporal change was highest with increasing elevation and latitude. Main conclusions: Fungal assemblage patterns demonstrate clear biogeographical patterns that relate the nutritional modes to their main environmental correlates of temperature, soil organic carbon and nitrogen deposition. With respect to global change impacts, the highest rates of compositional change by time suggest targeting higher latitudes and elevations for a better understanding of fungal dynamics. We, finally, suggest further examination of the ranges and dispersal abilities of fungi to better assess responses to global change.

    Data from: Explaining European fungal fruiting phenology with climate variability
    Andrew, Carrie ; Heegaard, Einar ; Høiland, Klaus ; Senn-Irlet, Beatrice ; Kuijper, T.W.M. ; Krisai-Greilhuber, Irmgard ; Kirk, Paul M. ; Heilmann-Clausen, Jacob ; Gange, Alan C. ; Egli, Simon ; Bässler, Claus ; Büntgen, Ulf ; Boddy, Lynne ; Kauserud, Håvard - \ 2018
    climate - fungi - fruit bodies - distribution - NDVI - nutritional mode - path analysis - phenology
    Here we assess the impact of geographically dependent (latitude, longitude and altitude) changes in bioclimatic (temperature, precipitation and primary productivity) variability on fungal fruiting phenology across Europe. Two main nutritional guilds of fungi, saprotrophic and ectomycorrhizal, were further separated into spring and autumn fruiters. We used a path‐analysis to investigate how biogeographic patterns in fungal fruiting phenology coincided with seasonal changes in climate and primary production. Across central to northern Europe, mean fruiting varied by approximately 25 days, primarily with latitude. Altitude affected fruiting by up to 30 days, with spring delays and autumnal accelerations. Fruiting was as much explained by the effects of bioclimatic variability as by their large‐scale spatial patterns. Temperature drove fruiting of autumnal ectomycorrhizal and saprotrophic, as well as spring saprotrophic groups, while primary production and precipitation were major drivers for spring‐fruiting ectomycorrhizal fungi. Species‐specific phenology predictors were not stable, instead deviating from the overall mean. There is significant likelihood that further climatic change, especially in temperature, will impact fungal phenology patterns at large spatial scales. The ecological implications are diverse, potentially affecting food webs (asynchrony), nutrient cycling and the timing of nutrient availability in ecosystems.
    Explaining European fungal fruiting phenology with climate variability
    Andrew, Carrie ; Heegaard, Einar ; Høiland, Klaus ; Senn-Irlet, Beatrice ; Kuyper, Thomas W. ; Krisai-Greilhuber, Irmgard ; Kirk, Paul M. ; Heilmann-Clausen, Jacob ; Gange, Alan C. ; Egli, Simon ; Bässler, Claus ; Büntgen, Ulf ; Boddy, Lynne ; Kauserud, Håvard - \ 2018
    Ecology 99 (2018)6. - ISSN 0012-9658 - p. 1306 - 1315.
    climate - distribution - Europe - fruit bodies - fungi - NDVI - nutritional mode - path analysis - phenology
    Here we assess the impact of geographically dependent (latitude, longitude, and altitude) changes in bioclimatic (temperature, precipitation, and primary productivity) variability on fungal fruiting phenology across Europe. Two main nutritional guilds of fungi, saprotrophic and ectomycorrhizal, were further separated into spring and autumn fruiters. We used a path analysis to investigate how biogeographic patterns in fungal fruiting phenology coincided with seasonal changes in climate and primary production. Across central to northern Europe, mean fruiting varied by approximately 25 d, primarily with latitude. Altitude affected fruiting by up to 30 d, with spring delays and autumnal accelerations. Fruiting was as much explained by the effects of bioclimatic variability as by their large-scale spatial patterns. Temperature drove fruiting of autumnal ectomycorrhizal and saprotrophic groups as well as spring saprotrophic groups, while primary production and precipitation were major drivers for spring-fruiting ectomycorrhizal fungi. Species-specific phenology predictors were not stable, instead deviating from the overall mean. There is significant likelihood that further climatic change, especially in temperature, will impact fungal phenology patterns at large spatial scales. The ecological implications are diverse, potentially affecting food webs (asynchrony), nutrient cycling and the timing of nutrient availability in ecosystems.
    Nucleus-specific expression in the multinuclear mushroom-forming fungus Agaricus bisporus reveals different nuclear regulatory programs
    Gehrmann, Thies ; Pelkmans, Jordi F. ; Ohm, Robin A. ; Vos, Aurin M. ; Sonnenberg, Anton S.M. ; Baars, Johan J.P. ; Wösten, Han A.B. ; Reinders, Marcel J.T. ; Abeel, Thomas - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)17. - ISSN 0027-8424 - p. 4429 - 4434.
    fungi - heterokaryon - Nuclear-specific expression - quantification - RNA-seq
    Many fungi are polykaryotic, containing multiple nuclei per cell. In the case of heterokaryons, there are different nuclear types within a single cell. It is unknown what the different nuclear types contribute in terms of mRNA expression levels in fungal heterokaryons. Each cell of the mushroom Agaricus bisporus contains two to 25 nuclei of two nuclear types originating from two parental strains. Using RNA-sequencing data, we assess the differential mRNA contribution of individual nuclear types and its functional impact. We studied differential expression between genes of the two nuclear types, P1 and P2, throughout mushroom development in various tissue types. P1 and P2 produced specific mRNA profiles that changed through mushroom development. Differential regulation occurred at the gene level, rather than at the locus, chromosomal, or nuclear level. P1 dominated mRNA production throughout development, and P2 showed more differentially up-regulated genes in important functional groups. In the vegetative mycelium, P2 up-regulated almost threefold more metabolism genes and carbohydrate active enzymes (cazymes) than P1, suggesting phenotypic differences in growth. We identified widespread transcriptomic variation between the nuclear types of A. bisporus. Our method enables studying nucleus-specific expression, which likely influences the phenotype of a fungus in a polykaryotic stage. Our findings have a wider impact to better understand gene regulation in fungi in a heterokaryotic state. This work provides insight into the transcriptomic variation introduced by genomic nuclear separation.
    How do you cultivate world's biggest mushroom?
    Vreeburg, S.M.E. - \ 2017
    Wageningen : WURcast
    fungi - meat alternates
    Sabine Vreeburg will talk about termites that cultivate fungus and growing mushrooms. Could mushrooms be the substitution of meat in the future?
    Data from: Trait-dependent distributional shifts in fruiting of common British fungi
    Gange, A.C. ; Heegaard, E. ; Boddy, L. ; Kirk, P.M. ; Halvorsen, R. ; Kuijper, T.W.M. ; Bässler, C. ; Diez, J. ; Heilman-Clausen, J. ; Høiland, K. ; Büntgen, U. ; Kauserud, H. - \ 2017
    fungal ecology - global change biology - community ecology - biogeography - fungi - Agaricomycetes
    Despite the dramatic phenological responses of fungal fruiting to recent climate warming, it is unknown whether spatial distributions of fungi have changed and to what extent such changes are influenced by fungal traits, such as ectomycorrhizal (ECM) or saprotrophic lifestyles, spore characteristics, or fruit body size. Our overall aim was to understand how climate and fungal traits determine whether and how species-specific fungal fruit body abundances have shifted across latitudes over time, using the UK national database of fruiting records. The data employed were recorded over 45 years (1970 – 2014), and include 853,278 records of Agaricales, Boletales and Russulales, though we focus only on the most common species (with more than 3,000 records each). The georeferenced observations were analysed by a Bayesian inference as a Gaussian Additive Model with a specification following a joint species distribution model. We used an offset, random contributions and fixed effects to isolate different potential biases from the trait-specific interactions with latitude/climate and time. Our main aim was assessed by examination of the three-way-interaction of trait, predictor (latitude or climate) and time. The results show a strong trait-specific shift in latitudinal abundance through time, as ECM species have become more abundant relative to saprotrophic species in the north. Along precipitation gradients, phenology was important, in that species with shorter fruiting seasons have declined markedly in abundance in oceanic regions, whereas species with longer seasons have become relatively more common overall. These changes in fruit body distributions are correlated with temperature and rainfall, which act directly on both saprotrophic and ECM fungi, and also indirectly on ECM fungi, through altered photosynthate allocation from their hosts. If these distributional changes reflect fungal activity, there will be important consequences for the responses of forest ecosystems to changing climate, through effects on primary production and nutrient cycling.
    Unravelling the genetic base of the meiotic recombination landscapes in two varieties of the button mushroom, Agaricus bisporus
    Sedaghat Telgerd, Narges - \ 2017
    Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): A.S.M. Sonnenberg. - Wageningen : Wageningen University - ISBN 9789463436953 - 142
    fungi - agaricus bisporus - mushrooms - genetics - breeding - meiosis - recombination - schimmels - agaricus bisporus - paddestoelen - genetica - veredelen - meiose - recombinatie

    The button mushroom, Agaricus bisporus var. bisporus, is one of the most cultivated mushrooms worldwide. Even though wild isolates of this variety have a broad genetic variation, the traditional and present-day hybrids only have a very narrow genetic base. The button mushroom has a typical meiotic recombination landscape (MRL) in which crossover (CO) events are predominantly restricted to the extreme ends of the chromosomes. This has been one of the main obstacles for mushroom breeders in improving or generating new mushroom hybrids due to a considerable linkage drag. A wild variety of A. bisporus, i.e., burnettii appeared to have CO spread more evenly across the genome. The existence of two extremely different MRLs in two compatible A. bisporus varieties offers an excellent opportunity to study the genetic basis for positioning CO in meiosis. The main objective of the research presented in this thesis initially was to examine meiosis of the var. burnettii in more detail and subsequently to identify genomic regions revealing the difference in MRL of the two A. bisporus varieties. The availability of genome sequences in the bisporus variety has produced many more informative markers such as SNP. We aimed to de novo sequence one of the haplotypes of a heterokaryotic strain of the burnettii variety using the PacBio sequencing technique and resequencing the other haplotype using Illumina HiSeq. In parallel to this, we used Genotyping by Sequencing (GBS) to construct the first linkage map of the burnettii variety, showing a more or less even distribution of COs across the genome. The constructed linkage map has also proved to be a useful tool for de novo assembly of the burnettii variety genome sequence. In addition, we performed comparative genome sequence studies between the burnettii variety and the previously sequenced genomes of two of the bisporus variety homokaryons, indicating high levels of collinearity between all three genomes. The only chromosomal rearrangement to be found was on chromosome 10, where an inversion of ~ 800 kb in the burnettii variety was detected compared to the var. bisporus genomes. As a starting point for unravelling the genetic basis underlying MRL in the A. bisporus, we performed quantitative trait loci (QTL) analysis using bisporus and burnettii varieties. An inter-varietal population was developed from a cross between a constituent nucleus of the bisporus and the burnettii variety. This population contains 178 haploid progenies which were genotyped by 210 SNP markers to construct a genetic linkage map, which proves to be a solid foundation for exploring the genetic control of MRL of A. bisporus. In addition, we performed a comparative genetic mapping study using the genetic maps of the bisporus variety Horst U1, the burnettii variety Bisp119/9 and the inter-varietal hybrid by selecting markers having similar positions in these three maps. In contrast to the bisporus variety where CO events are mainly restricted to chromosome ends, the burnettii variety shows a more or less equal distribution of CO events across the entire genome. The recombination landscape of the inter-varietal hybrid shows an intermediate pattern to that of both varieties. The MRL trait is expressed as a CO event in the offspring of each individual of the inter-varietal mapping population. For this reason, the individuals of the inter-varietal mapping population were intercrossed and outcrossed to generate three types of second generation hybrids. Two compatible tester homokaryons derived from the bisporus and burnettii varieties were used for outcrossing. Subsequently, the haploid progenies from each type of second generation hybrids were isolated to generate three types of segregating populations. The haploid progenies from segregating populations were genotyped with SNP markers covering the whole length of all the chromosomes. Recombination frequencies were determined at distal ends and elsewhere on the chromosomes and used to compare recombination frequencies between chromosomes within each population as well as between segregating populations across all chromosomes. A prerequisite for successful QTL mapping the MRL is to select segregating populations in which the segregation of MRL is clear. We observed that segregating populations outcrossed with the bisporus tester homokaryon were the most useful populations to generate haploid offspring in which COs are assessed for further QTL study of MRL at the time when this research was carried out. To map genomic regions involved in the different MRLs of A. bisporus, 71 homokaryotic offspring of the inter-varietal hybrid were outcrossed with an unrelated tester homokaryon of the bisporus variety. Subsequently, the haploid progenies were isolated from each hybrid and genotyped with SNP markers. Marker pairs were generated for the end regions of chromosomes to assess CO there or anywhere else on the chromosomes for each segregating population. QTL mapping analysis revealed two QTLs located on chromosome l and three others located on chromosomes IV, VI and VII. The QTLs identified span large parts of their respective chromosomes; therefore further strategies are needed for a more precise assessment and localisation of MRL.

    The role of strigolactones and the fungal microbiome in rice during drought adaptation
    Andreo Jimenez, Beatriz - \ 2017
    Wageningen University. Promotor(en): H.J. Bouwmeester, co-promotor(en): C. Ruyter-Spira. - Wageningen : Wageningen University - ISBN 9789463437028 - 205
    drought resistance - drought - abiotic injuries - rice - oryza sativa - plant-microbe interactions - nutrient uptake - defence mechanisms - hormones - fungi - genes - droogteresistentie - droogte - abiotische beschadigingen - rijst - oryza sativa - plant-microbe interacties - voedingsstoffenopname (planten) - verdedigingsmechanismen - hormonen - schimmels - genen

    Rice is the most important food crop in the world, feeding over half the world’s population. However, rice water use efficiency, defined by units of yield produced per unit of water used, is the lowest of all crops. The aim of this thesis was to study the effect of plant hormones and the root microbiome on drought tolerance in rice. The new plant hormone, strigolactone, was shown to be upregulated under drought and to regulate drought tolerance in interaction with the drought-hormone abscisic acid. Using a large collection of rice genotypes grown in the field, we showed that the composition of the root associated fungal microbiome is determined by the rice genotype and can contribute to drought tolerance.

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