Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2021
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Plants with roots and soil clumps transported over long distances in plant trading can harbor plant pathogenic oomycetes, facilitating disease outbreaks that threaten ecosystems, biodiversity, and food security. Tools to detect the presence of such oomycetes with a sufficiently high throughput and broad scope are currently not part of international phytosanitary testing regimes. In this work, DNA metabarcoding targeting the internal transcribed spacer (ITS) region was employed to broadly detect and identify oomycetes present in soil from internationally shipped plants. This method was compared to traditional isolation-based detection and identification after an enrichment step. DNA metabarcoding showed widespread presence of potentially plant pathogenic Phytophthora and Pythium species in internationally transported rhizospheric soil with Pythium being the overall most abundant genus observed. Baiting, a commonly employed enrichment method for Phytophthora species, led to an increase of golden-brown algae in the soil samples, but did not increase the relative or absolute abundance of potentially plant pathogenic oomycetes. Metabarcoding of rhizospheric soil yielded DNA sequences corresponding to oomycete isolates obtained after enrichment and identified them correctly but did not always detect the isolated oomycetes in the same samples. This work provides a proof of concept and outlines necessary improvements for the use of environmental DNA (eDNA) and metabarcoding as a standalone phytosanitary assessment tool for broad detection and identification of plant pathogenic oomycetes.
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Paal Krokene Bjørn Arild Hatteland Christer Magnusson Daniel Flø Iben Margrete Thomsen Johan A. Stenberg May Bente Brurberg Per Hans Micael Wendell Mogens Nicolaisen Simeon Rossmann Venche Talgø Beatrix Alsanius Sandra A.I. Wright Trond RafossAbstract
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2020
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Ahto Agan Rein Drenkhan Kalev Adamson Leho Tedersoo Halvor Solheim Isabella Børja Iryna Matsiakh Volkmar Timmermann Nina Elisabeth Nagy Ari HietalaAbstract
European ash (Fraxinus excelsior) is threatened by the invasive ascomycete Hymenoscyphus fraxineus originating from Asia. Ash leaf tissues serve as a route for shoot infection but also as a sporulation substrate for this pathogen. Knowledge of the leaf niche partitioning by indigenous fungi and H. fraxineus is needed to understand the fungal community receptiveness to the invasion. We subjected DNA extracted from unwashed and washed leaflets of healthy and diseased European ash to PacBio sequencing of the fungal ITS1-5.8S-ITS2 rDNA region. Leaflets from co-inhabiting rowan trees (Sorbus aucuparia) served as a reference. The overlap in leaflet mycobiomes between ash and rowan was remarkably high, but unlike in rowan, in ash leaflets the sequence read proportion, and the qPCR-based DNA amount estimates of H. fraxineus increased vigorously towards autumn, concomitant with a significant decline in overall fungal richness. The niche of ash and rowan leaves was dominated by epiphytic propagules (Vishniacozyma yeasts, the dimorphic fungus Aureobasidion pullulans and the dematiaceous hyphomycete Cladosporium ramotenellum and H. fraxineus), and endophytic thalli of biotrophs (Phyllactinia and Taphrina species), the indigenous necrotroph Venturia fraxini and H. fraxineus. Mycobiome comparison between healthy and symptomatic European ash leaflets revealed no significant differences in relative abundance of H. fraxineus, but A. pullulans was more prevalent in symptomatic trees. The impacts of host specificity, spatiotemporal niche partitioning, species carbon utilization profiles and life cycle traits are discussed to understand the ecological success of H. fraxineus in Europe. Further, the inherent limitations of different experimental approaches in the profiling of foliicolous fungi are addressed.
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Authors
Heidi Udnes Aamot Erik Lysøe Shiori Koga Katherine Ann Gredvig Nielsen Ulrike Böcker Guro Brodal Ruth Dill-Macky Anne Kjersti Uhlen Ingerd Skow HofgaardAbstract
The bread-making quality of wheat depends on the viscoelastic properties of the dough in which gluten proteins play an important role. The quality of gluten proteins is influenced by the genetics of the different wheat varieties and environmental factors. Occasionally, a near complete loss of gluten strength, measured as the maximum resistance towards stretching (Rmax), is observed in grain lots of Norwegian wheat. It is hypothesized that the loss of gluten quality is caused by degradation of gluten proteins by fungal proteases. To identify fungi associated with loss of gluten strength, samples from a selection of wheat grain lots with weak gluten (n = 10, Rmax < 0.3 N) and strong gluten (n = 10, Rmax ≥ 0.6 N) was analyzed for the abundance of fungal operational taxonomic units (OTUs) using DNA metabarcoding of the nuclear ribosomal Internal Transcribed Spacer (ITS) region ITS1. The DNA quantities for a selection of fungal pathogens of wheat, and the total amount of fungal DNA, were analyzed by quantitative PCR (qPCR). The mean level of total fungal DNA was higher in grain samples with weak gluten compared to grain samples with strong gluten. Heightened quantities of DNA from fungi within the Fusarium Head Blight (FHB) complex, i.e. Fusarium avenaceum, Fusarium graminearum, Microdochium majus, and Microdochium nivale, were observed in grain samples with weak gluten compared to those with strong gluten. Microdochium majus was the dominant fungus in the samples with weak gluten. Stepwise regression modeling based on different wheat quality parameters, qPCR data, and the 35 most common OTUs revealed a significant negative association between gluten strength and three OTUs, of which the OTU identified as M. majus was the most abundant. The same analysis also revealed a significant negative relationship between gluten strength and F. avenaceum detected by qPCR, although the DNA levels of this fungus were low compared to those of M. majus. In vitro growth rate studies of a selection of FHB species showed that all the tested isolates were able to grow with gluten as a sole nitrogen source. In addition, proteins secreted by these fungi in liquid cultures were able to hydrolyze gluten substrate proteins in zymograms, confirming their capacity to secrete gluten-degrading proteases. The identification of fungi with potential to influence gluten quality can enable the development of strategies to minimize future problems with gluten strength in food-grade wheat.