Monica Skogen

Lead Engineer

(+47) 452 19 095

Ås H7

Visiting address
Høgskoleveien 7, 1433 Ås


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.


Aquatic microbial diversity, composition, and dynamics play vital roles in sustaining water ecosystem functionality. Yet, there is still limited knowledge on bacterial seasonal dynamics in lotic environments. This study explores a temporal pattern of bacterial community structures in lotic freshwater over a 2-year period. The aquatic bacterial communities were assessed using Illumina MiSeq sequencing of 16S rRNA genes. Overall, the communities were dominated by α-, β-, and γ-Proteobacteria, Bacteroidetes, Flavobacteriia, and Sphingobacteriia. The bacterial compositions varied substantially in response to seasonal changes (cold vs. warm), but they were rather stable within the same season. Furthermore, higher diversity was observed in cold seasons compared to warm periods. The combined seasonal-environmental impact of different physico-chemical parameters was assessed statistically, and temperature, suspended solids, and nitrogen were determined to be the primary abiotic factors shaping the temporal bacterial assemblages. This study enriches particular knowledge on the seasonal succession of the lotic freshwater bacteria.

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Potato soft rot Pectobacteriaceae (SRP) cause large yield losses and are persistent in seed lots once established. In Norway, different Pectobacterium species are the predominant cause of soft rot and blackleg disease. This work aimed to evaluate the potential of real-time PCR for quantification of SRP in seed tubers, as well as investigating the status of potato seed health with respect to SRP in Norway. A total of 34 seed potato lots, including certified seeds, was grown and monitored over three consecutive years. All seed lots contained a quantifiable amount of SRP after enrichment, with very few subsamples being free of the pathogens. A high SRP prevalence based on a qPCR assay, as well as a high symptom incidence in certified seeds were observed, suggesting that current criteria for seed certification are insufficient to determine tuber health and predict field outcomes. Pectobacterium atrosepticum was the most abundant species in the examined seed lots and present in all lots. Consistently good performance of first generation seed lots with respect to blackleg and soft rot incidence, as well as low quantity of SRP in these seed lots demonstrated the importance of clean seed potatoes. Weather conditions during the growing season seemed to govern disease incidence and SRP prevalence more than seed grade. The impact of temperature, potato cultivar and Pectobacterium species on tuber soft rot development were further examined in tuber infection experiments, which showed that temperature was the most important factor in nearly all cultivars. Large-scale quantification of latent infection and predictive models that include contributing factors like weather, infecting bacterial species and cultivar are needed to reduce soft rot and blackleg.


The prevalence of Fusarium dry rot in potatoes produced in Norway was investigated in a survey for three consecutive years in the period 2010 to 2012. A total of 238 samples (comprising 23,800 tubers) were collected, representing different cultivars and production regions in Norway. Fusarium spp. were detected in 47% of the samples, with one to three species per sample. In total, 718 isolates of Fusarium spp. were recovered and identified to seven species. The most commonly isolated species was Fusarium coeruleum, comprising 59.6% of the total Fusarium isolates and found in 17.2% of the collected samples, followed by Fusarium avenaceum (27.2% of the isolates and found in 27.7% of the samples). Fusarium sambucinum was the third most prevalent species (6.4% in 8.8% of the samples) and Fusarium culmorum the fourth (5.2% in 6.3% of the samples). Less prevalent species included Fusarium cerealis, Fusarium graminearum, and Fusarium equiseti (<1% in 0.4 to 1.3% of the samples). F. coeruleum was the most prevalent species in northern and southwestern Norway, whereas F. avenaceum was dominating in eastern Norway. The potato cultivars Berber and Rutt were susceptible to all Fusarium spp. A new TaqMan real-time PCR assay specific for F. coeruleum was developed, which successfully identified Norwegian isolates. This and other previously developed real-time PCR assays targeting different Fusarium species were evaluated for their ability to detect latent infections in potatoes at harvest. This study provides new information on the current occurrence of different Fusarium species causing Fusarium dry rot in potatoes in Europe including areas far into the arctic in the north of Norway.