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
Authors
Paal KrokeneAbstract
No abstract has been registered
Abstract
No abstract has been registered
Authors
Ian K. Toth Marie-anne Barny May Bente Brurberg Guy Condemine Robert Czajkowski John G. Elphinstone Valérie Helias Steven B. Johnson Lucy N. Moleleki Minna Pirhonen Simeon Rossmann Leah Tsror Jacquie E. van der Waals Jan M. van der Wolf Frédérique Van Gijsegem Iris YedidiaAbstract
The soft rot Pectobacteriaceae (SRP) infect a wide range of plants worldwide and cause economic damage to crops and ornamentals but can also colonize other plants as part of their natural life cycle. They are found in a variety of environmental niches, including water, soil and insects, where they may spread to susceptible plants and cause disease. In this chapter, we look in detail at the plants colonized and infected by these pathogens and at the diseases and symptoms they cause. We also focus on where in the environment these organisms are found and their ability to survive and thrive there. Finally, we present evidence that SRP may assist the colonization of human enteric pathogens on plants, potentially implicating them in aspects of human/animal as well as plant health.
Authors
Jan M. van der Wolf Ivette Acuña Solke H. De Boer May Bente Brurberg Greig Cahill Amy O. Charkowski Teresa Coutinho Triona Davey Merete Wiken Dees Yeshitila Degefu Brice Dupuis John G. Elphinstone Jiaqin Fan Esmaeil Fazelisanagri Thomas Fleming Nahid Gerayeli Vladimir Gorshkov Valérie Helias Yves le Hingrat Steven B. Johnson Andreas Keiser Isabelle Kellenberger Xiang (Sean) Li Ewa Lojkowska Rodney Martin Juliana Perminow Olga Petrova Agata Motyka-Pomagruk Simeon Rossmann Santiago Schaerer Wojciech Sledz Ian K. Toth Leah Tsror Jacquie E. van der Waals Patrice de Werra Iris YedidiaAbstract
Soft rot Pectobacteriaceae (SRP) are ubiquitous on earth as there are records of findings from all continents where host plants are grown. This chapter describes information on soft rot diseases on these continents. For some countries, detailed information is provided by local experts on the SRP present, their economic damage, and the management strategies applied for their control. The focus of the chapter is mainly on SRP as causative agents of potato blackleg, although in specific cases details are provided on SRP in other host plants. In Europe, the SRP cause important economic losses mainly on potato, with most species described in the literature being found. In Latin America significant losses are also reported due to potato diseases caused by various Dickeya and Pectobacterium species, while in Australia and Oceania, recent outbreaks of D. dianthicola in potato have resulted in high economic losses. In Asia, however, SRP cause economic losses mainly in vegetable crops other than potato, while in North America SRP cause diseases on a wide range of crops (including potato and ornamental plants) in both field and storage. In Africa SRP are only known to occur in 17 of the 54 African countries but where it is known, potato is the most affected crop.
Abstract
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.
Authors
Line Nybakken Inger Sundheim Fløistad Melissa Magerøy Maren Lomsdal Solveig Strålberg Paal Krokene Johan AsplundAbstract
Nursery-grown Norway spruce Picea abies seedlings are often heavily attacked by the pine weevil Hylobius abietis on clear-cuts the first years after planting. Because the seedlings are not resource-limited during the growing phase in the nursery they are expected to invest less in defence than naturally regenerated seedlings already present on the clear-cuts. The latter have had to cope with various environmental stressors that could make them invest more in defence. We tested if naturally regenerated plants have stronger chemical defences than nursery-grown plants. Nursery-grown plants were planted in-between naturally regenerated plants on fresh clear cuts, and phenolic and terpene compounds in the stem bark were measured after one growing season. To test both constitutive and inducible defences, plants were either wounded, painted with methyl jasmonate (MeJA) to induce defences, or given a combination of both treatments. Growth and pine weevil attacks of the plants were registered. Nursery-grown plants had higher total concentrations of phenolic compounds and lower concentrations of terpenes than naturally regenerated plants. These opposite responses were reflected in very different compound profiles in the two plant types. We suggest the differences between plant types to be results of differences in plant age, stress level, genetic origin or possibly a combination of these factors. Most compounds showed no response to wounding, MeJA-treatment or wounding and MeJA-treatment combined, but the terpenes 3-carene, eucalyptol, limonene and para-cymene had higher concentrations in MeJA-treated nursery-grown plants than in control plants. These compounds are known to be effective in conifer resistance against weevils and bark beetles. Overall, 27% of our 400 study plants had signs of pine weevil damage after 3 ½ months in the field. However, treatment or plant type had no significant effect on whether plants were attacked or not and this might have been a result of the relatively low overall level of attacks in this study. Further studies are needed to disentangle the importance of plant age, stress level, genetic origin and resource availability for chemical defence mechanisms of young Norway spruce plants, as strengthening the natural resistance of nursery plants may be increasingly important in a future with less pesticide use.
Abstract
Methyl jasmonate (MeJA) treatment elicits induced resistance (IR) against pests and diseases in Norway spruce (Picea abies). We recently demonstrated using mRNA-seq that this MeJA-IR is associated with both a prolonged upregulation of inducible defenses and defense priming. Gene expression can be regulated at both a transcrip-tional and post-transcriptional level by small RNAs, including microRNAs (miRNAs). Here we explore the effects of MeJA treatment and subsequent challenge by wounding on the Norway spruce miRNA transcriptome. We found clusters of prolonged down- or upregulated miRNAs as well as miRNAs whose expression was primed after MeJA treatment and subsequent wounding challenge. Differentially expressed miRNAs included miR160, miR167, miR172, miR319, and the miR482/2118 superfamily. The most prominent mRNA targets predicted to be differentially expressed by miRNA activity belonged to the nucleotide-binding site leucine-rich repeat (NBS- LRR) family. Among other predicted miRNA targets were genes regulating jasmonic acid biosynthesis. Our re-sults indicate that miRNAs have an important role in the regulation of MeJA-IR in Norway spruce.
Authors
Ming Tian Xinmiao He Yanzhong Feng Wentao Wang Heshu Chen Ming Gong Di Liu Jihong Liu Clarke Andre van EerdeAbstract
The demand for animal protein has increased considerably worldwide, especially in China, where large numbers of livestock and poultry are produced. Antibiotics have been widely applied to promote growth and prevent diseases. However, the overuse of antibiotics in animal feed has caused serious environmental and health risks, especially the wide spread of antimicrobial resistance (AMR), which seriously affects animal and human health, food safety, ecosystems, and the sustainable future development of animal protein production. Unfortunately, AMR has already become a worldwide challenge, so international cooperation is becoming more important for combatting it. China’s efforts and determination to restrict antibiotic usage through law enforcement and effective management are of significance. In this review, we address the pollution problems of antibiotics; in particular, the AMR in water, soil, and plants caused by livestock and poultry manure in China. The negative impact of widespread and intensive use of antibiotics in livestock production is discussed. To reduce and mitigate AMR problems, we emphasize in this review the development of antibiotic substitutes for the era of antibiotic prohibition.
Authors
Natasha Sant'Anna Iwanicki Ana Beatriz Riguetti Zanardo Botelho Ingeborg Klingen Italo Delalibera Júnior Simeon Rossmann Erik LysøeAbstract
The genus Metarhizium is composed of species used in biological control programs of agricultural pests worldwide. This genus includes common fungal pathogen of many insects and mites and endophytes that can increase plant growth. Metarhizium humberi was recently described as a new species. This species is highly virulent against some insect pests and promotes growth in sugarcane, strawberry, and soybean crops. In this study, we sequenced the genome of M. humberi, isolate ESALQ1638, and performed a functional analysis to determine its genomic signatures and highlight the genes and biological processes associated with its lifestyle. The genome annotation predicted 10633 genes in M. humberi, of which 92.0% are assigned putative functions, and ∼17% of the genome was annotated as repetitive sequences. We found that 18.5% of the M. humberi genome is similar to experimentally validated proteins associated with pathogen–host interaction. Compared to the genomes of eight Metarhizium species, the M. humberi ESALQ1638 genome revealed some unique traits that stood out, e.g., more genes functionally annotated as polyketide synthases (PKSs), overrepresended GO-terms associated to transport of ions, organic and amino acid, a higher percentage of repetitive elements, and higher levels of RIP-induced point mutations. The M. humberi genome will serve as a resource for promoting studies on genome structure and evolution that can contribute to research on biological control and plant biostimulation. Thus, the genomic data supported the broad host range of this species within the generalist PARB clade and suggested that M. humberi ESALQ1638 might be particularly good at producing secondary metabolites and might be more efficient in transporting amino acids and organic compounds.
Authors
Beatrix Alsanius Christer Magnusson Mogens Nicolaisen Sandra A.I. Wright Per Hans Micael Wendell Paal Krokene Johan Stenberg Iben Margrete Thomsen Trond RafossAbstract
Key words: VKM, risk assessment, Norwegian Scientific Committee for Food and Environment, Norwegian Food Safety Authority, Norwegian Environment Agency, Biowaste, Compost, Plant health, organic waste, Phytosanitary safety, Biogas, Alien organisms Introduction The Norwegian Food Safety Authority (NFSA) and the Norwegian Environment Agency (NEA) have jointly asked the Norwegian Scientific Committee for food and environment for an assessment into treatment methods and validation methods for compost and digestate based on organic waste in relation to plant health and the spread of harmful alien organisms in Norway. The Norwegian Food Safety Authority will use the report in its supervisory work over companies that produce compost and digestate. The assessment will also provide important input for the regulatory development of several current regulations including regulations on indicator organisms that are used to validate new methods and ensure adequate security with regards to the survival of plant pests. The Norwegian Environment Agency wants to establish whether the methods used in the composting of garden waste and other types of plant waste today are able to ensure that the finished product does not become a source for the spread of harmful alien organisms. This will form the basis for the Norwegian Environment Agency’s guidelines relating to the precautionary provisions in the regulation on alien organisms. This request is limited to an assessment of plant pests and harmful alien organisms (hereinafter alien organisms). The survival of infectious diseases harmful to people and animals is considered in separate assessments. Methods We have conducted initiating workshops for identifying relevant fundamental processes and parameters, of relevant organisms and of relevant search terms for the literature surveys, as well as for discussion and validation. Visits to composting facilities and contact with stakeholders in Norway were also conducted. This information was further implemented in an extensive literature search. This assessment include/encompass organic waste and other materials that are currently treated in biogas and composting facilities, including garden and park waste (incl. soil), plant waste from garden centres, etc., food waste and waste from the food and animal feed industry (including grain/seed husks and waste from enterprises which package and process potatoes and vegetables), manure, bulking agents used in composting facilities, and husks from contracted grain/seed cleaners for sowing. We have used a quantitative risk assessment. The level of confidence in the risk assessment is described, and uncertainties and data gaps identified. Furthermore, we have used re-submission commenting and external expert reviewing before final approval and publication. ...........