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Gulkowska A.,Eawag - Swiss Federal Institute of Aquatic Science and Technology | Gulkowska A.,ETH Zurich | Gulkowska A.,Institute for Plant Production science IPS | Thalmann B.,Eawag - Swiss Federal Institute of Aquatic Science and Technology | And 3 more authors.
Chemosphere | Year: 2014

Soil incubation experiments using 14C-labelled sulfamethazine were carried out to assess the factors governing its nonextractable residue (NER) formation via nucleophilic addition reactions. Circumstantial evidence on possible mechanisms of NER formation was derived from a selective manipulation of soil samples. The amount of quinones in soil available for nucleophilic addition was a limiting factor as indicated by (i) an (initial) increase of NER formation by adding quinone precursors or enhancing their formation by manganese oxide addition and (ii) a decrease of NER formation by limiting the formation of quinones under anaerobic conditions. A slow NER formation with time under aerobic conditions is likely caused by covalent bonding as well, because no slow NER formation phase was observed under anaerobic conditions. © 2014 Elsevier Ltd.

Kohlschmid E.,Institute for Plant Production science IPS | Ruf D.,Institute for Plant Production science IPS
Environmental Science and Pollution Research | Year: 2016

Testing of effects on earthworms and non-target foliar arthropods is an integral part of the ecotoxicological risk assessment for the authorization of plant protection products. According to the new data requirements, which came into force in 2014 for active substances and in 2016 for plant protection products, the chronic earthworm toxicity test with Eisenia fetida based on reproductive, growth, and behavioral effects instead of the acute earthworm toxicity test based on mortality, has to be conducted routinely. Additional testing of effects on soil arthropods (Folsomia candida, Hyposaspis aculeifer) is required if the risk assessment of foliar applications raises concerns regarding non-target foliar arthropods (Aphidius rhopalosiphi, Typhlodromus pyri) or if the product is applied directly on or into the soil. Thus, it was investigated whether the sublethal earthworm endpoint is more sensitive than the sublethal soil arthropod endpoint for different types of pesticides and whether the risk assessment for non-target arthropods would trigger the testing of effects on soil arthropods in the cases where soil arthropods are more sensitive than earthworms. Toxicity data were obtained from Swiss ecotoxicological database, EFSA Conclusions and scientific literature. For insecticides and herbicides, no general conclusion regarding differences in sensitivity of either earthworms or soil arthropods based on sublethal endpoints were possible. For fungicides, the data indicated that in general, earthworms seemed to be more sensitive than soil arthropods. In total, the sublethal F. candida or H. aculeifer endpoint was lower than the sublethal E. fetida endpoint for 23 (34 %) out of 68 active substances. For 26 % of these 23 active substances, testing of soil arthropods would not have been triggered due to the new data requirement. These results based on sublethal endpoints show that earthworms and soil arthropods differ in sensitivity toward certain active substances and that the risk assessment for non-target foliar arthropods did not always trigger soil arthropod testing in the cases where soil arthropods were more sensitive than earthworms. © 2016 Springer-Verlag Berlin Heidelberg

Kiewnick S.,Institute for Plant Production science IPS | Frey J.E.,Institute for Plant Production science IPS | Braun-Kiewnick A.,Institute for Plant Production science IPS
Phytopathology | Year: 2015

Meloidogyne enterolobii is a quarantine root-knot nematode posing a major threat to agricultural production systems worldwide. It attacks many host plants, including important agricultural crops, ornamentals, and trees. M. enterolobii is a highly virulent and pathogenic root-knot nematode species, able to reproduce on plants resistant to other Meloidogyne spp. Significant crop damage has been reported in Asia, South America, Africa, the United States, France, and greenhouses in Switzerland. To identify potential introduction pathways and ensure appropriate phytosanitary measures and management strategies, accurate detection and identification tools are needed. Therefore, two real-time quantitative polymerase chain reaction (PCR) assays based on the second intergenic spacer region of the ribosomal DNA cistron and the cytochrome oxidase c subunit I (COI) gene using locked nucleic acid probes were developed and validated for fast and reliable detection and identification of M. enterolobii. Analytical specificity was confirmed with 16 M. enterolobii populations, 16 populations of eight closely related Meloidogyne spp., and four species from other nematode genera. Optimizing and testing the assays on two real-time PCR platforms revealed an analytical sensitivity of one juvenile in a background of 1,000 nematodes and the intended limit of detection of one juvenile per 100 ml of soil. Both assays performed equally well, with the COI-based assay showing a slightly better performance concerning detection of M. enterolobii target DNA in complex DNA backgrounds. © 2015 The American Phytopathological Society.

Gulkowska A.,Institute for Plant Production science IPS | Buerge I.J.,Institute for Plant Production science IPS | Poiger T.,Institute for Plant Production science IPS
Analytical and Bioanalytical Chemistry | Year: 2014

A sensitive and selective analytical method, based on online solid phase extraction coupled to LC-MS/MS, was developed and validated to determine traces of several recently introduced fungicides in surface water and wastewater. The list of target analytes included eight succinate dehydrogenase inhibitors (bixafen, boscalid, fluopyram, flutolanil, fluxapyroxad, isopyrazam, penflufen, and penthiopyrad), and two other fungicides with different modes of action, fenpyrazamine and fluopicolide. Detection and quantification limits in various matrices were in the range of 0.1 to 2 and 0.5 to 10 ng/L, respectively. Moderate signal suppression was observed in surface water (≤15 %) and wastewater (≤25 %) and was well compensated by the selected internal standard. The intra- and inter-day precisions were generally <10 and <20 %, respectively. The applicability of the method was demonstrated in a study on the occurrence of fungicides in the river Glatt, Switzerland, that drains a catchment area of 419 km2 with a substantial proportion of agricultural land. Of the studied compounds, only boscalid and fluopicolide were detected in flow-proportional weekly composite samples, generally at low concentrations up to 15 and 5 ng/L, respectively. While fluopicolide was detected in only 30 % of the samples above the LOD of 0.5 ng/L, boscalid was detected in all samples analyzed between March and October 2012. [Figure not available: see fulltext.] © 2014 Springer-Verlag Berlin Heidelberg.

Dupuis B.,Institute for Plant Production science IPS | Dupuis B.,Catholic University of Louvain
European Journal of Plant Pathology | Year: 2016

Potato virus Y (PVY) is responsible for major viral diseases in most potato seed areas. It is transmitted by aphids in a non-persistent manner, and it is spread in potato fields by the winged aphids flying from an infected source plant to a healthy one. Six different PVY strains groups affect potato crops: PVYC, PVYN, PVYO, PVYN:O, PVYNTN, and PVYN-Wi. Nowadays, PVYNTN and PVYN-Wi are the predominant strains in Europe and the USA. After the infection of the leaf and accumulation of the virus, the virus is translocated to the progeny tubers. It is known that PVYN is better translocated than PVYO, but little is known about the translocation of the other PVY strains. The translocation of PVY occurs faster in young plants than in old plants; this mature plant resistance is generally explained by a restriction of the cell-to-cell movement of the virus in the leaves. The mother tuber may play an important role in explaining mature plant resistance. PVY is able to pass from one stem to the other stems of the same plant through the vascular system of the mother tuber, but it is unknown whether this vascular link between stems is permanent during the whole life of the plant. Two greenhouse trials were set up to study the spread of PVY in the vascular system of the potato plant. The PVY-susceptible cultivar Charlotte was used for both trials. It was demonstrated that all stems growing from a PVY-infected tuber will become infected sooner or later, and that PVYN-Wi translocates more efficiently to progeny tubers than PVYNTN. It was also demonstrated that the progressive decay of the mother tuber in the soil reduces the possibility for virus particles to infect healthy stems through the vascular system of the mother tuber. This new element contributes to a better understanding of the mechanism of mature plant resistance. © 2016 The Author(s)

Reininger V.,ETH Zurich | Reininger V.,Institute for Plant Production science IPS | Schlegel M.,ETH Zurich
PLoS ONE | Year: 2016

Background: Phialocephala subalpina belongs to the Phialocephala fortinii s.l.-Acepphala applanata species complex (PAC) forming one of the major groups belonging to the dark septate endophytes (DSE). Depending on the strain, PAC was shown to form neutral to pathogenic associations with its host plant Picea abies. To understand PACs lifestyle we investigated the effect of presence/absence of Picea abies on the transcriptome of strain 6-70-1. Materials and Methods: PAC strain 6-70-1 was grown in liquid Pachlewski media either induced by its host plant Picea abies or without host plant as a control. Mycelia were harvested in a time course (1, 2, 3, 4, 7, 11, 18 days) with and without induction by the host plant and the fungal transcriptome revealed by Illumina sequencing. Differential gene expression analysis over the time course comparing control and treatment at each time point using the 'edgeR glm approach' and a gene enrichment analysis using GO categories were performed. Results: The three main functional groups within differentially expressed genes were 'metabolism', 'transport' and 'cell rescue, defense and virulence'. Additionally, genes especially involved in iron metabolism could be detected by gene set enrichment analysis. Conclusion: In conclusion, we found PAC strain 6-70-1 to be metabolically very active during colonization of its host plant Picea abies. A major shift in functional groups over the time course of this experiment could not be observed but GO categories which were found to be enriched showed different emphasis depending in the day post induction. © 2016 Reininger, Schlegel.

Gyorgy Z.,Corvinus University of Budapest | Vouillamoz J.F.,Institute for Plant Production science IPS | Ladanyi M.,Corvinus University of Budapest | Pedryc A.,Corvinus University of Budapest
Biochemical Systematics and Ecology | Year: 2014

Rhodiola rosea is a perennial adaptogenic medicinal plant found in the cool climates of the northern hemisphere. This species is highly variable both in morphological and phytochemical traits. The genetic diversity of five populations located in the Swiss Alps was studied with twelve SSR markers. However, only eight markers turned out to be informative in this study. The primer pairs for these eight SSR markers produced 37 fragments. The number of alleles per locus ranged from two to eight. The observed heterozygosity was between 0.09 and 1.0, whereas the expected heterozygosity was between 0.13 and 0.72. The genetic diversity was in the same range for all five populations. Principal coordinate analysis revealed that individuals from different populations did not cluster together, which confirmed that diversity within and among the populations were almost equivalent. The genetic fragmentation of this alpine species despite of its fragmented and isolated habitats, did not happened yet. The results of the present study on the genetic diversity were consistent with an earlier study on the chemical diversity with the same individuals. © 2014 Elsevier Ltd.

Gyorgy Z.,Szent Istvan University | Vouillamoz J.F.,Institute for Plant Production science IPS | Hohn M.,Szent Istvan University
Plant Systematics and Evolution | Year: 2016

Rhodiola rosea L. is an arctic–alpine perennial species. Genetic structure and relationships of 16 populations from the high mountains of Europe have been characterized by the use of microsatellite markers. Meanexpected heterozygosity (He) was 0.73, ranging from 0.51 to 0.74 in the populations studied. The genetic relationships among the populations revealed by both UPGMA and STRUCTURE analysis showed a clear clustering of the five Swiss Alps populations being well separated from all other populations. Next to these—also forming a distinct cluster—the populations from the Pyrenees were located. Another cluster contained the admixed group of individuals from Alpine and Carpathian populations including the Tatras. Norwegian samples were sister to the Alpine–Carpathian group and interestingly, the population from the Italian Dolomites showed a clearly distinct position. AMOVA revealed that the vast majority of the molecular variance was attributed to within-population variability (85 %) while only 11 % was among population variation, and 4 % among region variation. The weak genetic differentiation observed between the Eastern Alpine and Carpathian populations supports the existence of a former common glacial refugium and a shared history between the two regions. © 2016 Springer-Verlag Wien

Gassmann J.,Institute for Plant Production science IPS | Hunziker K.,Institute for Plant Production science IPS | Kellerhals M.,Institute for Plant Production science IPS
Acta Horticulturae | Year: 2014

Susceptibility of pome fruit genetic resources towards fire blight, caused by the bacterium Erwinia amylovora was evaluated with Swiss genetic resources. The tests were performed in a security glasshouse using a shoot inoculation tests. More than 200 different apple and pear genotypes were evaluated and revealed considerable differences in shoot susceptibility ranging from almost resistant to highly susceptible. Based on the results, some accessions were included in the apple breeding program as fire blight tolerant parents. Moreover, while considering also other agronomic and fruit quality characteristics, some accessions are currently recommended for fruit growing, especially on standards trees used for the production of apple juice and cider. Those standard trees are additionally contributing to a diverse, ecologically desirable landscape. © 2014, International Society for Horticultural Science. All rights reserved.

PubMed | Institute for Plant Production science IPS
Type: Journal Article | Journal: BMC microbiology | Year: 2017

While recent advances in next generation sequencing technologies have enabled researchers to readily identify countless microbial species in soil, rhizosphere, and phyllosphere microbiomes, the biological functions of the majority of these species are unknown. Functional studies are therefore urgently needed in order to characterize the plethora of microorganisms that are being identified and to point out species that may be used for biotechnology or plant protection. Here, we used a dual culture assay and growth analyses to characterise yeasts (40 different isolates) and their antagonistic effect on 16 filamentous fungi; comprising plant pathogens, antagonists, and saprophytes.Overall, this competition screen of 640 pairwise combinations revealed a broad range of outcomes, ranging from small stimulatory effects of some yeasts up to a growth inhibition of more than 80% by individual species. On average, yeasts isolated from soil suppressed filamentous fungi more strongly than phyllosphere yeasts and the antagonistic activity was a species-/isolate-specific property and not dependent on the filamentous fungus a yeast was interacting with. The isolates with the strongest antagonistic activity were Metschnikowia pulcherrima, Hanseniaspora sp., Cyberlindnera sargentensis, Aureobasidium pullulans, Candida subhashii, and Pichia kluyveri. Among these, the soil yeasts (C. sargentensis, A. pullulans, C. subhashii) assimilated and/or oxidized more di-, tri- and tetrasaccharides and organic acids than yeasts from the phyllosphere. Only the two yeasts C. subhashii and M. pulcherrima were able to grow with N-acetyl-glucosamine as carbon source.The competition assays and physiological experiments described here identified known antagonists that have been implicated in the biological control of plant pathogenic fungi in the past, but also little characterised species such as C. subhashii. Overall, soil yeasts were more antagonistic and metabolically versatile than yeasts from the phyllosphere. Noteworthy was the strong antagonistic activity of the soil yeast C. subhashii, which had so far only been described from a clinical sample and not been studied with respect to biocontrol. Based on binary competition assays and growth analyses (e.g., on different carbon sources, growth in root exudates), C. subhashii was identified as a competitive and antagonistic soil yeast with potential as a novel biocontrol agent against plant pathogenic fungi.

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