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Thonar C.,ETH Zurich | Thonar C.,Research Institute for Organic Agriculture | Erb A.,ETH Zurich | Jansa J.,ETH Zurich
Molecular Ecology Resources | Year: 2012

Quantitative real-time PCR (qPCR) is slowly becoming established as a tool to quantify abundance of different arbuscular mycorrhizal fungal (AMF) taxa in roots and in soil. Here, we describe the development and field validation of qPCR markers (i.e. primers with associated hydrolysis probes), targeting taxon-specific motifs in the nuclear large ribosomal subunit RNA genes. Design of such markers is complicated by the multinuclear and multigenomic cellular organization of these fungi and the high DNA sequence diversity within the smallest biologically relevant units (i.e. single-spore isolates). These limitations are further compounded by inefficient biomass production of these fungi, resulting in limited availability of pure genomic DNA (gDNA) of well-defined isolates for cross-specificity testing of the markers. Here we demonstrate, using a number of AMF isolates, the possibility to establish stringent qPCR running conditions allowing quantification of phylogenetically disjunctive AMF taxa. Further, we show that these markers can more generally be used to quantify abundance (i.e. number of target gene copies or amount of gDNA) of what is usually considered the level of AMF species, regardless of the isolate identities. We also illustrate the range of variation within qPCR signal strength across different AMF taxa with respect to the detected number of gene copies per unit amount of gDNA. This information is paramount for interpretation of the qPCR analyses of field samples. Finally, the field validation of these markers confirmed their potential to assess composition of field AMF communities and monitor the changes owing to agricultural practices such as soil tillage. © 2011 Blackwell Publishing Ltd. Source

Mayer J.,Institute for Sustainability science ISS | Gunst L.,Institute for Sustainability science ISS | Mader P.,Research Institute for Organic Agriculture | Samson M.-F.,French National Institute for Agricultural Research | And 4 more authors.
European Journal of Agronomy | Year: 2015

Long-term sustainability and high resource use efficiency are major goals for high quality baking wheat production throughout the world. Present strategies are low input systems such as organic agriculture or improved conventional systems (integrated). The fertilisation level and strategy, crop protection as well as preceding crop effects may modulate system performance with respect to wheat grain yield, quality and environmental performance of the systems.Our aim was to evaluate data of winter wheat (. Triticum aestivum L.) performance from the DOK long-term systems experiment in Switzerland comparing two mixed organic (biodynamic and bioorganic: BIODYN and BIOORG) and a mixed conventional cropping system (CONFYM) using mineral fertilisers and farmyard manure at two fertilisation intensities (level 1: 50% of standard fertilisation, level 2: standard fertilisation) since 1978. A conventional system was fertilised exclusively minerally at level 2 (CONMIN) and a control remained unfertilised (NOFERT). We compared crop yields, baking quality parameters, the nitrogen use efficiency and the effect of maize and potatoes as preceding crops obtained between 2003 and 2010 along with long-term soil sustainability parameters.The mean grain yields across both fertiliser levels of the organic cropping systems (BIODYN and BIOORG) were 64% of CONFYM, whereas crude protein contents were 79% of CONFYM at fertilisation level 2 and achieved 90% at level 1. The main driving factor of lower yields was a reduction of the numbers of ears per m2 and the thousand kernel weight. The apparent nitrogen use efficiency decreased with increasing N fertilisation. Doubling the organic fertilisation in the organic systems only slightly improved wheat grain yields but was not able to improve grain baking quality, due to low mineral N additions via slurry and farmyard manure. In contrast the effects of the preceding crop potatoes in comparison with preceding silage maize outperformed the organic fertilisation effects, resulting in 33% higher yields and 11% higher crude protein contents. The yield components recorded in the case of preceding potatoes demonstrated a more synchronised nutrient supply throughout the wheat development. Over all low input systems and both fertilisation levels in the conventional mixed farm system at half standard fertilisation (level 1) performed best with distinctly higher grain yields and crude protein contents than in the organic systems with standard fertilisation. However, all systems, organic and conventional, with the low or zero organic fertiliser inputs performed poorly considering the long-term soil quality parameters, indicating a degradation of soil quality. The DOK long-term experiment allows an integrated view on the performance of baking wheat production and long-term sustainability. The results emphasise the importance of a sufficient supply of soils with organic fertilisers as well as the need to improve the availability of organic nitrogen and synchrony between nutrient supply and demand in organic baking wheat production, beside the selection of a suitable preceding crop. © 2015 Elsevier B.V. Source

Suter F.,Research Institute for Organic Agriculture | Schmid A.,Research Institute for Organic Agriculture | Daniel C.,Research Institute for Organic Agriculture | Weibel F.P.,Research Institute for Organic Agriculture | Jenny M.,Research Institute for Organic Agriculture
Acta Horticulturae | Year: 2010

In recent years, an increasing market for blueberries has developed in Switzerland. Blueberries are well suited for organic production because few disease and insect pests are currently found under Swiss conditions. Soil conditions present the greatest obstacle to blueberry cultivation in that Swiss soils are often too alkaline and have low soil organic matter content. During a nine-year (1998-2006) field experiment on an alkaline soil, we tested the feasibility and plant performance of three peat-free cultivation systems (deep ditch, flat ditch, raised bed) and two acidification methods (sulfur or citric acid versus an untreated control). Cultivars were 'Bluecrop' and 'Reka'. The vegetative growth of the bushes was not significantly affected by the cultivation systems. However, the deep ditch system obtained produced significantly higher yields (6.04 kg) compared with the raised bed system (5.13 kg). The yield in the flat ditch system (5.96 kg) was not significantly different from either of the other two systems. Lowering pH levels in the substrate sufficiently (pH<4.8) was achieved only with sulfur (30 g/plant/y). The acidification treatments affected the shrub development and yields significantly. Compared with the untreated control, shrub volume (+43%) and accumulated yield (+55%) were greater in the treatment with application of sulfur. With the citric acid treatment, shrub volume and yield were increased by 12% and 9%, respectively. Root growth and biomass showed no differences between the cultivation systems. A flat ditch with pine sawdust combined with acidification by sulfur offers good plant growth and yield performance and is cheaper to install compared with deep ditch. Based on these results, we have recommended this cultivation system with sulfur applications for commercial blueberry production in regions with alkaline soils in Switzerland since 2005. Source

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