Assessing the phenotypic and genotypic diversity of <Emphasis Type="Italic">Sclerotinia sclerotiorum</Emphasis> in France

White mould caused by the ascomycete Sclerotinia sclerotiorum affects the production of many economically important crops. The incidence of this disease has recently increased in France, especially in melon crops, which were not affected much in the past. One possible explanation for this situation is the emergence of strains with particular characteristics, including increased aggressiveness to melon. To test this hypothesis, 200 isolates of S. sclerotiorum were collected from six host crops (bean, brassica oilseed rape, carrot, lettuce, melon, witloof chicory) in different regions. They were genotyped with 16 microsatellites markers. A subsample of 96 isolates were assessed for their aggressiveness on melon leaves. Overall, the isolates from melon did not show higher aggressiveness on melon leaves than those which originated from other host plants. Moreover, the melon isolates did not present distinctive genetic characteristics in comparison with those from other crops and shared several of the 128 identified multilocus haplotypes with isolates collected from carrot, witloof chicory and oilseed rape. Furthermore the Bayesian analysis of the genetic structure indicated that the host plant is not a structuring factor of the three genetic clusters identified, and it suggested instead the occurrence of an isolation-by-distance process. Possible consequences of these results for the management of white mould and alternative hypotheses to explain the recent changes in disease incidence are presented.     

Modeling combined continuous and ordinal outcomes in a clustered setting

Measurements of both continuous and categorical outcomes appear in many statistical problems. One such example is the study of teratology and developmental toxicity, where both the probability that a live fetus is malformed (ordinal) or of low birth weight (continuous) are important measures in the context of teratogenicity. Although multivariate methods of the analysis of continuous outcomes are well understood, methods for jointly continuous and discrete outcomes are less familiar. We propose a likelihood-based method that is an extension of the Plackett-Dale approach. Specification of the full likelihood will be avoided using pseudo-likelihood methodology. The estimation of safe dose levels as part of quantitative risk assessment will be illustrated based on a developmental toxicity experiment of diethylene glycol dimethyl ether in mice.     

Clonal and seasonal shifts in communities of saprotrophic microfungi and soil enzyme activities in the mycorrhizosphere of Salix spp.

The species‐specific microbial root and rhizosphere colonization contributes essentially to the plant nutrient supply. The species number and colonization densities of cultivable saprotrophic microfungi and the activities of nutrient‐releasing soil enzymes (protease, acid and alkaline phosphatase, arylsulfatase) were investigated in the rhizosphere of one low mycorrhizal (Salix viminalis) and one higher mycorrhizal (S. × dasyclados) willow clone at a Eutric Cambisol in N Germany. After soil washing, in total 32 and 28 saprotrophic microfungal species were isolated and identified microscopically from the rhizosphere of S. viminalis and S. × dasyclados, respectively. The fungal species composition changed within the growing season but the species number was always lower under S. × dasyclados than under S. viminalis. Under both willow clones, the fungal colonization density was largest in spring, and the species number was largest in autumn. Acid‐phosphatase activity (p < 0.001) and protease activity (p < 0.003) were significantly affected by the Salix clone, whereas arylsulfatase and alkaline‐phosphatase activities did not show clone‐specific differences. All enzyme activities reached their maxima in the summer sampling. Rhizosphere colonization with Acremonium butyri, Cladosporium herbarum, and Penicillium janthinellum contributed significantly to explain the activities of acid phosphatase. Rhizosphere colonization with Cylindrocarpon destructans, Penicillium spinulosum, Plectosphaerella cucumerina, and Trichoderma polysporum contributed significantly to explain the arylsulfatase activities. Effects of the saprotrophic fungal colonization densities on the protease activities in the rhizosphere were low. Acid‐ and alkaline‐phosphatase and arylsulfatase activities in the rhizosphere soil were stronger affected by the composition of the saprotrophic fungal communities than by the Salix clone itself. In conclusion, the colonization density of some saprotrophic microfungi in the rhizosphere contributed to explain shifts in soil‐enzyme activities of the P and S cycles under different willow clones.     

Development of a seven-target multiplex PCR for the simultaneous detection of transgenic soybean and maize in feeds and foods

The detection of genetically modified organisms (GMOs) in food and feed is an important issue for all the subjects involved in raw material control, food industry, and distribution. Because the number of GMOs authorized in the EU increased during the past few years, there is a need for methods that allow a rapid screening of products. In this paper, we propose a method for the simultaneous detection of four transgenic maize (MON810, Bt11, Bt 176, and GA21) and one transgenic soybean (Roundup Ready), which allows routine control analyses to be sped up. DNA was extracted either from maize and soybean seeds and leaves or reference materials, and the recombinant DNA target sequences were detected with 7 primer pairs, accurately designed to be highly specific for each investigated transgene. Cross and negative controls were performed to ensure the specificity of each primer pair. The method was validated on an interlaboratory ring test and good analytical parameters were obtained (LOD = 0.25%, Repeatability, (r) = 1; Reproducibility, (R) = 0.9). The method was then applied to a model biscuit made of transgenic materials baked for the purpose and to real samples such as feed and foodstuffs. On account of the high recognition specificity and the good detection limits, this multiplex PCR represents a fast and reliable screening method directly applicable in all the laboratories involved in raw material and food control.     

Erfassung der Variabilität von Bodenmerkmalen in einem Blindversuch auf Fahlerde mittels Methoden der räumlichen Statistik

Variability of soil parameters in a uniformity trial on a Luvisol evaluated by means of spatial statistics The relationships between soil parameters and indicators of soil genesis were investigated in a uniformity trial on Luvisol by means of classical and spatial statistics. The following properties were investigated in the topsoil (0–30 cm) and subsoil (31–40 cm): content of total carbon (C_t), content of clay plus fine silt (FAT), concentrations of available potassium (K) and phosphorus (P), and pH values. The depth loamy Bt horizon and microrelief were considered as indicators of soil genesis. Smoothing of the raw data by means of block kriging eliminated the small scale variability of all parameters. In this way, the rank correlation coefficients between soil parameters increased by factor 2 and were to 0.52 for C_t–FAT; 0.69 for C_t–K, and 0.55 for C_t–P in the top soil. The maps for smoothed data allowed a much better visual analysis of spatial distribution of investigated properties compared to the raw data. The significant correlations as well as the similarity of maps and variograms suggested that the spatial variability of FAT, C_t, K, and P in the top soil was determined by the same factors. The depth of the loamy Bt horizon and the relief were the most important factors defining the distribution of the investigated soil parameters. The rank correlation coefficients of the smoothed and detrended relief with the soil parameters amount to –0.63, –0.77, –0.71, and –0.57 for FAT, C_t, K, and P, respectively.     

Crop-specific differences in the concentrations of lipids in leachates from the root zone

Although lipids are involved in diverse soil processes and affect various soil properties, the contribution of rhizodeposits and the root zone to lipid concentrations and distributions in soils is unknown. For the first time, we determined the concentrations of alkanoic acids, n-alkanes and n-alkenes in root zone leachates and roots of maize and potato using gas chromatography/mass spectrometry (GC/MS). In total, the lipid concentrations of leachates were 100 μg g^?1 (maize) and 17 μg g^?1 (potato). The saturated n-alkanoic acids, ranging from n-C₁₄ to n-C₂₈ and having the maximum at n-C₂₂ (maize) and at n-C₁₆ (potato), were more abundant than the other compounds. Maize leachates had more alkanes (20 μg g^?1) than potato leachates (3.1 μg g^?1), but the members of the homologues were nearly the same. Comparison of these distributions with data for roots, microorganisms and soil indicated that the lipids in the leachates from the root zone mainly originated from abrasion of fine roots, rhizodeposits and rhizosphere microorganisms.     

Wirkungen technogener Druckbelastung auf die Spannungsverteilung und das Bodengefüge einer Schwarzerde aus Löß

Effect of wheeling on stress distribution and changes in the macro- and microstructure of a cambic phaeozem derived from loess The determination of stress induced changes in the poresystem due to repeated wheeling of a cambic phaeozem derived from loess as well as in the aggregate size distribution, arrangement, and stage are reported. It could be shown, that repeated wheeling always results in a further stress distribution to deeper depths and that the vertical stresses dominate with repeated wheeling. Furthermore the octahedral shear stresses and mean normal stresses exceed the maximum strength defined by the Mohr Coulomb failure line and define a further soil deformation. The process of aggregate deterioration can be verified by radiographs from which not only the changes in bulk density on a mesoscale can be derived but from which also the crack patterns can be defined for the different stages of structure deterioration. Under the well known assumption that pore water pressure is increased due to wheeling, soil compaction and consecutive soil homogenisation by kneading can be differentiated. The consequences for ecological parameters will be discussed.     

Evaluation of agro-industrial by-products as nutrient source for plant growth

Nutrient leaching from dry (COD) and wet (COW) coffee, sisal (SIS), brewery barley malt (BEB) and sugar cane (FIC) by-products, and linseed (LIC) and niger seed cakes (NIC), and uptake by maize were studied in a pot experiment with tropical Alfisol. After three months, soils were leached to recover labile plant nutrients, and root and shoot biomass was harvested. The leachate from FIC-amended soil had the highest concentration of inorganic P (0.90 μmol L^?1), whereas the highest concentrations of potassium (K) (48,088 μmol L^?1) and calcium (2566 μmol L^?1) were determined in leachates from COD and BEB treatments, respectively. The amendments significantly increased K uptake by maize proportional to the amount of K applied, but the effects for other plant nutrients were small. The results indicated that pre-decomposition of agro-industrial by-products may increase the nutrient release in tropical soils.     

Density,metabolic activity,and identity of cultivable rhizosphere bacteria on Salix viminalis in disturbed arable and landfill soils

The objective of this study was to provide fundamental data for a subsequent selection of willow growth and soil remediation promoting bacterial strains. The rhizosphere of willows (Salix viminalis) was screened for cultivable bacteria with high enzymatic activity (proteolytic, pectolytic, cellulolytic, amylolytic) and production of siderophores at four test sites with broad spectrum of anthropogenic soil disturbance: sewage‐sludge application, impoverishment by unfavorable arable use, ash dumping, and household‐waste depositing. The density of bacteria in the rhizosphere ranged from 7.92 to 8.56 log₁₀ of colony‐forming units per gram dry weight of soil and varied in a site‐ and willow‐clone‐specific manner. Within the 240 bacterial strains, a high diversity of metabolic activities was observed but was rarely combined in one strain (1.2% having six and 5.8% having five out of seven metabolic activities, respectively). The majority of strains (79.2%) revealed just one or two metabolic activities. Most common was a combination of lipolytic, proteolytic activities, and siderophore production as found in 13.8% of the bacterial strains. The 50 strains with the highest metabolic activity belonged predominantly to the Gammaproteobacteria (66%), the others to Flavobacteria (18%), Betaproteobacteria (8%), Actinobacteria (4%), and Bacilli (4%). The highest portion of cultivable strains of rhizosphere bacteria with high metabolic activities belonged to the genera Pseudomonas, Serratia, and Flavobacterium. We hypothesize that these genera include strains that support willow growth and soil remediation. Therefore, the described strain collection from the rhizosphere of S. viminalis provides a valuable basis for a subsequent selection of these candidates for applications in improvement of site adaptation of plants or remediation of soils.     

Innovative methods in soil phosphorus research: A review

Phosphorus (P) is an indispensable element for all life on Earth and, during the past decade, concerns about the future of its global supply have stimulated much research on soil P and method development. This review provides an overview of advanced state‐of‐the‐art methods currently used in soil P research. These involve bulk and spatially resolved spectroscopic and spectrometric P speciation methods (1 and 2D NMR, IR, Raman, Q‐TOF MS/MS, high resolution‐MS, NanoSIMS, XRF, XPS, (µ)XAS) as well as methods for assessing soil P reactions (sorption isotherms, quantum‐chemical modeling, microbial biomass P, enzymes activity, DGT, ³³P isotopic exchange, ¹⁸O isotope ratios). Required experimental set‐ups and the potentials and limitations of individual methods present a guide for the selection of most suitable methods or combinations.