Agroscope
  • Switzerland
Recent publications
Vertical ground reaction force (GRFz) measurements are the best tool for assessing horses’ weight-bearing lameness. However, collection of these data is often impractical for clinical use. This study evaluates GRFz predicted using data from body-mounted IMUs and long short-term memory recurrent neural networks (LSTM-RNN). Twenty-four clinically sound horses, equipped with IMUs on the upper-body (UB) and each limb, walked and trotted on a GRFz measuring treadmill (TiF). Both systems were time-synchronised. Data from randomly selected 16, 4, and 4 horses formed training, validation, and test datasets, respectively. LSTM-RNN with different input sets (All, Limbs, UB, Sacrum, or Withers) were trained to predict GRFz curves or peak-GRFz. Our models could predict GRFz shapes at both gaits with RMSE below 0.40 N.kg−1. The best peak-GRFz values were obtained when extracted from the predicted curves by the all dataset. For both GRFz curves and peak-GRFz values, predictions made with the All or UB datasets were systematically better than with the Limbs dataset, showing the importance of including upper-body kinematic information for kinetic parameters predictions. More data should be gathered to confirm the usability of LSTM-RNN for GRFz predictions, as they highly depend on factors like speed, gait, and the presence of weight-bearing lameness.
Romania has good agricultural resources and declining meat consumption, yet the country’s meat imports are on the rise. This study uses Balassa’s idea to link national trade patterns to worldwide ones and extends it, for the period between 2004 and 2019, to the ratio between prices and to the ratio between variables describing intra-industry trade. For price ratios, this study showed that Romania imported primarily inferior qualities of meat, particularly at the beginning of the study period. Regarding intra-industry trade, the Romanian trend moves in the opposite direction to the worldwide trend. Although, the trade of meat parts compared with whole/ half carcasses is on the rise internationally, it is declining in Romania, probably due to increasing competitiveness of the industry.
Listeria monocytogenes ( Lm ) accounts for serious public health and food safety problems owing to its stress resilience and pathogenicity. Based on their regulatory involvement in global gene expression events, cold-shock domain family proteins (Csps) are crucial in expression of various stress fitness and virulence phenotypes in bacteria. Lm possesses three Csps (CspA, CspB, and CspD) whose regulatory roles in the context of the genetic diversity of this bacterium are not yet fully understood. We examined the impacts of Csps deficiency on Lm nutrient metabolism and stress tolerance using a set of csp deletion mutants generated in different genetic backgrounds. Phenotype microarrays (PM) analysis showed that the absence of Csps in ∆ cspABD reduces carbon (C-) source utilization capacity and increases Lm sensitivity to osmotic, pH, various chemical, and antimicrobial stress conditions. Single and double csp deletion mutants in different Lm genetic backgrounds were used to further dissect the roles of individual Csps in these phenotypes. Selected PM-based observations were further corroborated through targeted phenotypic assays, confirming that Csps are crucial in Lm for optimal utilization of various C-sources including rhamnose and glucose as well as tolerance against NaCl, β-phenyethylamine (PEA), and food relevant detergent stress conditions. Strain and genetic lineage background-based differences, division of labour, epistasis, and functional redundancies among the Csps were uncovered with respect to their roles in various processes including C-source utilization, cold, and PEA stress resistance. Finally, targeted transcriptome analysis was performed, revealing the activation of csp gene expression under defined stress conditions and the impact of Csps on expression regulation of selected rhamnose utilization genes. Overall, our study shows that Csps play important roles in nutrient utilization and stress responses in Lm strains, contributing to traits that are central to the public health and food safety impacts of this pathogen.
Climate and land-use changes are main drivers of insect declines, but their combined effects have not yet been quantified over large spatiotemporal scales. We analysed changes in the distribution (mean occupancy of squares) of 390 insect species (butterflies, grasshoppers, dragonflies), using 1.45 million records from across bioclimatic gradients of Switzerland between 1980 and 2020. We found no overall decline, but strong increases and decreases in the distributions of different species. For species that showed strongest increases (25% quantile), the average proportion of occupied squares increased in 40 years by 0.128 (95% credible interval: 0.123–0.132), which equals an average increase in mean occupancy of 71.3% (95% CI: 67.4–75.1%) relative to their 40-year mean occupancy. For species that showed strongest declines (25% quantile), the average proportion decreased by 0.0660 (95% CI: 0.0613–0.0709), equalling an average decrease in mean occupancy of 58.3% (95% CI: 52.2–64.4%). Decreases were strongest for narrow-ranged, specialised, and cold-adapted species. Short-term distribution changes were associated to both climate changes and regional land-use changes. Moreover, interactive effects between climate and regional land-use changes confirm that the various drivers of global change can have even greater impacts on biodiversity in combination than alone. In contrast, 40-year distribution changes were not clearly related to regional land-use changes, potentially reflecting mixed changes in local land use after 1980. Climate warming however was strongly linked to 40-year changes, indicating its key role in driving insect trends of temperate regions in recent decades.
In this contribution, new data concerning the distribution of vascular flora alien to Italy are presented. It includes new records, confirmations, and status changes for Italy or for Italian administrative regions. Nomenclatural and distribution updates, published elsewhere, and corrections are provided as Suppl. material 1
The aim of this study was to combine the concept of prosumerism with the theory of the commons to develop the concept of commons prosumer (co-prosumer) in distinction to private prosumer (p-prosumer). While the p-prosumer prosumes for himself, the co-prosumer creates a social environment for social capital. We use energy and agriculture as two cases in point to illustrate that the concept of the prosumer‘s role appears in different contexts with varying attributes such as self-efficacy, sufficiency, or autarchy. However, independence and socially fragmented structures might lead to less resilience, whereas dependence structures could confer collective benefits. We propose a building block to fill the gap in the prosumer setting and balance individual and collective interests. By positioning the p-prosumer on a commons-based foundation, we make more explicit the dependence structures that build communities or networks to showcase possibilities that pave the way for shared and socially innovative structures of self-empowerment for infrastructure decision-making at different levels.
The impact of local biodiversity loss on ecosystem functioning is well established, but the role of larger-scale biodiversity dynamics in the delivery of ecosystem services remains poorly understood. Here we address this gap using a comprehensive dataset describing the supply of 16 cultural, regulating and provisioning ecosystem services in 150 European agricultural grassland plots, and detailed multi-scale data on land use and plant diversity. After controlling for land-use and abiotic factors, we show that both plot-level and surrounding plant diversity play an important role in the supply of cultural and aboveground regulating ecosystem services. In contrast, provisioning and belowground regulating ecosystem services are more strongly driven by field-level management and abiotic factors. Structural equation models revealed that surrounding plant diversity promotes ecosystem services both directly, probably by fostering the spill-over of ecosystem service providers from surrounding areas, and indirectly, by maintaining plot-level diversity. By influencing the ecosystem services that local stakeholders prioritized, biodiversity at different scales was also shown to positively influence a wide range of stakeholder groups. These results provide a comprehensive picture of which ecosystem services rely most strongly on biodiversity, and the respective scales of biodiversity that drive these services. This key information is required for the upscaling of biodiversity-ecosystem service relationships, and the informed management of biodiversity within agricultural landscapes.
Long-term field experiments (LTFEs) can provide an extensive overview on the effectiveness of phosphorus (P) management. In order to have a detailed insight into the availability and distribution of the P in soil as affected by organic and inorganic fertilizers (no P, triple-superphosphate (TSP), compost and compost + TSP), soil samples collected at a LTFE established in 1998 in Northern Germany at different sampling dates and soil depths were subjected to P characterization including the double-lactate method (P-dl) as standard soil test, the degree of P sorption (DPS), the sequential P fractionation and isotopic exchange kinetics. While the type of fertilizer had rarely an effect on the soil P pools, higher amounts of P applied resulted in increased values of P-dl, labile P fractions and P that was isotopically exchangeable within 1 min (p < 0.05). The DPS values varied from on average 40.2% (no P) to 47.2% (compost + TSP) with small variations during the experimental time. In contrast, significant shifts from less available to readily available P pools were measured between the sampling in autumn 2017 and spring 2019. The differences in the P budgets between the treatments corresponded to the differences of the total P stocks in 0–90 cm, yet with an estimated upward or downward movement of P between the soil depths as consequences of long-term deficit or surplus of fertilizer P. The use of complementary methods in this study contributed to a better understanding of the potential availability of P in soil in a long term perspective.
The 'genomic shock' hypothesis posits that unusual challenges to genome integrity such as whole genome duplication (WGD) may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and de-repression of transposable elements (TEs) in the immediate aftermath of WGD, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession 'Bhyb26'. We compared two independently-derived accessions of B. hybridum and their deeply diverged diploid progenitor species B. stacei and B. distachyon. The two B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-WGD genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced TE activation, though we find evidence supporting steady post-WGD TE activity in the older lineage. Gene loss in the older lineage was slightly biased toward one subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species' similarity in TE load may account for the subtlety of the observed genome dominance.
The high decline in liquid milk consumption in Western countries has been compensated by the increased consumption of processed dairy products and the rapidly increasing number of new plant-based beverages constantly introduced in the market, advertised as milk substitutes and placed on shelves near milk products. To provide better understanding about the nutritional value of these drinks compared with cow’s milk, 27 plant-based drinks of 8 different species and two milk samples were purchased from two big retailers in Switzerland, and their composition regarding protein, carbohydrate, fat, vitamin, and mineral contents and residue load [glyphosate, aminomethylphosphonic acid (AMPA), and arsenic] was analyzed quantitatively and qualitatively. Energy and nutrient intakes were calculated and compared with the dietary reference values for Germany, Austria and Switzerland (D-A-CH). In addition, the digestible indispensable amino acid score (DIAAS) was calculated to estimate the quality of the proteins. Milk contained more energy; fat; carbohydrate; vitamins C, B2, B12, and A; biotin; pantothenic acid; calcium; phosphorus; and iodine than most plant-based drinks. Soy drinks provided slightly more protein and markedly more vitamins B1 and B6, folic acid, and vitamins E and D2 (with supplemented vitamin D2) and K1, magnesium, manganese, iron, and copper than milk and the other plant-based drinks. However, with the exception of cow’s milk and soy drinks, which had > 3% protein, most milk alternatives contained ≤ 1% protein; therefore, they cannot be considered good protein sources. In regard to protein quality, milk was outstanding compared with all plant-based drinks and exhibited higher calculated DIAASs. Our results show that the analyzed plant-based drinks are not real alternatives to milk in terms of nutrient composition, even if the actual fortification is taken into account. Improved fortification is still an issue and can be optimized using the most bioavailable and soluble derivatives. Complete replacement of milk with plant-based drinks without adjusting the overall diet can lead to deficiencies of certain important nutrients in the long term.
To stop the ongoing decline of farmland biodiversity there are increasing claims for a paradigm shift in agriculture, namely from conserving and restoring farmland biodiversity at field scale (α‐diversity) to doing it at landscape scale (γ‐diversity). However, knowledge on factors driving farmland γ‐diversity is currently limited. Here, we quantified farmland γ‐diversity in 123 landscapes and analysed direct and indirect effects of abiotic and land‐use factors shaping it using structural equation models. The direction and strength of effects of factors shaping γ‐diversity were only partially consistent with what is known about factors shaping α‐diversity, and indirect effects were often stronger than direct effects or even opposite. Thus, relationships between factors shaping α‐diversity cannot simply be up‐scaled to γ‐diversity, and also indirect effects should no longer be neglected. Finally, we show that local mitigation measures benefit farmland γ‐diversity at landscape scale and are therefore a useful tool for designing biodiversity‐friendly landscapes. To stop the ongoing decline of farmland biodiversity there are increasing claims for a paradigm shift in agriculture, namely from conserving and restoring farmland biodiversity at the field scale (α‐diversity) to doing it at the landscape scale (γ‐diversity). By analysing 123 landscapes with structural equation models, this study demonstrates that the relationships between factors shaping α‐diversity cannot simply be up‐scaled to γ‐diversity, and that also indirect effects should taken into account when designing biodiversity‐friendly landscapes.
The under HS increased water intake and HP but unchanged feed intake and milk production suggest that cows were in beginning/mild heat stress | HS did not alter CH4 production | Reduced dietary NDF content did not mitigate HS | Future studies should investigate feeding strategies to mitigate mild heat stress and clarify the heat increment of digestible fibre
Unhealthy diets contribute to the increasing burden of non-communicable diseases. Annually, over 11 million deaths worldwide are attributed to dietary risk factors, with the vast majority of deaths resulting from cardiometabolic diseases (CMDs) including cardiovascular disease (∼10 million) and type II diabetes (∼339,000). As such, defining diets and dietary patterns that mitigate CMD risk is of great public health importance. Recently, the consumption of fermented foods has emerged as an important dietary strategy for improving cardiometabolic health. Fermented foods have been present in the human diet for over 10,000 years, but knowledge on whether their consumption benefits human health, and the molecular and microbiological mechanisms underpinning their purported health benefits, is relatively nascent. This review provides an overview of the definitions of fermented foods, types and qualities of fermented foods consumed in Europe and globally, possible mechanisms between the consumption of fermented foods and cardiometabolic health, as well as the current state of the epidemiological evidence on fermented food intake and cardiometabolic health. Finally, we outline future perspectives and opportunities for improving the role of fermented foods in human diets.
Background Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. Results We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. Conclusions Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry.
Background: Whereas the dietary intake of industrial trans fatty acids (iTFA) has been specifically associated with inflammation, cardiovascular disease, and type 2 diabetes, understanding the impact of dietary fats on human health remains challenging owing to their complex composition and individual effects of their lipid components on metabolism. The aim of this study is to profile the composition of blood, measured by the fatty acid (FAs) profile and untargeted metabolome of serum and the transcriptome of blood cells, in order to identify molecular signatures that discriminate dietary fat intakes. Methods: In a parallel study, the molecular effects of consuming dairy fat containing ruminant TFA (rTFA) or margarine containing iTFA were investigated. Healthy volunteers (n = 42; 45-69 y) were randomly assigned to diets containing margarine without TFA as major source of fat (wTFA control group with 0.4 g TFA per 100 g margarine), margarine with iTFA (iTFA group with 4.1 g TFA per 100 g margarine), or butter with rTFA (rTFA group with 6.3 g TFA per 100 g butter) for 4 weeks. The amounts of test products were individually selected so that fat intake contributed to 30-33% of energy requirements and TFA in the rTFA and iTFA groups contributed to up to 2% of energy intake. Changes in fasting blood values of lipid profiles (GC with flame-ionization detection), metabolome profiles (LC-MS, GC-MS), and gene expression (microarray) were measured. Results: Eighteen FAs, as well as 242 additional features measured by LC-MS (185) and GC-MS (54) showed significantly different responses to the diets (PFDR-adjusted < 0.05), mainly distinguishing butter from the margarine diets while gene expression was not differentially affected. The most abundant TFA in the butter, i.e. TFA containing (E)-octadec-11-enoic acid (C18:1 t11; trans vaccenic acid), and margarines, i.e. TFA containing (E)-octadec-9-enoic acid (C18:1 t9; elaidic acid) were reflected in the significantly different serum levels of TFAs measured after the dietary interventions. Conclusions: The untargeted serum metabolome differentiates margarine from butter intake although the identification of the discriminating features remains a bottleneck. The targeted serum FA profile provides detailed information on specific molecules differentiating not only butter from margarine intake but also diets with different content of iTFAs in margarine. Trial registration: ClinicalTrials.gov NCT00933322.
To defend themselves against pathogenic microorganisms, honey bees resort to social immunity mechanisms, such as the secretion of antibiotic compounds in the jelly they feed to their larvae. Whereas the bactericidal activity of jelly fed to queen larvae is well studied, little is known about the bioactivity of compositionally different jelly fed to worker larvae. However, the numerous worker larvae are likely to drive the spread of the microorganism and influence its virulence and pathogenesis. Diluted jelly or extracts are mostly used for jelly bioactivity tests, which may bias the evaluation of the pathogen’s resistance and virulence. Here, we compared the bactericidal effect of pure and diluted jellies destined for queen and worker larvae on Melissococcus plutonius , the etiological agent of the European foulbrood (EFB) disease of honey bees, and on a secondary invader bacteria, Enterococcus faecalis . We tested three strains of M. plutonius with varying virulence to investigate the association between resistance to antibacterial compounds and virulence. The resistance of the bacteria varied but was not strictly correlated with their virulence and was lower in pure than in diluted jelly. Resistance differed according to whether the jelly was destined for queen or worker larvae, with some strains being more resistant to queen jelly and others to worker jelly. Our results provide a biologically realistic assessment of host defenses via nutritive jelly and contribute to a better understanding of the ecology of M. plutonius and of secondary invaders bacteria in the honey bee colony environment, thus shedding light on the selective forces affecting their virulence and on their role in EFB pathogenesis.
A variety of organic feedstocks can be used for anaerobic digestion, resulting in digestates with different compositions, affecting the fertiliser value. Therefore, two experiments were conducted to assess (1) differences in the nitrogen (N) fertiliser value of seven digestates from different feedstocks in a 2-year field experiment with spring wheat, and (2) the degradability of organic matter (OM) in the digestates within an aerobic incubation experiment. In the field, mineral fertiliser equivalents were in a range of 18–60% (1st year) and 39–83% (2nd year). Fertiliser properties could describe 58.9–74.2% of the N offtake variance among digestates. In the incubation experiment, digestates produced 720–1900 mg CO 2 -C kg ⁻¹ . After 56 days, 61% of organic C added by food waste digestate has been mineralised, compared to 16–22% for the other digestates. Digestate composition (C/N, C org /N org , carbonate, cellulose, lignin, and crude fibre) could explain 90.4% of the CO 2 evolution. In both experiments, digested food waste stood out among digestates with the highest N offtake and highest OM mineralisation. In conclusion, differences in fertiliser value and OM degradability could be related to compositional variations. However, apart from food waste, the composition had only minor influence on digestate performance after soil application. Graphical Abstract
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481 members
Vincent Dietemann
  • Swiss Bee Research Center
Jana Collatz
  • Biosafety Group
Camps Cédric
  • Institute for Plant Production Sciences (IPS)
Barbara Walther
  • Food Microbial Systems
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Switzerland
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www.agroscope.ch