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Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences the structure and complexity of microbial communities. We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harbored a much more complex fungal network with significantly higher connectivity than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. We also found a strong negative association ( R 2  = 0.366; P  < 0.0001) between agricultural intensification and root fungal network connectivity. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH, and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales , Paraglomerales , and Diversisporales . Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome.

Aims Cover crops play an important role in soil fertility as they can accumulate large amounts of nutrients. This study aimed at understanding the nutrient uptake capacity of a wide range of cover crops and at assessing the relevance of acquisition strategies. Methods A field experiment was conducted to characterize 20 species in terms of leaf and root traits. Plant traits were related to nutrient concentration and shoot biomass production with a redundancy analysis. Acquisition strategies were identified using a cluster analysis. Results Root systems varied greatly among cover crop species. Five nutrient acquisition strategies were delineated. Significant amounts of nutrients (about 120 kg ha⁻¹ of nitrogen, 30 kg ha⁻¹ of phosphorus and 190 kg ha⁻¹ of potassium) were accumulated by the species in a short period. Nutrient acquisition strategies related to high accumulations of nutrients consisted in either high shoot biomass and root mass and dense tissues, or high nutrient concentrations and root length densities. Species with high root length densities showed lower C/N ratios. Conclusions The same amounts of nutrients were accumulated by groups with different acquisition strategies. However, their nutrient concentrations offer different perspectives in terms of nutrient release for the subsequent crop and nutrient cycling improvement.

AIMS: Biological nitrogen fixation by legumes is expected to play a greater role in future cropping systems. Our study evaluated 19 legume species grown as cover crops in Swiss agroecosystems. METHODS: Two field experiments were set up to monitor the biomass production and nitrogen content of 19 legumes and two non-legumes. The proportion of nitrogen derived from atmospheric N₂ (%Ndfa) was assessed using the ¹⁵N natural abundance method. In parallel, a pot experiment was set up to determine the species-specific B values necessary to apply this method. RESULTS: Some species produced an important amount of biomass in 3 months, up to 6.86 t/ha for Vicia faba. Five species, Lathyrus sativus, Pisum sativum, Vicia sativa, Vicia villosa, and V. faba, acquired more than 100 kg/ha of N through biological fixation. Important amounts of nitrogen were also derived from the soil. %Ndfa values showed high variability between and within species, ranging from 0 % to almost 100 %. CONCLUSIONS: Some legumes showed high N accumulation even in a short growing period, and could play an important role in fixing renewable nitrogen in crop rotation.

Core Ideas Cover crops provide ecosystem services linked to canopy cover development. Visual assessment of canopy cover is compared with two digital image analysis methods. Visual estimation is well correlated with image estimation but showed lower values. The choice of the canopy cover estimation method depends on the objective. Currently, in the context of agriculture, cover crops are crops cultivated with the sole aim of providing important ecosystem services such as erosion prevention. Many services offered by these crops are directly linked to the development of their vegetation, and especially of canopy cover. A proper estimation of this cover is thus necessary to evaluate cover crop performance. Many methods to estimate canopy cover exist, but differ in terms of effort and time needed to implement them. In this study, we compared visual assessment of canopy cover in the field with two methods of digital image analysis (Assess and Canopeo), for different cover crop species and vegetation types. Visual estimation was positively correlated with both type of image analysis estimations. However, it showed systematically lower values of canopy cover, especially at intermediate canopy cover values. The type of vegetation influenced the visual and digital image estimations, narrow leaf species being the most difficult to evaluate visually. This study showed that depending on its utilization, visual canopy cover assessment could be useful, especially when only relative estimation of canopy cover is needed. When absolute canopy cover estimation is needed, the use of digital image analysis should be preferred.

Identifying opportunities and limitations for closing yield gaps is essential for setting right the efforts dedicated to improve germplasm and agronomic practices. This study analyses genotypes × environments interaction (G × E), genetic progress, and grain yield stability under contrasting production systems. For this, we analyzed datasets obtained from three Swiss trial-networks of winter wheat that were designed to evaluate genotypes under organic farming conditions, conventional management with low-inputs (150 kg nitrogen (N) ha with no fungicide application) and conventional management with high-inputs (170 kg N ha with fungicide application). The datasets covered the periods from 1998 to 2018 for organic and conventional management with low-inputs and from 2008 to 2018 for conventional management with high-inputs. The trial-networks evaluated each year an average of 36 winter wheat genotypes that included released varieties, advanced breeding lines, and lines for registration and post-registration in Switzerland. We investigated within each trial-network the influence of years, genotypes, environments and their interactions on the total variance in grain yield and grain N concentration using variance components analyses. We further applied mixed models with regression features to dissect genetic components due to breeding efforts from non-genetic components. The genotype as a single factor or as a factor interacting with the environment or the year (G × E, G × year, and G × E × year) explained 13% (organic), 20% (conventional low-inputs), and 24% (conventional high-inputs) of the variance in grain yield, while the corresponding values for grain N concentration were 29%, 25%, and 32%. Grain yield has stagnated since 1990 for conventional systems while the trend under organic management was slightly negative. The dissection of a genetic component from the grain yield trends under conventional management showed that genetic improvements contributed with 0.58 and 0.68 t ha y with low- and high- inputs, respectively. In contrast, a significant genetic source in the grain yield trend under organic management was not detected. Therefore, breeding efforts have been less effective on the wheat productivity for organic farming conditions than for conventional ones.

Both soil quality degradation and climate change mitigation issues emphasize the need to increase, or at least stabilize, the topsoil organic carbon content (wt%) in arable land. This on-farm study aimed at measuring the impact of agricultural practices on changes in soil organic carbon (SOC) content over 10 years. A total of 120 fields belonging to 120 farms representative of the cropping systems and soil properties in Western Switzerland (Lake Geneva region) was randomly selected. The field 0–20 cm topsoil was sampled at a 10-years interval, and the corresponding cropping practices were gathered using farmer’s interviews and the mandatory records of yearly practices at field level in Swiss-farms. Only 1) organic matter inputs and 2) cover-crop intensity were significantly correlated to SOC increase while 3) the soil tillage intensity and 4) the soil saturation in carbon expressed as a SOC to clay content ratio were correlated to SOC decrease. Among others, temporary meadows were not correlated to changes in SOC content mainly due to increased tillage and decreased cover-crops between meadows. Organic farming did not correlate either with SOC changes due to the large tillage intensity applied for weed control. The observed SOC content changes ranged from −56‰ to +74‰ and were well explained by a linear regression model with additive effect of the four identified SOC change factors. The additivity of these factors means that farmers can emphasize the methods of their choice when regenerating their soils. This study advocates that strict no-till is not required at low carbon saturation level (small SOC:Clay ratio). However, as carbon saturation increases, conservation tillage and then no-till practices become necessary to further increase SOC contents. These findings are in accordance with previous studies showing that since 2015 SOC is increasing at more than +4‰ on average in the region and provide practical insights to further manage the transition of farming systems towards soil regeneration.

The new IMPACT 2002+ life cycle impact assessment methodology proposes a feasible implementation of a combined midpoint/damage approach, linking all types of life cycle inventory results (elementary flows and other interventions) via 14 midpoint categories to four damage categories. For IMPACT 2002+, new concepts and methods have been developed, especially for the comparative assessment of human toxicity and ecotoxicity. Human Damage Factors are calculated for carcinogens and non-carcinogens, employing intake fractions, best estimates of dose-response slope factors, as well as severities. The transfer of contaminants into the human food is no more based on consumption surveys, but accounts for agricultural and livestock production levels. Indoor and outdoor air emissions can be compared and the intermittent character of rainfall is considered. Both human toxicity and ecotoxicity effect factors are based on mean responses rather than on conservative assumptions. Other midpoint categories are adapted from existing characterizing methods (Eco-indicator 99 and CML 2002). All midpoint scores are expressed in units of a reference substance and related to the four damage categories human health, ecosystem quality, climate change, and resources. Normalization can be performed either at midpoint or at damage level. The IMPACT 2002+ method presently provides characterization factors for almost 1500 different LCI-results, which can be downloaded at http://www.epfl.ch/impact

ABSTRACT Introduction Environmental stressors on the agricultural field are increasing, from global warming to the rise of the human population. Among the resulting challenges, plant diseases remain one of the most important causes of crop losses worldwide. Chemical pesticides are used to protect crops, yet they often come with significant environmental risks to the farmers, water, pollinators, and soil diversity. It is crucial, therefore, to investigate non‐chemical alternatives to protect crops. Nevertheless, their effectiveness often varies and is difficult to predict, as results obtained under laboratory conditions rarely translate to the complex and dynamic environments of agricultural fields. Materials and Methods In this 3‐year on‐farm study, we compared the effects of chemical and alternative seed treatments (Thermoseed, electron beam, and mustard‐based treatments) on agronomic parameters (yield, protein, thousand grain weight, and micronutrients) as well as on the bacterial and fungal microbial communities associated with winter wheat. Results Neither the chemical nor the alternative seed treatments affected any of the agronomic parameters measured. The treatments had no effect on the microbial community. Because the seeds used had a low disease prevalence, it was not possible to assess the intrinsic efficacy of the alternative treatments. Conclusions The alternative treatments showed no evidence of phytotoxicity in our on‐farm field study, indicating their suitability for further evaluation. However, none of the treatments, including the synthetic treatment, had a positive effect when seeds carried a low pathogen load. Our results suggest that pesticide applications on seeds with low levels of seedborne pathogens may be unnecessary, unless soilborne pathogens are suspected to be present.