Evaluation des services et dis-services écosystémiques rendus par les cultures intermédiaires multi-services et par la biofumigation pour améliorer la productivité du tournesol

Le tournesol présente des atouts agro-écologiques (économe en intrants, tolérant à la sécheresse) et occupe une place importante parmi les cultures oléagineuses. La culture est semée après une interculture pendant laquelle le sol reste sans couverture, ce qui peut l’exposer à une lixiviation de nutriments. Aussi, deux bioagresseurs telluriques de la culture (Verticillium dahliae et Orobanche cumana) sont en expansion. L’interculture pourrait être valorisée par l’implantation de cultures intermédiaires multi-services (CIMS), telles que des Brassicacées pour leurs effets pièges à nitrates et leurs propriétés allélopathiques, qui permettent une production de molécules au potentiel biocide, notamment lors de son broyage et de son enfouissement (biofumigation). De plus, des Fabacées peuvent enrichir le sol en nitrates. Leur association pourrait induire une mutualisation de ces effets. L’objectif de la thèse était d’évaluer des services écosystémiques fournis par l’introduction de Brassicacées ou une Fabacée, seules ou associées, et de la biofumigation sur le tournesol. De potentiels dis-services sur des communautés microbiennes d’intérêt agronomique ont aussi été étudiés. Les CIMS choisies étaient la moutarde brune, le radis fourrager, la navette fourragère et la vesce du Bengale. Les expérimentations menées au laboratoire qui visaient à exposer V. dahliae et O. cumana à des broyats ont mis en évidence des régulations du développement du V. dahliae sur milieu de culture grâce aux Brassicacées et de la germination d’O. cumana (effet prédominant de la moutarde brune) et des effets plus variables des broyats sur le nombre de fixations ou d’émergences d’Orobanche. Au champ, la régulation de la Verticilliose est plus variable. Le radis fourrager semble être la CIMS la plus prometteuse pour lutter contre cette maladie, avec une réduction des dégâts ayant atteint 40% en 2016. Cependant, cette régulation pourrait dépendre de différents facteurs (météorologiques et techniques). Les effets des CIMS sur les quantités d’azote dans le sol et des rendements, en comparaison au sol nu, sont également variables en fonction des années et des CIMS. Une augmentation de l’azote (+50 kg.N.ha-1) a été observée en 2019, suite à de la vesce du Bengale. Une augmentation du rendement du tournesol a été observée (+0.7 t.ha-1) suite à la vesce du Bengale en 2020, mais des réductions (-0.5 à -0.6 t.ha-1) sont également à noter suite à un mélange. Aucun dis-service à l’égard de communautés microbiennes n’a été identifié durant ce travail de thèse. Les CIMS et la biofumigation, en particulier le radis fourrager ou la vesce du Bengale, auraient le potentiel de fournir des services écosystémiques, mais leur expression dépend des conditions météorologiques et de l’itinéraire cultural mis en place. Des travaux sont nécessaires afin de confirmer les effets observés, et pourraient s’appuyer sur une plus large diversité d’espèces et de variétés de radis, de vesces ainsi que de tournesols à évaluer. Des validations au sein de réseaux d’expérimentation chez des agriculteurs pourraient aussi être envisagées

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Assessment of ecosystem services and dis-services provided by cover crops and biofumigation to improve sunflower productivity

Le tournesol présente des atouts agro-écologiques (économe en intrants, tolérant à la sécheresse) et occupe une place importante parmi les cultures oléagineuses. La culture est semée après une interculture pendant laquelle le sol reste sans couverture, ce qui peut l’exposer à une lixiviation de nutriments. Aussi, deux bioagresseurs telluriques de la culture (Verticillium dahliae et Orobanche cumana) sont en expansion. L’interculture pourrait être valorisée par l’implantation de cultures intermédiaires multi-services (CIMS), telles que des Brassicacées pour leurs effets pièges à nitrates et leurs propriétés allélopathiques, qui permettent une production de molécules au potentiel biocide, notamment lors de son broyage et de son enfouissement (biofumigation). De plus, des Fabacées peuvent enrichir le sol en nitrates. Leur association pourrait induire une mutualisation de ces effets. L’objectif de la thèse était d’évaluer des services écosystémiques fournis par l’introduction de Brassicacées ou une Fabacée, seules ou associées, et de la biofumigation sur le tournesol. De potentiels dis-services sur des communautés microbiennes d’intérêt agronomique ont aussi été étudiés. Les CIMS choisies étaient la moutarde brune, le radis fourrager, la navette fourragère et la vesce du Bengale. Les expérimentations menées au laboratoire qui visaient à exposer V. dahliae et O. cumana à des broyats ont mis en évidence des régulations du développement du V. dahliae sur milieu de culture grâce aux Brassicacées et de la germination d’O. cumana (effet prédominant de la moutarde brune) et des effets plus variables des broyats sur le nombre de fixations ou d’émergences d’Orobanche. Au champ, la régulation de la Verticilliose est plus variable. Le radis fourrager semble être la CIMS la plus prometteuse pour lutter contre cette maladie, avec une réduction des dégâts ayant atteint 40% en 2016. Cependant, cette régulation pourrait dépendre de différents facteurs (météorologiques et techniques). Les effets des CIMS sur les quantités d’azote dans le sol et des rendements, en comparaison au sol nu, sont également variables en fonction des années et des CIMS. Une augmentation de l’azote (+50 kg.N.ha-1) a été observée en 2019, suite à de la vesce du Bengale. Une augmentation du rendement du tournesol a été observée (+0.7 t.ha-1) suite à la vesce du Bengale en 2020, mais des réductions (-0.5 à -0.6 t.ha-1) sont également à noter suite à un mélange. Aucun dis-service à l’égard de communautés microbiennes n’a été identifié durant ce travail de thèse. Les CIMS et la biofumigation, en particulier le radis fourrager ou la vesce du Bengale, auraient le potentiel de fournir des services écosystémiques, mais leur expression dépend des conditions météorologiques et de l’itinéraire cultural mis en place. Des travaux sont nécessaires afin de confirmer les effets observés, et pourraient s’appuyer sur une plus large diversité d’espèces et de variétés de radis, de vesces ainsi que de tournesols à évaluer. Des validations au sein de réseaux d’expérimentation chez des agriculteurs pourraient aussi être envisagées.Sunflower has agro-ecological benefits (low input, drought tolerant) and is an important oilseed crop. The crop is sown after an fallow period during which the soil remains uncovered, which can expose it to nutrient leaching. Also, two soilborne pests of the crop (Verticillium dahliae and Orobanche cumana) are expanding. Fallow period could be enhanced by sowing cover crops, such as Brassicaceae for their nitrate catching effects and allelopathic properties, which allow for the production of molecules with biocidal potential, especially during crushing and burial (biofumigation). In addition, Fabaceae can enhance nitrogen level in the soil. Their association could lead to a mutualisation of these effects. The objective of the thesis was to evaluate the ecosystem services provided by the introduction of Brassicaceae or a Fabaceae, as sole crop or as mixtures, and biofumigation on sunflower. Potential dis-services on microbial communities of agronomic interest were also studied. The selected cover crops were brown mustard, forage radish, turnip rape and purple vetch. Laboratory experiments involving exposure of V. dahliae and O. cumana to grinded tissues showed regulation of V. dahliae development on culture medium by Brassicaceae and of O. cumana germination (predominant effect of brown mustard) and more variable effects of grinded tissues on the number of Orobanche attachments or emergences. In the field, the regulation of Verticillium wilt is more variable. Fodder radish seems to be the most promising cover crop to control this disease, with a reduction in damage reaching 40% in 2016. However, this control could depend on different factors (meteorological and technical). The effects of cover crops on soil nitrogen levels and yields, compared to bare soil, are also variable depending on the year and the species of cover crops. An increase in nitrogen (+50 kg.N.ha-1) was observed in 2019, following purple vetch. An increase in sunflower yield was observed (+0.7 t.ha-1) following purple vetch in 2020, but reductions (-0.5 to -0.6 t.ha-1) were also noted. Finally, no dis-service to microbial communities was identified during this thesis work. Cover crops and biofumigation, in particular fodder radish or purple vetch, have the potential to provide ecosystem services, but their expression depends on the weather conditions and the crop itinerary. Further research is needed to confirm the observed effects, and could be based on a wider diversity of species and varieties of radish, vetch and sunflower to be evaluated. Validations within experimental networks of farmers could also be envisaged

Ecosystem Services Provided by Cover Crops and Biofumigation in Sunflower Cultivation

In south-western France, sunflowers are usually grown in short rotations and after a long fallow period during which soils are left bare. This practice can favour diseases, caused by soilborne fungi, such as sunflower verticillium wilt (SVW), as well as nitrate leaching, both of which can decrease yields. Growing cover crops during a fallow period is an agroecological practice that could provide ecosystem services and mitigate SVW. A Brassicaceae cover crop that causes biofumigation produces glucosinolates and liberate biocidal compounds that might regulate SVW biologically. Moreover, the green manure effect of the Fabaceae might increase soil mineral nitrogen (SMN). To go further, mixtures of Brassicaceae and Fabaceae might mutualise the benefits that each cover crop has in sole crops. A four-year field study in south-western France tested Brassicaceae (brown mustard, turnip rape and fodder radish) and Fabaceae (purple vetch) in sole crops or a mixture with two or three species during the fallow period, followed by biofumigation, and sunflower crop. The cover crops were characterised, SMN was measured, the SVW and yield were assessed and compared to those of the crop grown on soils left bare during the fallow period. Purple vetch as a sole crop cover crop significantly increased SMN before sunflower sowing but only in 2019. Fodder radish as a sole crop reduced SVW severity significantly, overall, 80 days after sowing, except in 2019, when weather conditions were unfavourable to biofumigation. Purple vetch as a sole crop also reduced significantly SVW severity in 2017 and 2020. Finally, sunflower yields after cover crops were higher than those after bare soils, only after purple vetch as a sole crop in 2020, with a mean increase of 0.77 t ha&minus;1. Mixtures of Brassicaceae and Fabaceae sowed at these densities resulted in an intermediate SMN level between those in sole crops and the bare soil and they did not significantly decrease SVW or increase yields. Our results suggest that cover crops, especially fodder radish or purple vetch, and biofumigation can provide ecosystem services for sunflower, instead of leaving soils bare during the fallow period. However, the extent of ecosystem services is markedly affected by soil and climatic conditions as well as other management practices

Evaluation des services et dis-services écosystémiques rendus par les cultures intermédiaires multi-services et par la biofumigation pour améliorer la productivité du tournesol

Sunflower has agro-ecological benefits (low input, drought tolerant) and is an important oilseed crop. The crop is sown after an fallow period during which the soil remains uncovered, which can expose it to nutrient leaching. Also, two soilborne pests of the crop (Verticillium dahliae and Orobanche cumana) are expanding. Fallow period could be enhanced by sowing cover crops, such as Brassicaceae for their nitrate catching effects and allelopathic properties, which allow for the production of molecules with biocidal potential, especially during crushing and burial (biofumigation). In addition, Fabaceae can enhance nitrogen level in the soil. Their association could lead to a mutualisation of these effects. The objective of the thesis was to evaluate the ecosystem services provided by the introduction of Brassicaceae or a Fabaceae, as sole crop or as mixtures, and biofumigation on sunflower. Potential dis-services on microbial communities of agronomic interest were also studied. The selected cover crops were brown mustard, forage radish, turnip rape and purple vetch. Laboratory experiments involving exposure of V. dahliae and O. cumana to grinded tissues showed regulation of V. dahliae development on culture medium by Brassicaceae and of O. cumana germination (predominant effect of brown mustard) and more variable effects of grinded tissues on the number of Orobanche attachments or emergences. In the field, the regulation of Verticillium wilt is more variable. Fodder radish seems to be the most promising cover crop to control this disease, with a reduction in damage reaching 40% in 2016. However, this control could depend on different factors (meteorological and technical). The effects of cover crops on soil nitrogen levels and yields, compared to bare soil, are also variable depending on the year and the species of cover crops. An increase in nitrogen (+50 kg.N.ha-1) was observed in 2019, following purple vetch. An increase in sunflower yield was observed (+0.7 t.ha-1) following purple vetch in 2020, but reductions (-0.5 to -0.6 t.ha-1) were also noted. Finally, no dis-service to microbial communities was identified during this thesis work. Cover crops and biofumigation, in particular fodder radish or purple vetch, have the potential to provide ecosystem services, but their expression depends on the weather conditions and the crop itinerary. Further research is needed to confirm the observed effects, and could be based on a wider diversity of species and varieties of radish, vetch and sunflower to be evaluated. Validations within experimental networks of farmers could also be envisaged.Le tournesol présente des atouts agro-écologiques (économe en intrants, tolérant à la sécheresse) et occupe une place importante parmi les cultures oléagineuses. La culture est semée après une interculture pendant laquelle le sol reste sans couverture, ce qui peut l’exposer à une lixiviation de nutriments. Aussi, deux bioagresseurs telluriques de la culture (Verticillium dahliae et Orobanche cumana) sont en expansion. L’interculture pourrait être valorisée par l’implantation de cultures intermédiaires multi-services (CIMS), telles que des Brassicacées pour leurs effets pièges à nitrates et leurs propriétés allélopathiques, qui permettent une production de molécules au potentiel biocide, notamment lors de son broyage et de son enfouissement (biofumigation). De plus, des Fabacées peuvent enrichir le sol en nitrates. Leur association pourrait induire une mutualisation de ces effets. L’objectif de la thèse était d’évaluer des services écosystémiques fournis par l’introduction de Brassicacées ou une Fabacée, seules ou associées, et de la biofumigation sur le tournesol. De potentiels dis-services sur des communautés microbiennes d’intérêt agronomique ont aussi été étudiés. Les CIMS choisies étaient la moutarde brune, le radis fourrager, la navette fourragère et la vesce du Bengale. Les expérimentations menées au laboratoire qui visaient à exposer V. dahliae et O. cumana à des broyats ont mis en évidence des régulations du développement du V. dahliae sur milieu de culture grâce aux Brassicacées et de la germination d’O. cumana (effet prédominant de la moutarde brune) et des effets plus variables des broyats sur le nombre de fixations ou d’émergences d’Orobanche. Au champ, la régulation de la Verticilliose est plus variable. Le radis fourrager semble être la CIMS la plus prometteuse pour lutter contre cette maladie, avec une réduction des dégâts ayant atteint 40% en 2016. Cependant, cette régulation pourrait dépendre de différents facteurs (météorologiques et techniques). Les effets des CIMS sur les quantités d’azote dans le sol et des rendements, en comparaison au sol nu, sont également variables en fonction des années et des CIMS. Une augmentation de l’azote (+50 kg.N.ha-1) a été observée en 2019, suite à de la vesce du Bengale. Une augmentation du rendement du tournesol a été observée (+0.7 t.ha-1) suite à la vesce du Bengale en 2020, mais des réductions (-0.5 à -0.6 t.ha-1) sont également à noter suite à un mélange. Aucun dis-service à l’égard de communautés microbiennes n’a été identifié durant ce travail de thèse. Les CIMS et la biofumigation, en particulier le radis fourrager ou la vesce du Bengale, auraient le potentiel de fournir des services écosystémiques, mais leur expression dépend des conditions météorologiques et de l’itinéraire cultural mis en place. Des travaux sont nécessaires afin de confirmer les effets observés, et pourraient s’appuyer sur une plus large diversité d’espèces et de variétés de radis, de vesces ainsi que de tournesols à évaluer. Des validations au sein de réseaux d’expérimentation chez des agriculteurs pourraient aussi être envisagées

Biofumigation to protect oilseed crops: focus on management of soilborne fungi of sunflower

Sunflower (Helianthus annuus L.) is one of the three most productive oilseed crops worldwide. Soilborne diseases limit yields and are challenging to manage. The fungi Verticillium dahliae, Sclerotinia sclerotiorum and Macrophomina phaseolina can survive in the soil for many years and spread. Following the ban on fumigants, biofumigation, which consists of growing, chopping and incorporating a Brassicaceae cover crop to allow biocidal compounds production in the soil, may be an alternative. Biocidal effects of the hydrolysis of glucosinolate into active compounds, such as isothiocyanates, have been shown in laboratory studies, but the effectiveness of biofumigation varies more in the field. The present study reviews the main factors that determine effective biofumigation to protect sunflower. Since the toxicity of isothiocyanates to pathogens varies widely among the latter, we reviewed studies that assessed the suppressive effect of products of glucosinolate hydrolysis on V. dahliae, S. sclerotiorum and M. phaseolina. Farmers can use many mechanisms to increase isothiocyanate production, which may protect sunflower crop effectively. Increasing biomass production and chopping the cover crop during mild temperatures and before rainy periods could increase biofumigation effectiveness. Further field experiments are needed to confirm the potential of biofumigation to control soilborne diseases of sunflower and assess potential disservices to beneficial soil communities, given their potential key role in the control of soilborne pathogens

Opportunités offertes par les plantes de services : la biofumigation

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