Is eco-efficiency in greenhouse gas emissions converging among European Union countries?

Eco-efficiency refers to the ability to produce more goods and services with less impact on the environment and less consumption of natural resources. This issue has become a matter of concern that is receiving increasing attention from politicians, scientists and researchers. Furthermore, greenhouse gases emitted as a result of production processes have a marked impact on the environment and are also the foremost culprit of global warming and climate change. This paper assesses convergence in eco-efficiency in greenhouse gas emissions in the European Union. Eco-efficiency is assessed at both country and greenhouse-gas-specific levels using Data Envelopment Analysis techniques and directional distance functions, as recently proposed by Picazo-Tadeo et al. (Eur J Oper Res, 220:798–809, 2012). Convergence is then evaluated using the Phillips and Sul (Econometrica, 75:1771–1855, 2007) approach that allows testing for the existence of convergence groups. Although the results point to the existence of different convergence clubs depending on the specific pollutant considered, they signal the existence of at least four clear groups of countries. The first two groups are core European Union high-income countries (Benelux, Germany, Italy, Austria, the United Kingdom and Scandinavian countries). A third club is made up of peripheral countries (Spain, Ireland, Portugal and Greece) together with some Eastern countries (Latvia and Slovenia), while the remaining clubs consist of groups containing Eastern European countries

Epidemiology of major diseases and structuration of root microbiomes : a comparative study between irrigated and lowland rice cultivation in Burkina Faso

Le riz constitue l’aliment de base de plus de la moitié de la population mondiale et sa consommation est en forte augmentation en Afrique de l’Ouest. De multiples contraintes affectent sa production, limitant ainsi les rendements rizicoles mondiaux, particulièrement au Burkina Faso où la production rizicole couvre à peine 47% des besoins des populations. Cela s’explique en partie par les dégâts causés par les agents pathogènes viraux, bactériens et fongiques. La compréhension de la dynamique spatiotemporelle des maladies et l'identification des facteurs de risque sont d'une importance capitale pour guider le déploiement de moyens de lutte efficaces car l’infection d’un hôte dépend de l’agent pathogène considéré mais aussi de la plante (génotype) et de l’environnement biotique et abiotique de la plante. Cet environnement biotique comprend les micro-organismes associés aux racines qui peuvent maintenant être appréhendés grâce aux techniques récentes de séquençage haut débit.Nous avons mené la présente étude entre 2016 et 2019 à l’ouest du Burkina Faso dans trois zones géographiques, comprenant chacune un périmètre irrigué, et un bas-fonds situé à proximité, donc un total de six sites. Tout d’abord, des entretiens ont été réalisé avec les agriculteurs pour mieux caractériser les pratiques agriculturales dans chacun des sites. Ils confirment que les deux systèmes de riziculture diffèrent en termes de pratiques culturales, avec notamment le repiquage, les deux saisons de riz, et une plus forte fertilisation minérale en riziculture irriguée.En outre, nous avons génotypé 77 échantillons de riz du Burkina Faso sur des milliers de SNP et analysé les données obtenues dans le cadre de la diversité génétique mondiale d'Oryza sativa. Tous les échantillons collectés au champ étaient assignés à Oryza sativa indica, sauf un correspondant au groupe Aus. Nous n’avons pas obtenu de différences entre la génétique des échantillons de riz des zones irriguées et celui des bas-fonds, à l'exception de Tengrela qui diffère de tous les autres sites, avec la présence de l’échantillon Aus et une différentiation forte par rapport aux cinq autres sites.De plus, nous avons visité annuellement des parcelles de riz et observé les symptômes foliaires afin de comparer les niveaux des quatre principales maladies du riz : la panachure jaune, la bactériose à stries foliaires, la pyriculariose et l’helminthosporiose entre deux systèmes rizicoles. Globalement la fréquence des symptômes (quatre maladies confondues) est plus élevée en riziculture irriguée que dans les bas-fonds. C’est aussi le cas spécifiquement pour la bactériose à stries foliaires et la pyriculariose. En revanche, la panachure jaune du riz est présente à forte fréquence et incidence dans certains sites (‘hotspots’), tandis que l’helminthosporiose est fréquente dans tous les sites. Les fréquences de co-occurrence sont plus élevées dans les périmètres irrigués que dans les bas-fonds.Enfin, nous avons caractérisé la diversité microbienne associées aux racines du riz par une approche de metabarcoding, c’est-à-dire un séquençage haut-débit des loci 16S pour les communautés bactériennes et ITS pour les communautés fongiques. Les principaux facteurs structurants ces communautés microbiennes sont le type de riziculture, la zone géographique, le site et le compartiment racinaire. Nous avons obtenu plus de diversité de procaryotes en riziculture irriguée (avec des réseaux plus complexes) que dans les bas-fonds, et identifié des phylotypes clés dans les communautés de chaque type de riziculture.Notre approche intégrative, qui s’inscrit dans le concept de ‘phytobiome’, contribue à une meilleure compréhension de la santé de la plante au sens large, dans le but de contrôler les bioagresseurs des cultures tout en protégeant la santé humaine et environnementale.Mots clés: Riz, riziculture irriguée, bas-fonds, maladies, Burkina Faso, diversité génétique, microbiomeRice is a staple food for more than half of the world's population and its consumption is increasing in West Africa. Multiple constraints affect its production, limiting global rice yields, particularly in Burkina Faso, where rice production covers barely 47% of the population's needs. This is partly due to damage caused by viral, bacterial and fungal pathogens. Understanding the spatiotemporal dynamics of diseases and identifying risk factors is of paramount importance in guiding the deployment of effective control measures, as host infection depends on the considered pathogen, but also on the plant (genotype), as well as the biotic and abiotic environment of the plant. This biotic environment includes the microorganisms associated with the roots, which can now be deciphered using recent high-throughput sequencing technologies.We conducted the present study between 2016 and 2019 in western Burkina Faso in three geographical areas, each of which included one irrigated perimeter, and a nearby lowland, resulting in a total of six sites. First, interviews were conducted with farmers to better characterize farming practices in each site. They confirmed that the two rice-growing systems differ in terms of cultural practices, including transplanting, two rice seasons, and higher mineral fertilization in irrigated rice.In addition, we genotyped 77 rice samples from Burkina Faso on thousands of SNPs and analyzed the resulting data in the context of global Oryza sativa genetic diversity. All samples collected in the field were assigned to Oryza sativa indica, except one corresponding to the Aus group. No differences were found between the genetics of the irrigated and lowland rice samples, with the exception of Tengrela, which differed from all other sites, with the presence of the Aus sample and a strong differentiation from the other five sites.In addition, we visited rice plots annually and observed leaf symptoms to compare the levels of the four major rice diseases: yellow mottle disease, bacterial leaf streak (BLS) disease, rice blast and brown spot between two rice systems. Our results show that overall the frequency of symptoms (all four diseases combined) is higher in irrigated rice than in lowland rice. This is also the case specifically for BLS and for rice blast. In contrast, rice yellow mottle disease is present at high frequency and incidence in some specific ('hotspots') sites, while brown spot is common in all sites. Co-occurrence are higher in irrigated areas than in lowland areas.Finally, we characterized the microbial diversity associated with rice roots using a metabarcoding approach, i.e. high-throughput sequencing of 16S loci for bacterial communities and ITS for fungal communities. The main factors structuring these microbial communities are the rice growing system, the geographical zone, the specific site and the root compartment. We obtained more prokaryotic diversity (and more complex networks) in irrigated rice, compared to rainfed lowlands and identified key phylotypes in the communities of each type of rice cultivation.Our integrative approach, inspired by the 'phytobiome' concept, contributes to a better understanding of plant health in the broadest sense, with the aim of controlling crop pests while protecting human and environmental health.Keywords: Rice, irrigated rice, lowland, diseases, Burkina Faso, genetic diversity, microbiom

Épidémiologie des maladies majeures et structuration des microbiomes racinaires : étude comparative entre rizicultures irriguée et de bas fond au Burkina Faso

Rice is a staple food for more than half of the world's population and its consumption is increasing in West Africa. Multiple constraints affect its production, limiting global rice yields, particularly in Burkina Faso, where rice production covers barely 47% of the population's needs. This is partly due to damage caused by viral, bacterial and fungal pathogens. Understanding the spatiotemporal dynamics of diseases and identifying risk factors is of paramount importance in guiding the deployment of effective control measures, as host infection depends on the considered pathogen, but also on the plant (genotype), as well as the biotic and abiotic environment of the plant. This biotic environment includes the microorganisms associated with the roots, which can now be deciphered using recent high-throughput sequencing technologies.We conducted the present study between 2016 and 2019 in western Burkina Faso in three geographical areas, each of which included one irrigated perimeter, and a nearby lowland, resulting in a total of six sites. First, interviews were conducted with farmers to better characterize farming practices in each site. They confirmed that the two rice-growing systems differ in terms of cultural practices, including transplanting, two rice seasons, and higher mineral fertilization in irrigated rice.In addition, we genotyped 77 rice samples from Burkina Faso on thousands of SNPs and analyzed the resulting data in the context of global Oryza sativa genetic diversity. All samples collected in the field were assigned to Oryza sativa indica, except one corresponding to the Aus group. No differences were found between the genetics of the irrigated and lowland rice samples, with the exception of Tengrela, which differed from all other sites, with the presence of the Aus sample and a strong differentiation from the other five sites.In addition, we visited rice plots annually and observed leaf symptoms to compare the levels of the four major rice diseases: yellow mottle disease, bacterial leaf streak (BLS) disease, rice blast and brown spot between two rice systems. Our results show that overall the frequency of symptoms (all four diseases combined) is higher in irrigated rice than in lowland rice. This is also the case specifically for BLS and for rice blast. In contrast, rice yellow mottle disease is present at high frequency and incidence in some specific ('hotspots') sites, while brown spot is common in all sites. Co-occurrence are higher in irrigated areas than in lowland areas.Finally, we characterized the microbial diversity associated with rice roots using a metabarcoding approach, i.e. high-throughput sequencing of 16S loci for bacterial communities and ITS for fungal communities. The main factors structuring these microbial communities are the rice growing system, the geographical zone, the specific site and the root compartment. We obtained more prokaryotic diversity (and more complex networks) in irrigated rice, compared to rainfed lowlands and identified key phylotypes in the communities of each type of rice cultivation.Our integrative approach, inspired by the 'phytobiome' concept, contributes to a better understanding of plant health in the broadest sense, with the aim of controlling crop pests while protecting human and environmental health.Keywords: Rice, irrigated rice, lowland, diseases, Burkina Faso, genetic diversity, microbiomeLe riz constitue l’aliment de base de plus de la moitié de la population mondiale et sa consommation est en forte augmentation en Afrique de l’Ouest. De multiples contraintes affectent sa production, limitant ainsi les rendements rizicoles mondiaux, particulièrement au Burkina Faso où la production rizicole couvre à peine 47% des besoins des populations. Cela s’explique en partie par les dégâts causés par les agents pathogènes viraux, bactériens et fongiques. La compréhension de la dynamique spatiotemporelle des maladies et l'identification des facteurs de risque sont d'une importance capitale pour guider le déploiement de moyens de lutte efficaces car l’infection d’un hôte dépend de l’agent pathogène considéré mais aussi de la plante (génotype) et de l’environnement biotique et abiotique de la plante. Cet environnement biotique comprend les micro-organismes associés aux racines qui peuvent maintenant être appréhendés grâce aux techniques récentes de séquençage haut débit.Nous avons mené la présente étude entre 2016 et 2019 à l’ouest du Burkina Faso dans trois zones géographiques, comprenant chacune un périmètre irrigué, et un bas-fonds situé à proximité, donc un total de six sites. Tout d’abord, des entretiens ont été réalisé avec les agriculteurs pour mieux caractériser les pratiques agriculturales dans chacun des sites. Ils confirment que les deux systèmes de riziculture diffèrent en termes de pratiques culturales, avec notamment le repiquage, les deux saisons de riz, et une plus forte fertilisation minérale en riziculture irriguée.En outre, nous avons génotypé 77 échantillons de riz du Burkina Faso sur des milliers de SNP et analysé les données obtenues dans le cadre de la diversité génétique mondiale d'Oryza sativa. Tous les échantillons collectés au champ étaient assignés à Oryza sativa indica, sauf un correspondant au groupe Aus. Nous n’avons pas obtenu de différences entre la génétique des échantillons de riz des zones irriguées et celui des bas-fonds, à l'exception de Tengrela qui diffère de tous les autres sites, avec la présence de l’échantillon Aus et une différentiation forte par rapport aux cinq autres sites.De plus, nous avons visité annuellement des parcelles de riz et observé les symptômes foliaires afin de comparer les niveaux des quatre principales maladies du riz : la panachure jaune, la bactériose à stries foliaires, la pyriculariose et l’helminthosporiose entre deux systèmes rizicoles. Globalement la fréquence des symptômes (quatre maladies confondues) est plus élevée en riziculture irriguée que dans les bas-fonds. C’est aussi le cas spécifiquement pour la bactériose à stries foliaires et la pyriculariose. En revanche, la panachure jaune du riz est présente à forte fréquence et incidence dans certains sites (‘hotspots’), tandis que l’helminthosporiose est fréquente dans tous les sites. Les fréquences de co-occurrence sont plus élevées dans les périmètres irrigués que dans les bas-fonds.Enfin, nous avons caractérisé la diversité microbienne associées aux racines du riz par une approche de metabarcoding, c’est-à-dire un séquençage haut-débit des loci 16S pour les communautés bactériennes et ITS pour les communautés fongiques. Les principaux facteurs structurants ces communautés microbiennes sont le type de riziculture, la zone géographique, le site et le compartiment racinaire. Nous avons obtenu plus de diversité de procaryotes en riziculture irriguée (avec des réseaux plus complexes) que dans les bas-fonds, et identifié des phylotypes clés dans les communautés de chaque type de riziculture.Notre approche intégrative, qui s’inscrit dans le concept de ‘phytobiome’, contribue à une meilleure compréhension de la santé de la plante au sens large, dans le but de contrôler les bioagresseurs des cultures tout en protégeant la santé humaine et environnementale.Mots clés: Riz, riziculture irriguée, bas-fonds, maladies, Burkina Faso, diversité génétique, microbiom

Épidémiologie des maladies majeures et structuration des microbiomes racinaires : étude comparative entre rizicultures irriguée et de bas fond au Burkina Faso

Rice is a staple food for more than half of the world's population and its consumption is increasing in West Africa. Multiple constraints affect its production, limiting global rice yields, particularly in Burkina Faso, where rice production covers barely 47% of the population's needs. This is partly due to damage caused by viral, bacterial and fungal pathogens. Understanding the spatiotemporal dynamics of diseases and identifying risk factors is of paramount importance in guiding the deployment of effective control measures, as host infection depends on the considered pathogen, but also on the plant (genotype), as well as the biotic and abiotic environment of the plant. This biotic environment includes the microorganisms associated with the roots, which can now be deciphered using recent high-throughput sequencing technologies.We conducted the present study between 2016 and 2019 in western Burkina Faso in three geographical areas, each of which included one irrigated perimeter, and a nearby lowland, resulting in a total of six sites. First, interviews were conducted with farmers to better characterize farming practices in each site. They confirmed that the two rice-growing systems differ in terms of cultural practices, including transplanting, two rice seasons, and higher mineral fertilization in irrigated rice.In addition, we genotyped 77 rice samples from Burkina Faso on thousands of SNPs and analyzed the resulting data in the context of global Oryza sativa genetic diversity. All samples collected in the field were assigned to Oryza sativa indica, except one corresponding to the Aus group. No differences were found between the genetics of the irrigated and lowland rice samples, with the exception of Tengrela, which differed from all other sites, with the presence of the Aus sample and a strong differentiation from the other five sites.In addition, we visited rice plots annually and observed leaf symptoms to compare the levels of the four major rice diseases: yellow mottle disease, bacterial leaf streak (BLS) disease, rice blast and brown spot between two rice systems. Our results show that overall the frequency of symptoms (all four diseases combined) is higher in irrigated rice than in lowland rice. This is also the case specifically for BLS and for rice blast. In contrast, rice yellow mottle disease is present at high frequency and incidence in some specific ('hotspots') sites, while brown spot is common in all sites. Co-occurrence are higher in irrigated areas than in lowland areas.Finally, we characterized the microbial diversity associated with rice roots using a metabarcoding approach, i.e. high-throughput sequencing of 16S loci for bacterial communities and ITS for fungal communities. The main factors structuring these microbial communities are the rice growing system, the geographical zone, the specific site and the root compartment. We obtained more prokaryotic diversity (and more complex networks) in irrigated rice, compared to rainfed lowlands and identified key phylotypes in the communities of each type of rice cultivation.Our integrative approach, inspired by the 'phytobiome' concept, contributes to a better understanding of plant health in the broadest sense, with the aim of controlling crop pests while protecting human and environmental health.Keywords: Rice, irrigated rice, lowland, diseases, Burkina Faso, genetic diversity, microbiomeLe riz constitue l’aliment de base de plus de la moitié de la population mondiale et sa consommation est en forte augmentation en Afrique de l’Ouest. De multiples contraintes affectent sa production, limitant ainsi les rendements rizicoles mondiaux, particulièrement au Burkina Faso où la production rizicole couvre à peine 47% des besoins des populations. Cela s’explique en partie par les dégâts causés par les agents pathogènes viraux, bactériens et fongiques. La compréhension de la dynamique spatiotemporelle des maladies et l'identification des facteurs de risque sont d'une importance capitale pour guider le déploiement de moyens de lutte efficaces car l’infection d’un hôte dépend de l’agent pathogène considéré mais aussi de la plante (génotype) et de l’environnement biotique et abiotique de la plante. Cet environnement biotique comprend les micro-organismes associés aux racines qui peuvent maintenant être appréhendés grâce aux techniques récentes de séquençage haut débit.Nous avons mené la présente étude entre 2016 et 2019 à l’ouest du Burkina Faso dans trois zones géographiques, comprenant chacune un périmètre irrigué, et un bas-fonds situé à proximité, donc un total de six sites. Tout d’abord, des entretiens ont été réalisé avec les agriculteurs pour mieux caractériser les pratiques agriculturales dans chacun des sites. Ils confirment que les deux systèmes de riziculture diffèrent en termes de pratiques culturales, avec notamment le repiquage, les deux saisons de riz, et une plus forte fertilisation minérale en riziculture irriguée.En outre, nous avons génotypé 77 échantillons de riz du Burkina Faso sur des milliers de SNP et analysé les données obtenues dans le cadre de la diversité génétique mondiale d'Oryza sativa. Tous les échantillons collectés au champ étaient assignés à Oryza sativa indica, sauf un correspondant au groupe Aus. Nous n’avons pas obtenu de différences entre la génétique des échantillons de riz des zones irriguées et celui des bas-fonds, à l'exception de Tengrela qui diffère de tous les autres sites, avec la présence de l’échantillon Aus et une différentiation forte par rapport aux cinq autres sites.De plus, nous avons visité annuellement des parcelles de riz et observé les symptômes foliaires afin de comparer les niveaux des quatre principales maladies du riz : la panachure jaune, la bactériose à stries foliaires, la pyriculariose et l’helminthosporiose entre deux systèmes rizicoles. Globalement la fréquence des symptômes (quatre maladies confondues) est plus élevée en riziculture irriguée que dans les bas-fonds. C’est aussi le cas spécifiquement pour la bactériose à stries foliaires et la pyriculariose. En revanche, la panachure jaune du riz est présente à forte fréquence et incidence dans certains sites (‘hotspots’), tandis que l’helminthosporiose est fréquente dans tous les sites. Les fréquences de co-occurrence sont plus élevées dans les périmètres irrigués que dans les bas-fonds.Enfin, nous avons caractérisé la diversité microbienne associées aux racines du riz par une approche de metabarcoding, c’est-à-dire un séquençage haut-débit des loci 16S pour les communautés bactériennes et ITS pour les communautés fongiques. Les principaux facteurs structurants ces communautés microbiennes sont le type de riziculture, la zone géographique, le site et le compartiment racinaire. Nous avons obtenu plus de diversité de procaryotes en riziculture irriguée (avec des réseaux plus complexes) que dans les bas-fonds, et identifié des phylotypes clés dans les communautés de chaque type de riziculture.Notre approche intégrative, qui s’inscrit dans le concept de ‘phytobiome’, contribue à une meilleure compréhension de la santé de la plante au sens large, dans le but de contrôler les bioagresseurs des cultures tout en protégeant la santé humaine et environnementale.Mots clés: Riz, riziculture irriguée, bas-fonds, maladies, Burkina Faso, diversité génétique, microbiom

Épidémiologie des maladies majeures et structuration des microbiomes racinaires : étude comparative entre rizicultures irriguée et de bas fond au Burkina Faso

Rice is a staple food for more than half of the world's population and its consumption is increasing in West Africa. Multiple constraints affect its production, limiting global rice yields, particularly in Burkina Faso, where rice production covers barely 47% of the population's needs. This is partly due to damage caused by viral, bacterial and fungal pathogens. Understanding the spatiotemporal dynamics of diseases and identifying risk factors is of paramount importance in guiding the deployment of effective control measures, as host infection depends on the considered pathogen, but also on the plant (genotype), as well as the biotic and abiotic environment of the plant. This biotic environment includes the microorganisms associated with the roots, which can now be deciphered using recent high-throughput sequencing technologies.We conducted the present study between 2016 and 2019 in western Burkina Faso in three geographical areas, each of which included one irrigated perimeter, and a nearby lowland, resulting in a total of six sites. First, interviews were conducted with farmers to better characterize farming practices in each site. They confirmed that the two rice-growing systems differ in terms of cultural practices, including transplanting, two rice seasons, and higher mineral fertilization in irrigated rice.In addition, we genotyped 77 rice samples from Burkina Faso on thousands of SNPs and analyzed the resulting data in the context of global Oryza sativa genetic diversity. All samples collected in the field were assigned to Oryza sativa indica, except one corresponding to the Aus group. No differences were found between the genetics of the irrigated and lowland rice samples, with the exception of Tengrela, which differed from all other sites, with the presence of the Aus sample and a strong differentiation from the other five sites.In addition, we visited rice plots annually and observed leaf symptoms to compare the levels of the four major rice diseases: yellow mottle disease, bacterial leaf streak (BLS) disease, rice blast and brown spot between two rice systems. Our results show that overall the frequency of symptoms (all four diseases combined) is higher in irrigated rice than in lowland rice. This is also the case specifically for BLS and for rice blast. In contrast, rice yellow mottle disease is present at high frequency and incidence in some specific ('hotspots') sites, while brown spot is common in all sites. Co-occurrence are higher in irrigated areas than in lowland areas.Finally, we characterized the microbial diversity associated with rice roots using a metabarcoding approach, i.e. high-throughput sequencing of 16S loci for bacterial communities and ITS for fungal communities. The main factors structuring these microbial communities are the rice growing system, the geographical zone, the specific site and the root compartment. We obtained more prokaryotic diversity (and more complex networks) in irrigated rice, compared to rainfed lowlands and identified key phylotypes in the communities of each type of rice cultivation.Our integrative approach, inspired by the 'phytobiome' concept, contributes to a better understanding of plant health in the broadest sense, with the aim of controlling crop pests while protecting human and environmental health.Keywords: Rice, irrigated rice, lowland, diseases, Burkina Faso, genetic diversity, microbiomeLe riz constitue l’aliment de base de plus de la moitié de la population mondiale et sa consommation est en forte augmentation en Afrique de l’Ouest. De multiples contraintes affectent sa production, limitant ainsi les rendements rizicoles mondiaux, particulièrement au Burkina Faso où la production rizicole couvre à peine 47% des besoins des populations. Cela s’explique en partie par les dégâts causés par les agents pathogènes viraux, bactériens et fongiques. La compréhension de la dynamique spatiotemporelle des maladies et l'identification des facteurs de risque sont d'une importance capitale pour guider le déploiement de moyens de lutte efficaces car l’infection d’un hôte dépend de l’agent pathogène considéré mais aussi de la plante (génotype) et de l’environnement biotique et abiotique de la plante. Cet environnement biotique comprend les micro-organismes associés aux racines qui peuvent maintenant être appréhendés grâce aux techniques récentes de séquençage haut débit.Nous avons mené la présente étude entre 2016 et 2019 à l’ouest du Burkina Faso dans trois zones géographiques, comprenant chacune un périmètre irrigué, et un bas-fonds situé à proximité, donc un total de six sites. Tout d’abord, des entretiens ont été réalisé avec les agriculteurs pour mieux caractériser les pratiques agriculturales dans chacun des sites. Ils confirment que les deux systèmes de riziculture diffèrent en termes de pratiques culturales, avec notamment le repiquage, les deux saisons de riz, et une plus forte fertilisation minérale en riziculture irriguée.En outre, nous avons génotypé 77 échantillons de riz du Burkina Faso sur des milliers de SNP et analysé les données obtenues dans le cadre de la diversité génétique mondiale d'Oryza sativa. Tous les échantillons collectés au champ étaient assignés à Oryza sativa indica, sauf un correspondant au groupe Aus. Nous n’avons pas obtenu de différences entre la génétique des échantillons de riz des zones irriguées et celui des bas-fonds, à l'exception de Tengrela qui diffère de tous les autres sites, avec la présence de l’échantillon Aus et une différentiation forte par rapport aux cinq autres sites.De plus, nous avons visité annuellement des parcelles de riz et observé les symptômes foliaires afin de comparer les niveaux des quatre principales maladies du riz : la panachure jaune, la bactériose à stries foliaires, la pyriculariose et l’helminthosporiose entre deux systèmes rizicoles. Globalement la fréquence des symptômes (quatre maladies confondues) est plus élevée en riziculture irriguée que dans les bas-fonds. C’est aussi le cas spécifiquement pour la bactériose à stries foliaires et la pyriculariose. En revanche, la panachure jaune du riz est présente à forte fréquence et incidence dans certains sites (‘hotspots’), tandis que l’helminthosporiose est fréquente dans tous les sites. Les fréquences de co-occurrence sont plus élevées dans les périmètres irrigués que dans les bas-fonds.Enfin, nous avons caractérisé la diversité microbienne associées aux racines du riz par une approche de metabarcoding, c’est-à-dire un séquençage haut-débit des loci 16S pour les communautés bactériennes et ITS pour les communautés fongiques. Les principaux facteurs structurants ces communautés microbiennes sont le type de riziculture, la zone géographique, le site et le compartiment racinaire. Nous avons obtenu plus de diversité de procaryotes en riziculture irriguée (avec des réseaux plus complexes) que dans les bas-fonds, et identifié des phylotypes clés dans les communautés de chaque type de riziculture.Notre approche intégrative, qui s’inscrit dans le concept de ‘phytobiome’, contribue à une meilleure compréhension de la santé de la plante au sens large, dans le but de contrôler les bioagresseurs des cultures tout en protégeant la santé humaine et environnementale.Mots clés: Riz, riziculture irriguée, bas-fonds, maladies, Burkina Faso, diversité génétique, microbiom

Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data.

Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome

The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso

International audienceDue to their potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer's fields from irrigated and rainfed lowlands in Burkina Faso, using an amplicon metabarcoding approach of the 16S rRNA gene (prokaryotes, three plant samples per field) and ITS (fungi, one sample per field). In addition to the expected structure by root compartments (root vs rhizosphere) and geographical zones, we showed that the rice production system is a major driver of microbiome structure. In irrigated systems, we found a higher diversity of prokaryotic communities from the rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands, while fungal communities exhibited an opposite pattern (higher richness in rainfed lowlands). Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, a higher abundance in rainfed lowlands was found for mycorrhizal fungi (both compartments) and rhizobia (rhizosphere only). Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for microbial engineering applications

Spatiotemporal Survey of Multiple Rice Diseases in Irrigated Areas Compared to Rainfed Lowlands in the Western Burkina Faso

International audienceMultiple constraints affect rice yields in West Africa. Among these constraints are viral, bacterial, and fungal pathogens. We aimed to describe the spatiotemporal patterns of occurrence and incidence of multiple rice diseases in farmers’ fields in contrasting rice growing systems in the western Burkina Faso. For this purpose, we selected a set of three pairs of sites, each comprising an irrigated area and a neighboring rainfed lowland, and studied them over four consecutive years. We first performed interviews with the rice farmers to better characterize the management practices at the different sites. This study revealed that the transplanting of rice and the possibility of growing rice twice a year are restricted to irrigated areas, while other practices, such as the use of registered rice cultivars, fertilization, and pesticides, are not specific but differ between the two rice growing systems. Then, we performed symptom observations at these study sites to monitor the following four diseases: yellow mottle disease, Bacterial Leaf Streak (BLS), rice leaf blast, and brown spot. The infection rates were found to be higher in irrigated areas than in rainfed lowlands, both when analyzing all observed symptoms together (any of the four diseases) and when specifically considering each of the two diseases: BLS and rice leaf blast. Brown spot was particularly prevalent in all six study sites, while yellow mottle disease was particularly structured geographically. Various diseases were frequently found together in the same field (co-occurrence) or even on the same plant (coinfection), especially in irrigated areas

Design of a new multiplex PCR assay for rice pathogenic bacteria detection and its application to infer disease incidence and detect co-infection in rice fields in Burkina Faso

International audienceCrop diseases are responsible for considerable yield losses worldwide and particularly in sub-Saharan Africa. To implement efficient disease control measures, detection of the pathogens and understanding pathogen spatio-temporal dynamics is crucial and requires the use of molecular detection tools, especially to distinguish different pathogens causing more or less similar symptoms. We report here the design a new molecular diagnostic tool able to simultaneously detect five bacterial taxa causing important diseases on rice in Africa: (1) Pseudomonas fuscovaginae, (2) Xanthomonas oryzae, (3) Burkholderia glumae and Burkholderia gladioli, (4) Sphingomonas and (5) Pantoea species. This new detection tool consists of a multiplex PCR, which is cost effective and easily applicable. Validation of the method is presented through its application on a global collection of bacterial strains. Moreover, sensitivity assessment for the detection of all five bacteria is reported to be at 0.5 ng DNA by μl. As a proof of concept, we applied the new molecular detection method to a set of 256 rice leaves collected from 16 fields in two irrigated areas in western Burkina Faso. Our results show high levels of Sphingomonas spp. (up to 100% of tested samples in one field), with significant variation in the incidence between the two sampled sites. Xanthomonas oryzae incidence levels were mostly congruent with bacterial leaf streak (BLS) and bacterial leaf blight (BLB) symptom observations in the field. Low levels of Pantoea spp. were found while none of the 256 analysed samples was positive for Burkholderia or Pseudomonas fuscovaginae. Finally, many samples (up to 37.5% in one studied field) were positive for more than one bacterium (co-infection). Documenting co-infection levels are important because of their drastic consequences on epidemiology, evolution of pathogen populations and yield losses. The newly designed multiplex PCR for multiple bacterial pathogens of rice is a significant improvement for disease monitoring in the field, thus contributing to efficient disease control and food safety

Virus-Bacteria Rice Co-Infection in Africa: Field Estimation, Reciprocal Effects, Molecular Mechanisms, and Evolutionary Implications

International audienceSimultaneous infection of a single plant by various pathogen species is increasingly recognized as an important modulator of host resistance and a driver of pathogen evolution. Because plants in agro-ecosystems are the target of a multitude of pathogenic microbes, co-infection could be frequent, and consequently important to consider. This is particularly true for rapidly intensifying crops, such as rice in Africa. This study investigated potential interactions between pathogens causing two of the major rice diseases in Africa: the Rice yellow mottle virus (RYMV) and the bacterium Xanthomonas oryzae pathovar oryzicola (Xoc) in order to: 1/ document virus-bacteria co-infection in rice in the field, 2/ explore experimentally their consequences in terms of symptom development and pathogen multiplication, 3/ test the hypothesis of underlying molecular mechanisms of interactions and 4/ explore potential evolutionary consequences. Field surveys in Burkina Faso revealed that a significant proportion of rice fields were simultaneously affected by the two diseases. Co-infection leads to an increase in bacterial specific symptoms, while a decrease in viral load is observed compared to the mono-infected mock. The lack of effect found when using a bacterial mutant for an effector specifically inducing expression of a small RNA regulatory protein, HEN1, as well as a viral genotype-specific effect, both suggest a role for gene silencing mechanisms mediating the within-plant interaction between RYMV and Xoc. Potential implications for pathogen evolution could not be inferred because genotype-specific effects were found only for pathogens originating from different countries, and consequently not meeting in the agrosystem. We argue that pathogen-pathogen-host interactions certainly deserve more attention, both from a theoretical and applied point of view