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As a consequence of its 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 western Burkina Faso, using an amplicon metabarcoding approach 16S (Prokaryotes, three plant sample per field) and ITS (fungi, one sample per field). In addition to the expected structure according to the root compartment (root vs. rhizosphere) and geographical zones, we show that the rice production system is a major driver of microbiome structure, both for prokaryotes and fungi. In irrigated systems, we found a higher diversity of prokaryotic communities from rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands. Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae and Bradyrhizobiaceae families in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, phylotypes assigned to putative phytobeneficial and pathogen species were found. Mycorrhizal fungi Glomeromycetes abundance was higher in rainfed lowlands. Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for potential microbial engineering applications.

We studied, at local scale, how the landscape dynamics of the Saloum and Casamance (Senegal) and The Gambia can reveal environmental crises and the resilience of agrarian. The method is based on remote sensing diachrony in land cover maps, field observations (landscape and botany), and interviews on recent landscape changes and agriculture. The results found that the relationships between agriculture and forest cover were complex and varied in space and time. However, some general trends appear: the period of drought prompted changes but with the rainfall recovery, a regeneration in the mangroves and a restoration in most rice crops happened. The changes stayed within the range of metastability, showing the strong resilience of the ecosystems and of most anthroposystems. Cet article étudie, à l’échelle locale comment les dynamiques des paysages du Saloum, de la Casamance (Sénégal) et de la Gambie peuvent informer sur les crises environnementales ou, au contraire, la résilience de ces systèmes agraires. La méthode est basée sur la production de cartes d’occupation du sol diachroniques par télédétection diachronique, des observations botaniques et paysagères sur le terrain et des enquêtes sur les changements récents des paysages et de l’agriculture. Les résultats obtenus indiquent que les relations entre agriculture et la couverture forestière ont été complexes et ont varié dans l’espace et dans le temps. Néanmoins certaines tendances générales apparaissent : la période de sécheresse a provoqué des changements mais, avec la reprise des pluies (fin des années 1990) s’observent une régénération des mangroves et une reprise de la riziculture dans la plupart des terroirs. Les changements sont donc restés dans le domaine de la métastabilité, et ont démontré une forte résilience écosystèmes et de la plupart des anthroposystèmes.

Meloidogyne spp. and Hirschmanniella spp. are among the most damaging plant-parasitic nematodes (PPNs). They threaten rice production, the main staple food in Asia. Cropping systems that promote natural biocontrol and plant tolerance to diseases are put forward as sustainable solutions to protect rice from these pests. In particular, cropping systems managed under conservation agriculture (CA) are promising because they improve soil health and functioning. We investigated the effects of two cropping system components in a Cambodian field, (i) CA practices, i.e., no-tillage with a cover crop Stylosanthes guianensis (cv. Nina), versus conventional plow-based tillage with no cover crop, and (ii) using IR504, IR64, Azucena and Zhonghua 11 rice varieties, on PPNs in roots and on communities (bacteria, fungi and nematodes) in the rhizosphere. We used a sequencing approach via amplicon barcoding to target microbial marker genes (16 S and ITS rRNA gene) and a microscopic approach to identify and quantify nematodes in the rhizosphere compartment. The variety had less effect than agricultural practices on the infection by PPNs and on the assembly of the three rhizosphere communities. Under CA, the abundance of PPNs extracted from the roots was reduced by 88%. Soil quality was substantially improved (+83% of total Kjeldahl nitrogen, +34% of available phosphorus, +10% of exchangeable potassium, +110% of soil organic carbon, +30% for the cation exchange capacity), thus providing more basal resources for microbial decomposers, especially fungi (+164% putative saprotrophs). Characterization of the three rhizosphere communities revealed a shift in the structure associated with soil enrichment. Both microbial richness (+3% for bacteria and +38% for fungi) and diversity (Shannon index, +11% for fungi and +5% for nematodes) increased. The relative abundance of taxa was modified by CA with notably more mycorrhizal fungi (+329% Glomeromycota spp.) and fewer Pratylenchidae nematodes (−92% Hirschmanniella spp.) in the rhizosphere. The reassembly of the communities using CA was associated with regulation of PPN populations. The reduction in Meloidogyne spp. abundance in roots (−64%) was correlated with the maturity of the food web (maturity index, +10% under CA) and with the increase in the relative abundance of omnivorous nematodes in the rhizosphere (+68% under CA). Seven years of CA in this field enabled the whole soil food web to mature thus creating a favorable niche for potentially predatory nematodes and microbes antagonistic against PPNs. This study confirms that CA is an alternative to nematicides to limit infection by PPNs in rice cropping systems.

International audience; Weeds are major biotic constraints to rice production worldwide. Compared to other sub-regions, weed communities of rice are not well described for East Africa and there is limited information on environmental factors affecting the distribution of species. This study aimed to address these knowledge gaps. Seasonally flooded rice production fields of 31 sites in Rwanda, Tanzania, Kenya and Uganda, across three altitude classes (Low: 1,000 m), were surveyed for weed species using quadrats. Data analyses involved multivariate approaches, non-parametric Kruskal–Wallis tests and logistic regressions, followed by calculation of ranked species abundance and Shannon Wiener Index diversity analyses. A total of 286 weed species, belonging to 59 families, were recorded with 42 species not previously reported as lowland rice weed in the sub-region. Twenty-four species were identified as abundant across altitudes. Weed species diversity was higher at medium altitudes compared to high and low altitudes. Significant patterns of floristic distinction between altitudinal classes were observed, with 80% of dissimilarity. The high altitude was dominated by Echinochloa colona, Leptochloa squarrosa and Sphaeranthus suaveolens, the medium altitude was dominated by Crassula granvikii, Pycreus lanceolatus and Ageratum conyzoides while the low altitude was dominated by E. colona, Cyperus difformis and Cyperus esculentus. The weed species composition of seasonally flooded rice fields in East Africa is diverse. Identification of a limited group of (24) commonly abundant weed species as well as the articulation of altitude-specific weed species groups will facilitate the development of better tailored weed control programmes.

Afin de suivre l’évolution de l’occupation du sol du bassin versant de la rivière Cau (nord du Vietnam), des images HRVIR 2 du satellite SPOT-4 ont été acquises fin novembre 2007 et début janvier 2008. Dans un premier temps, l’approche de classification hiérarchique avec le mode de classification « avec caractéristiques liées aux classes (class-related features) » a été développée et appliquée afin d’extraire sept classes d’occupation du sol pertinentes à la modélisation hydrologique, sans distinguer les rizières des autres types de culture. Cette approche a montré son efficacité, la précision globale de la classification étant de 91 %. Une diminution significative de la confusion entre les milieux urbains, les terres agricoles et les plantations a été remarquée par rapport à une classification antérieure d’une image LANDSAT-7 de 2003, dont la précision globale était de 78 %. Par la suite, afin de distinguer les rizières des autres types de culture, deux séries d’images du satellite RADARSAT-2 en bande-C (double polarisation et polarimétriques) ont été utilisées. Ces images ont été acquises de mai 2009 à mai 2010 et couvrent deux périodes de croissance du riz, soit la période de la principale récolte (saison traditionnelle du riz) et celle du printemps. Pour les images double polarisation, en mode standard (S5), une méthode de seuillage a été appliquée sur la variation temporelle du signal entre les images acquises en début de saison et celles à la mi-saison. Cette méthode a permis de détecter 74 % des rizières de la saison traditionnelle du riz et 63 % des rizières de la saison de riz du printemps, selon une comparaison avec des données statistiques de la province de Thai Nguyen. La précision globale de la classification obtenue, pour toutes les classes d’occupation du sol, est de 71 % pour la saison traditionnelle de riz et de 67 % pour la saison de riz du printemps. Pour les images polarimétriques, en mode fin (FQ21), la matrice de cohérence a été choisie pour identifier les rizières d’une zone hétérogène. La classification a été réalisée à l’aide de l’algorithme SVM (Support Vector Machine). Ces dernières informations ont ensuite été intégrées à la carte thématique dérivée d’images SPOT-4 pour obtenir la carte finale. Cette carte sert directement à la modélisation hydrologique. Les calculs des besoins en eau pour la culture du riz ont montré que les rizières prennent une grande proportion du débit total dans les deux sous-bassins versants utilisés en exemple. Ces calculs montrent l’importance de détecter les rizières si l’on souhaite réaliser des simulations hydrologiques réalistes sur le bassin versant de la rivière Cau et confirment une des hypothèses de nos travaux, qui est que l’identification des rizières sur la carte d’occupation du sol améliore les évaluations et prédictions liées au cycle hydrologique., In order to follow-up the evolution of land-cover in the Cau river watershed (northern Vietnam), SPOT-4 HRVIR 2 images were acquired at the end of November 2007 and at the beginning of January 2008. Initially, the hierarchical classification with class-related features approach has been developed and applied in order to extract seven land-cover classes relevant to hydrological modeling, without distinguishing between rice fields and other types of crop. This approach has proven to be effective, with overall classification accuracy of 91%. A significant decrease in confusion between urban areas, farmland and plantations was noted compared to a prior classification of a LANDSAT-7 image acquired in 2003 which had an overall accuracy of 78%. Subsequently, in order to distinguish paddy fields from other crop types, two series of RADARSAT-2 images which cover the centre region of the watershed were acquired during the second half of 2009 and the first half of 2010. One series of images were acquired as dual-polarization (like-polarization HH and cross-polarization HV) in standard mode (S5) and the others as quad-polarization in fine mode (FQ21). These images were acquired over a period which covers two rice growing periods, including the traditional crop season and the spring crop season. For dual polarization images (S5), a suitable thresholding method was applied to the ratio between images acquired at the beginning of the season and at the mid-season. This method detected 74% of rice fields in the traditional rice season and 63% of rice fields in the spring rice season, compared with statistical data from the province of Thai Nguyen. The overall classification accuracy for all land-cover classes is 71% for the traditional rice season and 67% for the spring rice season. As to the polarimetric images (FQ21), the coherence matrix was chosen to identify the rice fields of a heterogeneous zone. The classification was performed using the SVM (Support Vector Machine) algorithm. The latter information was then integrated into the thematic map derived from SPOT-4 images to obtain the final map. This map is directly used for hydrological modeling. Calculations of water requirements for rice cultivation have shown that rice fields take a large proportion of the total flow in the two sub-watersheds used as examples. These calculations show the importance of detecting rice fields when the realization of the realistic hydrological simulations on the Cau river watershed and to confirm the hypothesis that the identification of rice fields on the land-cover map improves assessments and predictions related to the hydrological cycle.

The aim of this research was to analyze greenhouse gas (GHG) emission in paddy rice–based cropping systems of the Middle Indo–Gangetic plains in India. Two paddy rice–based systems, namely paddy rice–wheat (PW) and paddy rice–potato–fallow (PP), were studied for GHG emission, net return (NR) and eco–efficiencies (EE). The PW (3354.9 ​± ​133.7 kgCO2eq ha−1 y−1) and PP (5096.3 ​± ​11.6 kgCO2eq ha−1 y−1) systems were observed to have significantly different GHG emissions. The most significant contributor to the GHG pool was fertilizer production, contributing about 40.3% and 46.1% in the PW and PP systems, respectively. On–farm direct nitrous oxide (N2O) emission was the second largest contributor to the GHG emission pool. Farm sizes significantly affected GHG emissions in the PW system, and medium farms (>3 ​ha) had higher GHG emission compared to other farm sizes. While the NR in the PP system was significantly higher (2504.3 ​± ​65.6 USD ha−1 y−1) compared to the PW system (1687.1 ​± ​90.6 USD ha−1 y−1) owing to better market prices of potato crop, it also performed slightly better on the EE scale (0.52 and 0.50 USD kgCO2 eq−1, respectively). In the PW system, comparatively larger farms were more eco–efficient than the smaller farms. However, the EE values for different farm sizes in the PP system were numerically and statistically similar. The results reported in this study may be beneficial to farmers to make decisions pertinent to sustainable management of agro inputs in paddy–based cropping systems and collective farming. Moreover, these results can even be utilized by governmental and non–governmental organizations for deciding support/subsidies to farmers in the study area.

Cette étude porte sur l'utilisation de l'imagerie satellite pour le suivi des cyclones et la caractérisation de leur impact. Deux événements récents sont étudiés à Madagascar : (i) Le cyclone Haruna, impactant la côte sud-ouest en février 2013, (ii) Le cyclone Enawo, touchant la côte nord-est en mars 2017. Le suivi de ces deux épisodes a montré la faisabilité de la mobilisation de l'imagerie satellitaire sur Madagascar pour une quantification des surfaces inondées associées aux cyclones. La combinaison des capteurs optiques et SAR (Synthetic Aperture Radar) à haute résolution temporelle et spatiale (HRS) abouti à : (i) un suivi en quasi temps réel d'Haruna par une surveillance des inondations pendant la crise et de la décrue en post-crise (ii) une cartographie des inondations en zone urbaine et dans les rizières de la région de Maroantsetra et Sambava, associées à Enawo, en combinant des images Sentinel-1 et 2, Pléiades et une démarche de cartographie participative.

International audience; An ethnobotanical study in lowland rice areas in East Africa was undertaken to assess farmers' knowledge on the usage of non-cultivated plants occurring in paddy fields, and to understand what rice farmers in this region do with useful species once they encounter them in their crop. Inventories of weed species in 19 rice schemes in Tanzania and Kenya were followed by interviews among 380 experienced rice farmers, community elders and traditional healers, grouped into 19 informant groups. Among informant groups, a high degree of consensus about uses of weeds growing in rice paddies was observed. From a total of 222 observed rice weed species, the informant groups identified 67 species with usages described in 1300 use reports. Among these 67 species, 20 are among the most commonly cited weed species in rice paddies in sub-Saharan Africa. Only in 42 cases (3% of the total use reports) did the farmers indicate that they collected (13 species) or spared (four species) these weeds during weeding. In all other cases, such plants were removed or killed during weeding, irrespective of their usefulness. Non-cultivated plants that are spared are those of which the putative agronomic qualities (i.e. for crop protection or soil improvement) are considered more important than their crop competition effects (i.e. Azolla filiculoides and Marsilea crenata) and those that are found in the field margins, which do not compete with the crop. Non-cultivated plants that are collected during weeding have food, fodder or medicinal purposes or a combination of purposes. The most cited species that are collected or spared during weeding were Bidens pilosa, Ipomoea aquatica, Corchorus olitorius and Stachytarpheta jamaicensis. This study revealed that lowland rice farmers in East Africa generally have a high level of understanding and consensus on the usefulness of the non-cultivated plants growing in lowland rice schemes. When they occur in their crop however, the vast majority of these species are primarily seen as weeds and consequently removed or killed.

This paper presents data collected in 2013, 2014 and 2015 on the cultural practices and agronomic performance of cropping systems in 500 lowland rice fields located in five regions of three West African countries, Benin, Mali and Sierra Leone. Data were collected in two stages. In the first stage, the main regions containing inland valleys were identified in each of the three countries and the most cultivated inland valley in each region was selected. Weather data were obtained from weather stations located close to the selected inland valleys. In regions with no weather stations, Tinytag data loggers were installed in the inland valleys to collect data on temperature, rainfall and relative humidity. In the second stage, the location and size of all the farmers' fields in each inland valley were determined using GPS devices. In 2013, soil samples were collected in each farmer's field and the soil physical-chemical properties were determined. Agronomic and socio-economic surveys were conducted to collect data on cultivated crops, crop sequences and management techniques using questionnaires and informal interviews. Crop yields were determined in each farmer's field in the growing season. The database contains a total of 131 variables divided into 9 themes: field characteristics, land preparation, field maintenance, irrigation, residue management, soil data, weather data, crop productions in the dry season and crop production in the rainy season.

Mali is a Sahelian country with a large climatic contrast from North to South. The current climatic and production evolutionary study is focused on the six major agro-climatic cereal production zones ranging from Kayes (400 mm) to Sikasso (>1000 mm) of rainfalls. Climatic data are rainfall records, daily maximum and minimum temperatures from 60 years of the six major synoptic weather observation stations. Data were analyzed on comparing average decades of the two normal periods of 30 years (1951-1980) and (1981-2010). Annual agronomic production data for millet, sorghum, maize and rice are derived from Mali's agricultural statistics base from 1984 to 2013. Main climatic results analyses indicate that climate change resulted in a decrease of 100 mm isohyets between the 2 periods of 30 years. The structure of the rainy season was little changed between these two periods since the average start of the season was delayed by 6 days and the average end date of the season became earlier by 4 days. Maximum temperatures increased significantly from + 0.44°C to + 1.53°C and minimum temperatures significantly increased from + 1.05°C to + 1.93°C in varying way depending on the sites. Statistics of major agronomic food crop production in Mali from 1984 to 2013 indicate an average increase of 985 to 4492 thousand tones, or 22% increase per year. There is a positive upward in saw tooth trend in Malian production from 1984 to 2013. This positive trend is the result of a combination of agricultural extension, agronomic research application and the management of small farmer holder in the Sahel. This evolution needs better study for drawing necessary right conclusions.

National audience

Madagascar est l’un des pays parmi les plus grands consommateurs de riz dans le monde avec 1,5kg de riz/hab./jour. En effet, la Grande île est aussi connue pour ces paysages de rizières et notamment dans la capitale. L’identité de la ville d’Antananarivo est associée aux rizières, qui témoignent de son passé culturel et historique. Aujourd’hui, le processus de remblaiement de ces parcelles de rizières favorise la création des quartiers informels qui sont appelés les« bas-quartiers ». Situés principalement dans la plaine, ces quartiers sous-équipés sont déconnectés de la ville, spatialement et socialement. Pourtant, sa proximité avec les rizières et le maintien de l’activité rurale constituent des qualités considérables pour le développement durable de la ville. C’est ce mode de vie conditionné par la culture du riz qui sera étudié dans ce mémoire sur trois échelles : la ville, le quartier et la maison. Ce mémoire est avant tout centré sur la riziculture dans la ville d’Antananarivo, mais peut également être une première approche sur ce que peut être la ville durable de demain avec la présence d’une agriculture de proximité dans la ville ; en réponse à la problématique d’aujourd’hui « Comment nourrir la planète ? ».

International audience; The Bradyrhizobium sp. DOA9 strain isolated from a paddy field has the ability to nodulate a wide spectrum of legumes. Unlike other bradyrhizobia, this strain has a symbiotic plasmid harboring nod, nif, and type 3 secretion system (T3SS) genes. This T3SS cluster contains all the genes necessary for the formation of the secretory apparatus and the transcriptional activator (TtsI), which is preceded by a nod-box motif. An in silico search predicted 14 effectors putatively translocated by this T3SS machinery. In this study, we explored the role of the T3SS in the symbiotic performance of DOA9 by evaluating the ability of a T3SS mutant (Omega rhcN) to nodulate legumes belonging to Dalbergioid, Millettioid, and Genistoid tribes. Among the nine species tested, four (Arachis hypogea, Vigna radiata, Crotalaria juncea, and Macroptilium atropurpureum) responded positively to the rhcN mutation (ranging from suppression of plant defense reactions, an increase in the number of nodules and a dramatic improvement in nodule development and infection), one (Stylosanthes hamata) responded negatively (fewer nodules and less nitrogen fixation) and four species (Aeschynomene americana, Aeschynomene afraspera, Indigofera tinctoria, and Desmodium tortuosum) displayed no phenotype. We also tested the role of the T3SS in the ability of the DOA9 strain to endophytically colonize rice roots, but detected no effect of the T3SS mutation, in contrast to what was previously reported in the Bradyrhizobium SUTN9-2 strain. Taken together, these data indicate that DOA9 contains a functional T3SS that interferes with the ability of the strain to interact symbiotically with legumes but not with rice.

Throughout Southeast Asia, government agencies are promoting good agricultural practices (GAP) standards for improving food safety, avoiding potential nontariff barriers to exports, and ultimately securing farmers' health and revenues. This paper presents an analysis of the adoption of a public standard in Thailand, the Rice Q-GAP where Q stands for “quality.” In the Central Plains of Thailand, a major rice production area, rice is produced by relatively small farms but with very intensive use of chemical inputs, making it challenging to promote production standards. Our study investigates the factors influencing the adoption of standards and the differences in cultivation practices between adopters and nonadopters. Governmental agencies have organized training activities throughout the country about rice production and Q-GAP standards. That training is likely to have an important influence on Q-GAP adoption. We investigate the potential selection bias in training delivery, using a recursive bivariate probit model whereby training is successively an explanatory variable for the Q-GAP adoption and a variable to be explained. Our model suggests that lack of labor availability is an essential factor related to nonadoption. Belonging to farmers associations and groups is also shown to be an important factor of adoption. Unexpectedly, training has a slight negative effect on Q-GAP adoption. A possible explanation is that when concrete information about the program is delivered, some farmers make an informed decision not to participate; this reinforces the idea that the main factors that could hamper further adoption are not related to information but to real farm constraints and farmers' rational behavior. The paper also found some small but significant differences in terms of farmers' practices related to adoption. The most convincing change is the reduction in the number of pesticide applications by adopters. (Resume d'auteur)

Bibliometric data about soil salinization suggests that around 1% of soil scientists invest on the subject allthough it concerns a large number of situations where the action of Man is often decisive. The study of the salt dynamics focuses on describing, understanding and predicting solute movement in the soil and the mechanisms that regulate them. Water flows and the ionic liquid phase diffusion are the main salts displacement vectors in and on the soil. The monitoring, the understanding and the prediction of water and solute flows beneficiate from different complementary approaches. First approach based on salt budget considers the soil compartment with two interfaces with the atmosphere and the aquifer. The intervention of regulatory processes can be internal or external to the soil. Agricultural practices for salinity remediation or prevention mobilize these processes. Illustration of the results obtained by salt budget approach is based on the analysis of salt inputs and outputs confirmed by observation and modeling in a rice field soil. During the flooding, field observations seem to reveal a contribution from a artesian salinity flow from the aquifer, while during the drying period the quantification of the evaporation is performed using soil water isotopic species of the molecule of water and chloride ions. Salt budget approach is complemented by the results of surface leaching of salts on the arid soil playas of the Chihuahuan Desert. Salinization may be regulated by feedback effects. For instance field organic matter amendment is one of the traditional methods of struggle against soil salinity shared by many traditions. Our work explains how organic inputs on rice field, allow to control pH, prevent dispersion of clays, with an acceptable methane production increase. Statistical relationships between soil salinity and frequency of surface vegetation organizations were established to illustrate their interactions. Finally, we discuss space organizations induced by salinization or desalination, in the case of plant mosaics or during the extension of salt patches. Prospects are guided by the fact that contamination of surface water and groundwater with pesticides in the Southern Mediterranean countries is very poorly documented, while the intensive irrigated agriculture in these countries is in constant struggle with constraints related to soil salinity induced by poor quality of irrigation and drainage water. The review of the literature shows that in arid situations, it is relatively common to observe positive correlations between the salinity of the water and soil and pesticides contents in surface water or groundwater. Some laboratory studies may identify, molecule by molecule, some explanatory physicochemical processes for these correlations. Nevertheless, insufficient data in Maghreb countries do not allow identifying the mechanisms involved in the environmental situations. Future research will study the mechanisms of the contamination of soil and water by pesticides, highlighting the role of salinity in the irrigated context in North Africa.; La bibliométrie sur les phénomènes entourant la salinisation des sols semblent indiquer qu'une modeste part (≈1%) de la communauté scientifique mondiale des sciences du sol s'investit régulièrement sur le sujet qui concerne pourtant des situations fréquentes où l’action de l’homme est souvent déterminante. L’étude de la dynamique saline s’attache à décrire, comprendre et prévoir les mouvements de solutés dans le sol et les mécanismes qui les régulent. Les flux hydriques et la diffusion ionique en phase liquide sont les principaux vecteurs de déplacement de sels dans et sur les sols. L'observation, la compréhension, la prédiction des flux d'eau et de solutés sont abordées selon différentes approches complémentaires. A l'origine, une démarche guidée par le bilan quantitatif considère un compartiment de sol avec ses deux interfaces avec l'atmosphère et l'aquifère. L'intervention de processus régulateurs qui peuvent être internes ou externes au sol est organisée en regard du compartiment sol et de ces interfaces. Les pratiques agricoles de remédiations ou de prévention vis à vis de la salinité sont situées par rapport aux processus qui les fondent. l’illustration des résultats acquis par des démarches de clôture du bilan salin s’appuie sur l’analyse des entrées et sorties dont on cherche à confirmer les termes dans un sol de rizière par observation et modélisation : d’une part pendant la submersion où les observations de terrain semble montrer une salinité issue d’un aquifère artésien d’autre part pendant les phases d’asséchement en s’appuyant sur la quantification de l’évaporation par la diffusion dans l’eau du sol des espèces isotopiques de la molécule d’eau et des ions chlorures. L’approche de bilan est complétée par le résultat du lessivage de surface des sels sur les sols arides des playas du désert de Chihuahua. En second lieu, nous illustrons les démarches d’étude qui incluent la prise en compte de certaines rétroactions vis-à-vis de la salinité, il s’agit d’abord des effets des amendements de matière organique qui est l’une des constantes dans les méthodes traditionnelles de lutte contre la salinité partagée par beaucoup de cultures. Nos travaux expliquent comment les apports de matière organiques en rizières en contexte de salinisation, permettent le contrôle du pH, la prévention de la dispersion des argiles, le tout avec une production de méthane qui reste acceptable. Par la suite nous nous utiliserons des liens statistiques entre salinité des sols, fréquence des organisations superficielles et la végétation pour illustrer leurs modes d’interactions. Enfin, nous abordons ce qui semble relever des logiques spatiales de la salinisation ou de la désalinisation, dans le cas de mosaïques végétales ou bien lors de l’extension de taches salines. Les perspectives de travaux sont guidées par le fait que la contamination des eaux de surfaces et souterraines par des pesticides dans les pays du Sud de la méditerranée est très faiblement documentée alors que l’agriculture irriguée intensive de ces pays est en confrontation constante avec des contraintes spécifiques liées à la salinité des sols et des eaux d’irrigation et de drainage. L’examen de la bibliographie montre que dans les situations des pays chauds et secs, il est relativement fréquent d’observer des corrélations positives entre la salinité des eaux et des sols et les teneurs en pesticides dans les eaux de surface ou souterraines. Les corrélations de terrain, insuffisamment nombreuses dans le sud de la méditerranée ne permettent pas de discerner aisément le poids des mécanismes qui sont en jeu dans des situations environnementales. Cependant quelques études expérimentales de laboratoire, permettent d’associer, molécule par molécule, quelques phénomènes physico-chimiques explicatifs de ces corrélations. La perspective est donc d’étudier les mécanismes de la contamination réelle des milieux en mettant en avant le rôle de la salinité liée à l’irrigation au Maghreb.

Background Leptospirosis is the most common bacterial zoonoses and has been identified as an important emerging global public health problem in Southeast Asia. Rodents are important reservoirs for human leptospirosis, but epidemiological data is lacking. Methodology/Principal Findings We sampled rodents living in different habitats from seven localities distributed across Southeast Asia (Thailand, Lao PDR and Cambodia), between 2009 to 2010. Human isolates were also obtained from localities close to where rodents were sampled. The prevalence of Leptospira infection was assessed by real-time PCR using DNA extracted from rodent kidneys, targeting the lipL32 gene. Sequencing rrs and secY genes, and Multi Locus Variable-number Tandem Repeat (VNTR) analyses were performed on DNA extracted from rat kidneys for Leptospira isolates molecular typing. Four species were detected in rodents, L. borgpetersenii (56% of positive samples), L. interrogans (36%), L. kirschneri (3%) and L. weilli (2%), which were identical to human isolates. Mean prevalence in rodents was approximately 7%, and largely varied across localities and habitats, but not between rodent species. The two most abundant Leptospira species displayed different habitat requirements: L. interrogans was linked to humid habitats (rice fields and forests) while L. borgpetersenii was abundant in both humid and dry habitats (non-floodable lands). Conclusion/Significance L. interrogans and L. borgpetersenii species are widely distributed amongst rodent populations, and strain typing confirmed rodents as reservoirs for human leptospirosis. Differences in habitat requirements for L. interrogans and L. borgpetersenii supported differential transmission modes. In Southeast Asia, human infection risk is not only restricted to activities taking place in wetlands and rice fields as is commonly accepted, but should also include tasks such as forestry work, as well as the hunting and preparation of rodents for consumption, which deserve more attention in future epidemiological studies., Author Summary Leptospirosis is the most prevalent bacterial zoonosis worldwide. Rodents are believed to be the main reservoirs of Leptospira, yet little epidemiological research has been conducted on rodents from Southeast Asia. Previous studies suggest that activities which place humans in microenvironments shared by rodents increase the probability of contracting leptospirosis. We therefore investigated the circulation of leptospiral species and strains in rodent communities and human populations in seven localities scattered throughout Southeast Asia; in Thailand, Lao PDR and Cambodia. Molecular typing assays were used to characterize leptospiral species and strains in both rodents and humans, which demonstrated common strains between humans and rodents. Additionally, we observed that the two most abundant leptospiral species; L. borgpetersenii and L. interrogans, have different habitat requirements, which supposes different modes of transmission. Lastly, in Southeast Asia, the risk of leptospiral transmission to humans is not solely limited to wetlands and rice paddy fields, but is also linked to forested areas, and activities such as the hunting and/or preparation of rodents for consumption.

International audience; While the spatial pattern of the highly pathogenic avian influenza H5N1 virus has been studied throughout Southeast Asia, little is known on the spatial risk factors for avian influenza in Africa. In the present paper, we combined serological data from poultry and remotely sensed environmental factors in the Lake Alaotra region of Madagascar to explore for any association between avian influenza and landscape variables. Serological data from cross-sectional surveys carried out on poultry in 2008 and 2009 were examined together with a Landsat 7 satellite image analysed using supervised classification. The dominant landscape features in a 1-km buffer around farmhouses and distance to the closest water body were extracted. A total of 1,038 individual bird blood samples emanating from 241 flocks were analysed, and the association between avian influenza seroprevalence and these landcape variables was quantified using logistic regression models. No evidence of the presence of H5 or H7 avian influenza subtypes was found, suggesting that only low pathogenic avian influenza (LPAI) circulated. Three predominant land cover classes were identified around the poultry farms: grassland savannah, rice paddy fields and wetlands. A significant negative relationship was found between LPAI seroprevalence and distance to the closest body of water. We also found that LPAI seroprevalence was higher in farms characterised by predominant wetlands or rice landscapes than in those surrounded by dry savannah. Results from this study suggest that if highly pathogenic avian influenza H5N1 virus were introduced in Madagascar, the environmental conditions that prevail in Lake Alaotra region may allow the virus to spread and persist.

This article is free to read on the publishers website Populations of the four major trophic groups of methanogens were enumerated by most probable numbers (MPN) on selective media in a sample of 13 soils representative of major types of rice soils. Dominant strains were isolated and their phenotypic and phylogenetic characteristics were studied. MPN counts ranged from 102 to 106 g−1 d.w. on H2, from 4 g−1 d.w. on acetate, from 5 on methanol, and from 50 to 106 on formate. In most soils, counts of hydrogenotrophs were higher than counts of acetotrophs, partly because acetotrophs were aggregated sarcinae difficult to separate into individual cells. Methylotrophs other than acetotrophic sarcinae were not recorded. In most soils, rods enumerated on formate were 5–400 times less abundant than those enumerated on H2, indicating that hydrogenotrophic-non-formatotrophic rods are probably dominant in ricefields. Dominant strains isolated comprised: 15 hydrogenotrophic-non-formatotrophic rods affiliated to Methanobacterium bryantii; three hydrogenotrophic-formatotrophic rods affiliated to Mb. formicicum; one hydrogenotrophic-formatotrophic rod not affiliated to a sequenced species; two sarcinae affiliated to Methanosarcina barkeri and Methanosarcina mazei; and one irregular coccus affiliated to Methanoculleus marisnigri– a species so far isolated from marine sediments only. Results from classical counts of methanogens and strains isolated from ricefields suggest the dominance of Methanobacterium spp. (mostly responsible for CH4 production from H2/CO2) and Methanosarcina spp. (mostly responsible for CH4 production from acetate) among culturable organisms. Both genera are probably ubiquitous. In particular, Mb. bryantii was isolated from 12 of the 13 soils.

Background: Predicting habitats prone to favor disease transmission is challenging due to confounding information on habitats, reservoirs, and diseases. Comparative analysis, which aims at investigating ecological and evolutionary patterns among species, is a tool that may help. The emergence of zoonotic pathogens is a major health concern and is closely linked to habitat modifications by human activities. Risk assessment requires a better knowledge of the interactions between hosts, parasites, and the landscape.Methods: We used information from a field spatial study that investigated the distribution of murid rodents, in various habitats of three countries in Southeast Asia, in combination with their status of infection by 10 taxa of microparasites obtained from the literature. Microparasite species richness was calculated by rodent species on 20,272 rodents of 13 species. Regression tree models and generalized linear models were used to explain microparasite diversity by the average distance between the trapping site and five categories of land cover: forest, steep agriculture land, flat agriculture land, water, and built-up surfaces. Another variable taken into account was the slope. Results: We found that microparasite diversity was positively associated with flat agriculture land, in this context mainly rice fields, and negatively associated with slope. Microparasite diversity decreased sharply a 100 m or less from flat agriculture land.Conclusion: We conclude that there is high microparasite circulation in rodents of flooded farmlands, meaning possibly a higher risk of disease for human inhabitants. Keywords: rodent-borne diseases; landscape; transmission ecology; comparative analysis(Published: 8 April 2013)Citation: Infection Ecology and Epidemiology 2013, 3: 20178 - http://dx.doi.org/10.3402/iee.v3i0.20178