International Journal of Agricultural Research, Innovation and Technology (IJARIT)
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Effects of ultramafic topsoil stockpiling during mine activities on its microbial diversity and other microbiological and physicochemical characteristics
No full textInternational audienceNowadays, ecological restoration is considered the best solution for the rehabilitation of mining-degraded areas, particularly when it concerns valuable ecosystems. This is the case in New Caledonia, a hot spot of biodiversity, with 82% of endemic plant species in ultramafic soils. The use of topsoil to restore mined areas is an important practice. However, topsoil stockpiling can reduce soil fertility. We studied the evolution of different properties of two topsoils stored in 10 m height piles on mined areas, in order to characterize possible degradations. The effects of storage duration, depth, and topsoil origin were analyzed, focusing mainly on bacterial and fungal diversity assessed after bar-coded pyrosequencing, and expressed by operational taxonomic units (OTU). Microbial activity (carbon dioxyde production), arbuscular mycorrhizal fungi (AMF) spore numbers, bulk density and different other physicochemical characteristics were also determined. The studied ultramafic soils were characterized by a relatively high microbial diversity with 45 bacterial phyla and 7 fungal phyla. Bacterial and fungal OTU numbers did not vary significantly after 12 months of storage, but the community structures of these groups were changed. AMF diversity was significantly reduced by the storage. Microbial activity, AMF spore numbers, soil organic carbon, total nitrogen, cation exchange capacity, and carbon to nitrogen ratio (C/N) decreased significantly starting from 3 to 9 months of topsoil storage. In contrast, soil bulk density and pH increased, and extractable concentrations of potentially toxic metals varied only slightly. All the changes induced by topsoil stockpiling in microbial population structure, AMF diversity, and other biotic and abiotic traits may negatively affect soil functions and create perturbations of the reconstructed ecosystems after revegetation. It is then necessary to reduce the storage of ultramafic topsoils as far as possible. In all cases, the stockpiling should not exceed six months before its use in ecosystem restoration. It is also recommended to reduce the height of the stockpiles, when possible, to 1 m or less to minimize the compaction and the anaerobiosis
Optimal Transport improves cell-cell similarity inference in single-cell omics data
No full textInternational audienceAbstract The recent advent of high-throughput single-cell molecular profiling is revolutionizing biology and medicine by unveiling the diversity of cell types and states contributing to development and disease. The identification and characterization of cellular heterogeneity is typically achieved through unsupervised clustering, which crucially relies on a similarity metric. We here propose the use of Optimal Transport (OT) as a cell-cell similarity metric for single-cell omics data. OT defines distances to compare, in a geometrically faithful way, high-dimensional data represented as probability distributions. It is thus expected to better capture complex relationships between features and produce a performance improvement over state-of-the-art metrics. To speed up computations and cope with the high-dimensionality of single-cell data, we consider the entropic regularization of the classical OT distance. We then extensively benchmark OT against state-of-the-art metrics over thirteen independent datasets, including simulated, scRNA-seq, scATAC-seq and single-cell DNA methylation data. First, we test the ability of the metrics to detect the similarity between cells belonging to the same groups (e.g. cell types, cell lines of origin). Then, we apply unsupervised clustering and test the quality of the resulting clusters. In our in-depth evaluation, OT is found to improve cell-cell similarity inference and cell clustering in all simulated and real scRNA-seq data, while its performances are comparable with Pearson correlation in scATAC-seq and single-cell DNA methylation data. All our analyses are reproducible through the OT-scOmics Jupyter notebook available at https://github.com/ComputationalSystemsBiology/OT-scOmics
Land use has little influence on the soil seed bank in a central African moist forest
No full textInternational audienceRegeneration of tropical forest occurs naturally and mainly through early secondary succession by soil seed banks. Here, we analyzed seed bank variation in density and diversity along a degradation gradient. We also explored the relationship (similarity in composition) between the seed and seedling banks and the overstory vegetation. The investigated forests were located at Dja Fauna Reserve and its surroundings, south-eastern Cameroon. We sampled 33 one-ha forest plots scattered in a protected area, in a logging concession and in community forests. Within each plot, we inventoried the seed bank in the litter and in four successive soil layers of 5 cm depth interval, and the standing vegetation. Seed density significantly varied with sampling depth but not between land use types. A total of 181 morphospecies were identified. Trees species accounted for 46% of seeds with pioneer species dispersed by animals dominating the seed bank. Species diversity and composition strongly varied with the sampling depth; the litter seed bank was more similar in composition to the soil seed bank than to the seedling bank, sapling, and forest stands. We highlighted the presence of a dense and diverse seed bank in each land use type. We also showed the differentiation of each sampling depth in terms of species composition, thus revealing their complementarity in the dynamics of natural regeneration. The dominance of pioneers in the seed bank and weak relationship with the overstory are universal for tropical forests and logically follow from forest succession after disturbance. Abstract in French is available with online material
Cross-sectional cycle threshold values reflect epidemic dynamics of COVID-19 in Madagascar
No full textInternational audienceAs the national reference laboratory for febrile illness in Madagascar, we processed samples from the first epidemic wave of COVID-19, between March and September 2020. We fit generalized additive models to cycle threshold (Ct) value data from our RT-qPCR platform, demonstrating a peak in high viral load, low-Ct value infections temporally coincident with peak epidemic growth rates estimated in real time from publicly-reported incidence data and retrospectively from our own laboratory testing data across three administrative regions. We additionally demonstrate a statistically significant effect of duration of time since infection onset on Ct value, suggesting that Ct value can be used as a biomarker of the stage at which an individual is sampled in the course of an infection trajectory. As an extension, the population-level Ct distribution at a given timepoint can be used to estimate population-level epidemiological dynamics. We illustrate this concept by adopting a recently-developed, nested modeling approach, embedding a within-host viral kinetics model within a population-level Susceptible-Exposed-Infectious-Recovered (SEIR) framework, to mechanistically estimate epidemic growth rates from cross-sectional Ct distributions across three regions in Madagascar. We find that Ct-derived epidemic growth estimates slightly precede those derived from incidence data across the first epidemic wave, suggesting delays in surveillance and case reporting. Our findings indicate that public reporting of Ct values could offer an important resource for epidemiological inference in low surveillance settings, enabling forecasts of impending incidence peaks in regions with limited case reporting
Numerical Study of the Air Conditioning of a Room by a Two-phase Thermosyphon Loop Using Meteorological Data from Mamou (Guinea)
No full textInternational audienceThis paper presents a numerical study of the air-conditioning of a room by a two-phase thermosyphon loop using meteorological data from the Mamou region (Guinea). The room is composed of a rectangular roof and a passenger compartment in the form of a parallelepiped. In addition, the air-conditioning unit that operates with methanol is composed of an evaporator, a condenser, a riser and a downcomer. The heat transfer modelling governing the habitat model and the air conditioning loop is based on the nodal method. The coupling of the system is done by convective transfer between the internal air of the habitat and the surface of the evaporator. The equations are solved by the implicit finite difference method. Thus, this resolution made it possible to determine the influence of the parameters on the model. This work presents results of the habitat with and without the air-conditioning loop for typical days in March of Mamou. These results show that the use of the air conditioning loop can contribute to lowering the internal air temperature. The value of the maximum temperature of the indoor air of the habitat with the air conditioner is about 299 K while that of the air without air conditioner is about 303 K. The variation of parameters such as temperature, wall thickness, incident solar flux, air exchange rate and evaporator surface has a significant impact on the operation of the air conditioner and on the temperature of the conditioned room. A low wall thickness or a high air exchange rate contributes to the temperature increase in the room. For a wall thickness of 10 cm, 15 cm or 40 cm, the air temperatures are 301.5 K, 297 K and 296.9 K respectively. However, for a habitat without an air conditioner the temperature is 303 K when the wall thickness is 15 cm
Strong-coupling emergence of dark states in XX central spin models
No full textInternational audienceIt was recently shown that the XX central spin model is integrable in the presence of a magnetic field perpendicular to the plane in which the coupling exists. A large number of its eigenstates are such that the central spin is not correlated to the environmental spins it is coupled to. In this work, we first demonstrate that the XX-central spin model remains integrable in the presence of an arbitrarily oriented magnetic field. We then show that, provided the coupling is strong enough, dark states can actually be found even in the presence of an in-plane magnetic field. We finally provide a simple explanation of this result and demonstrate its universality for a variety of distinct distributions of the coupling of the central spin to the various bath spins
Bottom-up assessment of local agriculture, forestry and urban waste potentials towards energy autonomy of isolated regions: Example of Réunion
No full textInternational audienceThis work assesses the role of biomass and municipal solid waste in isolated energy systems. For this, La Réunion, a French overseas territory in the Indian Ocean with a population of about 850,000, serves as a case study. Methodically, the study assesses technical biomass-based potentials based on an island-wide digital landscape model, detailed information on land use, soil, and climate, and a dynamic yield simulation tool, while technical waste-based energy potentials are calculated from local data. In total, 9 crops, 11 waste streams, and forested areas are considered. The potential contribution of biomass and waste to the energy system is studied in three scenarios. In all, unsustainable outcomes are avoided by valorizing only crop residues and applying sustainable harvesting rates to forests. Depending on the scenario, biomass or waste based energy could cover between 19% and 22% of 2019 electricity demand compared to an actual value of 6% (2019). Furthermore, prioritizing the production of secondary energy carriers allows to meet 8% of 2019 energy demand in the transport sector. These results are in good accordance with previous studies and scenarios on Réunion's energy transition. Given its bottom-up approach based on standard geoinformatic data, the proposed method is in principle transferable to other isolated regions, also in developing countries. A first, high-level assessment of four comparable island (states) shows that in three cases similar contributions of biomass and waste as in Réunion can be expected. As a next step, the purely technical assessment shall be complemented by economic considerations
Investigation of soil properties and pesticide intensity in crop lands at Tangail region of Bangladesh
Get PDFThe study was conducted to investigate the soil properties and pesticide intensity in rice, banana and brinjal growing agricultural land of Delduar and Sakhipur upazila of Tangail district during July 2019 to June 2020. Forty five soil samples were collected from different crop land at the study area and analyzed in the Soil Resource Development Institute to determine the soil properties as pH, total organic matter (OM), total nitrogen (N), available phosphorus (P), available sulfur (S), available zinc (Zn), exchangeable potassium (K), exchangeable magnesium (Mg) and exchangeable calcium (Ca). However, pesticide used intensity was also evaluated through questionnaire survey with farmers and stakeholders in the study area. Results showed that pH, OM, available N, exchangeable Ca and exchangeable Mg content were significantly higher in rice growing land than banana and brinjal. On the other hand, available P, exchangeable K and available Zn content were substantially higher in brinjal growing land than rice and banana. The OM showed significant positive correlation with soil pH, available N, available S, exchangeable Mg and exchangeable Ca (r=0.37, 0.99, 0.31, 0.59 and 0.63, respectively), indicated rice growing land built up these soil properties through increasing soil OM. The available P showed significant and positive correlation with K and Zn (r=0.55 and 0.74, respectively), but negative correlation with exchangeable Mg and exchangeable Ca (r=-0.53 and -0.32, respectively). The exchangeable K showed significant and positive correlation with available Zn (r=0.45) but negative correlation with exchangeable Mg (r=-0.37). The Mg showed significant negative correlation with available Zn (r=-0.45) but positive correlation with exchangeable Ca (r=0.87). Results also revealed that pesticide used intensity was higher in brinjal followed by banana and minimum in rice crop. Study suggests that farmers require up-to-date information on soil nutrient status so that they may use the proper utilization of fertilizers and avoid using excessive amounts of fertilizers and pesticides in their crop land.
Int. J. Agril. Res. Innov. Tech. 11(2): 85-94, Dec 202
The determinants of smallholder coffee producers’ market outlet choice decision in Debub ari district of South Omo Zone, SNNPR, Ethiopia
Get PDFThis study mainly aimed at analyzing coffee market chain and the determinants of coffee market outlet choice decision of smallholder coffee producers in the Debub Ari District. The descriptive statistics and econometric models were used to analyze the data. Multivariate probit model was used to identify factors affecting market outlet choices of the smallholder coffee producers. Both primary and secondary data were collected from the study area. The multi-stage sampling techniques have been employed for this study. A total of 194 coffee producer household heads have been randomly selected and interviewed with the help of pre-tested structured questionnaire. The focus group discussion and key informants interviews were conducted to supplement the formal data. The probability of choosing collector, wholesalers, retailer, processor, consumer’s outlets is 67.1%, 66.4%, 36.9%, 71.6% and 15.3%, respectively. The joint probabilities of households to jointly choose the four market outlets was 0.031% which is greater than the likely of not choosing all market outlets which is 0.003%. Access to credit negatively influenced retailer, processor and consumer market outlet choice, distance to the nearest market negatively influenced processor market outlet choices, market information, off-farm participation positively influenced retailer and consumer market outlets choices. Therefore, the intervention is needed to improve coffee marketing chain through promoting cooperatives, infrastructural development and timely market information for efficient marketing system in the study area.
Int. J. Agril. Res. Innov. Tech. 12(1): 166-173, June 202
Mapping and assessing ecosystem services in Europe's Overseas: A comparative analysis of MOVE case studies
No full textInternational audienceMapping and Assessment of Ecosystems and their Services (MAES) has been widely applied on the European Union (EU) mainland, whereas the EU Overseas entities still bear potential for implementation. This paper presents novel applications of the MAES procedure in the EU Outermost Regions and Overseas Countries and Territories ("EU Overseas"). Eight case studies from different geographical areas were analysed through a comparative assessment by applying an established framework following key steps in the MAES process, in order to stipulate lessons learned and recommendations for MAES in the EU Overseas. These key steps include the identification of policy questions, stakeholder networks and involvement, application of MAES methods, dissemination and communication and implementation. The case studies were conducted and analysed under the umbrella of the EU MOVE pilot project, including the Azores, the Canary Islands, Saint Martin, French Guiana, Martinique, Reunion Island and the Falkland Islands. Each case study represented different governance, policy and decision-making frameworks towards biodiversity and environmental protection. Case studies predominantly addressed the policy domains of Nature and Biodiversity Conservation and Marine and Maritime Policy. Ecosystem Services (ES) were assessed across a wide range of themes, biomes and scales, focusing on terrestrial, coastal and marine ecosystems. Results show that the implementation of the case studies was accompanied by extensive communication and dissemination activities. First success stories were visible, where the MAES exercise led to meaningful uptake of the ES concept to policies and decision-making. Yet, there is still work to be done - major bottlenecks were identified related to the MAES implementation centring around financial resources, training and technical expertise. Addressing these aspects can contribute to an enhanced implementation of MAES in the EU Overseas in the future