Search

The importance of soil biodiversity is increasingly recognized in agriculture and natural resource research and development. Yet, traditional soil biodiversity assessments are costly and time-consuming, limiting the extent and frequency of sampling and analysis in space and time. Flow cytometry (FCM) is a powerful technique to characterize cell communities due to its high robustness and accuracy, requiring only a short time for the characterization. Therefore, FCM could expand soil research capabilities by allowing the characterization of different aspects of bacterial biodiversity. However, this implementation of FCM requires the previous dispersion, separation and purification of bacteria from complex soil matrices. Moreover, soil monitoring programs or evaluation of soil management practices require high-throughput analysis. In this context, soil processing protocols need to consider not only an adequate recovery of undamaged, representative and pure soil bacteria, but also short-time processing requirements. Although soil processing protocols have been reported over time, to our knowledge, there is no recommended soil extraction protocol for high-throughput analysis of bacterial biodiversity by FCM. We reviewed the state-of-art of the use of flow cytometry in scientific research and the protocols used for the extraction of bacteria from soil. We analysed the literature to take stock of the diversity of methodologies for soil processing and applications of flow cytometry in bacterial characterization considering abundance, diversity, community structure and functional properties. This review provides several lines of evidence of the use of flow cytometry for soil bacterial biodiversity (SBB) characterization, highlighting its potential for soil monitoring and studies on soil bacterial community dynamics. The review also highlights and discusses the most relevant constraints and research gaps that need to be considered for high-throughput analysis of SBB by FCM, such as evaluation of scale-down, new reagents for and methods of purification, threshold of bacterial recovery efficiency and selection of a standardized and validated protocol. We proposed a protocol for soil bacterial extraction for high-throughput analysis of SBB by FCM and we provided detailed databases of systematized information that would be useful to the scientific community.

Caractériser la dynamique d’une forêt est essentiel pour la gestion forestière. Les houppiers des arbres forment un élément clé de cette dynamique ; mais, en forêt tropicale, les mesurer n’est pas simple. Cette étude teste l’utilisation d’images aériennes à haute résolution pour estimer la croissance diamétrique des arbres, en intégrant des mesures fines des houppiers détectés. Des ortho-images de 10 cm/pixel de résolution ont été obtenues à l’aide d’un drone à aile fixe sur une parcelle de 9 ha, installée dans la forêt de Yoko en République démocratique du Congo. Les inventaires menés sur les arbres de DHP ≥ 10 cm en 2008 et en 2016 ont permis d’avoir accès à différentes caractéristiques dendrométriques individuelles, dont le diamètre des arbres et leur tempérament, et de calculer des accroissements diamétriques. Des modèles linéaires mixtes ont été calibrés pour prédire l’accroissement de 163 arbres identifiés à la fois sur le terrain et sur les ortho-images en utilisant les variables quantifiées uniquement sur le terrain et/ou à partir de variables mesurées sur les ortho-images. Les images aériennes ont permis de détecter 23,4 % des arbres de DHP ≥ 10 cm inventoriés au sol, et représentant 75,1 % de la biomasse aérienne du peuplement. La probabilité de détection des arbres a varié en fonction de leur DHP : de 0,09 pour les arbres de DHP < 30 cm à 0,97 pour les arbres de DHP ≥ 60 cm. Les variables quantifiées par télédétection ajoutées aux variables de terrain ont permis d’améliorer significativement la prédiction de l’accroissement diamétrique. Les meilleurs modèles d’estimation des accroissements diamétriques contiennent notamment un terme caractérisant la dimension du houppier des arbres qui n’a pu être mesuré que par télédétection. Parmi les variables déterminées par télédétection, la superficie convexe du houppier est apparue la plus performante dans les modèles, et s’avère ainsi être la mesure la plus intéressante pour décrire la compétition entre les houppiers. Ces résultats ouvrent des perspectives pour construire de nouveaux outils d’acquisition de données au service de l’aménagement forestier.

Motivation Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) that are free of arbitrary global clustering thresholds. Here, we present swarm v3 to address issues of contemporary datasets that are growing towards tera-byte sizes. Results When compared with previous swarm versions, swarm v3 has modernized C++ source code, reduced memory footprint by up to 50%, optimized CPU-usage and multithreading (more than 7 times faster with default parameters), and it has been extensively tested for its robustness and logic. Availability and implementation Source code and binaries are available at https://github.com/torognes/swarm. Supplementary information Supplementary data are available at Bioinformatics online.

Transverse modal analysis of timber panels is a proven effective alternative method for approximating a material's elastic constants. Specific testing configurations, such as boundary conditions (BC) and location of sensor and impact, play a critical role in the accuracy of the results obtained from the experimental assessment. This article investigates signal-specific details, such as the signal quality factor, that directly relate to the damping properties and internal friction as well as frequency shifting obtained from six different BCs. A freely supported (FFFF), opposing minor sides (shorter length) simply supported, and major sides (longest length) free (SFSF), as well as the reverse of the SFSF configuration with minor sides free and major lengths simply supported (FSFS) and all sides simply supported (SSSS) setup, are investigated. Variations into the proposed methods used to achieve an FFFF supported system are also considered. A combination of experimental testing in parallel with finite element analysis was conducted to re-create the setup that would be used within a manufacturing facility for nondestructive assessment of full-size cross-laminated timber panels. The differences between all BC configurations for their resonance frequency quality and location indicate that a freely supported system provides higher-resolution results, good comparison of less than 10 percent error with the finite element analysis and experimental results, and advantages in a simple experimental setup for the intended application.

Vanilla flavor is derived from the cured fruits of two orchid species Vanilla planifolia and V. × tahitensis. About twenty other Vanilla species are also credited with scented fruits, but very little is known about their aromatic features. We investigated the aromatic compound content of the ripe fruits of 30 vanilla accessions obtained from eight species and three hybrids. Glucovanillin plus six phenolic and one anisic aglycones, extracted after enzymatic hydrolysis, were quantified by High-Performance Liquid Chromatography and Ultra-Violet detection. The analysis of the aromatic contents and the principal components showed clear-cut differences in the aromatic content of the species and varieties studied. The total content of aromatic compounds separated the three species most distantly related to V. planifolia, namely V. lindmaniana, V. crenulata and V. imperialis, from the other species notably by the absence of vanillin potential and a very low total aromatic potential (

Eight yam species (Dioscorea spp.) represented by 522 accessions (landraces and hybrids) were analysed for the individual sugars, catechins, phenolic acids and saponins contents of their tuber flours. Maltose, sucrose, glucose and fructose were quantified. Reducing sugars mean values were highly variable within species and ranged from 0.16%dry weight (DW) (SD ± 0.12) in D. dumetorum to 3.15%DW (±2.49) in D. esculenta. Maltose was detected only in D. esculenta. Chlorogenic acid, gallic acid and other phenolic acids ranged from 4.33 mg/g DW in D. bulbifera to 4.87 mg/g in D. alata and 9.55 mg/g in D. nummularia but were not detected in other species. Catechins (epicatechin and catechin) were highest in D. bulbifera bulbils (25.18 mg/g) and tubers (6.96 mg/g), and lowest in D. esculenta (0.32 mg/g). Their content is significantly correlated with dark flour colour and they most likely contribute to the oxidation of tuber flesh. Saponins (dioscin and gracillin) were quantified in only two species: D. cayenensis (5.94 mg/g, SD ± 3.78) and D. esculenta (3.74 mg/g, SD ± 3.72). Varietal selection may tend to reduce sugars levels and increase secondary metabolites with bioactive properties. HP-TLC is a suitable technique for the rapid quantification of compounds related to yam tuber flour quality.

Kava, the traditional beverage of the South Pacific Islands is prepared by cold water extraction of the fresh or dried roots and stumps of Piper methysticum Forst. (Piperaceae). Nutraceutical and pharmaceutical kava-based products manufactured in Europe from extracts obtained by solvents (acetone or ethanol) have been implicated in hepatotoxicity cases. Kava has been banned in Germany and, although the German Health Authorities have lost their case in the administrative court, the ban has produced a worldwide negative impact on kava's reputation as a safe product. Quality standards and control are now needed to enable the registration under the FAO/WHO Codex Alimentarius. The present paper reviews the most recent advances in analytical techniques (HPLC, NIRS, DNA analysis using SSRs and DArTs and HP-TLC) to detect unsuitable cultivars and raw material. These techniques are accurate and reliable but they are comparatively expensive and cumbersome for local traders and exporters in the South Pacific. A simple colorimetric test has been developed and represents a fairly convenient and cost efficient way of assessing the quality of traded kava. Possible strategies for improving the industry are discussed.

Non-aqueous Taylor dispersion analysis (TDA) was used for the size-characterization of natural and synthetic polyisoprenes (4 × 103–2 × 106 g/mol molar mass). Not only the weight-average hydrodynamic radius (Rh), but also the probability distribution of the hydrodynamic radius, were both derived from the Taylorgrams by a simple integration of the elution profile and by a more sophisticated constrained regularized linear inversion of the Taylorgram, respectively. Results in terms of size characterization (hydrodynamic radii between 2 and 100 nm) were compared to size exclusion chromatography coupled to a refractive index-based mass detector. Multimodal size distributions were resolved by TDA for industrial and natural polyisoprenes, with the advantage over the chromatographic technique that, in TDA, there is no abnormal elution of microaggregates (hydrodynamic radii ∼ 40–50 nm). Considering the importance and the difficulty of characterizing polyisoprene microaggregates, TDA appears as a promising and simple technique for the characterization of synthetic and natural rubber. (Resume d'auteur)

The present study aimed at evaluating the potential of diethyl ether extracts UV/visible (UV/vis) absorbance for assessing the suitability of commercial lots of kava (Piper methysticum). The UV/vis absorption spectra of diethyl ether root extracts of 15 cultivars clustered them into three groups in parallel to their known genetic relatedness and their chemical composition determined by GC–MS and LC–MS analyses. Absorption peaks at 250 nm and 290 nm respectively corresponded to kavain, the most health-promoting kavalactone, and dihydromethysticin a non-desirable kavalactone. The absorbance peak at 340–350 nm reflected the yellow coloration of the extract, which was mainly due to the undesirable flavokavins, desmethoxyyangonin and yangonin. Ratios of absorbance values at 250 nm and 290 nm significantly differentiated all three groups of cultivars, namely 'noble' which provide health benefits from 'two-day' and 'wichmannii' that are health damaging. These results provide a robust and rapid colorimetric test for routine control of a critical aspect of the quality of kava batches. (Resume d'auteur)

The coffee berry borer, Hypothenemus hampei (Ferrari), is a major insect pest of coffee crops worldwide. As part of a program of studies aimed at efficient and sustainable pest control, a study was conducted to determine the mating status of adult females in the broader context of studying pest dispersal behavior. To that end, it was deemed important to determine the morphology of the H. hampei female reproductive tract. This study focused on direct observation of the spermatheca of unmated, and colonizing adult females obtained from natural field populations with a high probability of having mated, and the description of all organs of the reproductive tract using established standard staining and microscopy techniques. Spermathecae were extracted from the samples and sorted according to their origin (unmated or colonizing females). The morphology of sperm present in the female spermathecae was compared with that of sperm taken directly from male testes. Two staining techniques using Giemsa and chlorazol black allowed spermatheca and sperm to be distinguished from other tissues. Under these conditions, a more precise description of the spermatheca was achieved, including the spermathecal duct and spermathecal muscles, spermathecal gland, and, for the first time, sperm when present. These techniques permitted the accurate and rapid determination of the presence or absence of sperm in the spermathecae of H. hampei females, thereby establishing their mating status. (Resume d'auteur)

International audience; In the present era of rapid global change, innovative monitoring methods can greatly enhance our ability to detect ecological disturbances and prioritise conservation areas in a timely and cost-effective manner. While Passive Acoustic Monitoring (PAM) has recently emerged as a promising tool for monitoring ecological states in marine environments, the specifics of how to apply this method remains poorly defined. In this study we examined how different combinations of sampling settings (frequency bandwidth, time of sampling (day/night), and sample duration) influenced the ability of two acoustic indices, the Sound Pressure Level (SPL) and the Acoustic Complexity Index (ACI), to discriminate different ecological states (ecostates) of coral reefs. We applied an iterative approach to select the most efficient and consistent combinations of sampling settings to use for these two acoustic indices, depending on the stability of their discriminating power across different time scales (successive days, moon phases, and seasons), and the minimum sampling effort required for reliable ecostate assessment. The ability of SPL and ACI to discriminate ecostate-specific soundscapes was more stable and required less sampling effort at nighttime. For indices calculated in the higher frequency band (> 2 kHz), very short recording times (≤20 min divided into 5 s samples) were sufficient to discriminate ecostates, whereas longer recording times (≥200 min divided into 5 min samples) were necessary when using indices calculated in the lower frequency bands (< 1 kHz). An optimised sampling scheme, i.e. the group of the five best combinations of settings to discern among coral reef ecostates, was determined at Reunion Island, Indian Ocean, then tested at New Caledonia, Pacific Ocean. Here, the classifications obtained through visual surveys and with the optimised acoustic sampling scheme were congruent. The concordance of our results with visual fish counts confirms the potential of ecoacoustics to rapidly and reliably characterise coral reefs' ecostate, allowing managers to prioritise conservation areas among numerous sites, and detect ecological changes over time. Our study provides clear guidelines for monitoring soundscapes by means of the ecoacoustic indices most widely used in the marine realm.

L'évolution des concepts phytopathologiques, avec l'amélioration des techniques de laboratoires et l'adoption de stratégies issues des difficultés surmontées, a permis, depuis 15 ans, de progresser dans la connaissance des maladies d'origine inconnue chez le cocotier et le palmier à huile. Ces stratégies peuvent être illustrées à l'aide de quelques exemples significatifs qui sont évoqués dans cette communication : étude de l'ultrastructure d'échantillons pré-définis par microcoscopie électronique, étude comparative des acides nucléiques dans les plantes malades et dans les plantes saines, identification des vecteurs de la maladie par exposition de plantes saines à un grand nombre d'insectes dans des cages

International audience; Aim: To understand how variations in precipitation and topographic wetness influence tree community assembly at both regional and landscape scales in tropical forests. Location: New Caledonia (SW Pacific). Methods: We sampled 40 tree communities in 0.04-ha plots laid along topographic gradients within two landscapes with contrasting precipitation. Within a dry (2,500 mm/year) landscape we used the Topographic Wetness Index (TWI) to sample communities in topographic position with low (e.g., ridges) and high (e.g., valleys) water accumulation. For each sampled species, we measured five functional traits involved in drought resistance and resource acquisition (wood density, leaf area, leaf specific area, leaf dry matter content, and leaf thickness). We first examined trait covariation across species. We then analysed how the functional composition of communities varied between landscapes (according to precipitation) and within landscapes (according to TWI), using trait-based statistics and null models. Results We identified two ecological trade-offs driving trait variation across species: (i) one opposing high hydraulic efficiency to drought resistance, related to a wood economic spectrum; and (ii) the other opposing resource acquisition to resource conservation, related to a leaf economic spectrum. Across landscapes, species with drought resistance strategies were favoured at lower precipitation. Within landscapes, drought resistant species were selected under low TWI in the dry landscape, while low TWI increased the abundance of species with conservative strategies in the wet landscape. Conclusions: Precipitation and topography jointly shape the functional composition of tree communities. At low precipitation, hydric constraints prevailed on ridges and upslopes by filtering drought resistant strategies along the wood economic spectrum. Contrastingly, higher precipitation relaxed the hydric constraints and resource availability became a primary driver of changing strategies along the leaf economic spectrum. Thus, the landscape scale influence of topography on processes driving community assembly and functional composition critically depends on the regional climatic context.

The mango fruit fly, Ceratitis (Ceratalaspis) cosyra, is a major agricultural pest affecting mango production in sub-Saharan Africa. Morphological differences between C. cosyra and five closely related Ceratitis (Ceratalaspis) species (C. discussa, C. pallidula, C. quinaria, C. silvestrii, C. striatella) are subtle, so that their identification often requires specialized expertise. A previous study based on nuclear molecular markers (microsatellites) showed cryptic genetic variation within C. cosyra with separate microsatellite genotypic clusters also occurring in sympatry. This study aimed at verifying whether DNA barcoding can (a) separate C. cosyra from morphologically similar Ceratitis (Ceratalaspis) species and (b) resolve the cryptic genetic variation previously observed within C. cosyra. A subset of 62 C. cosyra specimens previously genotyped at 16 microsatellite loci was subjected to DNA barcoding. This data set was integrated with 130 DNA barcodes of C. cosyra, C. discussa, C. quinaria, C. silvestrii and C. striatella. Neighbor Joining, maximum likelihood and Bayesian tree reconstructions confirmed the presence of two main C. cosyra genotypic groups and resolved well-supported groups corresponding to C. discussa, C. pallidula, C. striatella and to C. quinaria/C. silvestrii. The analysis of morphological characters did not show consistent morphological differences between the two groups of C. cosyra and called into question the morphological characters currently implemented in the identification of C. striatella. These results further support the hypothesis of cryptic speciation within the mango fruit fly and suggest that DNA barcoding represents a suitable complementary tool for the problematic diagnosis of C. cosyra and C. striatella.

Increasing research has highlighted the effects of changing climates on the occurrence and prevalence of toxigenic Aspergillus species producing aflatoxins. There is concern of the toxicological effects to human health and animal productivity following acute and chronic exposure that may affect the future ability to provide safe and sufficient food globally. Considerable research has focused on the detection of these toxins, based on the physicochemical and biochemical properties of the aflatoxin compounds, in agricultural products for human and animal consumption. As improvements in food security continue more regulations for acceptable levels of aflatoxins have arisen globally; the most stringent in Europe. These regulations are important for developing countries as aflatoxin occurrence is high significantly effecting international trade and the economy. In developed countries analytical approaches have become highly sophisticated, capable of attaining results with high precision and accuracy, suitable for regulatory laboratories. Regrettably, many countries that are affected by aflatoxin contamination do not have resources for high tech HPLC and MS instrumentation and require more affordable, yet robust equally accurate alternatives that may be used by producers, processors and traders in emerging economies. It is especially important that those companies wishing to exploit the opportunities offered by lucrative but highly regulated markets in the developed world, have access to analytical methods that will ensure that their exports meet their customers quality and safety requirements.This work evaluates the ToxiMet system as an alternative approach to UPLC–MS/MS for the detection and determination of aflatoxins relative to current European regulatory standards. Four commodities: rice grain, maize cracked and flour, peanut paste and dried distillers grains were analysed for natural aflatoxin contamination. For B1 and total aflatoxins determination the qualitative correlation, above or below the regulatory limit, was good for all commodities with the exception of the dried distillers grain samples for B1 for which no calibration existed. For B1 the quantitative R2 correlations were 0.92, 0.92, 0.88 (

Background The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its genome sequenced by next generation sequencing and bioinformatics analysis performed by RepeatExplorer pipeline. The clusters allowed the identification and characterization of repetitive elements (predominant contributors to most plant genomes). The aim of this study was to identify, characterize and map the repetitive DNA of P. edulis, providing important cytogenomic markers, especially sequences associated with the centromere. Results Three clusters of satellite DNAs (69, 118 and 207) and seven clusters of Long Terminal Repeat (LTR) retrotransposons of the superfamilies Ty1/Copy and Ty3/Gypsy and families Angela, Athila, Chromovirus and Maximus-Sire (6, 11, 36, 43, 86, 94 and 135) were characterized and analyzed. The chromosome mapping of satellite DNAs showed two hybridization sites co-located in the 5S rDNA region (PeSat_1), subterminal hybridizations (PeSat_3) and hybridization in four sites, co-located in the 45S rDNA region (PeSat_2). Most of the retroelements hybridizations showed signals scattered in the chromosomes, diverging in abundance, and only the cluster 6 presented pericentromeric regions marking. No satellite DNAs and retroelement associated with centromere was observed. Conclusion P. edulis has a highly repetitive genome, with the predominance of Ty3/Gypsy LTR retrotransposon. The satellite DNAs and LTR retrotransposon characterized are promising markers for investigation of the evolutionary patterns and genetic distinction of species and hybrids of Passiflora.

International audience; A local-based method for near-infrared spectroscopy predictions, the local partial least squares regression on global PLS scores (LPLS-S), is proposed in this work and compared with the usual local PLS (LPLS) regression approach. LPLS-S is based on the idea of replacing the original spectra with a global PLS score matrix before using the usual LPLS. This is done with the aim of increasing the speed of the calculations, which can be an important parameter for online applications in particular, especially when implemented on large databases. In this study, the performance of the two local approaches was compared in terms of efficiency and speed. It could be concluded that the root-mean-square error of prediction of LPLS and LPLS-S were 1.1962 and 1.1602, respectively, but the calculation speed for LPLS-S was more than 20 times faster than for the LPLS algorithm.

International audience; Direct-injection mass spectrometry (DIMS) techniques have evolved into powerful methods to analyse volatile organic compounds (VOCs) without the need of chromatographic separation. Combined to chemometrics, they have been used in many domains to solve sample categorization issues based on volatilome determination. In this paper, different DIMS methods that have largely outperformed conventional electronic noses (e-noses) in classification tasks are briefly reviewed, with an emphasis on food-related applications. A particular attention is paid to proton transfer reaction mass spectrometry (PTR-MS), and many results obtained using the powerful PTR-time of flight-MS (PTR-ToF-MS) instrument are reviewed. Data analysis and feature selection issues are also summarized and discussed. As a case study, a challenging problem of classification of dark chocolates that has been previously assessed by sensory evaluation in four distinct categories is presented. The VOC profiles of a set of 206 chocolate samples classified in the four sensory categories were analysed by PTR-ToF-MS. A supervised multivariate data analysis based on partial least squares regression-discriminant analysis allowed the construction of a classification model that showed excellent prediction capability: 97% of a test set of 62 samples were correctly predicted in the sensory categories. Tentative identification of ions aided characterisation of chocolate classes. Variable selection using dedicated methods pinpointed some volatile compounds important for the discrimination of the chocolates. Among them, the CovSel method was used for the first time on PTR-MS data resulting in a selection of 10 features that allowed a good prediction to be achieved. Finally, challenges and future needs in the field are discussed.

BGPI : équipe 7; International audience; Yellow leaf (YL) is a disease of sugarcane that is currently widespread throughout most American and Asian sugarcane-producing countries. However, its actual distribution in Africa remains largely unknown. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to facilitate and improve the detection of Sugarcane yellow leaf virus (SCYLV), the causal agent of YL. The RT-LAMP assay was found to be comparable with or superior to conventional RT-polymerase chain reaction (PCR) for the detection of SCYLV genotypes CUB and BRA in infected sugarcane 'C132-81' and 'SP71-6163', respectively. Additionally, 68 sugarcane samples that tested negative by RT-PCR were found positive by RT-LAMP, whereas the RT-LAMP assay failed to detect SCYLV in only 5 samples that tested positive by RT-PCR. Combining RT-PCR and RT-LAMP data enabled the detection of SCYLV in 86 of 183 Kenyan sugarcane plants, indicating high SCYLV prevalence throughout the country (ranging from 36 to 64% in individual counties). Seminested PCR assays were developed that enabled the amplification of a fragment encompassing the capsid protein coding region gene and its flanking 5' and 3' genomic regions. Sequences of this fragment for four Kenyan SCYLV isolates indicated that they shared 99.2 to 99.6% pairwise identity with one another and clearly clustered phylogenetically with SCYLV-BRA genotype isolates. To our knowledge, this is the first report of SCYLV in Kenya.

The management of livestock systems for technical, economic and environmental optimization requires an increasingly accurate formulation of rations and therefore a detailed knowledge on the feeds consumed by animals. Near-infrared spectrometry (NIRS), which has been used increasingly since the 1960s, is an analytical technique that allows rapid characterization of feeds or forage samples. The first applications developed were on the chemical composition of the feeds, but it is also possible to develop calibrations for the estimation of the nutritional value and the feed intake. Beyond these direct measurements on the feed, NIRS can also be applied to faeces to characterize the feeding of animals on rangelands. Joint consideration of feed and feces spectra can give a picture of how animals actually use feeds. Other possible uses of NIRS such as traceability or feed classification and botanical recognition of plants in grasslands are also described. The current technical developments, and in particular the miniaturization of spectrometers, make it possible to bring the instruments on the field to produce information as close as possible to its use. Other spectroscopic techniques that are alternative or complementary to NIRS such as mid-infrared spectroscopy, Raman spectroscopy or hyperspectral imaging will allow other measurement conditions and other applications., Le pilotage des systèmes d’élevage en vue d’une optimisation technique, économique et environnementale passe par une formulation des rations de plus en plus précise et nécessite donc une connaissance fine des aliments consommés par les animaux. La spectrométrie dans le proche infrarouge (SPIR), utilisée de façon croissante depuis les années 60, est une technique analytique permettant de caractériser rapidement des échantillons d’aliments ou de fourrages. Les premières applications concernaient la composition chimique des fourrages, mais il est également possible de développer des étalonnages pour une estimation de la valeur nutritive et de l’ingestion. Au-delà de ces mesures directes sur l’aliment, la SPIR peut être appliquée sur les fèces afin de caractériser l’alimentation d’animaux sur parcours. Le traitement conjoint des spectres des aliments et des fèces peut donner une vision de l’utilisation réellement faite des aliments par les animaux. D’autres utilisations possibles de la SPIR comme la traçabilité ou la classification des aliments ainsi que la reconnaissance botanique des végétaux dans les prairies sont aussi décrites. Les développements techniques actuels, et notamment la miniaturisation des spectromètres, permettent d’amener les instruments sur le terrain pour produire l’information au plus près de son utilisation. D’autres techniques spectroscopiques alternatives ou complémentaires à la SPIR comme la spectroscopie dans le moyen infrarouge, la spectroscopie Raman ou l’imagerie hyperspectrale permettront d’autres conditions de mesures et d’autres applications.

The aim of this study was to determine the multi-mycotoxin occurrence in cereal and oilseed products most consumed in Cote d’Ivoire. A total of 238 samples of rice (88 produced locally or imported), maize (79, cracked or flour) and peanut paste (71) were collected in the main markets of Abidjan, Bouake and Korhogo. An UHPLC-MS/MS method allowed the analysis of 77 mycotoxins. All the peanut paste samples were contaminated by aflatoxin B1 (AFB1) with 99% exceeding the EU limits of 2 μg kg−1 for AFB1 and 4 μg kg−1 for total aflatoxins (AFT: B1+B2+G1+G2), and concentrations reaching up to 4535 μg kg−1 (AFB1) and 8094 μg kg−1 (AFT). Maize (96%) and rice (57%) samples were also contaminated by AFB1 with 58% and 24% respectively above the EU limits and maximum levels of 80 μg kg−1 for maize and 14 μg kg−1 for rice. Only 6% of the cereal samples (3 rice and one maize samples) had ochratoxin A content above the EU limit (3 μg kg−1). Fumonisins and zearalenone were detected, respectively, in 91% and 8% of the maize samples, and in 18% and 5% of the rice samples but at levels below EU limits. Out of the 238 samples, 91% were contaminated with more than one mycotoxin including EU regulated mycotoxins and/or other mycotoxins mainly beauvericin (79% of the samples), equisetin (71%), aflatoxin M1 (45%), cyclopiazonic acid (32%), fumonisin B3 (29%), sterigmatocystin (24%), citrinin (18%), ochratoxin B (16%) and fusaric acid (15%). The peanut paste samples represented the highest risk to consumer health followed by maize and rice samples.

Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales.

Description du sujet. Le bilan des nutriments, l'homogénéité des andains ainsi que l'hygiénisation, évaluée par la température, de composts obtenus lors du co-compostage de boues de laiterie et de fumier de bovins ont été étudiés à la demande de l'industrie laitière réunionnaise qui souhaite développer la valorisation agronomique des boues de laiterie en satisfaisant les contraintes règlementaires de l'Ile de la Réunion. Objectifs. Les objectifs de cette expérimentation étaient d'évaluer la faisabilité d'un co-compostage de fumier de bovin avec des boues de laiterie et de statuer sur la qualité du compost produit. Méthode. Trois andains de fumier avec deux doses de boues de laiterie ont été mis en place (sur une base massique) : fumier seul (T), fumier ⅔ + boues ⅓ (B1) et fumier ½ + boues ½ (B2) présentant une densité brute de 305, 566 et 630 kg·m-3 et une porosité libre à l'air de 72 %, 48 % et 42 %, respectivement. Un retournement a été effectué après 21 jours. Le compostage a été prolongé durant 142 jours. Résultats. Les résultats obtenus montrent que les températures des tas atteignent 70 °C après deux jours de compostage et que l'hygiénisation (t > 55 °C) dure 40, 29 et 34 jours pour les andains T, B1et B2, respectivement. L'andain T a perdu 69 % de sa masse et 64 % de son volume initial pendant le compostage, l'andain B1, 71 % et 44 % et l'andain B2, 68 % et 49 %, respectivement. Les matières minérales et les éléments fertilisants se sont concentrés dans la matière sèche (MS). L'andain T a perdu 54 % de sa matière organique (MO) et 15 % de son azote (N), l'andain B1, 51 % et 42 % et l'andain B2, 56 % et 50 %, respectivement. Les teneurs en MS et en N deviennent plus homogènes au sein du tas pour les andains T et B1 contrairement au tas B2. Conclusions. Les composts obtenus sont conformes à la norme NFU 44-51 (T) et à la norme NFU 44-95 (B1 et B2), sauf pour le critère de teneur en MS pour ces derniers. Par rapport au compost de fumier de bovin, le compost avec ajout de boues (⅓) est enrichi (sur une base matière fraiche) en N (+ 15 %), en P (+ 40 %) et appauvri en K (- 20 %).

Food traceability is a growing consumer concern worldwide. Traceability is undertaken primarily at the administrative level, where the use of advanced analytical tools is not available. Nevertheless, the determination of geographical origin is a requirement of the traceability system for the import and export of foodstuffs (EU regulation 178/2002). The topics covered in this book include the history of traceability; legislations and rules; the actual traceability techniques and the potential analytical techniques for food traceability such as molecular methods (e.g. DGGE, SSCP), next generation sequencers (NGS), bio-captors, chromatographic techniques, isotopic analysis that are used for discrimination of organic food, fish, oils. The chromatographic techniques help in the use of volatile compounds analysis. The isotope analysis helps in distinguishing between chicken meat and vegetable oils. Ambient mass spectrometry is used for studying mycotoxines and alkaloids in foodstuffs and their management, food and feed authentication in olive and other plant oils, and wine. Vibrational methods (e.g. NMR and NIRS) are used to trace food by global spectrum. The book reviews the current and future techniques including metabolomic techniques. (Resume d'auteur)

Background: Ehrlichia ruminantium is the causal agent of heartwater, a fatal tropical disease affecting ruminants with important economic impacts. This bacterium is transmitted by Amblyomma ticks and is present in sub-Saharan Africa, islands in the Indian Ocean and the Caribbean, where it represents a threat to the American mainland.Methods: An automated DNA extraction method was adapted for Amblyomma ticks and a new qPCR targeting the pCS20 region was developed to improve E. ruminantium screening capacity and diagnosis. The first step in the preparation of tick samples, before extraction, was not automated but was considerably improved by using a Tissue Lyser. The new pCS20 Sol1 qPCR and a previously published pCS20 Cow qPCR were evaluated with the OIE standard pCS20 nested PCR.Results: pCS20 Sol1 qPCR was found to be more specific than the nested PCR, with a 5-fold increase in sensitivity (3 copies/reaction vs 15 copies/reaction), was less prone to contamination and less time-consuming. As pCS20 Sol1 qPCR did not detect Rickettsia, Anasplasma and Babesia species or closely related species such as Panola Mountain Ehrlichia, E. chaffeensis and E. canis, its specificity was also better than Cow qPCR. In parallel, a tick 16S qPCR was developed for the quality control of DNA extraction that confirmed the good reproducibility of the automated extraction. The whole method, including the automated DNA extraction and pCS20 Sol1 qPCR, was shown to be sensitive, specific and highly reproducible with the same limit of detection as the combined manual DNA extraction and nested PCR, i.e. 6 copies/reaction. Finally, 96 samples can be tested in one day compared to the four days required for manual DNA extraction and nested PCR.Conclusions: The adaptation of an automated DNA extraction using a DNA/RNA viral extraction kit for tick samples and the development of a new qPCR increased the accuracy of E. ruminantium epidemiological studies, as well as the diagnostic capabilities and turn-over time for surveillance of heartwater. This new method paves the way for large-scale screening of other bacteria and viruses in ticks as well as genetic characterization of ticks and tick-pathogen coevolution studies.

In a context of emergence or re-emergence of vector-borne diseases, certain species of Culicoides (Diptera: Ceratopogonidae) are involved in the transmission of certain viruses (Reoviridae: Orbivirus) and nematodes (Onchocercidae: Mansonella) in the Afrotropical region. However, the systematic and taxonomic schemes as well as the bio-ecology of species of veterinary interest remain to be explored. This work of integrative taxonomy aims to achieve (i) a systematic and taxonomic revision of species belonging to subgenera and groups of veterinary interest using a multi-marker molecular phylogeny and species delineation, and (ii) to develop molecular tools for studying the bioecology of species of veterinary interest and dynamics of their immature populations. Our results show (i) the presence of three monophyletic clades, the Imicola group, the Milnei group and the subgenus Remmia, (ii) a new species for science named C. sp. # 22 and affiliated into the subgenus Avaritia, Imicola group, (iii) the presence of a new undescribed species named C. sp. # 54 belonging to the Dasyops group, subgenus Avaritia, (iii) affiliating the Similis and Neavei species groups to the subgenus Synhelea, and (iv) cryptic species within C. oxystoma (subgenus Remmia). From a bioecological point of view, this work combining entomological follow-up and molecular identification with a library of barcode sequences allowed to describe the trophic behavior of C. imicola, C. kingi and C. oxystoma as well as their larval habitats in equine environments of the Niayes area in Senegal. This work completes the corpus of knowledge about the genus Culicoides in the Afrotropical region to improve our knowledge on the epidemiology of the transmitted pathogens and to propose research tracks to better control the immature and adult populations of the vector species in order to better anticipate and prevent Culicoides-borne diseases outbreaks.; Dans un contexte d’émergence ou de réémergence des maladies à transmission vectorielle, certaines espèces de Culicoides (Diptera : Ceratopogonidae) sont impliquées dans la transmission de certains virus (Reoviridae : Orbivirus) et de nématodes (Onchocercidae : Mansonella) en région Afrotropicale. Cependant, le schéma systématique et taxonomique ainsi que la bio-écologie des espèces d’intérêt vétérinaire restent à explorer. Ce travail de taxonomie intégrative a pour objectifs de réaliser (i) une révision systématique et taxonomique des espèces appartenant à des sous-genres et des groupes d’intérêt à partir de phylogénie moléculaire multi-marqueur et de délimitation d’espèces, et (ii) de développer des outils moléculaires pour l’étude de la bio-écologie des espèces d’intérêt vétérinaire et de la dynamique de leurs populations d’immatures. Nos résultats mettent en évidence (i) la présence de trois clades monophylétiques le groupe d’espèces Imicola, le groupe d’espèces Milnei et le sous-genre Remmia, (ii) une nouvelle espèce pour la science nommée C. sp. #22 et affiliée au sous-genre Avaritia, groupe Imicola, (iii) la présence d’une nouvelle espèce non-décrite nommée C. sp. #54 appartenant au groupe d’espèces Dasyops, sous-genre Avaritia, (iii) d’affilier les groupes d’espèces Similis et Neavei au sous-genre Synhelea et, (iv) de poser l’hypothèse d’une présence d’espèces cryptiques au sein de C. oxystoma (sous-genre Remmia). D’un point de vue bio-écologique, le travail réalisé combinant suivi entomologique et identification moléculaire avec une librairie de séquences barcodes a permis de décrire le comportement trophique de C. imicola, C. kingi et C. oxystoma ainsi que leurs habitats larvaires dans des environnements équins de la zone des Niayes au Sénégal. L’ensemble de ce travail permet de compléter le corpus de connaissances sur le genre Culicoides en région Afrotropicale afin d’améliorer la compréhension de l’épidémiologie des pathogènes transmis et proposer des pistes de recherches pour mieux contrôler les populations immatures et adultes des espèces vectrices afin de mieux anticiper et prévenir des évènements sanitaires.

International audience; The ISO-standardized RHIZOtest is used here for the first time to decipher how plant species, soil properties, and physical chemical properties of the nanoparticles and their transformation regulate the phytoavailability of nanoparticles. Two plants, tomato and fescue, were exposed to two soils with contrasted properties: a sandy soil poor in organic matter and a clay soil rich in organic matter, both contaminated with 1, 15, and 50 mg-kg(-1) of dissolved Ce-2(SO4)(3), bare and citrate coated CeO2 nanoparticles. All the results demonstrate that two antagonistic soil properties controlled Ce uptake. The clay fraction enhanced the retention of the CeO2 nanoparticles and hence reduced Ce uptake, whereas the organic matter content enhanced Ce uptake. Moreover, in the soil poor in organic matter, the organic citrate coating significantly enhanced the phytoavailability of the cerium by forming smaller aggregates thereby facilitating the transport of nanoparticles to the roots. By getting rid, of the dissimilarities between the root systems of the different plants and the normalizing the surfaces exposed to nanoparticles, the RHIZOtest demonstrated that the species of plant did not drive the phytoavailability, and provided evidence for soil plant transfers at concentrations lower than those usually cited in the literature and closer to predicted environmental concentrations.