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Distinct bacterial consortia established in ETBE-degrading enrichments from a polluted aquifer
No full textEthyl tert-butyl ether (ETBE) is a gasoline additive that became an important aquifer pollutant. The information about natural bacterial consortia with a capacity for complete ETBE degradation is limited. Here we assess the taxonomical composition of bacterial communities and diversity of the ethB gene (involved in ETBE biodegradation) in ETBE-enrichment cultures that were established from a gasoline-polluted aquifer, either from anoxic ETBE-polluted plume water (PW), or from an upstream non-polluted water (UW). We used a 16S rRNA microarray, and 16S rRNA and ethB gene sequencing. Despite the dissimilar initial chemical conditions and microbial composition, ETBE-degrading consortia were obtained from both PW and UW. The composition of ETBE-enrichment cultures was distinct from their initial water samples, reflecting the importance of the rare biosphere as a reservoir of potential ETBE degraders. No convergence was observed between the enrichment cultures originating from UW and PW, which were dominated by Mesorhizobium and Hydrogenophaga, respectively, indicating that distinct consortia with the same functional properties may be present at one site. Conserved ethB genes were evidenced in both PW and UW ETBE-enrichment cultures and in PW water. Our results suggest that the presence of ethB genes rather than the taxonomical composition of in situ bacterial communities indicate the potential for the ETBE degradation at a given site
Cultivated Olive Diversification at Local and Regional Scales: Evidence From the Genetic Characterization of French Genetic Resources
No full textMolecular characterization of crop genetic resources is a powerful approach to elucidate the origin of varieties and facilitate local cultivar management. Here we aimed to decipher the origin and diversification of French local olive germplasm. The 113 olive accessions of the ex situ collection of Porquerolles were characterized with 20 nuclear microsatellites plus their plastid haplotype. We then compared this collection to Mediterranean olive varieties from the Worldwide Olive Germplasm Bank of Marrakech, Morocco. High genetic diversity was observed within local French varieties, indicating a high admixture level, with an almost equal contribution from the three main Mediterranean gene pools. Nearly identical and closely related genotypes were observed among French and Italian/Spanish varieties. A high number of parent-offspring relationships were also detected among French varieties and between French and two Italian varieties ('Frantoio' and 'Moraiolo') and the Spanish variety ('Gordal Sevillana'). Our investigations indicated that French olive germplasm resulted from the diffusion of material from multiple origins followed by diversification based on parentage relationships between varieties. We strongly suggest that farmers have been actively selecting olives based on local French varieties. French olive agroecosystems more affected by unexpected frosts than southernmost regions could also be seen as incubators and as a bridge between Italy and Spain that has enhanced varietal olive diversification
Modelling temporal dynamics of Culicoides Latreille (Diptera: Ceratopogonidae) populations on Reunion Island (Indian Ocean), vectors of viruses of veterinary importance
No full textBackground Reunion Island regularly faces outbreaks of epizootic haemorrhagic disease (EHD) and bluetongue (BT), two viral diseases transmitted by haematophagous midges of the genus Culicoides (Diptera: Ceratopogonidae) to ruminants. To date, five species of Culicoides are recorded in Reunion Island in which the first two are proven vector species: Culicoides bolitinos, C. imicola, C. enderleini, C. grahamii and C. kibatiensis. Meteorological and environmental factors can severely constrain Culicoides populations and activities and thereby affect dispersion and intensity of transmission of Culicoides-borne viruses. The aim of this study was to describe and predict the temporal dynamics of all Culicoides species present in Reunion Island. Methods Between 2016 and 2018, 55 biweekly Culicoides catches using Onderstepoort Veterinary Institute traps were set up in 11 sites. A hurdle model (i.e. a presence/absence model combined with an abundance model) was developed for each species in order to determine meteorological and environmental drivers of presence and abundance of Culicoides. Results Abundance displayed very strong heterogeneity between sites. Average Culicoides catch per site per night ranged from 4 to 45,875 individuals. Culicoides imicola was dominant at low altitude and C. kibatiensis at high altitude. A marked seasonality was observed for the three other species with annual variations. Twelve groups of variables were tested. It was found that presence and/or abundance of all five Culicoides species were driven by common parameters: rain, temperature, vegetation index, forested environment and host density. Other parameters such as wind speed and farm building opening size governed abundance level of some species. In addition, Culicoides populations were also affected by meteorological parameters and/or vegetation index with different lags of time, suggesting an impact on immature stages. Taking into account all the parameters for the final hurdle model, the error rate by Normalized Root mean Square Error ranged from 4.4 to 8.5%. Conclusions To our knowledge, this is the first study to model Culicoides population dynamics in Reunion Island. In the absence of vaccination and vector control strategies, determining periods of high abundance of Culicoides is a crucial first step towards identifying periods at high risk of transmission for the two economically important viruses they transmit
ARSEINE - base de données régionalisées sur le bassin Seine-Normandie
No full textARSEINE est une base de données décrivant l’évolution des systèmes agricoles dominants sur les 50 dernières années à l’échelle du bassin hydrographique Seine-Normandie. Couplée à des outils de modélisation, cette base de données est utilisée pour appréhender à l’échelle d’un grand territoire l’impact au long terme des pratiques agricoles sur l’environnement
ABC’Terre : Integrating soil organic carbon variation into cropping systems greenhouse gases balance at a territorial scale
No full textInteractive effects of tree mixing and drought on a primary forest pest
No full textClimate change and biodiversity erosion are two major threats to the vitality of the world's forests. However, it is difficult to predict the extent to which tree diversity and environmental conditions interact to modify forest health, and in particular resistance and/or tolerance to insect pests. We used a tree diversity experiment with an irrigation treatment to investigate the effect of mixing and diluting host pines (Pinus pinaster) amongst broadleaved trees on pine stem borer (Dioryctria sylvestrella) infestations under contrasting drought conditions. We further tested whether the attack patterns of this primary pest resulted from direct effects of tree diversity and drought, or was indirectly mediated by their combined effects on pine vigor. The total number of stem borer attacks per plot significantly decreased with tree species richness, i.e., increased with the density of pines, being maximum in pure plots. There were more attacks in irrigated plots. Mixing pines with birches resulted in lower plot infestations but only in irrigated plots. The probability of individual tree being attacked was higher in irrigated plots and decreased with increasing pine density. More vigorous trees, i.e., with higher radial growth, were more likely to be attacked. We suggest that the pine stem borer is attracted by the volatile organic compounds released by the resin exuding from bark cracks. Bark fissuring increases with radial growth, which is enhanced by irrigation and reduced intraspecific competition in low-density pine plots. The presence of birch limits plot infestation, probably because it disrupts host-finding behavior through repellence by non-host volatiles. This phenomenon is mainly observed when pines are vigorous, i.e., when they are irrigated, and particularly attractive to the stem borer. Our results confirm that more severe droughts decrease the attacks by primary pests feeding on tree trunks, by reducing host tree vigor, and that focal tree species can obtain protection against specialized insect pests when mixed with non-host species. The functional characteristics of herbivorous insects are therefore to be taken into account in predicting the interactive effects of climate change and loss of diversity on forest health
Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves
No full textIn plants, RNA interference (RNAi) generates small interfering (si)RNAs from entire genomes of viruses, satellites and viroids. Therefore, deep small (s)RNA sequencing is a universal approach for virome reconstruction and RNAi characterization. We tested this approach on dried barley leaves from field surveys. Illumina sequencing of sRNAs from 2 plant samples identified in both plants Hordeum vulgare endornavirus (HvEV) and barley yellow mosaic bymovirus (BaYMV) and, additionally in one plant, a novel strain of Japanese soil-borne wheat mosaic furovirus (JSBWMV). De novo and reference-based sRNA assembly yielded complete or near-complete genomic RNAs of these viruses. While plant sRNAs showed broad size distribution, viral sRNAs were predominantly 21 and 22 nucleotides long with 5'-terminal uridine or adenine, and were derived from both genomic strands. These bona fide siRNAs are presumably processed from double-stranded RNA precursors by Dicer-like (DCL) 4 and DCL2, respectively, and associated with Argonaute 1 and 2 proteins. For BaYMV (but not HvEV, or JSBWMV), 24-nucleotide sRNAs represented the third most abundant class, suggesting DCL3 contribution to antibymovirus defence. Thus, viral siRNAs are well preserved in dried leaf tissues and not contaminated by non-RNAi degradation products, enabling both complete virome reconstruction and inference of RNAi components mediating antiviral defense
Unusual extracellular appendages deployed by the model strain Pseudomonas fluorescens C7R12
No full textPseudomonas fluorescens is considered to be a typical plant-associated saprophytic bacterium with no pathogenic potential. Indeed, some P. fluorescens strains are well-known rhizobacteria that promote plant growth by direct stimulation, by preventing the deleterious effects of pathogens, or both. Pseudomonas fluorescens C7R12 is a rhizosphere-competent strain that is effective as a biocontrol agent and promotes plant growth and arbuscular mycorrhization. This strain has been studied in detail, but no visual evidence has ever been obtained for extracellular structures potentially involved in its remarkable fitness and biocontrol performances. On transmission electron microscopy of negatively stained C7R12 cells, we observed the following appendages: multiple polar flagella, an inducible putative type three secretion system typical of phytopathogenic Pseudomonas syringae strains and densely bundled fimbria-like appendages forming a broad fractal-like dendritic network around single cells and microcolonies. The deployment of one or other of these elements on the bacterial surface depends on the composition and affinity for the water of the microenvironment. The existence, within this single strain, of machineries known to be involved in motility, chemotaxis, hypersensitive response, cellular adhesion and biofilm formation, may partly explain the strong interactions of strain C7R12 with plants and associated microflora in addition to the type three secretion system previously shown to be implied in mycorrhizae promotion
Implementation of a new food picture database in the context of fMRI and visual cognitive food-choice task in healthy volunteers
No full textThis pilot study aimed at implementing a new food picture database in the context of functional magnetic resonance imaging (fMRI) cognitive food-choice task, with an internal conflict or not, in healthy normal-weight adults. The database contains 170 photographs including starters, main courses, and desserts; it presents a broad-spectrum of energy content and is provided with portion weight and nutritional information. It was tested in 16 participants who evaluated the energy density and gave a liking score for all food pictures via numerical scales. First, volunteers were segregated into two groups according to their eating habits according to a food consumption frequency questionnaire (FCFQ) to assess whether the database might elicit different appreciations according to individual eating habits. Second, participants underwent fMRI cognitive food-choice task (van der Laan et al., 2014), using our picture database, in which they had to choose between high-energy (HE) and low-energy (LE) foods, under a similar liking (SL, foods with similar hedonic appraisals) condition or a different liking (DL, foods with different hedonic appraisals) condition. Participants evaluated correctly the caloric content of dishes (from r = 0.72 to r = 0.79, P < 0.001), confirming a good perception of the caloric discrepancies between food pictures. Two subgroups based on FCFQ followed by a principal component analysis (PCA) and a hierarchical ascendant classification (HAC) were defined, that is, Prudent-type (PTc, N = 9) versus Western-type (WTc, N = 7) consumers, where the WTc group showed higher consumption of HE palatable foods than PTc (P < 0.05). The WTc group showed a higher correlation between liking and caloric evaluation of the food pictures as compared to PTc (r = 0.77 and r = 0.36, respectively, P < 0.001), confirming that food pictures elicited variable responses according to contrasted individual eating habits. The fMRI analyses showed that the DL condition elicited the activation of dorsal anterior cingulate cortex (dACC), involved in internal conflict monitoring, whereas SL condition did not, and that LE food choice involved high-level cognitive processes with higher activation of the hippocampus (HPC) and fusiform gyrus compared to HE food choice. Overall, this pilot study validated the use of the food picture database and fMRI-based procedure assessing decision-making processing during a food choice cognitive task with and without internal conflict
TasselNetv2: in-field counting of wheat spikes with context-augmented local regression networks
No full textBackground: Grain yield of wheat is greatly associated with the population of wheat spikes, i.e., spike number m(-2). To obtain this index in a reliable and efficient way, it is necessary to count wheat spikes accurately and automatically. Currently computer vision technologies have shown great potential to automate this task effectively in a low-end manner. In particular, counting wheat spikes is a typical visual counting problem, which is substantially studied under the name of object counting in Computer Vision. TasselNet, which represents one of the state-of-the-art counting approaches, is a convolutional neural network-based local regression model, and currently benchmarks the best record on counting maize tassels. However, when applying TasselNet to wheat spikes, it cannot predict accurate counts when spikes partially present. Results: In this paper, we make an important observation that the counting performance of local regression networks can be significantly improved via adding visual context to the local patches. Meanwhile, such context can be treated as part of the receptive field without increasing the model capacity. We thus propose a simple yet effective contextual extension of TasselNet-TasselNetv2. If implementing TasselNetv2 in a fully convolutional form, both training and inference can be greatly sped up by reducing redundant computations. In particular, we collected and labeled a large-scale wheat spikes counting (WSC) dataset, with 1764 high-resolution images and 675,322 manually-annotated instances. Extensive experiments show that, TasselNetv2 not only achieves state-of-the-art performance on the WSC dataset (91.01% counting accuracy) but also is more than an order of magnitude faster than TasselNet (13.82 fps on 912 x 1216 images). The generality of TasselNetv2 is further demonstrated by advancing the state of the art on both the Maize Tassels Counting and ShanghaiTech Crowd Counting datasets. Conclusions: This paper describes TasselNetv2 for counting wheat spikes, which simultaneously addresses two important use cases in plant counting: improving the counting accuracy without increasing model capacity, and improving efficiency without sacrificing accuracy. It is promising to be deployed in a real-time system with high-throughput demand. In particular, TasselNetv2 can achieve sufficiently accurate results when training from scratch with small networks, and adopting larger pre-trained networks can further boost accuracy. In practice, one can trade off the performance and efficiency according to certain application scenarios. Code and models are made available at: https://tinyurl.com/TasselNetv2