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Multi-decadal to short-term beach and shoreline mobility in a complex river-mouth environment affected by mud from the amazon
No full textOn the 1500 km-long mud-dominated Guianas coast of South America, between the mouths of the two mega-rivers, the Amazon and the Orinoco, debouch numerous small rivers draining the humid tropical/equatorial Guiana Shield. The geomorphic development of the mouths of these rivers reflects interactions among water discharge, fluvial sediment load, and the alongshore migration of Amazon-derived mud banks alternating with inter-bank areas. The mouth of the Maroni River, astride the French Guiana-Suriname border, shows advanced estuarine infill and geomorphic development characterized by a western (downdrift) side comprising numerous recent cheniers and an eastern (updrift) side bound by an old (> 2000 years B. P.) chenier. A multidecadal analysis of the beach bounding this chenier shows little net overall mobility notwithstanding significant decadal to sub-decadal variation. The overall stability reflects the diversion of sand supply from the Maroni River toward the downdrift coast and limited sand supply by the smaller Mana River further east, and the south bank of which was contiguous with this beach. The variability in beach multi-decadal mobility reflects the influence, on waves, of alongshore-migrating banks (strong wave dissipation, limited beach mobility) and inter-bank areas (limited wave dissipation, larger beach mobility), highlighted by a comparison, in the current bank phase, of offshore and inshore waves. Erosion of the beach between 2011 and 2017 coincides with the sealing of the mouth of the Mana by muddy progradation in 2011 and mouth relocation several kilometers eastward. The morphodynamics of the beach and shorter-term fluctuations in budget are related to: (1) interaction with estuarine sand dunes mobilized by strong tidal currents on the adjacent shallow shoreface, (2) the influence of the Maroni channel, and (3) rapid encroachment of the leading edge of the shore-attached mud bank on the eastern part of the beach. The beach morphodynamics and evolution highlight, thus, embedded levels of influence: the Maroni at the local scale, and the net westward sedimenttransport system and bank and inter-bank alternations that affect the Guianas coast at a regional scale. The recent erosion poses a threat to the local communities by reducing beach space available for recreation and turtle-nesting
L’association de plantes compagnes aux protéagineux grains pour sécuriser leur production en agriculture conventionnelle et biologique
No full textLe réseau d’essais mis en place dans le cadre du projet PROGRAILIVE a permis de tester l’association
d’un protéagineux grains, semé à la même densité qu’en culture pure, avec une céréale, utilisée
comme plante de service mais récoltée, pour lever les freins liés à ces cultures (salissement, irrégularité
du rendement, …). Les essais ont été mis en place en Bretagne et Pays de la Loire, sur la féverole, le
pois protéagineux et le lupin, d’hiver et de printemps, en agriculture conventionnelle et biologique.
L’objectif est d’améliorer l’autonomie protéique des élevages du Grand Ouest. Concernant la gestion du salissement, l’association avec une céréale permet de mieux couvrir le sol et la céréale entre en concurrence avec les adventices. L’association présente donc à floraison un salissement plus faible que le protéagineux pur. Concernant le rendement, les résultats sont assez aléatoires (baisse ou augmentation). Dans le cas
particulier du pois, l’effet tuteur de la céréale permet d’augmenter la quantité de grains récoltée en cas
de verse. Le rendement total en grains (protéagineux + céréale) est toujours supérieur au protéagineux
seul. Concernant les données économiques, la marge semi-nette est très liée au rendement grain du
protéagineux. Selon les cas, la production complémentaire de céréales permet ou non de compenser
les surcoûts liés à l’association (semences, tri, absence d’aide PAC). Des parcelles ont également été suivies pour étudier les pratiques des agriculteurs sur ces cultures. Les itinéraires techniques sont très divers, ce qui reflète des objectifs et des motivations variées.Pulses are facing several technical issues (weed management, yield irregularity,…), resulting in
difficulties for their production. Trials were set up in the Western part of France to solve these problems,
using an intercrop with a cereal. The pulse is sowed at the same density as a sole crop and the cereal
at low density, to benefit from its presence but without important competition. The experiments were
conducted on winter and spring faba bean, pea and lupin, both in conventional and organic farming. The
main goal was to improve protein autonomy of breeding farms in the west part of France.[br/]
Regarding weed management, cereals have a better soil cover and are more competitive against
weeds. Therefore, the intercrop has a lower weed biomass than the pulse alone at flowering stage.
Regarding yield, results on intercropped pulse yield are variable (increase or decrease). In the case of
peas, the cereal can be a vertical support for the pea, thus allowing a better pea yield. The total yield
(pulse + cereal) is always higher in the intercrop than for the sole pulse.
Regarding economic data, the semi-net margin is strongly linked with the pulse grain yield. The
complementary cereal production may or may not compensate the over-costs generated by the
intercrop (extra seeds, separation, lack of CAP aids for intercrop plots), depending on the situations.
Plots were also observed to analyse farmer practices for those crops. Technical management is very
variable and that variability reflects the vast range of objectives and motivations of farmers to grow
pulses
SysVitSolVin - Impact de systèmes viticoles à faibles intrants sur la qualité des sols et la qualité sensorielle des productions
No full textDifférents systèmes viticoles sont évalués dans le cadre du programme ECOPHYTO pour fournir à la filière des nouveaux itinéraires techniques faiblement consommateurs d’intrants phytosanitaires. Les analyses réalisées sur les sols des sites systèmes viticoles étudiés, ont mis en évidence l’effet des pratiques sur le fonctionnement biogéochimique du sol. Les analyses combinées des paramètres microbiologiques du sol (diversité métabolique par Biolog® et biomasse bactérienne et fongique par qPCR) et de la minéralisation de l’azote ont permis de différencier les itinéraires en agriculture biologique de ceux en protection intégrée pour certains sites /systèmes étudiés. En effet, pour le site d’Aquitaine avec une vigne jeune et un sol sableux, le potentiel de minéralisation de l’azote est probablement lié à ces deux paramètres. En revanche pour un même cépage, des différences ont été
obtenues entre les itinéraires techniques (biologique ou intégré) au niveau de la minéralisation de l’azote, de la biomasse et de l’activité microbienne du sol d’un site Alsacien. Au niveau de la production, les résultats montrent que le profil sensoriel du vin, établit par un panel d’expert, est lié à la qualité de la grappe. Les attributs visuels et aromatiques sensoriels des vins ont permis de distinguer les sites en production AOP ainsi que les millésimes 2014 et 2015, mais non les systèmes en agriculture biologique de ceux intégrés. Finalement, la réduction drastique des herbicides dans la gestion des sols du vignoble n’a eu que des effets mineurs sur les caractéristiques sensorielles des baies de récolte et des vins
Evidence for Bisphenol B Endocrine Properties: Scientific and Regulatory Perspectives.
No full textThe substitution of bisphenol A (BPA) by bisphenol B (BPB), a very close structural analog, stresses the need to assess its potential endocrine properties.
This analysis aimed to investigate whether BPB has endocrine disruptive properties in humans and in wildlife as defined by the World Health Organization (WHO) definition used in the regulatory field, that is, a) adverse effects, b) endocrine activity, and c) plausible mechanistic links between the observed endocrine activity and adverse effects.
We conducted a systematic review to identify BPB adverse effects and endocrine activities by focusing on animal models and in vitro mechanistic studies. The results were grouped by modality (estrogenic, androgenic, thyroid hormone, steroidogenesis-related, or other endocrine activities). After critical analysis of results, lines of evidence were built using a weight-of-evidence approach to establish a biologically plausible link. In addition, the ratio of BPA to BPB potency was reported from studies investigating both bisphenols.
Among the 36 articles included in the analysis, 3 subchronic studies consistently reported effects of BPB on reproductive function. In rats, the 28-d and 48-week studies showed alteration of spermatogenesis associated with a lower height of the seminiferous tubules, the alteration of several sperm parameters, and a weight loss for the testis, epididymis, and seminal vesicles. In zebrafish, the results of a 21-d reproductive study demonstrated that exposed fish had a lower egg production and a lower hatching rate and viability. The in vitro and in vivo mechanistic data consistently demonstrated BPB's capacity to decrease testosterone production and to exert an estrogenic-like activity similar to or greater than BPA's, both pathways being potentially responsible for spermatogenesis impairment in rats and fish.
The available in vivo, ex vivo, and in vitro data, although limited, coherently indicates that BPB meets the WHO definition of an endocrine disrupting chemical currently used in a regulatory context
Water stress combined with sulfur deficiency in pea affects yield components but mitigates the effect of deficiency on seed globulin composition
No full textWater stress and sulfur (S) deficiency are two constraints increasingly faced by crops due to climate change and low-input agricultural practices. To investigate their interaction in the grain legume pea (Pisum sativum), sulfate was depleted at the mid-vegetative stage and a moderate 9-d water stress period was imposed during the early reproductive phase. The combination of the stresses impeded reproductive processes in a synergistic manner, reducing seed weight and seed number, and inducing seed abortion, which highlighted the paramount importance of sulfur for maintaining seed yield components under water stress. On the other hand, the moderate water stress mitigated the negative effect of sulfur deficiency on the accumulation of S-rich globulins (11S) in seeds, probably due to a lower seed sink strength for nitrogen, enabling a readjustment of the ratio of S-poor (7S) to 11S globulins. Transcriptome analysis of developing seeds at the end of the combined stress period indicated that similar biological processes were regulated in response to sulfur deficiency and to the combined stress, but that the extent of the transcriptional regulation was greater under sulfur deficiency. Seeds from plants subjected to the combined stresses showed a specific up-regulation of a set of transcription factor and SUMO ligase genes, indicating the establishment of unique regulatory processes when sulfur deficiency is combined with water stress. Moderate water stress combined with sulfur deficiency during seed development in pea synergistically affects reproductive processes, but mitigates the negative impact of the deficiency on the seed transcriptome and rebalances seed globulin composition
Deciphering the interplay between the genotoxic and probiotic activities of Escherichia coli Nissle 1917
No full textAlthough Escherichia coli Nissle 1917 (EcN) has been used therapeutically for over a century, the determinants of its probiotic properties remain elusive. EcN produces two siderophore-microcins (Mcc) responsible for an antagonistic activity against other Enterobacteriaceae. EcN also synthesizes the genotoxin colibactin encoded by the pks island. Colibactin is a virulence factor and a putative pro-carcinogenic compound. Therefore, we aimed to decouple the antagonistic activity of EcN from its genotoxic activity. We demonstrated that the pks-encoded ClbP, the peptidase that activates colibactin, is required for the antagonistic activity of EcN. The analysis of a series of ClbP mutants revealed that this activity is linked to the transmembrane helices of ClbP and not the periplasmic peptidase domain, indicating the transmembrane domain is involved in some aspect of Mcc biosynthesis or secretion. A single amino acid substitution in ClbP inactivates the genotoxic activity but maintains the antagonistic activity. In an in vivo salmonellosis model, this point mutant reduced the clinical signs and the fecal shedding of Salmonella similarly to the wild type strain, whereas the clbP deletion mutant could neither protect nor outcompete the pathogen. The ClbP-dependent antibacterial effect was also observed in vitro with other E. coli strains that carry both a truncated form of the Mcc gene cluster and the pks island. In such strains, siderophore-Mcc synthesis also required the glucosyltransferase IroB involved in salmochelin production. This interplay between colibactin, salmochelin, and siderophore-Mcc biosynthetic pathways suggests that these genomic islands were co-selected and played a role in the evolution of E. coli from phylogroup B2. This co-evolution observed in EcN illustrates the fine margin between pathogenicity and probiotic activity, and the need to address both the effectiveness and safety of probiotics. Decoupling the antagonistic from the genotoxic activity by specifically inactivating ClbP peptidase domain opens the way to the safe use of EcN
ANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
No full textBioinformatic tools for amplicon sequencing data analysis are continuously and rapidly evolving, thus integrating
We present an R workflow for 16S and ITS amplicons based sequencing. It is mainly based on the Dada2 and Phyloseq R packages. This workflow is based on several scripts in order to perform an analysis from fastq sequence files to final statistical analysis. The objective was to automate bioinformatic analyses to ensure reproducibility between projects trying to be versatile and simple to integrate new bioinformatic tools or statistical techniques.
ANOMALY use Amplicon Sequence Variant (ASV from Dada2 package) as taxonomic unit, allowing an easy and relevant sequence tracking between different environments and/or projects. Decontam package is included for an accurate and consistent detection of contaminant ASV and taxonomic assignment step relies on IDTAXA method. Our workflow is able to merge and check annotations from two taxonomic databases to unravel misannotation, discordance or inconsistency. The well known Phyloseq package provides the most common graphical representation, with additional statistics to assess significant impact of tested factors on microbial communities. The workflow incorporate multiple differential analyses (DESeq2 etc...) to reveal thin community contrast between conditions. Finally we are able to combine those results for cross-validation and thinner interpretation.
ANOMALY is a simple and customizable R workflow, that uses ASVs level for community characterization and integrates all assets of the up-to-date methods such as better sequence tracking, decontamination, merged taxonomic annotation, statistical tests, and cross-validated differential analysis
The bracteatus pineapple genome and domestication of clonally propagated crops
No full textDomestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops
Genetic diversity and population structure of the sweet leaf herb, Stevia rebaudiana B., cultivated and landraces germplasm assessed by EST-SSRs genotyping and steviol glycosides phenotyping.
No full textStevia rebaudiana (Asteraceae), native from Paraguay, accumulates steviol glycosides (SGs) into its leaves. These compounds exhibit acaloric intense sweet taste which answers to consumer demands for reducing daily sugar intake. Despite the developpement of S. rebaudiana cultivation all over the world, the development of new cultivars is very recent, in particular due to a colossal lack of (1) germplasm collection and breeding, (2) studies on genetic diversity and its structuring, (3) genomic tools.In this study, we developped 18 EST-SSR from 150,258 EST from The Compositae Genome Project of UC Davis ( http://compgenomics.ucdavis.edu/data/ ). We genotyped 145 S. rebaudiana individuals, issued from thirty-one cultivars and thirty-one landraces of various origins worldwide. Markers polymorphic information content (PIC) ranged between 0.60 and 0.84. An average of 12 alleles per locus and a high observed heterozygoty of 0.69 could be observed. The landraces revealed twice as many private alleles as cultivars. The genotypes could be clustered into 3 genetic populations. The landraces were grouped in the same cluster in which the oldest cultivars "Eirete" and "MoritaIII" type are also found. The other two clusters only include cultivated genotypes. One of them revealed an original genetic variability. SG phenotypes could not discriminate the three genetic clusters but phenotyping showed a wide range of composition in terms of bitter to sweet SGs.This is the first study of genetic diversity in Stevia rebaudiana involving 145 genotypes, including known cultivars as well as landrace populations of different origin. This study pointed out the structuration of S. rebaudiana germplasm and the resource of the landrace populations for genetic improvement, even on the trait of SG's composition
