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Sequencing, de novo assembly of Ludwigia plastomes, and comparative analysis within the Onagraceae family
No full textInternational audienceThe Onagraceae family, which belongs to the order Myrtales, consists of approximately 657 species and 17 genera. This family includes the genus Ludwigia L., which is comprised of 82 species. In this study, we focused on the two aquatic invasive species Ludwigia grandiflora subsp. hexapetala (Lgh) and Ludwigia peploides subsp. montevidensis (Lpm) largely distributed in aquatic environments in North America and in Europe. Both species have been found to degrade major watersheds leading ecological and economical damages. Genomic resources for Onagraceae are limited, with only Ludwigia octovalvis (Lo) plastid genome available for the genus Ludwigia L. at the time of our study. This scarcity constrains phylogenetic, population genetics, and genomic studies. To brush up genomic ressources, new complete plastid genomes of Ludwigia grandiflora subps. hexapetala (Lgh) and Ludwigia peploides subsp. montevidensis (Lpm) were generated using a combination of MiSeq (Illumina) and GridION (Oxford Nanopore) sequencing technologies. These plastomes were then compared to the published Ludwigia octovalvis (Lo) plastid genome, which was re-annotated by the authors. We initially sequenced and assembled the chloroplast (cp) genomes of Lpm and Lgh using a hybrid strategy combining short and long reads sequences. We observed the existence of two Lgh haplotypes and two potential Lpm haplotypes. Lgh, Lpm, and Lo plastomes were similar in terms of genome size (around 159 Kb), gene number, structure, and inverted repeat (IR) boundaries, comparable to other species in the Myrtales order. A total of 45 to 65 SSRs (simple sequence repeats), were detected, depending on the species, with the majority consisting solely of A and T, which is common among angiosperms. Four chloroplast genes (matK,accD, ycf2 and ccsA) were found under positive selection pressure, which is commonly associated with plant development, and especially in aquatic plants such as Lgh, and Lpm. Our hybrid sequencing approach revealed the presence of two Lgh plastome haplotypes which will help to advance phylogenetic and evolutionary studies, not only specifically for Ludwigia, but also the Onagraceae family and Myrtales order. To enhance the robustness of our findings, a larger dataset of chloroplast genomes would be beneficial
Quantifying intestinal lipolysis with MRI and TD-NMR: Proof of concept using dairy cream digested in vitro
No full textInternational audienceUnderstanding lipid digestion is crucial for promoting human health. Traditional methods for studying lipolysis face challenges in sample representativeness and pre-treatment, and cannot measure real-time lipolysis in vivo. Thus, non-invasive techniques like magnetic resonance imaging (MRI) need to be developed. This study assessedthe MRI water-fat separation method for monitoring in vitro intestinal digestion of dairy cream, supported by high-performance thin-layer chromatography (HP-TLC) and time-domain nuclear magnetic resonance (TDNMR). A clear distinction was found between the T2 of undigested lipids (~120 ms) and lipolytic products (0.1–15 ms). The short T2 of lipolytic products likely results from semi-crystalline structures formed with bile salts. While MRI methods cannot detect such fast-relaxing protons, it effectively quantified lipolysis by tracking the residual undigested lipids, showing high correlation with HP-TLC results (R2 = 0.93 and 0.95 for 13-s and 6-min MRI methods, respectively). The rapid 13-s MRI method offers strong potential for future in vivo applications
An evolutionary bouquet for roses
No full textInternational audienceThe genus Rosa, a member of Rosaceae family (along with apples, peaches and strawberries), makes up the most sales by value of all cut flowers sold in Europe and fifth of those in the USA1 (particularly driven by Valentine’s Day sales), in a global market for cut flowers that exceeds US $10 billion2. Roses are the top-selling deciduous shrubs and among the top five flowering plants sold in pots3. With 150 to 200 species accepted and more than 35,000 cultivars selected, understanding the evolution of this genus and the origins of both wild and cultivated taxa might have marked consequences not only for breeding (as current cultivars originate from only 7 to 10 species) but also for conservation decisions. At least two species are categorized as near-threatened or vulnerable in the International Union for the Conservation of Nature Global Red List; a few others are reported as invasive in some regions (for example, Rosa multiflora in the USA, Rosa rugosa in Europe and Rosa rubiginosa in South America and South Africa). In addition, the taxonomy of the genus Rosa is complicated by numerous polyploids and putative hybrids, and some peculiar species such as the pentaploid dog rose in which meiosis acts as apomictic taxa for three-fifths of the genome, whereas the remaining two-fifths of the genome is sexually transmitted. In this issue of Nature Plants, Cheng et al. provide a phylogenomic and phylogeographic analysis for the genus Rosa4
The Concept of Ecosystem Services and Its Application to Soil: Between Promises and Reality
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The role of fish in marine food webs
No full textInternational audienceFish employ mostly opportunistic size-based predation alongside a diverse array of feeding strategies. They occupy a wide range of trophic levels and fulfill diverse roles in marine food webs. This chapter presents the most common modeling approaches used to study the dynamics of fish within the food web. Using one of these approaches, we estimated that fish dominate the higher trophic levels (≥3) in biomass. We then present how fish contribute to trophic controls and the stability of marine food webs. By considering jointly the feeding dynamics and mobility patterns, we describe how fish facilitate the transfer of matter between ecosystems, both horizontally and vertically. Given their diverse roles, fish constitute a key element in marine food webs and contribute to various ecosystem services. Consequently, they have a crucial role to play in the implementation of ecosystem-based management strategies
Impact of ovotransferrin on the membrane integrity of Salmonella Enteritidis under egg-white conditions
No full textInternational audienceIntroduction - Eggs can mediate foodborne disease resulting in salmonellosis outbreaks that are most commonly caused by serovar Enteritidis. Ovotransferrin is a prominent egg-white antimicrobial glycoprotein belonging to the transferrin family, members of which exhibit powerful iron-chelating activity. However, several studies have also described the ability of transferrin proteins to disrupt bacterial membranes. This study aimed to investigate the antimicrobial activity of ovotransferrin toward Enteritidis membranes at 30°C under egg-white conditions. Materials and methods - This aim was supported by the deployment of a synthetic medium designed to mimic egg-white (matching the ionic composition and pH). The ability of ovotransferrin to induce bacterial membrane permeabilization in Enteritidis was investigated by measuring substrate accessibility to periplasmic -lactamase and cytosolic -galactosidase. Results - The depolarization of the inner membrane of Enteritidis was measured using a fluorescence probe [DiSC(5)]. The results show that ovotransferrin induces permeabilization of the outer membrane but not the inner membrane whereas egg white permeabilizes both membranes. In addition, the dissipation of the proton motive force by egg white was found to involve a contribution by ovotransferrin since this protein provoked inner-membrane depolarization. Discussion - It can thus be concluded that ovotransferrin exerts a membranes perturbation activity on S. Enteritidis under egg-white conditions, in addition to its well-known iron-chelation activity
Effects of digestate application, winter crop species and development on dissolved organic matter composition along the soil profile
No full textInternational audienceApplying organic waste products (OWPs) and sowing cover crops are agronomic practices to improve soil health. OWPs can be used in anaerobic digestion. Because microorganisms consume some of the labile molecules, persistent molecules accumulate in digestate. Few studies have investigated the transfer of dissolved organic matter (DOM) in soil that received digestate. Previously, effects of digestate application on dissolved organic carbon (DOC) were compared to those of the original pig slurry under wheat and a mustard catch crop for nine years at a lysimeter experimental site. DOC concentrations after digestate application were higher in the topsoil every year, due to crop development, but did not differ between treatments in the subsoil. The objectives of this study were to determine whether the observed differences in DOC concentrations caused DOM composition to differ, to identify sources (e.g., digestate, root exudation) that may have contributed to the DOM pool and to assess the DOM composition in the subsoil. The DOM composition of lysimeter samples and water extracts from the OWPs applied were analyzed by thermochemolysis coupled with gas chromatography and mass spectrometry, which identified plant- and microbial-derived biomarkers. Under mustard, the DOM pool seemed to contain mainly persistent molecules from digestate that were desorbed due to the increase in pH caused by nitrate uptake. Under wheat, the DOC pool seemed supplied by both digestate and root exudation. After applying digestate, plant-derived molecules decreased, while microbial-derived molecules increased, as depth increased, and molecules may have been sorbed from the topsoil to subsoil
Inducible MdAGG lectins in apple immunity toward fire blight: CRISPR/Cas9 validation and their potential for intragenesis approaches
No full textInternational audienceFire blight, caused by the bacterium Erwinia amylovora, represents a significant threat to apple (Malus domestica) production. Currently, only a limited number of genes effectively involved in resistance to E. amylovora have been identified. Seeking new resistance candidates, we focused on a multigene family encoding amaranthin-like lectins, which are highly upregulated following chemical elicitation by acibenzolar-S-methyl (ASM). These lectins are believed to contribute to downstream defense by promoting bacterial aggregation, which led to their designation as Malus domestica agglutinins (MdAGGs). When loss-offunction editions were introduced into MdAGG genes, the plant's ability to mount a fully effective defense response against fire blight upon ASM treatment was compromised, confirming the role of MdAGGs in fire blight resistance. Next, we coupled the pPPO16 promoter, endogenous to apple and known to be rapidly induced during E. amylovora infection, with the coding sequence of MdAGG10 to create apple lines with fire blight-inducible MdAGG10 expression. Early MdAGG10 expression in these lines significantly improved resistance to fire blight, and an additional ASM treatment further enhanced this resistance. In summary, we conclude that MdAGGs act as defense genes whose timely expression can provide effective resistance against E. amylovora.</div
Payments for environmental services with ecological thresholds: farmers’ preferences for a sponsorship bonus
No full textInternational audienceDesigning incentives for agri-environmental public good provision with threshold effects calls for payment mechanisms favouring critical mass participation and continuity of commitments at the landscape scale. We conducted a choice experiment to test the acceptability of a bonus in a scheme for improving river water quality in France. We introduce a sponsorship bonus each time the farmer convinces a peer into entering the scheme, which can be combined with a collective result bonus per hectare if the river reaches a higher step on the water quality scale. We consider the involvement of local financers could increase the willingness to pay beyond opportunity costs and income foregone and propose higher levels of payment than agri-environmental schemes. Results suggest a sponsorship bonus on its own is cost-effective. We characterize respondents' heterogeneity and identify three groups based on choice patterns: (i) "pro-environment individualists", (ii) "management change averse" farmers, and (iii) "pro-incentive" farmers
