Showing papers by "Institut national de la recherche agronomique published in 2022"

Short-term dynamic responses of soil properties and soil fauna under contrasting tillage systems

Abstract: Achieving sustainability is a worldwide current concern in agriculture that brings important challenges but also opportunities for rethinking agroecosystems. While many studies focused on tillage effects upon soil organisms, few of them have considered this into a temporal framework. In a study conducted in actual field conditions, we evaluated at short-term (7 months) the dynamic of several abiotic and biotic soil parameters under contrasting tillage systems. We hypothesised that (1) the reduction and especially the stopping of the soil mechanical perturbation lead overall to an improvement of the soil physical structure and the food resources available for soil fauna. (2) According to their specific ecological requirements, Collembola and Earthworms will show different dynamics of responses following alleviation of soil mechanical perturbation. (3) For a single group (either Collembola or earthworms), differences between tillage systems are dependent on the sampling period. We used a field set-up held on the INRA experimental station of Estrees-Mons (North of France). Three tillage systems were investigated: conventional tillage (with the soil inverted up to 25 cm depth) reduced tillage (limited to the first 7–8 cm depth) and no-tillage. Each treatment was replicated 4 times randomly (3 × 4 = 12 plots in total). Collembola and earthworms were sampled at each plot using standard methods. During the course of the experiment, two tillage operations were performed one in mid-March and one in mid-May. Samplings of soil fauna were performed on a regular basis according to tillage operation: 1 day before, and respectively 1; 7; 30; 49; 56; 104; 210 days after. Abiotic parameters (bulk density, SOC stock, Mean Weight Diameter (MWD) and aggregates size) and microflora (microbial and fungal biomass and their activity) were also monitored and used as explaining factors. Our findings showed that slightly reducing the intensity of soil mechanical perturbation, did not favour soil fauna. But, when stopping tillage, population sizes of earthworm and Collembola increased. This is related to the improvement of the distribution of, and accessibility to, organic matter as a basic food source (SOC stock, microbial and fungal biomass and their potential C mineralisation activity), the physical structure of the soil and the distribution of pore sizes as a space life (bulk density, MWD and aggregates size). Our kinetic study has shown that the different groups of soil fauna respond differently to mechanical soil disturbance. Overall, conservation tillage can foster one of the numerous services provided by the soil compartment, namely the soil biodiversity and therefore improve soil quality and health.

Evaluation of some nutritional quality criteria of seventeen Moroccan dates varieties and clones, fruits of date palm (Phoenix dactylifera L.).

Abstract: Date fruit is known to be the staple food in the Arab countries. It provides a lot of potential health benefits and can be the essential source of nutrients. The majority of Moroccan varieties are not characterized for their chemical, biochemical and quality properties. The aim of this work was to assess the chemical composition of 17 varieties of Moroccan date fruits (Phoenix dactylifera L.) and to determine their nutritive components. The analysis showed that the dates are rich in sugars (51.80-87.98%), they contain low concentration of proteins (1.09-2.80%) and lipids (0.16-0.39%). The predominant mineral is potassium (1055.26-1604.10 mg/100 g DW). Moreover, they contain high concentrations of malic acid (69.48-495.58 mg/100 g (DW)), oxalic acid (18.47-233.35 mg/100 g DW) and tartaric acid (115.70-484.168 mg/100 g DW). These results suggest that the date fruit are nutritious and can be an excellent source for human nutrition and health benefits.

Mapping of QTLs for citrus quality traits throughout the fruit maturation process on clementine (Citrus reticulata × C. sinensis) and mandarin (C. reticulata Blanco) genetic maps

Abstract: Abstract Citrus fruit quality is defined as the combination of physical and chemical traits; some of which may change during the ripening phase, e.g., acidity and sugar content. A clear understanding of their genetic control would be very helpful for marker-assisted breeding programs especially with regard to the juvenile phase and some reproductive features that hamper the selection of improved hybrids. A genetic study was thus performed on the heredity of quality traits and QTL detection based on segregation in a progeny generated from a cross between clementine cv “Commun” ( Citrus × reticulata cv clementine ) and mandarin cv “Willow leaf” ( C. reticulata Blanco). Parental and consensus genetic linkage maps were constructed using 645 SNP and SSR markers. These maps were represented by 10 linkage groups in clementine and 12 linkage groups in mandarin, representing 75% and 58% respectively of the previously published clementine reference map. A total of 16 traits, including fruit mass, equatorial diameter, juice percentage, total soluble solids, acidity, pH, glucose, fructose, sucrose, and citric and malic acid concentrations were evaluated at three maturation dates. High variations indicating transgressive segregation were found for all traits, with normal or close to normal distributions. QTL analysis performed using the multiple QTL model allowed the detection of 34 QTLs on the three maps. QTLs were distributed in different linkage groups and generally detected at only one date of the ripening phase. The percentage of total variation explained ranged from 12 to 37% per QTL. Major QTLs ( R 2 ≥ 30%) were detected for equatorial diameter, glucose, and fructose (expressed in percentage dry matter) on linkage groups 8 and 9. Co-localization of QTLs controlling correlated and uncorrelated traits were mainly found on linkage groups 2, 4, 8, and 9, particularly between fruit mass and acidity.

An Interior Point Method Applied to Flow Constraints in a Pressure-Dependent Water Distribution System

Abstract: This paper used the fusion of an active-set method (ASM) and an interior point method (IPM), with a Newton method, to solve for the steady-state flows, heads, and outflows of a pressure-dep...

The shaping of plant axes and crowns through tropisms and elasticity: an example of morphogenetic plasticity beyond the shoot apical meristem

Abstract: Shoot morphogenetic plasticity is crucial to the adaptation of plants to their fluctuating environments. Major insights into shoot morphogenesis have been compiled studying meristems, especially the shoot apical meristem (SAM), through a methodological effort in multiscale systems biology and biophysics. However, morphogenesis at the SAM is robust to environmental changes. Plasticity emerges later on during post-SAM development. The purpose of this review is to show that multiscale systems biology and biophysics is insightful for the shaping of the whole plant as well. More specifically, we review the shaping of axes and crowns through tropisms and elasticity, combining the recent advances in morphogenetic control using physical cues and by genes. We focus mostly on land angiosperms, but with growth habits ranging from small herbs to big trees. We show that generic (universal) morphogenetic processes have been identified, revealing feedforward and feedback effects of global shape on the local morphogenetic process. In parallel, major advances have been made in the analysis of the major genes involved in shaping axes and crowns, revealing conserved genic networks among angiosperms. Then, we show that these two approaches are now starting to converge, revealing exciting perspectives.

A newly evolved chimeric lysin motif receptor‐like kinase in <i>Medicago truncatula</i> spp. <i>tricycla</i> R108 extends its Rhizobia symbiotic partnership

Abstract: Rhizobial lipochitooligosaccharidic Nod factors (NFs), specified by nod genes, are the primary determinants of host specificity in the legume-Rhizobia symbiosis. We examined the nodulation ability of Medicago truncatula cv Jemalong A17 and M. truncatula ssp. tricycla R108 with the Sinorhizobium meliloti nodF/nodL mutant, which produces modified NFs. We then applied genetic and functional approaches to study the genetic basis and mechanism of nodulation of R108 by this mutant. We show that the nodF/nodL mutant can nodulate R108 but not A17. Using genomics and reverse genetics, we identified a newly-evolved, chimeric LysM receptor-like kinase gene in R108, LYK2bis, which is responsible for the phenotype and can allow A17 to gain nodulation with the nodF/nodL mutant. We found that LYK2bis is involved in nodulation by mutants producing non-O-acetylated NFs and interacts with the key receptor protein NFP. Many, but not all natural S. meliloti and S. medicae strains tested require LYK2bis for efficient nodulation of R108. Our findings reveal that a newly-evolved gene in R108, LYK2bis, extends nodulation specificity to mutants producing non-O-acetylated NFs and is important for nodulation by many natural Sinorhizobia. Evolution of this gene may present an adaptive advantage to allow nodulation by a greater variety of strains.

Dose response relationships between linseed or rapeseed oils supply and rumen microbial metabolism in continuous culture on maize silage-based diet

Abstract: Little quantitative information is available on how dietary lipids concurrently alter the main rumen microbial functions in relation with their incorporation level. In a three-period experiment, linseed (Linum usitatissimum, LO) and rapeseed (Brassica napus L., RO) oils were added at 0, 40 or 80 g/kg dry matter input (DMI) to five 1-L dual outflow fermenters that were on a maize silage-based diet for nine days per period. RO supply decreased butyrate specific production. The amount of hexoses fermented (HF) increased by 9% at 40 g/kg LO. The production of CH4 was lower at 80 g/kg LO by 46% compared with controls. Conversely, the supply of LO significantly increased H2 and H2S productions in an antagonistic mode. The specific productions of propionate, butyrate, CH4 and H2 were altered by LO. The supply of RO increased the ammonia daily outflow (by 23% at 40 g/kg) and decreased the organic N outflow (by 13% at 80 g/kg). The degradabilities of dietary fractions were not affected by RO, neither the OM partitioning between dietary, fermented and microbial outflows. The OM true degradability decreased at 80 g/kg LO compared with controls and 40 g/kg LO. When LO was supplied, isovalerate and ammonia-N outflows were higher, organic and microbial N outflows and EMPS were lower along with changes in the OM outflow partitioning. Overall microbial processes appeared to differ in their responses to fatty acids saturation. Moreover, most effects were present at 40 g/kg DMI and diminished or even plateaued at 80 g/kg DMI.HighlightsFour per cent oil lowered butyrate specific productionFour per cent Linseed oil lowered microbial protein synthesis efficiencyLinseed oil lowered methanogenesis in proportion to input level

L'analyse de la porosité: Application à l'étude du compactage des sols

Abstract: L’étude du compactage et de ses conséquences soulève de nombreux problèmes méthodologiques et notamment: Comment exprimer l’effet du compactage sur le sol ? Comment modéliser le processus de compactage des couches de surface sans satisfaire aux conditions d’homogénéité, d’isotropie et de continuité ? Comment évaluer en terme de risques pour la plante les effets du compactage ? L’auteur propose d’utiliser comme état de référence la masse volumique résultante de l’assemblage des constituants évaluée sur des agrégats de 2–3 mm de diamètre. Cette partition de l’espace poral en textural (intra-agrégats) et structural (inter-agrégats) permet une bonne interprétation du niveau de masse volumique, quelle que soit la teneur en eau. Une analyse du processus de compactage, en distinguant des comportements mécaniques texturaux et structuraux, est proposée. Des exemples de l’application de l’analyse des systèmes de porosité à l’étude des conséquences du compactage sont présentés et plus particulièrement l’interaction entre espace poral structural et transferts d’eau et de gaz (perméabilité, diffusivité) ainsi que les propriétés mécaniques résultantes. Several difficulties arise when studying soil compaction and its consequences on crop growth: How to express compaction responses in the soil ? How to predict soil compaction under wheel without assuming homogeneity, continuity and isotropy of top soil layers ? How to assess the real risks of crops consecutive to soil compaction ? The author proposes to use, as a reference state, the bulk density due only to the packing of soil constituants, which may be measured on aggregates of 2–3 mm diameter. This leads to a partition of pore space into “textural” (intra-aggregates) and “structural” (inter-aggregates) pore spaces, which allows a good interpretation of bulk density at any water content. An analysis of compaction process, distinguishing textural and structural mechanical behaviours is proposed. Examples of using this pore space partition for the study of the consequences of compaction are given. The interaction between structural pore space and water and gas transfer (permeability, diffusivity) as well as mechanical properties (soil strength) are emphasized.

Ecosystem Services Provided by Cover Crops and Biofumigation in Sunflower Cultivation

Abstract: In south-western France, sunflowers are usually grown in short rotations and after a long fallow period during which soils are left bare. This practice can favour diseases, caused by soilborne fungi, such as sunflower verticillium wilt (SVW), as well as nitrate leaching, both of which can decrease yields. Growing cover crops during a fallow period is an agroecological practice that could provide ecosystem services and mitigate SVW. A Brassicaceae cover crop that causes biofumigation produces glucosinolates and liberate biocidal compounds that might regulate SVW biologically. Moreover, the green manure effect of the Fabaceae might increase soil mineral nitrogen (SMN). To go further, mixtures of Brassicaceae and Fabaceae might mutualise the benefits that each cover crop has in sole crops. A four-year field study in south-western France tested Brassicaceae (brown mustard, turnip rape and fodder radish) and Fabaceae (purple vetch) in sole crops or a mixture with two or three species during the fallow period, followed by biofumigation, and sunflower crop. The cover crops were characterised, SMN was measured, the SVW and yield were assessed and compared to those of the crop grown on soils left bare during the fallow period. Purple vetch as a sole crop cover crop significantly increased SMN before sunflower sowing but only in 2019. Fodder radish as a sole crop reduced SVW severity significantly, overall, 80 days after sowing, except in 2019, when weather conditions were unfavourable to biofumigation. Purple vetch as a sole crop also reduced significantly SVW severity in 2017 and 2020. Finally, sunflower yields after cover crops were higher than those after bare soils, only after purple vetch as a sole crop in 2020, with a mean increase of 0.77 t ha−1. Mixtures of Brassicaceae and Fabaceae sowed at these densities resulted in an intermediate SMN level between those in sole crops and the bare soil and they did not significantly decrease SVW or increase yields. Our results suggest that cover crops, especially fodder radish or purple vetch, and biofumigation can provide ecosystem services for sunflower, instead of leaving soils bare during the fallow period. However, the extent of ecosystem services is markedly affected by soil and climatic conditions as well as other management practices.

On making physics relevant to society in general and to scientists in particular: Closing the epistemic gap

Abstract: Physics has a bad press: it is seen by a majority of people as a boring discipline ever since their High School days. There is no glamour to it, just toil and pain, and for many who engaged in it, the end sight is often unemployment. Could it be that physicists don't know how to communicate what their discipline entails to? I will be tackling the problematic of making physics relevant to society and to the scientists in general. I will also be dealing with the methodological and educational aspects of teaching and practicing physics, and the need to close the epistemic gap between physics teaching and the physicist's understanding ... By the way, do physicists understand physics?

10 PW peak power femtosecond laser pulses at ELI-NP

Abstract: We report on the generation and delivery of 10 PW peak power laser pulses, using the High Power Laser System (HPLS) at the Extreme Light Infrastructure – Nuclear Physics (ELI-NP).

PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time

Abstract: Abstract Background High-throughput phenotyping platforms allow the study of the form and function of a large number of genotypes subjected to different growing conditions (GxE). A number of image acquisition and processing pipelines have been developed to automate this process, for micro-plots in the field and for individual plants in controlled conditions. Capturing shoot development requires extracting from images both the evolution of the 3D plant architecture as a whole, and a temporal tracking of the growth of its organs. Results We propose PhenoTrack3D, a new pipeline to extract a 3D+t reconstruction of maize at organ level from plant images. It allows the study of plant architecture and individual organ development over time during the entire growth cycle. PhenoTrack3D improves a former method limited to 3D reconstruction at a single time point [Artzet et al ., 2019] by (i) a novel stem detection method based on deep-learning and (ii) a new and original multiple sequence alignment method to perform the temporal tracking of ligulated leaves. Our method exploits both the consistent geometry of ligulated leaves over time and the unambiguous topology of the stem axis. Growing leaves are tracked afterwards with a distance-based approach. This pipeline is validated on a challenging dataset of 60 maize hybrids imaged daily from emergence to maturity in the PhenoArch platform (ca. 250,000 images). Stem tip was precisely detected over time (RMSE < 2.1cm). 97.7% and 85.3% of ligulated and growing leaves respectively were assigned to the correct rank after tracking, on 30 plants x 43 dates. The pipeline allowed to extract various development and architecture traits at organ level, with good correlation to manual observations overall, on random subsets of 10 to 355 plants. Conclusions We developed a novel phenotyping method based on sequence alignment and deep-learning. It allows to characterise automatically and at a high-throughput the development of maize architecture at organ level. It has been validated for hundreds of plants during the entire development cycle, showing its applicability to the GxE analyses of large maize datasets.

Evolution of bacterial persistence to antibiotics during a 50,000-generation experiment in an antibiotic-free environment.

Abstract: Failure of antibiotic therapies causes > 700,000 deaths yearly and involves both bacterial resistance and persistence. Persistence results in the relapse of infections by producing a tiny fraction of pathogen survivors that stay dormant during antibiotic exposure. From an evolutionary perspective, persistence is either a 'bethedging strategy' that helps to cope with stochastically changing environments or an unavoidable minimal rate of 'cellular errors' that lock the cells in a low activity state. Here, we analyzed the evolution of persistence over 50,000 bacterial generations in a stable environment by improving a published method that estimates the number of persister cells based on the growth of the reviving population. Our results challenged our understanding of the factors underlying persistence evolution. In one case, we observed a substantial decrease in persistence proportion, suggesting that the naturally observed persistence level is not an unavoidable minimal rate of 'cellular errors'. However, although there was no obvious environmental stochasticity, in most cases the persistence level was maintained during 50,000 bacterial generations, and even increased in few cases.