French Higher Education Institution in Agriculture, Food, Horticultural and Landscape Sciences

Currently, parental care is becoming increasingly perceived as male and female cooperation, instead of being primarily shaped by sexual conflict. Most studies examining cooperating performance consider coordination of parental activities, and doing so focuses on a short time-window including only one stage of breeding (i.e., incubation or chick rearing period). Here, we considered the cooperation of breeding partners, investigating the coordination of parental care in a long-lived seabird species with long and extensive biparental care, the Dovekie (or Little Auk), Alle alle, and looked at the issue throughout the breeding season. Previous studies on this species revealed coordinated chick provisioning, but parental coordination during incubation remains unstudied. Using video recordings collected over the course of two breeding seasons, we tested whether coordination was subject to small-scale changes within each stage and whether there was a relationship between coordination levels across the two stages. We found that the level of parental coordination is overall high and increases during the incubation period but decreases through the chick rearing phases. There were some inter-annual differences in the coordination level both at the incubation and chick rearing stages. We also found some dependency between the coordination during the incubation and chick rearing periods. All these results suggest that coordination is not a fixed behavior but breeding-phase dependent. The present study thus provides insights into how parental care and parents’ cooperation is shaped by brood needs and conditions. It also highlights a relationship between coordination levels during chick rearing and incubation periods, suggesting some extent of temporal dependence in coordination of parental performance within the breeding season.

The loggerhead turtle ( Caretta caretta ) South Pacific subpopulation is classified as 'Critically Endangered’ in the International Union for Conservation of Nature’s Red List, based on its estimated demographic decline. The Southern Province of New Caledonia shelters two distinct major nesting areas for this subpopulation, aggregating approximately 10–25% of all reported nesting activities at the ocean basin scale. A prejudicial knowledge gap subsisted in whether the nesting population of these two nesting areas are part of a single or two distinct Management Unit(s), which could have significant implications for conservation strategies to be implemented. Based on a dataset collected from November 2016 to March 2023, we evaluated the sex-specific connectivity of loggerhead turtles over various temporal scales using three complementary methodologies: satellite telemetry (intra-annual), Capture-Mark-Recapture surveys (inter-annual) and molecular analysis (inter-generations). Our results suggest that reproductive populations from both nesting areas form a unique genetic stock, and that the gene flow is presumably ensured by males, contrasting with the high fidelity to nesting areas shown by females. Considering that both nesting areas show heterogeneous habitat conformations and substantial differences in the associated threat levels, this study highlights the importance to consider both the site-specific aspects and the more global Management Unit scale to ensure a prioritized and coherent conservation strategy. Not considering those aspects could result in management failure and loss of local population segments.

The management of food fermentation is still largely based on empirical knowledge, as the dynamics of microbial communities and the underlying metabolic networks that produce safe and nutritious products remain beyond our understanding. Although these closed ecosystems contain relatively few taxa, they have not yet been thoroughly characterized with respect to how their microbial communities interact and dynamically evolve. However, with the increased availability of metataxonomic data sets on different fermented vegetables, it is now possible to gain a comprehensive understanding of the microbial relationships that structure plant fermentation. In this study, we applied a network-based approach to the integration of public metataxonomic 16S data sets targeting different fermented vegetables throughout time. Specifically, we aimed to explore, compare, and combine public 16S data sets to identify shared associations between amplicon sequence variants (ASVs) obtained from independent studies. The workflow includes steps for searching and selecting public time-series data sets and constructing association networks of ASVs based on co-abundance metrics. Networks for individual data sets are then integrated into a core network, highlighting significant associations. Microbial communities are identified based on the comparison and clustering of ASV networks using the “stochastic block model” method. When we applied this method to 10 public data sets (including a total of 931 samples) targeting five varieties of vegetables with different sampling times, we found that it was able to shed light on the dynamics of vegetable fermentation by characterizing the processes of community succession among different bacterial assemblages. IMPORTANCE Within the growing body of research on the bacterial communities involved in the fermentation of vegetables, there is particular interest in discovering the species or consortia that drive different fermentation steps. This integrative analysis demonstrates that the reuse and integration of public microbiome data sets can provide new insights into a little-known biotope. Our most important finding is the recurrent but transient appearance, at the beginning of vegetable fermentation, of amplicon sequence variants (ASVs) belonging to Enterobacterales and their associations with ASVs belonging to Lactobacillales. These findings could be applied to the design of new fermented products.

The study explored the sociocultural influences on sugar consumption in three distinct countries: New Zealand, France, and Singapore. It employed the theory of planned behavior (TPB) alongside consumer perception and acceptance factors, such as sugar consciousness, product labeling, sugar substitution with sweeteners, and perceived flavor, to investigate participants’ behaviors regarding various yogurt types. Data was gathered through web surveys in each country, analyzed through partial least squares (PLS)–confirmatory factor analysis to create country‐specific conceptual frameworks, and then validated using PLS‐path modeling to assess the correlations between TPB and consumer perception constructs. The results indicated that perceived behavioral control positively influenced intentions to reduce sugar intake in participants from New Zealand and Singapore. Sugar consciousness exhibited a positive correlation with behavioral intentions across all three countries, suggesting heightened awareness of sugar intake motivates individuals to cut back. Notably, the presence of labels and claims showed negative correlation with perceived flavor, among the participants from New Zealand and France, suggesting that food researchers must navigate a delicate balance between labels and flavor to successfully design and market sugar‐reduced products. Further analysis, PLS‐multigroup analysis revealed significant difference in the impact of subjective norms on attitude between participants from different countries. Singaporeans placed stronger value on others’ approval for consuming less sugar‐sweetened yogurt, whereas French and New Zealand participants had a more neutral stance. This study's novelty lies in its comprehensive exploration of sociocultural factors, integration of TPB with consumer perception constructs, and tailoring of analysis to each country's cultural context, thereby enhancing our understanding of multicultural sugar consumption patterns.

Fish spawning phenology is a major concern for conservation and fisheries management. New intensive data sources such as GPS-based tracking data or high resolution catch declaration data are progressively becoming available in the field of marine ecology. These benefit from high spatio-temporal resolution and open new research avenues to investigate inter-annual and seasonal variability of phenology. In this paper, we illustrate how catch declarations modeling coupled with spatio-temporal dimension reduction methods known as Empirical Orthogonal Functions (EOF) can be used to synthetize spatio-temporal signals in fish distribution; Specifically, we address the following questions; (1) can we identify spatio-seasonal patterns that can be interpreted in terms of seasonal migration between essential habitats? (2) can we identify changes in the phenology? (3) are those changes related to environmental drivers? The analysis is illustrated through the analysis of the reproduction phenology on three key commercial species in the Bay of Biscay (Hake, Sole and Sea Bass). The EOF analysis on these species emphasizes strong seasonal spatio-temporal patterns that correspond to migration patterns between feeding areas and reproduction areas. Based on this methodology, we identify seasonal variations in the timing of the reproduction and we relate these to Sea Surface Temperature, a key driver of fish reproduction.

The International Council for the Exploration of the Sea (ICES) typically provides advice on fishing opportunities on a stock-by-stock basis. Nevertheless, levels of total allowable catch (TAC) are sometimes set for a collection of stocks and species (i.e. a common TAC). An explicit expectation of these is that landings will scale with ICES advice, especially when ICES advice is used to calculate the common TAC. This expectation is tested for skates and rays in the Northeast Atlantic, spanning 26 stocks, 8 species, and 3 ecoregions. Using ICES landings and ICES advice data from 2016 to 2022, we show that landings of several stocks and species have overshot their respective ICES advice, whereas others have undershot. Specifically, some stocks of blonde ray (Raja brachyura) in North Sea and Celtic Seas ecoregions are being landed at a rate that often exceeds double its ICES advice. By collating species based on their ICES assessment category and life-history traits, we find that those considered data-poor and potentially most vulnerable to fishing are consistently landed at higher-than-expected rates in the Celtic Seas. This study questions the appropriateness of a common TAC for skates and rays and calls for shifts towards the use of single-stock catch allocations and the application of advanced stock assessment methodologies.

Fishers have intensively used drifting fish aggregating devices (DFADs) over the last three decades to facilitate their catch of tropical tunas. DFADs increase purse‐seine efficiency, potentially increasing tuna fishing mortality. They could also have impacts on tuna natural mortality and reproductive potential, and assessing the consequences of their presence at sea on tuna populations is a challenge. The use of DFADs results in a major increase in the number of floating objects, which are spatially heterogeneous at sea. To date, no converging scientific results exist regarding the effects of DFADs on the large‐scale movements and behaviour of tuna, mainly due to the difficulty of disentangling the respective roles of DFADs and environmental factors. Some biological indices show that tuna condition is lower when associated to a floating object than in a free‐swimming school. However, it is not clear whether this is the cause or the consequence of the association nor if it has long‐term effects on individuals' fitness. Further scientific progress requires (i) the collection of time series of indicators to monitor habitat change, individual behaviour, individual fitness, and population dynamics and (ii) experimental studies to identify the underlying behavioural and biological processes involved in associative behaviour. The extent of the modification of the surface habitat by the massive deployment of DFADs and the current uncertainty of the possible long‐term consequences on the individual fitness and dynamics of tuna populations argue for the need for increased awareness of this issue by Regional Fisheries Management Organisations regulating tuna fishing.

Copper-based plant protection products (PPPs) are widely used in both conventional and organic farming, and to a lesser extent for non-agricultural maintenance of gardens, greenspaces, and infrastructures. The use of copper PPPs adds to environmental contamination by this trace element. This paper aims to review the contribution of these PPPs to the contamination of soils and waters by copper in the context of France (which can be extrapolated to most of the European countries), and the resulting impacts on terrestrial and aquatic biodiversity, as well as on ecosystem functions. It was produced in the framework of a collective scientific assessment on the impacts of PPPs on biodiversity and ecosystem services in France. Current science shows that copper, which persists in soils, can partially transfer to adjacent aquatic environments (surface water and sediment) and ultimately to the marine environment. This widespread contamination impacts biodiversity and ecosystem functions, chiefly through its effects on phototrophic and heterotrophic microbial communities, and terrestrial and aquatic invertebrates. Its effects on other biological groups and biotic interactions remain relatively under-documented.

Introduction Simple sequence repeats (SSR), also known as microsatellites, are crucial molecular markers in both animals and plants. Despite extensive previous research on SSRs, the development of microsatellite markers in Brassica crops remains limited and inefficient. Methods Krait software was used to identify microsatellites by genome-wide and marker development based on three recently sequenced basic species of Brassica crops in the triangle of U (Brassica rapa, B. nigra and B. oleracea), as well as three allotetraploids (B. juncea, B. napus and B. carinata) using public databases. Subsequently, the primers and the characteristics of microsatellites for most of them were accordingly designed on each chromosome of each of the six Brassica species, and their physical locations were identified,and the cross-transferability of primers have been carried out. In addition, a B-genome specific SSR marker was screened out. Results A total of 79341, 92089, 125443, 173964, 173604, and 222160 SSR loci have been identified from the whole genome sequences of Brassica crops within the triangle of U crops, B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. napus (AACC), B. juncea (AABB) and B. carinata (BBCC), respectively. Comparing the number distribution of the three allotetraploid SSR loci in the three subgenomes AA, BB and CC, results indicate that the allotetraploid species have significant reduction in the number of SSR loci in the genome compared with their basic diploid counterparts. Moreover, we compared the basic species with their corresponding varieties, and found that the microsatellite characters between the allotetraploids and their corresponding basic species were very similar or almost identical. Subsequently, each of the 40 SSR primers was employed to investigate the polymorphism potential of B. rapa (85.27%), B. nigra (81.33%) and B. oleracea (73.45%), and B. rapa was found to have a higher cross-transfer rate among the basic species in the triangle of U. Meanwhile, a B-genome specific SSR marker, BniSSR23228 possessing the (AAGGA)3 sequence characteristics was obtained, and it located in chromosome B3 with a total length of 97 bp. Discussion In this study, results suggest that the pattern of distribution may be highly conserved during the differentiation of basic Brassica species and their allotetraploid counterparts. Our data indicated that the allotetraploidization process resulted in a significant reduction in SSR loci in the three subgenomes AA, BB and CC. The reasons may be partial gene dominated chromosomal homologous recombination and rearrangement during the evolution of basic diploid species into allotetraploids. This study provides a basis for future genomics and genetic research on the relatedness of Brassica species.

Phytopathogens are a threat for global food production and security. Emergence or re‐emergence of plant pathogens is highly dependent on the environmental conditions affecting pathogen spread and survival. Under climate change, a geographic expansion of pathogen distribution poleward has been observed, potentially resulting in disease outbreaks on crops and wild plants. Therefore, estimating the adaptive potential of plants to novel epidemics and describing the underlying genetic architecture is a primary need to propose agricultural management strategies reducing pathogen outbreaks and to breed novel plant cultivars adapted to pathogens that might spread under climate change. To address this challenge, we inoculated Pseudomonas syringae strains isolated from Arabidopsis thaliana populations from south‐west of France on the highly genetically polymorphic TOU‐A A . thaliana population from north‐east France. While no adaptive potential was identified in response to most P . syringae strains, the TOU‐A population displayed a variable disease response to the JACO‐CL strain belonging to the P . syringae phylogroup 7 (PG7). This strain carried a reduced type III secretion system (T3SS) characteristic of the PG7 as well as flexible genomic traits and potential novel effectors. Genome‐wide association mapping on 192 TOU‐A accessions revealed a polygenic architecture of disease response to JACO‐CL. The main quantitative trait locus (QTL) region encompasses two R genes and the AT5G18310 gene encoding ubiquitin hydrolase, a target of the AvrRpt2 P . syringae effector. Altogether, our results pave the way for a better understanding of the genetic and molecular basis of the adaptive potential in an ecologically relevant A . thaliana – P . syringae pathosystem.

Live weight (LW) is a key and conventional indicator for monitoring and assessing overall animal performance and welfare, representing the progress through different physiological stages, while providing close indication of individual physical and health status. Measuring LW in practice is still, however, quite rare and infrequent under commercial sheep farming conditions, mainly because sessions are time-consuming, stressful either for the operator or the animals. A Walk-over-Weighing (WoW) system was tested in this experiment lasting 14 weeks (i.e. 3 weeks for acclimation and adaptation and 11 weeks for data collection). We validated its use for routine and frequent monitoring of growth rate in postweaned Merinos d’Arles ewe lambs (n = 100), reared under Mediterranean grazing conditions. The necessity for an initial adaptation period of the animals was confirmed. Also, the importance of conducting an effective data cleaning procedure of the raw database automatically collected by the WoW was corroborated. Adaptation of naive ewe lambs enabled the required voluntary passages across the weighing platform and a high volume of individual and daily data after 2–3 weeks. Close monitoring of individual growth was then possible after performing sound data cleaning. A good agreement was demonstrated between WoW LW and a reference LW value (measured with a standard static scale). At the individual level, even with the lowest number of LW values collected with WoW, it was possible to monitor variations in LW at daily intervals. The establishment of an early warning system to help farmer decision-making could therefore be possible. Our results show interesting prospects for more accurate and frequent monitoring of LW in grazing sheep without human intervention, compared to what is currently carried out on commercial farms.

Eelgrass supports diverse benthic communities that ensure a variety of ecosystem functions. To better understand the ecological processes that shape community composition in eelgrass at local and regional scales, taxonomic and functional α-and β-diversity were quantified for communities inhabiting five meadows in France. The extent to which environmental factors affected local and regional benthic communities was quantified by considering their direct and indirect effects (through morphological traits of eelgrass) using piecewise structural equation modeling (pSEM). Communities supported by eelgrass had higher species abundances, as well as taxo-nomic and functional diversity compared to nearby bare sediments. No significant differences were found between communities from the center relative to the edges of meadows, indicating that both habitats provide similar benefits to biodiversity. The presence of a few abundant species and traits suggests moderate levels of habitat filtering and close associations of certain species with eelgrass. Nevertheless, high turnover of a large number of rare species and traits was observed among meadows , resulting in meadows being characterized by their own distinct communities. High turnover indicates that much of the community is not specific to eelgrass, but rather reflects local species pools. pSEM showed that spatial variation in community composition (β-diversity) was primarily affected by environmental conditions, with temperature, current velocity, and tidal amplitude being the most significant explanatory variables. Local richness and abundance (α-diversity) were affected by both environment and morphological traits. Importantly, morphological traits of Zostera marina were also influenced by environmental conditions, revealing cascading effects of the environment on assemblages. In sum, the environment exerted large effects on community structure at both regional and local scales, while plant traits were only pertinent in explaining local diversity. This complex interplay of processes acting at multiple scales with indirect effects should be accounted for in conservation efforts that target the protection of biodiversity.

The growing incidence of human diseases involving inflammation and increased gut permeability makes the quest for protective functional foods more crucial than ever. Propionibacterium freudenreichii (Pf) is a beneficial bacterium used in the dairy and probiotic industries. Selected strains exert anti-inflammatory effects, and the present work addresses whether the Pf CIRM-BIA129, consumed daily in a preventive way, could protect mice from acute colitis induced by dextran sodium sulfate (DSS), and more precisely whether it could protect from intestinal epithelial breakdown induced by inflammation. Pf CIRM-BIA129 mitigated colitis severity and inhibited DSS-induced permeability. It limited crypt length reduction and promoted the expression of Zonula Occludens-1 (ZO-1), without reducing interleukin-1beta mRNA ( il-1ß) expression. In vitro, Pf CIRM-BIA129 prevented the disruption of a Caco-2 monolayer induced by pro-inflammatory cytokines. It increased transepithelial electrical resistance (TEER) and inhibited permeability induced by inflammation, along with an increased ZO-1 expression. Extracellular vesicles (EVs) from Pf CIRM-BIA129, carrying the surface layer protein (SlpB), reproduced the protective effect of Pf CIRM-BIA129. A mutant strain deleted for slpB (ΔslpB), or EVs from this mutant strain, had lost their protective effects, and worsened both DSS-induced colitis and inflammation in vivo. These results shown that P. freudenreichii CIRM-BIA129 daily consumption has the potential to greatly alleviate colitis symptoms and, particularly, to counter intestinal epithelial permeability induced by inflammation by restoring ZO-1 expression through mechanisms involving S-layer protein B. They open new avenues for the use of probiotic dairy propionibacteria and/or postbiotic fractions thereof, in the context of gut permeability.

Bread wheat can be infected and/or contaminated by several genera of mycotoxin producing fungi. In the European Union, several mycotoxins are subject to defined limits for human consumption. Speculation has arisen about the potential higher contamination level of mycotoxins produced by Fusarium species in organic compared to conventional production systems. So far, many studies have focused on the level of mycotoxins, highlighting comparable levels in organic and conventional farming. In this long-term study, we monitored, each year over a 13-year period in several sites in France and for a set of bread wheat genotypes, the incidence of four fungal genera on bread wheat grains from both conventional low input and organic farming. During this long period of monitoring, we used the same morphological characterization of fungal colonies. The results obtained highlighted two general trends. First, the incidence of the genus Fusarium in grains was generally lower than or equal to 1% in more than 60% of ‘year × site’ combinations, both in low-input and organic farming conditions. In contrast, the genus Alternaria was dominant in the vast majority of combinations. Second, the main explanatory factors of the incidence of fungus on grains, independently of the genus and the farming conditions, were the year and the ‘year × site’ interaction, suggesting the dominant influence of the environmental conditions of the year and the site on the relative development of the fungal genera in/on grains. According to these results, organic or low-input production of bread wheat does not represent a significant risk for the development of Fusarium head blight in France.

Climate variability and increasing drought events have become significant concerns in recent years. However, there is limited published research on body weight (BW) change of dairy heifers with different genetic merit when grazing on drought impacted pastures in southern Australia. Achieving target body weight (BW) is vital for dairy heifers, especially during critical stages like mating and calving. This study aimed to assess dry matter (DM) intake, BW change, urinary nitrogen excretion, and grazing behaviours of high vs. low genetic dairy heifers grazing pasture during a 43-day experimental period in a drought season. Forty-eight Holstein Friesian heifers grazed on ryegrass-dominant pasture and were divided into two groups based on their high and low Balanced Performance Index (HBPI and LBPI, respectively). Each group was further stratified into six plots, with similar BW, resulting in four heifers per replication group. Data from the five measurement days were averaged for individual cows to analyse the dry matter intake, nitrogen intake and nitrogen excretion. The statistical model included the treatment effect of BPI (H and L) and means were analysed using ANOVA. The pasture quality was poor, with metabolizable energy 9.3 MJ/Kg DM and crude protein 5.9% on a DM basis. Nitrogen intake and urinary nitrogen excretion were significantly higher (p < 0.05) in HBPI compared to the LBPI. However, despite these differences, the study did not find any advantages of having HBPI heifer grazing on low quality forage in terms of BW performance.

Environmental DNA (eDNA) metabarcoding is a method to detect taxa from environmental samples. It is increasingly used for marine biodiversity surveys. As it only requires water collection, eDNA metabarcoding is less invasive than scientific trawling and might be more cost effective. Here, we analysed data from both sampling methods applied in the same scientific survey targeting Northeast Atlantic fish in the Bay of Biscay. We compared the methods regarding the distribution of taxonomic, phylogenetic, and functional diversity. We found that eDNA captured more taxonomic and phylogenetic richness than bottom trawling and more functional richness at the local scale. eDNA was less selective than trawling and detected species in local communities spanning larger phylogenetic and functional breadths, especially as it detected large pelagic species that escaped the trawl, even though trawling detected more flat fish. eDNA indicated differences in fish community composition that were comparable to those based on trawling. However, consistency between abundance estimates provided by eDNA metabarcoding and trawl catches was low, even after accounting for allometric scaling in eDNA production. We conclude that eDNA metabarcoding is a promising method that can complement scientific trawling for multi-component biodiversity monitoring based on presence/absence, but not yet for abundance.

The study of macroinvertebrates using computer vision is in its infancy and still faces multiple challenges including destructive sampling, low signal-to-noise ratios, and the complexity to choose a model algorithm among multiple existing ones. In order to deal with those challenges, we propose here a new framework, dubbed 'MacroNet,’ for the monitoring, i.e., detection and identification at the morphospecies level, of live aquatic macroinvertebrates. This framework is based on an enhanced RetinaNet model. Pre-processing steps are suggested to enhance the characterization propriety of the original algorithm. The images are split into fixed-size tiles to better detect and identify small macroinvertebrates. The tiles are then fed as an input to the model, and the resulting bounding box is assembled. We have optimized the anchor boxes generation process for high detection performance using the k-medoid algorithm. In order to enhance the localization accuracy of the original RetinaNet model, the complete intersection over union loss has been integrated as a regression loss to replace the standard loss (a smooth l1 norm). Experimental results show that MacroNet outperforms the original RetinaNet model on our database and can achieve on average 74.93% average precision (AP), depending on the taxon identity. In our database, taxa were identified at various taxonomic levels, from species to order. Overall, the proposed framework offers promising results for the non-lethal and cost-efficient monitoring of live freshwater macroinvertebrates.

There is growing interest in using the ecosystem services framework for environmental risk assessments of chemicals, including plant protection products (PPPs). Although this topic is increasingly discussed in the recent scientific literature, there is still a substantial gap between most ecotoxicological studies and a solid evaluation of potential ecotoxicological consequences on ecosystem services. This was recently highlighted by a collective scientific assessment (CSA) performed by 46 scientific experts who analyzed the international science on the impacts of PPPs on biodiversity, ecosystem functions, and ecosystem services. Here, we first point out the main obstacles to better linking knowledge on the ecotoxicological effects of PPPs on biodiversity and ecological processes with ecosystem functions and services. Then, we go on to propose and discuss possible pathways for related improvements. We describe the main processes governing the relationships between biodiversity, ecological processes, and ecosystem functions in response to effects of PPP, and we define categories of ecosystem functions that could be directly linked with the ecological processes used as functional endpoints in investigations on the ecotoxicology of PPPs. We then explore perceptions on the possible links between these categories of ecosystem functions and ecosystem services among a sub-panel of the scientific experts from various fields of environmental science. We find that these direct and indirect linkages still need clarification. This paper, which reflects the difficulties faced by the multidisciplinary group of researchers involved in the CSA, suggests that the current gap between most ecotoxicological studies and a solid potential evaluation of ecotoxicological consequences on ecosystem services could be partially addressed if concepts and definitions related to ecological processes, ecosystem functions, and ecosystem services were more widely accepted and shared within the ecotoxicology community. Narrowing this gap would help harmonize and extend the science that informs decision-making and policy-making, and ultimately help to better address the trade-off between social benefits and environmental losses caused by the use of PPPs.