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Étangs piscicoles et services écosystémiques : Relations entre pratiques de gestion, maintien de la biodiversité et stockage de carbone
No full textEurope is home to a large number of “pond landscapes”, many with origins dating back to the Middle Ages and a historic vocation for fish farming. Despite their man-made nature, these environments are known for their capacity to harbor significant biodiversity, with rare, even endemic or endangered species. With the abandonment of fish farming, combined with other threats such as climate change, a significant number of these ponds have disappeared in recent decades. Until recently, and despite the important role they can play, these small water bodies have been neglected in research, but also in public policies.In this PhD thesis work, we looked at the effects of different fish farming management practices on ecosystem services provided by fish ponds. First, we analyzed the practice of drying-out ponds and its impact on both biodiversity and fish yields. Secondly, we explored the impacts of different fish density management on macrophyte community characteristics. And finally, we studied fish ponds as potential carbon sinks or sources, and the effects of management practices on these carbon balances.To contribute to the scientific knowledge on these topics, we capitalized on historical data collected in the Dombes region (Ain, France) since 2007, but also on data collected as part of the European PONDERFUL project, between 2021 and 2022, in Dombes and Midden-Limburg (Belgium). We analyzed data on water and sediment physico-chemistry, as well as biodiversity (macrophytes, phytoplankton and macroinvertebrates), carbon storage and emissions, and fish farming management practices (time since the last dry year, fish stocking, fertilization).Our results show that drying-out is a major agroecological practice for extensive pond fish farming. This voluntary draining facilitates the recolonization of macrophytes and their diversity when the pond is re-watered. The second year in water is characterized by an "unstable state" of equilibrium between the two primary producers. This state appears to be favorable to biodiversity, production and carbon storage. Intensification of production, through increased fish densities, nevertheless has negative effects on macrophyte species richness. It also impacts community structure. Ponds used for fish farming have subsets of species that nest in the richer communities of ponds managed without fish. We were also able to show a very high degree of variability in the carbon balances of 20 fish ponds. On average, monitored ponds appear to be carbon sinks, with around 4 tonnes of CO2 equivalent stored per hectare over 6 months. The dry year, on the other hand, is characterized by high greenhouse gas emissions.All these elements confirm that fish ponds, combined with extensive practices, can provide numerous ecosystem services. Fish production is not incompatible with biodiversity conservation. The sustainability of these environments in European landscapes, and of the ecosystem services they provide, depends on the maintenance of these management practices. Even if it seems possible to reconcile provisioning and support services, in the future it will be necessary to establish a hierarchy of desired services, particularly in view of the inverse effects that certain management practices may have.L'Europe renferme de nombreux paysages d'étangs, pour beaucoup avec une origine pouvant remonter au Moyen-âge et une vocation historique de production piscicole. Ces milieux, malgré qu'ils soient anthropisés, sont connus pour leur capacité à présenter une biodiversité importante, avec des espèces rares, voir endémiques ou menacées. Avec l'abandon de la pisciculture, combiné à d'autres menaces comme le changement climatique, un nombre significatif de ces étangs ont disparus au cours des dernières décennies. Jusqu'à récemment, et ce malgré le rôle important qu'ils peuvent jouer, ces petits plans d'eau ont de plus été négligés en Recherche, mais également par les politiques publiques.Dans ce travail de thèse nous nous sommes intéressés aux effets de différentes pratiques de gestion piscicoles sur certains services écosystémiques rendus par les étangs piscicoles. Dans un premier temps, nous avons analysé la pratique de l'assec et ses impacts à la fois sur la biodiversité et sur la productivité en poissons. Dans un second temps, nous avons exploré les impacts de différentes gestions de la densité piscicole sur les caractéristiques des communautés de macrophytes. Et enfin, nous avons étudié les étangs piscicoles comme potentiels puits ou sources de carbone, et les effets des pratiques de gestion sur ces bilans carbone.Pour compléter les connaissances scientifiques sur ces thématiques, nous avons capitalisé sur des données historiques collectées en Dombes (Ain, France) depuis 2007, mais également sur des données collectées dans le cadre du projet européen PONDERFUL, entre 2021 et 2022, en Dombes et dans le Midden-Limburg (Belgique). Nous avons analysé à la fois des données sur la physico-chimie de l'eau et des sédiments, ainsi que des données de biodiversité (macrophytes, phytoplancton et macroinvertébrés), de stockage et d'émissions de carbone, ainsi que sur les pratiques de gestion piscicoles (distance au dernier assec, empoissonnage, fertilisation).Nos résultats démontrent que l'assec constitue une pratique agroécologique majeure pour la pisciculture extensive en étang. Cet assèchement volontaire favorise la recolonisation des macrophytes ainsi que leur diversité lors de la remise en eau. La deuxième année en eau est caractérisée par un “état instable” d'équilibre entre les deux producteurs primaires. Cet état apparait comme étant favorable à la fois à la biodiversité, à la production mais également au stockage du carbone. L'intensification de la production, à travers une augmentation des densités piscicoles, a néanmoins des effets négatifs sur la richesse spécifique des macrophytes. Elle impacte également la structure des communautés. Les étangs piscicoles possèdent des sous-ensembles d'espèces, nichés dans les communautés plus riches des étangs gérés sans poissons. Nous avons également pu montrer une très forte variabilité sur les bilans carbone réalisés sur 20 étangs piscicoles. En moyenne, les étangs monitorés apparaissent comme étant plutôt des puits de carbone, à hauteur d'environ 4 tonnes de CO2 équivalent stocké par hectare et sur 6 mois. La phase d'assec est quant à elle caractérisée par des émissions de gaz à effet de serre importantes.Tous ces éléments permettent de confirmer que les étangs piscicoles, associés à des pratiques extensives, peuvent fournir de nombreux services écosystémiques. La production piscicole n'est pas antinomique de la conservation de la biodiversité. La pérennité de ces milieux dans les paysages européens, et des services fournis, passe par le maintien de ces pratiques de gestion. Même si concilier les services d'approvisionnement et de support semble possible, à l'avenir, une hiérarchisation des services souhaités sera nécessaire, notamment au regard des effets inverses que peuvent avoir certaines pratiques de gestion
Quels sont les facteurs qui influencent l'attitude des consommateurs à l'égard des protéines alternatives ?
No full textInternational audienceAchieving the sustainability of protein is central to creating a sustainable food system. Current meat consumption patterns require a paradigm shift, as the status quo is unsustainable. However, at present, consumer participation in this shift is limited necessitating a change in consumer behaviour. This review seeks to understand consumer willingness to consume alternative proteins (cultured meat, edible insects, plant and fermentation-based proteins) and the factors influencing their decisions, considering variations across protein categories and cultural backgrounds. Understanding these factors is vital for designing interventions that effectively enhance acceptance levels. Consumer behaviour is complex, influenced by a spectrum of personal and societal factors, which must be interpreted within the specific context of the target society or demographic segment
Determining the footprint of breeding in the seed microbiome of a perennial cereal
No full textInternational audienceBackground Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays. ResultsIntermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria , Alphaproteobacteria , and Bacilli , which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia , and Pseudomonas , was transmitted to the next plant generation or shared with offspring seeds. ConclusionOverall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs
Teaching methods and tips for embedded food systems education
No full textInternational audienceThis booklet provides tested and successfully implemented innovative teaching concepts and practices and teaching tips for embedded food systems education. They were developed based on the input collected from workshops with teachers in different European universities. The examples and tips include the description of the teaching practices or concept regarding skills and resources needed, methods to be used, suitability for study programme level(s), needed prerequisites of students, and obstacles to overcome if identified. Target groups are lecturers and teacher in higher education or peoples working in vocational training. We hope to provide a useful guide who to enrich teaching in embedded food systems. For more details and practical information, the authors of the different teaching tips can be contacted for sharing about the teaching experience
Impacts environnementaux, sociaux et éthiques des aliments à base de cellules cultivées Incertitudes et zones d’ombre autour de la « viande de culture »
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Development of a regionalized dynamic weighting method for the environmental impact of alternative protein sources
No full textInternational audienceAccurate environmental analysis is central to addressing food product impacts, yet uncertainty shrouds the effectiveness of life cycle assessment (LCA) weighting methods, particularly for alternative protein foods and different countries. Our approach characterizes environmental impact weighting based on total or specific production impacts at the country level, facilitating relevance assessment. We have developed an innovated methodology to calculate weights for alternative foods such as crickets, mealworms, black soldier flies, cultured meat, Chlorella , and Spirulina . This method integrates their country-level eco-potential linked to environmental impacts, and addresses challenges in existing methodologies-policy changes, contextual adaptation, method specificity, intangible values. Relative impact weights, normalized by arable land and population, cover greenhouse gas emissions, land use, water use and energy use. Eco-potential points for alternative protein sources are derived by dividing their impact values by the relative country-level weights. In addition, eco-potential points for conventional protein sources are calculated for comparison, highlighting disparities. The results show a dynamic eco-potential influenced by evolving country-level per capita impacts that influence food product impacts. Comparison of literature based LCAs with our weighted country-level impacts highlights an alignment between absolute emissions and relative impact weightings in certain cases. Moreover, we have developed a parallel methodology to calculate eco-potential points for selected alternative food proteins based on protein supply in countries. This calculation is based on 17 years of data and multiplies the protein supply by the average environmental impact of selected sources (GHGE, water, land and energy use). This results in country-level weighted impacts (CWI), or eco-potential points that are aligned with protein supply. Combining the CWI from the four indicators gives the combined eco-potential values for selected alternative proteins. The comparison of the product’s CWIs for GWP, WU, EU and LU showed that certain impact categories with higher CWI or eco-potential points can contribute to the higher combined eco-potential point. The eco-potential points of different impact categories also varied between countries
Generation of Systemic Chimeras via Rabbit Induced Pluripotent Stem Cells Reprogrammed with KLF2, ERAS, and PRMT6
No full textSummary Little is known about the molecular underpinnings of pluripotent stem cells’ (PSCs) ability to colonize the epiblast of preimplantation embryos and generate chimeras. In our study, using rabbit PSCs as a model system, we conducted unbiased screening of a cDNA library that encodes a panel of 36 pluripotency factors. From this screening, we identified KLF2, ERAS and PRMT6, whose overexpression confers the ability for self-renewal in a KOSR/FGF2-free culture medium supplemented with LIF, activin A, PKC and WNT inhibitors. The reprogrammed cells acquired transcriptomic and epigenetic features of naive pluripotency, including the reactivation of the 2 nd X-chromosome. Leveraging these PSC lines, we determined the transcriptomic signature of embryonic colonization-competence, demonstrating transcriptional repression of genes involved in MAPK, WNT, HIPPO, and EPH signaling pathways, alongside the activation of genes involved in amino-acid metabolism, NF-kB signaling, and p53 pathway. Remarkably, a subset of reprogrammed cells, expressing CD75 at a high level, gained the ability to produce chimeric fetuses with a high contribution from PSCs in all lineages
H3K9 post-translational modifications regulate epiblast/primitive endoderm specification in rabbit blastocysts
No full textInternational audiencePost-translational modifications of histone H3 on lysine 9, specifically acetylation (H3K9ac) and tri-methylation (H3K9me3), play a critical role in regulating chromatin accessibility. However, the role of these modifications in lineage segregation in the mammalian blastocyst remains poorly understood. We demonstrate that di- and trimethylation marks, H3K9me2 and H3K9me3, decrease during cavitation and expansion of the rabbit blastocyst. Notably, H3K9me3 levels are particularly low in inner cell mass cells at the onset of blastocyst formation but increase again just before gastrulation. Conversely, H3K9ac is abundant in early blastocyst stages but decreases during the transition from the inner cell mass to the epiblast. These distinct distribution patterns correlate with high expression levels of methyltransferases (EHMT1, EHMT2, SETDB1) and deacetylases (HDAC1, HDAC2, HDAC5) in expanding blastocysts. Functionally, inhibiting H3K9me2/3 through an EHMT1/2 inhibitor disrupts primitive endoderm segregation, whereas enhancing histone acetylation (including H3K9ac) using a class I HDAC inhibitor promotes epiblast expansion at the expense of the primitive endoderm. These modifications impact the expression of genes associated with pluripotency and lineage determination, underscoring the importance of H3K9 modifications in embryonic cell fate decisions
The microbiome of a perennial cereal differs from annual winter wheat only in the root endosphere
No full textInternational audienceThe intensification of agriculture has led to environmental degradation, including the loss of biodiversity. This has prompted interest in perennial grain cropping systems to address and mitigate some of these negative impacts. In order to determine if perennial grain cultivation promotes a higher microbial diversity, we assessed the endophytic microbiota of a perennial grain crop (intermediate wheatgrass, Thinopyrum intermedium L.) in comparison to its annual counterpart, wheat (Triticum aestivum L.). The study covered three sampling sites in a pan-European gradient (Sweden, Belgium, France), two plant genotypes, three plant compartments (roots, stems, and leaves) and two sampling timepoints. We observed that the host genotype effect was mainly evident in the belowground compartment, and only to a lesser extent in the aboveground tissues, with a similar pattern at all three sampling sites. Moreover, intermediate wheatgrass roots harboured a different bacterial community composition and higher diversity and richness compared to their annual counterparts. The root bacterial diversity was influenced by several soil chemical parameters, such as the carbon:nitrogen ratio, but also soil microbial parameters, such as soil respiration and dehydrogenase activity.Consistent findings across time and space suggest stable mechanisms in microbiota assembly associated with perennial grain cropping, underscoring their potential role in supporting biodiversity within sustainable agricultural systems
