The PHYTOFUEL project aims at promoting valorisation processes of the plant biomasses collected at polluted sites managed by eco-innovative phytotechnologies. It will draw on the phytomanagement field trials developed at the partners institutes that are in progress in France, UK, Italy, Poland and Belgium. The valuation considered in PHYTOFUEL is the exploitation of an annual resource, present in large amounts on plots of phytomanagement and whose valorization potential is little mastered. However, as the woody biomass needs to be also valorized, the impact of biomass harvest on the environment needs to be investigated. PHYTOFUEL responds to the constraint of scarcity of resources by proposing a new source of biofuels from marginal surfaces, constituting a complementary resource of interest for the French plant-based biofuels industries. The solutions developed during the project will have both applicatory and innovative character. It involves introduction of industrial crops selection and management practices on the marginal lands, which are not currently used for production purposes. These solutions will also take into account the post-harvesting operations required to convert the industrial crops into bio-based products (storage and pre-treatment at dispersed geographic locations) and the mass losses related to these operations. The proposed solutions are also the basis for the creation of the resource base for the decentralized and prosumer energetics, which will not compete with food and forage production. The PHYTOFUEL multidisciplinary consortium will consists of expertise from 9-12 partners from at least 6 EU-countries in biology, ecology, economics, forestry, landscape modeling, stakeholder engagement, management and communication. PHYTOFUEL aims at deepening and extending the level of biological material processing, leading to the emergence of new products and new markets, based on academic research. The used materials in PHYTOFUEL cover trees, crops and plantations, and subsequent generations of waste and residues from primary and secondary processes. WP1 (biomass production) partners will ensure full availability of biomasses from marginal lands and their procurement to WP2 (Pre-treatment) and WP3 (innovative biofuel production) partners. These materials will be used in the production of novel, more complete, environmentally-safe biofuels, to be implemented and used in industrial processes. PHYTOFUEL makes use of biomass obtained from renewable biological resources of plant origin, which will be processed in a thermal or chemical manner. PHYTOFUEL seeks for a rational management of available resources, widening the use of renewable energy. It creates conditions for the bioeconomy development in rural and suburban areas. As a synthesis the WP4 "Sustainability" partners will benefit from environmental, economic and social data obtained from WP1-WP3, that will strengthen competitiveness of the European countries and impact the bioeconomy sector, which is one of the challenge of the European Commission, as stated in its recent 2018 communication (COM(2018) 673 final).

Pressures on ecosystems have reached such an unprecedented rate that many ecosystems have been irreversibly damaged and that many animal populations have declined since the 1950s. Although human pressures on ecosystems have been identified, the mechanisms of biodiversity decline (i.e. relative importance of each pressure in the decline, temporality of events…) are poorly known. One reason is the lack of long-term data on population monitoring to study the impact of human pressures from past to present on animal populations and communities. REPAST proposes to use a retrospective multidisciplinary approach to study the impact of environmental pressures on the decline of bats through the study of guano cores collected in bat roosts. In caves or buildings, bat droppings (guano) fall to the ground and accumulate chronologically until reaching substantial thickness over time, and constitute historical archives containing temporally situated information about bat populations, environmental context, and human pressures. REPAST will test the general hypothesis that one or several stressors (habitat and climate changes, exposure to pollutants) will be associated to temporal variations of biological responses (pathogen prevalence, shift in diet, genetic diversity, bat richness). On 10 cores already sampled in bat colonies located in Burgundy Franche-Comté region, a robust chronology based on proxies used for paleoecological studies (14C, 137Cs, 210Pb concentrations) will be performed. The feasibility study done within the last 2 years shows that the cores date back from at least the 1950s, one being much older. Temporal variations of some anthropogenic pressures will also be reconstructed. Pollens will be studied on the cores to reconstruct the foraging areas (habitat) characteristics. The concentrations of some pollutants (~20 metals, 17 persistent organic pollutants including DDT and PCBs, and neonicotinoids) will be measured along the cores. Climate changes will be studied using meteorological data from 76 stations active since the 1940s across the region. Guano cores will also provide biological descriptors of bat colonies, which will be related to human pressures indices. The richness and composition of bat colonies, their diet using a metabarcoding approach, their exposure to eukaryotic pathogens, and their genetic diversity (using guano and Museum specimens already collected) will be reconstructed over time. Finally, historical archives and current counts from NGOs working in bat conservation will allow reconstructing the pattern of demographic trends and extinction risk of bat species since the 1940s. As the various anthropogenic pressures may act directly or indirectly on the biological responses, the complex set of variables measured in REPAST will be analysed using the structural equation modelling (SEM) framework. SEM’s causal diagrams will be constructed, based on explicit causal assumptions/hypotheses related to the mechanisms supposed to be involved between one or several pressures to one or several biological responses. The nature and the pattern of associations (what stressor(s) is(are) linked to what response(s) and how (from long and continuous associations to sudden shifts)) will improve our understanding of the mechanism(s) of bat decline. NGOs and stakeholders of bat roosts will be fully involved in the project and have already took part in the sampling process and share their data (e.g. bat counts). Apart from the classical scientific exploitation of the results (international meetings and articles), the large public will also be informed and invited to participate (e.g. in indicating colonies with guano accumulation unknown from NGOs) through a specific website and conferences. REPAST will allow gaining insights in the understanding of the mechanisms underlying the decline and the temporality of bat decline (and resilience) and, as some of the stressors still occur, may allow to predict and prevent new declines.

Dark septate endophytes (DSEs) are a polyphyletic assemblage of Ascomycetes that colonize plant roots and are originally characterized by the accumulation of high concentrations of melanin in their hyphae. It has been hypothesized that this trait could be advantageous to both partners in plant-DSE associations in response to a variety of biotic and abiotic stresses. However, evidence for the contribution of high melanization of DSEs to stress mitigation is still lacking. Secondly, we hypothesize that melanin plays a role in root penetration by hyphae and subsequent colonization, because melanization is analogously required for virulent fungal pathogens to successfully infect animal and plant tissues. In this French-German collaborative project, we aim to better understand the melanization process in the DSE model Leptodontidium sp., including the study of regulatory mechanisms modulating melanization. Moreover, complementary genetic, pharmacological, physico-chemical, physiological and omics approaches contributed by the Franco-German partners will be used to decipher the role that melanin might play in the competitiveness of Leptodontidium sp. for plant colonization and in the high tolerance of Leptodontidium sp. to a range of abiotic and biotic stresses. The consortium is composed of researchers from four laboratories having complementary expertise in microbiology, plant-microbe interactions under stress conditions, fungal ecology, multi-omics analyses and bioinformatics. Particular techniques and topics are genetic transformation of DSEs and atomic force microscopy (Université of Lorraine - P1), miRNA analyses and metal stress (Université de Bourgogne Franche-Comté - P2), epigenetics and RNAseq analysis (Friedrich Schiller University Jena - P3), and interactions between fungi and mycoparasites (Wismar University of Applied Sciences - P4). Therefore, answering the questions and testing the hypotheses concerning the role of melanin for DSEs and for DSE-plant interactions can only be achieved by the combined activities of the French-German team. Understanding the mechanisms that mitigate environmental stress for DSEs and for plants colonized by DSEs could contribute to the exploitation of this relevant fungal resource for the sustainable and economically meaningful production of crops that face increasing constraints, including the presence of mycophagous and plant-pathogenic organisms in the rhizosphere, exposure to contaminants, and climate change impacts such as drought and heat. Consequently, we also aim to ensure wide dissemination of the project results to the scientific community, society and stakeholders in agriculture, horticulture and forestry.

The excessive use of antibiotics has led to emergence of bacteria strains, which are resistant to a range of antimicrobials, including first-choice agents for the treatment of humans. By 2050, the death toll caused by the antimicrobial resistance could exceed the one related to cancer and diabetes combined. In light of this emergency, antimicrobial peptides have the potential to become valuable antimicrobial weapons because they offer potential broad-spectrum and rapid bactericidal activity. However, their toxicities and poor specificities limit their clinical use. To overcome these drawbacks, we will develop hybrid delivery systems based on aptamers and mesoporous silica nanoparticles. Very high in vitro antimicrobial activities with very high specificities are expected.

Pathogenic bacteria are a permanent threat for Humanity even the discovery of antibiotics led to the fade-out of mass epidemies. Nevertheless, human being faces more and more antibiotic-resistant bacterial strains. Thus, the constant development of innovative antibiotics is crucial, especially against Gram-negative bacteria found in many lethal infections. The current antibiotic arsenal is mainly composed of organic compounds when organometallic derivatives appear to be reserved principally to cancer. However, the toxicity profiles of current last resort antibiotics make now organometallic derivatives competitive. More particularly, gold(I) complexes have shown impressive bactericidal properties on Gram-positive pathogens, but these chemical entities poorly cross the bacterial envelope of Gram-negative bacteria. Bacterial iron uptake systems are gates through the envelope. Siderophores are small iron(III) chelating molecules secreted by bacteria to promote iron acquisition. Siderophores are able to use bacterial iron uptake systems to cross bacterial membrane reaching therefore bacterial inner space. Siderophores could be thus used as vectors to promote accumulation of bactericidal metals into Gram-negative bacteria using a so-called Trojan horse strategy. In our approach gold(I) complexes will be conjugated to siderophore vectors through linkers. The recognition of the ferric-siderophores by specific outer membrane transporters will lead to the uptake of the whole conjugate inside the bacterium. This approach will, at one and at the same time, increase the penetration of organometallic species and reduce the peripheral toxicity of gold(I) for host cells. Vectors to be used in our approach will be analogues of enterobactin, desferrioxamin B (DFOB), pyoverdine and pyochelin, four siderophores used by Gram-negative pathogens and P. aeruginosa more particularly. These vectors will be synthesized in the team of partner 1 (Dr. Gaëtan MISLIN, UMR7242 BSC, Illkirch) and will be generated with alkyne or azide functions. These functions will be used for the conjugation of gold(I) complexes by azide-alkyne cycloaddition (CAA, click chemistry). These gold(I) complexes will be prepared by partner 2 (Dr. Sylvain GAILLARD, UMR6507 LCMT, Caen) in the form of N-heterocyclic carbene (NHC). The conjugates synthesized in the present project will be tested by Partner 3 (Pr Katy JEANNOT, UMR6249 Besançon), primarily on P. aeruginosa. This screening will be then extended to other pathogenic bacteria with a specific focus on critical Gram-negative pathogens from a collection of resistant clinical isolates. ADME-Tox study will be performed on the more promising conjugates in order to assess the therapeutic potential of our approach. The emergence of resistance is a crucial consideration in the development of new antimicrobial compounds with longer shelf life. Our study aims also to assess the potential of our conjugates to induce resistance, both to themselves and to commercially available antimicrobials (cross-resistance). Additionally, we will characterize the mechanisms of resistance developed and evaluate the susceptibility of our compounds against previously identified mechanisms, as well as strains exhibiting reduced susceptibility or resistance to cefiderocol (the sole Trojan Horse antibiotic marketed so far). The structure of the project, the methodologies used and the expertise of the partners should allow the production of conjugates siderophores-gold(I) that are both effective against Gram-negative bacteria and have a toxicity compatible with use in humans.