Quaternary ammonium compounds (QACs) are widely used non-therapeutic biocides that can have a range of unintended environmental consequences, including harmful effects on natural microbial communities and biogeochemical cycles. BITTER-PROPHECY will investigate sources, fate and transport of QACs in mixed land use catchments, quantify their natural attenuation and evaluate their impacts on the activity of denitrifying microbes. A field survey will be complemented with laboratory experiments to establish the role organic matter and environmental minerals in modulating the mobility of QACs, and the effects of exposure to QACs on denitrification capacity. The effects of QACs will be determined on strains of nitrate reducing bacteria, as well as on natural denitrifying communities inhabiting natural sediments. Ultimately, the results will help characterize, sources, transport and risks related to QACs in the environment and their impact on ecosystem functioning

The deep subsurface is conventionally thought as a carbon and energy-poor environment, with limited microbial growth and biogeochemical process rates. In recent years, there has been increasing evidence of the existence of deep microbial communities, able to actively respond to changes in hydrological and geochemical changes. These subsurface communities are thought to catalyse a large array of redox reactions but their impact on geochemical processes, rates and fluxes have remained largely elusive so far. IRONSTONE assembles an interdisciplinary team of scientists with complementary expertise in Earth sciences, microbial ecology and fluid mechanics to explore the interplay between hydrological, geochemical and microbial processes in the critical zone. The central hypothesis that will be tested is that flow and chemical gradients enhance microbial activity at depth by promoting the formation of redox driven habitats and triggering biogeochemical processes that would not occur in homogeneous environments. By investigating the mechanisms and scales that control these microbial hot spots and hot moments, IRONSTONE will provide a new understanding of how microbially enhanced reactivity influence landscape-scale biogeochemical fluxes. For this purpose, IRONSTONE will focus on iron oxidation and iron oxidizing bacteria (FeOB). Iron redox transformations play a central role in global biogeochemical cycles and FeOB are primary producer of organic carbon that potentially strongly influence deep microbial communities. We recently demonstrated that mixing between superficial oxygenated water and deep iron-rich groundwater drives the formation of microoxic environments, where FeOB can thrive in deep fractured rocks. This mechanism is likely representative of the dynamics of other microorganisms that depend on electron donors and acceptors that are spatially segregated, leading to strongly enhanced microbial activity in mixing zones. As such, it may profoundly change representations and models of deep subsurface environments. IRONSTONE will rely on an original methodology coupling microfluidics, genomics, geochemistry and hydrology to understand and quantify the dynamics of FeOB hot spots and their impact on critical zone cycles and fluxes. This methodology may be extended to a range of microorganisms and reactions. IRONSTONE will make the most of the rapid developments in microfluidics and microimaging to interrogate the concept of geochemical gradients at microscale. Innovative microfluidic devices and experiments will allow observing growth, distribution and morphology of mineralized FeOB colonies subjected to precise concentrations or gradients of O2 and Fe(II) (WP1). These microscale observation will be combined with the characterization of reactive pathways and geochemical fluxes associated to FeOB hot spots formation and degradation (WP2). For this, IRONSTONE will couple metagenomics and metatranscriptomics, isotopic labelling, and microimaging, molecular and thermodynamics approaches. Upscaling to field scale will be investigated using novel tracer tests based on continuous dissolved gas and isotopic measurements, including isotopic fractionation of O2, to quantify microbiological controls on reactions and elemental fluxes (WP3). The highly interdisciplinary approach developed in IRONSTONE will thus provide new opportunities to understand how spatial heterogeneity and temporal variation of environmental conditions affect the dynamics of microbial growth and the kinetics of microbially catalyzed reactions in the subsurface, leading to a new framework to integrate deep microbial dynamics in critical zone cycles and fluxes.

Gene regulation plays an essential role in shaping species differences and modulating phenotypes across development and environmental conditions. It essentially works through the recruitment of trans-acting intermediates to cis-acting DNA sequences affecting the expression of the nearby gene. While gene expression regulation is central in molecular, cellular, developmental, and system biology, its detailed mechanisms have relatively little been incorporated into modern evolutionary theory. We previously discovered two processes specific to gene expression evolution in diploids, cis-regulator runaway and divergence. They arise because of (i) transient dominance modifications that automatically occur following the evolution of cis-acting regulatory elements and (ii) coevolution of these cis-acting elements with trans-acting regulators. We have shown that accounting for these processes calls into question a half-century of theory on sex chromosome evolution and may completely rejuvenate empirical and theoretical work in this field. Here, we will develop the evolutionary theory of cis- and trans-regulators at full scale and empirically test its core features and predictions. Specifically, there are sound reasons to believe that this new theory also has the potential to revolutionize our understanding of other fundamental and enigmatic features of eukaryotic life. It may be a crucial missing element for illuminating the deep evolutionary mysteries of (i) the origin of eukaryotic genome complexity and (ii) the structure of eukaryotic gene regulatory networks. It also may explain (iii) how and why sex – asex transitions fail or succeed and, therefore, why eukaryotic sex is maintained. CisTransEvol offers a radically new groundbreaking approach to important problems in evolutionary biology. If successful, it will be a tremendous advance in our understanding of eukaryotic life-forms and provides a general framework for gene expression evolution in eukaryotes.

Climate change is the biggest challenge that we are facing for food production. Increase in atmospheric carbon dioxide, in temperature and in variability of precipitation, directly affect the abiotic environment of crops, their geographical distribution and their biotic interactions, leading to increased crop vulnerability. Rethinking new strategies that will mitigate these impacts is a priority for agriculture. Compared with domesticated forms monitored by humans, crop wild relatives are facing continuous challenges in their natural environments and encompass more genetic diversity. Therefore, they constitute an untapped reservoir of alleles, which could be used to increase adaptive capacity of cultivated species in the face of global changes. Genetic exploitation of wild relatives in crop improvement is a key alternative strategy to the massive use of inputs, and promotes the sustainability of agroecosystems. It is however conditioned by cross compatibilities between wild and domesticated forms, and fertility of the resulting progenies. The DOMISOL project aims at characterizing the extent and molecular nature of reproductive barriers between wild and domesticated forms, and at investigating the underlying evolutionary processes. Owing to their recent divergence, barriers between wild and domesticates are incomplete and can therefore be ‘caught in the act’ in their set-up. We propose here to focus on 14 wild/domesticates systems representing a low to high continuum of divergence, in order to undertake a comparative approach. We are pursuing two major objectives. The first one is to take advantage of this broad diversity of systems to perform a quantitative assessment of reproductive barriers in F1 hybrids obtained from wild x domesticates crosses; and to investigate the links between these barriers, the evolutionary history these forms, their phenotypic and genomic divergence, in order to infer the evolutionary parameters that determine the strength of reproductive isolation. The second one is to focus on three of the 14 systems to refine our understanding of the molecular mechanisms underlying reproductive isolation. This includes the description of transcriptional changes in healthy versus unhealthy F1 hybrids, as well as the detection of segregation distortions in F1 and F2 progenies that will be used subsequently for mapping loci involved in hybrid fitness defects. DOMISOL brings together complementary expertise of four partners in the production and valorization of genetic resources, agronomy, evolutionary genomics, plant genetics and modeling. This ambitious project is an exceptional opportunity to produce unique genetic material on several systems and datasets that will serve as bases for collaborations among actors of the plant genetics and genomics community in France. The outcomes will provide a better understanding of the processes at work in the early stages of reproductive isolation, and their consequences on fitness-related traits; but will also help to characterize the extent and genetic nature of barriers to reproduction between wild and cultivated forms. This is an essential step to overcome them and exploit the full reservoir of adaptive alleles to improve crop sustainability in agro-ecosystems. We will take advantage of the data produced for teaching activities to illustrate the application of high-throughput sequencing in plant breeding, and to raise general public awareness of the importance of preserving wild populations.

Strawberry, raspberry and cherry farmers lack solutions to control the invasive pest Drosophila suzukii (DS). Here, we will maturate the Sterile Insect Technique (SIT) targeting DS. SIT has shown great efficacy to control many insects in foreign countries. It prevents reproduction by wild females through their mating with sterile males of the same species, which are mass-produced, sterilised and regularly released in large numbers. Females that mate with them produce non-viable eggs, hence reducing the population over generations. DS SIT will be deployed in semi-enclosed environments such as greenhouses and netted orchards. Key initial technical elements have been reached, positioning DS SIT at a TRL of 4: the rearing process and pupae sterilization are mastered at a small-scale; a high-performance genetic line selected by the project leader greatly reduced female fertility when competing with wild males, in laboratory trials. This project will mature the technology to TRL 7 thanks to: (1) scale-up and optimization of the operational steps (production capacity, handling, packaging, transport, adult sterilization); in order to (2) evaluate various parameters of efficacy in operational conditions; taking into account (3) the integration and consequences of DS SIT on both farming practices and the surrounding environment; and allowing to (4) propose organizational scenarios to implement DS SIT at the territorial level based on stakeholders’ engagements. We will combine prototyping, field testing, in-situ monitoring, laboratory investigations and socio-economic studies. Laboratory-scale research will enable tweaking various operational levers to increase quality and effectiveness. By increasing the testing scale - from experimental greenhouses to operational contexts in commercial farms - will we identify practical challenges and impacts. A socio-economical approach will unveil how to deploy DS SIT for the protection of these three commodities. Strawberry, raspberry and cherry farmers are the future users and core stakeholders. Crops grown under tunnels or protected by nets are the targets of this project; due to DS abundance, control in open field is not a current goal. This project is led by the ambition to create a commercial entity for DS SIT services (production, release, monitoring). The operational trials will allow assessing the benefits-costs in view of large-scale deployment, both for industry, users and stakeholders. The SIT is an alternative to chemical insecticides. Due to a lack of sustainable solutions, current DS control mostly relies either on molecules subjected to temporary authorizations, or the costly manual sorting of infested fruit. Successful SIT actions nest into Integrated Pest Management strategies (IPM). Mandatory changes on pests and diseases management will include the fine-scale monitoring of DS and the adaptation of sterile releases to field observations. Technical support to growers and education is hence mandatory. The sustainability of the solution will rely on the active participation and regional coordination of users and stakeholders. To this effect, we will elaborate organizational scenarios of integrated strategies meeting their constraints. SIT long-lasting adoption through stakeholders’ involvement, will have positive impacts for environment, health and society. The SIT participates to the agroecology transition and a renewed relationship between growers and pests. Our transdisciplinary consortium has background in ecology, mathematics and socio-economy. All partners are involved in SIT pilot projects or in the pioneering of DS SIT and have worked together in the past. INRAE coordinates the project, closely with the economic partner CTIFL, with the common goal of developing a commercial solution. Due to their position in French agronomy R&D, partners are best placed to disseminate project results to different audiences including value chain actors.