Despite the fact that vaccine use in poultry is greater than in any other farmed species, the mechanisms by which they induce protection, particularly at mucosal surfaces, are poorly understood. Many diseases constraining avian productivity and welfare affect the respiratory tract and are multi-factorial. A better understanding of responses in the respiratory tract to bacterial and viral infections, co-infections and vaccines is needed to control endemic production diseases. Avian pathogenic Escherichia coli (APEC) cause severe respiratory and systemic disease, threatening food security and avian welfare at a time of increasing global demand. Infections frequently involve sepsis, inflammation of visceral organs and reduced egg yield/quality, with losses through early mortality, reduced productivity and product condemnation. The expansion of free-range production systems will increase the incidence of colibacillosis through greater exposure of birds to environmental pathogens, stress and injury associated with forming a social hierarchy. Importantly, APEC infections are frequently associated with respiratory viral infections. The nature and consequences of host-pathogen interactions during APEC (co-)infections are poorly understood. Virulence factors of APEC, antagonistic or synergistic effects of co-infection and the basis of immunity and resistance are ill-defined. The EC-wide ban on prophylactic antibiotic use and transmissible resistance render poultry susceptible to APEC infection. Existing vaccines confer limited serogroup-specific protection. This project will advance understanding of mucosal immune responses in the avian respiratory tract. It will provide a comprehensive description of the respiratory tract immune system, leading to new tools to study immune responses and improved understanding of the mechanism and site of antigen presentation in the lung. We will thereby identify correlates of resistance and susceptibility to, and the impact of viral infections on the outcome of, APEC infection. Using transgenic chickens we will further characterise the role of antigen-presenting cells and humoral immunity during APEC infection and vaccination, for example by using our unique MacRed chickens (in which all cells of the mononuclear phagocyte lineage (macrophages, monocytes and dendritic cells) express a fluorescent protein driven by the chicken CSF-1 receptor), and immunoglobulin knock-out chickens (which lack the B cell receptor and thus antibody).

Antibiotic resistance is a significant and increasing problem in many bacterial pathogens that infect animals and humans. Escherichia coli is among the most important of these pathogens, because of its role in intestinal, urinary tract and respiratory disease, and septicaemia in a variety of livestock species, including poultry; and also because many serotypes of E. coli that are associated with extra-intestinal infections in animals and humans are closely related. Antibiotic resistance in E. coli strains is increasing worldwide and this resistance can be maintained even after reducing or withdrawing antibiotic use (Tadesse, 2012). Treatment of E. coli infections in animals and humans thus requires a new and sustainable approach. This consortium will isolate viruses which infect bacteria (bacteriophages, or 'phages') which specifically target surface bacterial determinants of virulence and/or antibiotic resistance transfer. We will isolate phages from the environment, surface water, farms, drains and sewage which are able to infect a range of Avian Pathogenic Escherichia coli (APEC) serotypes. These will be characterised in vitro, and bacteriophage biocontrol candidates will be selected for evaluation in an E. coli septicaemia model in chickens. Selection of the phage will be based on the ability to infect a wide range of pathogenic E. coli strains, in vitro phage replication kinetics, and lack of/minimal host resistance. The potential issue of E. coli resistance to phage infection will be addressed by (i) targeting surface receptors which are important for virulence and/or antibiotic resistance, (ii) the use of cocktails of phages which target different receptors, and (iii) studying the CRISPR-Cas system of wild strains of E. coli to determine its role in phage resistance and its epidemiology and evolution during phage infection. The phage therapy company Ampliphibio is a partner and has collaborated with consortium members for more than 15 years through its UK subsidiary Biocontrol Ltd. This approach can synergise with the development of new drugs and has the potential to provide a sustainable platform for control of antibiotic-resistant pathogens which could easily be extrapolated to many other animal pathogens.

Soil organic carbon (SOC) is a keystone for most soil functions and associated soil ecosystem services (e.g., biomass production, ?ood and erosion mitigation, etc.). SOC is also the main part of the large soil organic matter reservoir feeding soil life with energy and nutrients, and increasing SOC stocks can help mitigate climate change. The SOC reservoir has been strongly depleted by human land-use. Restoring SOC stocks using more sustainable management practices has been suggested as a way to improve soil health while mitigating global warming. Soils contain organic carbon with highly contrasted residence times, ranging from a few hours to millennia. This is due to the complex combination of mechanisms driving its persistence. The di?erent organic matter forms of SOC support di?erent functions in soils. SOC with short residence times is easily metabolized, and sustains soil biological activity, but is rapidly respired as CO2 and lost to the atmosphere. Conversely, persistent SOC with long residence time can lock up C and thus mitigate climate change, but does not fuel biological activity. Our insu?cient knowledge of SOC kinetic pools partitioning hampers e?orts to estimate soil health, and limits the accuracy of model projections of the fate of the SOC reservoir at all spatial scales. Qualitative methods have been developed for decades to estimate the proportions of stable or active SOC fractions such as the widely used POM/MAOM physical SOC fractionation schemes. Recently, a method based on Rock-Eval® thermal analysis data and the PARTYsoc machine-learning model has enabled quantifying the size of SOC fractions that are stable or active at the century-scale. With the FREACS project, our ?rst objective is to quantify SOC fractions (POM/MAOM and centennially stable/active), their saturation level and their subsequent SOC storage potential on topsoil and subsoil samples from 6 soil networks: EU LUCAS Soil, French RMQS and RENECOFOR, Finnish network of farms, German and New Zealand agricultural soil networks. We will also deliver machine-learning models to predict all SOC fractions using quicker and cheaper vis-NIR and MIR soil spectroscopy or widely available environmental data. Our second objective is to decipher the mechanisms explaining long-term SOC persistence by studying a subset of 200 soils with a wide range of centennially stable SOC content. We will characterize the chemical (pyrogenic C & C, H, O, N, P stoichiometry of organic matter), mineralogical (clays & oxi-hydroxides) and microbial (microbial necromass & energy return on investment of SOC use) properties of these topsoils and subsoils to determine the relative contribution of these factors to long-term SOC persistence. Our third objective is to will evaluate the sensitivity of SOC fractions to changes in land-cover or management practice and to use maps of SOC fractions to improve the accuracy of SOC dynamics models simulations. The state-of-the-art ORCHIDEE Land Surface model, RothC and Yasso SOC models will be re-calibrated to match SOC fractions data and used to simulate more accurately SOC stock evolution and associated greenhouse gas emissions under contrasting land-use and soil management scenarios by 2050. Our fourth objective is to ensure access to all data produced in the project and to produce maps of SOC fractions and improved SOC projections for EU and New Zealand that FREACS will deliver in a public data visualization website dedicated to the various interested stakeholders. FREACS will leverage the complementary and recognized skills of all project partners (Biogeochemistry, Mineralogy, Microbial ecology, Pedology, Pedometrics, Data science, Web design). The results will bring key insights on the understanding of SOC sequestration on regional and continental scales and will also be used by a private company to develop an innovative rating system for SOC and soil health, ensuring impact far beyond the academic world.

Climate change affects mountain forests by increasing the intensity and frequency of disturbances such as drought, insect and pathogen outbreaks, fire, wind and ice storms. As a result widespread tree mortality has been reported in recent decades. Most mountain forests support a rich community of organisms, so the loss or replacement of any tree species implies a change in species composition and a financial and economic cost. Understanding which species are lost and which are resilient to these environmental changes is crucial in order to take reasoned management decisions for mitigation. In addition, the presence of large numbers of dead trees and the replacement of dying native trees by exotic species have an impact on human inhabitants, tourists, and forest owners and can lead to local social conflicts over whether resources should be expended on maintaining traditional landscapes. To study the impact of climate change and forest management on the biodiversity of highland forests, we will quantify changes in species richness and composition of a wide range of terrestrial and freshwater organisms, along tree-dieback gradients of four highland conifers in European and Chinese mountains, using cutting-edge molecular technology. We will also measure changes in functional diversity for several focal groups recognized as regulators and indicators of key water and soil processes and ecosystem services. To study the perception of climate change by local populations and the socioeconomic impact of climate-induced mountain forest diebacks and tree replacement strategies on local communities we will carry out both qualitative and quantitative surveys in Europe and China. This project involves a multidisciplinary team of ecologists, sociologists, economists, geographers, forest entomologists, limnologists, mycologists, molecular biologists, forest managers and policy makers. We will work with stakeholders to disseminate the results of the project and facilitate the adoption of newly generated tools and indicators by policy makers.