Rodent-borne microparasitic infectious diseases (e.g. LCMv), including those transmitted by the rodents’ ectoparasites (e.g. TBE), are of increasing concern for public health. Rodents themselves are also a threat to food security because they damage agricultural crops and food stores. Effective control of these emerging and re-emerging diseases (and the rodent hosts themselves) requires a full understanding of the parasite-host dynamic. This dynamic is likely to be altered where hosts are coinfected with prevalent endemic macroparasite species (e.g. helminths), which change host demography and may interact directly with microparasites via the host’s immune system. Using empirical data from a typical European temperate forest in the Autonomous Province of Trent (PAT), Northern Italy, this project will: i) first assesses which macro- and microparasites interactions exist among the common parasite community in this region (using advanced statistical methods), ii) develop a mathematical modelling framework to assess the long term dynamics of the rodent and parasite community and to simulate the outcome of a range of different parasite and host control strategies and iii) use this model to develop a co-ordinated ‘OneHealth’ plan for both rodent and parasite control in PAT .

Calls to stem biodiversity loss have generally focussed on the plight of charismatic vertebrates (mammals, birds, fish, amphibians) and to some extent, insects (like butterflies). However, although the abundance and diversity of microbial and helminth communities inhabiting the gastrointestinal tract have been demonstrated of critical importance to health in both humans and non-human animals, this microbiodiversity has rarely been considered within a conservation framework. Using recently collected fecal samples from two free-ranging tropical non-human primate species with contrasting ecological parameters, WILDGUT proposes a multi-disciplinary approach to investigate the four-way interplay between habitat changes, host species, and gut micro- and macro-parasites in natural environments. The results will lead to a better understanding of the impact of human activities on microbiodiversity, and whether such changes could have an effect on wildlife health, and ultimately to a species’ conservation status. Thus, the project will explore whether the comparison of gut microbiota and helminth community diversity, functions and interaction between intact and degraded habitats can be used to develop new indices to estimate host health and informing conservation strategies.

The first aim of the project is to prove a general mechanism for plant protection from abiotic stresses (such as temperature and ozone stress) exerted by volatile isoprenoids (VIPs). Recent studies advanced the hypothesis that VIPs may function as effective antioxidants in plants by directly reacting with reactive oxygen species (ROS) that accumulate upon abiotic stress, producing oxidized VIPs. However, this mechanism is yet to be confirmed. During the outgoing phase (Harvard University, Cambridge MA, USA) the objective described above will be addressed via a comprehensive experimental approach that will be carried out on the model plant Arabidopsis (wild-type and isoprene-emitting transgenic Arabidopsis), on a plant species (Quercus rubra) that emits very large quantities of VIPs and on grapevine, a crop of outmost importance in the European economy. During the return phase (FEM, Trento, Italy) the multidisciplinary expertise gained in the outgoing period will be fully employed to study the grapevine germplasm owned by the return institution and new grapevine varieties selected or genetically modified for the emission of specific VIPs, which have recently been developed by a partner research group, in collaboration with the applicant. The final objectives of the project are 1) to prove that VIPs act as effective antioxidant on grapevine leading to an improved ozone stress resistance and 2) to integrate screening for VIP emission in the host institution grapevine breeding program in order to improve stress resistance of new grapevine varieties.

Apple scab caused by Venturia inaequalis is the major constraint to apple production worldwide, causing severe economic losses. As current commercial cultivars are highly susceptible to scab, introduction of new scab-resistant cultivars will reduce the intensive use of pesticides now required to control this disease. Although the ‘Geneva’ apple is an important source of resistance for breeding, its complex scab resistance has not been properly characterized. In preliminary studies, we mapped to chromosome 4 of ‘Geneva’ a 5 cM region containing three genes conferring both dominant and recessive scab resistance, which corresponds to a 2 Mbp region containing nine candidate NBS-LRR resistance genes on the physical map of ‘Golden Delicious’ (GD). This provided the first evidence of recessive genetic control of apple scab resistance. In this project proposal, we will further characterize this complex locus, employing next generation sequencing, together with bioinformatics and functional analysis of disease candidate resistance genes (CRGs): (1) we will sequence the resistance locus in ‘Geneva’ and identify CRGs that are polymorphic (presence/absence, or sequence polymorphism) between the resistant ‘Geneva’ and the susceptible GD; (2) we will clone each CRG with its native promoter, terminator and introns; and (3) transform susceptible lines with the individual CRGs to evaluate their effect on the level of disease resistance and its race-specific spectrum. This will not only build a better understanding of the genetic basis of apple scab resistance and the gene-for-gene relationships between the pathogen and the host, but it will enable the development of molecular markers for breeding new ‘sprayfree’ cultivars with durable scab resistance.

The current global biodiversity crisis requires rapid, inexpensive and reliable methods of detecting the main threats to species’ survival: pathogens, habitat change, and loss of genetic diversity1. Equally crucial are solutions for stemming biodiversity loss: we lack vital models that determine how these threats interact, which would help prioritise conservation efforts. Recently, CRI-CG has discovered for one species of frog over a relatively small geographic area that eDNA extracted from water samples captures more genetic diversity than analyses using tissue samples (UNESCO-funded project ACQUAVIVA). The same eDNA can be used to detect amphibian pathogens. NIPMAP will apply this knowledge in an innovative way by: i) optimizing this eDNA approach to estimate mtDNA diversity in four amphibian taxa (two caudates, two anurans) and pathogen diversity (principal pathogens: Bd, Bsal, Rv) across the eastern Italian Alps; ii) using these data to inform individual-based and spatially explicit simulations of host movements and pathogen transmission37; iii) integrating parameters from i-ii with skin microbiota and other health indices, as well as iv) environmental variables at each sample site, to generate correlative models (e.g. GLMMs and SDMs) and potential distribution maps to direct conservation management decisions. We will also pilot two innovative eDNA protocols: one to measure nuclear DNA diversity (to measure current gene flow and dispersal rates) and one to understand microbiota function using metatranscriptomics. These interdisciplinary tools will be integrated into a workflow that will be applicable to animal taxa anywhere on the planet.