Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program

The effectiveness of environmental protection measures is based on the early identification and diagnosis of anthropogenic pressures. Similarly, restoration actions require precise monitoring of changes in the ecological quality of ecosystems, in order to highlight their effectiveness. Monitoring the ecological quality relies on bioindicators, which are organisms revealing the pressures exerted on the environment through the composition of their communities. Their implementation, based on the morphological identification of species, is expensive because it requires time and experts in taxonomy. Recent genomic tools should provide access to reliable and high-throughput environmental monitoring by directly inferring the composition of bioindicators’ communities from their DNA (metabarcoding). The French-Swiss program SYNAQUA (INTERREG France-Switzerland 2017–2019) proposes to use and validate the tools of environmental genomic for biomonitoring and aims ultimately at their implementation in the regulatory bio-surveillance. SYNAQUA will test the metabarcoding approach focusing on two bioindicators, diatoms, and aquatic oligochaetes, which are used in freshwater biomonitoring in France and Switzerland. To go towards the renewal of current biomonitoring practices, SYNAQUA will (1) bring together different actors: scientists, environmental managers, consulting firms, and biotechnological companies, (2) apply this approach on a large scale to demonstrate its relevance, (3) propose robust and reliable tools, and (4) raise public awareness and train the various actors likely to use these new tools. Biomonitoring approaches based on such environmental genomic tools should address the European need for reliable, higher-throughput monitoring to improve the protection of aquatic environments under multiple pressures, guide their restoration, and follow their evolution.     

Modelling spatial zero-inflated continuous data with an exponentially compound Poisson process

A parsimonious model is presented as an alternative to delta approaches to modelling zero-inflated continuous data. The data model relies on an exponentially compound Poisson process, also called the law of leaks (LOL). It represents the process of sampling resources that are spatially distributed as Poisson distributed patches, each containing a certain quantity of biomass drawn from an exponential distribution. In an application of the LOL, two latent structures are proposed to account for spatial dependencies between zero values at different scales within a hierarchical Bayesian framework. The LOL is compared to the delta-gamma (ΔΓ) distribution using bottom-trawl survey data. Results of this case study emphasize that the LOL provides slightly better fits to learning samples with a very high proportion of zero values and small strictly positive abundance data. Additionally, it offers better predictions of validation samples.     

Adaptation potential of ecosystem-based management to climate change in the eastern Canadian boreal forest

Ecosystem-based management (EBM) of forests is gaining acceptance for its focus on the maintenance of the long-term integrity of ecosystem processes, but climate change challenges this view because of its impacts on these very processes. We have therefore evaluated the robustness of EBM to projected climate change, considering the role of climate on forest growth and fire regime in a boreal forest of eastern Canada. A climate sensitive growth index model was calibrated for three commercial species and used to project the evolution of merchantable volume for two climate scenarios (B1 and A2) under conventional and EBM strategies. Current burn rate and burn rates under future climate scenarios were also considered. Under the most extreme projected climate scenario, the periodic timber supply could be reduced by up to 79% through direct (growth reduction) and indirect (fire) effects. However, ecological indicators show that EBM is a more robust forest management strategy than conventional one demonstrating its adaptation potential to climate change at least in the short term.     

Proposal for standardized prenatal ultrasound assessment of the fetus with congenital diaphragmatic hernia by the European reference network on rare inherited and congenital anomalies (ERNICA)

Congenital diaphragmatic hernia is a rare disease associated with high mortality and morbidity. Antenatal ultrasound screening identifies more than 70% of cases, providing the opportunity for in utero referral to a tertiary care center for expert assessment and perinatal management. Additional genetic and morphologic assessment may be used to rule out associated anomalies. In isolated cases, the outcome may be predicted prenatally by medical imaging. The combination of lung size and liver herniation is a widely accepted method to stratify fetuses into groups with an increasing degree of pulmonary hypoplasia and corresponding mortality rates. Ultrasound measurement of the observed to expected lung-to-head ratio (o/e LHR) is most widely used. The o/e LHR is an independent predictor of survival and short-term morbidity. Finally, evaluation of stomach position has recently been introduced as an indirect method to estimate severity of the disease in left-sided defects, as it has been shown to correlate with the proportion of intrathoracic liver. Herein, we propose a protocol for the standardized ultrasound assessment of fetuses with isolated CDH and individualized prediction of neonatal outcome.