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.     

Innovation through collaboration: scaling up solutions for sustainable development

The open collaborative philosophy employed in the success of open source (OS) software can be applied to hardware design. Specifically, the development of OS appropriate technologies (OSAT) can improve sustainable development efforts worldwide. Yet, widespread OSAT use is far from ubiquitous. Given that lack of communication, access to information and poor collaboration are among the largest barriers to a more effective OSAT dissemination, this paper explores opportunities to overcome such obstacles using four techniques: (1) collaborative online platforms, (2) crowd-sourcing, (3) the concept of knowledge commons, and (4) enabled educational institutions through service learning and applied research. The results are analyzed, and conclusions are drawn that outline paths to higher multiuser collaboration for OSAT deployment.     

Packaging waste and the polluter pays principle: a taxation solution

Packaging waste has become a focus for attention by policy‐makers in a number of countries. This article offers a simple policy measure — a packaging tax or levy — which serves the required aims of policy, namely: reducing waste at source; increasing the rate of recycling; and consistency with the polluter pays principle. The tax is illustrated in the context of beverage containers in the UK and Japan. The merits of the proposal are its simplicity and flexibility. The article suggests that the relevant environmental damages are captured by waste disposal costs and litter. Other life cycle impacts, such as emissions from energy use, could be included but only if there are not more efficient ways of regulating them.     

Derelict land: the case for a strategic approach

This paper examines the rationale underlying the ‘strategic approach’ to the prevention and reclamation of derelict land proposed in research recently published by the Department of the Environment. It outlines the main features and the processes involved in this approach and indicates the form and content of the documentation which might accompany its adoption. The paper focuses upon the tasks involved in the preparation of strategies for derelict land but the principles it examines will have wider application in other policy fields. It concludes with an examination of the practical problems which the adoption of a strategic approach may entail and the ways in which it would enhance the activities of the recently announced Urban Regeneration Agency for England.     

Non-invasive fetal genotyping for maternal alleles with droplet digital PCR: A comparative study of analytical approaches

Objectives

To develop a flexible droplet digital PCR (ddPCR) workflow to perform non-invasive prenatal diagnosis via relative mutation dosage (RMD) for maternal pathogenic variants with a range of inheritance patterns, and to compare the accuracy of multiple analytical approaches.

Methods

Cell free DNA (cfDNA) was tested from 124 archived maternal plasma samples: 88 cases for sickle cell disease and 36 for rare Mendelian conditions. Three analytical methods were compared: sequential probability ratio testing (SPRT), Bayesian and z-score analyses.

Results

The SPRT, Bayesian and z-score analyses performed similarly well with correct prediction rates of 96%, 97% and 98%, respectively. However, there were high rates of inconclusive results for each cohort, particularly for z-score analysis which was 31% overall. Two samples were incorrectly classified by all three analytical methods; a false negative result predicted for a fetus affected with sickle cell disease and a false positive result predicting the presence of an X-linked IDS variant in an unaffected fetus.

Conclusions

ddPCR can be applied to RMD for diverse conditions and inheritance patterns, but all methods carry a small risk of erroneous results. Further evaluation is required both to reduce the rate of inconclusive results and explore discordant results in more detail.     

Monitoring Australian Rangeland Sites Using Landscape Function Indicators and Ground- and Remote-Based Techniques

If the goal for managing rangelands is to achieve a balance between production and conservation, then monitoring is essential to detect change and apply corrective action. In some range-land areas of northern Australia, monitoring has detected a tilt in the production-conservation balance towards excessive production. How big is this imbalance? Can it shift back? Robust monitoring is needed to answer these questions. The aim is to know what to monitor, and where. For example, to detect changes caused by livestock on rangeland forage production and soil erosion, indicators linking grazing disturbances to landscape function are needed, that is, indicators that signal how well landscapes are capturing, concentrating, and utilizing scarce water, nutrient, and organic resources. Studies in Australia and the USA document that simple vegetation and soil patch attributes can be measured as indicators of the 'state of health' of landscape function. For example, field and remote sensing-based grazing studies in Australia document that landscapes with a high cover of perennial plant patches function effectively to capture runoff water and nutrients in sediments, whereas landscapes with a low cover of these patches do not — they are dysfunctional — as indicated by large patches of bare soil. Aerial videography is proving to be a robust technique for measuring indicators of landscape function such as small patches of vegetation and the extent of bare soil. These indicators typically have a sigmoidal response to grazing impacts. We illustrate that if these indicators are measured on monitoring sites established near the sigmoidal 'point of inflection’ then small changes in these indicators can be detected.