A comprehensive review of catchment water quality monitoring using a tiered framework of integrated sensing technologies.

Due to the growing threat of climate change, new advances in water quality monitoring strategies are needed now more than ever. Reliable and robust monitoring practices can be used to improve and better understand catchment processes affecting the water quality. In recent years the deployment of long term in-situ sensors has increased the temporal and spatial data being obtained. Furthermore, the development and research into remote sensing using satellite and aerial imagery has been incrementally integrated into catchments for monitoring areas that previously might have been impossible to monitor, producing high-resolution data that has become imperative to catchment monitoring. The use of modelling in catchments has become relevant as it enables the prediction of events before they occur so that strategic plans can be put in place to deal with or prevent certain threats. This review highlights the monitoring approaches employed in catchments currently and examines the potential for integration of these methods. A framework might incorporate all monitoring strategies to obtain more information about a catchment and its water quality. The future of monitoring will involve satellite, in-situ and air borne devices with data analytics playing a key role in providing decision support tools. The review provides examples of successful use of individual technologies, some combined approaches and identifies gaps that should be filled to achieve an ideal catchment observation system.

The application of CRISPR-Cas for single species identification from environmental DNA.

We report the first application of CRISPR-Cas technology to single species detection from environmental DNA (eDNA). Organisms shed and excrete DNA into their environment such as in skin cells and faeces, referred to as environmental DNA (eDNA). Utilising eDNA allows noninvasive monitoring with increased specificity and sensitivity. Current methods primarily employ PCR-based techniques to detect a given species from eDNA samples, posing a logistical challenge for on-site monitoring and potential adaptation to biosensor devices. We have developed an alternative method; coupling isothermal amplification to a CRISPR-Cas12a detection system. This utilises the collateral cleavage activity of Cas12a, a ribonuclease guided by a highly specific single CRISPR RNA. We used the target species Salmo salar as a proof-of-concept test of the specificity of the assay among closely related species and to show the assay is successful at a single temperature of 37°C with signal detection at 535 nM. The specific assay, detects at attomolar sensitivity with rapid detection rates (<2.5 hr). This approach simplifies the challenge of building a biosensor device for rapid target species detection in the field and can be easily adapted to detect any species from eDNA samples from a variety of sources enhancing the capabilities of eDNA as a tool for monitoring biodiversity.