Biodiversity is the foundation of all ecosystem services indispensable to people’s health, survival and well-being, but is quickly eroded by anthropogenic changes. Human-related disturbances affect all ecosystems by disrupting major interdependent abiotic and biotic factors, threatening biodiversity and the provision of ecosystem services. These unprecedented threats are likely to increase in the next decades, stressing the need to understand and document how ecosystems respond to global changes in their composition, functioning and services to effectively protect and rebuild terrestrial and marine life.
The principal species responses to anthropogenic disturbances are the modification of species assemblages, and particularly the local loss of sensitive species or the establishment of invaders, leading to a declining and biodiversity homogenisation. However, compared with the documentation of global change impact on the physical environments (e.g. temperature, pH etc.), existing methods for monitoring biodiversity fall short of the needs to quickly document changes in ecosystems. In order to guide human coexistence with nature, we need novel, fast and efficient biodiversity information gathering systems to quantify consequences of the ongoing degradation of habitats, but also to communicate the positive effects of ongoing ecosystem restoration efforts.
The current process of performing environmental DNA (eDNA) analyses is both time-consuming and expensive, requiring well-equipped laboratories and trained personnel. There is a pressing need for testing methods that can be deployed in the field, especially given the lessons from the COVID-19 pandemic, where CRISPR/Cas techniques have demonstrated quick and rapid diagnostics. CRISPR/Cas systems, originally a bacterial defence mechanism, have been adapted for medical diagnostics, such as DETECTR and SHERLOCK, offering near-immediate results at the point of care.
This project proposes applying CRISPR/Cas technology to biodiversity monitoring through eDNA. While successful in detecting fish species in eDNA samples, challenges include the need for rapid and easy DNA extraction and amplification in the field. The researchers have developed a rapid extraction protocol to address this gap. Performing extractions and amplifications directly on-site reduces the risk of contamination and facilitates quick results. The proposed workflow integrates rapid field extraction and amplification with CRISPR/Cas detection, aiming to overcome challenges in biodiversity monitoring. The major advantage lies in its field applicability, providing immediate species detection and enabling anyone, including citizens in regions affected by biodiversity loss, to conduct assessments.
« The project's uniqueness lies in its ambition to create a rapid extraction field device, democratizing biodiversity monitoring worldwide. »
To further enhance field applicability, the ETH research team suggest consolidating the extraction and amplification setup into a single field device, named the eDNAxtractor. This automated machine would handle all pipetting and incubation steps, requiring users only to load prepared consumables. The eDNAxtractor has the potential to simplify sample processing, reduce contamination risks, and make biodiversity monitoring accessible globally, including in developing countries where biodiversity is rich. The project's uniqueness lies in its ambition to create a rapid extraction field device, democratizing biodiversity monitoring worldwide.