Offshore biodiversity monitoring using an automated eDNA sampler

Marine biodiversity is under increasing pressure due to anthropogenic impacts, environmental change, and climate warming. This has led to a growing need for monitoring and documenting existing marine biodiversity. However, there are several challenges associated with documenting marine biodiversity largely due to the high cost of traditional methods for generating biodiversity data. One emerging monitoring method is the analysis of environmental DNA (eDNA), which is defined as genetic material collected directly from the environment, outside of living hosts. eDNA can be easily collected through water filtration and it can be analyzed to detect either single species using quantitative PCR (qPCR) or analyzed for broader species communities using metabarcoding. Despite its potential, eDNA also presents several fundamental challenges, some of which are particularly relevant for remote offshore marine biodiversity monitoring. These include the need for dedicated vessel time, which significantly increases operational costs and the time lag associated with analyzing the samples.
We present data from four different field campaigns using a so-called ecogenomic sensor, the second-generation Environmental Sample Processor (2G-ESP). This instrument is a unique, autonomous and stationary eDNA sampler and analyzer that can operate at sea for several months, depending on power supply, while being remotely controlled by scientists on land. During deployment, the 2G-ESP can collect samples and analyze them using qPCR, with results accessible to scientists on land in real time. It can also store filters for subsequent analysis post deployment, using either qPCR or metabarcoding methods, enabling the analysis of broader species communities. Hence the 2G-ESP offers a possibility to mitigate some of the limitations normally associated with marine offshore eDNA monitoring.
Here, we present the practical and analytical challenges encountered, along with results from the four deployments focusing on biodiversity assessment of a wide range of species including fish, elasmobranchs and marine mammals. We show how the instrument can be used for real-time species detection and how temporal offshore eDNA sampling can be used to better cover full biodiversity in an area. In the end we provide an overview of the potential applications of this technology in future offshore biodiversity monitoring.