Using environmental (e)DNA sequencing for aquatic biodiversity surveys: a beginner's guide

Biological surveys are needed to monitor and assess the health of ecosystems and the species within them. However, morphology-based biodiversity surveys can be invasive, time consuming and financially expensive. Recently, environmental (e)DNA sequencing has been demonstrated as a potential alternative to morphological-based surveys because it enables the rapid and inexpensive detection of multiple taxa from DNA present in the environment. Numerous studies have shown that eDNA-based biodiversity surveys can provide considerable information about aquatic ecosystem function and health. Therefore, this molecular method has the potential to improve how current aquatic biological surveys are conducted. Currently, most eDNA literature is aimed at an audience with a moderate to advanced knowledge of DNA sequencing, creating a barrier for many ecologists who lack DNA sequencing expertise but wish to apply such methods to their research. The aim of this review is to provide guidance to non-geneticists regarding sequencing eDNA for aquatic biodiversity surveys and to highlight the requirements that need to be considered before the technique can be effectively incorporated into biomonitoring programs. Specifically, we provide details and recommendations on some of the major principles, from sample collection to bioinformatic analyses. For those areas where specific recommendations cannot be given, we have provided references to suitable literature.