Anya Kardailsky , Benjamín Durán-Vinet, Georgia Nester, Marcelle E Ayad, Eric J Raes, Gert-Jan Jeunen, Allison K Miller, Philip McVey, Shannon Corrigan, Matthew W Fraser, Priscilla Goncalves, Stephen Burnell, Adam J Bennet, Sebastian Rauschert, Philipp E Bayer

Characterising biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA biomonitoring is limited by biases towards certain species and the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics of eDNA enables the collection of whole ecosystem data by sequencing all molecules present, allowing characterisation and identification. CRISPR-Cas based methods have the potential to improve the efficiency of eDNA metagenomic sequencing of low abundant target organisms and simplify data analysis by enrichment of target species or non-target DNA depletion prior to sequencing. Implementation of CRISPR-Cas in eDNA has been limited due to a lack of interest and support in the past. This perspective synthesizes current approaches of CRISPR-Cas to study underrepresented taxa and advocate for further application and optimization of depletion and enrichment methods of eDNA using CRISPR-Cas, holding promise for eDNA biomonitoring.