Biomonitoring of freshwater streams using bulk eDNA and CRISPR-Cas enrichment

Miss Anya Kardailsky¹, Dr Eddy Dowle¹, Dr Christoph Matthaei¹, Dr Neil Gemmell¹, Dr Gert-Jan Jeunen¹

¹University Of Otago, Dunedin, New Zealand

Abstract:

Freshwater quality in many New Zealand catchments is declining due to increased agricultural use, urban development and other anthropogenic effects. Traditional methods of biomonitoring of freshwater stream health uses microscopic analyses that are biased, costly, slow and require a high degree of specialist taxonomic knowledge, all of which limits its use and effectiveness. In this study, bulk eDNA samples of freshwater macroinvertebrates collected from local streams are used to assess the application of CRISPR-Cas enrichment approaches to generate biomass estimates, increase the sensitivity of rare species identification, and decrease biomonitoring costs. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) is a bacterial immune system that has been adapted for both DNA editing and enrichment due to its highly specific DNA targeting ability. I assess if this technology can overcome the biases that have limited genomic biomonitoring in the past and prevented quantitative measures of stream health. This method is compared to traditional metabarcoding approaches to assess accuracy, sensitivity and opportunities for the application of the CRISPR technique in molecular biomonitoring. This study presents an exciting opportunity to expand the field of genomic-based biomonitoring techniques and allow for faster, cheaper, more accurate measures of stream health.

Biography:

Biography to come