DNA barcoding and metabarcoding of highly diverse aquatic mites (Acarina) can improve their use in routine biological monitoring

Abstract

Context Acarina are commonly collected in macroinvertebrate surveys used to monitor freshwater ecosystems. However, they can be difficult to identify morphologically requiring considerable taxonomic skill for identification to finer taxonomic levels. Therefore, in biomonitoring they are identified to subclass despite high species diversity and varied environmental responses. DNA barcoding individuals and DNA metabarcoding of bulk samples enables species to be accurately and routinely identified. However, poor DNA barcode coverage of Australian aquatic mites has hampered their use in DNA studies. Aims Here, we aim to generate DNA barcodes for mites from Greater Melbourne, Australia. Key results For many specimens, we link DNA barcodes to genus-level morphological identifications using genetic analysis of DNA barcodes to understand biodiversity. We then test if new DNA barcodes can improve identification of mites in samples processed with DNA metabarcoding. We found Australian aquatic mites showed high diversity with many DNA barcodes represented by single specimens. Conclusions Increased mite DNA barcode library coverage improved their detection using DNA metabarcoding. Implications Given high species diversity, much effort will be required to improve DNA barcode coverage for aquatic mites in Australia and integrate barcodes with species level taxonomy, allowing Acarina to be better incorporated into DNA-based biological monitoring.