X-rays have little impact on estimates of biodiversity from marine sedimentary ancient DNA metabarcoding

Abstract

Sedimentary ancient DNA (sedaDNA) recovered from marine sediments offers valuable insights into past ocean biodiversity through ecosystem reconstructions ranging from decadal to glacial-interglacial timescales. The current best-practice in ancient DNA research is to collect new sediment cores with clean sampling protocols in an effort to prevent modern DNA contamination and minimize post-collection DNA degradation. However, new core collection can pose a barrier to research due to the high costs associated with project-specific expeditions; it also excludes leveraging existing sediment core archives. In general, the recommendation is founded on an abundance of caution rather than evidence-based guidelines. Here, we present a comparative study on the impacts of X-Radiography sediment analysis and different extraction methods on marine sedaDNA outcomes in an archived core to help develop such guidelines. We found that exposure to standard X-ray imaging had no significant impact on sedaDNA recovery, co-extraction of inhibitors (e.g. humic acids), metabarcoding diversity metrics, community structure or composition. The extraction method, however, has a significant impact on sedaDNA recovery/inhibition, diversity metrics, community structure, and composition. Laboratory methodological design for marine sedaDNA studies is, therefore, a critical consideration for future research, whereas standard X-ray screening by marine geoscientists appears benign to the parameters measured. Our results support the use of archived sediments for prospective sedaDNA work, thus reducing a considerable barrier to the field.