Unlocking the molecular time-capsules of Antarctic sponge specimens - recovering historical eDNA from various preservation methods
Marine sponges have recently been investigated as natural environmental DNA (eDNA) samplers. The ability of marine sponges to accumulate eDNA through their filter-feeding strategy enables an exciting opportunity to reconstruct past ecosystems with high temporal and spatial precision by extracting historical eDNA (heDNA) from museum-stored sponge specimens. While vast numbers of marine sponges have been gathered over centuries, various preservation methods have been employed to store these archived specimens in scientific collections, thereby potentially influencing heDNA recovery success. Here, we investigate whether preservation method choice, including (i) ethanol submersion, (ii) frozen, and (iii) dried, impacts heDNA signal recovery from 30 museum-stored Antarctic sponge specimens through a 16S fish metabarcoding approach. In total, we detected 64 fish heDNA signals and successfully recovered heDNA from sponge specimens irrespective of the preservation method. Furthermore, detection consistency, investigated through five replicated biopsy extractions from each specimen, did not differ between storage methods, though was impacted by sponge taxonomy. Incidence frequency analysis, on the other hand, identified frozen specimens needing significantly increased replication due to detection inconsistencies compared to ethanol-submerged and dried specimens. Additionally, ordination revealed heDNA signal composition differed between preservation methods and influenced by location and depth. Hence, caution is warranted when comparing heDNA signals from sponge specimens stored using different preservation strategies. Our results show the successful recovery of heDNA from marine sponge specimens, thereby enabling scientists to recreate past ecosystem states with a spatial and temporal resolution previously unattainable.