Details

Autor(en) / Beteiligte

• Thomson‐Laing, Georgia
• Howarth, Jamie D.
• Atalah, Javier
• Vandergoes, Marcus J.
• Rees, Andrew
• Steiner, Konstanze
• Thomson‐Laing, Jacob
• Wood, Susanna A.

Titel

Detection of fish and mussel DNA in lake sediment cores depends on location, species, and molecular method

Ist Teil von

• Environmental DNA (Hoboken, N.J.), 2023-11, Vol.5 (6), p.1484-1504

Ort / Verlag

Hoboken: John Wiley & Sons, Inc

Erscheinungsjahr

2023

Quelle

Wiley Online Library - AutoHoldings Journals

Beschreibungen/Notizen

• Environmental DNA provides an opportunity to track long‐term changes in biological communities in lake ecosystems but the detection of macroorganisms, such as freshwater fish and mussels, in sedimentary DNA (sedDNA) has only been successfully reported in a few studies to date. Factors such as low abundance of the target organisms, sampling location, the molecular approach used, and DNA quantity may influence detection, though studies exploring these factors are lacking. In the present study, sediment cores were collected from a depocenter and nearshore site in a small shallow lake where some historical fish survey data was available. DNA was extracted from the sediment core and analyzed for Anguilla australis (shortfin eel), Echyridella menziesii (freshwater mussel), and Perca fluviatilis (European perch) using droplet digital PCR (ddPCR) and general fish (class Actinopterygii) and macroinvertebrates using metabarcoding. The data from the historical fish surveys (last 20 years) aligned with the molecular data except for a lack of Anguilla dieffenbachii (longfin eel) DNA detection. Generalized additive mixed model analysis showed significantly higher detections in samples from the nearshore compared to depocenter core, which is most likely related to habitat of the target species. Differential detection of target species was likely caused by their ecology and locality. The ddPCR assays were more sensitive (88 ± 3% of samples with positive detections) than metabarcoding (48 ± 10%). However, the metabarcoding enabled the detection of additional fish species. Target species detection was negatively impacted by a reduction in total DNA concentration in older sediments. This research highlights that current molecular techniques used to target fish and mussel sedDNA can result in inconsistent temporal and spatial detection of species, especially in older sediments. We recommend that the methodology and interpretation of sedDNA results need to be considered in the context of species ecology, abundance, and DNA concentrations. In this study, we assess how within‐lake location, target species, molecular method, and sediment age affects the detection of freshwater fish and mussel sedDNA in a historical sediment core archive from a shallow, lowland lake in Aotearoa New Zealand. Using targeted species droplet digital PCR assays and metabarcoding, we report the successful detection of fish and mussel DNA in lake sediment dating back to approximately 1250 CE. The results provide context and recommendations for future work in this area, specifically that methodology and interpretation of sedDNA results need to be considered in the context of species ecology, abundance, and historical DNA limitations.