Temporal and spatial variability of mudflat and mangrove foraminiferal eDNA assemblages and its implication for sea-level reconstruction

Reconstructing relative sea level (RSL) is essential for understanding coastal evolution and mitigating impacts of climate change. Foraminiferal assemblages are established proxies for past sea levels, but their composition can vary seasonally and spatially, affecting the reliability of morphological reconstructions. Environmental DNA (eDNA) enables high-resolution, non-invasive monitoring of foraminiferal communities and supports high-precision RSL reconstruction. However, the spatiotemporal stability of eDNA assemblages in (sub)tropical intertidal zones—and their influence on RSL reconstruction—remains uncertain. We conducted a two-year eDNA monitoring study at three intertidal stations of varying tidal elevation in Hong Kong, sampling during both dry and wet seasons to assess variability in mangrove and mudflat environments. Mid-mangrove eDNA communities exhibited temporal and spatial stability. In contrast, eDNA assemblages in mudflat and upper-mangrove environments, particularly among monothalamous foraminifera taxa, showed pronounced seasonal shifts primarily driven by environmental changes. Despite this variability in the upper-mangrove, eDNA-based elevation estimates in mangrove consistently aligned with observed elevations (within 95% credible intervals), demonstrating reliability of RSL reconstructions in these environments. However, samples from mudflats, especially during the wet season, exhibited an overprediction bias, reflecting their heightened sensitivity to seasonal and exogenous eDNA inputs. These findings highlight the need to account for seasonal and environmental variability in eDNA-based RSL reconstruction. Stable mangroves are optimal for transfer functions, while transitional/mudflat zones require caution due to higher variability. Our study provides guidance for foraminiferal eDNA application in complex, dynamic coastal settings.