DNA Metabarcoding Unveils a Decade of Dietary Shifts in Prey Fishes of an Estuarine Dolphin

Estuarine and coastal ecosystems face increasing threats from climate change and anthropogenic pressures, negatively impacting producers and primary consumers. This disruption at the base of the food chain leads to a significant decline in fish stocks due to the depletion of prey resources, ultimately affecting top marine predators within the ecosystem. This study utilized 18S rRNA metabarcoding to investigate decadal (2013–2023) dietary shifts in three key prey fish species of the endangered Indo-Pacific humpback dolphin (Sousa chinensis)—Bighead Croaker (Collichthys lucida), Chinese Gizzard Shad (Clupanodon thrissa), and Dotted Gizzard Shad (Konosirus punctatus)—in the Pearl River Estuary (PRE), China. The results indicated that all species exhibited generalist feeding strategies, primarily consuming arthropods (crustaceans) and Bacillariophyta (phytoplankton); however, both prey categories showed significant declines in species richness by 2023 (arthropods: a 40–72% reduction; Bacillariophyta: a 17–65% reduction). Furthermore, PERMANOVA confirmed significant temporal dietary divergence (P<0.05), with intensified niche partitioning between C. lucida and the other species, while dietary overlap between C. thrissa and K. punctatus decreased from 62% (2013) to 28% (2023). Additionally, phytoplankton, the foundation of the trophic pyramid, experienced a 20% decline in species richness, potentially triggering bottom-up effects that threaten the food availability of apex predators. Conversely, among the three species studied, C. lucida exhibited greater dietary plasticity, while clupeids showed trophic niche compression. This study highlights how climate change and anthropogenic pressures have restructured PRE food webs. These shifts may exacerbate humpback dolphin population declines by limiting prey accessibility.