Seasonal trophic flexibility and diet–resource decoupling in Branchiostoma belcheri assessed using eDNA metabarcoding

Branchiostoma belcheri , once abundant in Xiamen, has declined sharply since mid-20th-century harvesting, underscoring the need for dietary evidence to guide habitat restoration. We surveyed 33 stations across four seasons in 2023, sampling B. belcheri and habitat surface sediments with concurrent environmental measurements, and profiled gut contents and co-occurring benthic resources using eukaryotic 18S rDNA (V4) metabarcoding. Ninety gut-content metabarcoding revealed a broad trophic spectrum spanning 32 phyla, with clear seasonal turnover: fungal peaks (dominated by Ascomycota/Basidiomycota) in spring, diatom dominance in summer, a mixed fungi–diatom phase in autumn, and increased zooplankton and diatom contributions in winter. Redundancy analysis linked diet composition primarily to temperature, dissolved oxygen, chlorophyll a , and suspended solids (adjusted R² ≈ 0.20), indicating strong environmental control of food availability. Comparisons with habitat surface sediments exposed consistent diet–resource mismatches, most notably low ingestion of sediment-dominant Chrysophyceae and enrichment of fungi in guts, implicating selective uptake based on particle traits and quality rather than abundance alone. These findings refine the traditional “microalgae-plus-detritus” view by demonstrating that marine fungi and diverse protists form substantial components of the diet and that B. belcheri functions as a conduit from the microbial loop to higher consumers. Recognizing and maintaining habitat surface-sediment conditions that support seasonally key fungal and algal prey can improve habitat restoration and inform captive feeding strategies for reintroduction.