Bulk nitrogen isotopes in sediments are often used in paleoceanographic studies. However, they are often influenced by various sources and diagenetic processes—including inorganic nitrogen, terrestrial nitrogen, secondary microbial nitrogen, and differential degradation—making it difficult to accurately reflect the paleo-ecological conditions. Nitrogen-containing organic molecules, including individual amino acids (AAs) and chlorophyll degradation products such as maleimides (MALs), along with their nitrogen isotopes, can potentially constrain the aforementioned complex source-sink processes, thereby advancing the field of nitrogen isotope paleoceanography. Here these potentials are investigated through integrated analyses of bulk organic and AA- and MAL-specific δ¹⁵N measurements, as well as the AAs- and MALs-derived degradation indices, in surface sediments from the South China Sea (SCS).

Our results show that bulk sedimentary δ¹⁵N_org (range 5.0–6.3‰; mean 5.6 ± 0.3‰) in the SCS increases with water depth (R² = 0.62). This trend is likely driven by increasing oxygen exposure time and cumulative microbial deamination with water depth during water-column settling and sea-floor retention, as evidenced by elevated divergence among δ¹⁵N_AA signatures (i.e., ΣV values, mean 3.3‰) and systematically decreasing TOC and TON with depth. The δ¹⁵N of phenylalanine (δ¹⁵N_Phe) is usually considered to reflect that of primary producers; in the oligotrophic SCS, it should also represent the isotopic baseline of N nutrients. However, sedimentary δ¹⁵N_Phe (mean 10.8‰) exceeds the SCS baseline by ~5.3‰, reflecting extensive microbial overprinting. Comparatively, δ¹⁵N of total hydrolyzable AAs (δ¹⁵N_THAA) is weakly diagenetically influenced (δ¹⁵N_THAA vs. ΣV, R² = 0.13), and an offset of 7.6 ± 1.0‰ is proposed for the SCS δ¹⁵N baseline calculations. Nevertheless, the typical δ¹⁵N_AAs distribution pattern between trophic and source AAs is largely preserved in sediments and the tropical position (TP), derived from the δ¹⁵N difference between Phe and Glx, can be corrected according to the linear relationship between TP and ΣV (R² = 0.57).

The difference (ε_MAL) between δ¹⁵N_MAL and δ¹⁵N_org can potentially be used to reconstruct relative contributions of sedimentary organic matter from eukaryotic and prokaryotic (cyanobacteria) phytoplankton. After correcting for water depth influence, the calculated ε_MAL values (2.4±1.7 ‰) from our sediment data reveal contributions of ~48% eukaryotic and ~52% prokaryotic primary producers to export production. Interestingly, the relative contributions are broadly consistent with modern water-column surveys of the SCS phytoplankton community, suggesting that prokaryotic production is efficiently exported without significant attenuation. Collectively, our study shows that δ¹⁵N of AAs and MALs, along with bulk δ¹⁵N, are powerful tools in the study of marine paleoecology.