Origin, trophic transfer and recycling of particulate organic matter in two upwelling bays of Humboldt Current System: Insights from compound-specific isotopic compositions of amino acids

Abstract

The Chilean upwelling bays are highly productive ecosystems shaped by their interactions with the open ocean. Although significant knowledge exists regarding their hydrodynamic and ecological processes, the spatial dynamics of trophic transfer and heterotrophic resynthesis of organic matter remain insufficiently understood. To address these knowledge gaps, we conducted a compound-specific isotope analysis of amino acids (CSIAA) on suspended and sinking particulate organic matter from Mejillones and Antofagasta bays, two oceanographic environments characterized by contrasting hydrodynamic conditions and topographic orientations. In Mejillones Bay, the CSIAA trophic positions for metazoan (1.7 ± 0.5) and protozoan (2.3 ± 0.3) were significantly higher compared to those in Antofagasta Bay (metazoans: 1.3 ± 0.6; protozoans: 1.5 ± 0.3), highlighting protozoans as primary trophic vectors. MixSIAR analysis indicated that phytoplankton is a key source of particulate organic matter in both bays; however, Mejillones Bay exhibited a greater proportion of microbially degraded organic matter. Enhanced heterotrophic resynthesis in Mejillones Bay (ΣV: 1.9-2.5) was associated with lower oxygen levels, increased concentrations of NO₂ ⁻ , and heightened stratification of the water column. Additionally, depth-dependent variations in δ15N for phenylalanine and threonine indicated a greater solubilization of particles, which contributed to a reduction in the export of particulate organic matter (averaging 9 ± 2 mg C/m²/d). These findings underscore the critical role of the intricate interactions between the bay's topographic features and the physical and biological processes that ultimately influence the cycling trajectories of particulate organic matter in upwelling bays.

Fig 1. Geographical context of the study area in northern Chile, shaped by the cold Humboldt Current flowing northward along the western coast of South America and the southward-moving Peru-Chile Undercurrent (left panel).

A detailed view of Mejillones and Antofagasta bays shows the nine sampling stations: blue circles indicate all general sampling locations, while red circles highlight the three stations in each bay where additional stable N and C isotope analyses were conducted (right panel). Reprinted from https://cran.r-project.org/web/packages/ggOceanMaps/index.html under a CC BY license, with permission from Dr. Edgart Flores, original copyright 2025.”.

Fig 2. Vertical profiles of temperature (°C), salinity, dissolved oxygen (

µM), pH, and T-S diagrams for MB and AB.

Fig 3. Vertical profiles of (A)

δ¹⁵N-NO₃^-, (B) N*, and (C) apparent oxygen utilization (AOU) in the water columns of MB and AB. Data are presented as mean ± standard deviation values.

Fig 4. Vertical profiles of (A) TP _Metazoan; (B) TP _Protozoan, (C) ΣV; (D)

δ¹⁵N Phe, and (E) δ¹⁵N Thr in the water columns of MB and AB. Data are presented as mean ± standard deviation values.

Fig 5. Relative fractional contribution of POM from the main end-members (i.e., zooplankton, MDOM, fecal pellets, and phytoplankton) based on

δ¹⁵N at varying depths (5–20 m and 35–45 m) in MB and AB, estimated with the MixSIAR mixing model (Stable Isotope Analysis in R).

Fig 6. Relative fractional contribution of POM to sediment traps from the main end-members (zooplankton, MDOM, fecal pellets, phytoplankton, and water column POM), based on

δ¹⁵N values. Results for (A) MB and (B) AB were estimated by the MixSIAR mixing model.

Fig 7. Vertical patterns of apparent isotopic fractionation (εx/Glu) for Gly and Ser in the water columns of (A) MB and (B) AB.

Data are presented as mean ± standard deviation values.

Fig 8. Spatial distributions of mean oxygen inventories, stratification values, sea surface temperatures (SST), and average NO₂^- concentrations are presented for MB (A-D) and AB (E-H).