Marine food webs are highly compartmentalized and characterizing the trophic niches among consumers is important for predicting how impact from human activities affect the structuring and functioning of marine food webs. Biomarkers such as bulk stable isotopes have proven to be powerful tools to elucidate trophic niches, but they may lack in resolution, particularly when spatio-temporal variability in a system is high. To close this gap, we investigated whether carbon isotope (δ¹³C ) patterns of essential amino acids (EAAs), also termed d13CAA fingerprints, can characterize niche differentiation in a highly dynamic marine system. Specifically, we tested the ability of d13CAA fingerprints to differentiate trophic niches among six functional groups and ten individual species in the Baltic Sea. We also tested whether fingerprints of the common zooplanktivorous fishes, herring and sprat, differ among four Baltic Sea regions with different biochemical conditions and phytoplankton assemblages. Additionally, we investigated how these results compared to bulk C and N isotope data for the same sample set. We found significantly different d13CAA fingerprints among all six functional groups. Species differentiation was in comparison less distinct, due to partial convergence of the species’ fingerprints within functional groups. Herring and sprat displayed region specific d13CAA fingerprints indicating that this approach could be used as a migratory marker. Niche metrics analyses showed that bulk isotope data had a lower power to differentiate between trophic niches than 13CAA fingerprinting. We conclude that d13CAA fingerprinting has a strong potential to advance our understanding of ecological niches, and trophic linkages from producers to higher trophic levels in dynamic marine systems. Given how management practices of marine resources and habitats are reshaping the structure and function of marine food webs, implementing new and powerful tracer methods are urgently needed to improve the knowledge base for policy makers.

Baltic Sea fish samples collected during the cruise AL476 with the research vessel ALKOR in April 2016. All tissue samples were freeze dried. Samples for d13C amino acid analysis were first hydrolyzed in 6 N HCl at 110°C for 20 h before derivatizing the amino acids to N-acetyl methyl esters. The samples were analysed at the Leibniz Laboratory at Kiel University.

Elemental content and bulk isotope values were determined at the Stable Isotope Facility of the Experimental Ecology Group, GEOMAR, Kiel.

The isotope ratios are expressed relative to international standards; Vienna Pee Dee Belemnite (VPDB) for carbon and atmospheric air for nitrogen.