Knowledge of how zooplankton can utilize cyanobacteria to sustain their nitrogen (N) demand for essential compounds like amino acids (AAs) is a key to predicting responses of higher trophic levels in terms of production and food web structure to future enhanced water column stratification. We explored the natural abundances of bulk N and AA‐specific nitrogen isotopes (δ15N) in particulate organic matter and mesozooplankton size‐fraction samples from three vertically separated water bodies in the central Baltic Sea during two summertime cyanobacteria blooms. The combination of plankton community and isotope data together with environmental variables helped to identify a mechanism of diazotrophic AA supply (synthesized during N2 fixation) for mesozooplankton, that largely depended on the sea surface temperature which regulated the access to the diazotrophic N‐based food web in the surface water (SW). We found that in the warmer summer, thermophilic cladocerans (e.g., Bosmina spp.) benefited most from diazotrophic AAs in the SW (19.8°C), while only in the colder summer, temperate copepods (e.g., Temora longicornis) ascended from the subjacent winter water into the SW (16.2°C) and incorporated diazotrophic AAs. Trophic position estimates based on the phenylalanine and glutamic acid δ15N signatures revealed that the diazotrophic AA supply into mesozooplankton was mainly indirect via feeding on mixo‐ and heterotrophic diets. Significantly enriched δ15N signatures in phenylalanine in the deep mesozooplankton (mainly copepods of Pseudo‐ and Paracalanus spp.) from the bottom water (BW) that was a region of the suboxic zone point to a reliance on a local food web. Mesozooplankton in the BW was feeding on diets of heterotrophic origin and probably profited from the heterotrophic re‐synthesis of AAs originating from sinking organic matter, as well as from the indirect incorporation of de novo synthesized AAs that most likely originated from chemoautotrophic bacteria or archaea communities in the suboxic zone. Our findings suggest that indirect feeding on diazotrophs and chemoautotrophs will be principal ways of amino acid supply for zooplankton in future enhanced stratified aquatic systems. Only a relatively small increase in temperature may restrict temperate key species from diazotrophic N‐based food webs in the mixed layer.

Changes in the complexity of planktonic food webs may be expected in future aquatic systems due to increases in sea surface temperature and an enhanced stratification of the water column. Under these conditions, the growth of unpalatable, filamentous, N2‐fixing cyanobacterial blooms, and their effect on planktonic food webs will become increasingly important. The planktonic food web structure in aquatic ecosystems at times of filamentous cyanobacterial blooms is currently unresolved, with discordant lines of evidence suggesting that herbivores dominate the mesozooplankton or that mesozooplankton organisms are mainly carnivorous. Here, we use a set of proxies derived from amino acid nitrogen stable isotopes from two mesozooplankton size fractions to identify changes in the nitrogen source and the planktonic food web structure across different microplankton communities. A transition from herbivory to carnivory in mesozooplankton between more eutrophic, near‐coastal sites and more oligotrophic, offshore sites was accompanied by an increasing diversity of microplankton communities with aging filamentous cyanobacterial blooms. Our analyses of 124 biotic and abiotic variables using multivariate statistics confirmed salinity as a major driver for the biomass distribution of non‐N2‐fixing microplankton species such as dinoflagellates. However, we provide strong evidence that stratification, N2 fixation, and the stage of the cyanobacterial blooms regulated much of the microplankton diversity and the mean trophic position and size of the metabolic nitrogen pool in mesozooplankton. Our empirical, macroscale data set consistently unifies contrasting results of the dominant feeding mode in mesozooplankton during blooms of unpalatable, filamentous, N2‐fixing cyanobacteria by identifying the at times important role of heterotrophic microbial food webs. Thus, carnivory, rather than herbivory, dominates in mesozooplankton during aging and decaying cyanobacterial blooms with hitherto uncharacterized consequences for the biogeochemical functions of mesozooplankton.

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Cyanobacteria are the main autotrophs and N 2 -fixing (diazotrophic) organisms in large parts of the oligotrophic global ocean, where generally all heterotrophic production depends on their activity. Amino acids (AAs) from cyanobacteria are essential macronutrients for these heterotrophic food webs, yet little is known about the de novo synthesis of AAs during N 2 fixation. Through a combination of bulk and amino acid nitrogen (AAN) specific analyses of field based N 2 fixation experiments, we demonstrate that the de novo synthesis of 13 AAs accounted for the majority of bulk N 2 fixation rates at four stations in the central Baltic Sea in July 2015. Slow AA turnover times of 87 6 14 d coincided with low phosphate concentrations and high cellcarbon biomasses of unicellular cyanobacteria. Very fast turnover times of 17 6 3 d coincided with high phosphate concentrations and undecayed Nodularia spumigena cells, but unexpectedly also with phosphate depletion and decayed N. spumigena cells. In a decayed bloom, volumetric N 2 fixation rates into AAN provided a much better estimate of the net incorporation of N 2 into biomass than fixation into bulk nitrogen that rather reflected gross N 2 fixation. In an undecayed bloom, the turnover times of 13 AAs can be predicted from a single bulk N 2 fixation rate. This is the first direct evidence that the very late, decayed stage of a cyanobacteria bloom can be a flashpoint of very fast AA turnover during N 2 fixation with hitherto uncharacterized consequences for heterotrophic food webs and diazotroph N inputs to the global ocean. Highlights 1. Cyanobacteria composition and bloom stage can be critical factors for amino acid (AA) turnover. 2. In a decaying bloom, amino acid nitrogen based volumetric rates reflected net N 2 fixation. 3. Bulk nitrogen based volumetric rates in a decaying bloom reflected gross N 2 fixation. 4. In undecayed blooms, AA turnover can be predicted from single bulk N 2 fixation rates. 5. Decaying cyanobacteria blooms can be flashpoints of AA turnover during N 2 fixation.

Increasing sea surface temperatures (SST) and blooms of lipid‐poor, filamentous cyanobacteria can change mesozooplankton metabolism and foraging strategies in marine systems. Lipid shortage and imbalanced diet may challenge the build‐up of energy pools of lipids and proteins, and access to essential fatty acids (FAs) and amino acids (AAs) by copepods. The impact of cyanobacterial blooms on individual energy pools was assessed for key species temperate Temora longicornis and boreal Pseudo‐/Paracalanus spp. that dominated field mesozooplankton communities isolated by seasonal stratification in the central Baltic Sea during the hot and the cold summer. We looked at (a) total lipid and protein levels, (b) FA trophic markers and AA composition, and (c) compound‐specific stable carbon isotopes (δ13C) in bulk mesozooplankton and in a subset of parameters in particulate organic matter. Despite lipid‐poor cyanobacterial blooms, the key species were largely able to cover both energy pools, yet a tendency of lipid reduction was observed in surface animals. Omni‐ and carnivory feeding modes, FA trophic makers, and δ13C patterns in essential compounds emphasized that cyanobacterial FAs and AAs have been incorporated into mesozooplankton mainly via feeding on mixo‐ and heterotrophic (dino‐) flagellates and detrital complexes during summer. Foraging for essential highly unsaturated FAs from (dino‐) flagellates may have caused night migration of Pseudo‐/Paracalanus spp. from the deep subhalocline waters into the upper waters. Only in the hot summer (SST>19.0°C) was T. longicornis submerged in the colder subthermocline water (~4°C). Thus, the continuous warming trend and simultaneous feeding can eventually lead to competition on the preferred diet by key copepod species below the thermocline in stratified systems. A comparison of δ13C patterns of essential AAs in surface mesozooplankton across sub‐basins of low and high cyanobacterial biomasses revealed the potential of δ13C‐AA isoscapes for studies of commercial fish feeding trails across the Baltic Sea food webs.