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Cyanobacteria are the main autotrophs and N2‐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 N2fixation. Through a combination of bulk and amino acid nitrogen (AAN) specific analyses of field based N2fixation experiments, we demonstrate that the de novo synthesis of 13 AAs accounted for the majority of bulk N2fixation rates at four stations in the central Baltic Sea in July 2015. Slow AA turnover times of 87 ± 14 d coincided with low phosphate concentrations and high cell‐carbon biomasses of unicellular cyanobacteria. Very fast turnover times of 17 ± 3 d coincided with high phosphate concentrations and undecayed Nodularia spumigenacells, but unexpectedly also with phosphate depletion and decayed N. spumigenacells. In a decayed bloom, volumetric N2fixation rates into AAN provided a much better estimate of the net incorporation of N2into biomass than fixation into bulk nitrogen that rather reflected gross N2fixation. In an undecayed bloom, the turnover times of 13 AAs can be predicted from a single bulk N2fixation 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 N2fixation with hitherto uncharacterized consequences for heterotrophic food webs and diazotroph N inputs to the global ocean.

We report on methane enrichments that were observed during summer in the upper water column of the Gotland Basin, central Baltic Sea. In the eastern part of the basin, methane concentrations just below the thermocline varied between 15 nM and 77 nM, in contrast to the western part where no methane enrichments could be detected. Stable carbon isotope ratios of methane (δ13C‐CH4of −67.6‰) indicated its in situ biogenic origin from CO2reduction, which was supported by clonal sequences that clustered with Methanomicrobiaceae, a family of methanogenic Archaea. Incubation experiments with a Temora longicornisdominated seston fraction obtained from the relevant depth showed a positive correlation between seston concentration and methane production rates. Our results, in combination with previous literature outcomes, suggest that the methane enrichment in the eastern basin might be sustained by a diet‐consumer relationship between the dinoflagellate Dinophysis norvegicaand the copepod T. longicornis. However, our mass balance indicates that a local methane production of 110 pmol L−1d−1was needed to maintain the methane enrichment, and that the estimated production rate from our incubation experiments of 0.3 pmol CH4d−1per adult T. longicornis(about 1 pmol L−1d−1) was too low to maintain the methane enrichment by zooplankton associated methane production only. These calculations also showed that methane was consumed below the thermocline and not transported into the upper‐ocean, suggesting that other sources in the mixed layer in the range of 95 pmol L−1d−1are needed to maintain the observed methane air–sea flux.

The mean trophic position (TP) of mesozooplankton largely determines how much mass and energy is available for higher trophic levels like fish. Unfortunately, the ratio of herbivores to carnivores in mesozooplankton is difficult to identify in field samples. Here, we investigated changes in the mean TP of mesozooplankton in a highly dynamic environment encompassing four distinct habitats in the southern South China Sea: the Mekong River plume, coastal upwelling region, shelf waters, and offshore oceanic waters. We used a set of variables derived from bulk and amino acid nitrogen stable isotopes from particulate organic matter and four mesozooplankton size fractions to identify changes in the nitrogen source and TP of mesozooplankton across these habitats. We found clear indications of a shift in N sources for biological production from nitrate in near‐coastal waters with shallow mixed layer depths toward an increase in diazotroph‐N inputs in oceanic waters with deep mixed layer depths where diazotrophs shaped the phytoplankton community. The N source shift was accompanied by a lengthening of the food chain (increase in the TP). This may provide further support for the connection between diazotrophy and the indirect routing of N through the marine food web. Our combined bulk and amino acid δ15N approach also allowed us to estimate the trophic enrichment (TE) of mesozooplankton across the entire regional ecosystem. When put in the context of literature values, a high TE of 5.1‰ suggested a link between ecosystem heterogeneity and the less efficient transfer of mass and energy across trophic levels. Zooplankton are one of the central pillars of the marine food web and form an important link between the production of organic matter by phytoplankton and biomass at higher trophic levels (e.g., fish). Of particular interest are mesozooplankton (0.2–20 mm in size), which encompass a diverse assemblage of animals utilizing a range of feeding strategies, including herbivory, omnivory, and carnivory. Since mass and energy are lost with each trophic step, their prevailing feeding strategy determines the availability of mass and energy to the upper food web. The exact relationship between carnivores and herbivores in mesozooplankton has so far only been studied with complex experiments or in homogenous environments. We have now resolved zooplankton feeding relationships in a highly dynamic marine environment. Specifically, we used stable nitrogen isotopes in amino acids and bulk organic matter in combination with a habitat‐delineating method for phytoplankton to directly determine the ratio of carnivores to herbivores in zooplankton from dynamic habitats in the South China Sea. The mass and energy transfer across trophic levels is less efficient in such variable marine environments compared to stable open ocean systems. These findings represent a big step toward understanding the dynamics of planktonic food webs in general. Trophic structure of mesozooplankton is regulated by similar environmental factors such as phytoplankton assemblagesDiazotrophy and nutrient availability correlated with enhanced mesozooplankton carnivory in a complex tropical marine ecosystemMass and energy transfer across trophic levels of planktonic food webs are less efficient in spatially and temporally variable ecosystems Trophic structure of mesozooplankton is regulated by similar environmental factors such as phytoplankton assemblages Diazotrophy and nutrient availability correlated with enhanced mesozooplankton carnivory in a complex tropical marine ecosystem Mass and energy transfer across trophic levels of planktonic food webs are less efficient in spatially and temporally variable ecosystems