Reconstructing plankton food web interactions with DNA metabarcoding

This study is published in Molecular Ecology and shows for the first time the natural diet of zooplankton under temporal variation of food resources.

Knowledge of zooplankton in situ diet is critical for accurate assessment of marine ecosystem function and structure, but due to methodological constraints, there is still a limited understanding of ecological networks in marine ecosystems. Several target consumers, including copepods and cladocerans, were investigated by sequencing 16S rRNA and 18S rRNA genes to identify prokaryote and eukaryote potential prey present in their guts. During the spring phytoplankton bloom, we found a dominance of diatom and dinoflagellate trophic links to copepods. During the summer period, zooplankton including cladocerans showed a more diverse diet dominated by cyanobacteria and heterotrophic prey. Our study suggests that copepods present trophic plasticity, changing their natural diet over seasons, and adapting their feeding strategies to the available prey spectrum, with some species being more selective. We did not find a large overlap of prey consumed by copepods and cladocerans, based on prey diversity found in their guts, suggesting that they occupy different roles in the trophic web. This study represents the first molecular approach to investigate several zooplankton–prey associations under seasonal variation, and highlights how, unlike other techniques, the diversity coverage is high when using DNA, allowing the possibility to detect a wide range of trophic interactions in plankton communities.

Spring (March, April) and summer (June, July, August) zooplankton trophic interactions for (a) 16S and (b) 18S rRNA gene reads represented as coloured segments in circos plots. Zooplankton consumers are shown at the top and associated prey on the bottom of the plot. The width of the connection ribbons represents the relative abundance of a particular prey of that consumer and the width of each
prey taxon segment is proportional to the relative abundance of each prey considering all samples. Copepod (i.e., Maxillopoda) and parasitic (i.e., order Syndiniales) sequences are excluded in the plots.

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