This study includes time series of 18S ribosomal DNA gene metabarcoding data covering from Aug-2016 to Jun-2018.

Changes in protists biodiversity and community structure in the coastal lagoon of the Mar Menor after the phytoplankton bloom that produced the collapse of the ecosystem in 2016 were analyzed. The analyses were based on a time series of 18S ribosomal DNA gene metabarcoding data covering from Aug-2016 to Jun-2018. Relative abundances of amplicon sequence variants (ASVs) assigned at least to order level were classified within four tropic modes (autotrophic, dinoflagellates, heterotrophic and Syndiniales) and used to network analyses based on co-occurrence matrices. This postbloom period was characterized by large fluctuation in phytoplankton biomass, including phases with chlorophyll a concentration lower than 1.0 ?g L-1 and peaks above 12.7 ?g L-1. Cluster and NMDS analyses permitted distinguishing three communities featuring periods with different productivity level. ASVs assigned to the four trophic modes contributed significantly to these differences. The comparisons among the networks built for each period show that average degree and stability changed with the Chl a levels of the lagoon; specifically, low productivity conditions lead to higher stability. These changes in network topology occurred along with changes in the number of modules that increased during the period of highest productivity implying a reshuffling of the networks into sub-networks (modules) of ASV dense aggregates. Since the centrality was lower during low chlorophyll a concentration period, the higher modularity at high Chl a concentration implies that the network is re-organized around a comparatively lower amount of ASVs, which are strongly connected and might lead to higher vulnerability. Our results support the hypothesis that plankton network structure is modulated by changing nutrient levels emphasizing the importance of trophic interactions in shaping the plankton community's response. Our work underscores the importance of considering the whole plankton communities in the eutrophication surveillance programs.