Quantifying long‐term recurrence in planktonic microbial eukaryotes

Abstract

How much temporal recurrence is present in microbial assemblages is still an unanswered ecological question. Even though marked seasonal changes have been reported for whole microbial communities, less is known on the dynamics and seasonality of individual taxa. Here, we aim at understanding microbial recurrence at three different levels: community, taxonomic group and operational taxonomic units (OTUs). For that, we focused on a model microbial eukaryotic community populating a long‐term marine microbial observatory using 18S rRNA gene data from two organismal size fractions: the picoplankton (0.2–3 µm) and the nanoplankton (3–20 µm). We have developed an index to quantify recurrence in particular taxa. We found that community structure oscillated systematically between two main configurations corresponding to winter and summer over the 10 years studied. A few taxonomic groups such as Mamiellophyceae or MALV‐III presented clear recurrence (i.e., seasonality), whereas 13%–19% of the OTUs in both size fractions, accounting for ~40% of the relative abundance, featured recurrent dynamics. Altogether, our work links long‐term whole community dynamics with that of individual OTUs and taxonomic groups, indicating that recurrent and non‐recurrent changes characterize the dynamics of microbial assemblages.

Time series are critical to understand microbial plankton diversity and ecology

“…have developed a new Recurrence Index (RI) to specifically address this question on a rich data set of plankton samples collected monthly over 10 years at the Blanes Bay Microbial Observatory (Mediterranean Sea) and submitted to 18S rRNA gene metabarcoding analysis. For both eukaryotes and prokaryotes, a recurrent observation in previous marine plankton metabarcoding analyses is that diversity is most often dominated by rare OTUs occurring at very low frequencies and in single or very few samples(Pedrós-Alió, 2006) Giner et al (2019). corroborated this expectation and, by applying their RI index, they found that only 13% and 19% of the pico-and nano-eukaryotic OTUs, respectively, showed seasonality.…”

“…For both eukaryotes and prokaryotes, a recurrent observation in previous marine plankton metabarcoding analyses is that diversity is most often dominated by rare OTUs occurring at very low frequencies and in single or very few samples (Pedrós‐Alió, ). Giner et al () corroborated this expectation and, by applying their RI index, they found that only 13% and 19% of the pico‐ and nano‐eukaryotic OTUs, respectively, showed seasonality. However, these OTUs represented a large proportion of the sequence reads (39% and 37%, respectively), indicating that they are quantitatively important members of the small‐size eukaryotic plankton community.…”

“…Analyzing that information is challenging because planktonic eukaryotic community structures are complex, with hundreds or thousands of different OTUs, most of them exhibiting at first glimpse a rather sporadic temporal behavior. Giner et al () have developed a new Recurrence Index (RI) to specifically address this question on a rich data set of plankton samples collected monthly over 10 years at the Blanes Bay Microbial Observatory (Mediterranean Sea) and submitted to 18S rRNA gene metabarcoding analysis. For both eukaryotes and prokaryotes, a recurrent observation in previous marine plankton metabarcoding analyses is that diversity is most often dominated by rare OTUs occurring at very low frequencies and in single or very few samples (Pedrós‐Alió, ).…”

“…In a From the Cover article in this issue of Molecular Ecology, Giner et al (2019) introduce a new Recurrence Index (RI) to specifically look for seasonality in time-series metabarcoding data. They inspected the temporal dynamics of all operational taxonomic units (OTUs) in a rich sequence data set of pico-and nanoplanktonic eukaryotes in samples collected monthly during 10 years.…”

“…However, this averaging approach misses the finegrain information contained in the temporal dynamics of each individual OTU. Analyzing that information is challenging because planktonic eukaryotic community structures are complex, with hundreds or thousands of different OTUs, most of them exhibiting at first glimpse a rather sporadic temporal behavior Giner et al (2019). have developed a new Recurrence Index (RI) to specifically address this question on a rich data set of plankton samples collected monthly over 10 years at the Blanes Bay Microbial Observatory (Mediterranean Sea) and submitted to 18S rRNA gene metabarcoding analysis.…”