Temporal Dynamics of Microbial Plankton Diversity at a Long-Term Ecological Monitoring Site

Microbial marine eukaryotes play a key role in ocean trophic dynamics, as they comprise a large proportion of both primary producers and primary consumers. The advent of high-throughput amplicon sequencing with environmental samples has uncovered far greater eukaryotic diversity than previous methods, but much of this diversity remains unclassified and uncharacterized. Here we describe eukaryotic community diversity at the Scripps Institution of Oceanography pier, a long-term ecological monitoring site in the California current ecosystem. This site is well suited for a temporal study as other data, including chlorophyll, temperature, and cyanobacteria counts, have been collected on a weekly basis for over a decade. The compilation of community 18S sequence data at seventeen time points over several years reveals that the eukaryotic microbial composition is highly dynamic. By defining and classifying Operational Taxonomic Units (OTUs) we found that approximately a quarter of this diversity remains unclassified. While some OTUs were ubiquitous temporally, less than 1% were present during all times sampled and the majority of OTUs were members of the ‘rare biosphere’-- present at low levels during only one or a few time points. With this time series we can explore factors, both environmental and biological, underlying the temporal differences in the eukaryotic community. We additionally used our sequence data to examine the environmental relevance of lab isolates from the pier sampling site, including both heterotrophic nanoflagellate grazers and common autotrophs. We found these model species to be relatively rare in the overall community over time, but this was partially dependent on whether the conventional 97% similarity cutoff for species-level OTU assignment was used. This raises important questions about whether this cutoff is appropriate within all taxa.