Long-term dynamics of phytoplankton, protistan, and prokaryotic communities at the San Pedro Ocean Time-series

16S and 18S rRNA sequencing has been widely used for microbiome analyses. However, they are rarely used at the same time for investigating interactions between eukaryotic microbes and prokaryotes. As these relationships can be inferred using species co-occurrence patterns together with evidence from culture experiments, simultaneous amplification of 16S and 18S rRNA with universal primers in a single PCR reaction significantly improves sampling efficiency, and also allows all organisms to be evaluated on a common scale. This study used the universal primers (515Y/926R) to investigate marine microbial communities at the San Pedro Ocean Time-series (SPOT) during 2000-2018, focusing on two size fractions (0.2-1.2 µm and 1.2-80 µm). The processing pipeline we developed is able to separate community composition into protistan (18S rRNA), phytoplankton (plastidal 16S rRNA), free-living and particle-associated prokaryotes (16S rRNA) communities. The results show that phytoplankton, protistan, and prokaryotic communities all have strong seasonality at the surface and the deep chlorophyll maximum (DCM). However, only the free-living prokaryotes exhibited a relatively stable dynamic without decreasing in average similarity over time, whereas the particle-associated fraction and protists were more variable. The different dynamics between free-living and particle-associated prokaryotes imply that they might be driven by different ecological processes (bottom-up vs. top-down controls) due to their lifestyles.