Changes in the community composition of marine microbial eukaryotes across multiple temporal scales of measurement

Microbial eukaryotes are critical components of marine ecosystems, contributing to vital ecological and biogeochemical processes, but fundamental knowledge regarding patterns of spatial and temporal variability of natural assemblages of these taxa is limited. Sequence-based and fragment-based genetic approaches were used to characterize changes in community composition and structure of microbial eukaryote assemblages across multiple timescales (days, months, seasons, years). Short-term temporal changes in community composition and structure were characterized for a 3-day bottle incubation experiment that consisted of 3 treatments (a control, inorganic nutrient enrichment, and organic nutrient enrichment). Inorganic and organic enrichments resulted in dramatic changes in community structure and substantially influenced richness estimates, but community composition and structure also responded rapidly and significantly even without nutrient additions. The relative abundance of some initially rare taxa increased dramatically, implying that some taxa comprising the 'rare biosphere' responded to take on ecologically important roles under changing environmental conditions. Long-term temporal patterns of variability (monthly, seasonal and interannual) in the composition of natural assemblages of microbial eukaryotes were examined at the San Pedro Ocean Time-series (SPOT) station for 237 samples collected from four depths on cruises between September 2000 and December 2010. The spatiotemporal variability of microbial eukaryote assemblages indicated the presence of distinct communities within and below the euphotic zone at the SPOT station. Month-to-month community similarity values (∼51-61%) were relatively high for assemblages at all depths, but assemblages at 5 m were temporally more dynamic compared to deeper assemblages. Seasonality was apparent for microbial eukaryote assemblages within and below the euphotic zone at 5 m and 150 m, but not at the deep chlorophyll maximum (DCM) which varied in depth seasonally, or at 500 m. Microbial eukaryote assemblages exhibited cyclical patterns in nearly half of all the years and depths examined in this study, with an annual resetting of communities during winter. Interannual variability was apparent at all depths and was a major factor influencing community composition at our study site. Network analysis based on global Spearman correlations identified highly correlated temporal patterns between microbial eukaryote taxa for samples collected between September 2000 and December 2003, indicating the presence of unique guilds of microbial eukaryote taxa at each depth with coordinated responses over the 3 years. Our results provide new insight into the temporal changes within natural assemblages of microbial eukaryotes on multiple timescales of variability, an essential step for linking changes in microbial eukaryote communities brought about by environmental fluctuations to overall ecosystem function.