Temporal variation of Skeletonema community composition from a long-term time series in Narragansett Bay identified using high-throughput DNA sequencing

Phytoplankton species cannot always be identified by their morphology using light microscopy, which makes inferring the ecological and biogeochemical importance of individual species a difficult task. Here, a combination of microscopy and high-throughput DNA sequencing was used to examine morphologically cryptic and pseudo-cryptic species in the diatom genus Skeletonema from the Long-Term Plankton Time Series in Narragansett Bay (NBay), where Skeletonema is ecologically important, comprising up to 99% of microplankton cells in surface waters. The 28S rDNA from mock phytoplankton communities comprising known species was amplified and sequenced using newly developed Skeletonema-specific primers. The relative abundances of species in the sequence data did not match expected abundances, suggesting that 28S copy number can vary greatly, even among closely related diatom species. The 28S rDNA was also amplified from 75 field samples collected from 2008 to 2013. A total of 7 Skeletonema species were identified, including 5 newly detected species from NBay. Skeletonema species composition was highly seasonal and significantly correlated with water temperature. Winter-spring and summer-autumn communities were significantly different and characterized by low and high species richness, respectively. Species abundance during winter-spring was quantified by combining sequence data with light microscopy counts, revealing Skeletonema marinoi as the numerically dominant species during the winter-spring bloom. Seasonal variation in Skeletonema composition suggests that, although morphologically similar, species in this genus are likely adapted to different environmental conditions, raising the possibility that species composition of this important bloom-forming genus may shift as water temperatures in NBay increase due to anthropogenic influences.