Diatom community transcriptomic response to nitrate and silicon limitation

Diatoms serve as the major link between the marine carbon and silicon (Si) biogeochemical cycles through their contributions to primary productivity and requirement for Si for cell wall formation. Although several laboratory culture-based studies have investigated the molecular response of diatoms to Si starvation and replenishment, diatom silicon metabolism has been understudied in natural populations. In this study, we conducted a series of manipulative, deck-board incubations using surface water collected near Monterey Bay in the California Current Ecosystem. Measurements of silica production were coupled with metatranscriptomic analysis of communities incubated with and without added Si to explore the underlying molecular response of diatom communities to silicon availability. Rapid utilization of nutrients created steep gradients in silicic acid and nitrate in the surface ocean with low silicic acid concentrations leading to limitation of silica production and cell growth at two of the three stations. Despite silica production rates ranging from 0.20 to 1.21 d^-1, metatranscriptomic analysis revealed no differences in expression of diatom silicon transporters – proteins responsible for the uptake and transport of Si – and minimal variation in total diatom gene expression between unamended and +Si samples. In contrast we found was a strong downregulation of carbon and nitrogen assimilation pathways that was predominantly driven by the gradient in nitrate rather than Si availability, suggesting a broader physiological impact of nitrogen stress on these communities. These data suggest that differences in rates of silica production cannot be resolved at the transcriptional level and that silicon transporter expression may not be a robust marker of physiological Si limitation.