Combining In Situ and Culture-based ‘Omic and Biogeochemical Measures to Identify the Physiological Ecology of a Blooming Diatom in the Amazon River Plume

The Amazon River is the largest riverine fresh water input to the ocean and forms a plume that may extend over 1.3 x 10⁶ km², providing a significant source of nutrients that contributes to enhanced regional export flux and carbon sequestration. While we know that the enriched nutrient environment of the plume should promote phytoplankton success, it is difficult to discern the physiological basis of one organism’s success over another. Characterizing the physiological ecology of individual species is increasingly tractable with the application of ‘omic approaches in situ. In the spring of 2013, a large centric diatom of the genus Coscinodiscus was observed in a mesohaline region of the Amazon River plume at high abundance relative to other diatoms both in the surface low salinity lens and in sediment traps deployed in this region. Using a combination of physiological, biogeochemical, rate, and ‘omic measurements, the metabolic state of the blooming Coscinodiscus species was examined in situ and in incubation experiments designed to characterize the physiological response to changes in nutrient supply ratios. In addition to field measurements, an isolate of the blooming Coscinodiscus species was brought into uni-algal culture and used to generate a de novo transcriptome assembly spanning gene sets expressed over a range of physiological conditions. This unique aspect of the research approach provided a reference transcriptome for improved (6 fold) identification of Coscinodiscus metatranscriptome reads. Taken together, the data from this multi-faceted approach, indicate the strong control of nitrogen on Coscinodiscus physiology in this system, as evidenced by cell counts and chlorophyll patterns as well as the modulation of Coscinodiscus marker genes like a nitrogen-regulated nitrate transporter. Future work that uses a similar approach may be a valuable path forward in discerning the physiological ecology of key species in other systems.