Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

The ocean's biological pump strips nutrients out of the surface waters and exports them into the thermocline and deep waters. If there were no return path of nutrients from deep waters, the biological pump would eventually deplete the surface waters and thermocline of nutrients; surface biological productivity would plummet. Here we make use of the combined distributions of silicic acid and nitrate to trace the main nutrient return path from deep waters by upwelling in the Southern Ocean and subsequent entrainment into subantarctic mode water. We show that the subantarctic mode water, which spreads throughout the entire Southern Hemisphere and North Atlantic Ocean, is the main source of nutrients for the thermocline. We also find that an additional return path exists in the northwest corner of the Pacific Ocean, where enhanced vertical mixing, perhaps driven by tides, brings abyssal nutrients to the surface and supplies them to the thermocline of the North Pacific. Our analysis has important implications for our understanding of large-scale controls on the nature and magnitude of low-latitude biological productivity and its sensitivity to climate change.