Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for ∼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.

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The size of 30 small (2–60 µm) phytoplankton species was examined with a microscope and a Coulter Counter before and after fixation. Acid Lugol’s iodine caused cells to shrink immediately. The shrinkage effect was constant for concentrations of 1–10% Lugol’s iodine (in seawater). For optically measured cells fixed in 2% Lugol’s iodine, volume of live cells = 1.33 × (volume of fixed cells). Coulter Counter and optically measured volumes did not agree. For live cells, optical cell volume = 1.24–2.04 × (Coulter Counter determined volume); this difference is likely due to inaccurate volume measurements of non‐spherical cells by the Coulter Counter and by inaccurate microscopy resulting from optical distortions (errors of <0.5 µm in cell dimensions). Cell quota estimates were presented following the relation y = ax^b, where x = optically measured cell volume (µm³), y = any cell constituent (pg cell⁻¹), and a and b are constants. The constants a and b were 0.109 and 0.991 for carbon, 0.0172 and 1.023 for nitrogen, 0.043 and 1.058 for protein, and 0.00428 and 0.917 for Chl a. Our relation of carbon to volume differs from other literature values, in which there is no consensus. Our data can be used to determine carbon, nitrogen, protein, and Chl a estimates from field material that has been fixed with Lugol’s iodine, observed live, optically measured, or Coulter Counter measured; however, the variability in published data suggests that any of these estimates will have a large potential error.

The physiological processes of natural phytoplankton mortality due to environmental stress (vs. that caused by sedimentation and predation) are poorly understood. Cell survival was examined in batch cultures of the diatom Thalassiosira weissflogii and the chlorophyte Dunaliella tertiolecta during deprivation of fixed nitrogen or light. Despite severe impairment of photosynthetic efficiencies, both species remained viable during 2 weeks of N starvation. Under N stress, a specific protease was induced in the diatom, overall activity of proteases doubled, and there was gradual, selective loss of certain proteins, especially ribulose 1,5‐bisphosphate carboxylase/oxygenase. Light‐deprived diatoms were virtually unaffected, but the chlorophyte underwent catastrophic cell death after about 6 d of darkness. Cell death coincided with a large increase in protease activity and the induction of a specific protease. Although we cannot completely rule out roles for viruses or bacteria in the losses of cells, the consistent timing, the unique response to stress, and the coincident expression of a specific protease strongly suggest that the process is a form of autocatalyzed cell death, such as apoptosis. While of uncertain adaptive significance, phytoplankton cell death may have implications for species succession and cycling of organic matter in aquatic ecosysterns.

The effects of nitrogen starvation on photosynthetic efficiency were examined in three unicellular algae by measuring changes in the quantum yield of fluorescence with a pump-and-probe method and thermal efficiency (i.e. the percentage of trapped energy stored photochemically) with a pulsed photoacoustic method together with the inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea to distinguish photosystems I and II (PSI and PSII). Measured at 620 nm, maximum thermal efficiency for both photosystems was 32% for the diatom Thalassiosira weissflogii (PSII:PSI ratio of 2:1), 39% for the green alga Dunaliella tertiolecta (PSII:PSI ratio of 1:1), and 29% for the cyanobacterium Synechococcus sp. PCC 7002 (PSII:PSI ratio of 1:2). Nitrogen starvation decreased total thermal efficiency by 56% for T. weissflogii and by 26% for D. tertiolecta but caused no change in Synechococcus. Decreases in the number of active PSII reaction centers (inferred from changes in variable fluorescence) were larger: 86% (T. weissflogii), 65% (D. tertiolecta), and 65% (Synechococcus). The selective inactivation of PSII under nitrogen starvation was confirmed by independent measurements of active PSII using oxygen flash yields and active PSI using P700 reduction. Relatively high thermal efficiencies were measured in all three species in the presence of the PSII inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, suggesting the potential for significant cyclic electron flow around PSI. Fluorescence or photoacoustic data agreed well; in T. weissflogii, the functional cross-sectional area of PSII at 620 nm was estimated to be the same using both methods (approximately 1.8 x 102 A2). The effects of nitrogen starvation occur mainly in PSII and are well represented by variable fluorescence measurements.