Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.

Significance: As global CO ₂ levels rise and fossil fuel abundance decreases, the development of alternative fuels becomes increasingly imperative. Biologically derived fuels, and specifically those from microalgae, are promising sources, but improvements throughout the production process are required to reduce cost. Increasing lipid yields in microalgae without compromising growth has great potential to improve economic feasibility. We report that disrupting lipid catabolism is a practical approach to increase lipid yields in microalgae without affecting growth or biomass. We developed transgenic strains through targeted metabolic engineering that show increased lipid accumulation, biomass, and lipid yields. The target enzyme’s ubiquity suggests that this approach can be applied broadly to improve the economic feasibility of algal biofuels in other groups of microalgae.

In spite of attractive attributes, diatoms are underrepresented in research and literature related to the development of microalgal biofuels. Diatoms are highly diverse and have substantial evoluti...

Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa.

A major challenge in the development of microalgal strains for large-scale production is the optimization of biomass accumulation and production of fuel-relevant molecules such as triacylglycerol. Selecting targets for genetic manipulation approaches will require a fundamental understanding of the organization and regulation of carbon metabolic pathways in these organisms. Functional genomic and metabolomics data is becoming easier to obtain and process, however interpreting the significance of these data in a physiological context is challenging since the metabolic framework of all microalgae remains poorly understood. Owing to a complex evolutionary history, diatoms differ substantially from many other photosynthetic organisms in their intracellular compartmentation and the organization of their carbon partitioning pathways. A comparative analysis of the genes involved in carbon partitioning metabolism from Thalassiosira pseudonana, Phaeodactylum tricornutum, and Fragilariopsis cylindrus revealed that diatoms have conserved the lower half of glycolysis in the mitochondria, the upper half of glycolysis (including key regulatory enzymes) in the cytosol, and several mitochondrial carbon partitioning enzymes. However, some substantial differences exist between the three diatoms investigated, including the translocation of metabolic pathways to different compartments, selective maintenance and horizontal acquisition of genes, and differential gene family expansions. A key finding is that metabolite transport between intracellular compartments is likely to play a substantial role in the regulation of carbon flux. Analysis of the carbon partitioning components in the mitochondria suggests an important role of this organelle as a carbon flux regulator in diatoms. Differences between the analyzed species are specific examples of how diatoms may have modified their carbon partitioning pathways to adapt to environmental niches during the diversification of the group. This comparative analysis highlights how even core central pathways can be modified considerably within a single algal group, and enables the identification of suitable targets for genetic engineering to enhance biofuel precursor production