Project: Genomic and Transcriptomic Comparison of Iron and Light Physiology in Coastal and Oceanic Diatoms

Project description from NSF award abstract:
Diatoms are among the most important primary producers in the ocean. Coastal species can respond to dynamic inputs of nutrients into the surface ocean and form large biomass blooms. Phytoplankton growth in much of the ocean is limited by one nutrient or another, and species that persist in these environments must be able to function under these low nutrient conditions. Oceanic diatom species have lower Fe requirements for growth and may have evolved to subsist in low Fe environments by changing the composition of Fe-demanding metabolic pathways. Iron and light responsive pathways are intimately linked because of the large Fe requirement of photosynthesis and the potential for both to limit growth and the efficiency of the biological carbon pump. Physiological and field studies have shown that many diatoms are susceptible to Fe/light co-limitation, but we lack information on the biochemical basis for co-limitation and how this differs between diatom species. This project will use a combination of genomics tools to investigate how coastal and oceanic diatoms in the ecologically important Thalassiosira genus respond to differing conditions of Fe and light. The investigators will compare the genome sequence of the oceanic diatom T. oceanica, which has recently been sequenced by the PI in collaboration with Illumina, Inc., to published diatom genomes to identify potential differences and similarities in the Fe and light metabolism in oceanic and coastal diatoms. They will use normalized libraries of Expressed Sequence Tags (EST) to characterize the transcriptome of T. oceanica, an oceanic strain of T. weissflogii, and the coastal diatom T. rotula grown in a matrix of Fe-limiting and replete conditions and at low and growth-saturating light levels. And they will quantify gene expression levels for the transcriptome-wide response in these experiments using digital gene expression (DGE), and use the EST data to map the DGE tags. Data from the DGE and EST experiments will be used to compare how diatom metabolism responds to variable light and Fe concentrations and to identify target genes for following limitation in natural diatom populations. Expression of these genes will be monitored in time-course experiments with additional manipulations of Fe and light levels to identify gene markers indicative of different physiological states using quantitative PCR (qPCR). The investigators will also design antibodies to a select number of proteins to monitor protein expression, and they will use qPCR and antibodies to follow responses in diatom communities in field samples collected from a cruise transitioning between Fe-replete and Fe-limiting environments as part of other funded research efforts. This work will further our understanding of how diatoms are adapted to different environments and what the genetic basis for their ecological success may be. Results from this work will help us predict how diatoms may respond to changing light regimes as a result of increased stratification due to climate change and help predict if species from different habitats will have similar or varied responses.