Transcriptional responses of three model diatoms to nitrate limitation of growth

Abstract

Diatoms are among the most diverse groups of phytoplankton in the ocean. Despite their widely recognized influence on ocean ecosystems and global biogeochemistry, little is known about the impact of this diversity on large-scale processes. Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three diatoms -Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries -to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. The three species shared 5583 clusters of orthologous genes based on OrthoMCL clustering of publically available diatom genomes. These clusters represent 30-54% of the predicted genes in each diatom genome. Less than 5% of genes within these core clusters displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling. Characterization of these finely tuned responses will help to better predict which types of diatoms will bloom under which sets of environmental factors.

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

“…Specific genes in this set included, but were not limited to, those genes associated with N assimilation (e.g., glutamate dehydrogenase, glutamine synthase, nitrate reductase), dissolved organic N utilization (e.g., urease, aminopeptidase, amino acid transport system), P scavenging (e.g., phosphate transporter, NPT), and DOP utilization (e.g., phosphatases) (Dataset 2). A number of these genes have been shown to be N-or P-responsive in transcriptional studies with cultures of the diatom T. pseudonana (56,61), and transporters and enzymes for the processing of organic N or P, as observed here, are well known to be RR in many phytoplankton (56,(62)(63)(64). Overall, these genes demonstrated patterns of regulation in situ (Fig.…”

Nitrate Reductase Knockout Uncouples Nitrate Transport from Nitrate Assimilation and Drives Repartitioning of Carbon Flux in a Model Pennate Diatom

“…FAME composition in both wild-type and NR-KO14 cells was dominated by C16:0, C16:1, and C20:5 FAs (Supplemental Figures 7A to 7E), consistent with previous reports for diatom FAME composition (Abida et al, 2015;Shen et al, 2016;Yu et al, 2009). As previous studies have established (Bender et al, 2014;Hockin et al 2012;Li et al, 2014;Rismani-Yazdi et al, 2012;Shifrin and Chisholm, 1981;Yang et al 2013;Yoon et al, 2012), N-limited conditions in photosynthetic microalgae induce accumulation of lipids, predominantly TAG, which is stored in lipid droplets. Therefore, it was not surprising to observe very rapid increases in TAG accumulation in NR-KO14 cells ( Figure 8C) as N-stress is sensed amid NO 3 2 -replete conditions.…”

“…Shortly after NO 3 2 is introduced to NR-KO14 cells, expression levels of key functional and metabolic gene clusters indirectly related to N-assimilation are sharply downregulated. Despite ample extra-and intracellular NO 3 2 , transcript profiles for these clusters respond similarly to those observed in wild-type cells under N-stress (Alipanah et al 2015;Bender et al, 2014;Juergens et al, 2015;Levitan et al, 2015;Schmollinger at al., 2014). However, in contrast to wild-type cells which gradually acclimate to a dwindling supply of N-product, the response in NR-KO14 cells is quite rapid.…”

“…Much recent work has focused both on characterizing the genes and metabolic pathways that induce lipid biosynthesis and on identifying routes and regulators that could be harnessed to substantially increase TAG production without negatively affecting growth (Alipanah et al, 2015;Ge et al, 2014;Hildebrand et al, 2012;Levitan et al, 2015;Radakovits et al, 2010;Trentacoste et al, 2013;Yang et al, 2013;Yoon et al, 2012). Deleterious impacts of NO 3 2 depletion include reduction of photosynthetic capacity, C-fixation, and N-assimilation and cessation of growth (Alipanah et al, 2015;Bender et al, 2014;Hockin et al, 2012;Syrett et al, 1986;Turpin, 1991).…”

Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean

“…3). This decrease in transcript abundance may be indicative of nitrogen and vitamin limitation based on the pattern in other organisms (40,41), but the regulation of these targets in haptophytes is poorly understood. Metal transport proteins were significantly increased for haptophytes in E1-E3 and indicated metabolic strategies following the addition of resources that differ from diatoms.…”