Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation

Abstract

Marine primary productivity is iron (Fe)-limited in vast regions of the contemporary oceans, most notably the high nutrient low chlorophyll (HNLC) regions. Diatoms often form large blooms upon the relief of Fe limitation in HNLC regions despite their prebloom low cell density. Although Fe plays an important role in controlling diatom distribution, the mechanisms of Fe uptake and adaptation to low iron availability are largely unknown. Through a combination of nontargeted transcriptomic and metabolomic approaches, we have explored the biochemical strategies preferred by Phaeo dactylum tricornutum at growth-limiting levels of dissolved Fe. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport, and nitrate assimilation, were down-regulated. Our results show that this retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electrons by mitochondrial alternative oxidase (AOX) and non-photochemical quenching (NPQ), and augmented Fe-independent oxidative stress responses. Iron limitation leads to the elevated expression of at least three gene clusters absent from the Thalassiosira pseudonana genome that encode for components of iron capture and uptake mechanisms.

Fig. 1.

Hypothetical cellular pathways and processes in iron-limited pennate diatom cells. All roman green or red type depicts gene transcripts found to be up- or down-regulated, respectively. Italicized and underlined green type indicates metabolites found to be enriched relative to total protein in iron-limited cells. DF, diffusion factor; EPS, extracellular polymeric substances; FR, ferric reductase; HMA, heavy metal-associated; PCD, programmed cell death; ROS, reactive oxygen species.

Fig. 2.

Iron-regulated gene clusters in P. tricornutum. With the exception of FRE2, the iron-regulated cluster genes are absent from the T. pseudonana genome. Putative components of the Fe uptake system are shown in brown. The number of ESTs retrieved from the Fe limited EST library and the R statistic are provided. R > 12 indicates a statistically significant enrichment of ESTs in the Fe limited library relative to 11 other Fe-replete EST libraries (14). qRT-PCR data are given in Table S1.

Fig. 3.

Venn diagram of the distribution of proteins upregulated by iron limitation in P. tricornutum. Distribution of homologs (E ≤ 10⁻⁵, ≥50% coverage, ≥30% percent identity) to proteins in other lineages and the centric diatom T. pseudonana is depicted.