Diatom Proteomics Reveals Unique Acclimation Strategies to Mitigate Fe Limitation

Abstract

Phytoplankton growth rates are limited by the supply of iron (Fe) in approximately one third of the open ocean, with major implications for carbon dioxide sequestration and carbon (C) biogeochemistry. To date, understanding how alteration of Fe supply changes phytoplankton physiology has focused on traditional metrics such as growth rate, elemental composition, and biophysical measurements such as photosynthetic competence (Fv/Fm). Researchers have subsequently employed transcriptomics to probe relationships between changes in Fe supply and phytoplankton physiology. Recently, studies have investigated longer-term (i.e. following acclimation) responses of phytoplankton to various Fe conditions. In the present study, the coastal diatom, Thalassiosira pseudonana, was acclimated (10 generations) to either low or high Fe conditions, i.e. Fe-limiting and Fe-replete. Quantitative proteomics and a newly developed proteomic profiling technique that identifies low abundance proteins were employed to examine the full complement of expressed proteins and consequently the metabolic pathways utilized by the diatom under the two Fe conditions. A total of 1850 proteins were confidently identified, nearly tripling previous identifications made from differential expression in diatoms. Given sufficient time to acclimate to Fe limitation, T. pseudonana up-regulates proteins involved in pathways associated with intracellular protein recycling, thereby decreasing dependence on extracellular nitrogen (N), C and Fe. The relative increase in the abundance of photorespiration and pentose phosphate pathway proteins reveal novel metabolic shifts, which create substrates that could support other well-established physiological responses, such as heavily silicified frustules observed for Fe-limited diatoms. Here, we discovered that proteins and hence pathways observed to be down-regulated in short-term Fe starvation studies are constitutively expressed when T. pseudonana is acclimated (i.e., nitrate and nitrite transporters, Photosystem II and Photosystem I complexes). Acclimation of the diatom to the desired Fe conditions and the comprehensive proteomic approach provides a more robust interpretation of this dynamic proteome than previous studies.

Diatom Transcriptional and Physiological Responses to Changes in Iron Bioavailability across Ocean Provinces

“…This supports that diatoms may be capable of shuffling energy pools into either the CCM or RubisCO production depending on Fe bioavailability. Interestingly, in laboratory-based proteomic analyses with cultures of the coastal diatom T. pseudonana, RubisCO was similarly more highly expressed under Fe limitation, while PEPC protein levels were higher under Fe-replete conditions (Nunn et al, 2013). Consistent with our hypothesis, Hopkinson et al (2010) attributed increases in biomass following CO 2 -enrichment of an Fe-limited phytoplankton community in the HNLC Northeast Pacific Ocean to downregulation of the CCM in order to conserve iron and photosynthetically-produced energy.…”

Toward a Regional Classification to Provide a More Inclusive Examination of the Ocean Biogeochemistry of Iron-Binding Ligands

“…Carbohydrate exudation products tend to be linked to nutrient limitation and the stationary growth phase of cells (e.g., Myklestad, 1977;Liu et al, 2001), such as at the decline of a phytoplankton bloom when cells continue to fix carbon photosynthetically but have insufficient nutrients available for macromolecular synthesis (e.g., Boyd et al, 2005). To date, a clear link between phytoplankton Fe limitation and the specific production of exopolymeric substances is missing but putative proteomic evidence has been presented (Nunn et al, 2013). However, EPS release is not be restricted to surface waters; bacterial exopolymers were reported in the deep-ocean, including hydrothermal vents (e.g., Nichols et al, 2005), but their specific role(s) within Fe biogeochemistry remains unknown.…”

Central role for ferritin in the day/night regulation of iron homeostasis in marine phytoplankton

“…Earlier studies have shown that the uptake rates per unit of cell surface are similar among species with different iron requirements and as a consequence smaller cells with higher surface-to-volume ratios are favored under iron limitation (10,11). Acclimation to low iron induces rapid changes in the Photosystem (PS) II-to-PSI ratio and a global remodeling of the photosynthetic machinery (12), the down-regulation of nitrogen-reducing enzymes such as Fe-dependent nitrate and nitrite reductases, and the upregulation of enzymes involved in nitrogen recycling (13). In oceanic diatoms, metabolic adaptation to iron limitation involves a decrease of PSI and cytochrome b6/f requirements (14) and the utilization of copper-dependent plastocyanin instead of cytochrome c 6 (15,16).…”