Genetic and physiological responses to light quality in a deep ocean ecotype of Ostreococcus, an ecologically important photosynthetic picoeukaryote

Abstract Phytoplankton are exposed to dramatic variations in light quality when cells are carried by upwelling or downwelling currents or encounter sediment. We investigated the potential impact of light quality changes in Ostreococcus, a key marine photosynthetic picoeukaryote, by analysing changes in its transcriptome, pigment content, and photophysiology after acclimation to monochromatic red, green, or blue light. The clade B species RCC809, isolated from the deep euphotic zone of the tropical Atlantic Ocean, responded to blue light by accelerating cell division at the expense of storage reserves and by increasing the relative level of blue-light-absorbing pigments. It responded to red and green light by increasing its potential for photoprotection. In contrast, the clade A species OTTH0595, which originated from a shallow water environment, showed no difference in photosynthetic properties and minor differences in carotenoid contents between light qualities. This was associated with the loss of candidate light-quality responsive promoter motifs identified in RCC809 genes. These results demonstrate that light quality can have a major influence on the physiology of eukaryotic phytoplankton and suggest that different light quality environments can drive selection for diverse patterns of responsiveness and environmental niche partitioning.

The following Supporting Information is available for this article:           Table S1.Lists of differentially expressed genes identified for RCC809 in pairwise comparisons between red and green, red and blue, or blue and green light conditions.Table S2.Light quality-responsive genes related to the cell cycle.
Table S3.Light quality-responsive genes with roles in photosystem II assembly.S2.Table S1 Lists of differentially expressed genes identified in pairwise comparisons between red and green, red and blue, or blue and green light conditions (provided as a separate Excel file).
Table S2 Light quality-responsive genes related to the cell cycle.Genes indicated as "Up in blue / Down in green" were identified as up-regulated in blue light relative to red and green light, as well as down-regulated in green light relative to red and blue light.

Fig. S1 .
Fig. S1.Spectroradiometer analysis of the three light conditions used in our experiments.

Fig. S2 .
Fig. S2.Validation of the use of absorbance at 550 nm (OD 550 nm) to estimate the cell abundance of Ostreococcus cultures.

Fig. S3 .
Fig. S3.Examples of cell cycle-related genes upregulated under blue light.

Fig. S4 .
Fig. S4.Effect of light quality on the expression of Calvin cycle-related genes.

Fig. S5 .
Fig. S5.Effect of light quality on the expression of glycolysis and starch synthesis-related genes.

Fig. S6 .
Fig. S6.Effect of light quality on the expression of fatty acid synthesis-related genes.

Fig. S7 .
Fig. S7.Effect of light quality on the expression of TCA cycle-related genes.

Fig. S8 .
Fig.S8.Effect of light quality on the expression of terpenoid biosynthesis-related genes.

Fig. S9 .
Fig. S9.Effect of light quality on the expression of porphyrin and chlorophyll metabolism-related genes.

Fig. S10 .
Fig. S10.Effect of light quality on the expression of carotenoid biosynthesis-related genes.

Fig. S11 .
Fig. S11.Effect of light quality on the expression of Ostreococcus RCC809 genes encoding photoreceptors.Fig. S12.Examples of HPLC chromatograms illustrating the range of pigments detected in the (A) RCC809 and (B) OTTH0595 ecotypes of Ostreococcus.

Fig. S1 .
Fig. S1.Spectroradiometer analysis of the three light conditions used in our experiments.Peak wavelengths were 650.5 nm for red light, 545 nm for green light, and 467.5 nm for blue light.Total Iight intensity was 4 µmol photons m ˉ2 s ˉ1 (4 µE) under all conditions, as indicated by the area under the curves.

Fig. S4 .
Fig. S4.Effect of light quality on the expression of Calvin cycle-related genes.(A-C) RuBisCO Fig. S5.Effect of light quality on the expression of glycolysis and starch synthesis-related genes.(A) Annotated KEGG pathway diagram.Steps of the pathway where expression of enzymes is affected by light quality are indicated by numbered, colour-coded labels.Colours indicate the wavelengths that induce the response.Darker colours indicate induction, lighter colours indicate repression.(B) Corresponding genes and their light quality responses.

BFig. S7 .
Fig. S6.Effect of light quality on the expression of fatty acid synthesis-related genes.(A) Annotated KEGG pathway diagram.(B) Corresponding genes and their light quality responses.
Fig. S8.Effect of light quality on the expression of terpenoid biosynthesis-related genes.(A)

BFig. S10 .Fig. S11 .
Fig. S10.Effect of light quality on the expression of carotenoid biosynthesis-related genes.(A) Figure 4.2 HPLC chromatograms of Ostreococcus sp.RCC809 and OTH95 pigments grown under different light qualities (a) RCC809 exposed to 72 hours of low intensity blue light.The presence and separation time for the two chlorophyll b-like pigments can be seen just before chl-b and are marked with blue arrows.(b) OTH95 exposed to 72 hours of low intensity red light.The chlorophyll b-like pigments seen in RCC809 were not found in OTH95.
blue Single-stranded DNA-binding protein, DNA replication Od05g01780 Down in blue DNA replication licensing factor, protein ubiquitination Od07g01730 Down in blue Lysine-specific demethylase 8, protein binding Od07g02050 Down in blue Predicted, GTPase activity, chloroplast fission, cell division Od07g04740 Down in blue Cell division FtsY homolog, chloroplastic, GTP binding Od10g01360 Down in blue Resistance-nodulation-cell division superfamily Od01g04460 Down in green DNA replication licensing factor Mcm6, helicase Od02g01320 Down in green DNA replication licensing factor Mcm7 helicase Od02g01330 Down in green DNA replication licensing factor Mcm7 helicase Od02g02310 Down in green DNA replication licensing factor Mcm3 helicase Od05g00150 Down in green Replication factor C subunit 3 DNA replication Od10g01480 Down in green ATP-dependent helicase/nuclease DNA2 isoform X1, 5'-flap DNA replication, Okazaki fragment processing Od17g03020 Down in green P4 family, helicase activity, ATP binding, DNA replication Od01g02860 Up in blue Histone H3, nucleosomal DNA binding, meiotic chromosome separation Od02g03320 Up in blue Predicted, peptide dephosphorylation, positive regulation of cell cycle, G2/M phase transition Od02g03690 Up in blue Serine/threonine-protein kinase 24, regulation of cell cycle Od02g03890 Up in blue Condensin complex component, non-smc subunit, mitotic chromosome condensation, cell division

Table S3
Light-quality responsive genes with roles in photosystem II assembly.