Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging

Abstract

Eukaryotic phytoplankton have a small global biomass but play major roles in primary production and climate. Despite improved understanding of phytoplankton diversity and evolution, we largely ignore the cellular bases of their environmental plasticity. By comparative 3D morphometric analysis across seven distant phytoplankton taxa, we observe constant volume occupancy by the main organelles and preserved volumetric ratios between plastids and mitochondria. We hypothesise that phytoplankton subcellular topology is modulated by energy-management constraints. Consistent with this, shifting the diatom Phaeodactylum from low to high light enhances photosynthesis and respiration, increases cell-volume occupancy by mitochondria and the plastid CO₂-fixing pyrenoid, and boosts plastid-mitochondria contacts. Changes in organelle architectures and interactions also accompany Nannochloropsis acclimation to different trophic lifestyles, along with respiratory and photosynthetic responses. By revealing evolutionarily-conserved topologies of energy-managing organelles, and their role in phytoplankton acclimation, this work deciphers phytoplankton responses at subcellular scales.

Fig. 1. Cellular volume and external features of selected phytoplankton cells revealed by FIB-SEM imaging.

Green branches of the phylogenetic tree of eukaryotes represent photosynthetic lineages (adapted from ref. ). A 3D scan view of cell morphology of selected phytoplankton members (Mammiellophyceae (Micromonas RCC 827), Prymnesiophyceae (Emiliania RCC 909), Bacillariophyceae (Phaeodactylum Pt1 8.6), Pelagophyceae (Pelagomonas RCC 100), Dinophyceae (Symbiodinium RCC 4014 clade A), Cyanidiophyceae (Galdieria SAG21.92) and Eustigmatophyceae (Nannochloropsis CCMP526) is shown with a linear scale bar of 1 µm and a voxel scale of 1 µm³. Specific cellular features (cell walls, the flagellum in Micromonas, the raphe in Phaeodactylum, the coccosphere in Emiliania) are visible. For every species, three cells were reconstructed and morphometrically analysed. Data represent cell volumes ± s.d. for every species.

Fig. 2. Internal cell architecture of phytoplankton cells.

a Sections through cellular 3D volumes, segmented from FIB-SEM images of whole cells of Micromonas (stack of frames in Supplementary Movie 1), Pelagomonas (Supplementary Movie 2), Nannochloropsis (Supplementary Movie 3), Galdieria (Supplementary Movie 4), Emiliania (Supplementary Movie 5), Phaeodactylum (Supplementary Movie 6) and Symbiodinium (Supplementary Movie 7). Sections are representatives micrographs of an experiment repeated three times with similar results Scale bar: 1 µm. b Segmentations highlight the main subcellular compartments: green: plastids (containing thylakoids and pyrenoids—light green—in some cell types); red: mitochondria; blue: nuclei (with different intensities of staining possibly corresponding to euchromatin—light blue—heterochromatin—blue and the nucleolus—dark blue); grey: other compartments. Segmentations are representatives tomograms of an experiment repeated three times with similar results. c Volume occupancy by the different subcellular compartments in different microalgal cells. Top plot: % of cell-volume occupation; bottom plot: absolute volume sizes. Data refer to three cells ± s.d. for every species.

Fig. 3. Morphometric analysis of phytoplankton members.

a 3D topology of the main organelles (green: plastids; red: mitochondria; blue: nuclei) in the different cell types. b Volume relationships in different subcellular compartments, as derived from quantitative analysis of microalgal 3D models. c Surface relationships in different subcellular compartments, as derived from quantitative analysis of microalgal 3D models. Three cells were considered for every taxum. Stars: Emiliania; squares: Galdieria; hexagons: Micromonas; circles: Pelagomonas; triangles: Phaeodactylum; suns: Nannochloropsis. Symbiodinium cells were not considered in this analysis, because their size, which largely exceeds the other (Supplementary Fig. 3), prevents a meaningful analysis of the volume/surface relationships.

Fig. 4. Proximity between plastids and mitochondria in different phytoplankton members.

Green: plastid surface. Red: mitochondria surface. Magenta: proximity surface (i.e. points at a distance ≤30 nm (panel a) or ≤90 nm (panel b) between mitochondria and plastids. Data refer to three cells ± s.d. for every species.

Fig. 5. Architecture of the mitochondria and plastids of different phytoplankton taxa.

a Topology of the plastid. Whole plastid images and focus on the CO₂-fixing compartment (pyrenoid) topology in Emiliania, Phaeodactylum, Micromonas and Symbiodinium cells. The 3D reconstruction displays the thylakoid network (dark green) crossing the pyrenoid matrix (light green). If present (Micromonas and Symbiodinium), a starch layer surrounding the pyrenoid is shown in grey. The histogram recapitulates volume occupancy by sub-plastidial structures (thylakoids, matrix, starch, pyrenoid). Note that starch is cytosolic in Symbiodinium, and therefore its volume is not considered in the graph. b Topology of mitochondrial compartments. Red: mitochondrial matrix; yellow: cristae. The histogram recapitulates volume occupancy by mitochondrial subcompartments (in the matrix and within the cristae). See Supplementary Fig. 4 for sections through plastids and mitochondria.

Fig. 6. Structural analysis of light acclimation in Phaeodactylum tricornutum.

a Cells were imaged at two different light regimes: LL (40 µmol photons m⁻² s⁻¹, left) and HL (350 µmol photons m⁻² s⁻¹, right). Scale bar: 1 µm. b Volume occupancy by the plastids (dark green), mitochondria (red) and pyrenoid (light green) in the two conditions. Data refer to three cells ± s.d. for each growth condition. c Respiratory activities (red) and photosynthetic capacities (green) are indicated for LL (left) and HL (right) cells. Data refer to three biological samples ± s.d. for each growth condition. d Plastid-mitochondria proximity surface points in LL and HL cells, measured at ≤30 nm (grey) and ≤90 nm (black). At both distances, proximity areas points are increased by around 25% (blue) upon HL transition. Data refer to three cells ± s.d. for each growth condition.

Fig. 7. Plastid-mitochondria interactions are modified by trophic regimes in Nannochloropsis.

a Cells were imaged after growth in phototrophic (left) and mixotrophic (right) conditions. Sections are representatives micrographs of an experiment repeated three times with similar results. Scale bar: 2 µm. b Cell growth in phototrophic conditions (black) and mixotrophic conditions (orange). Data refer to three biological samples ± s.d. for each growth condition. c Oxygen consumption (respiration) and evolution (photosynthesis). Data refer to six biological samples ± s.d. for each growth condition. d Cell-volume occupancy by the different subcellular compartments in different microalgal cells. Green: plastid; red: mitochondria; blue: nuclei; white: storage vesicles; grey: other. Data refer to five cells ± s.d. for each growth condition. Scale bar: 2 µm. e analysis of proximity surface points (magenta) between plastid (green) and mitochondria (red). Data refer to five cells ± s.d. for each growth condition.