Reminiscent of the pre-diatom? A hitherto undescribed scaly bolidophyte Lepidoparma frigida gen. et sp. nov. in a new order Lepidoparmales based on morphology, phylogeny, and ecology

Abstract

The class Bolidophyceae, which consists of small phytoplankton distributed worldwide, is the sister group of diatoms. This class has contained only one order, the Parmales, until now. In this study, we established a new order Lepidoparmales Kamakura & S.Sato ord. nov. and a new family Lepidoparmaceae Kamakura & S.Sato fam. nov., within the Bolidophyceae, and described Lepidoparma frigida Kamakura & S.Sato gen. et sp. nov. from the Sea of Okhotsk. We conducted a comprehensive comparison of L. frigida with diatoms and other parmaleans through analysis of its molecular phylogeny, morphology, ultrastructure, ontogeny, distribution, and lipid composition. The cell surface of L. frigida is covered with numerous siliceous scales with radial patterns similar to centric diatom valves; this character distinguishes it from other known parmaleans. Intriguingly, its appearance resembles the hypothesized "pre-diatom," which was proposed to be a precursor to primitive diatoms. The discovery and characterization of L. frigida will provide valuable insights into the evolutionary processes of both diatoms and bolidophytes and shed light on their common ancestor.

Keywords: biomineralization; marine phytoplankton; picoplankton; silica mineralization; taxonomy.

FIGURE 1

LM and SEM images of Lepidoparma frigida NIES‐4679. (a) Bright‐field LM image. (b) Fluorescence image of (a). The chloroplast autofluorescence appears in red, and the SYBR Green‐stained nucleus appears in green. (c, d) SEM images showing cells surrounded by scales. Scale bars = 1 μm.

FIGURE 2

TEM images of the ultrathin sections of Lepidoparma frigida NIES‐4679. (a) General ultrastructure in an interphase cell. The chloroplast (Chl), mitochondrion (M), and Golgi body (G) are visible around the nucleus (n). (b) Enlarged view of (a), focusing on the chloroplast, Golgi body, and nucleus. The arrowhead indicates the continuity between the outermost membranes of the nucleus and the chloroplast. (c) Longitudinal sections of microtubules in an interphase cell. Arrowheads indicate arrays of short microtubules. (d1–d6) Serial sections of the mitotic spindle in metaphase. The interpolar microtubules (iMTs) and other spindle microtubules (MTs) emanate from the poles toward the center of condensed chromatins (Chr). Arrowheads indicate intact sites of the outer nuclear envelope as examples, which were identified based on the alignment of ribosomes attached to the outer nuclear membrane, since the membrane itself is difficult to discern. Double arrowheads indicate regions where some microtubules appear to extend toward the chromatin mass itself. Scale bars = 500 nm (a, d1) and 100 nm (b, c). Figures d1–d6 share a scale bar.

FIGURE 3

TEM images showing SDVs in ultrathin sections (a–d) and scale formation (e–l) in Lepidoparma frigida NIES‐4679. (a) A silica deposition vesicle distant from the plasma membrane. (b, c) Silica deposition vesicles and a flat vesicle (FV) adjacent to the plasma membrane. (d1–d10) A vesicle containing multiple scales. (e) Earliest stage of scale formation. (f) Rib elongation. (g, h) The rib tips join the outline of the scale. In (g), a circular space (indicated by the arrow) is visible at the structural center, whereas it is missing in (h). (i) Silicification processes and vertical morphogenesis. Arrowheads indicate two examples of knobs. (j) Process of elongation of the projection at the scale center. (k, l) Developed scales. Scale bars = 100 nm. Figures d1–d10 share a scale bar, as do Figures e–l.

FIGURE 4

Maximum likelihood trees based on nuclear 18S rRNA gene. (a) Tree based on the sequences >800 bp. (b) Subtree of the tree based on the sequences of the V4 region, showing the clade including L. frigida. For sequences obtained from public databases, the GenBank accession number or metaPR² ASV code (asterisk) is appended at the end of each name. Values at nodes indicate ultrafast bootstrap support. Bootstrap values below 70 are omitted. Clade names are according to the classifications of Ban et al. (2023), Ichinomiya et al. (2016) and Kuwata et al. (2018).

FIGURE 5

Comparison of chloroplast genome organizations in parmaleans. The tree showing the phylogenetic relationships among Lepidoparma frigida and seven parmaleans, excluding the outgroup diatom Thalassiosira pseudonana, on the basis of 62 common single‐copy chloroplast genes. Bootstrap values are indicated at each node. Yellow blocks represent the 16S rRNA gene (rrs: Smaller block) and 23S/5S rRNA genes (rrl/rrf: Larger block) genes. Other genes are represented by blue‐green blocks, with genes sharing the same annotation filled in with the same color. Gray shading between the genomes indicates regions of similarity identified by BLASTn.

FIGURE 6

Sampling stations around Hokkaido (Japan), current systems, and abundance of Lepidoparma. (a) Sampling in the Pacific Ocean in May 2016. (b) Sampling in the Sea of Okhotsk in June 2016. Red and blue lines and the blue area indicate warm and cold water currents and cold water masses, respectively. (c) Under‐ice water sampling in the Notoro‐ko Lagoon in February 2016. Closed and open circles indicate stations where Lepidoparma cells were detected and not detected, respectively. ESC, the East Sakhalin Current; CO, the Coastal Oyashio; OC, the Oyashio Current; OSICW, Okhotsk Sea Intermediate Cold Water; SWC, the Soya Warm Current.