Research Article |
Corresponding author: Kui-Dong Xu ( kxu@qdio.ac.cn ) Academic editor: Bing Liu
© 2023 Fei-Chao Du, Yu-Hang Li, Kui-Dong Xu.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Du F-C, Li Y-H, Xu K-D (2023) Morphology and molecular phylogeny of Pleurosigma pacificum sp. nov. (Pleurosigmataceae), a new tropical pelagic species from the Western Pacific Ocean. PhytoKeys 227: 99-108. https://doi.org/10.3897/phytokeys.227.103890
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A new species of pelagic diatom, Pleurosigma pacificum sp. nov., is described from the tropical Western Pacific Ocean. It has the typical features of Pleurosigma, including a slightly sigmoid raphe, intersected transverse and oblique striae, and loculate areolae with external opening slits and internal poroids. Morphologically, P. pacificum belongs to a species group of Pleurosigma with lanceolate valves, including P. atlanticum Heiden & Kolbe, P. nubecula W. Smith, P. indicum Simonsen, and P. simonsenii Hasle. However, P. pacificum differs by its smaller lanceolate valve and smaller intersection angle as well as elliptical areolae without a silica bar. The SSU rDNA and rbcL sequence data place P. pacificum in a basal position relative to other species of Pleurosigma. Our molecular phylogenetic analyses did not support the monophyly of lanceolate and slightly sigmoid species. Thus, the sigmoidality of valve outline cannot be considered as a criterion to define the species group.
Marine diatoms, morphology, new species, phylogeny, Pleurosigma, Western Pacific Ocean
Pleurosigma is a group of diatoms that is widely disturbed in brackish to marine environments (
In this paper, we describe a new species of Pleurosigma isolated from the tropical Western Pacific Ocean by using light microscopy (LM) and scanning electron microscopy (SEM). Its phylogenetic position is determined by DNA sequence.
Phytoplankton samples were collected from upper 200 m water column by using a phytoplankton net (64 µm mesh), on the Western Pacific Ocean (7°0.26'N, 141°59.63'E). Single cells of diatoms were isolated using capillary pipettes and cultivated in F/2 medium. Cultures were maintained at 24–26 °C under a light intensity of 120–150 µmol photon/m2/s, with a light/dark cycle of 12:12 h. Five milliliters of vegetative cells were fixed with 2.5% glutaraldehyde and then cleaned with hydrogen peroxide (
The DNA was extracted and sequenced according to the method described in
Primers used to amplify SSU rDNA, LSU rDNA, rbcL and psbC fragments for P. pacificum.
Name | Marker | Sequence (5′ to 3′) | Reference |
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SSU1 | SSU | AACCTGGTTGATCCTGCCAGT | ( |
ITS1DR | SSU | CCTTGTTACGACTTCACCTTCC | ( |
D1R | LSU | ACCCGCTGAATTTAAGCATA | ( |
D3Ca | LSU | ACGAACGATTTGCACGTCAG | ( |
rbcL 66+ | rbcL | TTAAGGAGAAATAAATGTCTCAATCTG | ( |
rbcL 1444- | rbcL | GCGAAATCAGCTGTATCTGTW G | ( |
psbC+ | psbC | CACGACCWGAATGCCACCAAT | ( |
psbC- | psbC | ACAGGMTTYGCTTGGTGGAGTGG | ( |
To examine the phylogenetic position of P. pacificum, a two-gene dataset (SSU rDNA–rbcL) including 30 recognized species and 12 unnamed strains, was used to construct the phylogenetic trees (Suppl. material
The SSU rDNA and rbcL sequences were aligned using MAFFT v.7.313 (
Valves lanceolate, gradually tapering towards the subacute ends, 45.0–51.5 µm long and 13.0–15.6 µm wide (Fig.
A–F LM photographs of P. pacificum A–D cleaned frustules showing parallel transverse striae under LM E valve center showing a roundish central area (arrowhead) F funnel-shaped terminal area in apical position G–L SEM photographs of P. pacificum G internal view of the whole valve H internal valve central area showing straight, slight expanded raphe fissures (arrowhead) and nodule bordered by two arched bars I internal raphe fissures terminate in helictoglossae at the apices (arrowhead) J external view of the whole valve showing the terminal fissures curving into opposite directions K external central area of valve showing straight, simple raphe fissures (arrowhead) L terminal fissures (arrowhead). Scale bars: 10 μm (A–F); 5 μm (G, J); 1 μm (H, I, K, L).
In SEM, internally, raphe fissures terminate in helictoglossae at apices, orientated in opposite direction to one another (Fig.
MBMCAS286904, an example is illustrated in Fig.
MBMCAS286905, an example is illustrated in Fig.
7°0.26'N, 141°59.63'E, the upper 200 m water column in the tropical Western Pacific Ocean.
Named after the Pacific Ocean where the species was discovered.
Pleurosigma pacificum is a planktonic species known only from the type locality. The water temperature was 28.5 °C and salinity about 33.4 during sampling.
The BLASTn search showed that the SSU rDNA sequence of P. pacificum shares 97.65% identity with an uncultured marine eukaryote (KC771201). The rbcL gene sequence of P. pacificum shares 92.54% identity with P. intermedium (NC_066077). The ML, BI and MP phylogenetic tree based on the concatenated SSU rDNA and rbcL gene showed that P. pacificum belongs to the clade of the genus Pleurosigma with high support (IQ-TREE ultrafast bootstrap value = 99, Mrbayes posterior probability = 1.00, MP standard boostrap value = 77 and MP jacknife value = 85). The P. pacificum is basal to all other species of Pleurosigma, and branched earlier than the two slightly sigmoid species, P. planctonicum and P. intermedium (Fig.
Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees based on the concatenated SSU rDNA and rbcL sequences. The values on each node indicate ML bootstrap and Bayesian posterior probabilities (%), respectively. Only bootstrap values over 50% are shown on the tree. Black dot indicate ML/BI = 100/1.00. The asterisk indicates the topological incongruence between ML and BI trees.
The valves of Pleurosigma pacificum sp. nov. possess intersected transverse and oblique striae, opposite curved raphe distal endings, two internal central bars, and loculate areolae with an internal poroids and an external slit opening. These are considered to be the main characters of the genus Pleurosigma (
The morphological data place P. pacificum in a group of species, which includes P. nubecula W. Smith, P. indicum Simonsen, P. simonsenii Hasle, and P. atlanticum Heiden & Kolbe, with lanceolate valves and a straight raphe (Table
Comparison of morphological features of Pleurosigma pacificum sp. nov. with similar species.
Characteristics | P. pacificum sp. nov. | P. simonsenii # | P. indicum | P. atlanticum | P. nubecula |
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Length (µm) | 45.0–51.5 | 300–600 | 70–90 | 69–76 | 82–85 |
Width (µm) | 13.0–15.6 | 40–75 | 8–11 | 13.0–16.5 | 16 |
Raphe angle | 2–3° | ND | 2.5–2.6° | 1.2° | 1.2–1.9° |
Transverse striae in 10 µm | 21–22 | 28–30 | 23–28 | 20 | 25–26 |
Oblique striae in 10 µm | 21–23 | 30 | 20–24 | 20 | 23–25 |
Stria angle | 32–35° | 60° | 44–48° | 60° | 60–61° |
Valve outline | lanceolate | Lanceolate, slightly sigmoid | Lanceolate, slightly sigmoid | Lanceolate | Narrowly lanceolate |
Raphe | Straight, slightly deflected near the apices | Straight, sigmoid before the ends | Straight, eccentric towards the ends | Straight, slightly deflected at poles | Very slightly deflected |
Apices | Subacute | very acute | Subacute | Blunt rounded obtuse | Subacute |
Internal view areolae | elliptical without bars | ND | elliptical, bisected by a narrow silica bar | ND | elliptical, bisected by a narrow silica bar |
Sources | This study (n = 20) |
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Heiden and Kolbe (1928) |
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The definition of the genus Pleurosigma has undergone constant debate and modifications (
This work was supported by the National Natural Science Foundation of China (Grant numbers 42276099 and 31800171). This work was also supported by Oceanographic Data Center, Institute of Oceanology, Chinese Academy of Sciences. We are very grateful to two reviewers and the editors for their careful revisions and constructive comments. We are also grateful to staff of the Research Vessel KEXUE for sample collection.
No conflict of interest was declared.
No ethical statement was reported.
No funding was reported.
Conceptualization: KDX. Funding acquisition: YHL. Investigation: FCD. Methodology: YHL. Supervision: KDX. Writing - original draft: FCD. Writing - review and editing: YHL, KDX.
Fei-Chao Du https://orcid.org/0009-0005-0674-5761
Yu-Hang Li https://orcid.org/0000-0002-5546-1774
Kui-Dong Xu https://orcid.org/0000-0002-5186-519X
All of the data that support the findings of this study are available in the main text or Supplementary Information.
GenBank accession of SSU rDNA and rbcL gene sequences
Data type: tables (pdf file)
Explanation note: GenBank accession of SSU rDNA and rbcL gene sequences derived from the species used in the phylogenetic analysis.
Maximum parsimony (MP) phylogenetic trees based on the concatenated SSU rDNA and rbcL gene sequences
Data type: figure (pdf file)