Psammina yokosukae, Gooday & Ishitani & Chen & Holzmann & Richirt & Seike & Yamashita & Tsuchiya & Nomaki, 2025

Gooday, Andrew J., Ishitani, Yoshiyuki, Chen, Chong, Holzmann, Maria, Richirt, Julien, Seike, Koji, Yamashita, Momo, Tsuchiya, Masashi & Nomaki, Hidetaka, 2025, Integrative taxonomy of new xenophyophores (Rhizaria, Foraminifera) from the abyssal northwest Pacific, European Journal of Taxonomy 1004, pp. 144-189 : 149-152

Psammina yokosukae sp. nov.

urn:lsid:zoobank.org:act:8F06D3F4-DE75-46FD-8701-0D6C1379EB9E

Figs 2A–B , 3–4 , 5D–G , 6–7 , 8A–E ; Supp. file 2: Figs S4A–B, S 5A–B , Supp. file 3: µCT video 1

Diagnosis

Species of Psammina with free, epifaunal test comprising system of undulating, sometimes fan-shaped, plates up to> 5 cm in overall extent. In places, surface displays vague concentric zones defined by slightly raised lineations and traversed by low radial ridges. Micro-CT scans reveal internal structures, often rather poorly defined, corresponding to these surface features. Obvious apertures absent. Test wall friable, comprising mineral grains of varying sizes (generally <100 µm) and occasional biogenic particles. Interior partly filled with agglutinated mineral grains that are larger (>300 µm) than those constituting the wall. Stercomare forms branching and anastomosing strings and masses of variable width (~70 to>200 µm) that occupy spaces between internal grains with no clear pattern. Granellare yellowish-brown, branching, thread-like (width ~10 to 34 µm), in places attached to grain surfaces; barite crystals rare.

Etymology

Named for the RV Yokosuka, support ship for the HOV Shinkai 6500.

Material examined

Holotype NW PACIFIC OCEAN – 32.5° N (west of Kuroshio Extension Observatory (KEO)) • 32°34.81′ N, 143°46.24′ E; depth 5509 m; 22 Oct. 2022; H. Nomaki leg.; Dive 1659 of HOV Shinkai 6500, core Red#3; GenBank accession nos: PP662675 to PP662677; National Museum of Nature and Science, Tsukuba, Japan, reg. no. TNS Pr691 . The specimen is preserved in a core in 10% buffered formalin.

Paratype

NW PACIFIC OCEAN – 32.5° N (west of KEO) • 1 spec.; same data as for holotype; Dive 1659 of HOV Shinkai 6500, core Red#5; National Museum of Nature and Science, Tsukuba, Japan, reg. no. TNS Pr691 . The specimen was frozen at sea and only available as fragments .

Description

Overall test morphology

The in situ seafloor photograph of the holotype ( Fig. 2A ) shows a group of about five main plate-like elements that are curved or undulating with sinuous and often upturned margins. The plates are orientated in different directions but merge together into one structure. Near one end of the test, there is an open-ended, chimney-like feature that is also visible in the shipboard photograph (Supp. file 2: Fig. S4A ). The seafloor photograph of the paratype (TNS Pr693) is similar, although it comprises fewer, relatively larger plates ( Fig. 2B ).

The recovered holotype measures 5.5 cm × 3.7 cm in maximum extent when viewed from above ( Fig. 3B ) and extends ~ 2.7 cm above the sediment surface. The test is composed of plates that are ~0.60–1.0 mm (mean 0.81 ± 0.11 mm, n = 11) thick. It is strongly asymmetrical, with one side low lying, or even slightly buried under resedimented material ( Figs 3A–B , 4C–D, G–H ), and the other side upstanding. Supp. file 3: µCT video 1 gives a clear impression of its structure. The low-lying side comprises two mainly separate plates with strongly upturned rims. These, and particularly the larger of the two, merge with, and to some extent buttress, the more prominent upstanding part of the test. This part can be thought of as comprising two components. One is a branched plate, the upper part of which forms a U-shaped trough with undulating side ( Fig. 3A, E ). One side of the trough merges with the second component, a fairly flat semicircular fan that is a visually conspicuous feature in Figs 3C , 4A–D , and shown in detail in Fig. 3D–G . In side view, the fan appears to be linked with the abovementioned tubular chimney-like structure ( Fig. 3A–C, G ), but the µCT video (Supp. file 3) clearly shows that this feature develops at the end of one side of the U-shaped trough, after it has merged with the fan-shaped plate. Another approximately circular, somewhat larger but less regular feature is located in the central part of the test. It is largely obscured by other test elements but can be seen at a few points in the video.

Surface ornamentation, test structure and composition

In light photographs of the holotype, the test surface displays a vague pattern of concentric zones. These can be seen most clearly under very oblique lighting, notably on the prominent semicircular plate ( Fig. 3G ; Supp. file 2: Fig. S5B ). Where the boundaries between the zones are most clearly developed ( Fig. 3G ), they appear to be shallow steps, suggesting that later zones overlap earlier ones. Superimposed on these zones are low radial ridges separated by shallow furrows, which are equally indistinct. The same pattern is clearer in μCT images of the holotype than in visible light. When the test is rendered more transparent in μCT scans, it is almost entirely occupied by concentric zones and radial features. Although the pattern of lineations is obvious on the semicircular plate ( Fig. 3C–D ), the individual features are often indistinct and discontinuous.

The test wall is fairly friable, 180–320 µm (mean 267 ±56 µm, n = 15) thick, and light greyish in colour when dry. It is continuous around the margin and devoid of obvious apertures. Seen through the wall of the core tube, the surface is peppered with a variable density of larger grains ( Fig. 3F–G ; Supp. file 2: Fig. S5B ). Under a stereo microscope, the surface appears noticeably granular and comprises a rather heterogeneous mixture of mineral grains of various sizes ( Fig. 5D, F ). Some larger ones are dark and there is a sprinkling of whitish and orange grains, but most are pale or transparent.

In SEM images of the paratype, the surface is quite uneven at a scale of 100–200 µm ( Fig. 6A–D ). The main constituents are mineral grains amongst which are scattered some biogenic remains. mainly radiolarian fragments, but also diatom fragments. The outer wall is not sharply delimited from the test interior ( Fig. 6G ). In addition to empty space, the interior is occupied by a variety of particles (‘internal xenophyae’) of different shapes and sizes that are dominated visually (although not numerically) by grains that are larger (200–300 µm) than those forming the outer layer ( Fig. 7A–D ). These include sharp-edged shards of volcanic glass, and porous and fibrous particles, possibly also of volcanic origin, in addition to radiolarian fragments.

The relatively few test fragments in which the interior was examined directly did not display welldefined partitions corresponding to the internal structures visible in μCT renders ( Fig. 3C–D ). However, two or perhaps three poorly-defined internal partitions can be seen in an SEM image showing the interior exposed at the edge of a test fragment ( Fig. 6A ); a broken cross section of the test shows similar features ( Fig. 6G ). Vague radial structures are sometimes also discernible when the test interior is viewed by light microscopy ( Fig. 5E ). The poorly defined nature of these features probably reflects the fact that the internal agglutination is dominated bys coarse-grained particles. This probably also explains why individual radial features are sometimes indistinct and discontinuous in µCT renders ( Fig. 3D ).

Stercomare and granellare

In addition to internal particles, the test contains stercomare and granellare. The dark stercomare forms branches that to some extent anastomose, as well as more irregular masses ( Figs 5G , 6F , 8A ). At least in the test fragments examined, they did not follow any clear trend but occupied the irregular spaces between the large internal xenophyae. The branches vary greatly in width, from ~70 µm to more than 200 µm. They have a thin, transparent organic sheath, ~1 µm thick, that encloses masses of spherical to ovoid stercomata, each stercome ranging in size from 12 to 30 µm (typically 12–20 µm) ( Figs 5G , 6H ).

The granellare forms narrow thread-like strings, yellowish-brown in colour (a darker golden-brown when dried), that branch throughout the test interior ( Figs 5G , 7A–D , 8A ). They measure 10–40 µm in width (usually 14–25 µm; mean 20.7 ±6.17 µm, n=50) and occupy only a very small proportion of the interior space. The branches weave between the internal xenophyae and in places are attached to the surfaces of grains, from which they are difficult to dislodge. The organic sheath that surrounds the cytoplasm is ~0.1– 0.2 µm thick and shrinks creating longitudinal wrinkles when dried on an SEM stub ( Fig. 7E ). Granellare fragments viewed in glycerol under a compound microscope show the cytoplasm with small inclusions of various kinds, including a few refractive particles that are presumably mineral grains ( Fig. 8D–E ), although these do not resemble typical barite crystals. There was little evidence for intracellular barite crystals in SEM images. None were visible through the granellare walls ( Fig. 7E ). Various inclusions could be seen within the cytoplasm where the granellare tube was ruptured, but only a single crystal-like particle yielded EDS peaks for Ba ( Fig. 7H ), suggesting that barite crystals are not common.

Molecular characterisation

Psammina yokosukae sp. nov. branches as sister to Psammina tenuis Gooday & Holzmann, 2020 . The grouping is supported by a BV of 89%. The sequenced fragment of the 18S gene of P. yokosukae contains 1038–1039 nucleotides and the GC content is 36 %.

Remarks

Phylogenetic reconstruction shows that Psammina yokosukae sp. nov. is closely related to P. tenuis . In terms of morphology, the granellare branches of both species are similar in being narrow ( P. yokosukae 12–22 µm; P. tenuis 10–30 µm) and attached for part of their length to internal test particles. The two species are also similar in having basically plate-like tests. An in situ photograph of the unique specimen of P. tenuis on the seafloor shows a relatively simple plate, strongly curved around a vertical axis, growing up vertically from the surface of a polymetallic nodule ( Gooday et al. 2020a: fig. 5a therein). This is somewhat reminiscent of the holotype of P. yokosukae but is much simpler than the cluster of plates that make up the test of the new species. Concentric lines are more clearly developed in P. tenuis than in P. yokosukae , but there is no sign of the radial lineations that are dimly visible in the new species. These differences in test morphology support the genetic distinction between P. yokosukae sp. nov. and P. tenuis . Given the variability of many xenophyophores, an important caveat is that the overall test morphology is known in detail for only one specimen of both species. Nevertheless, the fact that the test wall is composed largely of radiolarian shells in P. tenuis but largely of mineral grains in P. yokosukae , and the presence of more numerous internal particles in P. yokosukae , supports the conclusion that these are different species.

Figures

Fig. 2. Seafloor images. A–B. Psammina yokosukae sp. nov. A. Holotype, reg. no. TNS Pr691. B. Paratype, reg. no. TNS Pr693. C–D. Psammina contorta sp. nov. C. Paratype, reg. no. TNS Pr694. D. Holotype, reg. no. TNS Pr695; the rounded object on the left side is the ‘Pebble-shaped, honeycombed xenophyophore’ informally described below. The arrowhead (A) indicates the chimney-like feature referred to in the text.

Fig. 3. Psammina yokosukae sp. nov., holotype, reg. no. TNS Pr691. A–D. Micro-CT renders showing surface structures (A–B) and inner structures (C–D) of the test on the core surface. A. Oblique view from above. B. View from directly above. C. Side view showing concentric zones traversed by radial features. D. Detail of largest fan-shaped plate. E–G. Light photographs taken through the side of the plastic core tube.E. Main upstanding part of test. F–G. Two plates with concentric zones and low radial ridges. The arrowheads (A–C, G) indicate the chimney-like feature referred to in the text.

Fig. 4. Psammina yokosukae sp. nov., holotype, reg. no. TNS Pr691. A–B, E–F. Micro-CT renders of complete test from different angles, showing surface structure. C–D, G–H. Corresponding light photographs taken through the side of the plastic core tube; note optical distortion due to curvature of tube wall.

Fig. 5. Stereo microscope images. A–C. Psammina contorta sp. nov. A. Fragment of holotype, reg. no. TNS Pr695.B. Fragment of paratype, reg. no. TNS Pr694.C. Detail of holotype surface.D–G. Psammina yokosukae sp. nov., fragments of holotype, reg. no. TNS Pr691. D. Outer surface of fragment. E. View of broken test edge showing wall and interior with dark stercomare. F. Closer view of test wall. G. Interior of fragment showing dark stercomare mass comprising accumulation of stercomata (tiny waste pellets) and two thin granellare branches (arrowed). A–D, F taken in Geneva; E, G taken at JAMSTEC.

Fig. 6. Psammina yokosukae sp. nov., SEM images (secondary electron mode) of fragment of paratype, reg. no. TNS Pr693. A. Entire test fragment showing outer surface with interior exposed at the edge. B–D. Progressively closer views of test surface. E. Detail showing outer surface of test and coarsergrained internal surface. F. Internal surface showing stercomare (arrowed). G. Broken showing vague internal partitions. H. Detail of stercomare showing stercomata and enclosing membrane.

Fig. 7. Psammina yokosukae sp. nov., SEM images (secondary electron mode) of fragment of paratype, reg. no. TNS Pr693. A. Entire test fragment showing inner surface. B. Closer views of inner surface. C–D. Closer views of two other fragments. E–H. Granellare. E. Surface of granellare showing crinkled surface of organic tube. F. Fragment with ruptured part indicated by arrowhead. G. Detail of ruptured granellare showing thin organic tube and heterogeneous contents. H. Detail of ruptured granellare showing interior with inclusions, including a crystal (arrowed) that yielded an EDX peak for Ba. Arrowheads in B–D indicate granellare strands.

Fig. 8. Light microscope images. A–E. Psammina yokosukae sp. nov., fragments of holotype, reg. no. TNS Pr691. A. Test interior showing damaged stercomare; fine granellare strands also visible. B. Granellare fragments dissected from test for molecular analyses. C. Closer view of granellare fragments. D–E. Granellare fragments immersed in glycerol on a glass slide and viewed with transmitted light in compound microscope. F–G. Psammina contorta sp. nov., granellare fragments from paratype, reg. no. TNS Pr694, viewed in glycerol, as described for D–E. Images A–C were taken in Geneva, D–G in Southampton.