Eukaryotic richness in the abyss: insights from pyrotag sequencing

Background: The deep sea floor is considered one of the most diverse ecosystems on Earth. Recent environmental DNA surveys based on clone libraries of rRNA genes confirm this observation and reveal a high diversity of eukaryotes present in deep-sea sediment samples. However, environmental clone-library surveys yield only a modest number of sequences with which to evaluate the diversity of abyssal eukaryotes. Methodology/Principal Findings: Here, we examined the richness of eukaryotic DNA in deep Arctic and Southern Ocean samples using massively parallel sequencing of the 18S ribosomal RNA (rRNA) V9 hypervariable region. In very small volumes of sediments, ranging from 0.35 to 0.7 g, we recovered up to 7,499 unique sequences per sample. By clustering sequences having up to 3 differences, we observed from 942 to 1756 Operational Taxonomic Units (OTUs) per sample. Taxonomic analyses of these OTUs showed that DNA of all major groups of eukaryotes is represented at the deep-sea floor. The dinoflagellates, cercozoans, ciliates, and euglenozoans predominate, contributing to 17%, 16%, 10%, and 8% of all assigned OTUs, respectively. Interestingly, many sequences represent photosynthetic taxa or are similar to those reported from the environmental surveys of surface waters. Moreover, each sample contained from 31 to 71 different metazoan OTUs despite the small sample volume collected. This indicates that a significant faction of the eukaryotic DNA sequences likely do not belong to living organisms, but represent either free, extracellular DNA or remains and resting stages of planktonic species. Conclusions/Significance: In view of our study, the deep-sea floor appears as a global DNA repository, which preserves genetic information about organisms living in the sediment, as well as in the water column above it. This information can be used for future monitoring of past and present environmental changes.French ANR Aquaparadox; ANR DeepOases; Swiss National Science Foundation [31003A-125372]; WM Keck foundationinfo:eu-repo/semantics/publishedVersio

Virtualia 2016. La réalité virtuelle au service de la recherche: Actes du séminaire organisé par le CIREVE à Caen (19 octobre 2016),

International audienceLe séminaire Virtualia est né en 2006 en même temps que le Centre Interdisciplinaire de Réalité Virtuelle (CIREVE) de l’Université de Caen Normandie. Son objectif est de permettre aux équipes associées au CIREVE d’exposer leurs méthodologies et les résultats de leurs travaux dans le domaine de la Réalité Virtuelle, tout en s’ouvrant à des communications extérieures. Il a connu quatre éditions de 2006 à 2009.2016 fut l’occasion de relancer VIRTUALIA et de concrétiser le partenariat avec les Universités de Rouen et du Havre dans le cadre de la COMUE. Une Structure Fédérative de Recherche « CIREVE » est en effet en cours de labellisation au sein de Normandie Université. 2016 est également une année importante car elle marque à la fois le dixième anniversaire du CIREVE et la finalisation d’une plate-forme de réalité virtuelle normande, unique en son genre sur le territoire français. Elle est composée d’une salle immersive quatre faces de 45 m2, équipée d’un tapis roulant particulièrement adapté pour l’analyse de la marche en temps réel (GRAIL de Motek Medical). Les calculateurs de cette salle immersive sont mutualisés avec un amphithéâtre attenant de 150 places, de manière que les expérimentations effectuées avec un sujet unique dans la salle immersive puissent être suivies par un auditoire nombreux (besoins de formation notamment). Les équipes utilisent le matériel au fur et à mesure des développements informatiques et de nouveaux protocoles d’expérimentation germent dans l’esprit des chercheurs qui voient dans la réalité virtuelle des possibilités de tests jamais atteintes.Une centaine de chercheurs utilise régulièrement le plateau technique CIREVE, dans des visées de recherche qui leur sont propres. Il est toutefois apparu qu’un certain nombre de problématiques concernaient toutes les disciplines et qu’une partie de la réflexion sur les mondes virtuels pouvait être mutualisée. Le séminaire VIRTUALIA permet d’offrir un espace de rencontre à ces chercheurs, issus d’horizons différents, pour discuter de l’utilisation de l’outil d’un point de vue épistémologique. Il est par exemple capital de s’interroger sur la notion de présence. Le sujet se comporte-il de la même façon dans l’environnement virtuel et dans le monde réel ? Les chemins de circulation choisis dans le modèle virtuel sont-ils les mêmes que ceux qui seraient empruntés en réalité ? Les conclusions établies dans le modèle virtuel sont-elles directement transposables à la réalité ? Un des enjeux du travail est d’évaluer la pertinence subjective des modèles virtuels, ce qui est capital avant de généraliser leur utilisation dans des actions de formation par exemple. L’utilisation d’une technologie n’est jamais complètement neutre. Dans le cadre des mondes virtuels, l’interaction de l’homme avec le monde de synthèse n’est possible qu’au travers de logiciels et d’interfaces matérielles. Il faut s’assurer que les processus cognitifs soient adéquats avant de s’interroger sur le résultat des simulations. Naturellement, le séminaire permet également à chaque discipline d’exposer les résultats des dernières recherches réalisées grâce à la réalité virtuelle.Les domaines scientifiques concernés par la réalité virtuelle sont multiples : les civilisations et les patrimoines culturels, la médecine, les neurosciences, la psychologie, les sciences du mouvement et du sport, l’ingénierie, l’informatique. L’Université de Caen Normandie étant pluridisciplinaire, le spectre des utilisations est très large. Elles se répartissent en trois axes principaux et un axe en émergence :LA REPRÉSENTATION : la réalité virtuelle permet de représenter et de visualiser, interactivement et en trois dimensions, des environnements disparus, dégradés, inaccessibles, ou des environnements futurs.Domaines concernés : civilisations, patrimoine, linguistique...L'EXPÉRIMENTATION : en permettant d'interagir en temps réel avec un monde numérique 3D, la réalité virtuelle offre de nouvelles perspectives d'expérimentations dans des environnements de plus en plus proches du réel et en même temps parfaitement contrôlables.Domaines concernés : santé, neuropsychologie, psychologie, activités physiques et sportives...LA CREATION ET LE DEVELOPPEMENT D’OUTILS : les informaticiens créent et testent des applications concernant les méthodes de navigation en monde virtuel, de restitution de la réalité.Domaine concerné : informatique.LA FORMATION (axe en émergence) : par la représentation de la connaissance, par les diverses possibilités d'expérimentation, la réalité virtuelle est un formidable outil de formation.Domaines concernés : sciences du langage, médecine, informatique (serious game, simulation...).Une partie importante de la réflexion développée lors du séminaire Virtualia 2016 a été consacrée aux enjeux sociétaux liés à la réalité virtuelle : notions de mémoire, d’apprentissage des gestes techniques, d’être humain « augmenté » etc. Les articles publiés attestent du savoir-faire, bien réel cette fois, que le CIREVE a acquis en termes de création de mondes virtuels pour représenter, expérimenter et former. La publication des actes du séminaire Virtualia vise à mettre en lumière des recherches particulièrement innovantes qui s’effectuent dans un cadre technologique exceptionnel.- S. Madeleine, Virtualia 2016. Introduction (et direction de l'édition)- J. Grieu, F. Lecroq, Th. Galinho, H. Boukachour, Environnements industriels virtualisés et processus d’apprentissage- Ph. Brunet, J. Dehut, Images 3D et humanités numériques : modélisation et restitution du geste théâtral- G. Lecouvey, J. Gonneaud, N. Legrand, G. Rauchs, F. Eustache, B. Desgranges, Réalité virtuelle et mémoire- N. Benguigui, C. Mandil, M. Mallek, L. Lejeune, R. Thouvarecq, Étude des liens entre perception et action dans des environnements virtuels- E.-G. Dupuy, A. Maneuvrier, E. Vlamynck, S. Besnard, B. Bienvenu, L.-M. Decker, Le syndrome d’Ehlers-Danlos type hypermobile : évolution des stratégies posturales en réponse à un programme de rééducation à visée somesthésique- C. Weismann-Arcache, Réalité virtuelle et humain augmenté : subjectivation, désubjectivation ?- L. Haddouk, Réalité psychique en visioconsultatio

New insights into the diversity of deep-sea benthic foraminifera

Les foraminifères benthiques sont une composante majeure des fonds océaniques. Leur importance dans le cycle du carbone est largement reconnue et ils sont couramment utilisés en paléocéanographie en tant que marqueurs des changements climatiques. Cependant, nos connaissances croissantes à leur sujet nous dévoilent peu à peu que ce vaste phylum retient encore quelques secrets, notamment quant à sa diversité et à la distribution géographique de ses espèces. Dans cette thèse sont décrits deux nouveaux genres de foraminifères agglutinés : Capsammina patelliformis et Shinkaiya lindsayi. Leur morphologies, spectaculairement différentes, illustrent parfaitement l'étendue de la richesse des foraminifères monothalames. Comme d'autres xenophyophores, S. lindsayi présente un réseau interne de conglomérats digestifs (stercomata) mais se distingue aussi par l'absence de cristaux de barite dans son cytoplasme. Des analyses élémentaires ont révélé que ce foraminifère géant (8 cm de diamètre) concentrait de grandes quantités de métaux, dont l'uranium, à l'intérieur de ses stercomata, contribuant ainsi à modifier la composition chimique du sédiment..

Shinkaiya Lecroq & Gooday & Tsuchiya & Pawlowski 2009, GEN. NOV.

SHINKAIYA GEN. NOV. Type species: Shinkaiya lindsayi gen. et sp. nov. Generic diagnosis: Large xenophyophore: at least 8 cm in diameter and 5-cm high. Test fragile, approximately cylindrical in shape, and forming tightly-meshed, reticulated structure composed of bar-shaped elements (~ 0.5 cm in diameter), separated by open spaces. Test with smooth outer surface; wall relatively thick, soft, weakly cemented, and composed of fine sediment particles. Scattered internal xenophyae (agglutinated particles), mainly radiolarian tests, present. Derivation of name: The name of the new genus is derived from the Japanese submersible Shinkai 6500, operated by JAMSTEC, which was used to collect the specimen. Remarks: The new genus resembles species of the genus Syringammina, in particular the type species Sy. fragilissima. The genera are similar in the general shape and construction of the test, which consists of a framework of bar-like elements, forming a tightlymeshed, often reticulated structure. Another species, Syringammina reticulata Gooday, 1996, has a similar arrangement of test elements, although the body form is flattened rather than domed. The main morphological difference between the new genus and Syringammina is the nature of the test wall. In Syringammina, the wall is brittle, with a smooth inner surface, and consists of ‘tightly cemented xenophyae’ (Tendal, 1972). These comprise mainly fine sand grains and small foraminiferan tests in Sy. fragilissima. Shinkaiya, on the other hand, is characterized by a relatively thick wall that is soft rather than brittle, and consists mainly of clay-sized sediment particles. Unlike Syringammina, in which the particles are confined to the test wall, the lumen of the test in Shinkaiya includes scattered internal xenophyae. Our distinction of these two genera is supported by molecular data showing an important genetic distance between Sh. lindsayi sp. nov. and Sy. corbicula. Unfortunately, DNA sequences are not yet available for Sy. fragilissima.Published as part of Lecroq, Béatrice, Gooday, Andrew John, Tsuchiya, Masashi & Pawlowski, Jan, 2009, A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis, pp. 455-464 in Zoological Journal of the Linnean Society 156 (3) on page 457, DOI: 10.1111/j.1096-3642.2008.00493.x, http://zenodo.org/record/468774

Shinkaiya LINDSAYI GEN. ET, GEN. ET SP. NOV.

SHINKAIYA LINDSAYI GEN. ET SP. NOV. Diagnosis: As for genus. Derivation of name: The species is named after the biologist Dhugal Lindsay, who collected the specimen. Type specimen: The single specimen (and therefore the holotype) was recovered from a push core taken by the Shinkai 6500 submersible from the North Pacific, east of the Japan Trench (38°14.8175′N, 147°00.1885′E; water depth, 5435 m). The major fragment is deposited in the National Museum of Nature and Science, Tokyo (registration number: NSMT-Pr 241). MORPHOLOGICAL DESCRIPTION Test form and structure: The test forms a short, approximately cylindrical structure, with a fairly flat upper surface. It measures at least 8 cm in diameter, with ~ 5 cm of test being exposed above the sediment surface. At the base of the test, 1–2 cm long root-like structures extend into the sediment. The test comprises a system of anastomosing branches, typically 0.5 cm in diameter, forming a meshwork with open spaces ranging from 1 to 3 cm in size (Fig. 2A, B). On the upper surface of the test, these branches tend to form an approximately reticulated pattern. The test wall is delicate, soft, and 300-Mm thick. It is light brown in colour, and is mainly composed of fine-grain sediment particles with scattered darker particles, and with occasional larger radiolarian tests (up to 200 Mm in diameter) and quartz grains (Fig. 3D). Test interior: Usually, the test branches are basically hollow, but there are some internal xenophyae, mainly isolated radiolarian tests, but also quartz grains and sponge spicules (Fig. 3A). Occasionally, the two sides of the test adjoin, leaving almost no lumen. Cytology: The interior contains prominently developed granellare and stercomare strands, which are intimately intertwined inside the test branches, but without any obvious connections between them (Fig. 2D). The stercomare and granellare are not equally distributed within the specimen. Some test branches contain stercomare but no granellare, although the reverse has not been observed. The granellare strands are pale yellowish (strawcoloured), and branch in an irregular manner (Fig. 2D). The diameter is highly variable (50– 200 Mm). Sometimes, a thick granellare section gives rise to a cluster of four or five much narrower branches. Where the granellare runs along the length of a test section, the branches may merge; however, these anastomose are not common in the test fragments examined. The organic sheath is very thin, delicate, and has a non-reflective surface (Fig. 3C). No granellae (barite crystals) are visible within the cytoplasm when squashed preparations of granellare fragments are viewed under a high-power microscope. The DAPI staining of the cytoplasm revealed numerous nuclei (roughly 15 ¥ 105 mm-3), of between 2 and 4 Mm in diameter (Fig. 2E, F). Although the cytoplasmic ultrastructure had been largely destroyed by freezing, nuclei and a Golgi apparatus were recognizable in TEM sections, and at least one stercome was present within the cytoplasm. Barite crystals were not observed in any of the sections examined. The stercomare system occupies a greater volume of the test interior than the granellare (Fig. 2C). The strands are usually attached loosely to the inner surface of the wall, but in places they project into the test lumen (Fig. 3A). They are dark grey, almost black, and the thin organic sheath that encloses the stercomata masses has a distinctly reflective, slightly iridescent surface. The strands range from 30 to 200 Mm in diameter, and their width is often uneven; lobate sections separated by constrictions sometimes develop. Some branches end blindly with rounded terminations. Anastomoses have not been observed, although branches sometimes adjoin without merging. Branching, which is usually dichotomous, may be very frequent. The branches often run in different directions. However, in the more tubular sections of the test, the stercomare strands extend for 100 Mm without branching, and run more or less parallel with the granellare strands. The stercomata are between 10 and 15 Mm in diameter (Fig. 3B). The TEM observations reveal that the organic envelope enclosing the stercomare is of even thickness: 1-Mm thick (Fig. 3E). The envelope appears rather homogeneous and featureless, except for an outer layer that in places separates from the underlying part to form a loop-like structure (Fig. 3F). An iron peak is evident in the EDAX spectra. The TEM sections of stercomare revealed the presence of cytoplasm associated with stercomata (Fig. 3E, F). The cytoplasm is present around the margins of the stercomare mass, but is inside the organic envelope. Stercomata are composed mainly of flake-like mineral particles. The EDAX microanalysis revealed peaks for silica, aluminium, magnesium, and iron, suggesting that these particles are composed of clay minerals. Barium was also detected within the stercomata. In one case, this element was associated with a crystal. The barite composition of this crystal, however, remains uncertain, because it also yielded a peak for calcium. A sharp peak for titanium was associated with another crystal, presumably rutile. LIFE POSITION The specimen was epibenthic. It projected from the seafloor, with the root-like lower part being buried in the sediment. It was found among numerous other unidentified xenophyophores of different sizes. MOLECULAR CHARACTERIZATION The total length of the SSU rDNA was 4054 bp, and all of the clones sequenced were identical. The sequence alternates between conserved regions and variable regions among foraminiferans, with a long insertion of 624 bp starting in the variable region E23 at position 1744 bp (Fig. 1). The GC content of Sh. lindsayi sp. nov. (32.2%) is similar to that of Sy. corbicula (34.1%). The sequence divergence between the two xenophyophores is 23.6%, whereas it is 30.2% between Sh. lindsayi sp. nov. and R. algaeformis. In the phylogenetic tree obtained by the ML method (Fig. 4), Sh. lindsayi sp. nov. clusters with Sy. corbicula, and the two xenophyophores form a sister group of R. algaeformis. This topology is supported by high bootstrap values (94 and 100%, respectively). The clade consisting of Sh. lindsayi sp. nov., Sy. corbicula, and R. algaeformis branches at the base of polythalamous (multichambered) foraminiferans, including rotaliids, textulariids, and robertinids. REMARKS As discussed above, the new species is similar to some species of Syringammina in the construction of the test from reticulated bar-like elements. There is a particular resemblance between Sh. lindsayi sp. nov. and Sy. reticulata in the constant diameter, dimensions, and arrangement of the tubes (compare Fig. 2A with Gooday, 1996: pl. 7). However, in addition to the differences in wall structure noted above, the overall morphology of the test is distinctly flattened in Sy. reticulata, but is more or less equidimensional in Sh. lindsayi sp. nov. ELEMENTAL COMPOSITION Mass spectrometry analyses were performed separately on pieces of the stercomare, granellare, and on intact fragments of the specimen, as well as on environmental samples from the area where the specimen was collected (site 1037) (Fig. 5). Aluminium, barium, and magnesium were present inside the stercomare, where concentrations were more than 30% higher than in the sediment. These elements were less abundant in the granellare than in the surrounding sediment (site 1037). They occur in roughly the same concentration in the intact fragment (mainly test) and in the environment. Consistent with microscopic observations of barite crystals, barium occurs in the stercomata but not in the cytoplasm. Lead, mercury, and uranium concentrations are also higher (two, four, and six times higher, respectively) inside the stercomare than in the sediment. The concentration of mercury in the granellare is 12 times that in the sediment.Published as part of Lecroq, Béatrice, Gooday, Andrew John, Tsuchiya, Masashi & Pawlowski, Jan, 2009, A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis, pp. 455-464 in Zoological Journal of the Linnean Society 156 (3) on pages 457-461, DOI: 10.1111/j.1096-3642.2008.00493.x, http://zenodo.org/record/468774

Figure 3 in A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis

Figure 3. Shinkaiya lindsayi gen. et sp. nov. A, scanning electron micrograph (SEM) of an open tube, showing its inner surface with many radiolarian tests, a granellare string (right-hand arrow), and a stercomare string (left-hand arrow). B, SEM image of an open stercomare string, containing stercomata (spherical pellets). C, SEM image of the organic sheath of the granellare. D, SEM image showing details of the external surface of the test, with agglutinated material. E, F, transmission electronic microscopy (TEM) images of a stercomare section, showing its wall (W), stercomata (S), and cytoplasm (C). Scale bars: 100 Mm (A), 10 Mm (B–D), 2 Mm (E), 1 Mm (F).Published as part of <i>Lecroq, Béatrice, Gooday, Andrew John, Tsuchiya, Masashi & Pawlowski, Jan, 2009, A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis, pp. 455-464 in Zoological Journal of the Linnean Society 156 (3)</i> on page 460, DOI: 10.1111/j.1096-3642.2008.00493.x, <a href="http://zenodo.org/record/10114806">http://zenodo.org/record/10114806</a&gt

Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments

Deep-sea floors represent one of the largest and most complex ecosystems on Earth but remain essentially unexplored. The vastness and remoteness of this ecosystem make deep-sea sampling difficult, hampering traditional taxonomic observations and diversity assessment. This problem is particularly true in the case of the deep-sea meiofauna, which largely comprises small-sized, fragile, and difficult-to-identify metazoans and protists. Here, we introduce an ultra-deep sequencing-based metagenetic approach to examine the richness of benthic foraminifera, a principal component of deep-sea meiofauna. We used Illumina sequencing technology to assess foraminiferal richness in 31 unsieved deep-sea sediment samples from five distinct oceanic regions. We sequenced an extremely short fragment (36 bases) of the small subunit ribosomal DNA hypervariable region 37f, which has been shown to accurately distinguish foraminiferal species. In total, we obtained 495,978 unique sequences that were grouped into 1,643 operational taxonomic units, of which about half (841) could be reliably assigned to foraminifera. The vast majority of the operational taxonomic units (nearly 90%) were either assigned to early (ancient) lineages of soft-walled, single-chambered (monothalamous) foraminifera or remained undetermined and yet possibly belong to unknown early lineages. Contrasting with the classical view of multichambered taxa dominating foraminiferal assemblages, our work reflects an unexpected diversity of monothalamous lineages that are as yet unknown using conventional micropaleontological observations. Although we can only speculate about their morphology, the immense richness of deep-sea phylotypes revealed by this study suggests that ultra-deep sequencing can improve understanding of deep-sea benthic diversity considered until now as unknowable based on a traditional taxonomic approach