Molecular data reveal high taxonomic diversity of allogromiid Foraminifera in Explorers Cove (McMurdo Sound,Antarctica)

Allogromiids are organic-walled or agglutinated, single-chambered Foraminifera, common in deep-sea and polar benthic communities. The simple forms and paucity of distinctive features make allogromiid identification difficult by traditional means. Molecular phylogenetic methods offer alternative tools for species identification and are used here to investigate allogromiid diversity. We obtained 135 partial small-subunit ribosomal DNA sequences of allogromiids collected in Explorers Cove, McMurdo Sound, Antarctica. In contrast to the 27 morphotypes identified, phylogenetic analysis revealed 49 molecular types (considered separate species) that differ by more than 5% of sequence divergence. The 49 genetic types form 28 molecular supra-groups that differ by more than 20% and probably represent distinct genera or families. Large genetic distances separating the molecular types indicate unexpectedly high taxonomic diversity. Comparison of our data with sequences of non-Antarctic allogromiids suggests that Explorers Cove species might be endemic and only distantly related to comparable northern hemisphere fauna.     

Deep-Sea Biodiversity in the Mediterranean Sea: The Known,the Unknown,and the Unknowable

Deep-sea ecosystems represent the largest biome of the global biosphere, but knowledge of their biodiversity is still scant. The Mediterranean basin has been proposed as a hot spot of terrestrial and coastal marine biodiversity but has been supposed to be impoverished of deep-sea species richness. We summarized all available information on benthic biodiversity (Prokaryotes, Foraminifera, Meiofauna, Macrofauna, and Megafauna) in different deep-sea ecosystems of the Mediterranean Sea (200 to more than 4,000 m depth), including open slopes, deep basins, canyons, cold seeps, seamounts, deep-water corals and deep-hypersaline anoxic basins and analyzed overall longitudinal and bathymetric patterns. We show that in contrast to what was expected from the sharp decrease in organic carbon fluxes and reduced faunal abundance, the deep-sea biodiversity of both the eastern and the western basins of the Mediterranean Sea is similarly high. All of the biodiversity components, except Bacteria and Archaea, displayed a decreasing pattern with increasing water depth, but to a different extent for each component. Unlike patterns observed for faunal abundance, highest negative values of the slopes of the biodiversity patterns were observed for Meiofauna, followed by Macrofauna and Megafauna. Comparison of the biodiversity associated with open slopes, deep basins, canyons, and deep-water corals showed that the deep basins were the least diverse. Rarefaction curves allowed us to estimate the expected number of species for each benthic component in different bathymetric ranges. A large fraction of exclusive species was associated with each specific habitat or ecosystem. Thus, each deep-sea ecosystem contributes significantly to overall biodiversity. From theoretical extrapolations we estimate that the overall deep-sea Mediterranean biodiversity (excluding prokaryotes) reaches approximately 2805 species of which about 66% is still undiscovered. Among the biotic components investigated (Prokaryotes excluded), most of the unknown species are within the phylum Nematoda, followed by Foraminifera, but an important fraction of macrofaunal and megafaunal species also remains unknown. Data reported here provide new insights into the patterns of biodiversity in the deep-sea Mediterranean and new clues for future investigations aimed at identifying the factors controlling and threatening deep-sea biodiversity.     

Les ostracodes et foraminifères associés des dépôts de l’Éocène moyen et supérieur de la coupe de Jebel Serj (Tunisie centrale). Intérêt biostratigraphique,paléoécologique et paléobiogéographique

The ostracod fauna collected from the Cherahil formation that crops out at the Jebel Serj section (central Tunisia) contains 24 species belonging to 12 genera. These ostracods are associated with 9 genera of benthic Foraminifera (including 4 Nummulites species) and 7 genera of planktonic Foraminifera. The biostratigraphic study of ostracod assemblages results to the recognition of 6 biozones which are correlated with Lutetian-Priabonian. The Shannon Weaver, Margalef and equitability indices point to internal platform netritic conditions, with minor fluctuations in depth and oxygenation. The palaeobiogeographic distribution of ostracod species found in the study area of Central of Tunisia establishes a good connexion with the basins developed in Northern Africa (Tunisia, Algeria, Libya and Mauritania) and the Middle East (Egypt and Jordan).     

Nouvelles données micropaléontologiques(Foraminifères planctoniques et petits Foraminifères benthiques) sur le stratotype bordelais du Burdigalien

The present work deals with the microfauna of small benthonic and planktonic Foraminifera from the Burdigalian stratotype of Aquitaine basin (France) and from a few outcrops in the stratotype vicinity showing the upper or lower boundary of the stratotype.Benthonic fauna is rich: more than 250 species divided in 92 genera have been collected. The most frequent are hyaline Foraminifera (Pararotalia, Elphidium, Asterigerina, Florilus, Virgulopsis, Bolivina). The miocene feature is more pronounced than in the Aquitanian stratotype.Planktonic Foraminifera are much less abundant:only 20 species. However, some of them authorize to place the stratotype (or its equivalent l. s.) in N5 Blow's zone and perhaps in the basel N6 zone.The figurations of many species are made withthe scanning electronic microscope.     

Deep-sea asellote isopods of the north-east Atlantic: the family Dendrotionidae and some new ectoparasitic copepods

A new species of Dendromunna and two new species of Dendrotion are described from abundant material collected in the Rockall Trough region of the north-east Atlantic. The taxonomy of the little known benthic deep-sea asellote isopod family Dendrotionidae is reviewed and keys provided for genera and species. Also diagnosed and described are two new species belonging to a new genus of siphonostomatoid copepod found as ectoparasites on the walking legs of the new Dendromunna. The new parasites belong in the Rhizorhina group of genera within the family Nicothoidae.     

Les travaux micropaléontologiques d’Alcide d’Orbigny

D’Orbigny has created the order of Foraminifera for minute animals classed, at this time, amongst Cephalopoda, and proposed the first classification of this order in 1826, laying the foundations of micropalaeontology. All along his life, he described, figured or clarified diagnosis of about 1500 recent and fossil species. His collections, stored in the National Museum of Natural History in Paris, represent an inestimable patrimony and are still actively consulted. Several micropalaeontologists had contributed to their valorisation and recognised the validity of most of his species. Nowadays, one hundred and two are considered as type species of genera.     

Deep-sea origin and in-situ diversification of chrysogorgiid octocorals

The diversity, ubiquity and prevalence in deep waters of the octocoral family Chrysogorgiidae Verrill, 1883 make it noteworthy as a model system to study radiation and diversification in the deep sea. Here we provide the first comprehensive phylogenetic analysis of the Chrysogorgiidae, and compare phylogeny and depth distribution. Phylogenetic relationships among 10 of 14 currently-described Chrysogorgiidae genera were inferred based on mitochondrial (mtMutS, cox1) and nuclear (18S) markers. Bathymetric distribution was estimated from multiple sources, including museum records, a literature review, and our own sampling records (985 stations, 2345 specimens). Genetic analyses suggest that the Chrysogorgiidae as currently described is a polyphyletic family. Shallow-water genera, and two of eight deep-water genera, appear more closely related to other octocoral families than to the remainder of the monophyletic, deep-water chrysogorgiid genera. Monophyletic chrysogorgiids are composed of strictly (Iridogorgia Verrill, 1883, Metallogorgia Versluys, 1902, Radicipes Stearns, 1883, Pseudochrysogorgia Pante & France, 2010) and predominantly (Chrysogorgia Duchassaing & Michelotti, 1864) deep-sea genera that diversified in situ. This group is sister to gold corals (Primnoidae Milne Edwards, 1857) and deep-sea bamboo corals (Keratoisidinae Gray, 1870), whose diversity also peaks in the deep sea. Nine species of Chrysogorgia that were described from depths shallower than 200 m, and mtMutS haplotypes sequenced from specimens sampled as shallow as 101 m, suggest a shallow-water emergence of some Chrysogorgia species.     

The spirotheca of the foraminifer Quasifusulina

A SEM study on the test wall of Quasifusulina has demonstrated that the ultrastructures in the spirotheca Quasifusulina different from those of related fusulinid genera, such as Fusulinella and Triticites. The primary wall structure is prokerotheca rather than diaphanotheca or keriotheca, as previously described. The peculiar wall structures of Quasifusulina may represent a previously unknown type of spirotheca in fusulinid Foraminifera. □ Foraminifera, ultrastructure, spirotheca, biomineralization, Carboniferous, Permian.     

New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes

Background

Two deep-sea eels collected from the Western Pacific Ocean are described in this study. Based on their morphological characteristics, the two deep-sea eel specimens were assumed to belong to the cusk-eel family Ophidiidae and the cutthroat eel family Synaphobranchidae.

Methods and results

To accurately identify the species of the deep-sea eel specimens, we sequenced the mitochondrial genes (cytochrome c oxidase subunit I [COI] and 16S ribosomal RNA [16S rRNA]). Through molecular phylogenetic analysis based on mtDNA COI and 16S rRNA gene sequences, these species clustered with the genera Bassozetus and Synaphobranchus, suggesting that the deep-sea eel specimens collected are two species from the genera Bassozetus and Synaphobranchus in the Western Pacific Ocean, respectively.

Conclusions

This is the first study to report new records of the genera Bassozetus and Synaphobranchus from the Western Pacific Ocean based on COI and 16S rRNA genes

     

Marine mites (Halacaroidea: Acari): a geographical and ecological survey

Halacarid mites (Acari), with almost 700 species described, inhabit marine and freshwater habitats. The majority of genera are recorded from at least two ocean basins or continents. There is no evidence of endemic genera, in either littoral faunal provinces or in deep-sea regions. Copidognathus, a genus comprising 1/4 of all species described, is found in almost all geographic regions, depths and habitats. Other genera dominate or are restricted to cold waters, to warm waters or to distinct habitats.Corresponding habitats on either side of the boreal Atlantic Ocean harbour congeneric, identical, sibling or morphologically similar species. The fauna in the western Atlantic is less diverse than that in the eastern. Amphiatlantics are restricted to certain genera. Transatlantic distribution is independent of the niche inhabited.Of the marine halacarid species recorded from the boreal western Atlantic, 41% are amphiatlantics, while only one species is recorded from both the Caribbean and the Mediterranean. The Caribbean and the Mediterranean faunas are dominated by genera in which amphiatlantics are unknown.Most of the Black Sea species of the genus Halacarellus also occur in the Baltic, North Sea or North Atlantic, whereas the Copidognathus fauna of the Black Sea is similar to that of the Mediterranean.Halacarids are thought to be an ancient taxon, with most genera probably having been present since the Mesozoic and with several species having an age of at least 50 million years. Evidence for their antiquity is found in the distributional pattern of marine and limnic genera and species, in the lack of endemic genera despite low fecundity and lack of dispersal stages, and in the fact that amphiatlantics are restricted to certain genera without relationships to the niches inhabited.     

Advances in Taxonomy,Ecology, and Biogeography of Dirivultidae (Copepoda) Associated with Chemosynthetic Environments in the Deep Sea

Background

Copepoda is one of the most prominent higher taxa with almost 80 described species at deep-sea hydrothermal vents. The unique copepod family Dirivultidae with currently 50 described species is the most species rich invertebrate family at hydrothermal vents.

Methodology/Principal Findings

We reviewed the literature of Dirivultidae and provide a complete key to species, and map geographical and habitat specific distribution. In addition we discuss the ecology and origin of this family.

Conclusions/Significance

Dirivultidae are only present at deep-sea hydrothermal vents and along the axial summit trough of midocean ridges, with the exception of Dirivultus dentaneus found associated with Lamellibrachia species at 1125 m depth off southern California. To our current knowledge Dirivultidae are unknown from shallow-water vents, seeps, whale falls, and wood falls. They are a prominent part of all communities at vents and in certain habitat types (like sulfide chimneys colonized by pompei worms) they are the most abundant animals. They are free-living on hard substrate, mostly found in aggregations of various foundation species (e.g. alvinellids, vestimentiferans, and bivalves). Most dirivultid species colonize more than one habitat type. Dirivultids have a world-wide distribution, but most genera and species are endemic to a single biogeographic region. Their origin is unclear yet, but immigration from other deep-sea chemosynthetic habitats (stepping stone hypothesis) or from the deep-sea sediments seems unlikely, since Dirivultidae are unknown from these environments. Dirivultidae is the most species rich family and thus can be considered the most successful taxon at deep-sea vents.     

深海钻探计划(DSDP)31航次296站晚新生代介形类

本文研究了深海钻探(DSDP)31航次296站晚新生代介形类动物群的性质及其古海洋学意义.此站钻孔上部上新统至全新统以超微浮游生物软泥和粘土为主的16块岩芯中,共分析获得介形类化石8属11种,计有:Poseidonamicus major Benson, P. anteropunctatus Whatley et al., P. punctatus Whatley et al., Pennyella dorsoserrata (Brady), Henryhowella sp., Pterygocythere mucronalatum (Brady), Abyssocythere sp., Abyssocythereis sulcatoperforata (Brady), Pelecocythere sp., Krithe sp. 1和Krithe sp.2.这些介形类属种均为冷海域深海区介形类分子.由此表明,西北太平洋边缘地区在晚新生代曾为一深海区.在第四纪,其深度可能和现今296站的深度大致相当;在上新世,其深度可能更深一些.研究结果证实,深海底栖介形类属种的分布具全球性;在相当长的地质时期内,介形类属种的形态和壳饰都非常稳定,无明显变化.同时,进一步证实,介形类个体大小变化与深度相关,同一种介形类壳体随水域深度加深而增大.     

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

The deep‐sea floor is inhabited by a number of unusual and enigmatic taxa, unknown in shallow waters. These include the xenophyophores, a group of giant protists that construct fragile agglutinated tests. Here, we describe Shinkaiya lindsayi gen. et sp. nov. , a new xenophyophore collected by the submersible Shinkai 6500 at a depth of 5435 m near the Japan Trench. The phylogenetic analysis performed on its complete small‐subunit ribosomal DNA (SSU rDNA) sequence confirms that Sh. lindsayi sp. nov. is a foraminiferan that is closely related to another xenophyophore, Syringammina corbicula Richardson, 2001, and to a monothalamous (single‐chambered) foraminiferan Rhizammina algaeformis Brady, 1879. In terms of morphology, the new genus resembles Syringammina, but its test wall is thicker, softer, and more weakly cemented. Moreover, the SSU rDNA sequences of the two genera are highly divergent. Mass spectra analyses reveal unusually high concentrations of some elements, such as lead, uranium, and mercury. The granellare system (the cytoplasm and the organic sheath that encloses it) is apparently devoid of barite crystals, which are usually abundant as intracellular inclusions in xenophyophores, but is rich in mercury (with 12 times the concentration of mercury found in the surrounding sediment). Fecal pellets retained within a tubular system (stercomare) concentrate heavy metals, including lead and uranium (respectively, two and six times more than that of the sediment). Based on a comparison of the compositions of the agglutinated test wall, the granellare, the stercomare, and the surrounding sediment, we discuss the impact of xenophyophores on their habitat. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 455–464.     

Sponges Collected by the Swedish Deep Sea Expedition

The paper deals with sponges collected in the Atlantic by the Swedish Deep Sea Expedition. The collection contains six species of the genera Malaco-saccus, Chonelasma, heptonema, Asbestopluma , and Chondrocladia , which are well known from the deep-sea. Three new species are described, viz. Asbestopluma quadriserialis sp.n., Chondrocladia al-batrossi sp.n., and C. burtoni sp.n. A survey of the knowledge of the Atlantic deep-sea sponge fauna shows that 118 species are at present known from depths of more than 2 000 m. About 35% of the species were found four or more times, whereas about 47% are known only from the type locality. 63 species were taken more than once, and 50 species are known also from depths of less than 2 000 m.     

Nouvelles données micropaléontologiques(Foraminifères planctoniques et petits Foraminifères benthiques) sur le stratotype de l'Aquitanien

The authors study the microfauna of small benthonic and planktonic Foraminifera from the Aquitanian stratotype and of a few exposures in the stratotype vicinity.Benthonic microfauna is rich: more than 150species have been collected; among them Miliolidae mainly belonging to the genera Quinqueloculina and Miliola.Planktonic Foraminifera are much less abundant:only 20 species. They authorize to place the stratotype at the boundary of N4–N5 Blow's zones.The figurations of many species are made withthe scanning electronic microscope.     

The Foraminifera of the Pitcairn Islands

Foraminifera were recovered from 18 samples collected in the Pitcairn Islands, 12 from Henderson Island (including the best and most comprehensive collections) and three each from Oeno Atoll and Pitcairn Island itself. Although both algae and sediment samples were collected, the living Foraminifera came, almost exclusively, from phytal (attached or clinging) habitats. Foraminifera in the sediment samples are mainly thanatocoenoses. The fauna is an exclusively calcareous, relatively low diversity assemblage, dominated by large soritids [Marginopora, Amphisorus, Sorites) and Amphistegina , all of which are ubiquitous throughout the tropical Pacific. These larger Foraminifera are usually accompanied by small miliolids in particular, as well as by small attached Foraminifera (discorbids and the like). Typical reefal Foraminifera are generally under-represented. So far, no endemic species have been found. Of more significance, perhaps, is the apparent absence of Calcarina , small rotaliids, elphidiids and agglutinating species, so common in the western Pacific islands. One sample of fossil Foraminifera was analysed, from a shelly sand (c. 30 m above present sea-level) on Henderson Island. Though, for the most part, like the Recent assemblages, this was characterized by Archaias , a soritid which was not found in any of the modern collections made by the 1991– 92 Expedition. This could either be a sampling artifact or refer to a real environmental change since the Pleistocene.     

Amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone

To examine the occurrence in other deep-sea bacteria of two amino acid substitutions (Ala-180 and His-229) in malate dehydrogenase (MDH) found previously in the deep-sea piezophilic Moritella sp. strain 2D2, we cloned and sequenced MDH genes of deep-sea piezophilic Moritella and Shewanella strains isolated from intestinal contents of deep-sea fishes, as well as other Moritella species from deep-sea water and sediments: M. marina, M. japonica, and M. yayanosii. The piezophilic Moritella strains had a Val residue or an Ala residue at position 180 and all the Moritella strains except for one had a His residue at position 229. However, four piezophilic-strain-specific substitutions at positions 103, 111, 229, and 283 were found to be completely conserved in the MDH of the intestinal Moritella strains of deep-sea fishes, indicating the substitutions may be habitat-specific. The piezophilic Shewanella strains had a Val residue and a Gln residue at positions 180 and 229, respectively. However, the MDHs of the Shewanella strains had five piezophilic-strain-specific substitutions at positions 61, 65, 107, 161, and 202. Therefore, the enzymatic strategies for responding to deep-sea high pressure environments of the MDHs between the genera Moritella and Shewanella are potentially different. Moreover, homology modeling shows these substitutions found in the MDHs of both genera except for position 229 in the subunit interface are located on the exposed region of the MDH molecules, indicating the substitutions may be related to the hydration state of the molecules.     

Optical parameters of euphausiid eyes as a function of habitat depth

Summary The relationships between habitat depth, eye diameter relative to body length, and the dimensions of rhabdoms and crystalline cones have been examined for 13 species of three oceanic euphausiid genera with habitats ranging from near-surface waters to the deep-sea. Rate of eye growth decreases with depth. Longer rhabdoms may increase the visual sensitivity to point and extended light sources by an eye of a particular size with depth. Larger interommatidial angles suggest that visual acuity decreases at depth. Depth-related changes in euphausiid eyes are considered with respect to the probable roles of vision and bioluminescence in the deep-sea. Unusual features of the eyes of several species are described.     

A review of the pelagic ophidioid fish genus Brotulataenia with descriptions of two new species

An osteological study and a taxonomic diagnosis are presented for the mesopelagic, oviparous ophidioid fish genus Brotulataenia. Its relationships are probably with a large group of benthic deep-sea oviparous genera. Brotulataenia has been known previously from three North Atlantic specimens assigned to two species. The present study is based on 33 specimens from the North and South Atlantic and Pacific Oceans and the Indian Ocean, and placed in four species, two of which are described as new. Two species are excessively elongate and are interpreted as being derived forms; they are lighter in color than are the two short-bodied species and may live higher in the water column.