Monothalamous (single-chambered) foraminifers are a major component of the benthic meiofauna in high latitude regions. Several morphologically similar species are common in the Arctic and Antarctic. However, it is uncertain whether these morphospecies are genetically identical, or whether their accurate identification is compromised by a lack of distinctive morphological features. To determine the relationship between Arctic and Antarctic species, we have compared SSU rDNA sequences of specimens belonging to four morphotaxa: Micrometula , Psammophaga , Gloiogullmia , and one morphospecies Hippocrepinella hirudinea from western Svalbard (Arctic) and McMurdo Sound (Antarctic). Wherever possible, we include in our analyses representatives of these taxa from the deep Arctic and Southern Oceans, as well as from Northern European fjords. We found that in all cases, the bipolar populations were clearly distinct genetically. As expected, Arctic specimens were usually more closely related to those from Northern Europe than to their Antarctic representatives. The deep-sea specimens from Weddell Sea branched as a sister to the McMurdo Sound population, while those from the Arctic Ocean clustered with ones from Norwegian fjords. Our study has revealed a high number of cryptic species within each of the examined genera, and demonstrates the unexplored potential of monothalamous foraminifers for use as a tool to evaluate the origin and biogeography of polar meiofauna.

Despite its often featureless appearance, the deep-ocean floor includes some of the most diverse habitats on Earth. However, the accurate assessment of global deep-sea diversity is impeded by a paucity of data on the geographical ranges of bottom-dwelling species, particularly at the genetic level. Here, we present molecular evidence for exceptionally wide distribution of benthic foraminifera, which constitute the major part of deep-sea meiofauna. Our analyses of nuclear ribosomal RNA genes revealed high genetic similarity between Arctic and Antarctic populations of three common deep-sea foraminiferal species (Epistominella exigua, Cibicides wuellerstorfi and Oridorsalis umbonatus), separated by distances of up to 17 000 km. Our results contrast with the substantial level of cryptic diversity usually revealed by molecular studies, of shallow-water benthic and planktonic marine organisms. The very broad ranges of the deep-sea foraminifera that we examined support the hypothesis of global distribution of small eukaryotes and suggest that deep-sea biodiversity may be more modest at global scales than present estimates suggest.

Despite its often featureless appearance, the deep-ocean floor includes some of the most diverse habitats on Earth. However, the accurate assessment of global deep-sea diversity is impeded by a paucity of data on the geographical ranges of bottom-dwelling species, particularly at the genetic level. Here, we present molecular evidence for exceptionally wide distribution of benthic foraminifera, which constitute the major part of deep-sea meiofauna. Our analyses of nuclear ribosomal RNA genes revealed high genetic similarity between Arctic and Antarctic populations of three common deep-sea foraminiferal species (Epistominella exigua, Cibicides wuellerstorfi and Oridorsalis umbonatus), separated by distances of up to 17, 000 km. Our results contrast with the substantial level of cryptic diversity usually revealed by molecular studies, of shallow-water benthic and planktonic marine organisms. The very broad ranges of the deep-sea foraminifera that we examined support the hypothesis of global distribution of small eukaryotes and suggest that deep-sea biodiversity may be more modest at global scales than present estimates suggest.

Macroevolutionary relations among main lineages of Foraminifera have traditionally been inferred from the small subunit ribosomal genes (SSU rDNA). However, important discrepancies in the rates of SSU rDNA evolution between major lineages led to difficulties in accurate interpretation of SSU-based phylogenetic reconstructions. Recently, actin and β-tubulin sequences have been used as alternative markers of foraminiferal phylogeny and their analyses globally confirm results obtained with SSU rDNA. In order to test new protein markers, we sequenced a fragment of the largest subunit of the RNA polymerase II (RPB1), a nuclear encoded single copy gene, for 8 foraminiferal species representing major orders of Foraminifera. Analyses of our data robustly confirm previous SSU rDNA and actin phylogenies and show (i) the paraphyly and ancestral position of monothalamid Foraminifera; (ii) the independent origin of miliolids; (iii) the monophyly of rotaliids, including buliminids and globigerinids; and (iv) the polyphyly of planktonic families Globigerinidae and Candeinidae. Additionally, the RPB1 phylogeny suggests Allogromiidae as the most ancestral foraminiferal lineage. In the light of our study, RPB1 appears as a valuable phylogenetic marker, particularly useful for groups of protists showing extreme variations of evolutionary rates in ribosomal genes.

Biodiversity in deep-sea sediments is extraordinarily rich at a local scale. It is disputable, however, to what extent the high local species richness of abyssal faunas can be extrapolated to larger spatial scales. The accurate assessment of regional and global deep-sea diversity is impeded by a lack of data on dispersal ranges of species at the ocean floor, particularly at the genetic level. To test the capability for long-distance dispersal of deep-sea foraminiferal species, we examined the genetic diversity of Arctic and Antarctic populations of three common, deep-sea rotaliids, Epistominella exigua, Cibicides wuellerstorfi and Oridorsalis umbonatus, collected during recent R/V Polarstern cruises, including the ANDEEP III campaign in the Southern Ocean. Our analyses revealed no significant genetic differences between polar populations of the examined morphospecies, even in an extremely variable ITS region of the ribosomal DNA. This result provides strong evidence that a high gene flow occurs between populations of deep-sea species separated by long distances. The genetic homogeneity of Arctic and Antarctic deep-sea foraminifera suggests that deep-sea biodiversity may be more modest at regional and global scales than present estimates suggest. Anuár io do Inst i tu to de Geociências UFRJ ISSN 0101-9759 Vol. 29 1 / 2006 p. 558

The present field study uses Spongia officinalis for assessing trace metals occurrence in time and space within Mediterranean rocky communities. Nine sites were selected in the Marseille area for studying spatial trends in 12 metal concentrations. Long term changes in 8 metal concentrations were assessed at sites that had been sampled before and 12 years after the opening of a treatment plant. Spongia officinalis highly concentrated all the trace metal surveyed excepted Hg and Cd. The overall contamination level registered provided a classification of the study sites which is congruent with that given by other studies on pollutant accumulation in neighbouring sandy-bottoms or benthic assemblages. Among the metals studied, Fe, Pb, Cr are those that best highlighted a pollution gradient. In the present study, only Cd concentration did not vary in space. Except for Ni, all pollutant concentrations clearly decreased between 1984 and 1999. This very impressive decrease in heavy metal concentrations within the Marseille area represents an indisputable evidence of the improvement of the seawater quality resulting from 12 years' operation of the Marseille sewage plant. Moreover, the significant decrease also recorded in the reference population at Port-Cros might reflect an overall improvement in the seawater quality of the NW Mediterranean.

Summary. Gromia oviformis is a common marine rhizopod, possessing a large ovoid membraneous theca that resembles the tests of certain monothalamous (single-chambered) foraminifers. In fact, the genus Gromia was initially classified among the Foraminifera, but because of its non-granular, filose pseudopodia it was later included among filopodia-bearing protists (the Filosea). Recent molecular phylogenies suggested that Gromia branches among Cercozoa, a heterogeneous assemblage of mainly amoeboid protists, which show some affinities to Foraminifera. To test how closely related are Gromia and Foraminifera, we have analysed the sequences of actin, large subunit of the RNA polymerase II (RPB1) and small subunit (SSU) rRNA genes. We also analysed the structure of the polyubiquitin gene of G. oviformis. Our analyses show that Gromia’s actin is specifically related to one of the two actin genes families known in Foraminifera. In RPB1-based phylogenies, Gromia appears as the closest relative of Foraminifera, while in the SSU rRNA trees it branches as sister to Foraminifera and Haplosporidia. We identified also a single serine insertion in the polyubiquitin of Gromia, similar to that found in Foraminifera, Plasmodiophorida and some Cercozoa. Altogether, these findings support the hypothesis that the morphological resemblance between Gromia and Foraminifera may be due to a shared common ancestor. If further analyses of protein-coding genes including a more representative sampling of Cercozoa confirm this relationship, then the molecular study of G. oviformis will be of key importance for understanding the origin of Foraminifera.

Plant peroxidases (class III peroxidases, E.C. 1.11.1.7) are secreted glycoproteins known to be involved in the mechanism of cell elongation, in cell wall construction and differentiation, and in the defense against pathogens. They usually form large multigenic families in angiosperms. The recent completion of rice (Oryza sativa japonica c.v. Nipponbare) genome sequencing allowed drawing up the full inventory of the genes encoding class III peroxidases in this plant. We found 138 peroxidase genes distributed among the 12 rice chromosomes. In contrast to several other gene families studied so far, peroxidase genes are twice as numerous in rice as in Arabidopsis. This large number of genes results from various duplication events that were tentatively traced back using a phylogenetic tree based on the alignment of conserved amino acid sequences. We also searched for peroxidase encoding genes in the major phyla of plant kingdom. In addition to gymnosperms and angiosperms, sequences were found in liverworts, mosses and ferns, but not in unicellular green algae. Two rice and one Arabidopsis peroxidase genes appeared to be rather close to the only known sequence from the liverwort Marchantia polymorpha. The possible relationship of these peroxidases with the putative ancestor of peroxidase genes is discussed, as well as the connection between the development of the class III peroxidase multigenic family and the emergence of the first land plants.

Phylogenetic analysis of small and large subunits of rDNA genes suggested that Foraminifera originated early in the evolution of eukaryotes, preceding the origin of other rhizopodial protists. This view was recently challenged by the analysis of actin and ubiquitin protein sequences, which revealed a close relationship between Foraminifera and Cercozoa, an assemblage of various filose amoebae and amoeboflagellates that branch in the so-called crown of the SSU rDNA tree of eukaryotes. To further test this hypothesis, we sequenced a fragment of the largest subunit of the RNA polymerase II (RPB1) from five foraminiferans, two cercozoans and the testate filosean Gromia oviformis. Analysis of our data confirms a close relationship between Foraminifera and Cercozoa and points to Gromia as the closest relative of Foraminifera.

Ubiquitin is a 76 amino acid protein with a remarkable degree of evolutionary conservation. Ubiquitin plays an essential role in a large number of eukaryotic cellular processes by targeting proteins for proteasome-mediated degradation. Most ubiquitin genes are found as head-to-tail polymers whose products are posttranslationally processed to ubiquitin monomers. We have characterized polyubuiquitin genes from the photosynthetic amoeboflagellate Chlorarachnion sp. CCMP 621 (also known as Bigelowiella natans) and found that they deviate from the canonical polyubiquitin structure in having an amino acid insertion at the junction between each monomer, suggesting that polyubiquitin processing in this organism is unique among eukaryotes. The gene structure indicates that processing likely cleaves monomers at the amino terminus of the insertion. We examined the phylogenetic distribution of the insertion by sequencing polyubiquitin genes from several other eukaryotic groups and found it to be confined to Cercozoa (including Chlorarachnion, Lotharella, Cercomonas, and Euglypha) and Foraminifera (including Reticulomyxa and Haynesina). This character strongly suggests that Cercozoa and Foraminifera are close relatives and form a new “supergroup” of eukaryotes.