Marina Montresor

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing.

Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the worlds oceans.

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.

Deep carbon export from a Southern Ocean iron-fertilized diatom bloom

Fertilization of the ocean by adding iron compounds has induced diatom-dominated phytoplankton blooms accompanied by considerable carbon dioxide drawdown in the ocean surface layer. However, because the fate of bloom biomass could not be adequately resolved in these experiments, the timescales of carbon sequestration from the atmosphere are uncertain. Here we report the results of a five-week experiment carried out in the closed core of a vertically coherent, mesoscale eddy of the Antarctic Circumpolar Current, during which we tracked sinking particles from the surface to the deep-sea floor. A large diatom bloom peaked in the fourth week after fertilization. This was followed by mass mortality of several diatom species that formed rapidly sinking, mucilaginous aggregates of entangled cells and chains. Taken together, multiple lines of evidence—although each with important uncertainties—lead us to conclude that at least half the bloom biomass sank far below a depth of 1,000 metres and that a substantial portion is likely to have reached the sea floor. Thus, iron-fertilized diatom blooms may sequester carbon for timescales of centuries in ocean bottom water and for longer in the sediments.

Intraspecific diversity in Scrippsiella trochoidea (Dinopbyceae): evidence for cryptic species

Abstract Scrippsiella trochoidea is a widely distributed neritic dinoflagellate that produces calcareous resting cysts. We assessed the level of intraspecific diversity at the molecular, morphological and physiological levels among 15 strains identified as S. trochoidea and isolated from the Gulf of Naples (Italy, Mediterranean Sea), and an additional isolate from the Faeroe Islands. We investigated the morphology of motile cells and cysts, mating modality, encystment success, and growth rates at different light irradiances. The ribosomal DNA internal transcribed spacer (ITS) region was sequenced to infer phylogenetic relationships among the S. trochoidea strains and closely related species. The molecular analysis revealed a well-supported lineage comprising strains with a Scrippsiella plate pattern. Within this clade, a number of distinct ITS haplotypes were recorded but the relationships among them were only partially resolved. The 16 S. trochoidea isolates grouped into five single-strain clades and three multi-strain clades. The grouping of haplotypes in a series of distinct clades suggests the existence of cryptic species within what has previously been considered a single species, based on the morphological features of the motile cells and cysts. Some of the ITS haplotypes were distinguishable visually, based on minor morphological features of the motile cells and cysts, but in two cases morphologically almost identical strains fell into different clades. Our results showed that the majority of the strains are homothallic; only S. trochoidea v. aciculifera from the Faeroe Islands is heterothallic. Cyst production rates were notable for their diversity, even among strains grouping with the same ITS haplotype, as were growth rates at different light irradiances. Based on phylogenetic results, two new combinations are proposed: S. operosa (Deflandre) Montresor comb. nov. and S. infula (Deflandre) Montresor comb. nov.

Bipolar distribution of the cyst-forming dinoflagellate Polarella glacialis

Morphological investigations of motile cells and cysts of a small dinoflagellate (strain CCMP 2088) isolated from Canadian Arctic waters were carried out under both light and scanning electron microscopy. This species strongly resembled Polarella glacialis (strain CCMP 1383), which up to now was known only from Antarctic sea ice. The photosynthetic pigment composition of strain CCMP 2088 is typical of dinoflagellates, with peridinin as a major accessory pigment. Phylogenetic relationships between the two strains and other dinoflagellate species were inferred from SSU nrDNA using Neighbour Joining and weighted parsimony analyses. Our results showed that strain CCMP 2088 and P. glacialis (strain CCMP 1383) grouped in the same clade (Suessiales clade), showing high similarity values (0.99%). Morphological and molecular data support the assignment of the Arctic strain to P. glacialis. The free-living Gymnodinium simplex and the two P. glacialis strains have a basal position in the Suessiales clade, as compared to Symbiodinium spp.

Thick-shelled, grazer-protected diatoms decouple ocean carbon and silicon cycles in the iron-limited Antarctic Circumpolar Current

Significance Silica-shelled diatoms dominate marine phytoplankton blooms and play a key role in ocean ecology and the global carbon cycle. We show how differences in ecological traits of dominant Southern Ocean diatom species, observed during the in situ European Iron Fertilization Experiment (EIFEX), can influence ocean carbon and silicon cycles. We argue that the ecology of thick-shelled diatom species, selected for by heavy copepod grazing, sequesters silicon relative to other nutrients in the deep Southern Ocean and underlying sediments to the detriment of diatom growth elsewhere. This evolutionary arms race provides a framework to link ecology with biogeochemistry of the ocean. Diatoms of the iron-replete continental margins and North Atlantic are key exporters of organic carbon. In contrast, diatoms of the iron-limited Antarctic Circumpolar Current sequester silicon, but comparatively little carbon, in the underlying deep ocean and sediments. Because the Southern Ocean is the major hub of oceanic nutrient distribution, selective silicon sequestration there limits diatom blooms elsewhere and consequently the biotic carbon sequestration potential of the entire ocean. We investigated this paradox in an in situ iron fertilization experiment by comparing accumulation and sinking of diatom populations inside and outside the iron-fertilized patch over 5 wk. A bloom comprising various thin- and thick-shelled diatom species developed inside the patch despite the presence of large grazer populations. After the third week, most of the thinner-shelled diatom species underwent mass mortality, formed large, mucous aggregates, and sank out en masse (carbon sinkers). In contrast, thicker-shelled species, in particular Fragilariopsis kerguelensis, persisted in the surface layers, sank mainly empty shells continuously, and reduced silicate concentrations to similar levels both inside and outside the patch (silica sinkers). These patterns imply that thick-shelled, hence grazer-protected, diatom species evolved in response to heavy copepod grazing pressure in the presence of an abundant silicate supply. The ecology of these silica-sinking species decouples silicon and carbon cycles in the iron-limited Southern Ocean, whereas carbon-sinking species, when stimulated by iron fertilization, export more carbon per silicon. Our results suggest that large-scale iron fertilization of the silicate-rich Southern Ocean will not change silicon sequestration but will add carbon to the sinking silica flux.

Toxic Pseudo-nitzschia multistriata (Bacillariophyceae) from the Gulf of Naples: morphology, toxin analysis and phylogenetic relationships with other Pseudo-nitzschia species

The genus Pseudo-nitzschia includes several species capable of producing domoic acid, the causative agent of Amnesic Shellfish Poisoning. Some of these species have been recorded frequently in the Gulf of Naples. For one of the species, P. multistriata, which has been recurrently found in our sampling area since 1995, this is the first report for European waters. Here we provide further details on the fine structure of this species. Pseudo-nitzschia multistriata was the only one found to produce domoic acid among all the Pseudo-nitzschia species from the Gulf of Naples, and this finding raises the number of potentially toxic species in this genus to nine. Phylogenetic relationships among several Pseudo-nitzschia species were assessed using the hypervariable domains (D1–D3) of the large subunit (LSU) rDNA. The match between the phylogeny obtained and important taxonomic characters used in this genus are discussed. Results show that P. multistriata clusters with wider species lacking a central larger interspace in the raphe. Close genetic relationships were determined between P. fraudulenta and P. subfraudulenta, and between P. pungens and P. multiseries. Genetic differences among these pairs of species are comparable to those among isolates of P. pseudodelicatissima from the Gulf of Naples, indicating high intraspecific genetic diversity of Pseudo-nitzschia species in the relatively conserved LSU region. This could explain the problematic results obtained when testing a match between species-specific Pseudo-nitzschia LSU probes and our sequences.

LIFE CYCLE, SIZE REDUCTION PATTERNS, AND ULTRASTRUCTURE OF THE PENNATE PLANKTONIC DIATOM PSEUDO-NITZSCHIA DELICATISSIMA (BACILLARIOPHYCEAE)†

Pseudo‐nitzschia delicatissima (Cleve) Heiden is a very common pennate planktonic diatom found in temperate marine waters, where it is often responsible for blooms. Recently, three distinct internal transcribed spacer types have been recorded during a P. delicatissima bloom in the Gulf of Naples (Mediterranean Sea, Italy), which suggests the existence of cryptic diversity. We carried out mating experiments with clonal strains belonging to the most abundant internal transcribed spacer type. Pseudo‐nitzschia delicatissima is heterothallic and produces two functional anisogametes per gametangium. The elongated auxospore possesses a transverse and a longitudinal perizonium. The sexual phase was observed to occur over a wide size spectrum, spanning 19–80 μm and corresponding to almost the whole range of cell length observed for P. delicatissima. We also investigated cell morphology, valve ultrastructure and morphometry of parental, F1‐generation strains, and the progeny of crosses between parental and F1 strains. Although ultrastructural features match those described for P. delicatissima, variability in cell shape was recorded in the largest cells of the F1 generation as well as in valves with an abnormal arrangement of poroids. As many other diatoms, P. delicatissima undergoes size reduction over its life cycle, and cells of different size showed differences in growth rates and the amount of size reduction per cell cycle. Cells between 60 and 30 μm in length showed the fastest growth and the slowest rates of size reduction per generation. In culture, P. delicatissima cells can decrease to 8 μm in length; however, such small cells (≤30 μm) are not recorded in the sea, and this raises interesting questions about the factors that control their survival in the natural environment.

POLARELLA GLACIALIS, GEN. NOV., SP. NOV. (DINOPHYCEAE): SUESSIACEAE ARE STILL ALIVE!

The culture CCMP 1383, obtained from sea‐ice brine collected in McMurdo Sound (Ross Sea, Antarctica), is a small gymnodinioid dinoflagellate. This species is very abundant in the upper land‐fast sea ice, where it can both grow and overwinter as a spiny encysted stage. The motile vegetative stage and the cyst produced in the culture were studied by scanning electron microscopy (SEM) and transmission electron micrscopy (TEM). The amphiesma of the vegetative cells is constituted by thin vesicles that are organized into nine latitudinal series of plates: three in the epitheca, two in the cingulum, and four in the hypotheca. The same tabulation is reflected in the cyst wall by acicular processes arising from the center of paraplates, with the exception of the paracingulum, in which acicular processess are absent. On the basis of the peculiar plate pattern of this dinoflagellate, we establish the new genus Polarella and the new species Polarella glacialis (family Suessiaceae, order Suessiales). This species has a remarkable similarity with fossil Suessiaceae cysts dating back to the Triassic and Jurassic and represents, up to now, the only extant member of the subfamily Suessiaceae. Phylogenetic analysis based on the small‐subunit ribosomal RNA gene confirmed the placement of this species in the order Suessiales and its close relationship with the genus Symbiodinium Freudenthal.

Morphology, phylogeny, and sexual cycle of Pseudo-nitzschia mannii sp. nov. (Bacillariophyceae): a pseudo-cryptic species within the P. pseudodelicatissima complex

A. Amato and M. Montresor. 2008. Morphology, phylogeny, and sexual cycle of Pseudo-nitzschia mannii sp. nov. (Bacillariophyceae): a pseudo-cryptic species within the P. pseudodelicatissima complex. Phycologia 47: 487–497. DOI: 10.2216/07-92.1 There is increasing evidence that cryptic and pseudo-cryptic species are widespread in several diatom taxa. This is the case with the genus Pseudo-nitzschia, which includes chain-forming pennate diatoms that bloom both in coastal and open ocean waters. In the last years, up to 10 new species have been described on the basis of morphological and molecular investigations, and some of them are only distinguishable on the basis of minute ultrastructural features of their siliceous frustule. We here describe the morphology of the vegetative cell and sexual stages of Pseudo-nitzschia mannii sp. nov., and present an ITS2-based phylogeny to illustrate genetic relationships between P. mannii sp. nov. and the closest congeneric species. On the basis of ribosomal and chloroplastidial gene phylogenies, P. mannii is closely related to P. calliantha, from which it can be differentiated by its slightly wider cells and a different arrangement of the poroid sectors. The analysed strains did not produce the ASP-toxin domoic acid.