Assembly processes and functional diversity of marine protists and their rare biosphere.

Background: The mechanisms shaping the rare microbial biosphere and its role in ecosystems remain unclear. We developed an approach to study ecological patterns in the rare biosphere and use it on a vast collection of marine microbiomes, sampled in coastal ecosystems at a regional scale. We study the assembly processes, and the ecological strategies constituting the rare protistan biosphere.

Longest sediment flows yet measured show how major rivers connect efficiently to deep sea.

Here we show how major rivers can efficiently connect to the deep-sea, by analysing the longest runout sediment flows (of any type) yet measured in action on Earth. These seafloor turbidity currents originated from the Congo River-mouth, with one flow travelling >1,130 km whilst accelerating from 5.2 to 8.

Coupling high frequency monitoring and bioassay experiments to investigate a harmful algal bloom in the Bay of Seine (French-English Channel).

Coastal ecosystems are increasingly threatened by eutrophication and dystrophy. In this context, the full pattern of a bloom dominated by the dinoflagellate, Lepidodinium chlorophorum, was investigated by a high frequency monitoring buoy equipped with sensors allowing nutrients and photosynthesis measurements. An increase of the N/P ratio affected phytoplankton physiology leading to bloom collapse with a slight oxygen depletion.

Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front.

Oceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample.

A simple method for the preparation and injection of gas mixtures into a gas chromatograph using a two-component device.

Environmental sciences are expanding and are based on standardized and certified calibrations when measurements are required. When a gaseous composition is quantified, commercial standards are used. Here, we report on a two-component device for the preparation and injection of gas mixtures at the appropriate levels of pressure and volume.

Direct Monitoring Reveals Initiation of Turbidity Currents From Extremely Dilute River Plumes.

Rivers (on land) and turbidity currents (in the ocean) are the most important sediment transport processes on Earth. Yet how rivers generate turbidity currents as they enter the coastal ocean remains poorly understood. The current paradigm, based on laboratory experiments, is that turbidity currents are triggered when river plumes exceed a threshold sediment concentration of ~1 kg/m.

Oceanic mantle reflections in deep seismic profiles offshore Sumatra are faults or fakes.

In the late 90's, some faults identified within oceanic crust were demonstrated to be artifacts arising from out-of-plane scattering along linear sediment-buried fault scarps. Symmetrical mantle reflections observed southwest northern Sumatra on seismic reflection profiles have been identified as faults cutting through the upper mantle down to unprecedented depths reaching ~45 km. Seawater being conveyed along sub-vertical re-activated fracture zones (FZs) to the upper mantle, the mantle portions of FZs are serpentinized and act as mirrors for seismic rays.

Novel Widespread Marine Oomycetes Parasitising Diatoms, Including the Toxic Genus : Genetic, Morphological, and Ecological Characterisation.

Parasites are key drivers of phytoplankton bloom dynamics and related aquatic ecosystem processes. Yet, the dearth of morphological and molecular information hinders the assessment of their diversity and ecological role. Using single-cell techniques, we characterise morphologically and molecularly, intracellular parasitoids infecting four potentially toxin-producing and one species on the North Atlantic coast.

Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network.

Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group.

Heterogeneous distribution in sediments and dispersal in waters of Alexandrium minutum in a semi-enclosed coastal ecosystem.

Within the framework of research aimed at using genetic methods to evaluate harmful species distribution and their impact on coastal ecosystems, a portion of the ITS1rDNA of Alexandrium minutum was amplified by real-time PCR from DNA extracts of superficial (1-3cm) sediments of 30 subtidal and intertidal stations of the Bay of Brest (Brittany, France), during the winters of 2013 and 2015. Cell germinations and rDNA amplifications of A. minutum were obtained for sediments of all sampled stations, demonstrating that the whole bay is currently contaminated by this toxic species.

Analysis of hydrogen and methane in seawater by "Headspace" method: Determination at trace level with an automatic headspace sampler.

"Headspace" technique is one of the methods for the onboard measurement of hydrogen (H) and methane (CH) in deep seawater. Based on the principle of an automatic headspace commercial sampler, a specific device has been developed to automatically inject gas samples from 300ml syringes (gas phase in equilibrium with seawater). As valves, micro pump, oven and detector are independent, a gas chromatograph is not necessary allowing a reduction of the weight and dimensions of the analytical system.

Dissolved Organic Carbon in the North Atlantic Meridional Overturning Circulation.

The quantitative role of the Atlantic Meridional Overturning Circulation (AMOC) in dissolved organic carbon (DOC) export is evaluated by combining DOC measurements with observed water mass transports. In the eastern subpolar North Atlantic, both upper and lower limbs of the AMOC transport high-DOC waters. Deep water formation that connects the two limbs of the AMOC results in a high downward export of non-refractory DOC (197 Tg-C·yr(-1)).

Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest (France).

The multiannual dynamic of the cyst-forming and toxic marine dinoflagellate Alexandrium minutum was studied over a time scale of about 150 years by a paleoecological approach based on ancient DNA (aDNA) quantification and cyst revivification data obtained from two dated sediment cores of the Bay of Brest (Brittany, France). The first genetic traces of the species presence in the study area dated back to 1873 ± 6. Specific aDNA could be quantified by a newly developed real-time PCR assay in the upper core layers, in which the germination of the species (in up to 17-19-year-old sediments) was also obtained.

Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.

Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources.

Biophysical interactions control the size and abundance of large phytoplankton chains at the Ushant tidal front.

Phytoplankton blooms are usually dominated by chain-forming diatom species that can alter food pathways from primary producers to predators by reducing the interactions between intermediate trophic levels. The food-web modifications are determined by the length of the chains; however, the estimation is biased because traditional sampling strategies damage the chains and, therefore, change the phytoplankton size structure. Sedimentological studies around oceanic fronts have shown high concentrations of giant diatom mats (>1 cm in length), suggesting that the size of diatom chains is underestimated in the pelagic realm.

Cellular and biochemical responses of the oyster Crassostrea gigas to controlled exposures to metals and Alexandrium minutum.

Effects of simultaneous exposure of Pacific oyster, Crassostrea gigas, to both a harmful dinoflagellate that produces Paralytic Shellfish Toxins (PST), Alexandrium minutum, and cadmium (Cd) and copper (Cu), were assessed. Oysters were exposed to a mix of Cd-Cu with two different diets (i.e.

Physical proximity may promote lateral acquisition of bacterial symbionts in vesicomyid clams.

Vesicomyid clams harbor intracellular sulfur-oxidizing bacteria that are predominantly maternally inherited and co-speciate with their hosts. Genome recombination and the occurrence of non-parental strains were recently demonstrated in symbionts. However, mechanisms favoring such events remain to be identified.

Effects of oil exposure and dispersant use upon environmental adaptation performance and fitness in the European sea bass, Dicentrarchus labrax.

The worldwide increasing recourse to chemical dispersants to deal with oil spills in marine coastal ecosystems is a controversial issue. Yet, there exists no adequate methodology that can provide reliable predictions of how oil and dispersant-treated oil can affect relevant organism or population-level performance. The primary objective of the present study was to examine and compare the effects of exposure to untreated oil (weathered Arabian light crude oil), chemically dispersed oil (Finasol, TOTAL-Fluides) or dispersant alone, upon the ability of fish for environmental adaptation.

Panmixia in a fragmented and unstable environment: the hydrothermal shrimp Rimicaris exoculata disperses extensively along the Mid-Atlantic Ridge.

Dispersal plays a fundamental role in the evolution and persistence of species, and especially for species inhabiting extreme, ephemeral and highly fragmented habitats as hydrothermal vents. The Mid-Atlantic Ridge endemic shrimp species Rimicaris exoculata was studied using microsatellite markers to infer connectivity along the 7100-Km range encompassing the sampled sites. Astonishingly, no genetic differentiation was found between individuals from the different geographic origins, supporting a scenario of widespread large-scale dispersal despite the habitat distance and fragmentation.

First respiration estimates of cold-seep vesicomyid bivalves from in situ total oxygen uptake measurements.

Vesicomyid bivalves are one of the most abundant symbiont-bearing species inhabiting deep-sea reducing ecosystems. Nevertheless, except for the hydrothermal vent clam Calyptogena magnifica, their metabolic rates have not been documented, and only assessed with ex situ experiments. In this study, gathering benthic chamber measurements and biomass estimation, we give the first in situ assessment of the respiration rate of these bivalves.

Distribution of anaerobic methane-oxidizing and sulfate-reducing communities in the G11 Nyegga pockmark, Norwegian Sea.

Pockmarks are seabed geological structures sustaining methane seepage in cold seeps. Based on RNA-derived sequences the active fraction of the archaeal community was analysed in sediments associated with the G11 pockmark, in the Nyegga region of the Norwegian Sea. The anaerobic methanotrophic Archaea (ANME) and sulfate-reducing bacteria (SRB) communities were studied as well.

Methanogenic diversity and activity in hypersaline sediments of the centre of the Napoli mud volcano, Eastern Mediterranean Sea.

Submarine mud volcanoes are a significant source of methane to the atmosphere. The Napoli mud volcano, situated in the brine-impacted Olimpi Area of the Eastern Mediterranean Sea, emits mainly biogenic methane particularly at the centre of the mud volcano. Temperature gradients support the suggestion that Napoli is a cold mud volcano with moderate fluid flow rates.

Archaeal populations in hypersaline sediments underlying orange microbial mats in the Napoli mud volcano.

Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor.

A functional study of transforming growth factor-beta from the gonad of Pacific oyster Crassostrea gigas.

The transforming growth factor (TGF)-β superfamily is a group of important growth factors involved in multiple processes such as differentiation, cell proliferation, apoptosis and cellular growth. In the Pacific oyster Crassostrea gigas, the oyster gonadal (og) TGF-β gene was recently characterized through genome-wide expression profiling of oyster lines selected to be resistant or susceptible to summer mortality. Og TGF-β appeared specifically expressed in the gonad to reach a maximum when gonads are fully mature, which singularly contrasts with the pleiotropic roles commonly ascribed to most TGF-β family members.