Air‐Sea Turbulent Fluxes From a Wave‐Following Platform During Six Experiments at Sea
Auteurs : Denis Bourras (MIO), Rémi Cambra, Louis Marié, Marie‐Noëlle Bouin, Lucio Baggio, Hubert Branger, Houda Beghoura, Gilles Reverdin, Boris Dewitte, Aurélien Paulmier, Christophe Maes, Fabrice Ardhuin, Ivane Pairaud, Philippe Fraunié (MIO) , Christopher Luneau, Danièle Hauser
JGR Oceans - First published: 18 June 2019
Turbulent fluxes at the air‐sea interface are estimated with data collected in 2011 to 2017 with a low‐profile platform during six experiments in four regions. The observations were carried out with moderate winds (2–10 m/s) and averaged wave heights of 1.5 m. Most of the time, there was a swell, with an averaged wave age (the ratio between wave phase speed and wind speed) being equal to 2.8 ± 1.6. Three flux calculation methods are used, namely, the eddy covariance (EC), the inertial dissipation (ID), and the bulk methods. For the EC method, a spectral technique is proposed to correct wind data from platform motion. A mean bias affecting the friction velocity (u*) is then evaluated. The comparison between EC u* and ID u* estimates suggests that a constant imbalance term (ϕimb) equal to 0.4 is required in the ID method, possibly due to wave influence on our data. Overall, the confidence in the calculated u* estimates is found to be on the order of 10%. The values of the drag coefficient (CD) are in good agreement with the parameterizations of Smith (1988, https://doi.org/10.1029/JC093iC12p15467) in medium‐range winds and of Edson et al. (2013, https://doi.org/10.1175/JPO‐D‐12‐0173.1) in light winds. According to our data, the inverse wave age varies linearly with wind speed, as in Edson et al. (2013, https://doi.org/10.1175/JPO‐D‐12‐0173.1), but our estimates of the Charnock coefficient do not increase with wind speed, which is possibly related to sampling swell‐dominated seas. We find that the Stanton number is independent from wind speed.
Christelle Desnues (MIO), co-auteur de "Global phylogeography and ancient evolution of the widespread human gut virus crAssphage"
Auteurs : Robert A. Edwards, Alejandro A. Vega, Holly M. Norman, Maria Ohaeri, Kyle Levi, Elizabeth A. Dinsdale, Ondrej Cinek, Ramy K. Aziz, Katelyn McNair, Jeremy J. Barr, Kyle Bibby, Stan J. J. Brouns, Adrian Cazares, Patrick A. de Jonge, Christelle Desnues (MIO), Samuel L. Díaz Muñoz, Peter C. Fineran, Alexander Kurilshikov, Rob Lavigne, Karla Mazankova, David T. McCarthy, Franklin L. Nobrega, Alejandro Reyes Muñoz, German Tapia, Nicole Trefault, Alexander V. Tyakht, Pablo Vinuesa, Jeroen Wagemans, Alexandra Zhernakova, Frank M. Aarestrup, Gunduz Ahmadov, Abeer Alassaf, Josefa Anton, Abigail Asangba, Emma K. Billings, Vito Adrian Cantu, Jane M. Carlton, Daniel Cazares, Gyu-Sung Cho, Tess Condeff, Pilar Cortés, Mike Cranfield, Daniel A. Cuevas, Rodrigo De la Iglesia, Przemyslaw Decewicz, Michael P. Doane, Nathaniel J. Dominy, Lukasz Dziewit, Bashir Mukhtar Elwasila, A. Murat Eren, Charles Franz, Jingyuan Fu, Cristina Garcia-Aljaro, Elodie Ghedin, Kristen M. Gulino, John M. Haggerty, Steven R. Head, Rene S. Hendriksen, Colin Hill, Heikki Hyöty, Elena N. Ilina, Mitchell T. Irwin, Thomas C. Jeffries, Juan Jofre, Randall E. Junge, Scott T. Kelley, Mohammadali Khan Mirzaei, Martin Kowalewski, Deepak Kumaresan, Steven R. Leigh, David Lipson, Eugenia S. Lisitsyna, Montserrat Llagostera, Julia M. Maritz, Linsey C. Marr, Angela McCann, Shahar Molshanski-Mor, Silvia Monteiro, Benjamin Moreira-Grez, Megan Morris, Lawrence Mugisha, Maite Muniesa, Horst Neve, Nam-phuong Nguyen, Olivia D. Nigro, Anders S. Nilsson, Taylor O’Connell, Rasha Odeh, Andrew Oliver, Mariana Piuri, Aaron J. Prussin II, Udi Qimron, Zhe-Xue Quan, Petra Rainetova, Adán Ramírez-Rojas, Raul Raya, Kim Reasor, Gillian A. O. Rice, Alessandro Rossi, Ricardo Santos, John Shimashita, Elyse N. Stachler, Lars C. Stene, Ronan Strain, Rebecca Stumpf, Pedro J. Torres, Alan Twaddle, MaryAnn Ugochi Ibekwe, Nicolás Villagra, Stephen Wandro, Bryan White, Andy Whiteley, Katrine L. Whiteson, Cisca Wijmenga, Maria M. Zambrano, Henrike Zschac
Nature Microbiology (2019)
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
New Insights of the Sicily Channel and Southern Tyrrhenian Sea Variability
Auteurs : Menna, M.; Poulain, P.; Ciani, D.; Doglioli, A. (MIO); Notarstefano, G.; Gerin, R.; Rio, M.; Santoleri, R.; Gauci, A.; Drago, A.
Water 2019, 11(7), 1355; https://doi.org/10.3390/w11071355
Received: 31 May 2019 / Revised: 24 June 2019 / Accepted: 27 June 2019 / Published: 29 June 2019
The dynamics of the Sicily Channel and the southern Tyrrhenian Sea are highly influenced by the seasonal variability of the Mediterranean basin-wide circulation, by the interannual variability of the numerous mesoscale structures present in the Channel, and by the decadal variability of the adjacent Ionian Sea. In the present study, all these aspects are investigated using in-situ (Lagrangian drifter trajectories and Argo float profiles) and satellite data (Absolute Dynamic Topography, Sea Level Anomaly, Sea Surface Temperature, wind products) over the period from 1993 to 2018. The availability of long time series of data and high-resolution multi-sensor surface currents allow us to add new details on the circulation features and on their driving mechanisms and to detect new permanent eddies not yet described in literature. The structures prevailing in winter are mainly driven by wind, whereas those prevailing in summer are regulated by topographical forcing on surface currents. The strength of the surface structures located at the western entrance of the Ionian Sea and of the mesoscale activity along the northern Sicily coast is modulated by the large-scale internal variability. The vertical hydrological characteristics of these mesoscale eddies are delineated using the Argo float profiles inside these structures.
Accounting for ocean connectivity and hydroclimate in fish recruitment fluctuations within transboundary metapopulations
Auteurs : Manuel Hidalgo, Vincent Rossi (MIO), Pedro Monroy, Enrico Ser‐Giacomi, Emilio Hernández‐García, Beatriz Guijarro, Enric Massutí, Francisco Alemany, Angelique Jadaud, José Luis Perez, Patricia Reglero
First published: 30 May 2019
Marine resources stewardships are progressively becoming more receptive to an effective incorporation of both ecosystem and environmental complexities into the analytical frameworks of fisheries assessment. Understanding and predicting marine fish production for spatially and demographically complex populations in changing environmental conditions is however still a difficult task. Indeed, fisheries assessment is mostly based on deterministic models that lack realistic parameterizations of the intricate biological and physical processes shaping recruitment, a cornerstone in population dynamics. We use here a large metapopulation of a harvested fish, the European hake (Merluccius merluccius), managed across transnational boundaries in the northwestern Mediterranean, to model fish recruitment dynamics in terms of physics‐dependent drivers related to dispersal and survival. The connectivity among nearby subpopulations is evaluated by simulating multi‐annual Lagrangian indices of larval retention, imports, and self‐recruitment. Along with a proxy of the regional hydroclimate influencing early life stages survival, we then statistically determine the relative contribution of dispersal and hydroclimate for recruitment across contiguous management units. We show that inter‐annual variability of recruitment is well reproduced by hydroclimatic influences and synthetic connectivity estimates. Self‐recruitment (i.e., the ratio of retained locally produced larvae to the total number of incoming larvae) is the most powerful metric as it integrates the roles of retained local recruits and immigrants from surrounding subpopulations and is able to capture circulation patterns affecting recruitment at the scale of management units. We also reveal that the climatic impact on recruitment is spatially structured at regional scale due to contrasting biophysical processes not related to dispersal. Self‐recruitment calculated for each management unit explains between 19% and 32.9% of the variance of recruitment variability, that is much larger than the one explained by spawning stock biomass alone, supporting an increase of consideration of connectivity processes into stocks assessment. By acknowledging the structural and ecological complexity of marine populations, this study provides the scientific basis to link spatial management and temporal assessment within large marine metapopulations. Our results suggest that fisheries management could be improved by combining information of physical oceanography (from observing systems and operational models), opening new opportunities such as the development of short‐term projections and dynamic spatial management.
Implementation of an end-to-end model of the Gulf of Lions ecosystem (NW Mediterranean Sea). II. Investigating the effects of high trophic levels on nutrients and plankton dynamics and associated feedbacks
Auteurs : Frédéric Diaz (MIO), Daniela Bănaru (MIO ), Philippe Verley , Yunne JaiShin
Volume 405, 1 August 2019, Pages 51-68
The end-to-end OSMOSE-GoL model parameterized, calibrated and evaluated for the Gulf of Lions ecosystem (Northwestern Mediterranean Sea) has been used to investigate the effects of introducing two-ways coupling between the dynamics of Low and High Trophic Level groups.
The use of a fully dynamic two-ways coupling between the models of Low and High Trophic Levels organisms provided some insights in the functioning of the food web in the Gulf of Lions. On the whole microphytoplankton and mesozooplankton were found to be preyed upon by High Trophic Levels planktivorous groups at rates lower than 20% and 30% of their respective natural mortality rates, but these relatively low rates involved some important alterations in the infra-seasonal and annual cycles of both High and Low Trophic Levels groups. They induced significant changes in biomass, fisheries landings and food web interactions by cascading effects. Spatial differential impacts of High Trophic Levels predation on plankton are less clear except in areas in which primary productivity is high. Higher predation rates on plankton groups were encountered within the area of the Rhone river’s influence and in areas associated to the presence of mesoscale eddies in the Northwestern part of the Gulf of Lions, especially. Generally, the pressure of the High Trophic Levels predation was the highest in areas of highest biomass whatever the plankton group considered.
The two-ways coupling between Low and High Trophic Levels models revealed both bottom-up and top-down controls in the ecosystem with effects on planktivorous species similar to those observed in the field. The use of the end-to-end model enabled to propose a set of potential mechanisms that may explain the observed decrease in small pelagic catches by the French Mediterranean artisanal fisheries over the last decade.
Macro-litter in surface waters from the Rhone River: Plastic pollution and loading to the NW Mediterranean Sea
Auteurs : Javier Castro-Jiménez (MIO), Daniel González,Fernández, Michel Fornier (MIO), Natascha Schmidt (MIO ), Richard Sempéré (MIO)
Marine Pollution Bulletin
Volume 146, September 2019, Pages 60-66
We present here the first estimates of floating macro-litter in surface waters from the Rhone River, based on monthly visual observations during 1-year period (2016–2017). Plastic represented 77% of the identified items, confirming its predominance in riverine floating litter. Fragments (2.5–50 cm) and Single Use Plastics (i.e. bags, bottles and cover/packaging) were among the most abundant items. Frequent non-plastic floating litter were paper items such as packaging material and newspapers, and metal items (mostly cans), representing 14% and 5% of total litter, respectively. A lower-end estimate resulted in ∼223,000 plastic items (∼0.7 t of plastic) transported annually by the Rhone surface waters to the Gulf of Lion (NW Mediterranean Sea). Floating macro-plastics are only a fraction of the total plastic export by the Rhone. Our study highlights the current discrepancy between field observations and theoretical estimations. Improvements are needed to harmonize data collection methodologies for field studies and model validation.
" Libre accès au document donné par Elsevier jusqu'au 27 juillet : https://authors.elsevier.com/a/1ZB9i,ashtxtq "
Production of Current by Syntrophy Between Exoelectrogenic and Fermentative Hyperthermophilic Microorganisms in Heterotrophic Biofilm from a Deep-Sea Hydrothermal Chimney
Auteurs : Guillaume Pillot (MIO) , Sylvain Davidson (MIO) ,Richard Auria (MIO), Yannick Combet-Blanc (MIO); Anne Godfroy, Pierre-Pol Liebgott (MIO)
First Online: 11 May 2019
To study the role of exoelectrogens within the trophic network of deep-sea hydrothermal vents, we performed successive subcultures of a hyperthermophilic community from a hydrothermal chimney sample on a mix of electron donors in a microbial fuel cell system. Electrode (the electron acceptor) was swapped every week to enable fresh development from spent media as inoculum. The MFC at 80 °C yielded maximum current production increasing from 159 to 247 mA m−2 over the subcultures. The experiments demonstrated direct production of electric current from acetate, pyruvate, and H2 and indirect production from yeast extract and peptone through the production of H2 and acetate from fermentation. The microorganisms found in on-electrode communities were mainly affiliated to exoelectrogenic Archaeoglobales and Thermococcales species, whereas in liquid media, the communities were mainly affiliated to fermentative Bacillales and Thermococcales species. The work shows interactions between fermentative microorganisms degrading complex organic matter into fermentation products that are then used by exoelectrogenic microorganisms oxidizing these reduced compounds while respiring on a conductive support. The results confirmed that with carbon cycling, the syntrophic relations between fermentative microorganisms and exoelectrogens could enable some microbes to survive as biofilm in extremely unstable conditions.
Schematic representation of cross-feeding between fermentative and exoelectrogenic microbes on the surface of the conductive support. B, Bacillus/Geobacillus spp.; Tc, Thermococcales; Gg, Geoglobus spp.; Py, pyruvate; Ac, acetate.
Amino acids promote black carbon aggregation and microbial colonization in coastal waters off Vietnam
Auteurs : Mar Benavides (MIO) Thuoc Chu Van, Xavier Mari (MIO)
Science of The Total Environment - Volume 685, 1 October 2019, Pages 527-532
The combustion of fossil fuels and biomass produces pyrogenic organic matter usually known as ‘black carbon’ (BC), which are transported across the atmosphere as particulate aerosol, eventually deposited on land and oceans. Soil studies have investigated the potential microbial colonization and remineralization of BC particles, but this process has been seldom studied in marine waters. BC provides a significant input of organic carbon to the oceans, yet its fate and role in biogeochemical cycling remains unknown. Here we explored the microbial colonization of BC particles in coastal seawater samples collected in Halong Bay (northern Vietnam). Using high-resolution mass spectrometry and microscopy methods, we observed an increasing colonization of BC particles by marine microbes in the presence of amino acids. Our results suggest that natural organic matter (NOM) present in seawater may promote the microbial colonization and eventual remineralization of BC particles. Future experiments should explore the potential microbial remineralization of BC particles to unveil the role of this massive source of carbon to marine ecosystems.
Impact of sterilization methods on dissolved trace metals concentrations in complex natural samples: Optimization of UV irradiation
Auteurs : Sandrine Chifflet (MIO), Marianne Quéméneur (MIO), Aude Barani (MIO), Bernard Angeletti, Morgane Didry (MIO) Gérald Grégori (MO) NathaliePradel (MIO)
MethodsX Volume 6, 2019, Pages 1133-1146
Received 12 March 2019, Accepted 18 April 2019, Available online 22 April 2019.
Sterilization is essential for discriminating biotic responses from abiotic reactions in laboratory experiments investigating biogeochemical processes of complex natural samples. However, the conventional methods used to effectively sterilize materials or culture media do not allow sterilizing complex natural samples while maintaining biogeochemical balances. The aim of this study was to develop a low-cost and easy-to-use method to obtain geochemically unmodified and sterilized samples from complex lacustrine or coastal marine ecosystems. In preliminary assays, the impact of several sterilization methods (autoclaving, chemical poisoning, microwave, UV irradiation) on the trace metals balances was studied using borosilicate glass (BG), fluorinated ethylene-propylene (FEP) or polyethylene terephthalate (PET) bottles. Unlike other methods, UV sterilization had minor effects on the distribution of dissolved trace metals. Additional tests using complex lacustrine and coastal marine samples under 10 g/L sediments were performed using a homemade UV sterilization chamber designed to simultaneously irradiate a large number samples. Results showed:
• very reproducible UV tests in BG and FEP bottles
• faster sterilization using FEP bottles than using BG bottles
• low variations of dissolved trace metals concentrations, except for Al, Cu, Fe and Zn
Vertical Motions and Their Effects on a Biogeochemical Tracer in a Cyclonic Structure Finely Observed in the Ligurian Sea
Auteurs : Rousselet L. (MIO), Doglioli AM (MIO)., de Verneil, A., Pietri, A., Della Penna, A., Berline, L.(MIO). , Marrec, P., Gregori, G (MIO), Thyssen, M.(MIO), Carlotti, F.(MIO), Barillon, S.(MIO), Simon-Bot, F.(MIO), Bonal, M., d'Ovidio, F. and Petrenko, A.A. (MIO), (2019)
JGR Oceans : First published: 23 April 2019
Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the ω‐equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3‐D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low‐salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3‐D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG ω‐equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3‐D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3‐D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics.
Frontiers in Fine-Scale in situ Studies: Opportunities During the SWOT Fast Sampling Phase
Authors : D’Ovidio F, Pascual A, Wang J, Doglioli AM (MIO), Jing Z, Moreau S, Grégori G (MIO), Swart S, Speich S, Cyr F, Legresy B, Chao Y, Fu L and Morrow RA (2019)
Front. Mar. Sci., 30 April 2019 | https://doi.org/10.3389/fmars.2019.00168
Résumé : Conceived as a major new tool for climate studies, the Surface Water and Ocean Topography (SWOT) satellite mission will launch in late 2021 and will retrieve the dynamics of the oceans upper layer at an unprecedented resolution of a few kilometers. During the calibration and validation (CalVal) phase in 2022, the satellite will be in a 1-day-repeat fast sampling orbit with enhanced temporal resolution, sacrificing the spatial coverage. This is an ideal opportunity – unique for many years to come – to coordinate in situ experiments during the same period for a focused study of fine scale dynamics and their broader roles in the Earth system. Key questions to be addressed include the role of fine scales on the ocean energy budget, the connection between their surface and internal dynamics, their impact on plankton diversity, and their biophysical dynamics at the ice margin.
Liquid chromatographic isolation of individual carbohydrates from environmental matrices for stable carbon analysis and radiocarbon dating
Auteurs : Amel Nouara (MIO), Christos Panagiotopoulos (MIO), Jérôme Balesdent, Kalliopi Violaki (MIO), Edouard Bard, Yoann Fagault, Daniel James Repeta, Richard Sempéré (MIO)
Analytica Chimica Acta - Volume 1067, 27 August 2019, Pages 137-146
Carbohydrates are among the most abundant organic molecules in both aquatic and terrestrial ecosystems; however, very few studies have addressed their isotopic signature using compound-specific isotope analysis, which provides additional information on their origin (δ13C) and fate (Δ14C). In this study, semi-preparative liquid chromatography with refractive index detection (HPLC-RI) was employed to produce pure carbohydrate targets for subsequent offline δ13C and Δ14C isotopic analysis. δ13C analysis was performed by elemental analyzer-isotope ratio mass spectrometer (EA-IRMS) whereas Δ14C analysis was performed by an innovative measurement procedure based on the direct combustion of the isolated fractions using an elemental analyzer coupled to the gas source of a mini carbon dating system (AixMICADAS). In general, four successive purifications with Na+, Ca2+, Pb2+, and Ca2+ cation-exchange columns were sufficient to produce pure carbohydrates. These carbohydrates were subsequently identified using mass spectrometry by comparing their mass spectra with those of authentic standards.
The applicability of the proposed method was tested on two different environmental samples comprising marine particulate organic matter (POM) and total suspended atmospheric particles (TSP). The obtained results revealed that for the marine POM sample, the δ13C values of the individual carbohydrates ranged from −18.5 to −16.8‰, except for levoglucosan and mannosan, which presented values of −27.2 and −26.2‰, respectively. For the TSP sample, the δ13C values ranged from −26.4 to −25.0‰. The galactose and glucose Δ14C values were 19 and 43‰, respectively, for the POM sample. On the other hand, the levoglucosan radiocarbon value was 33‰ for the TSP sample. These results suggest that these carbohydrates exhibit a modern age in both of these samples. Radiocarbon HPLC collection window blanks, measured after the addition of phthalic acid (14C free blank), ranged from −988 to −986‰ for the abovementioned compounds, indicating a very small background isotopic influence from the whole purification procedure. Overall, the proposed method does not require derivatization steps, produces extremely low blanks, and may be applied to different types of environmental samples.
How closely do mercury trends in fish and other aquatic wildlife track those in the atmosphere? – Implications for evaluating the effectiveness of the Minamata Convention
Auteurs : Feiyue Wang , Peter M.Outridge, Xinbin Feng, Bo Meng,, Lars-EricHeimbürger-Boavida (MIO) Robert P.Mason
Science of The Total Environment
Volume 674, 15 July 2019, Pages 58-70
The Minamata Convention to reduce anthropogenic mercury (Hg) emissions entered into force in 2017, and attention is now focused on how to best monitor its effectiveness at reducing Hg exposure to humans. A key question is how closely Hg concentrations in the human food chain, especially in fish and other aquatic wildlife, will track the changes in atmospheric Hg that are expected to occur following anthropogenic emission reductions. We investigated this question by evaluating several regional groups of case studies where Hg concentrations in aquatic biota have been monitored continuously or intermittently for several decades. Our analysis shows that in most cases Hg time trends in biota did not agree with concurrent Hg trends in atmospheric deposition or concentrations, and the divergence between the two trends has become more apparent over the past two decades. An over-arching general explanation for these results is that the impact of changing atmospheric inputs on biotic Hg is masked by two factors: 1) The aquatic environment contains a large inventory of legacy emitted Hg that remains available for bio-uptake leading to a substantial lag in biotic response time to a change in external inputs; and 2) Biotic Hg trends reflect the dominant effects of changes in multi-causal, local and regional processes (e.g., aquatic or terrestrial biogeochemical processes, feeding ecology, climate) that control the speciation, bioavailability, and bio-uptake of both present-day and legacy emitted Hg. Globally, climate change has become the most prevalent contributor to the divergence. A wide range of biotic Hg outcomes can thus be expected as anthropogenic atmospheric Hg emissions decline, depending on how these processes operate on specific regions and specific organisms. Therefore, evaluating the effectiveness of the Minamata Convention will require biomonitoring of multiple species that represent different trophic and ecological niches in multiple regions of the world.
Out of the Mediterranean? Post‐glacial colonization pathways varied among cold‐water coral species
Auteurs : Joana Boavida (MIO), Ronan Becheler, Marvin Choquet, Norbert Frank, Marco Taviani, Jean‐François Bourillet, Anne‐Leila Meistertzheim, Anthony Grehan, Alessandra Savini, Sophie Arnaud‐Haond
Journal of Biogeography. 2019;1–17 - https://doi.org/10.1111/jbi.13570
Aim: To infer cold‐water corals’ (CWC) post‐glacial phylogeography and assess the role of Mediterranean Sea glacial refugia as origins for the recolonization of the northeastern Atlantic Ocean.
Location: Northeastern Atlantic Ocean and Mediterranean Sea.
Taxon: Lophelia pertusa, Madrepora oculata.
Methods: We sampled CWC using remotely operated vehicles and one sediment core for coral and sediment dating. We characterized spatial genetic patterns (microsatellites and a nuclear gene fragment) using networks, clustering and measures of genetic differentiation.
Results: Inferences from microsatellite and sequence data were congruent, and showed a contrast between the two CWC species. Populations of L. pertusa present a dominant pioneer haplotype, local haplotype radiations and a majority of endemic variation in lower latitudes. Madrepora oculata populations are differentiated across the northeastern Atlantic and genetic lineages are poorly admixed even among neighbouring sites.
Conclusions: Our study shows contrasting post‐glacial colonization pathways for two key habitat‐forming species in the deep sea. The CWC L. pertusa has likely undertaken a long‐range (post‐glacial) recolonization of the northeastern Atlantic directly from refugia located along southern Europe (Mediterranean Sea or Gulf of Cadiz). In contrast, the stronger genetic differentiation of M. oculata populations mirrors the effects of long‐term isolation in multiple refugia. We suggest that the distinct and genetically divergent, refugial populations initiated the post‐glacial recolonization of the northeastern Atlantic margins, leading to a secondary contact in the northern range and reaching higher latitudes much later, in the late Holocene. This study highlights the need to disentangle the influences of present‐day dispersal and evolutionary processes on the distribution of genetic polymorphisms, to unravel the influence of past and future environmental changes on the connectivity of cosmopolitan deep‐sea ecosystems associated with CWC.
Pressure-Retaining Sampler and High-Pressure Systems to Study Deep-Sea Microbes Under in situ Conditions
Auteurs : Marc Garel (MIO), Patricia Bonin (MIO), Séverine Martini, Sophie Guasco (MIO), Marie Roumagnac (MIO), Nagib Bhairy (MIO), Fabrice Armougom (MIO) and Christian Tamburini (MIO)
Front. Microbiol., 09 April 2019 | https://doi.org/10.3389/fmicb.2019.00453
Abstract : The pelagic realm of the dark ocean is characterized by high hydrostatic pressure, low temperature, high-inorganic nutrients, and low organic carbon concentrations. Measurements of metabolic activities of bathypelagic bacteria are often underestimated due to the technological limitations in recovering samples and maintaining them under in situ environmental conditions. Moreover, most of the pressure-retaining samplers, developed by a number of different labs, able to maintain seawater samples at in situ pressure during recovery have remained at the prototype stage, and therefore not available to the scientific community. In this paper, we will describe a ready-to-use pressure-retaining sampler, which can be adapted to use on a CTD-carousel sampler. As well as being able to recover samples under in situ high pressure (up to 60 MPa) we propose a sample processing in equi-pressure mode. Using a piloted pressure generator, we present how to perform sub-sampling and transfer of samples in equi-pressure mode to obtain replicates and perform hyperbaric experiments safely and efficiently (with <2% pressure variability). As proof of concept, we describe a field application (prokaryotic activity measurements and incubation experiment) with samples collected at 3,000m-depth in the Mediterranean Sea. Sampling, sub-sampling, transfer, and incubations were performed under in situ high pressure conditions and compared to those performed following decompression and incubation at atmospheric pressure. Three successive incubations were made for each condition using direct dissolved-oxygen concentration measurements to determine the incubation times. Subsamples were collected at the end of each incubation to monitor the prokaryotic diversity, using 16S-rDNA/rRNA high-throughput sequencing. Our results demonstrated that oxygen consumption by prokaryotes is always higher under in situ conditions than after decompression and incubation at atmospheric pressure. In addition, over time, the variations in the prokaryotic community composition and structure are seen to be driven by the different experimental conditions. Finally, within samples maintained under in situ high pressure conditions, the active (16S rRNA) prokaryotic community was dominated by sequences affiliated with rare families containing piezophilic isolates, such as Oceanospirillaceae or Colwelliaceae. These results demonstrate the biological importance of maintaining in situ conditions during and after sampling in deep-sea environments.
Biogeochemical Impacts of a Black Carbon Wet Deposition Event in Halong Bay, Vietnam
Auteurs : Xavier Mari (MIO), Benjamin Guinot, Chu Van Thuoc, Justine Brune, Jean-Pierre Lefebvre, Pradeep Ram Angia Sriram, Patrick Raimbault (MIO), Thorsten Dittmar and Jutta Niggemann
Front. Mar. Sci. (2019) DOI: 10.3389/fmars.2019.00185
Abstract : Black carbon (BC) is emitted to the atmosphere during biomass, biofuel, and fossil fuel combustion, and leaves the atmosphere via dry or wet deposition on land and on the ocean. On a global scale, wet deposition accounts for about 80% of the total atmospheric BC inputs to the ocean. The input of BC particles to the ocean can enrich surface waters with carbon and associated elements, and owing to high porosity and surface-active properties, BC can alter biogeochemical cycles by sorbing dissolved compounds and promoting aggregation. The rain-mediated input of BC to the ocean and its consequences on nutrient concentrations and particle dynamics were studied in Halong Bay, Vietnam, during a 24-h cycle impacted by short and heavy rainfall events. This study suggests that once introduced in the surface ocean via wet deposition, BC sorbs dissolved organic matter (DOM) and stimulates aggregation processes. The observed wet deposition events were characterized by sudden and pulsed inputs of BC particles that created a thin layer of sinking surface-active aggregates, acting as a net-like scavenger for DOM, nutrients (especially phosphate), and small particles. In addition, the wet deposition events coincided with an enrichment of nutrients in the surface microlayer, with an excess input of nitrogen relative to phosphorus leading to an increase of the molar N:P ratio from 24:1 to 37:1. In the underlying water, the molar N:P ratio also increased (i.e., from 39:1 to 64:1), and this can be attributed to the preferential scavenging of dissolved P-compounds on sinking BC-aggregates.
Implementation of an end-to-end model of the Gulf of Lions ecosystem (NW Mediterranean Sea). I. Parameterization, calibration and evaluation
Auteurs : Daniela Bănaru (MIO), Fréderic Diaz (MIO), Philippe Verley, Rose Campbell, Jonathan Navarro (MIO), ChristopheYohia (MIO), Ricardo Oliveros-Ramos, Capucine Mellon-Duval, Yunne-Jai Shin
Ecological Modelling : Volume 401, 1 June 2019, Pages 1-19
Abstract : An end-to-end model named OSMOSE-GoL has been built for the Gulf of Lions, the main French Mediterranean fishing area. This spatialized dynamic model links the coupled hydrodynamic and biogeochemical model Eco3M-S/SYMPHONIE (LTL – low trophic level model) to OSMOSE (HTL – high trophic level model). It includes 15 compartments of living organisms, five from the LTL model (i.e. nanophytoplankton, microphytoplankton, nanozooplankton, microzooplankton and mesozooplankton) and ten from the HTL model (northern krill, southern shortfin squid, European pilchard, European anchovy, European sprat, Atlantic horse mackerel, Atlantic mackerel, blue whiting, European hake and Atlantic bluefin tuna). With the exception of northern krill and European sprat, all HTL species are commercially exploited and undergo fisheries mortality pressure. The modeled species represent more than 70% of annual catches in this area. This paper presents the parameterization, calibration and evaluation of this model with satellite data for phytoplankton and with biomass, landings, diet and trophic level data for HTL groups. For most species, the diets in output of OSMOSE-GoL are similar to field and literature data in terms of dominant prey groups and species. However, some differences were observed. Various reasons may explain the mismatch between the modeled diet and field data. Benthic prey sometimes observed in the stomach content of the HTL predators were not modeled in OSMOSE-GoL. Field studies were carried out at specific periods and locations, while our data concern the period 2001–2004 and the entire modeled domain. Inter- and intra-annual variations in spatial distribution and density of prey may also explain these differences. The model estimates trophic level values similar to those cited in the literature for all the HTL compartments. These values are also close to the trophic levels estimated by a previous Ecopath model for the same area and period. Even though some improvements are still possible, this model may already be of use to explore fishery or Marine Protected Areas scenarios for socio-ecosystem management issues.
The ups and downs of a canopyforming seaweed over a span of more than one century
Autheurs : Aurélie Blanfuné, Charles François Boudouresque, Marc Verlaque & Thierry Thibaut (tous du MIO)
Scientific Reportsvolume 9, Article number: 5250 (2019)
Asbtract : Canopy-forming seaweeds constitute marine forests that deliver ecosystem services. The worldwide range shift, sharp decline or loss of many of these forests, caused by the cumulative impact of increasing human pressure and climate change, have been widely documented. Contrasting examples, reflecting higher than expected resilience, have been more rarely reported. Here, we took the opportunity of having at our disposal a two-century suite of documents (herbarium vouchers, articles) and a ~120-year observation period, dealing with a long-lived brown seaweed, Cystoseira mediterranea, along a well-explored Mediterranean coastline in the Gulf of Lions, to depict the fate of its populations. In addition, we provided baselines for future surveys, with a high degree of accuracy. The northernmost population, scattered on rare suitable substrates, gradually declined and has been extinct since the 1980s. The length of shore occupied by the southern population showed a long-term decline trend, with two sharp minima followed by partial recovery. The causes of the decline differ between sites and periods: coastal development, pollution, competition with mussels, heatwaves and exceptional storms. Overall, the Gulf of Lions populations reflects long-lasting resilience, higher than expected, and a health status that is better than that reported for many other canopy-forming seaweeds.
A Novel Highly Efficient Device for Growing Micro-Aerophilic Microorganisms
Auteurs : Maxime Fuduche (MIO) , Sylvain Davidson (MIO), Céline Boileau (MIO), Long-Fei Wu and Yannick Combet-Blanc (MIO)
Front. Microbiol., 19 March 2019 | https://doi.org/10.3389/fmicb.2019.00534
Abstract : This work describes a novel, simple and cost-effective culture system, named the Micro-Oxygenated Culture Device (MOCD), designed to grow microorganisms under particularly challenging oxygenation conditions. Two microaerophilic magnetotactic bacteria, a freshwater Magnetospirillum gryphiswaldense strain MSR-1 and a marine Magnetospira sp. strain QH-2, were used as biological models to prove the efficiency of the MOCD and to evaluate its specifications. Using the MOCD, growth rates of MSR-1 and QH-2 increased by four and twofold, respectively, when compared to traditional growing techniques using simple bottles. Oxystat-bioreactors have been typically used and specifically designed to control low dissolved oxygen concentrations, however, the MOCD, which is far less sophisticated was proven to be as efficient for both MSR-1 and QH-2 cultures with regard to growth rate, and even better for MSR-1 when looking at cell yield (70% increase). The MOCD enables a wide range of oxygenation conditions to be studied, including different O2-gradients. This makes it an innovative and ingenious culture device that opens up new parameters for growing microaerobic microorganisms.
A Glider-Compatible Optical Sensor for the Detection of Polycyclic Aromatic Hydrocarbons in the Marine Environment
Authors : Frédéric Cyr, Marc Tedetti (MIO), Florent Besson, Nagib Bhairy (MIO) and Madeleine Goutx (MIO)
Front. Mar. Sci., 18 March 2019 | https://doi.org/10.3389/fmars.2019.00110
Cette étude présente le MiniFluo-UV, un capteur de fluorescence compatible avec les planeurs océaniques, qui cible la détection des hydrocarbures aromatiques polycycliques (HAP) dans le milieu marin. Deux MiniFluos peuvent être installés sur un planeur, chacun équipé de deux canaux optiques (un HAP est mesuré par canal). Cette configuration permet de mesurer jusqu'à 4 HAP fluorescents différents : le naphtalène, le phénanthrène, le fluorène et le pyrène. Des tests en laboratoire sur les produits pétroliers (pétrole brut et diesel Maya) ainsi que sur des échantillons marins situés à proximité de zones industrielles (ports urbains et installations offshore) ont révélé que la concentration des quatre HAP ciblés représentait entre 62% et 97% de la concentration totale d'HAP détectée en échantillons (HAP P16 déterminés par des protocoles internationaux standard). Les tests de laboratoire ont également révélé que, pour les applications marines, l’étalonnage de la fraction de pétrole brut adaptée à l’eau (WAF) est plus approprié que celui des étalons purs (STD). En effet, la fluorescence des HAP est constituée en grande partie de composés alkylés qui ne sont pas pris en compte avec l’étalonnage STD. Les résultats de trois déploiements de planeurs dans des niveaux de complexité croissants (un essai en laboratoire, une admission sur le terrain en mode non autonome et une mission totalement autonome) sont également présentés. Au cours des déploiements sur le terrain, l’ensemble MiniFluo-planeur « SeaExplorer » a pu détecter des gradients de concentration des eaux marines au large d’un port méditerranéen (<80ngL−1) ainsi que des zones d’hydrocarbures dans les eaux de surface d’un champ d’exploitation pétrolière en Mer du Nord (<200ngL−1, principalement du naphtalène).
Biochemical composition and energy content of size-fractionated zooplankton east of the Kerguelen Islands
Authors : Mireille Harmelin-Vivien (MIO), Daniela Bӑnaru (MIO) , Charlotte Dromard, Melanie Ourgaud (MIO), François Carlotti
Polar Biology, Springer Verlag, 2019, 42 (3), pp.603-617. 10.1007/s00300-019-02458-8
Food quality is recognized as a key parameter of food web functioning in which zooplankton plays a crucial role not only in linking lower to upper trophic levels but also in transforming the quality of the organic matter available to predators. The influence of size and taxonomic group composition of zooplankton in these processes was assessed in eastern Kerguelen waters (Southern Ocean) at the onset of the spring bloom in 2011. Biochemical (lipids, proteins and carbohydrates) and elemental (carbon and nitrogen) composition were measured in five size—fractions of bulk zooplankton ranging from 80 µm to > 2000 µm and in large copepods, euphausiids, annelids and salps, and energy content was derived from biochemical contents. Proteins were the dominant component of zooplankton dry weight (21.5% dw), followed by lipids (8.9% dw), soluble carbohydrates (2.2% dw) and insoluble carbohydrates (1.0% dw). A concentration increase with zooplankton size for all biochemical components was observed, particularly stronger for proteins and lipids. Copepods and salps provided, respectively, the highest and the lowest amount of lipids and energy. A four-fold increase in energy content was observed from the smallest to the largest fraction inducing a significant ncrease (> 10 kJ g dw) in the quality of zooplankton matter. This may explain why large zooplankton represent a major food resource for numerous fish, seabirds and marine mammals in the Southern Ocean. Such unique results are required to better quantify energy dynamics in polar food webs.
Evidence of high N2 fixation rates in the temperate northeast Atlantic
Authors : Debany Fonseca-Batista, Xuefeng Li, Virginie Riou (MIO), Valérie Michotey(MIO), Florian Deman1, François Fripiat5, Sophie Guasco (MIO), Natacha Brion, Nolwenn Lemaitre, Manon Tonnard, Morgane Gallinari6, Hélène Planquette, Frédéric Planchon, Géraldine Sarthou, Marc Elskens, Julie LaRoche, Lei Chou, Frank Dehairs
Biogeosciences, 16, 999–1017, 2019
Abstract. : Diazotrophic activity and primary production (PP) were investigated along two transects (Belgica BG2014/14 and GEOVIDE cruises) off the western Iberian Margin and the Bay of Biscay in May 2014. We report substantial N2fixation activitiesat 8 of the 10 stations sampled, ranging overallbetween 81 and 384 μmol N m-2d-1(0.7 to 8.2 nmol N L-1d-1),withtwo sites close to the Iberian Margin between 38.8° N and 40.7° N yieldingrates 25reachingup to 1355 and 1533 μmol N m-2d-1(65 and 45 nmol N L-1d-1at surface level, respectively).Although diazotrophic activity was not detected at two northern stations in the central Bay of Biscay, when converted to carbon uptake using Redfield stoichiometry, N2fixation at the eight other sites generally contributed to 1–3% of euphotic layer daily PP, and up to 25% and 23%, respectively at the two most active sites. In the Atlantic Ocean, N2fixation rates exceeding 1000 μmol N m-2d-1have previously only been reported in the temperate and tropical western North 30Atlantic waters having coastal, shelf or mesohaline characteristics, as opposed to the mostly open ocean conditions studied here.At the two sites where N2fixation activity wasthe highest; nifHsequences assigned to theprymnesiophyte-symbiont CandidatusAtelocyanobacterium thalassa (UCYN-A)dominated the nifH sequence pool recovered from DNA samples, whilethe remaining sequences, as for all the ones recovered from the other sites,belonged exclusively to non-cyanobacterialphylotypes. Previous studies in the Iberian Basin have systematically 35reported lower N2fixation rates (from < 0.1 to 140 μmol N m-2d-1), as compared to those found in the presentstudy, and this regardless of whether the bubble-addition method or the dissolution method were applied. Earlier studiesin the Iberian region wereconductedlargely outside the bloom period,unlike the present work which was carried out in spring, yet in all cases the assessment of nifHgene diversity, suggests a predominance of UCYN-A and non-cyanobacterial diazotrophs. We support that the unexpectedly high N2fixation activitiesrecorded at the time of our 40study werepromoted by the availability of phytoplankton-derived organic matter produced during the spring bloom, as evidencedby the significant surface particulate organic carbon concentrations,andby the presence of excess phosphorus signature in surface waters, particularly atthe sites with extreme activities. Our findings stress the need2for a more detailed monitoring of oceanic N2fixation in productive waters of the temperate North Atlantic to better constrain the basin-scale nitrogen input to the ocean inventory
Bacterial Bioluminescence: Light Emission in Photobacterium phosphoreum Is Not Under Quorum-Sensing Control
Authors : Lisa Tanet, Christian Tamburini, Chloé Baumas, Marc Garel, Gwénola Simon and Laurie Casalot (all MIO)
Frontiers in Microbiology March 2019, Volume 10, Article 365
Abstract : Bacterial-bioluminescence regulation is often associated with quorum sensing. Indeed, many studies have been made on this subject and indicate that the expression of the light-emission-involved genes is density dependent. However, most of these studies have concerned two model species, Aliivibrio fischeri and Vibrio campbellii. Very few works have been done on bioluminescence regulation for the other bacterial genera. Yet, according to the large variety of habitats of luminous marine bacteria, it would not be surprising to find different light-regulation systems. In this study, we used Photobacterium phosphoreum ANT-2200, a piezophilic bioluminescent strain isolated from Mediterranean deep-sea waters (2200-m depth). To answer the question of whether or not the bioluminescence of P. phosphoreum ANT-2200 is under quorum-sensing control, we focused on the correlation between growth and light emission through physiological, genomic and, transcriptomic approaches. Unlike A. fischeri and V. campbellii, the light of P. phosphoreum ANT-2200 immediately increases from its initial level. Interestingly, the emitted light increases at much higher rate at the low cell density than it does for higher cell-density values. The expression level of the light-emission-involved genes stays constant all along the exponential growth phase. We also showed that, even when more light is produced, when the strain is cultivated at high hydrostatic pressure, no change in the transcription level of these genes can be detected. Through different experiments and approaches, our results clearly indicate that, under the tested conditions, the genes, directly involved in the bioluminescence in P. phosphoreum ANT-2200, are not controlled at a transcriptomic level. Quite obviously, these results demonstrate that the light emission of the strain is not density dependent, which means not under quorum-sensing control. Through this study, we point out that bacterial-bioluminescence regulation should not, from now on, be always linked with the quorum-sensing control.
Synthesis review of the Gulf of Gabes (eastern Mediterranean Sea, Tunisia): Morphological, climatic, physical oceanographic, biogeochemical and fisheries features
Auteurs : Béjaoui Béchir , Sana Ben Ismail, Achref Othmani, Olfa Ben Abdallah-Ben Hadj Hamida, Cristèle Chevalier (MIO), Wafa Feki-Sahnoun, Ali Harzallah, Nader Ben Hadj Hamida, Riadh Bouaziz, Salem Dahech, Frédéric Diaz (MIO), Khouthir Tounsi, Cherif Sammari, Marc Pagano (MIO), Malika Bel Hassen
Estuarine, Coastal and Shelf Science, 219, 395-408
DOI : 10.1016/j.ecss.2019.01.006
•The coastal morphology of the Gulf of Gabes is characterized by beaches, cliffs and wetlands.
•The climate of the Gulf of Gabes is characterized by temperate and hot subtropical Saharan climate.
•The water circulation and water level are closely associated with tides.
•The Gulf of Gabes is considered as the most productive area in the Mediterranean.
Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized Marine Coastal Area
Authors : Clément Coclet (MIO), Cédric Garnier (MIO), Gaël Durrieu (MIO), Dario Omanović, Sébastien D’Onofrio (MIO), Christophe Le Poupon (MIO), Jean-Ulrich Mullot, Jean-François Briand and Benjamin Misson (MIO)
Front. Microbiol., 22 February 2019 - https://doi.org/10.3389/fmicb.2019.00257
Abstract : Unraveling the relative importance of both environmental conditions and ecologicalprocesses regulating bacterioplankton communities is a central goal in microbialecology. Marine coastal environments are among the most urbanized areas and as aconsequence experience environmental pressures. The highly anthropized Toulon Bay(France) was considered as a model system to investigate shifts in bacterioplanktoncommunities along natural and anthropogenic physicochemical gradients during a1-month survey. In depth geochemical characterization mainly revealed strong andprogressive Cd, Zn, Cu, and Pb contamination gradients between the entrance ofthe Bay and the north-western anthropized area. On the other hand, low-amplitudenatural gradients were observed for other environmental variables. Using 16S rRNAgene sequencing, we observed strong spatial patterns in bacterioplankton taxonomicand predicted function structure along the chemical contamination gradient. Variationpartitioning analysis demonstrated that multiple metallic contamination explained thelargest part of the spatial biological variations observed, but DOC and salinity werealso significant contributors. Network analysis revealed that biotic interactions were farmore numerous than direct interactions between microbial groups and environmentalvariables. This suggests indirect effects of the environment, and especially trace metals,on the community through a few taxonomic groups. These spatial patterns werealso partially found for predicted bacterioplankton functions, thus indicating a limitedfunctional redundancy. All these results highlight both potential direct influences of tracemetals contamination on coastal bacterioplankton and indirect forcing through bioticinteractions and cascading.
Keywords : coastal ecosystem, metal contamination gradients, bacterioplankton community structure, functional prediction, co-occurrence network
Toward science-oriented validations of coastal altimetry: Application to the Ligurian Sea
Authors : M.Meloni, J.Bouffard, A.M.Dogliolic (MIO), A.Petrenko (MIO), G.Valladeaud
Remote Sensing of Environment
Volume 224, April 2019, Pages 275-288 - https://doi.org/10.1016/j.rse.2019.01.028
Abstract : This study is a preliminary contribution to the European Space Agency's efforts aimed at establishing reference in situ networks specifically targeted to validate coastal altimetry. For this purpose, we processed and cross-compared conjointly improved altimetry data and in situ measurements acquired over the Ligurian Sea – a coastal region of the Mediterranean characterised by complex, fine-scale and rapidly evolving oceanic features. We made use of several kinds of multi-sensor in situ observations located along SARAL and Jason-2 tracks. The main objectives of the study were to assess improved coastal oriented validation strategies, including the usage of a new in situ platform (Moving Vessel Profiler), while better understanding potential differences owing to physical content inconsistency and instrumental or data processing limitations. The results show remarkable agreements over spatial scales of few tens of kilometres, paving the way for the deployment of future in situ networks and the definition of science-oriented diagnostics targeted to assess the capability of present and future high-resolution altimetric missions in resolving small-scale physical features.
Keywords : Coastal altimetry Mesoscale Validation and verification Northern current
Pascal Hingamp (MIO) co-auteur de Minimum Information about an Uncultivated Virus Genome (MIUViG)
In Nature Biotechnology volume 37, pages 29–37 (2019)
Authors : Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P (MIO), Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.
Abstract : We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
A Mild-Slope System for Bragg Scattering of Water Waves by Sinusoidal Bathymetry in the Presence of Vertically Sheared Currents
Authors : Kostas Belibassakis, Julien Touboul (MIO), Elodie Laffitte (MIO), Vincent Rey (MIO).
Received : 12 October 2018 / Accepted : 29 December 2018 / Published : 7 January 2019
J. Mar. Sci. Eng. 2019, 7(1), 9 ; doi:10.3390/jmse7010009
Abstract : Extended mild-slope models (MMSs) are examined for predicting the characteristics of normally incident waves propagating over sinusoidal bottom topography in the presence of opposing shearing currents. It is shown that MMSs are able to provide quite good predictions in the case of Bragg scattering of waves over rippled bathymetry without a current, but fail to provide good predictions concerning the resonant frequency in the additional presence of a current. In order to resolve the above mismatch, a two-equation mild-slope system (CMS2) is derived from a variational principle based on the representation of the wave potential expressed as a superposition of the forward and backward components. The latter system is compared against experimentally measured data collected in a wave flume and is shown to provide more accurate predictions concerning both the resonant frequency and the amplitude of the reflection coefficient. Future work will be devoted to the examination of the derived model for a more general wave system over realistic seabed topography. View Full-Text
Keywords : wave-current interaction ; sinusoidal bathymetry ; resonant reflection ; mild-slope equation ; coupled-mode system
Damage-related protein turnover explains inter-specific patterns of maintenance rate and suggests modifications of the DEB theory
Authors : Olivier Maury, Jean-Christophe Poggiale (MIO), Olivier Aumont
Journal of Sea Research, Elsevier, 2019, 143, pp.35-47
Abstract : Maintenance is the energy that living organisms are bound to use to maintain their structure in a viable state. It includes all the metabolic and physiological costs that are not directly associated to the production of biomass (growth and reproduction) or to development (maturation). In the framework of the DEB theory, somatic maintenance rate can either be proportional to organism structural volume V or, more marginally, to structural surface V 2/3. Being mostly associated to similar metabolic processes, volume specific maintenance costs are not expected to vary substantially at both intra-and interspecific levels. In the DEB theory, the volume-specific maintenance rate is therefore supposed to keep constant from birth to death and to remain approximately constant between species. However, a recent meta-analysis of DEB parameters estimated using the Add-my-Pet collection (Kooijman, 2014) reveals troubling patterns apparently violating this inter-specific scaling rule and challenging the DEB theory. It is indeed shown in this study that empirically-derived volume-specific maintenance rates scale approximately with, and display a very high variability around this trend. Overall, estimated maintenance rates in Add-my-Pet span over three to four orders of magnitude, thus invalidating the assumption of constant maintenance rate between species, which underpins the covariation rules for parameter values of the DEB theory. In an attempt to address this major problem for the DEB theory, we propose a simple physiological mechanism that would simultaneously explain the apparent decrease of volume-specific maintenance rate with ultimate size and its apparent variability for a given range of maximum size. Our proposition consists in making protein (and more generally structure) turnover explicit in maintenance and linking protein damage rate to aerobic metabolism and the production of ROS, which are decreasing with both structural volume and maximum structural volume. We show that this implies that the actual volume specific maintenance rate varies both at the intra- and inter-specific levels in a range very similar to what is observed in the Add-my Pet data estimations. If true, this implies that the apparent decrease of volume-specific maintenance rate with ultimate size is an artefact and it requires modifications of the standard DEB theory in order to capture empirical inter-specific scaling patterns of DEB parameters while keeping the consistency of the theory at both intra- and inter-specific levels.
Spatio-temporal variability in benthic exchanges at the sediment-water interface of a shallow tropical coastal lagoon (south coast of Gulf of Mexico)
Authors : Christian Grenz (MIO), Montserrat Moreno (MIO), Karline Soetaert, Lionel Denis, Pascal Douillet (MIO), Renaud Fichez (MIO)
Estuarine, Coastal and Shelf Science
Volume 218, 5 March 2019, Pages 368-380
Abstract : The sediment in Laguna de Términos, the largest and shallowest system in the Southwest portion of the Gulf of Mexico features a broad range of ecological and hydrobiological characteristics driven by annual weather cycles (dry and wet seasons), causing large salinity gradients during the wet season due to large river discharges. Four sampling campaigns were carried out during the wet and the dry seasons in 2009 and 2010 on a selection of 13 out of 35 stations. Measurements of Sediment Oxygen Demand (SOD) and nutrient fluxes at the sediment-water interface were performed using lab incubations with 15 cm diameter sediment cores. SOD fluctuated between 1327 ± 161 and 2248 ± 359 μmol m −2 h −1 for dry and wet seasons respectively. Silicate effluxes were also significantly higher during the wet seasons (89.4 ± 15.9 μmol m −2 h −1) than during the dry season (46.5 ± 11.4 μmol m −2 h −1). PO 4 fluxes were low all over the study period without seasonal trend. No significant difference was measured for DIN fluxes but there was a tendency for DIN uptake during the wet season (−2.9 ± 18.8 μmol m −2 h −1) and conversely an efflux during the dry season (24.3 ± 7.3 μmol m −2 h −1). SOD correlated to organic matter and chloropigment content of the sediments while silicate fluxes responded to enhanced chloropigments in the sediments. During both seasons, total benthic nutrient fluxes overwhelmed largely riverine inputs and benthic carbon mineralization rates approximated a significant proportion of the pelagic organic carbon production. We conclude that benthic processes in Laguna de Términos are largely driven by weather variability and that they contribute substantially to carbon and nutrient budgets in this shallow subtropical system.