Recent publications

A Novel Highly Efficient Device for Growing Micro-Aerophilic Microorganisms

Authors : Maxime Fuduche (MIO) , Sylvain Davidson (MIO),   Céline Boileau (MIO), Long-Fei Wu and Yannick Combet-Blanc (MIO)

Front. Microbiol., 19 March 2019 |

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.

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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 |

Abstract :  This study presents the MiniFluo-UV, an ocean glider-compatible fluorescence sensor that targets the detection of polycyclic aromatic hydrocarbons (PAHs) in the marine environment. Two MiniFluos can be installed on a glider, each equipped with two optical channels (one PAH is measured per channel). This setup allows the measurement of up to 4 different fluorescent PAHs: Naphthalene, Phenanthrene, Fluorene and Pyrene. Laboratory tests on oil products (Maya crude oil and Diesel fuel) as well as on marine samples near industrial areas (urban harbor and offshore installations) revealed that the concentration of the four PAHs targeted accounted for 62–97% of the total PAH concentration found in samples (P16 PAHs determined by standard international protocols). Laboratory tests also revealed that for marine applications, the calibration on Water Accommodated Fraction (WAF) of crude oil is more appropriate than the one on pure standards (STD). This is because PAH fluorescence is constituted in large part of alkylated compounds that are not considered with STD calibration. Results from three glider deployments with increasing levels of complexity (a laboratory trial, a field mission in non-autonomous mode and a fully autonomous mission) are also presented. During field deployments, the MiniFluo-glider « SeaExplorer » package was able to detect concentration gradients from offshore marine waters toward the head of a Mediterranean harbor ( < 80ngL−1) as well as hydrocarbon patches at the surface waters of an oil and gas exploitation field in the North Sea (< 200ngL−1, mainly Naphthalene).

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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

doi: 10.3389/fmicb.2019.00365

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.

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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  -

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


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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 -

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


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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.


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.


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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


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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.


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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.


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