Pressure-Retaining Sampler and High-Pressure Systems to Study Deep-Sea Microbes Under in situ Conditions

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

The REINFORCE Project: Inviting Citizen Scientists to analyse KM3NeT data

Large research infrastructures have opened new observational windows, allowing us to study the structure of matter up to the entire Universe. However, society hardly observes these developments through education and outreach activities. This induces a gap between frontier science and society that may create misconceptions about the content, context, and mission of public funded science. In this context, the main goal of the European Union’s Horizon 2020 "Science with and for Society" REINFORCE project (REsearch INfrastructure FOR Citizens in Europe) is to minimize the knowledge gap between large research infrastructures and society through Citizen Science. A series of activities is being developed on the Zooniverse platform, in four main fields of frontier physics involving large research infrastructures: gravitational waves with the VIRGO interferometer, particle physics with the ATLAS detector at LHC, neutrinos with the KM3NeT telescope, and cosmic rays at the interface of geoscience and archeology. Using real and simulated data, Citizen Scientists will help building a better understanding of the impact of the environment on these very high precision detectors as well as creating new knowledge. This poster describes REINFORCE, with a special emphasis on the Deep Sea Hunter demonstrator involving the KM3NeT neutrino telescope, in order to show practical examples of Citizen Science activities that will be proposed through the project.Article signat per 297 autors/es: M.Ageron, S. Aiello, A. Albert, M. Alshamsi, S. Alves Garre, Z. Aly, A. Ambrosone, F. Ameli, M. Andre, G. Androulakis, M. Anghinolfi, M. Anguita, G. Anton, M. Ardid, S. Ardid, W. Assal, J. Aublin, C. Bagatelas, B. Baret, S. Basegmez du Pree, M. Bendahman, F. Benfenati, E. Berbee, A. M. van den Berg, V. Bertin, S. Beurthey, V. van Beveren, S. Biagi, M. Billault, M. Bissinger, M. Boettcher, M. Bou Cabo, J. Boumaaza, M. Bouta, C. Boutonnet, G. Bouvet, M. Bouwhuis, C. Bozza, H.Brânzas, R. Bruijn, J. Brunner, R. Bruno, E. Buis, R. Buompane, J. Busto, B. Caiffi, L. Caillat, D. Calvo, S. Campion, A. Capone, H. Carduner, V. Carretero, P. Castaldi, S. Celli;, R. Cereseto, M. Chabab, C. Champion, N. Chau, A. Chen, S. Cherubini, V. Chiarella, T. Chiarusi, M. Circella, R. Cocimano, J. A. B. Coelho, A. Coleiro, M. Colomer Molla, S. Colonges, R. Coniglione, A. Cosquer, P. Coyle, M. Cresta, A. Creuso, A. Cruz, G. Cuttone, A. D’Amico, R. Dallier, B. De Martino, M. De Palma, I. Di Palma, A. F. Díaz, D. Diego- Tortosa, C. Distefano, A. Domi, C. Donzaud, D. Dornic, M. Dörr, D. Drouhin, T. Eberl, A. Eddyamoui, T. van Eeden, D. van Eijk, I. El Bojaddaini, H. Eljarrari, D. Elsaesser, A. Enzenhöfer, V. Espinosa, P. Fermani, G. Ferrara, M. D. Filipovic, F. Filippini, J. Fransen, L. A. Fusco, D. Gajanana, T. Gal, J. García Méndez, A. Garcia Soto, E. Garçon, F. Garufi, C. Gatius, N. Geißelbrecht, L. Gialanella, E. Giorgio, S. R. Gozzini, R. Gracia, K. Graf, G. Grella, D. Guderian, C. Guidi, B. Guillon, M. Gutiérrez, J. Haefner, S. Hallmann, H. Hamdaoui, H. van Haren, A. Heijboer, A. Hekalo, L. Hennig, S. Henry, J. J. Hernández-Rey, J. Hofestädt, F. Huang,W. Idrissi Ibnsalih, A. Ilioni, G. Illuminati, C.W. James, D. Janezashvili, P. Jansweijer, M. de Jong, P. de Jong, B. J. Jung, M. Kadler, P. Kalaczynski, O. Kalekin,U. F. Katz, F. Kayzel, P.Keller, N. R. Khan Chowdhury, G. Kistauri, F. van der Knaap, P. Kooijman, A. Kouchner, M. Kreter, V. Kulikovskiy, M. Labalme, P. Lagier, R. Lahmann, P. Lamare, M. Lamoureux, G. Larosa, C. Lastoria, J. Laurence, A. Lazo, R. Le Breton, E. Le Guirriec, S. Le Stum, G. Lehaut, O. Leonardi, F. Leone, E. Leonora, C. Lerouvillois, J. Lesrel, N. Lessing, G. Levi, M. Lincetto, M. Lindsey Clark, T. Lipreau, C. LLorens Alvarez, A. Lonardo, F. Longhitano, D. Lopez-Coto, N. Lumb, L. Maderer, J. Majumdar, J. Manczak, A. Margiotta, A. Marinelli, A. Marini, C. Markou, L. Martin, J. A. Martínez-Mora, A. Martini, F. Marzaioli, S. Mastroianni, K.W. Melis, G. Miele, P. Migliozzi, E. Migneco, P. Mijakowski, L. S. Miranda, C. M. Mollo, M. Mongelli, A. Moussa, R. Muller, P. Musico, M. Musumeci, L. Nauta, S. Navas, C. A. Nicolau, B. Nkosi, B. Ó Fearraigh, M. O’Sullivan, A. Orlando, G. Ottonello, S. Ottonello, J. Palacios González5, G. Papalashvili, R. Papaleo, C. Pastore, A. M. Paun, G. E. Pavalas, G. Pellegrini, C. Pellegrino, M. Perrin-Terrin, V. Pestel, P. Piattelli, C. Pieterse, O. Pisanti, C. Poirè, V. Popa, T. Pradier, F. Pratolongo, I. Probst, G. Pühlhofer, S. Pulvirenti, G. Quéméner, N. Randazzo, A. Rapicavoli, S. Razzaque, D. Real, S. Reck, G. Riccobene, L. Rigalleau, A. Romanov, A. Rovelli, J. Royon, F. Salesa Greus, D. F. E. Samtleben, A. Sánchez Losa, M. Sanguineti, A. Santangelo, D. Santonocito, P. Sapienza, J. Schmelling, J. Schnabel, M. F. Schneider, J. Schumann, H. M. Schutte, J. Seneca, I. Sgura, R. Shanidze, A. Sharma, A. Sinopoulou, B. Spisso, M. Spurio, D. Stavropoulos, J. Steijger, S. M. Stellacci, M. Taiuti, F. Tatone, Y. Tayalati, E. Tenllado, D. Tézier, T. Thakore, S. Theraube, H. Thiersen, P. Timmer, S. Tingay, S. Tsagkli, V. Tsourapis, E. Tzamariudaki, D. Tzanetatos, C. Valieri, V. Van Elewyck, G. Vasileiadis, F. Versari, S. Viola, D. Vivolo, G. de Wasseige, J.Wilms, R.Wojaczynski, E. deWolf, T. Yousfi, S. Zavatarelli, A. Zegarelli, D. Zito, J. D. Zornoza, J. Zúñiga, N. ZywuckaPostprint (published version

Global Trends in Marine Plankton Diversity across Kingdoms of Life

35 pages, 18 figures, 1 table, supplementary information https://doi.org/10.1016/j.cell.2019.10.008.-- Raw reads of Tara Oceans are deposited at the European Nucleotide Archive (ENA). In particular, newly released 18S rRNA gene metabarcoding reads are available under the number ENA: PRJEB9737. ENA references for the metagenomics reads corresponding to the size fraction < 0.22 μm (for prokaryotic viruses) analyzed in this study are included in Gregory et al. (2019); see their Table S3. ENA references for the metagenomics reads corresponding to the size fraction 0.22-1.6/3 μm (for prokaryotes and giruses) correspond to Salazar et al. (2019) (see https://zenodo.org/record/3473199). Imaging datasets from the nets are available through the collaborative web application and repository EcoTaxa (Picheral et al., 2017) under the address https://ecotaxa.obs-vlfr.fr/prj/412 for regent data, within the 3 projects https://ecotaxa.obs-vlfr.fr/prj/397, https://ecotaxa.obs-vlfr.fr/prj/398, https://ecotaxa.obs-vlfr.fr/prj/395 for bongo data, and within the 2 projects https://ecotaxa.obs-vlfr.fr/prj/377 and https://ecotaxa.obs-vlfr.fr/prj/378 for WP2 data. A table with Shannon values and multiple samples identifiers, plus a table with flow cytometry data split in six groups are available (https://doi.org/10.17632/p9r9wttjkm.1). Contextual data from the Tara Oceans expedition, including those that are newly released from the Arctic Ocean, are available at https://doi.org/10.1594/PANGAEA.875582The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservationTara Oceans (which includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Ocean Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org/). We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the Study of Global Ocean Systems Ecology and Evolution FR2022/Tara Oceans-GOSEE), the European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Ministry of Research, and the French Government “Investissements d’Avenir” programs OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), the PSL∗ Research University (ANR-11-IDEX-0001-02), as well as EMBRC-France (ANR-10-INBS-02). Funding for the collection and processing of the Tara Oceans data set was provided by NASA Ocean Biology and Biogeochemistry Program under grants NNX11AQ14G, NNX09AU43G, NNX13AE58G, and NNX15AC08G (to the University of Maine); the Canada Excellence research chair on remote sensing of Canada’s new Arctic frontier; and the Canada Foundation for Innovation. We also thank agnès b. and Etienne Bourgois, the Prince Albert II de Monaco Foundation, the Veolia Foundation, Region Bretagne, Lorient Agglomeration, Serge Ferrari, Worldcourier, and KAUST for support and commitment. The global sampling effort was enabled by countless scientists and crew who sampled aboard the Tara from 2009–2013, and we thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expeditions. We are also grateful to the countries who graciously granted sampling permission. We thank Stephanie Henson for providing ocean carbon export data and are also grateful to the other researchers who kindly made their data available. We thank Juan J. Pierella-Karlusich for advice regarding single-copy genes. C.d.V. and N.H. thank the Roscoff Bioinformatics platform ABiMS (http://abims.sb-roscoff.fr) for providing computational resources. C.B. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program (grant agreement 835067) as well as the Radcliffe Institute of Advanced Study at Harvard University for a scholar’s fellowship during the 2016-2017 academic year. M.B.S. thanks the Gordon and Betty Moore Foundation (award 3790) and the National Science Foundation (awards OCE#1536989 and OCE#1829831) as well as the Ohio Supercomputer for computational support. S.G.A. thanks the Spanish Ministry of Economy and Competitiveness (CTM2017-87736-R), and J.M.G. is grateful for project RT2018-101025-B-100. F.L. thanks the Institut Universitaire de France (IUF) as well as the EMBRC platform PIQv for image analysis. M.C.B., D.S., and J.R. received financial support from the French Facility for Global Environment (FFEM) as part of the “Ocean Plankton, Climate and Development” project. M.C.B. also received financial support from the Coordination for the Improvement of Higher Education Personnel of Brazil (CAPES 99999.000487/2016-03)Peer Reviewe

Modulation of Brain β-Endorphin Concentration by the Specific Part of the Y Chromosome in Mice

International audienceBackground: Several studies in animal models suggest a possible effect of the specific part of the Y-chromosome (Y NPAR) on brain opioid, and more specifically on brain b-endorphin (BE). In humans, male prevalence is found in autistic disorder in which observation of abnormal peripheral or central BE levels are also reported. This suggests gender differences in BE associated with genetic factors and more precisely with Y NPAR. Methodology/Principal Findings: Brain BE levels and plasma testosterone concentrations were measured in two highly inbred strains of mice, NZB/BlNJ (N) and CBA/HGnc (H), and their consomic strains for the Y NPAR. An indirect effect of the Y NPAR on brain BE level via plasma testosterone was also tested by studying the correlation between brain BE concentration and plasma testosterone concentration in eleven highly inbred strains. There was a significant and major effect (P,0.0001) of the Y NPAR in interaction with the genetic background on brain BE levels. Effect size calculated using Cohen's procedure was large (56% of the total variance). The variations of BE levels were not correlated with plasma testosterone which was also dependent of the Y NPAR. Conclusions/Significance: The contribution of Y NPAR on brain BE concentration in interaction with the genetic background is the first demonstration of Y-chromosome mediated control of brain opioid. Given that none of the genes encompassed by the Y NPAR encodes for BE or its precursor, our results suggest a contribution of the sex-determining region (Sry, carried by Y NPAR) to brain BE concentration. Indeed, the transcription of the Melanocortin 2 receptor gene (Mc2R gene, identified as the proopiomelanocortin receptor gene) depends on the presence of Sry and BE is derived directly from proopiomelanocortin. The results shed light on the sex dependent differences in brain functioning and the role of Sry in the BE system might be related to the higher frequency of autistic disorder in males

Insights into the Biodiversity, Behavior, and Bioluminescence of Deep-Sea Organisms Using Molecular and Maritime Technology

Since its founding, the Monterey Bay Aquarium Research Institute (MBARI) has pioneered unique capabilities for accessing the deep ocean and its inhabitants through focused peer relationships between scientists and engineers. This focus has enabled breakthroughs in our understanding of life in the sea, leading to fundamental advances in describing the biology and the ecology of open-ocean and deep-sea animals. David Packard’s founding principle was the application of technological advances to studying the deep ocean, in part because he recognized the critical importance of this habitat in a global context. Among other fields, MBARI’s science has benefited from applying novel methodologies in molecular biology and genetics, imaging systems, and in situ observations. These technologies have allowed MBARI’s bioluminescence and biodiversity laboratory and worldwide collaborators to address centuries-old questions related to the biodiversity, behavior, and bio-optical properties of organisms living in the water column, from the surface into the deep sea. Many of the most interesting of these phenomena are in the midwater domain—the vast region of ocean between the sunlit surface waters and the deep seafloor

Global, regional, and national burden of diabetes from 1990 to 2021, with projections of prevalence to 2050: a systematic analysis for the Global Burden of Disease Study 2021

Background Diabetes is one of the leading causes of death and disability worldwide, and affects people regardless of country, age group, or sex. Using the most recent evidentiary and analytical framework from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD), we produced location-specific, age-specific, and sex-specific estimates of diabetes prevalence and burden from 1990 to 2021, the proportion of type 1 and type 2 diabetes in 2021, the proportion of the type 2 diabetes burden attributable to selected risk factors, and projections of diabetes prevalence through 2050. Methods Estimates of diabetes prevalence and burden were computed in 204 countries and territories, across 25 age groups, for males and females separately and combined; these estimates comprised lost years of healthy life, measured in disability-adjusted life-years (DALYs; defined as the sum of years of life lost [YLLs] and years lived with disability [YLDs]). We used the Cause of Death Ensemble model (CODEm) approach to estimate deaths due to diabetes, incorporating 25 666 location-years of data from vital registration and verbal autopsy reports in separate total (including both type 1 and type 2 diabetes) and type-specific models. Other forms of diabetes, including gestational and monogenic diabetes, were not explicitly modelled. Total and type 1 diabetes prevalence was estimated by use of a Bayesian meta-regression modelling tool, DisMod-MR 2.1, to analyse 1527 location-years of data from the scientific literature, survey microdata, and insurance claims; type 2 diabetes estimates were computed by subtracting type 1 diabetes from total estimates. Mortality and prevalence estimates, along with standard life expectancy and disability weights, were used to calculate YLLs, YLDs, and DALYs. When appropriate, we extrapolated estimates to a hypothetical population with a standardised age structure to allow comparison in populations with different age structures. We used the comparative risk assessment framework to estimate the risk-attributable type 2 diabetes burden for 16 risk factors falling under risk categories including environmental and occupational factors, tobacco use, high alcohol use, high body-mass index (BMI), dietary factors, and low physical activity. Using a regression framework, we forecast type 1 and type 2 diabetes prevalence through 2050 with Socio-demographic Index (SDI) and high BMI as predictors, respectively. Findings In 2021, there were 529 million (95% uncertainty interval [UI] 500–564) people living with diabetes worldwide, and the global age-standardised total diabetes prevalence was 6·1% (5·8–6·5). At the super-region level, the highest age-standardised rates were observed in north Africa and the Middle East (9·3% [8·7–9·9]) and, at the regional level, in Oceania (12·3% [11·5–13·0]). Nationally, Qatar had the world’s highest age-specific prevalence of diabetes, at 76·1% (73·1–79·5) in individuals aged 75–79 years. Total diabetes prevalence—especially among older adults—primarily reflects type 2 diabetes, which in 2021 accounted for 96·0% (95·1–96·8) of diabetes cases and 95·4% (94·9–95·9) of diabetes DALYs worldwide. In 2021, 52·2% (25·5–71·8) of global type 2 diabetes DALYs were attributable to high BMI. The contribution of high BMI to type 2 diabetes DALYs rose by 24·3% (18·5–30·4) worldwide between 1990 and 2021. By 2050, more than 1·31 billion (1·22–1·39) people are projected to have diabetes, with expected age-standardised total diabetes prevalence rates greater than 10% in two super-regions: 16·8% (16·1–17·6) in north Africa and the Middle East and 11·3% (10·8–11·9) in Latin America and Caribbean. By 2050, 89 (43·6%) of 204 countries and territories will have an age-standardised rate greater than 10%.Peer ReviewedPostprint (published version

Machine learning techniques to characterize functional traits of plankton from image data

Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms

The Dark Ocean Is Full of Lights

International audienc

Distribution and quantification of bioluminescence as an ecological trait in the deep sea benthos

Bioluminescence is a prominent functional trait used for visual communication. A recent quantification showed that in pelagic ecosystems more than 75% of individual macro-planktonic organisms are categorized as able to emit light. In benthic ecosystems, only a few censuses have been done, and were based on a limited number of observations. In this study, our dataset is based on observations from remotely operated vehicle (ROV) dives conducted from 1991–2016, spanning 0–3,972 m depth. Data were collected in the greater Monterey Bay area in central California, USA and include 369,326 pelagic and 154,275 epibenthic observations at Davidson Seamount, Guide Seamount, Sur Ridge and Monterey Bay. Because direct observation of in situ bioluminescence remains a technical challenge, taxa from ROV observations were categorized based on knowledge gained from the literature to assess bioluminescence status. We found that between 30–41% of the individual observed benthic organisms were categorized as capable of emitting light, with a strong difference between benthic and pelagic ecosystems. We conclude that overall variability in the distribution of bioluminescent organisms is related to the major differences between benthic and pelagic habitats in the deep ocean. This study may serve as the basis of future investigations linking the optical properties of various habitats and the variability of bioluminescent organism distributions