Artículos de revistas: "Tara-Pacific expedition"

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Flores, J. M., G. Bourdin, O. Altaratz, M. Trainic, N. Lang-Yona, E. Dzimban, S. Steinau et al. "Marine Aerosols: Measurements by the Tara Pacific Expedition". Bulletin of the American Meteorological Society 101, n.º 6 (junio de 2020): 499–504. http://dx.doi.org/10.1175/bams-d-18-0224.a.

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BOISSIN, E., C. POGOREUTZ, A. PEY, N. GRAVIER-BONNET y S. PLANES. "Millepora platyphylla (Cnidaria, Hydrozoa) range extended back to the Eastern Pacific, thanks to a new record from Clipperton Atoll". Zootaxa 4668, n.º 4 (12 de septiembre de 2019): 599–600. http://dx.doi.org/10.11646/zootaxa.4668.4.11.

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The fire coral Millepora platyphylla Hemprich & Ehrenberg, 1834 (Cnidaria, Hydrozoa) has a widespread Indo-Pacific distribution observed from the surface to 40 m (Razak & Hoeksema 2003). However, its extirpation from the East Pacific (Gulf of Chiriqui, Panama) was documented after the 1982-1983 bleaching event (Glynn & Weerdt 1991). Here, we report the discovery of 5 colonies of M. platyphylla from the eastern Pacific, specifically at Clipperton Atoll, during the TARA Pacific expedition (www.taraexpeditions.org).

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RIAUX-GOBIN, CATHERINE, ANDRZEJ WITKOWSKI, RICHARD W. JORDAN, VALERIANO PARRAVICINI y SERGE PLANES. "Cocconeis kurakakea, a new diatom species from Nukutavake (Tuamotu Archipelago, South Pacific): description and comparison with C. diruptoides and C. pseudodiruptoides". Phytotaxa 349, n.º 2 (11 de mayo de 2018): 115. http://dx.doi.org/10.11646/phytotaxa.349.2.2.

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During the ‘Tara Pacific 2016–2018 Expedition’, marine benthic diatom samples were collected from several Tuamotu atolls in the South Pacific. Preparation and examination of these samples were conducted following standard methods including light and scanning electron microscopy. A small-celled taxon from the genus Cocconeis Ehrenb. (Bacillariophyceae) is described from the Nukutavake reef, and compared to several other taxa for which the definition is not always clear (e.g., Cocconeis diruptoides Hust. and Cocconeis pseudodiruptoides Foged). The new taxon is present only on one of the investigated Tuamotu atolls, possibly indicating local endemism.

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Flores, J. M., G. Bourdin, O. Altaratz, M. Trainic, N. Lang-Yona, E. Dzimban, S. Steinau et al. "Tara Pacific Expedition’s Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans: Overview and Preliminary Results". Bulletin of the American Meteorological Society 101, n.º 5 (1 de mayo de 2020): E536—E554. http://dx.doi.org/10.1175/bams-d-18-0224.1.

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Abstract Marine aerosols play a significant role in the global radiative budget, in clouds’ processes, and in the chemistry of the marine atmosphere. There is a critical need to better understand their production mechanisms, composition, chemical properties, and the contribution of ocean-derived biogenic matter to their mass and number concentration. Here we present an overview of a new dataset of in situ measurements of marine aerosols conducted over the 2.5-yr Tara Pacific Expedition over 110,000 km across the Atlantic and Pacific Oceans. Preliminary results are presented here to describe the new dataset that will be built using this novel set of measurements. It will characterize marine aerosols properties in detail and will open a new window to study the marine aerosol link to the water properties and environmental conditions.

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Miguel-Gordo, Maria, Sandra Gegunde, Kevin Calabro, Laurence K. Jennings, Amparo Alfonso, Grégory Genta-Jouve, Jean Vacelet, Luis M. Botana y Olivier P. Thomas. "Bromotryptamine and Bromotyramine Derivatives from the Tropical Southwestern Pacific Sponge Narrabeena nigra". Marine Drugs 17, n.º 6 (30 de mayo de 2019): 319. http://dx.doi.org/10.3390/md17060319.

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So far, the Futuna Islands located in the Central Indo-Pacific Ocean have not been inventoried for their diversity in marine sponges and associated chemical diversity. As part of the Tara Pacific expedition, the first chemical investigation of the sponge Narrabeena nigra collected around the Futuna Islands yielded 18 brominated alkaloids: seven new bromotryptamine derivatives 1–7 and one new bromotyramine derivative 8 together with 10 known metabolites of both families 9–18. Their structures were deduced from extensive analyses of nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS) data. In silico metabolite anticipation using the online tool MetWork revealed the presence of a key and minor biosynthetic intermediates. These 18 compounds showed almost no cytotoxic effect up to 10 µM on human neuroblastoma SH-SY5Y and microglia BV2 cells, and some of them exhibited an interesting neuroprotective activity by reducing oxidative damage.

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Planes, Serge, Denis Allemand, Sylvain Agostini, Bernard Banaigs, Emilie Boissin, Emmanuel Boss, Guillaume Bourdin et al. "The Tara Pacific expedition—A pan-ecosystemic approach of the “-omics” complexity of coral reef holobionts across the Pacific Ocean". PLOS Biology 17, n.º 9 (23 de septiembre de 2019): e3000483. http://dx.doi.org/10.1371/journal.pbio.3000483.

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Lucena, Teresa, Isabel Sanz-Sáez, David R. Arahal, Silvia G. Acinas, Olga Sánchez, Carlos Pedrós-Alió, Rosa Aznar y María J. Pujalte. "Mesonia oceanica sp. nov., isolated from oceans during the Tara oceans expedition, with a preference for mesopelagic waters". International Journal of Systematic and Evolutionary Microbiology 70, n.º 7 (1 de julio de 2020): 4329–38. http://dx.doi.org/10.1099/ijsem.0.004296.

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Strain ISS653T, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bacterium, strictly aerobic and chemoorganotrophic, slightly halophilic (1–15 % NaCl) and mesophilic (4–37 °C), oxidase- and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15 : 0, iso-C15 : 0 2-OH, and iso-C17 : 0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2 %), Salegentibacter mishustinae (93.1 %) and Mesonia mobilis (92.9 %) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81 % AAI; 78.9 % ANI), M. phycicola (76 % AAI; 76.3 % ANI), Mesonia maritima (72 % AAI, 74.9 % ANI), Mesonia hippocampi (64 % AAI, 70.8 % ANI) and Mesonia algae (68 % AAI; 72.2 % ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653T in a clade with species of the genus Mesonia . We conclude that strain ISS653T represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653T (=CECT 9532T=LMG 31236T) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans.

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Cornejo, M., L. Bravo, M. Ramos, O. Pizarro, J. Karstensen, M. Gallegos, M. Correa-Ramirez, N. Silva, L. Farias y L. Karp-Boss. "Biogeochemical characteristics of a long-lived anticyclonic eddy in the eastern South Pacific Ocean". Biogeosciences Discussions 12, n.º 17 (2 de septiembre de 2015): 14481–506. http://dx.doi.org/10.5194/bgd-12-14481-2015.

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Abstract. Eastern boundary upwelling systems are characterized by high productivity that often leads to subsurface hypoxia on the shelf. Mesoscale eddies are important, frequent, and persistent features of circulation in these regions, transporting physical, chemical and biological properties from shelves to the open ocean. In austral fall of 2011, during the Tara Oceans expedition, a subsurface layer (200–400 m) in which the concentration of oxygen was very low (< 2 μmol kg−1 of O2) was observed in the eastern South Pacific, ~ 900 km offshore (30° S, 81° W). Satellite altimetry combined with CTD observations associated the local oxygen anomaly with an intrathermocline, anticyclonic, mesoscale eddy with a diameter of about 150 km. The eddy contained Equatorial Subsurface Water (ESSW) that at this latitude is normally restricted near the coast. Undersaturation (44 %) of nitrous oxide (N2O) and nitrite accumulation (> 0.5 μM) gave evidence for denitrification in this water mass. Based on satellite altimetry, we tracked the eddy back to its region of formation on the coast of central Chile (36.1° S, 74.6° W). We estimate that the eddy formed in April 2010. Field studies conducted on the Chilean shelf in June 2010 provided approximate information on initial O2 and N2O concentrations of "source water" in the region at the time of eddy formation. Concentrations of both O2 and N2O in the oxygen minimum zone (OMZ) of the offshore eddy were lower than its surroundings or "source water" on the shelf, suggesting that these chemical species were consumed as the eddy moved offshore. Estimates of apparent oxygen utilization rates at the OMZ of the eddy ranged from 0.29 to 44 nmol L−1 d−1 and the rate of N2O consumption was 3.92 nmol L−1 d−1. Our results show that mesoscale eddies in the ESP not only transport physical properties of the ESSW from the coast to the ocean interior, but also export and transform biogeochemical properties, creating suboxic environments in the oligotrophic region of the eastern South Pacific. Suboxic water masses that are advected by eddies act as hotspots for denitrification and loss of fixed nitrogen from the system.

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Dror, Tom, J. Michel Flores, Orit Altaratz, Guy Dagan, Zev Levin, Assaf Vardi y Ilan Koren. "Sensitivity of warm clouds to large particles in measured marine aerosol size distributions – a theoretical study". Atmospheric Chemistry and Physics 20, n.º 23 (9 de diciembre de 2020): 15297–306. http://dx.doi.org/10.5194/acp-20-15297-2020.

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Abstract. Aerosol size distribution has major effects on warm cloud processes. Here, we use newly acquired marine aerosol size distributions (MSDs), measured in situ over the open ocean during the Tara Pacific expedition (2016–2018), to examine how the total aerosol concentration (Ntot) and the shape of the MSDs change warm clouds' properties. For this, we used a toy model with detailed bin microphysics initialized using three different atmospheric profiles, supporting the formation of shallow to intermediate and deeper warm clouds. The changes in the MSDs affected the clouds' total mass and surface precipitation. In general, the clouds showed higher sensitivity to changes in Ntot than to changes in the MSD's shape, except for the case where the MSD contained giant and ultragiant cloud condensation nuclei (GCCN, UGCCN). For increased Ntot (for the deep and intermediate profiles), most of the MSDs drove an expected non-monotonic trend of mass and precipitation (the shallow clouds showed only the decreasing part of the curves with mass and precipitation monotonically decreasing). The addition of GCCN and UGCCN drastically changed the non-monotonic trend, such that surface rain saturated and the mass monotonically increased with Ntot. GCCN and UGCCN changed the interplay between the microphysical processes by triggering an early initiation of collision–coalescence. The early fallout of drizzle in those cases enhanced the evaporation below the cloud base. Testing the sensitivity of rain yield to GCCN and UGCCN revealed an enhancement of surface rain upon the addition of larger particles to the MSD, up to a certain particle size, when the addition of larger particles resulted in rain suppression. This finding suggests a physical lower bound can be defined for the size ranges of GCCN and UGCCN.

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Cornejo D'Ottone, Marcela, Luis Bravo, Marcel Ramos, Oscar Pizarro, Johannes Karstensen, Mauricio Gallegos, Marco Correa-Ramirez, Nelson Silva, Laura Farias y Lee Karp-Boss. "Biogeochemical characteristics of a long-lived anticyclonic eddy in the eastern South Pacific Ocean". Biogeosciences 13, n.º 10 (20 de mayo de 2016): 2971–79. http://dx.doi.org/10.5194/bg-13-2971-2016.

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Abstract. Mesoscale eddies are important, frequent, and persistent features of the circulation in the eastern South Pacific (ESP) Ocean, transporting physical, chemical and biological properties from the productive shelves to the open ocean. Some of these eddies exhibit subsurface hypoxic or suboxic conditions and may serve as important hotspots for nitrogen loss, but little is known about oxygen consumption rates and nitrogen transformation processes associated with these eddies. In the austral fall of 2011, during the Tara Oceans expedition, an intrathermocline, anticyclonic, mesoscale eddy with a suboxic (< 2 µmol kg−1 of O2), subsurface layer (200–400 m) was detected ∼ 900 km off the Chilean shore (30° S, 81° W). The core of the eddy's suboxic layer had a temperature-salinity signature characteristic of Equatorial Subsurface Water (ESSW) that at this latitude is normally restricted to an area near the coast. Measurements of nitrogen species within the eddy revealed undersaturation (below 44 %) of nitrous oxide (N2O) and nitrite accumulation (> 0.5 µM), suggesting that active denitrification occurred in this water mass. Using satellite altimetry, we were able to track the eddy back to its region of formation on the coast of central Chile (36.1° S, 74.6° W). Field studies conducted in Chilean shelf waters close to the time of eddy formation provided estimates of initial O2 and N2O concentrations of the ESSW source water in the eddy. By the time of its offshore sighting, concentrations of both O2 and N2O in the subsurface oxygen minimum zone (OMZ) of the eddy were lower than concentrations in surrounding water and “source water” on the shelf, indicating that these chemical species were consumed as the eddy moved offshore. Estimates of apparent oxygen utilization rates at the OMZ of the eddy ranged from 0.29 to 44 nmol L−1 d−1 and the rate of N2O consumption was 3.92 nmol L−1 d−1. These results show that mesoscale eddies affect open-ocean biogeochemistry in the ESP not only by transporting physical and chemical properties from the coast to the ocean interior but also during advection, local biological consumption of oxygen within an eddy further generates conditions favorable to denitrification and loss of fixed nitrogen from the system.

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Planes, Serge y Denis Allemand. "Insights and achievements from the Tara Pacific expedition". Nature Communications 14, n.º 1 (1 de junio de 2023). http://dx.doi.org/10.1038/s41467-023-38896-6.

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Belser, Caroline, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec et al. "Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition". Scientific Data 10, n.º 1 (1 de junio de 2023). http://dx.doi.org/10.1038/s41597-023-02204-0.

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AbstractCoral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

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Lombard, Fabien, Guillaume Bourdin, Stéphane Pesant, Sylvain Agostini, Alberto Baudena, Emilie Boissin, Nicolas Cassar et al. "Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems". Scientific Data 10, n.º 1 (1 de junio de 2023). http://dx.doi.org/10.1038/s41597-022-01757-w.

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AbstractThe Tara Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.

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Gorsky, Gabriel, Guillaume Bourdin, Fabien Lombard, Maria Luiza Pedrotti, Samuel Audrain, Nicolas Bin, Emmanuel Boss et al. "Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018)". Frontiers in Marine Science 6 (11 de diciembre de 2019). http://dx.doi.org/10.3389/fmars.2019.00750.

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Lang-Yona, Naama, J. Michel Flores, Rotem Haviv, Adriana Alberti, Julie Poulain, Caroline Belser, Miri Trainic et al. "Terrestrial and marine influence on atmospheric bacterial diversity over the north Atlantic and Pacific Oceans". Communications Earth & Environment 3, n.º 1 (20 de mayo de 2022). http://dx.doi.org/10.1038/s43247-022-00441-6.

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AbstractThe diversity of microbes and their transmission between ocean and atmosphere are poorly understood despite the implications for microbial global dispersion and biogeochemical processes. Here, we survey the genetic diversity of airborne and surface ocean bacterial communities sampled during springtime transects across the northwest Pacific and subtropical north Atlantic as part of the Tara Pacific Expedition. We find that microbial community composition is more variable in the atmosphere than in the surface ocean. Bacterial communities were more similar between the two surface oceans than between the ocean and the overlying atmosphere. Likewise, Pacific and Atlantic atmospheric microbial communities were more similar to each other than to those in the ocean beneath. Atmospheric community composition over the Atlantic was dominated by terrestrial and specifically, dust-associated bacteria, whereas over the Pacific there was a higher prevalence and differential abundance of marine bacteria. Our findings highlight regional differences in long-range microbial exchange and dispersal between land, ocean, and atmosphere.

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Canesi, Marine, Eric Douville, Paolo Montagna, Marco Taviani, Jarosław Stolarski, Louise Bordier, Arnaud Dapoigny et al. "Differences in carbonate chemistry up-regulation of long-lived reef-building corals". Scientific Reports 13, n.º 1 (18 de julio de 2023). http://dx.doi.org/10.1038/s41598-023-37598-9.

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AbstractWith climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016–2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ωcf) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ωcf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus.

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Galand, Pierre E., Hans-Joachim Ruscheweyh, Guillem Salazar, Corentin Hochart, Nicolas Henry, Benjamin C. C. Hume, Pedro H. Oliveira et al. "Diversity of the Pacific Ocean coral reef microbiome". Nature Communications 14, n.º 1 (1 de junio de 2023). http://dx.doi.org/10.1038/s41467-023-38500-x.

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AbstractCoral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.

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Voolstra, Christian R., Benjamin C. C. Hume, Eric J. Armstrong, Guinther Mitushasi, Barbara Porro, Nicolas Oury, Sylvain Agostini et al. "Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation". npj Biodiversity 2, n.º 1 (7 de julio de 2023). http://dx.doi.org/10.1038/s44185-023-00020-8.

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AbstractTropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016–2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals—Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla—across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.

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Trainic, Miri, J. Michel Flores, Iddo Pinkas, Maria Luiza Pedrotti, Fabien Lombard, Guillaume Bourdin, Gabriel Gorsky et al. "Airborne microplastic particles detected in the remote marine atmosphere". Communications Earth & Environment 1, n.º 1 (diciembre de 2020). http://dx.doi.org/10.1038/s43247-020-00061-y.

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AbstractAnthropogenic pollution from marine microplastic particles is a growing concern, both as a source of toxic compounds, and because they can transport pathogens and other pollutants. Airborne microplastic particles were previously observed over terrestrial and coastal locations, but not in the remote ocean. Here, we collected ambient aerosol samples in the North Atlantic Ocean, including the remote marine atmosphere, during the Tara Pacific expedition in May-June 2016, and chemically characterized them using micro-Raman spectroscopy. We detected a range of airborne microplastics, including polystyrene, polyethylene, polypropylene, and poly-silicone compounds. Polyethylene and polypropylene were also found in seawater, suggesting local production of airborne microplastic particles. Terminal velocity estimations and back trajectory analysis support this conclusion. For technical reasons, only particles larger than 5 µm, at the upper end of a typical marine atmospheric size distribution, were analyzed, suggesting that our analyses underestimate the presence of airborne microplastic particles in the remote marine atmosphere.

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Reddy, Maggie M., Corentine Goossens, Yuxiang Zhou, Slimane Chaib, Delphine Raviglione, Florence Nicolè, Benjamin C. C. Hume et al. "Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean". Communications Earth & Environment 4, n.º 1 (8 de agosto de 2023). http://dx.doi.org/10.1038/s43247-023-00942-y.

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AbstractCoral reefs are considered one of the most emblematic ecosystems in our oceans, but their existence is increasingly threatened by climate change. In this study, natural populations of two reef-building coral genera, Pocillopora spp. and Porites spp., and one hydrocoral Millepora cf. platyphylla from two different marine provinces in the Pacific Ocean were investigated using a multi-omics approach as part of the Tara Pacific expedition. Here, we propose a standardised method consisting of a biphasic extraction method followed by metabolomics analysis using mass spectrometry for the lipidome and 1H nuclear magnetic resonance for hydrophilic metabolites. Our study assessed a broad range of the metabolome and is the first to identify and add 24 compounds by NMR and over 200 lipids by MS analyses for corals. Metabolic profiles were distinct among genera but not within genotypes of the cnidarian corals. Although endosymbiotic dinoflagellates of the family Symbiodiniaceae are known to play a central role in the metabolomic signature of the coral holobiont, they did not account for all differences. This suggests that a combined effect by different members of the coral holobiont and an interaction with the environment might be at play. Our study provides foundational knowledge on the coral holobiont metabolome.

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Carradec, Quentin, Julie Poulain, Emilie Boissin, Benjamin C. C. Hume, Christian R. Voolstra, Maren Ziegler, Stefan Engelen, Corinne Cruaud, Serge Planes y Patrick Wincker. "A framework for in situ molecular characterization of coral holobionts using nanopore sequencing". Scientific Reports 10, n.º 1 (28 de septiembre de 2020). http://dx.doi.org/10.1038/s41598-020-72589-0.

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Abstract Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 h. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.

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Noel, Benjamin, France Denoeud, Alice Rouan, Carol Buitrago-López, Laura Capasso, Julie Poulain, Emilie Boissin et al. "Pervasive tandem duplications and convergent evolution shape coral genomes". Genome Biology 24, n.º 1 (1 de junio de 2023). http://dx.doi.org/10.1186/s13059-023-02960-7.

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Abstract Background Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

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Veglia, Alex J., Kalia S. I. Bistolas, Christian R. Voolstra, Benjamin C. C. Hume, Hans-Joachim Ruscheweyh, Serge Planes, Denis Allemand et al. "Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes". Communications Biology 6, n.º 1 (1 de junio de 2023). http://dx.doi.org/10.1038/s42003-023-04917-9.

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AbstractEndogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

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