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  • 1
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    The Phaeodactylum genome reveals the evolutionary history of diatom genomes (2008)
    Nature Publishing Group
    In:  Nature, 456 . pp. 239-244.
    Details
    Publication Date: 2017-03-06
    Description: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth1, 2. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology3, 4, 5. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (approx40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.
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  • 2
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    Pan genome of the phytoplankton Emiliania underpins its global distribution (2013)
    Nature Publishing Group
    In:  Nature, 499 (7457). pp. 209-213.
    Details
    Publication Date: 2019-03-05
    Description: Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO 2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO 2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions. © 2013 Macmillan Publishers Limited. All rights reserved.
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  • 3
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    Abyssal undular vortices in the Eastern Mediterranean basin (2012)
    Nature Publishing Group
    In:  Nature Communications, 3 . p. 834.
    Details
    Publication Date: 2015-09-28
    Description: Abyssal temperature and velocity observations performed within the framework of the Neutrino Mediterranean Observatory, a project devoted to constructing a km3-scale underwater telescope for the detection of high-energy cosmic neutrinos, demonstrate cross-fertilization between subnuclear physics and experimental oceanography. Here we use data collected south of Sicily in the Ionian abyssal plain of the Eastern Mediterranean (EM) basin to show for the first time that abyssal vortices exist in the EM, at depths exceeding 2,500 m. The eddies consist of chains of near-inertially pulsating mesoscale cyclones/anticyclones. They are embedded in an abyssal current flowing towards North-Northwest. The paucity of existing data does not allow for an unambiguous determination of the vortex origin. A local generation mechanism seems probable, but a remote genesis cannot be excluded a priori. The presence of such eddies adds further complexity to the discussion of structure and evolution of water masses in the EM.
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  • 4
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    Rapid rates of growth and collapse of Monowai submarine volcano in the Kermadec Arc (2012)
    Nature Publishing Group
    In:  Nature Geoscience, 5 (7). pp. 510-515.
    Details
    Publication Date: 2017-02-20
    Description: Most of Earth’s volcanoes are under water. As a result of their relative inaccessibility, little is known of the structure and evolution of submarine volcanoes. Advances in navigation and sonar imaging techniques have made it possible to map submarine volcanoes in detail, and repeat surveys allow the identification of regions where the depth of the sea floor is actively changing. Here we report the results of a bathymetric survey of Monowai submarine volcano in the Tonga–Kermadec Arc, which we mapped twice within 14 days. We found marked differences in bathymetry between the two surveys, including an increase in seafloor depth up to 18.8 m and a decrease in depth up to 71.9 m. We attribute the depth increase to collapse of the volcano summit region and the decrease to growth of new lava cones and debris flows. Hydroacoustic T-wave data reveal a 5-day-long swarm of seismic events with unusually high amplitude between the surveys, which directly link the depth changes to explosive activity at the volcano. The collapse and growth rates implied by our data are extremely high, compared with measured long-term growth rates of the volcano, demonstrating the pulsating nature of submarine volcanism and highlighting the dynamic nature of the sea floor.
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  • 5
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    Synchronous basin-wide formation and redox-controlled preservation of a Mediterranean sapropel (2008)
    Nature Publishing Group
    In:  Nature Geoscience, 1 . pp. 606-610.
    Details
    Publication Date: 2017-02-22
    Description: Organic-rich sedimentary units called sapropels have formed repeatedly in the eastern Mediterranean Sea, in response to variations of solar radiation. Sapropel formation is due to a change either in the flux of organic matter to the sea floor from productivity changes or in preservation by bottom-water oxygen levels. However, the relative importance of surface-ocean productivity versus deep-water preservation for the formation of these organic-rich shale beds is still being debated, and conflicting interpretations are often invoked1, 2, 3, 4, 5, 6, 7. Here we analyse at high resolution the differences in the composition of the most recent sapropel, S1, in a suite of cores covering the entire eastern Mediterranean basin. We demonstrate that during the 4,000 years of sapropel formation, surface-water salinity was reduced and the deep eastern Mediterranean Sea, below 1,800 m depth, was devoid of oxygen. This resulted in the preferential basin-wide preservation of sapropel S1 with different characteristics above and below 1,800 m depth as a result of different redox conditions. We conclude that climate-induced stratification of the ocean may therefore contribute to enhanced preservation of organic matter in sapropels and potentially also in black shales.
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  • 6
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    Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes (2013)
    Nature Publishing Group
    In:  The ISME Journal, 7 . pp. 555-567.
    Details
    Publication Date: 2019-09-23
    Description: Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO2 in the seabed. The emission of CO2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO2-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO2 concentration, indicating that microbial activity and community structure are sensitive to CO2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (13–30 cm in depth) characterized by high CO2. Measurement of the potential sulfate reduction rate at pH conditions of 3–9 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO2-seep sedimentary environment; however, CO2 and pH in the deep-sea sediment were found to severely impact the activity and structure of the microbial community.
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  • 7
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    Biological and chemical sulfide oxidation in a Beggiatoa inhabited marine sediment (2007)
    Nature Publishing Group
    In:  The ISME Journal, 1 (4). pp. 341-353.
    Details
    Publication Date: 2016-05-25
    Description: The ecological niche of nitrate-storing Beggiatoa, and their contribution to the removal of sulfide were investigated in coastal sediment. With microsensors a clear suboxic zone of 2-10cm thick was identified, where neither oxygen nor free sulfide was detectable. In this zone most of the Beggiatoa were found, where they oxidize sulfide with internally stored nitrate. The sulfide input into the suboxic zone was dominated by an upward sulfide flux from deeper sediment, whereas the local production in the suboxic zone was much smaller. Despite their abundance, the calculated sulfide-oxidizing capacity of the Beggiatoa could account for only a small fraction of the total sulfide removal in the sediment. Consequently, most of the sulfide flux into the suboxic layer must have been removed by chemical processes, mainly by precipitation with Fe2+ and oxidation by Fe(III), which was coupled with a pH increase. The free Fe2+ diffusing upwards was oxidized by Mn(IV), resulting in a strong pH decrease. The nitrate storage capacity allows Beggiatoa to migrate randomly up and down in anoxic sediments with an accumulated gliding distance of 4m before running out of nitrate. We propose that the steep sulfide gradient and corresponding high sulfide flux, a typical characteristic of Beggiatoa habitats, is not needed for their metabolic performance, but rather used as a chemotactic cue by the highly motile filaments to avoid getting lost at depth in the sediment. Indeed sulfide is a repellant for Beggiatoa.
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  • 8
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    The acceleration of oceanic denitrification during deglacial warming (2013)
    Nature Publishing Group
    In:  Nature Geoscience, 6 (7). pp. 579-584.
    Details
    Publication Date: 2019-09-23
    Description: Over much of the ocean’s surface, productivity and growth are limited by a scarcity of bioavailable nitrogen. Sedimentary δ15N records spanning the last deglaciation suggest marked shifts in the nitrogen cycle during this time, but the quantification of these changes has been hindered by the complexity of nitrogen isotope cycling. Here we present a database of δ15N in sediments throughout the world’s oceans, including 2,329 modern seafloor samples, and 76 timeseries spanning the past 30,000 years. We show that the δ15N values of modern seafloor sediments are consistent with values predicted by our knowledge of nitrogen cycling in the water column. Despite many local deglacial changes, the globally averaged δ15N values of sinking organic matter were similar during the Last Glacial Maximum and Early Holocene. Considering the global isotopic mass balance, we explain these observations with the following deglacial history of nitrogen inventory processes. During the Last Glacial Maximum, the nitrogen cycle was near steady state. During the deglaciation, denitrification in the pelagic water column accelerated. The flooding of continental shelves subsequently increased denitrification at the seafloor, and denitrification reached near steady-state conditions again in the Early Holocene. We use a recent parameterization of seafloor denitrification to estimate a 30–120% increase in benthic denitrification between 15,000 and 8,000 years ago. Based on the similarity of globally averaged δ15N values during the Last Glacial Maximum and Early Holocene, we infer that pelagic denitrification must have increased by a similar amount between the two steady states.
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  • 9
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    Subduction of the oceanic Hikurangi Plateau and its impact on the Kermadec arc (2014)
    Nature Publishing Group
    In:  Nature Communications, 5 (Article 4923).
    Details
    Publication Date: 2019-09-23
    Description: Large igneous province subduction is a rare process on Earth. A modern example is the subduction of the oceanic Hikurangi Plateau beneath the southern Kermadec arc, offshore New Zealand. This segment of the arc has the largest total lava volume erupted and the highest volcano density of the entire Kermadec arc. Here we show that Kermadec arc lavas south of B32°S have elevated Pb and Sr and low Nd isotope ratios, which argues, together with increasing seafloor depth, forearc retreat and crustal thinning, for initial Hikurangi Plateau—Kermadec arc collision B250 km north of its present position. The combined data set indicates that a much larger portion of the Hikurangi Plateau (the missing Ontong Java Nui piece) than previously believed has already been subducted. Oblique plate convergence caused southward migration of the thickened and buoyant oceanic plateau crust, creating a buoyant ‘Hikurangi’ me´lange beneath the Moho that interacts with ascending arc melts.
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  • 10
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    Modern-style plate subduction preserved in the Palaeoproterozoic West African craton (2012)
    Nature Publishing Group
    In:  Nature Geoscience, 5 (1). pp. 60-65.
    Details
    Publication Date: 2019-08-28
    Description: The timing of onset of modern-style plate tectonics is debated. The apparent lack of blueschist metamorphism--a key indicator of modern plate subduction--in rocks aged more than about 1 billion years calls into question the existence of plate tectonics during the Archaean and Palaeoproterozoic eras. Instead, plate tectonics and subduction could have either not occurred at that time, or could have proceeded differently owing to warmer conditions in the early Earth mantle. Here we use thermodynamic models to investigate the formation conditions of metamorphic minerals in the 2.2-2.0Gyr old West African metamorphic province. We find a record of blueschist metamorphism in these rocks. We show that minerals such as chlorite and phengite formed at high pressures of 10-12 kbar, low temperatures of 400-450°C and under a geothermal gradient of 10-12°Ckm-1. These conditions are typical of modern subduction zones. We therefore suggest that modern-style plate tectonics existed during the Palaeoproterozoic era. We conclude that ancient blueschist metamorphism may exist in other parts of the world, but the identification of these rocks has so far been hampered by methodological problems associated with deciphering their pressure and temperature evolution.
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