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  • Nature Publishing Group
  • 2015-2019  (63)
  • 2010-2014
  • 1990-1994
  • 1985-1989
  • 2015  (63)
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  • 2015-2019  (63)
  • 2010-2014
  • 1990-1994
  • 1985-1989
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  • 1
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    Dynamic feeder dyke systems in basaltic volcanoes: the exceptional example o fthe 1809 Etna eruption (Italy) (2015)
    Nature Publishing Group
    Details
    Publication Date: 2017-04-04
    Description: In this paper, we describe the 1809 eruption of Mt. Etna, Italy, which represents one historical rare case in which it is possible to observe details of the internal structure of the feeder system. This is possible thanks to the presence of two large pit craters located in the middle of the eruptive fracture field that allow studying a section of the shallow feeder system. Along the walls of one of these craters, we analysed well-exposed cross sections of the uppermost 15–20 m of the feeder system and related volcanic products. Here, we describe the structure, morphology and lithology of this portion of the 1809 feeder system, including the host rock which conditioned the propagation of the dyke, and compare the results with other recent eruptions. Finally, we propose the dynamic model of the magma behaviour inside a laterally-propagating feeder dyke, demonstrating how this dynamic triggered important changes in the eruptive style (from effusive/Strombolian to phreatomagmatic) during the same eruption. Our results are also useful for hazard assessment related to the development of flank eruptions, potentially the most hazardous type of eruption from basaltic volcanoes in densely urbanized areas, such as Mt. Etna.
    Description: Published
    Description: 1-11
    Description: 2T. Tettonica attiva
    Description: 2V. Dinamiche di unrest e scenari pre-eruttivi
    Description: 3V. Dinamiche e scenari eruttivi
    Description: 4V. Vulcani e ambiente
    Description: 6A. Monitoraggio ambientale, sicurezza e territorio
    Description: N/A or not JCR
    Description: open
    Keywords: feeder dyke ; basaltic volcanoes ; flank eruptions ; Etna ; volcanic hazards ; sill ; volcanic rift ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas ; 04. Solid Earth::04.08. Volcanology::04.08.04. Thermodynamics ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk ; 05. General::05.02. Data dissemination::05.02.03. Volcanic eruptions
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Recent Arctic tundra fire initiates widespread thermokarst development (2015)
    Nature Publishing Group
    In:  EPIC3Scientific Reports, Nature Publishing Group, 5, pp. 15865, ISSN: 2045-2322
    Details
    Publication Date: 2015-10-31
    Description: Fire-induced permafrost degradation is well documented in boreal forests, but the role of fires in initiating thermokarst development in Arctic tundra is less well understood. Here we show that Arctic tundra fires may induce widespread thaw subsidence of permafrost terrain in the first seven years following the disturbance. Quantitative analysis of airborne LiDAR data acquired two and seven years post-fire, detected permafrost thaw subsidence across 34% of the burned tundra area studied, compared to less than 1% in similar undisturbed, ice-rich tundra terrain units. The variability in thermokarst development appears to be influenced by the interaction of tundra fire burn severity and near-surface, ground-ice content. Subsidence was greatest in severely burned, ice-rich upland terrain (yedoma), accounting for ~50% of the detected subsidence, despite representing only 30% of the fire disturbed study area. Microtopography increased by 340% in this terrain unit as a result of ice wedge degradation. Increases in the frequency, magnitude, and severity of tundra fires will contribute to future thermokarst development and associated landscape change in Arctic tundra regions.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 3
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    Growth of a deep-water, predatory fish is influenced by the productivity of a boundary current system (2015)
    Nature Publishing Group
    In:  EPIC3Nature Scientific Reports, Nature Publishing Group
    Details
    Publication Date: 2017-01-20
    Description: The effects of climate change on predatory fishes in deep shelf areas are difficult to predict because complex processes may govern food availability and temperature at depth. We characterised the net impact of recent environmental changes on hapuku (Polyprion oxygeneios), an apex predator found in continental slope habitats (〉200 m depth) by using dendrochronology techniques to develop a multi-decadal record of growth from otoliths. Fish were sampled off temperate south-western Australia, a region strongly influenced by the Leeuwin Current, a poleward-flowing, eastern boundary current. The common variance among individual growth records was relatively low (3.4%), but the otolith chronology was positively correlated (r = 0.61, p 〈 0.02) with sea level at Fremantle, a proxy for the strength of the Leeuwin Current. The Leeuwin Current influences the primary productivity of shelf ecosystems, with a strong current favouring growth in hapuku. Leeuwin Current strength is predicted to decline under climate change models and this study provides evidence that associated productivity changes may flow through to higher trophic levels even in deep water habitats.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
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    Acidification reduced growth rate but not swimming speed of larval sea urchins (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 5 (2015): 9764, doi:10.1038/srep09764.
    Description: Swimming behaviors of planktonic larvae impact dispersal and population dynamics of many benthic marine invertebrates. This key ecological function is modulated by larval development dynamics, biomechanics of the resulting morphology, and behavioral choices. Studies on ocean acidification effects on larval stages have yet to address this important interaction between development and swimming under environmentally-relevant flow conditions. Our video motion analysis revealed that pH covering present and future natural variability (pH 8.0, 7.6 and 7.2) did not affect age-specific swimming of larval green urchin Strongylocentrotus droebachiensis in still water nor in shear, despite acidified individuals being significantly smaller in size (reduced growth rate). This maintenance of speed and stability in shear was accompanied by an overall change in size-corrected shape, implying changes in swimming biomechanics. Our observations highlight strong evolutionary pressure to maintain swimming in a varying environment and the plasticity in larval responses to environmental change.
    Description: K.C. was supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution (WHOI), with funding provided by the Coastal Ocean Institute, the Croucher Foundation, and the Royal Swedish Academy of Sciences. S.D. was financially supported by the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg (http://www.cemeb.science.gu.se/) and a Linnaeus grant from the Swedish Research Councils VR and Formas. Additional funding was provided from the European Seventh Framework Programme under grant agreement 265847.
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Irreversibly increased nitrogen fixation in Trichodesmium experimentally adapted to elevated carbon dioxide (2015)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    Description: This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 6 (2015): 8155, doi:10.1038/ncomms9155.
    Description: Nitrogen fixation rates of the globally distributed, biogeochemically important marine cyanobacterium Trichodesmium increase under high carbon dioxide (CO2) levels in short-term studies due to physiological plasticity. However, its long-term adaptive responses to ongoing anthropogenic CO2 increases are unknown. Here we show that experimental evolution under extended selection at projected future elevated CO2 levels results in irreversible, large increases in nitrogen fixation and growth rates, even after being moved back to lower present day CO2 levels for hundreds of generations. This represents an unprecedented microbial evolutionary response, as reproductive fitness increases acquired in the selection environment are maintained after returning to the ancestral environment. Constitutive rate increases are accompanied by irreversible shifts in diel nitrogen fixation patterns, and increased activity of a potentially regulatory DNA methyltransferase enzyme. High CO2-selected cell lines also exhibit increased phosphorus-limited growth rates, suggesting a potential advantage for this keystone organism in a more nutrient-limited, acidified future ocean.
    Description: Grant support was provided by U.S. National Science Foundation OCE 1260490 and OCE 1143760 to D.A.H., E.A.W., and F.-X.F, and OCE 1260233, OCE OA 1220484, and G.B. Moore Foundation 3782 and 3934 to M.A.S.© The Author(s), [year].
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Minimum entropy decomposition : unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 968–979, doi:10.1038/ismej.2014.195.
    Description: Molecular microbial ecology investigations often employ large marker gene datasets, for example, ribosomal RNAs, to represent the occurrence of single-cell genomes in microbial communities. Massively parallel DNA sequencing technologies enable extensive surveys of marker gene libraries that sometimes include nearly identical sequences. Computational approaches that rely on pairwise sequence alignments for similarity assessment and de novo clustering with de facto similarity thresholds to partition high-throughput sequencing datasets constrain fine-scale resolution descriptions of microbial communities. Minimum Entropy Decomposition (MED) provides a computationally efficient means to partition marker gene datasets into ‘MED nodes’, which represent homogeneous operational taxonomic units. By employing Shannon entropy, MED uses only the information-rich nucleotide positions across reads and iteratively partitions large datasets while omitting stochastic variation. When applied to analyses of microbiomes from two deep-sea cryptic sponges Hexadella dedritifera and Hexadella cf. dedritifera, MED resolved a key Gammaproteobacteria cluster into multiple MED nodes that are specific to different sponges, and revealed that these closely related sympatric sponge species maintain distinct microbial communities. MED analysis of a previously published human oral microbiome dataset also revealed that taxa separated by less than 1% sequence variation distributed to distinct niches in the oral cavity. The information theory-guided decomposition process behind the MED algorithm enables sensitive discrimination of closely related organisms in marker gene amplicon datasets without relying on extensive computational heuristics and user supervision.
    Description: AME was supported by a G. Unger Vetlesen Foundation grant to the Marine Biological Laboratory and the Alfred P Sloan Foundation.
    Repository Name: Woods Hole Open Access Server
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  • 7
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    The Kallisti Limnes, carbon dioxide-accumulating subsea pools (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 5 (2015): 12152, doi:10.1038/srep12152.
    Description: Natural CO2 releases from shallow marine hydrothermal vents are assumed to mix into the water column, and not accumulate into stratified seafloor pools. We present newly discovered shallow subsea pools located within the Santorini volcanic caldera of the Southern Aegean Sea, Greece, that accumulate CO2 emissions from geologic reservoirs. This type of hydrothermal seafloor pool, containing highly concentrated CO2, provides direct evidence of shallow benthic CO2 accumulations originating from sub-seafloor releases. Samples taken from within these acidic pools are devoid of calcifying organisms, and channel structures among the pools indicate gravity driven flow, suggesting that seafloor release of CO2 at this site may preferentially impact benthic ecosystems. These naturally occurring seafloor pools may provide a diagnostic indicator of incipient volcanic activity and can serve as an analog for studying CO2 leakage and benthic accumulations from subsea carbon capture and storage sites.
    Description: This research was supported by the Eurofleets Caldera 2012 Project (EU), a NASA Astrobiology Science & Technology for Exploring Planets grant #NNX09AB76G (USA), a CAREER Award grant #OCE-0955674 to R. Camilli from the National Science Foundation (USA), and IPGP (France).
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 6 (2015): 8933, doi:10.1038/ncomms9933.
    Description: Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.
    Description: his project is funded in part by the Gordon and Betty Moore Foundation Grant GBMF2609, National Science Foundation Grants OCE1038006 (G.J.D.) and OCE-1038055 (J.A.B), National Natural Science Foundation of China (grant no. 41506163), Natural Science Foundation of Guangdong Province (grant no. 2014A030310056), Shenzhen City (grant no. JCY20140828163633985 and KQCX2015032416053646) and SZU (grant no. 000066) (M.L.)
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Monitoring brain activity with protein voltage and calcium sensors (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 5 (2015): 10212, doi:10.1038/srep10212.
    Description: Understanding the roles of different cell types in the behaviors generated by neural circuits requires protein indicators that report neural activity with high spatio-temporal resolution. Genetically encoded fluorescent protein (FP) voltage sensors, which optically report the electrical activity in distinct cell populations, are, in principle, ideal candidates. Here we demonstrate that the FP voltage sensor ArcLight reports odor-evoked electrical activity in the in vivo mammalian olfactory bulb in single trials using both wide-field and 2-photon imaging. ArcLight resolved fast odorant-responses in individual glomeruli, and distributed odorant responses across a population of glomeruli. Comparisons between ArcLight and the protein calcium sensors GCaMP3 and GCaMP6f revealed that ArcLight had faster temporal kinetics that more clearly distinguished activity elicited by individual odorant inspirations. In contrast, the signals from both GCaMPs were a saturating integral of activity that returned relatively slowly to the baseline. ArcLight enables optical electrophysiology of mammalian neuronal population activity in vivo.
    Description: Supported by US NIH DC005259, WCI 2009-003 from the National Research Foundation of Korea, a James Hudson Brown – Alexander Brown Coxe fellowship from Yale University, and a Ruth L. Kirschstein National Research Service Award DC012981.
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Seasonality in submesoscale turbulence (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 6 (2015): 6862, doi:10.1038/ncomms7862.
    Description: Although the strongest ocean surface currents occur at horizontal scales of order 100 km, recent numerical simulations suggest that flows smaller than these mesoscale eddies can achieve important vertical transports in the upper ocean. These submesoscale flows, 1–100 km in horizontal extent, take heat and atmospheric gases down into the interior ocean, accelerating air–sea fluxes, and bring deep nutrients up into the sunlit surface layer, fueling primary production. Here we present observational evidence that submesoscale flows undergo a seasonal cycle in the surface mixed layer: they are much stronger in winter than in summer. Submesoscale flows are energized by baroclinic instabilities that develop around geostrophic eddies in the deep winter mixed layer at a horizontal scale of order 1–10 km. Flows larger than this instability scale are energized by turbulent scale interactions. Enhanced submesoscale activity in the winter mixed layer is expected to achieve efficient exchanges with the permanent thermocline below.
    Description: J.C. and R.F. acknowledge financial support under grants ONR-N00014-09-1-0458 and NSF-OCE-1233832; J.M.K. under grants ONR-N00014-11-1-0165 and NSERC-327920-2006; J.G. under grant ONR-N00014-12-1-0105.
    Repository Name: Woods Hole Open Access Server
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  • 11
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    Multi-jet propulsion organized by clonal development in a colonial siphonophore (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 6 (2015): 8158, doi:10.1038/ncomms9158.
    Description: Physonect siphonophores are colonial cnidarians that are pervasive predators in many neritic and oceanic ecosystems. Physonects employ multiple, clonal medusan individuals, termed nectophores, to propel an aggregate colony. Here we show that developmental differences between clonal nectophores of the physonect Nanomia bijuga produce a division of labour in thrust and torque production that controls direction and magnitude of whole-colony swimming. Although smaller and less powerful, the position of young nectophores near the apex of the nectosome allows them to dominate torque production for turning, whereas older, larger and more powerful individuals near the base of the nectosome contribute predominantly to forward thrust production. The patterns we describe offer insight into the biomechanical success of an ecologically important and widespread colonial animal group, but, more broadly, provide basic physical understanding of a natural solution to multi-engine organization that may contribute to the expanding field of underwater-distributed propulsion vehicle design.
    Description: This work is a product of US National Science Foundation grant OCE-1155084 to K.R.S. and CBET-1511721 to J.H.C., OCE-1061182 to S.P.C. and OCE-1061628 to J.O.D.
    Repository Name: Woods Hole Open Access Server
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  • 12
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    Suction-based propulsion as a basis for efficient animal swimming (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 6 (2015): 8790, doi:10.1038/ncomms9790.
    Description: A central and long-standing tenet in the conceptualization of animal swimming is the idea that propulsive thrust is generated by pushing the surrounding water rearward. Inherent in this perspective is the assumption that locomotion involves the generation of locally elevated pressures in the fluid to achieve the expected downstream push of the surrounding water mass. Here we show that rather than pushing against the surrounding fluid, efficient swimming animals primarily pull themselves through the water via suction. This distinction is manifested in dominant low-pressure regions generated in the fluid surrounding the animal body, which are observed by using particle image velocimetry and a pressure calculation algorithm applied to freely swimming lampreys and jellyfish. These results suggest a rethinking of the evolutionary adaptations observed in swimming animals as well as the mechanistic basis for bio-inspired and biomimetic engineered vehicles.
    Description: Funding for this research was provided by the US Office of Naval Research and the US National Science Foundation.
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  • 13
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    High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © International Society for Microbial Ecology, 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISMEJournal 9 (2015): 2725–2739, doi:10.1038/ismej.2015.68.
    Description: The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 μM) or 10x (700 μM) the ocean surface water concentrations yielded positive growth in 4–6% of replicate dilutions, whereas 〈1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enriched with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them.
    Description: This research was funded by the Gordon and Betty Moore Foundation through Grant GBMF3298 to DJR and EFD, GBMF #3777 (to EFD) and NSF Science and Technology Center grant EF0424599 (to EFD), and the Simons Foundation (to EFD and DR).
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  • 14
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    Profiling molecular and behavioral circadian rhythms in the non-symbiotic sea anemone Nematostella vectensis (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 5 (2015): 11418, doi:10.1038/srep11418.
    Description: Endogenous circadian clocks are poorly understood within early-diverging animal lineages. We have characterized circadian behavioral patterns and identified potential components of the circadian clock in the starlet sea anemone, Nematostella vectensis: a model cnidarian which lacks algal symbionts. Using automatic video tracking we showed that Nematostella exhibits rhythmic circadian locomotor activity, which is persistent in constant dark, shifted or disrupted by external dark/light cues and maintained the same rate at two different temperatures. This activity was inhibited by a casein kinase 1δ/ε inhibitor, suggesting a role for CK1 homologue(s) in Nematostella clock. Using high-throughput sequencing we profiled Nematostella transcriptomes over 48 hours under a light-dark cycle. We identified 180 Nematostella diurnally-oscillated transcripts and compared them with previously established databases of adult and larvae of the symbiotic coral Acropora millepora, revealing both shared homologues and unique rhythmic genes. Taken together, this study further establishes Nematostella as a non-symbiotic model organism to study circadian rhythms and increases our understanding about the fundamental elements of circadian regulation and their evolution within the Metazoa.
    Description: This work was supported by the Israel-US Binational Science Foundation to OL and AMT (Award 2011187). Additional support was provided by the WHOI Early Career Scientist Award to AMT.
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  • 15
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    A TEX86 surface sediment database and extended Bayesian calibration (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Data 2 (2015): 150029, doi:10.1038/sdata.2015.29.
    Description: Quantitative estimates of past temperature changes are a cornerstone of paleoclimatology. For a number of marine sediment-based proxies, the accuracy and precision of past temperature reconstructions depends on a spatial calibration of modern surface sediment measurements to overlying water temperatures. Here, we present a database of 1095 surface sediment measurements of TEX86, a temperature proxy based on the relative cyclization of marine archaeal glycerol dialkyl glycerol tetraether (GDGT) lipids. The dataset is archived in a machine-readable format with geospatial information, fractional abundances of lipids (if available), and metadata. We use this new database to update surface and subsurface temperature calibration models for TEX86 and demonstrate the applicability of the TEX86 proxy to past temperature prediction. The TEX86 database confirms that surface sediment GDGT distribution has a strong relationship to temperature, which accounts for over 70% of the variance in the data. Future efforts, made possible by the data presented here, will seek to identify variables with secondary relationships to GDGT distributions, such as archaeal community composition.
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  • 16
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    Response of plant nutrient stoichiometry to fertilization varied with plant tissues in a tropical forest (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 5 (2015): 14605, doi:10.1038/srep14605.
    Description: Plant N:P ratios are widely used as indices of nutrient limitation in terrestrial ecosystems, but the response of these metrics in different plant tissues to altered N and P availability and their interactions remains largely unclear. We evaluated changes in N and P concentrations, N:P ratios of new leaves (〈1 yr), older leaves (〉1 yr), stems and mixed fine roots of seven species after 3-years of an N and P addition experiment in a tropical forest. Nitrogen addition only increased fine root N concentrations. P addition increased P concentrations among all tissues. The N × P interaction reduced leaf and stem P concentrations, suggesting a negative effect of N addition on P concentrations under P addition. The reliability of using nutrient ratios as indices of soil nutrient availability varied with tissues: the stoichiometric metrics of stems and older leaves were more responsive indicators of changed soil nutrient availability than those of new leaves and fine roots. However, leaf N:P ratios can be a useful indicator of inter-specific variation in plant response to nutrients availability. This study suggests that older leaf is a better choice than other tissues in the assessment of soil nutrient status and predicting plant response to altered nutrients using nutrients ratios.
    Description: This work was funded by Natural Science Foundation of China (31300419), NSFC-Guangdong Joint Project (U1131001), National Basic Research Program of China (2011CB403200), Innovation Foundation of Guangdong Forestry (2012KJCX013-02, 2014KJCX021-03) and the “Strategic Priority Research Program” of the Chinese Academy of Sciences (XDA05070307).
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  • 17
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    Polychromatic polarization microscope : bringing colors to a colorless world (2015)
    Nature Publishing Group
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 5 (2015): 17340, doi:10.1038/srep17340.
    Description: Interference of two combined white light beams produces Newton colors if one of the beams is retarded relative to the other by from 400 nm to 2000 nm. In this case the corresponding interfering spectral components are added as two scalars at the beam combination. If the retardance is below 400 nm the two-beam interference produces grey shades only. The interference colors are widely used for analyzing birefringent samples in mineralogy. However, many of biological structures have retardance 〈100 nm. Therefore, cells and tissues under a regular polarization microscope are seen as grey image, which contrast disappears at certain orientations. Here we are proposing for the first time using vector interference of polarized light in which the full spectrum colors are created at retardance of several nanometers, with the hue determined by orientation of the birefringent structure. The previously colorless birefringent images of organelles, cells, and tissues become vividly colored. This approach can open up new possibilities for the study of biological specimens with weak birefringent structures, diagnosing various diseases, imaging low birefringent crystals, and creating new methods for controlling colors of the light beam.
    Description: This publication was made possible by Grant Number R01-GM101701 from the National Institute of General Medical Sciences, National Institutes of Health.
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    Shallow methylmercury production in the marginal sea ice zone of the central Arctic Ocean (2015)
    Nature Publishing Group
    In:  EPIC3Scientific Reports, Nature Publishing Group, 5(10318), ISSN: (online): 2045-2322
    Details
    Publication Date: 2016-11-29
    Description: Methylmercury (MeHg) is a neurotoxic compound that threatens wildlife and human health across the Arctic region. Though much is known about the source and dynamics of its inorganic mercury (Hg) precursor, the exact origin of the high MeHg concentrations in Arctic biota remains uncertain. Arctic coastal sediments, coastal marine waters and surface snow are known sites for MeHg production. Observations on marine Hg dynamics, however, have been restricted to the Canadian Archipelago and the Beaufort Sea (〈79°N). Here we present the first central Arctic Ocean (79–90°N) profiles for total mercury (tHg) and MeHg. We find elevated tHg and MeHg concentrations in the marginal sea ice zone (81–85°N). Similar to other open ocean basins, Arctic MeHg concentration maxima also occur in the pycnocline waters, but at much shallower depths (150–200 m). The shallow MeHg maxima just below the productive surface layer possibly result in enhanced biological uptake at the base of the Arctic marine food web and may explain the elevated MeHg concentrations in Arctic biota. We suggest that Arctic warming, through thinning sea ice, extension of the seasonal sea ice zone, intensified surface ocean stratification and shifts in plankton ecodynamics, will likely lead to higher marine MeHg production.
    Repository Name: EPIC Alfred Wegener Institut
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    Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton (2015)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © International Society for Microbial Ecology, 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 1365–1377, doi:10.1038/ismej.2014.221.
    Description: Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers.
    Description: This research was supported by a Marie Curie International Incoming Fellowship FUNSEXDEPHYND to PvD within the 7th European Community Framework Programme, FONDECYT Projects 1110575 (to PvD) and 312004 (to DM-F), the French Agence Nationale de la Recherche/Investissements d’Avenir Grants POSEIDON and OCEANOMICS (Grant No. ANR-11-BTBR-0008 to CdV and IP), the European ERA-net program BiodivERsA under the BioMarks project (to EMB), funding from NASA and NSF (Grants NNX11AF55G and EF-0424599 to DMG and SD), the Genoscope 2007-2008 sequencing initiative and the PACES research program of the Alfred Wegener Helmholtz Institute Helmhotz Centre for Polar and Marine Research.
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    Satellite remote sensing data can be used to model marine microbial metabolite turnover (2015)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 166–179, doi:10.1038/ismej.2014.107.
    Description: Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes’ predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value 〈10−6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ~3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology.
    Description: This work was supported by the US Department of Energy under Contract DE-AC02-06CH11357 and by the Howard Hughes Medical Institute.
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    A single genus in the gut microbiome reflects host preference and specificity (2015)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 90–100, doi:10.1038/ismej.2014.97.
    Description: Delineating differences in gut microbiomes of human and animal hosts contributes towards understanding human health and enables new strategies for detecting reservoirs of waterborne human pathogens. We focused upon Blautia, a single microbial genus that is important for nutrient assimilation as preliminary work suggested host-related patterns within members of this genus. In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping. Our analysis revealed 13 host-specific oligotypes that occurred exclusively in fecal samples of humans (three oligotypes), swine (six oligotypes), cows (one oligotype), deer (one oligotype), or chickens (two oligotypes). We identified an additional 171 oligotypes that exhibited differential abundance patterns among all the host species. Blautia oligotypes in the human population obtained from sewage and fecal samples displayed remarkable continuity. Oligotypes from only 10 Brazilian human fecal samples collected from individuals in a rural village encompassed 97% of all Blautia oligotypes found in a Brazilian sewage sample from a city of three million people. Further, 75% of the oligotypes in Brazilian human fecal samples matched those in US sewage samples, implying that a universal set of Blautia strains may be shared among culturally and geographically distinct human populations. Such strains can serve as universal markers to assess human fecal contamination in environmental samples. Our results indicate that host-specificity and host-preference patterns of organisms within this genus are driven by host physiology more than dietary habits.
    Description: This study was funded by the NIH grant R01AI091829-01A1 to SLM.
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    A daily global mesoscale ocean eddy dataset from satellite altimetry (2015)
    Nature Publishing Group
    In:  Scientific Data, 2 (Art. Nr. 150028).
    Details
    Publication Date: 2017-10-24
    Description: Mesoscale ocean eddies are ubiquitous coherent rotating structures of water with radial scales on the order of 100 kilometers. Eddies play a key role in the transport and mixing of momentum and tracers across the World Ocean. We present a global daily mesoscale ocean eddy dataset that contains ~45 million mesoscale features and 3.3 million eddy trajectories that persist at least two days as identified in the AVISO dataset over a period of 1993–2014. This dataset, along with the open-source eddy identification software, extract eddies with any parameters (minimum size, lifetime, etc.), to study global eddy properties and dynamics, and to empirically estimate the impact eddies have on mass or heat transport. Furthermore, our open-source software may be used to identify mesoscale features in model simulations and compare them to observed features. Finally, this dataset can be used to study the interaction between mesoscale ocean eddies and other components of the Earth System.
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    Discovery of microbial natural products by activation of silent biosynthetic gene clusters (2015)
    Nature Publishing Group
    In:  Nature Reviews Microbiology, 13 (8). pp. 509-523.
    Details
    Publication Date: 2020-06-23
    Description: Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities and a wide variety of applications in medicine and agriculture, such as the treatment of infectious diseases and cancer, and the prevention of crop damage. Genomics has revealed that many microorganisms have far greater potential to produce specialized metabolites than was thought from classic bioactivity screens; however, realizing this potential has been hampered by the fact that many specialized metabolite biosynthetic gene clusters (BGCs) are not expressed in laboratory cultures. In this Review, we discuss the strategies that have been developed in bacteria and fungi to identify and induce the expression of such silent BGCs, and we briefly summarize methods for the isolation and structural characterization of their metabolic products.
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    Littoral lichens as a novel source of potentially bioactive Actinobacteria (2015)
    Nature Publishing Group
    In:  Scientific Reports, 5 (1).
    Details
    Publication Date: 2017-12-21
    Description: Cultivable Actinobacteria are the largest source of microbially derived bioactive molecules. The high demand for novel antibiotics highlights the need for exploring novel sources of these bacteria. Microbial symbioses with sessile macro-organisms, known to contain bioactive compounds likely of bacterial origin, represent an interesting and underexplored source of Actinobacteria. We studied the diversity and potential for bioactive-metabolite production of Actinobacteria associated with two marine lichens ( Lichina confinis and L. pygmaea ; from intertidal and subtidal zones) and one littoral lichen ( Roccella fuciformis ; from supratidal zone) from the Brittany coast (France), as well as the terrestrial lichen Collema auriforme (from a riparian zone, Austria). A total of 247 bacterial strains were isolated using two selective media. Isolates were identified and clustered into 101 OTUs (98% identity) including 51 actinobacterial OTUs. The actinobacterial families observed were: Brevibacteriaceae, Cellulomonadaceae, Gordoniaceae, Micrococcaceae, Mycobacteriaceae, Nocardioidaceae, Promicromonosporaceae, Pseudonocardiaceae, Sanguibacteraceae and Streptomycetaceae. Interestingly, the diversity was most influenced by the selective media rather than lichen species or the level of lichen thallus association. The potential for bioactive-metabolite biosynthesis of the isolates was confirmed by screening genes coding for polyketide synthases types I and II. These results show that littoral lichens are a source of diverse potentially bioactive Actinobacteria.
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    Water column methanotrophy controlled by a rapid oceanographic switch (2015)
    Nature Publishing Group
    In:  Nature Geoscience, 8 (5). pp. 378-382.
    Details
    Publication Date: 2020-11-23
    Description: Large amounts of the greenhouse gas methane are released from the seabed to the water column1, where it may be consumed by aerobic methanotrophic bacteria2. The size and activity of methanotrophic communities, which determine the amount of methane consumed in the water column, are thought to be mainly controlled by nutrient and redox dynamics3–7. Here, we report repeated measurements of methanotrophic activity and community size at methane seeps west of Svalbard, and relate them to physical water mass properties and modelled ocean currents. We show that cold bottom water, which contained a large number of aerobic methanotrophs, was displaced by warmer water with a considerably smaller methanotrophic community within days. Ocean current simulations using a global ocean/sea-ice model suggest that this water mass exchange is consistent with short-term variations in the meandering West Spitsbergen Current. We conclude that the shift from an offshore to a nearshore position of the current can rapidly and severely reduce methanotrophic activity in the water column. Strong fluctuating currents are common at many methane seep systems globally, and we suggest that they affect methane oxidation in the water column at other sites, too.
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    Biological ramifications of climate-change-mediated oceanic multi-stressors (2015)
    Nature Publishing Group
    In:  Nature Climate Change, 5 (1). pp. 71-79.
    Details
    Publication Date: 2017-02-24
    Description: Climate change is altering oceanic conditions in a complex manner, and the concurrent amendment of multiple properties will modify environmental stress for primary producers. So far, global modelling studies have focused largely on how alteration of individual properties will affect marine life. Here, we use global modelling simulations in conjunction with rotated factor analysis to express model projections in terms of regional trends in concomitant changes to biologically influential multi-stressors. Factor analysis demonstrates that regionally distinct patterns of complex oceanic change are evident globally. Preliminary regional assessments using published evidence of phytoplankton responses to complex change reveal a wide range of future responses to interactive multi-stressors with 〈20–300% shifts in phytoplankton physiological rates, and many unexplored potential interactions. In a future ocean, provinces will encounter different permutations of change that will probably alter the dominance of key phytoplankton groups and modify regional productivity, ecosystem structure and biogeochemistry. Consideration of regionally distinct multi-stressor patterns can help guide laboratory and field studies as well as the interpretation of interactive multi-stressors in global models.
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    Lessons learned from ocean acidification research (2015)
    Nature Publishing Group
    In:  Nature Climate Change, 5 (1). pp. 12-14.
    Details
    Publication Date: 2017-04-13
    Description: Reflection on the rapidly growing field of ocean acidification research highlights priorities for future research on the changing ocean.
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    Continental crust generated in oceanic arcs (2015)
    Nature Publishing Group
    In:  Nature Geoscience, 8 (4). pp. 321-327.
    Details
    Publication Date: 2017-12-19
    Description: Thin oceanic crust is formed by decompression melting of the upper mantle at mid-ocean ridges, but the origin of the thick and buoyant continental crust is enigmatic. Juvenile continental crust may form from magmas erupted above intraoceanic subduction zones, where oceanic lithosphere subducts beneath other oceanic lithosphere. However, it is unclear why the subduction of dominantly basaltic oceanic crust would result in the formation of andesitic continental crust at the surface. Here we use geochemical and geophysical data to reconstruct the evolution of the Central American land bridge, which formed above an intra-oceanic subduction system over the past 70Myr. We find that the geochemical signature of erupted lavas evolved from basaltic to andesitic about 10Myr ago - coincident with the onset of subduction of more oceanic crust that originally formed above the Galápagos mantle plume. We also find that seismic P-waves travel through the crust at velocities intermediate between those typically observed for oceanic and continental crust. We develop a continentality index to quantitatively correlate geochemical composition with the average P-wave velocity of arc crust globally. We conclude that although the formation and evolution of continents may involve many processes, melting enriched oceanic crust within a subduction zone - a process probably more common in the Archaean - can produce juvenile continental crust.
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    Evolution of extreme stomach pH in bilateria inferred from gastric alkalization mechanisms in basal deuterostomes (2015)
    Nature Publishing Group
    In:  Scientific Reports, 5 (10421).
    Details
    Publication Date: 2017-12-19
    Description: The stomachs of most vertebrates operate at an acidic pH of 2 generated by the gastric H+/K+-ATPase located in parietal cells. The acidic pH in stomachs of vertebrates is believed to aid digestion and to protect against environmental pathogens. Little attention has been placed on whether acidic gastric pH regulation is a vertebrate character or a deuterostome ancestral trait. Here, we report alkaline conditions up to pH 10.5 in the larval digestive systems of ambulacraria (echinoderm + hemichordate), the closest relative of the chordate. Microelectrode measurements in combination with specific inhibitors for acid-base transporters and ion pumps demonstrated that the gastric alkalization machinery in sea urchin larvae is mainly based on direct H+ secretion from the stomach lumen and involves a conserved set of ion pumps and transporters. Hemichordate larvae additionally utilized HCO 3- transport pathways to generate even more alkaline digestive conditions. Molecular analyses in combination with acidification experiments supported these findings and identified genes coding for ion pumps energizing gastric alkalization. Given that insect larval guts were also reported to be alkaline, our discovery raises the hypothesis that the bilaterian ancestor utilized alkaline digestive system while the vertebrate lineage has evolved a strategy to strongly acidify their stomachs.
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    The effect of nutrients on carbon and nitrogen fixation by the UCYN-A–haptophyte symbiosis (2015)
    Nature Publishing Group
    In:  The ISME Journal, 9 (7). pp. 1635-1647.
    Details
    Publication Date: 2015-07-16
    Description: Symbiotic relationships between phytoplankton and N-2-fixing microorganisms play a crucial role in marine ecosystems. The abundant and widespread unicellular cyanobacteria group A (UCYN-A) has recently been found to live symbiotically with a haptophyte. Here, we investigated the effect of nitrogen (N), phosphorus (P), iron (Fe) and Saharan dust additions on nitrogen (N-2) fixation and primary production by the UCYN-A-haptophyte association in the subtropical eastern North Atlantic Ocean using nifH expression analysis and stable isotope incubations combined with single-cell measurements. N-2 fixation by UCYN-A was stimulated by the addition of Fe and Saharan dust, although this was not reflected in the nifH expression. CO2 fixation by the haptophyte was stimulated by the addition of ammonium nitrate as well as Fe and Saharan dust. Intriguingly, the single-cell analysis using nanometer scale secondary ion mass spectrometry indicates that the increased CO2 fixation by the haptophyte in treatments without added fixed N is likely an indirect result of the positive effect of Fe and/or P on UCYN-A N-2 fixation and the transfer of N-2-derived N to the haptophyte. Our results reveal a direct linkage between the marine carbon and nitrogen cycles that is fuelled by the atmospheric deposition of dust. The comparison of single-cell rates suggests a tight coupling of nitrogen and carbon transfer that stays balanced even under changing nutrient regimes. However, it appears that the transfer of carbon from the haptophyte to UCYN-A requires a transfer of nitrogen from UCYN-A. This tight coupling indicates an obligate symbiosis of this globally important diazotrophic association.
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    Solar forcing synchronizes decadal North Atlantic climate variability (2015)
    Nature Publishing Group
    In:  Nature Communications, 6 (8268).
    Details
    Publication Date: 2017-04-12
    Description: Quasi-decadal variability in solar irradiance has been suggested to exert a substantial effect on Earth’s regional climate. In the North Atlantic sector, the 11-year solar signal has been proposed to project onto a pattern resembling the North Atlantic Oscillation (NAO), with a lag of a few years due to ocean-atmosphere interactions. The solar/NAO relationship is, however, highly misrepresented in climate model simulations with realistic observed forcings. In addition, its detection is particularly complicated since NAO quasi-decadal fluctuations can be intrinsically generated by the coupled ocean-atmosphere system. Here we compare two multi-decadal ocean-atmosphere chemistry-climate simulations with and without solar forcing variability. While the experiment including solar variability simulates a 1–2-year lagged solar/NAO relationship, comparison of both experiments suggests that the 11-year solar cycle synchronizes quasi-decadal NAO variability intrinsic to the model. The synchronization is consistent with the downward propagation of the solar signal from the stratosphere to the surface.
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    Boundaries of the Peruvian oxygen minimum zone shaped by coherent mesoscale dynamics (2015)
    Nature Publishing Group
    In:  Nature Geoscience, 8 (12). pp. 937-940.
    Details
    Publication Date: 2017-02-20
    Description: Dissolved oxygen in sea water affects marine habitats and biogeochemical cycles. Oceanic zones with oxygen deficits represent 7% of the volume and 8% of the area of the oceans, and are thought to be expanding. One of the most pronounced lies in the region off Peru, where mesoscale activity in the form of fronts and eddies is strong. Here, we study the dynamics of the Peruvian oxygen minimum zone in a Lagrangian framework, using a coupled physical-biogeochemical numerical model and finite-size Lyapunov exponent fields, to evaluate the role of mesoscale activity. We find that, at depths between 380 and 600 m, mesoscale structures have two distinct roles. First, their mean positions and paths delimit and maintain the oxygen minimum zone boundaries. Second, their high-frequency fluctuations inject oxygen across the oxygen minimum zone boundaries and eddy fluxes are one order of magnitude higher than mean oxygen fluxes. We conclude that these eddy fluxes contribute to the ventilation of the Peruvian oxygen minimum zone.
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    Local adaptation constrains the distribution potential of heat-tolerant Symbiodinium from the Persian/Arabian Gulf (2015)
    Nature Publishing Group
    In:  The ISME Journal, 9 (12). pp. 2551-2560.
    Details
    Publication Date: 2021-04-23
    Description: The symbiotic association of corals and unicellular algae of the genus Symbiodinium in the southern Persian/Arabian Gulf (PAG) display an exceptional heat tolerance, enduring summer peak temperatures of up to 36 °C. As yet, it is not clear whether this resilience is related to the presence of specific symbiont types that are exclusively found in this region. Therefore, we used molecular markers to identify the symbiotic algae of three Porites species along 〉1000 km of coastline in the PAG and the Gulf of Oman and found that a recently described species, Symbiodinium thermophilum, is integral to coral survival in the southern PAG, the world’s hottest sea. Despite the geographic isolation of the PAG, we discovered that representatives of the S. thermophilum group can also be found in the adjacent Gulf of Oman providing a potential source of thermotolerant symbionts that might facilitate the adaptation of Indian Ocean populations to the higher water temperatures expected for the future. However, corals from the PAG associated with S. thermophilum show strong local adaptation not only to high temperatures but also to the exceptionally high salinity of their habitat. We show that their superior heat tolerance can be lost when these corals are exposed to reduced salinity levels common for oceanic environments elsewhere. Consequently, the salinity prevailing in most reefs outside the PAG might represent a distribution barrier for extreme temperature-tolerant coral/Symbiodinium associations from the PAG.
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    Extensive phenotypic plasticity of a Red Sea coral over a strong latitudinal temperature gradient suggests limited acclimatization potential to warming (2015)
    Nature Publishing Group
    In:  Scientific Reports, 5 (8940).
    Details
    Publication Date: 2019-09-23
    Description: Global warming was reported to cause growth reductions in tropical shallow water corals in both, cooler and warmer, regions of the coral species range. This suggests regional adaptation with less heat-tolerant populations in cooler and more thermo-tolerant populations in warmer regions. Here, we investigated seasonal changes in the in situ metabolic performance of the widely distributed hermatypic coral Pocillopora verrucosa along 12 degrees latitudes featuring a steep temperature gradient between the northern (28.5 degrees N, 21-27 degrees C) and southern (16.5 degrees N, 28-33 degrees C) reaches of the Red Sea. Surprisingly, we found little indication for regional adaptation, but strong indications for high phenotypic plasticity: Calcification rates in two seasons (winter, summer) were found to be highest at 28-29 degrees C throughout all populations independent of their geographic location. Mucus release increased with temperature and nutrient supply, both being highest in the south. Genetic characterization of the coral host revealed low inter-regional variation and differences in the Symbiodinium clade composition only at the most northern and most southern region. This suggests variable acclimatization potential to ocean warming of coral populations across the Red Sea: high acclimatization potential in northern populations, but limited ability to cope with ocean warming in southern populations already existing at the upper thermal margin for corals
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    Crucial role of Black Sea warming in amplifying the 2012 Krymsk precipitation extreme (2015)
    Nature Publishing Group
    In:  Nature Geoscience, 8 (8). pp. 615-619.
    Details
    Publication Date: 2017-04-12
    Description: Over the past 60 years, both average daily precipitation intensity and extreme precipitation have increased in many regions1, 2, 3. Part of these changes, or even individual events4, 5, have been attributed to anthropogenic warming6, 7. Over the Black Sea and Mediterranean region, the potential for extreme summertime convective precipitation has grown8 alongside substantial sea surface temperature increase. A particularly devastating convective event experienced in that region was the July 2012 precipitation extreme near the Black Sea town of Krymsk9. Here we study the effect of sea surface temperature (SST) increase on convective extremes within the region, taking the Krymsk event as a showcase example. We carry out ensemble sensitivity simulations with a convection-permitting atmospheric model and show the crucial role of SST increase in the extremeness of the event. The enhancement of lower tropospheric instability due to the current warmer Black Sea allows deep convection to be triggered, increasing simulated precipitation by more than 300% relative to simulations with SSTs characteristic of the early 1980s. A highly nonlinear precipitation response to incremental SST increase suggests that the Black Sea has exceeded a regional threshold for the intensification of convective extremes. The physical mechanism we identify indicates that Black Sea and Mediterranean coastal regions may face abrupt amplifications of convective precipitation under continued SST increase, and illustrates the limitations of thermodynamical bounds for estimating the temperature scaling of convective extremes.
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    Subducting seamounts control interplate coupling and seismic rupture in the 2014 Iquique earthquake area (2015)
    Nature Publishing Group
    In:  Nature Communications, 6 . p. 8267.
    Details
    Publication Date: 2017-12-19
    Description: To date, the parameters that determine the rupture area of great subduction zone earthquakes remain contentious. On 1 April 2014, the Mw 8.1 Iquique earthquake ruptured a portion of the well-recognized northern Chile seismic gap but left large highly coupled areas un-ruptured. Marine seismic reflection and swath bathymetric data indicate that structural variations in the subducting Nazca Plate control regional-scale plate-coupling variations, and the limited extent of the 2014 earthquake. Several under-thrusting seamounts correlate to the southward and up-dip arrest of seismic rupture during the 2014 Iquique earthquake, thus supporting a causal link. By fracturing of the overriding plate, the subducting seamounts are likely further responsible for reduced plate-coupling in the shallow subduction zone and in a lowly coupled region around 20.5°S. Our data support that structural variations in the lower plate influence coupling and seismic rupture offshore Northern Chile, whereas the structure of the upper plate plays a minor role.
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    Efficient removal of recalcitrant deep-ocean dissolved organic matter during hydrothermal circulation (2015)
    Nature Publishing Group
    In:  Nature Geoscience, 8 (11). pp. 856-860.
    Details
    Publication Date: 2021-04-23
    Description: Oceanic dissolved organic carbon (DOC) is an important carbon pool, similar in magnitude to atmospheric CO2, but the fate of its oldest forms is not well understood. Hot hydrothermal circulation may facilitate the degradation of otherwise un-reactive dissolved organic matter, playing an important role in the long-term global carbon cycle. The oldest, most recalcitrant forms of DOC, which make up most of oceanic DOC, can be recovered by solid-phase extraction. Here we present measurements of solid-phase extractable DOC from samples collected between 2009 and 2013 at seven vent sites in the Atlantic, Pacific and Southern oceans, along with magnesium concentrations, a conservative tracer of water circulation through hydrothermal systems. We find that magnesium and solid-phase extractable DOC concentrations are correlated, suggesting that solid-phase extractable DOC is almost entirely lost from solution through mineralization or deposition during circulation through hydrothermal vents with fluid temperatures of 212-401°C. In laboratory experiments, where we heated samples to 380°C for four days, we found a similar removal efficiency. We conclude that thermal degradation alone can account for the loss of solid-phase extractable DOC in natural hydrothermal systems, and that its maximum lifetime is constrained by the timescale of hydrothermal cycling, at about 40 million years
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    Discovery of symbiotic nitrogen fixation and chemoautotrophy in cold-water corals (2015)
    Nature Publishing Group
    In:  Scientific Reports, 5 . p. 17962.
    Details
    Publication Date: 2016-11-03
    Description: Cold-water corals (CWC) are widely distributed around the world forming extensive reefs at par with tropical coral reefs. They are hotspots of biodiversity and organic matter processing in the world’s deep oceans. Living in the dark they lack photosynthetic symbionts and are therefore considered to depend entirely on the limited flux of organic resources from the surface ocean. While symbiotic relations in tropical corals are known to be key to their survival in oligotrophic conditions, the full metabolic capacity of CWC has yet to be revealed. Here we report isotope tracer evidence for efficient nitrogen recycling, including nitrogen assimilation, regeneration, nitrification and denitrification. Moreover, we also discovered chemoautotrophy and nitrogen fixation in CWC and transfer of fixed nitrogen and inorganic carbon into bulk coral tissue and tissue compounds (fatty acids and amino acids). This unrecognized yet versatile metabolic machinery of CWC conserves precious limiting resources and provides access to new nitrogen and organic carbon resources that may be essential for CWC to survive in the resource-depleted dark ocean.
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    Atlantic multi-decadal oscillation covaries with Agulhas leakage (2015)
    Nature Publishing Group
    In:  Nature Communications, 6 (10082).
    Details
    Publication Date: 2019-02-25
    Description: The interoceanic transfer of seawater between the Indian Ocean and the Atlantic, ‘Agulhas leakage’, forms a choke point for the overturning circulation in the global ocean. Here, by combining output from a series of high-resolution ocean and climate models with in situ and satellite observations, we construct a time series of Agulhas leakage for the period 1870–2014. The time series demonstrates the impact of Southern Hemisphere westerlies on decadal timescales. Agulhas leakage shows a correlation with the Atlantic Multi-decadal Oscillation on multi-decadal timescales; the former leading by 15 years. This is relevant for climate in the North Atlantic
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    Effects of long-term variability on projections of twenty-first century dynamic sea level (2015)
    Nature Publishing Group
    In:  Nature Climate Change, 5 (4). pp. 343-347.
    Details
    Publication Date: 2017-04-13
    Description: Sea-level rise1 is one of the most pressing aspects of anthropogenic global warming with far-reaching consequences for coastal societies. However, sea-level rise did2, 3, 4, 5, 6, 7 and will strongly vary from coast to coast8, 9, 10. Here we investigate the long-term internal variability effects on centennial projections of dynamic sea level (DSL), the local departure from the globally averaged sea level. A large ensemble of global warming integrations has been conducted with a climate model, where each realization was forced by identical CO2 increase but started from different atmospheric and oceanic initial conditions. In large parts of the mid- and high latitudes, the ensemble spread of the projected centennial DSL trends is of the same order of magnitude as the globally averaged steric sea-level rise, suggesting that internal variability cannot be ignored when assessing twenty-first-century DSL trends. The ensemble spread is considerably reduced in the mid- to high latitudes when only the atmospheric initial conditions differ while keeping the oceanic initial state identical; indicating that centennial DSL projections are strongly dependent on ocean initial conditions.
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    Policy: Five priorities for the UN Sustainable Development Goals - Comment (2015)
    Nature Publishing Group
    In:  Nature, 520 (7548). pp. 432-433.
    Details
    Publication Date: 2019-09-23
    Description: Restructure data-gathering and evaluation networks to address climate change, energy, food, health and water provision, say Yonglong Lu and colleagues.
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    Pacific origin of the abrupt increase in Indian Ocean heat content during the warming hiatus (2015)
    Nature Publishing Group
    In:  Nature Geoscience, 8 (6). pp. 445-449.
    Details
    Publication Date: 2017-12-19
    Description: Global mean surface warming has stalled since the end of the twentieth century1, 2, but the net radiation imbalance at the top of the atmosphere continues to suggest an increasingly warming planet. This apparent contradiction has been reconciled by an anomalous heat flux into the ocean3, 4, 5, 6, 7, 8, induced by a shift towards a La Niña-like state with cold sea surface temperatures in the eastern tropical Pacific over the past decade or so. A significant portion of the heat missing from the atmosphere is therefore expected to be stored in the Pacific Ocean. However, in situ hydrographic records indicate that Pacific Ocean heat content has been decreasing9. Here, we analyse observations along with simulations from a global ocean–sea ice model to track the pathway of heat. We find that the enhanced heat uptake by the Pacific Ocean has been compensated by an increased heat transport from the Pacific Ocean to the Indian Ocean, carried by the Indonesian throughflow. As a result, Indian Ocean heat content has increased abruptly, which accounts for more than 70% of the global ocean heat gain in the upper 700 m during the past decade. We conclude that the Indian Ocean has become increasingly important in modulating global climate variability.
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    Ocean science: The origins of a climate oscillation (2015)
    Nature Publishing Group
    In:  Nature, 521 (7553). pp. 428-430.
    Details
    Publication Date: 2017-12-19
    Description: An index of water-circulation strength in the North Atlantic Ocean has been derived from sea-level measurements. This provides fresh evidence of the ocean's leading role in multidecadal climate variability. See Letter p.508
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    How and when plume zonation appeared during the 132 Myr evolution of the Tristan Hotspot (2015)
    Nature Publishing Group
    In:  Nature Communications, 6 (7799).
    Details
    Publication Date: 2019-09-23
    Description: Increasingly, spatial geochemical zonation, present as geographically distinct, subparallel trends, is observed along hotspot tracks, such as Hawaii and the Galapagos. The origin of this zonation is currently unclear. Recently zonation was found along the last B70 Myr of the Tristan-Gough hotspot track. Here we present new Sr–Nd–Pb–Hf isotope data from the older parts of this hotspot track (Walvis Ridge and Rio Grande Rise) and re-evaluate published data from the Etendeka and Parana flood basalts erupted at the initiation of the hotspot track. We show that only the enriched Gough, but not the less-enriched Tristan, component is present in the earlier (70–132 Ma) history of the hotspot. Here we present a model that can explain the temporal evolution and origin of plume zonation for both the Tristan-Gough and Hawaiian hotspots, two end member types of zoned plumes, through processes taking place in the plume sources at the base of the lower mantle.
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    Ocean acidification increases the accumulation of toxic phenolic compounds across trophic levels (2015)
    Nature Publishing Group
    In:  Nature Communications, 6 (8714).
    Details
    Publication Date: 2019-09-23
    Description: Increasing atmospheric CO2 concentrations are causing ocean acidification (OA), altering carbonate chemistry with consequences for marine organisms. Here we show that OA increases by 46–212% the production of phenolic compounds in phytoplankton grown under the elevated CO2 concentrations projected for the end of this century, compared with the ambient CO2 level. At the same time, mitochondrial respiration rate is enhanced under elevated CO2 concentrations by 130–160% in a single species or mixed phytoplankton assemblage. When fed with phytoplankton cells grown under OA, zooplankton assemblages have significantly higher phenolic compound content, by about 28–48%. The functional consequences of the increased accumulation of toxic phenolic compounds in primary and secondary producers have the potential to have profound consequences for marine ecosystem and seafood quality, with the possibility that fishery industries could be influenced as a result of progressive ocean changes
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    Diversity of key players in the microbial ecosystems of the human body (2015)
    Nature Publishing Group
    In:  Scientific Reports, 5 . p. 15920.
    Details
    Publication Date: 2020-11-09
    Description: Coexisting bacteria form various microbial communities in human body parts. In these ecosystems they interact in various ways and the properties of the interaction network can be related to the stability and functional diversity of the local bacterial community. In this study, we analyze the interaction network among bacterial OTUs in 11 locations of the human body. These belong to two major groups. One is the digestive system and the other is the female genital tract. In each local ecosystem we determine the key species, both the ones being in key positions in the interaction network and the ones that dominate by frequency. Beyond identifying the key players and discussing their biological relevance, we also quantify and compare the properties of the 11 networks. The interaction networks of the female genital system and the digestive system show totally different architecture. Both the topological properties and the identity of the key groups differ. Key groups represent four phyla of prokaryotes. Some groups appear in key positions in several locations, while others are assigned only to a single body part. The key groups of the digestive and the genital tracts are totally different.
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    Institutional coordination of global ocean observations (2015)
    Nature Publishing Group
    In:  Nature Climate Change, 5 (1). pp. 4-6.
    Details
    Publication Date: 2019-09-23
    Description: A sustainable global ocean observation system requires timely implementation of the framework for ocean observing. The recent Qingdao Global Ocean Summit highlighted the need for a more coherent institutional response to maintain an integrated ocean-observing system.
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    Ocean currents generate large footprints in marine palaeoclimate proxies (2015)
    Nature Publishing Group
    In:  Nature Communications, 6 (6521).
    Details
    Publication Date: 2019-02-25
    Description: Fossils of marine microorganisms such as planktic foraminifera are among the cornerstones of palaeoclimatological studies. It is often assumed that the proxies derived from their shells represent ocean conditions above the location where they were deposited. Planktic foraminifera, however, are carried by ocean currents and, depending on the life traits of the species, potentially incorporate distant ocean conditions. Here we use high-resolution ocean models to assess the footprint of planktic foraminifera and validate our method with proxy analyses from two locations. Results show that foraminifera, and thus recorded palaeoclimatic conditions, may originate from areas up to several thousands of kilometres away, reflecting an ocean state significantly different from the core site. In the eastern equatorial regions and the western boundary current extensions, the offset may reach 1.5 °C for species living for a month and 3.0 °C for longer-living species. Oceanic transport hence appears to be a crucial aspect in the interpretation of proxy signals.
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    Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection (2015)
    Nature Publishing Group
    In:  The ISME Journal, 9 (3). pp. 670-682.
    Details
    Publication Date: 2017-04-13
    Description: Microbiota provide their hosts with a range of beneficial services, including defense from external pathogens. However, host-associated microbial communities themselves can act as a source of opportunistic pathogens depending on the environment. Marine poikilotherms and their microbiota are strongly influenced by temperature, but experimental studies exploring how temperature affects the interactions between both parties are rare. To assess the effects of temperature, temperature stress and infection on diversity, composition and dynamics of the hemolymph microbiota of Pacific oysters (Crassostrea gigas), we conducted an experiment in a fully-crossed, three-factorial design, in which the temperature acclimated oysters (8 or 22 °C) were exposed to temperature stress and to experimental challenge with a virulent Vibrio sp. Strain. We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. We found that the microbial dynamics and composition of communities in healthy animals (including infection survivors) were significantly affected by temperature and temperature stress, but not by infection. The response was mediated by changes in the incidence and abundance of operational taxonomic units (OTUs) and accompanied by little change at higher taxonomic levels, indicating dynamic stability of the hemolymph microbiome. Dead and moribund oysters, on the contrary, displayed signs of community structure disruption, characterized by very low diversity and proliferation of few OTUs. We can therefore link short-term responses of host-associated microbial communities to abiotic and biotic factors and assess the potential feedback between microbiota dynamics and host survival during disease.
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    Fossil fuels in a trillion tonne world (2015)
    Nature Publishing Group
    In:  Nature Climate Change, 5 (5). pp. 419-423.
    Details
    Publication Date: 2017-12-19
    Description: The useful energy services and energy density value of fossil carbon fuels could be retained for longer timescales into the future if their combustion is balanced by CO2 recapture and storage. We assess the global balance between fossil carbon supply and the sufficiency (size) and capability (technology, security) of candidate carbon stores. A hierarchy of value for extraction-to-storage pairings is proposed, which is augmented by classification of CO2 containment as temporary (〈1,000 yr) or permanent (〉100,000 yr). Using temporary stores is inefficient and defers an intergenerational problem. Permanent storage capacity is adequate to technically match current fossil fuel reserves. However, rates of storage creation cannot balance current and expected rates of fossil fuel extraction and CO2 consequences. Extraction of conventional natural gas is uniquely holistic because it creates the capacity to re-inject an equivalent tonnage of carbon for storage into the same reservoir and can re-use gas-extraction infrastructure for storage. By contrast, balancing the extraction of coal, oil, biomass and unconventional fossil fuels requires the engineering and validation of additional carbon storage. Such storage is, so far, unproven in sufficiency.
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    Deformation-related volcanism in the Pacific Ocean linked to the Hawaiian–Emperor bend (2015)
    Nature Publishing Group
    In:  Nature Geoscience, 8 (5). pp. 393-397.
    Details
    Publication Date: 2019-09-23
    Description: Ocean islands, seamounts and volcanic ridges are thought to form above mantle plumes. Yet, this mechanism cannot explain many volcanic features on the Pacific Ocean floor and some might instead be caused by cracks in the oceanic crust linked to the reorganization of plate motions. A distinctive bend in the Hawaiian–Emperor volcanic chain has been linked to changes in the direction of motion of the Pacific Plate, movement of the Hawaiian plume, or a combination of both. However, these links are uncertain because there is no independent record that precisely dates tectonic events that affected the Pacific Plate. Here we analyse the geochemical characteristics of lava samples collected from the Musicians Ridges, lines of volcanic seamounts formed close to the Hawaiian–Emperor bend. We find that the geochemical signature of these lavas is unlike typical ocean island basalts and instead resembles mid-ocean ridge basalts. We infer that the seamounts are unrelated to mantle plume activity and instead formed in an extensional setting, due to deformation of the Pacific Plate. 40Ar/39Ar dating reveals that the Musicians Ridges formed during two time windows that bracket the time of formation of the Hawaiian–Emperor bend, 53–52 and 48–47 million years ago. We conclude that the Hawaiian–Emperor bend was formed by plate–mantle reorganization, potentially triggered by a series of subduction events at the Pacific Plate margins.
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    Points of significance: Bayesian statistics (2015)
    Nature Publishing Group
    In:  Nature Methods, 12 (5). pp. 377-378.
    Details
    Publication Date: 2020-06-24
    Description: Today’s predictions are tomorrow’s priors
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    Long-term response of oceans to CO2 removal from the atmosphere (2015)
    Nature Publishing Group
    In:  Nature Climate Change, 5 (12). pp. 1107-1113.
    Details
    Publication Date: 2017-04-11
    Description: Carbon dioxide removal (CDR) from the atmosphere has been proposed as a measure for mitigating global warming and ocean acidification. To assess the extent to which CDR might eliminate the long-term consequences of anthropogenic CO2 emissions in the marine environment, we simulate the effect of two massive CDR interventions with CO2 extraction rates of 5 GtC yr(-1) and 25 GtC yr(-1), respectively, while CO2 emissions follow the extended RCP8.5 pathway. We falsify two hypotheses: the first being that CDR can restore pre-industrial conditions in the ocean by reducing the atmospheric CO2 concentration back to its pre-industrial level, and the second being that high CO2 emissions rates (RCP8.5) followed by CDR have long-term oceanic consequences that are similar to those of low emissions rates (RCP2.6). Focusing on pH, temperature and dissolved oxygen, we find that even after several centuries of CDR deployment, past CO2 emissions would leave a substantial legacy in the marine environment.
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    The re-emergence of natural products for drug discovery in the genomics era (2015)
    Nature Publishing Group
    In:  Nature Reviews Drug Discovery, 14 (2). pp. 111-129.
    Details
    Publication Date: 2020-06-23
    Description: Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein–protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.
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    Genome-wide maps of recombination and chromosome segregation in human oocytes and embryos show selection for maternal recombination rates (2015)
    Nature Publishing Group
    In:  Nature Genetics, 47 (7). pp. 727-735.
    Details
    Publication Date: 2020-06-25
    Description: Crossover recombination reshuffies genes and prevents errors in segregation tha't Iead to extra or missing chromosomes (aneuploidy) in human eggs, a major cause of pregnancy failure and congenital disorders. Here we generate genome-wide maps of cro~sovers and chromosome segregation patterns by recovering all three products of single female meioses. Genotyping 〉4 millioninformative SNPs from 23 complete meioses allowed us to map 2,032 maternal and 1,342 paternal crossovers and to infer the segregation patterns of 529 chromosome pairs. We uncover a new reverse chromosome segregation pattern in which both homologsseparate their sister chromatids at meiosis I; detect selection for higher recombination rates in the female germ line by the elimination of aneuploid embryos; and report chromosomal drive against non recombinant chromatids at meiosis II. Collectively, our findings show !hat recombination not only affects homolog segregation at meiosis I but also the fate of sister chromatids at meiosis II.
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    A novel hydrogen oxidizer amidst the sulfur-oxidizing Thiomicrospira lineage (2015)
    Nature Publishing Group
    In:  The ISME Journal, 9 (3). pp. 696-707.
    Details
    Publication Date: 2019-01-17
    Description: Thiomicrospira species are ubiquitously found in various marine environments and appear particularly common in hydrothermal vent systems. Members of this lineage are commonly classified as sulfur-oxidizing chemolithoautotrophs. Although sequencing of Thiomicrospira crunogena's genome has revealed genes that encode enzymes for hydrogen uptake activity and for hydrogenase maturation and assembly, hydrogen uptake ability has so far not been reported for any Thiomicrospira species. We isolated a Thiomicrospira species (SP-41) from a deep sea hydrothermal vent and demonstrated that it can oxidize hydrogen. We show in vivo hydrogen consumption, hydrogen uptake activity in partially purified protein extracts and transcript abundance of hydrogenases during different growth stages. The ability of this strain to oxidize hydrogen opens up new perspectives with respect to the physiology of Thiomicrospira species that have been detected in hydrothermal vents and that have so far been exclusively associated with sulfur oxidation.
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    Microbiology: Exclusive networks in the sea (2015)
    Nature Publishing Group
    In:  Nature, 522 (7554). pp. 36-37.
    Details
    Publication Date: 2019-03-05
    Description: The identification of an exchange of nutrients and signalling molecules between a planktonic alga and a bacterium demonstrates that targeted mutualistic interactions occur across domains of life in the oceans. See Letter p.98
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    Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter (2015)
    Nature Publishing Group
    In:  ISME Journal, 9 (8). pp. 1747-1763.
    Details
    Publication Date: 2019-03-05
    Description: Particles in aquatic environments host distinct communities of microbes, yet the evolution of particlespecialized taxa and the extent to which specialized microbial metabolism is associated with particles is largely unexplored. Here, we investigate the hypothesis that a widely distributed and uncultivated microbial group - the marine group II euryarchaea (MGII) - interacts with living and detrital particulate organic matter (POM) in the euphotic zone of the central California Current System. Using fluorescent in situ hybridization, we verified the association of euryarchaea with POM. We further quantified the abundance and distribution of MGII 16S ribosomal RNA genes in size-fractionated seawater samples and compared MGII functional capacity in metagenomes from the same fractions. The abundance of MGII in free-living and 〈3 μm fractions decreased with increasing distance from the coast, whereas MGII abundance in the 0.8-3 lm fraction remained constant. At several offshore sites, MGII abundance was highest in particle fractions, indicating that particle-attached MGII can outnumber free-living MGII under oligotrophic conditions. Compared with free-living MGII, the genome content of MGII in particleassociated fractions exhibits an increased capacity for surface adhesion, transcriptional regulation and catabolism of high molecular weight substrates. Moreover, MGII populations in POM fractions are phylogenetically distinct from and more diverse than free-living MGII. Eukaryotic phytoplankton additions stimulated MGII growth in bottle incubations, providing the first MGII net growth rate measurements. These ranged from 0.47 to 0.54 d-1. However, MGII were not recovered in wholegenome amplifications of flow-sorted picoeukaryotic phytoplankton and heterotrophic nanoflagellates, suggesting that MGII in particle fractions are not physically attached to living POM. Collectively, our results support a linkage between MGII ecophysiology and POM, implying that marine archaea have a role in elemental cycling through interactions with particles. © 2015 International Society for Microbial Ecology. All rights reserved.
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    Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? (2015)
    Nature Publishing Group
    In:  Scientific Reports, 5 (1). Art.Nr. 10134.
    Details
    Publication Date: 2019-03-05
    Description: Algae with secondary plastids of a red algal origin, such as ochrophytes (photosynthetic stramenopiles), are diverse and ecologically important, yet their evolutionary history remains controversial. We sequenced plastid genomes of two ochrophytes, Ochromonas sp. CCMP1393 (Chrysophyceae) and Trachydiscus minutus (Eustigmatophyceae). A shared split of the clpC gene as well as phylogenomic analyses of concatenated protein sequences demonstrated that chrysophytes and eustigmatophytes form a clade, the Limnista, exhibiting an unexpectedly elevated rate of plastid gene evolution. Our analyses also indicate that the root of the ochrophyte phylogeny falls between the recently redefined Khakista and Phaeista assemblages. Taking advantage of the expanded sampling of plastid genome sequences, we revisited the phylogenetic position of the plastid of Vitrella brassicaformis, a member of Alveolata with the least derived plastid genome known for the whole group. The results varied depending on the dataset and phylogenetic method employed, but suggested that the Vitrella plastids emerged from a deep ochrophyte lineage rather than being derived vertically from a hypothetical plastid-bearing common ancestor of alveolates and stramenopiles. Thus, we hypothesize that the plastid in Vitrella, and potentially in other alveolates, may have been acquired by an endosymbiosis of an early ochrophyte.
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    Strong and deep Atlantic meridional overturning circulation during the last glacial cycle (2015)
    Nature Publishing Group
    In:  Nature Geoscience, 517 (7532). pp. 73-76.
    Details
    Publication Date: 2019-09-23
    Description: Extreme, abrupt Northern Hemisphere climate oscillations during the last glacial cycle (140,000 years ago to present) were modulated by changes in ocean circulation and atmospheric forcing. However, the variability of the Atlantic meridional overturning circulation (AMOC), which has a role in controlling heat transport from low to high latitudes and in ocean CO2 storage, is still poorly constrained beyond the Last Glacial Maximum. Here we show that a deep and vigorous overturning circulation mode has persisted for most of the last glacial cycle, dominating ocean circulation in the Atlantic, whereas a shallower glacial mode with southern-sourced waters filling the deep western North Atlantic prevailed during glacial maxima. Our results are based on a reconstruction of both the strength and the direction of the AMOC during the last glacial cycle from a highly resolved marine sedimentary record in the deep western North Atlantic. Parallel measurements of two independent chemical water tracers (the isotope ratios of 231Pa/230Th and 143Nd/144Nd), which are not directly affected by changes in the global cycle, reveal consistent responses of the AMOC during the last two glacial terminations. Any significant deviations from this configuration, resulting in slowdowns of the AMOC, were restricted to centennial-scale excursions during catastrophic iceberg discharges of the Heinrich stadials. Severe and multicentennial weakening of North Atlantic Deep Water formation occurred only during Heinrich stadials close to glacial maxima with increased ice coverage, probably as a result of increased fresh-water input. In contrast, the AMOC was relatively insensitive to submillennial meltwater pulses during warmer climate states, and an active AMOC prevailed during Dansgaard–Oeschger interstadials (Greenland warm periods).
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    Complementary effects of species and genetic diversity on productivity and stability of sown grasslands (2015)
    Nature Publishing Group
    Details
    Publication Date: 2022-09-21
    Description: Plant species diversity regulates the productivity1–3 and stability2,4 of natural ecosystems, along with their resilience to disturbance5,6. The influence of species diversity on the productivity of agronomic systems is less clear7–10. Plant genetic diversity is also suspected to influence ecosystem function3,11–14, although empirical evidence is scarce. Given the large range of genotypes that can be generated per species through artificial selection, genetic diversity is a potentially important leverage of productivity in cultivated systems. Here we assess the effect of species and genetic diversity on the production and sustainable supply of livestock fodder in sown grasslands, comprising single and multispecies assemblages characterized by different levels of genetic diversity, exposed to drought and non-drought conditions. Multispecies assemblages proved more productive than monocultures when subject to drought, regardless of the number of genotypes per species present. Conversely, the temporal stability of production increased only with the number of genotypes present under both drought and non-drought conditions, and was unaffected by the number of species. We conclude that taxonomic and genetic diversity can play complementary roles when it comes to optimizing livestock fodder production in managed grasslands, and suggest that both levels of diversity should be considered in plant breeding programmes designed to boost the productivity and resilience of managed grasslands in the face of increasing environmental hazards.
    Type: Article , PeerReviewed
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  • 62
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    Massive nitrous oxide emissions from the tropical South Pacific Ocean (2015)
    Nature Publishing Group
    Details
    Publication Date: 2023-09-19
    Description: Nitrous oxide is a potent greenhouse gas and a key compound in stratospheric ozone depletion. In the ocean, nitrous oxide is produced at intermediate depths through nitrification and denitrification, in particular at low oxygen concentrations. Although a third of natural emissions of nitrous oxide to the atmosphere originate from the ocean, considerable uncertainties in the distribution and magnitude of the emissions still exist. Here we present high-resolution surface measurements and vertical profiles of nitrous oxide that include the highest reported nitrous oxide concentrations in marine surface waters, suggesting that there is a hotspot of nitrous oxide emissions in high-productivity upwelling ecosystems along the Peruvian coast. We estimate that off Peru, the extremely high nitrous oxide supersaturations we observed drive a massive efflux of 0.2–0.9 Tg of nitrogen emitted as nitrous oxide per year, equivalent to 5–22% of previous estimates of global marine nitrous oxide emissions. Nutrient and gene abundance data suggest that coupled nitrification–denitrification in the upper oxygen minimum zone and transport of resulting nitrous oxide to the surface by upwelling lead to the high nitrous oxide concentrations. Our estimate of nitrous oxide emissions from the Peruvian coast surpasses values from similar, highly productive areas.
    Type: Article , PeerReviewed
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  • 63
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    A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity (2015)
    Nature Publishing Group
    Details
    Publication Date: 2023-11-29
    Description: Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a key enzyme of the Calvin cycle, which is responsible for most of Earth's primary production. Although research on RubisCO genes and enzymes in plants, cyanobacteria and bacteria has been ongoing for years, still little is understood about its regulation and activation in bacteria. Even more so, hardly any information exists about the function of metagenomic RubisCOs and the role of the enzymes encoded on the flanking DNA owing to the lack of available function-based screens for seeking active RubisCOs from the environment. Here we present the first solely activity-based approach for identifying RubisCO active fosmid clones from a metagenomic library. We constructed a metagenomic library from hydrothermal vent fluids and screened 1056 fosmid clones. Twelve clones exhibited RubisCO activity and the metagenomic fragments resembled genes from Thiomicrospira crunogena. One of these clones was further analyzed. It contained a 35.2 kb metagenomic insert carrying the RubisCO gene cluster and flanking DNA regions. Knockouts of twelve genes and two intergenic regions on this metagenomic fragment demonstrated that the RubisCO activity was significantly impaired and was attributed to deletions in genes encoding putative transcriptional regulators and those believed to be vital for RubisCO activation. Our new technique revealed a novel link between a poorly characterized gene and RubisCO activity. This screen opens the door to directly investigating RubisCO genes and respective enzymes from environmental samples.
    Type: Article , PeerReviewed
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