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  • Oxford University Press  (26)
  • Frontiers Media S.A.  (24)
  • Blackwell Publishing Ltd
  • 2025-2025
  • 2020-2023  (54)
  • 1985-1989
  • 2021  (39)
  • 2020  (15)
  • 1
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    How to Find Aquifer Statistics Utilizing Pumping Tests? Two Field Studies Using welltestpy (2021)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publication Date: 2022-04-01
    Description: We present a workflow to estimate geostatistical aquifer parameters from pumping test data using the Python package welltestpy. The procedure of pumping test analysis is exemplified for two data sets from the Horkheimer Insel site and from the Lauswiesen site, Germany. The analysis is based on a semi‐analytical drawdown solution from the upscaling approach Radial Coarse Graining, which enables to infer log‐transmissivity variance and horizontal correlation length, beside mean transmissivity, and storativity, from pumping test data. We estimate these parameters of aquifer heterogeneity from type‐curve analysis and determine their sensitivity. This procedure, implemented in welltestpy, is a template for analyzing any pumping test. It goes beyond the possibilities of standard methods, for example, based on Theis' equation, which are limited to mean transmissivity and storativity. A sensitivity study showed the impact of observation well positions on the parameter estimation quality. The insights of this study help to optimize future test setups for geostatistical aquifer analysis and provides guidance for investigating pumping tests with regard to aquifer statistics using the open‐source software package welltestpy.
    Description: Article impact statement: We present a workflow to infer parameters of subsurface heterogeneity from pumping test data exemplified at two sites using welltestpy.
    Description: German Federal Environmental Foundation (DBU) http://dx.doi.org/10.13039/100007636
    Keywords: ddc:551.49
    Language: English
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  • 2
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    Importance of sources of variability, scales and experimental design: A case study about the effects of biochar and slurry application on soil properties in agricultural silty loam soils (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-04-01
    Description: In designed experiments, different sources of variability and an adequate scale of measurement need to be considered, but not all approaches in common usage are equally valid. In order to elucidate the importance of sources of variability and choice of scale, we conducted an experiment where the effects of biochar and slurry applications on soil properties related to soil fertility were studied for different designs: (a) for a field‐scale sampling design with either a model soil (without natural variability) as an internal control or with composited soils, (b) for a design with a focus on amendment variabilities, and (c) for three individual field‐scale designs with true field replication and a combined analysis representative of the population of loess‐derived soils. Three silty loam sites in Germany were sampled and the soil macroaggregates were crushed. For each design, six treatments (0, 0.15 and 0.30 g slurry‐N kg−1 with and without 30 g biochar kg−1) were applied before incubating the units under constant soil moisture conditions for 78 days. CO2 fluxes were monitored and soils were analysed for macroaggregate yields and associated organic carbon (C). Mixed‐effects models were used to describe the effects. For all soil properties, results for the loess sites differed with respect to significant contributions of fixed effects for at least one site, suggesting the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils to be made and showed that site:slurry:biochar and site:slurry interactions were not negligible for macroaggregate yields. The use of a model soil as an internal control enabled observation of variabilities other than those related to soils or amendments. Experiments incorporating natural variability in soils or amendments resulted in partially different outcomes, indicating the need to include all important sources of variability. Highlights Effects of biochar and slurry applications were studied for different designs and mixed‐effects models were used to describe the effects. Including an internal control allowed observation of, e.g., methodological and analytical variabilities. The results suggested the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils. The results indicated the need to include all important sources of variability.
    Keywords: ddc:631.4
    Language: English
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  • 3
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    Do tree species affect decadal changes in soil organic carbon and total nitrogen stocks in Danish common garden experiments? (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-04-01
    Description: Temperate forest soils are often considered as an important sink for atmospheric carbon (C), thereby buffering anthropogenic CO2 emissions. However, the effect of tree species composition on the magnitude of this sink is unclear. We resampled a tree species common garden experiment (six sites) a decade after initial sampling to evaluate whether forest floor (FF) and topsoil organic carbon (Corg) and total nitrogen (Nt) stocks changed in dependence of tree species (Norway spruce—Picea abies L., European beech—Fagus sylvatica L., pedunculate oak—Quercus robur L., sycamore maple—Acer pseudoplatanus L., European ash—Fraxinus excelsior L. and small‐leaved lime—Tilia cordata L.). Two groups of species were identified in terms of Corg and Nt distribution: (1) Spruce with high Corg and Nt stocks in the FF developed as a mor humus layer which tended to have smaller Corg and Nt stocks and a wider Corg:Nt ratio in the mineral topsoil, and (2) the broadleaved species, of which ash and maple distinguished most clearly from spruce by very low Corg and Nt stocks in the FF developed as mull humus layer, had greater Corg and Nt stocks, and narrow Corg:Nt ratios in the mineral topsoil. Over 11 years, FF Corg and Nt stocks increased most under spruce, while small decreases in bulk mineral soil (esp. in 0–15 cm and 0–30 cm depth) Corg and Nt stocks dominated irrespective of species. Observed decadal changes were associated with site‐related and tree species‐mediated soil properties in a way that hinted towards short‐term accumulation and mineralisation dynamics of easily available organic substances. We found no indication for Corg stabilisation. However, results indicated increasing Nt stabilisation with increasing biomass of burrowing earthworms, which were highest under ash, lime and maple and lowest under spruce. Highlights We studied if tree species differences in topsoil Corg and Nt stocks substantiate after a decade. The study is unique in its repeated soil sampling in a multisite common garden experiment. Forest floors increased under spruce, but topsoil stocks decreased irrespective of species. Changes were of short‐term nature. Nitrogen was most stable under arbuscular mycorrhizal species.
    Description: Deutsche Forschungsgemeinschaff (DFG)
    Keywords: ddc:551.9 ; ddc:631.41
    Language: English
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  • 4
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    Natural Radioactivity of the Crystalline Basement Rocks of the Peloritani Mountains (North-Eastern Sicily, Italy): Measurements and Radiological Hazard (2021)
    Oxford University Press
    Details
    Publication Date: 2022-03-02
    Description: Crystalline rocks can produce dangerous radiation levels on the basis of their content in radioisotopes. Here, we report radiological data from 10 metamorphic and igneous rock samples collected from the crystalline basement of the Peloritani Mountains (southern Italy). In order to evaluate the radiological properties of these rocks, the gamma radiation and the radon emanation have been measured. Moreover, since some of these rocks are employed as building materials, we assess the potential hazard for population connected to their use. Gamma spectroscopy was used to measure the 226Ra, 232Th and 40K activity concentration, whereas the radon emanation was investigated by using a RAD 7 detector. The results show 226Ra, 232Th and 40K activity concentration values ranging from (17 ± 4) to (56 ± 8) Bq kg-1, (14 ± 3) to (77 ± 14) Bq kg-1 and (167 ± 84) to (1760 ± 242) Bq kg-1, respectively. Values of the annual effective dose equivalent outdoor range from 0.035 to 0.152 mSv y-1, whereas the gamma index is in the range of 0.22-0.98. The 222Rn emanation coefficient and the 222Rn surface exhalation rate vary from (0.63 ± 0.3) to (8.27 ± 1.6)% and from (0.12 ± 0.03) to (2.75 ± 0.17) Bq m-2 h-1, respectively. The indoor radon derived from the building use of these rocks induces an approximate contribution to the annual effective dose ranging from 8 to 176 μSv y-1. All the obtained results suggest that the crystalline rocks from the Peloritani Mountains are not harmful for the residential population, even though they induce annual effective doses due to terrestrial gamma radiation above the worldwide average values. Moreover, their use as building materials does not produce significant health hazards connected to the indoor radon exposure.
    Description: Published
    Description: 452–464
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carroll, E. L., Ott, P. H., McMillan, L. F., Galletti Vernazzani, B., Neveceralova, P., Vermeulen, E., Gaggiotti, O. E., Andriolo, A., Baker, C. S., Bamford, C., Best, P., Cabrera, E., Calderan, S., Chirife, A., Fewster, R. M., Flores, P. A. C., Frasier, T., Freitas, T. R. O., Groch, K., Hulva, P., Kennedy, A., Leaper, R., Leslie, M. S., Moore, M., Oliveira, L., Seger, J., Stepien, E. N., Valenzuela, L. O., Zerbini, A., & Jackson, J. A. Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground. Journal of Heredity, 111(3), (2020): 263-276, doi:10.1093/jhered/esaa010.
    Description: As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile–Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile–Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile–Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile–Peru.
    Description: This work was supported by the EU BEST 2.0 medium grant 1594 and UK DARWIN PLUS grant 057 and additional funding from the World Wildlife Fund GB107301. The collection of the Chile–Peru sample was supported by the Global Greengrants Fund and the Pacific Whale Foundation. The collection of the Brazilian samples was supported through grants by the Brazilian National Research Council to Paulo H. Ott (CNPq proc. n° 144064/98-7) and Paulo A.C. Flores (CNPq proc. n° 146609/1999-9) and with support from the World Wildlife Fund (WWF-Brazil). The collection of the South African samples was supported by the Global Greengrants Fund, the Pacific Whale Foundation and Charles University Grant Agency (1140217). E.L.C. was partially supported by a Rutherford Discovery Fellowship from the Royal Society of New Zealand. This study forms part of the Ecosystems component of the British Antarctic Survey Polar Sciences for Planet Earth Programme, funded by the Natural Environment Research Council.
    Keywords: population structure ; connectivity ; migration ; gene flow
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Transfer learning: Improving neural network based prediction of earthquake ground shaking for an area with insufficient training data (2021)
    Oxford University Press
    Details
    Publication Date: 2022-03-16
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: In a recent study (Jozinovi\'c et al, 2020) we showed that convolutional neural networks (CNNs) applied to network seismic traces can be used for rapid prediction of earthquake peak ground motion intensity measures (IMs) at distant stations using only recordings from stations near the epicenter. The predictions are made without any previous knowledge concerning the earthquake location and magnitude. This approach differs from the standard procedure adopted by earthquake early warning systems (EEWSs) that rely on location and magnitude information. In the previous study, we used 10 s, raw, multistation waveforms for the 2016 earthquake sequence in central Italy for 915 events (CI dataset). The CI dataset has a large number of spatially concentrated earthquakes and a dense station network. In this work, we applied the CNN model to an area around the VIRGO gravitational waves observatory sited near Pisa, Italy. In our initial application of the technique, we used a dataset consisting of 266 earthquakes recorded by 39 stations. We found that the CNN model trained using this smaller dataset performed worse compared to the results presented in the original study by Jozinovi\'c et al. (2020). To counter the lack of data, we adopted transfer learning (TL) using two approaches: first, by using a pre-trained model built on the CI dataset and, next, by using a pre-trained model built on a different (seismological) problem that has a larger dataset available for training. We show that the use of TL improves the results in terms of outliers, bias, and variability of the residuals between predicted and true IMs values. We also demonstrate that adding knowledge of station positions as an additional layer in the neural network improves the results. The possible use for EEW is demonstrated by the times for the warnings that would be received at the station PII.
    Description: RISE (Union's Horizon 2020 research and innovation programme, grant agreement No.821115)
    Description: Published
    Description: 704–718
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics ; machine learning ; ground motion prediction ; seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    Seismogenic Structure Orientation and Stress Field of the Gargano Promontory (Southern Italy) From Microseismicity Analysis (2021)
    Frontiers Media S.A.
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    Publication Date: 2021-11-30
    Description: Historical seismic catalogs report that the Gargano Promontory (southern Italy) was affected in the past by earthquakes with medium to high estimated magnitude. From the instrumental seismicity, it can be identified that the most energetic Apulian sequence occurred in 1995 with a main shock of MW = 5.2 followed by about 200 aftershocks with a maximum magnitude of 3.7. The most energetic earthquakes of the past are attributed to right-lateral strike-slip faults, while there is evidence that the present-day seismicity occur on thrust or thrust-strike faults. In this article, we show a detailed study on focal mechanisms and stress field obtained by micro-seismicity recorded from April 2013 until the present time in the Gargano Promontory and surrounding regions. Seismic waveforms are collected from the OTRIONS Seismic Network (OSN), from the Italian National Seismic Network (RSN), and integrated with data from the Italian National Accelerometric Network (RAN) in order to provide a robust dataset of earthquake localizations and focal mechanisms. The effect of uncertainties of the velocity model on fault plane solutions (FPS) has been also evaluated indicating the robustness of the results. The computed stress field indicates a deep compressive faulting with maximum horizontal compressive stress, SHmax, trending NW-SE. The seismicity pattern analysis indicates that the whole crust is seismically involved up to a depth of 40 km and indicates the presence of a low-angle seismogenic surface trending SW-NE and dipping SE-NW, similar to the Gargano–Dubrovnik lineament. Shallower events, along the eastern sector of the Mattinata Fault (MF), are W-E dextral strike-slip fault. Therefore, we hypothesized that the seismicity is locally facilitated by preexisting multidirectional fractures, confirmed by the heterogeneity of focal mechanisms, and explained by the different reactivation processes in opposite directions over the time, involving the Mattinata shear zone.
    Description: Published
    Description: 589332
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Gargano promontory ; OTRIONS local seismic network ; focal mechanisms ; stress field ; microseismicity ; mattinata fault ; gargano-dubrovnik lineament ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    In situ Skeletal Growth Rates of the Solitary Cold-Water Coral Tethocyathus endesa From the Chilean Fjord Region (2021)
    Frontiers Media S.A.
    In:  EPIC3Frontiers in Marine Science, Frontiers Media S.A., 8(757702), ISSN: 22967745
    Details
    Publication Date: 2022-01-10
    Description: Cold-water corals (CWC) can be found throughout a wide range of latitudes (79°N–78°S). Since they lack the photosymbiosis known for most of their tropical counterparts, they may thrive below the euphotic zone. Consequently, their growth predominantly depends on the prevalent environmental conditions, such as general food availability, seawater chemistry, currents, and temperature. Most CWC communities live in regions that will face CaCO3 undersaturation by the end of the century and are thus predicted to be threatened by ocean acidification (OA). This scenario is especially true for species inhabiting the Chilean fjord system, where present-day carbonate water chemistry already reaches values predicted for the end of the century. To understand the effect of the prevailing environmental conditions on the biomineralization of the CWC Tethocyathus endesa, a solitary scleractinian widely distributed in the Chilean Comau Fjord, a 12-month in situ experiment was conducted. The in situ skeletal growth of the test corals was assessed at two sites using the buoyant weight method. Sites were chosen to cover the naturally present carbonate chemistry gradient, with pH levels ranging between 7.90 ± 0.01 (mean ± SD) and 7.70 ± 0.02, and an aragonite saturation (Ωarag) between 1.47 ± 0.03 and 0.98 ± 0.05. The findings of this study provide one of the first in situ growth assessments of a solitary CWC species, with a skeletal mass increase of 46 ± 28 mg per year and individual, at a rate of 0.03 ± 0.02% day. They also indicate that, although the local seawater chemistry can be assumed to be unfavorable for calcification, growth rates of T. endesa are comparable to other cold-water scleractinians in less corrosive waters (e.g., Lophelia pertusa in the Mediterranean Sea).
    Repository Name: EPIC Alfred Wegener Institut
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  • 9
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    Analysis of Swarm Satellite Magnetic Field Data Before the 2016 Ecuador (Mw = 7.8) Earthquake Based on Non-negative Matrix Factorization (2021)
    Frontiers Media S.A.
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    Publication Date: 2021-10-28
    Description: In this paper, based on non-negative matrix factorization (NMF), we analyzed the ionosphere magnetic field data of the Swarm Alpha satellite before the 2016 (Mw = 7. 8) Ecuador earthquake (April 16, 0.35°N, 79.93°W), including the whole data collected under quiet and disturbed geomagnetic conditions. The data from each track were decomposed into basis features and their corresponding weights. We found that the energy and entropy of one of the weight components were more concentrated inside the earthquake-sensitive area, which meant that this weight component was more likely to reflect the activity inside the earthquake-sensitive area. We focused on this weight component and used five times the root mean square (RMS) to extract the anomalies. We found that for this weight component, the cumulative number of tracks, which had anomalies inside the earthquake-sensitive area, showed accelerated growth before the Ecuador earthquake and recovered to linear growth after the earthquake. To verify that the accelerated cumulative anomaly was possibly associated with the earthquake, we excluded the influence of the geomagnetic activity and plasma bubble. Through the random earthquake study and low-seismicity period study, we found that the accelerated cumulative anomaly was not obtained by chance. Moreover, we observed that the cumulative Benioff strain S, which reflected the lithosphere activity, had acceleration behavior similar to the accelerated cumulative anomaly of the ionosphere magnetic field, which suggested that the anomaly that we obtained was possibly associated with the Ecuador earthquake and could be described by one of the Lithosphere–Atmosphere–Ionosphere Coupling (LAIC) models.
    Description: This research was supported by the National Natural Science Foundation of China under Grant No. 41974084 and the International Cooperation Project of Department of Science and Technology of Jilin Province No. 20200801036GH.
    Description: Published
    Description: 621976
    Description: 7T. Variazioni delle caratteristiche crostali e "precursori"
    Description: JCR Journal
    Keywords: Ecuador earthquake ; cumulative number of anomalous tracks ; Swarm satellites magnetic field ; non-negative matrix factorization decomposition ; 04.05. Geomagnetism ; 01.02. Ionosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    Editorial: Bridging Environmental Magnetism With Biogeophysics to Study Biogeochemical Processes of Today (2021)
    Frontiers Media S.A.
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    Publication Date: 2021-11-29
    Description: Since the first studies on biogeophysics in the early 2000s our understanding of how biogeochemical processes affect geophysical signatures has significantly improved. This interdisciplinary field now incorporates and integrates environmental and rock magnetism with traditional biological and geochemical methods to interpret geophysical signatures in highly dynamic environments (e.g., biogeochemical hotspots, contamination plumes). Environmental magnetism, in particular, can trace environmental changes by identifying magnetic mineral transformations induced from several biogeochemical processes. This Special Issue includes papers that present applications of environmental and rock magnetism in biogeophysics and discuss their impact on Earth Sciences.
    Description: Published
    Description: 757171
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Keywords: environmental magnetism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
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    Probabilistic Tsunami Hazard and Risk Analysis: A Review of Research Gaps (2021)
    Frontiers Media S.A.
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    Publication Date: 2021-12-14
    Description: Tsunamis are unpredictable and infrequent but potentially large impact natural disasters. To prepare, mitigate and prevent losses from tsunamis, probabilistic hazard and risk analysis methods have been developed and have proved useful. However, large gaps and uncertainties still exist and many steps in the assessment methods lack information, theoretical foundation, or commonly accepted methods. Moreover, applied methods have very different levels of maturity, from already advanced probabilistic tsunami hazard analysis for earthquake sources, to less mature probabilistic risk analysis. In this review we give an overview of the current state of probabilistic tsunami hazard and risk analysis. Identifying research gaps, we offer suggestions for future research directions. An extensive literature list allows for branching into diverse aspects of this scientific approach.
    Description: Published
    Description: 628772
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
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  • 12
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    Editorial: Submarine Active Faults: From Regional Observations to Seismic Hazard Characterization (2021)
    Frontiers Media S.A.
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    Publication Date: 2021-12-15
    Description: Since the beginning of the XXI Century, our society has witnessed a number of catastrophic earthquakes with devastating consequences (e.g., Sumatra 2004, Haiti 2010, Japan 2010, Nepal 2015, Italy 2009 and 2016). Localizing the active faults and understanding their earthquake history is key to improve modern probabilistic seismic hazard assessment (PSHA) and, thus, to mitigate the consequences of future events. Seismicity models to characterize the earthquake frequency in a region in PSHA studies have been traditionally based on archaeological, historical and instrumental earthquake records. However, the rapid advance of active tectonics and paleoseismological studies has resulted in the development of seismicity models for faults, since they allow characterizing the active faults, reconstructing their 3D geometry at depth, and determining their past earthquake history and seismic potential based on the interpretation of the geological record. Traditionally, active tectonics and paleoseismological research had been mainly conducted to study onshore active faults. However, the occurrence of the offshore Sumatra (2004) and Japan (2010) earthquakes and consequent tsunamis, which caused tens of thousands of casualties and extensive and severe damage and economic losses, have brought into sharp focus the need to better understand the geohazards related to submarine active faults. In the last few years, the availability of offshore geological and geophysical data at various scales (e.g., deep and shallow borehole, wide angle seismic profiles, tomography, 3D and 2D seismic reflection surveys, high resolution bathymetry or seafloor imaging) has allowed for a better definition of offshore fault systems. These studies focused on accurately constraining the kinematic, architecture and linkage of active faults, and, in some cases, identify recent earthquake ruptures or recognize and date individual events. In addition, underwater active tectonics and paleoseismological studies benefit from: (1) low erosional rates that preserve fault morphology and segmentation; (2) continuous sedimentation in time and space that allows for local and/or regional stratigraphic and chronostratigraphic correlations; (3)multiscale seafloor mapping and sub-seafloor seismic imaging; and 4) absence–or lowest amount–of human modification. This Research Topic includes fourteen published articles focused in the study of underwater active tectonic regions or active fault systems around the world
    Description: Published
    Description: 809205
    Description: 2T. Deformazione crostale attiva
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
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    Paroxysms at Stromboli Volcano (Italy): Source, Genesis and Dynamics (2021)
    Frontiers Media S.A.
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    Publication Date: 2021-12-15
    Description: Deciphering the triggering mechanisms of violent explosive activity is of broad interest for understanding the dynamics of basaltic open-vent volcanic systems. For nearly 1300 years Stromboli has been renowned not only for its continuous degassing activity and mild explosions at the summit craters, but also for short-lived, violent explosive events of variable scale, known as major explosions and paroxysms. Here, we focus on the 1456 and 1930 paroxysms and on the most recent events, in July and August 2019 at Stromboli. We show that shallow phenomena such as flank collapse, lava outpouring through fractures opening, or partial emptying of the shallow conduit, only speed up volatile-rich magma ascent by increasing the decompression rate, whereas pressurization of the crustal system and the deep refilling by magma and its CO2-rich gas phase play a major role in triggering paroxysms. Moreover, we present new data on the geochemistry of the 2019 bulk pumice, along with a compilation of data from the literature, chemical profiles in olivine crystals, and the physical parameters of explosive eruptions of wide ranging magnitude and intensity. For small and large paroxysms, timescales were derived from Fe–Mg diffusion profiles in olivine. In both types of explosion, the last phases of crystallization-diffusion indicate rapid magma ascent rates of two to ten days prior to eruption. Trace element concentrations (Nb, La and Ba) and ratios (Rb/Th) indicate that the 2019 pumice samples plot in the domain of magma batches erupted within the last 20 years at Stromboli. As a whole, there is no correlation between magma geochemistry and magnitude or intensity of explosive eruptions, which span a range of ∼3 orders of magnitude (from major explosions to large paroxysms) based on estimates of erupted tephra volumes. In contrast, olivine compositions are a good proxy for erupted tephra volumes and magma flux. The correlation among physical and chemical parameters, which is valid for the overall spectrum of eruptions, implies that the magmatic source ultimately controls eruptive dynamics.
    Description: Published
    Description: 593339
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: Stromboli, paroxysms, diffusion profiles, olivine
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  • 14
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    Volcanic Lakes in Africa: The VOLADA_Africa 2.0 Database, and Implications for Volcanic Hazard (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-13
    Description: Here we introduce the updated, interactive and open-access database for African volcanic lakes, country by country. The previous database VOLADA (VOlcanic LAke DAta Base, Rouwet et al., 2014) reported 96 volcanic lakes for Africa. This number is now revised and established at 220, converting VOLADA_Africa 2.0 in the most comprehensive resource for African volcanic lakes: 81 in Uganda, 37 in Kenya, 33 in Cameroon, 28 in Madagascar, 19 in Ethiopia, 6 in Tanzania, 2 in Rwanda, 2 in Sudan, 2 in D.R. Congo, 1 in Libya, and 9 on the minor islands around Africa. We present the current state-of-the-art of arguably all the African volcanic lakes that the global experts and regional research teams are aware of, and provide hints for future research directions, with a special focus on the volcanic hazard assessment. All lakes in the updated database are classified for their genetic origin and their physical and chemical characteristics, and level of study. The predominant rift-related volcanism in Africa favors basaltic eruptive products, leading to volcanoes with highly permeable edifices (e.g. scoria), and hence less-developed hydrothermal systems. Basal aquifers accumulate under large volcanoes and in rift depressions providing a potential scenario for phreatomagmatic volcanism. This hypothesis, based on a morphometric analysis and volcanological research from literature, conveys the predominance of maar lakes in large monogenetic fields in Africa (e.g. Uganda, Cameroon, Ethiopia), and the absence of high-activity crater lakes, generally found at arc-volcanoes. Considering the large number of maar lakes in Africa (172), within similar geotectonic settings and meteoric conditions as in Cameroon, it is somewhat surprising that “only” from Lake Monoun and Lake Nyos fatal CO2 bursts have been recorded. Explaining why other maars did not erupt in such fashion is a question that can only be answered by enhancing insights into physical limnology and fluid geochemistry of the so far poorly studied lakes. From a hazard perspective, there is an urgent need to tackle this task as a community.
    Description: Published
    Description: 717798
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Modeling Tsunamis Generated by Submarine Landslides at Stromboli Volcano (Aeolian Islands, Italy): A Numerical Benchmark Study (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-15
    Description: We present a benchmark study aimed at identifying the most effective modeling approach for tsunami generation, propagation, and hazard in an active volcanic context, such as the island of Stromboli (Italy). We take as a reference scenario the 2002 landslide-generated tsunami event at Stromboli simulated to assess the relative sensitivity of numerical predictions to the landslide and the wave models, with our analysis limited to the submarine landslide case. Two numerical codes, at different levels of approximation, have been compared in this study: the NHWAVE three-dimensional non-hydrostaticmodel in sigma-coordinates and theMultilayer-HySEA model. In particular, different instances of Multilayer-HySEA with one or more vertical discretization layers, in hydrostatic and non-hydrostatic formulation and with different landslide models have been tested. Model results have been compared for the maximum runup along the shores of Stromboli village, and the waveform sampled at four proximal sites (two of them corresponding to the locations of the monitoring gauges, offshore the Sciara del Fuoco). Both rigid and deformable (granular) submarine landslide models, with volumes ranging from 7 to 25 million of cubic meters, have been used to trigger the water waves, with different physical descriptions of the mass movement. Close to the source, the maximum surface elevation and the resulting runup at the Stromboli village shores obtainedwith hydrostatic and non-hydrostaticmodels are similar. However, hydrostatic models overestimate (with respect to non-hydrostatic ones) the amplitude of the initial positive wave crest, whose height increases with the distance. Moreover, as expected, results indicate significant differences between the waveforms produced by the different models at proximal locations. The accuratemodeling of near-field waveforms is particularly critical at Stromboli in the perspective of using the installed proximal sea-level gauges, together with numerical simulations, to characterize tsunami source in an early-warning system. We show that the use of non-hydrostatic models, coupled with a multilayer approach, allows a better description of the waveforms. However, the source description remains the most sensitive (and uncertain) aspect of the modeling. We finally show that non-hydrostatic models, such as Multilayer-HySEA, solved on accelerated GPU architectures, exhibit the optimal trade-off between accuracy and computational requirements, at least for the envisaged problem size and for what concerns the proximal wave field of tsunamis generated by volcano landslides. Their application and future developments are opening new avenues to tsunami early warning at Stromboli.
    Description: Published
    Description: 628652
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
    Keywords: landslide ; tsunami ; volcano ; Stromboli ; numerical simulation ; benchmark ; hazard assessment ; 04.08. Volcanology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 16
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    A High Resolution Reanalysis for the Mediterranean Sea (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-22
    Description: In order to be able to forecast the weather and estimate future climate changes in the ocean, it is crucial to understand the past and the mechanisms responsible for the ocean variability. This is particularly true in a complex area such as the Mediterranean Sea with diverse dynamics like deep convection and overturning circulation. To this end, effective tools are ocean reanalyses or reconstructions of the past ocean state. Here we present a new physical reanalysis of the Mediterranean Sea at high resolution, developed in the Copernicus Marine Environment Monitoring Service (CMEMS) framework. The hydrodynamic model is based on the Nucleus for European Modelling of the Ocean (NEMO) combined with a variational data assimilation scheme (OceanVar). The model has a horizontal resolution of 1/24° and 141 unevenly distributed vertical z* levels. It provides daily and monthly temperature, salinity, current, sea level and mixed layer depth as well as hourly fields for surface velocities and sea level. ECMWF ERA-5 atmospheric fields force the model and daily boundary conditions in the Atlantic are taken from a global reanalysis. The reanalysis covers the 33 years from 1987 to 2019. Initialized from SeaDataNet climatology in January 1985, it reaches a nominal state after a 2-years spin-up. In-situ data from CTD, ARGO floats and XBT are assimilated into the model in combination with satellite altimetry observations. This reanalysis has been validated and assessed through comparison to in-situ and satellite observations as well as literature climatologies. The results show an overall improvement of the comparison with observations and a better representation of the main dynamics of the region compared to a previous, lower resolution (1/16°), reanalysis. Temperature and salinity RMSD are decreased by respectively 14 and 18%. The salinity biases at depth of the previous version are corrected. Climate signals show continuous increase of the temperature and salinity, confirming estimates from observations and other reanalysis. The new reanalysis will allow the study of physical processes at multi-scales, from the large scale to the transient small mesoscale structures and the selection of climate indicators for the basin.
    Description: Published
    Description: 702285
    Description: 4A. Oceanografia e clima
    Description: JCR Journal
    Keywords: ocean ; mediterranean sea ; reanalysis ; numerical modelling ; observations ; data assimilation ; multi-scale
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 17
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    The Seismicity of Lipari, Aeolian Islands (Italy) From One-Month Recording of the LIPARI Array (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-22
    Description: Seismic activity in volcanic settings could be the signature of processes that include magma dynamics, hydrothermal activity and geodynamics. The main goal of this study is to analyze the seismicity of Lipari Island (Southern Tyrrhenian Sea) to characterize the dynamic processes such as the interaction between pre-existing structures and hydrothermal processes affecting the Aeolian Islands. We deployed a dense seismic array of 48 autonomous 3-component nodes. For the first time, Lipari and its hydrothermal field are investigated by a seismic array recording continuously for about a month in late 2018 with a 0.1–1.5 km station spacing. We investigate the distribution and evolution of the seismicity over the full time of the experiment using self-organized maps and automatic algorithms. We show that the sea wave motion strongly influences the background seismic noise. Using an automatic template matching approach, we detect and locate a seismic swarm offshore the western coast of Lipari. This swarm, made of transient-like signals also recognized by array and polarization analyses in the time and frequency domains, is possibly associated with the activation of a NE-SW fault. We also found the occurrence of hybrid events close to the onshore Lipari hydrothermal system. These events suggest the involvement of hot hydrothermal fluids moving along pre-existing fractures. Seismological analyses of one month of data detect signals related to the regional tectonics, hydrothermal system and sea dynamics in Lipari Island.
    Description: Published
    Description: 678581
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
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    Application of Subspace-Based Detection Algorithm to Infrasound Signals in Volcanic Areas (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-23
    Description: Infrasonic signals investigation plays a fundamental role for both volcano monitoring purpose and the study of the explosion dynamics. Proper and reliable detection of weak signals is a critical issue in active volcano monitoring. In particular, in volcanic acoustics, it has direct consequences in pinpointing the real number of generated events (amplitude transients), especially when they exhibit low amplitude, are close in time to each other, and/or multiple sources exist. To accomplish this task, several algorithms have been proposed in literature; in particular, to overcome limitations of classical approaches such as short-time average/long-time average and cross-correlation detector, in this paper a subspace-based detection technique has been implemented. Results obtained by applying subspace detector on real infrasound data highlight that this method allows sensitive detection of lower energy events. This method is based on a projection of a sliding window of signal buffer onto a signal subspace that spans a collection of reference signals, representing similar waveforms from a particular infrasound source. A critical point is related to subspace design. Here, an empirical procedure has been applied to build the signal subspace from a set of reference waveforms (templates). In addition, in order to determine detectors parameters, such as subspace dimension and detection threshold, even in presence of overlapped noise such as infrasonic tremor, a statistical analysis of noise has been carried out. Finally, the subspace detector reliability and performance, have been assessed by performing a comparison among subspace approach, cross correlation detector and short-time average/long-time average detector. The obtained confusion matrix and extrapolated performance indices have demonstrated the potentiality, the advantages and drawbacks of the subspace method in tracking volcanic activity producing infrasound events. This method revealed to be a good compromise in detecting low-energy and very close in time events recorded during Strombolian activity
    Description: Published
    Description: 579923
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
    Keywords: infrasound signal ; trigger algorithm ; infrasound volcano monitoring ; strombolian activity ; etna volcano ; infrasonic tremor ; subspace detector ; infrasound events ; solid earth ; 04.08. Volcanology ; 04.06. Seismology
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  • 19
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    Deep Magma Transport Control on the Size and Evolution of Explosive Volcanic Eruptions (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-11-29
    Description: Explosive eruptions are the surface manifestation of dynamics that involve transfer of magma from the underground regions of magma accumulation. Evidence of the involvement of compositionally different magmas from different reservoirs is continuously increasing to countless cases. Yet, models of eruption dynamics consider only the uppermost portion of the plumbing system, neglecting connections to deeper regions of magma storage. Here we show that the extent and efficiency of the interconnections between different magma storage regions largely control the size of the eruptions, their evolution, the causes of their termination, and ultimately their impact on the surrounding environment. Our numerical simulations first reproduce the magnitude-intensity relationship observed for explosive eruptions on Earth and explain the observed variable evolutions of eruption mass flow rates. Because deep magmatic interconnections are largely inaccessible to present-day imaging capabilities, our results motivate the need to better image and characterize extant magma bodies.
    Description: Published
    Description: 681083
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
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  • 20
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    The Seismicity of Ischia Island, Italy: An Integrated Earthquake Catalogue From 8th Century BC to 2019 and Its Statistical Properties (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-01
    Description: Ischia is a densely inhabited and touristic volcanic island located in the northern sector of the Gulf of Naples (Italy). In 2017, the Mw 3.9 Casamicciola earthquake occurred after more than one century of seismic quiescence characterized only by minor seismicity, which followed a century with three destructive earthquakes (in 1828, 1881, and 1883). These events, despite their moderate magnitude (Mw 〈 5.5), lead to dreadful effects on buildings and population. However, an integrated catalogue systematically covering historical and instrumental seismicity of Ischia has been still lacking since many years. Here, we review and systematically re-analyse all the available data on the historical and instrumental seismicity, to build an integrated earthquake catalogue for Ischia with a robust characterization of existing uncertainties. Supported by new or updated macroseismic datasets, we significantly enriched existing catalogues, as the Italian Parametric Earthquake Catalogue (CPTI15) that, with this analysis, passed from 12 to 57 earthquakes with macroseismic parametrization. We also extended back by 6 years the coverage of the instrumental catalogue, homogenizing the estimated seismic parameters. The obtained catalogue will not only represent a solid base for future local hazard quantifications, but also it provides the unique opportunity of characterizing the evolution of the Ischia seismicity over centuries. To this end, we analyse the spatial, temporal, and magnitude distributions of Ischia seismicity, revealing for example that, also in the present long-lasting period of volcanic quiescence, is significantly non-stationary and characterized by a b-value larger than 1.
    Description: This work benefited of the agreement between Istituto Nazionale di Geofisica e Vulcanologia and the Italian Presidenza del Consiglio dei Ministri, Dipartimento della Protezione Civile (DPC).
    Description: Published
    Description: 629736
    Description: 4T. Sismicità dell'Italia
    Description: 6SR VULCANI – Servizi e ricerca per la società
    Description: 1IT. Reti di monitoraggio e sorveglianza
    Description: 4IT. Banche dati
    Description: JCR Journal
    Keywords: Ischia island ; Volcano seismicity ; Seismic catalogue ; Completeness analysis ; Ensemble modelling ; Frequency size distribution ; Poisson process ; 04.06. Seismology ; 04.08. Volcanology ; 05.02. Data dissemination ; 05.04. Instrumentation and techniques of general interest
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  • 21
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    Gas Emissions From the Western Aleutians Volcanic Arc (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-06
    Description: The Aleutian Arc is remote and highly active volcanically. Its 4,000 km extent from mainland Alaska to Russia’s Kamchatka peninsula hosts over 140 volcanic centers of which about 50 have erupted in historic times. We present data of volcanic gas samples and gas emission measurements obtained during an expedition to the western-most segment of the arc in September 2015 in order to extend the sparse knowledge on volatile emissions from this remote but volcanically active region. Some of the volcanoes investigated here have not been sampled for gases before this writing. Our data show that all volcanoes host high-temperature magmatic-hydrothermal systems and have gas discharges typical of volcanoes in oceanic arcs. Based on helium isotopes, the western Aleutian Arc segment has minimal volatile contributions from the overriding crust. Volcanic CO2 fluxes from this arc segment are small, compared to the emissions from volcanoes on the Alaska Peninsula and mainland Alaska. The comparatively low CO2 emissions may be related to the lower sediment flux delivered to the trench in this part of the arc.
    Description: Published
    Description: 786021
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: JCR Journal
    Keywords: Aleutians ; volcano ; gas ; volatiles ; geochemistry ; 04.08. Volcanology ; 04.01. Earth Interior
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  • 22
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    Azimuthal anisotropy from Eikonal Tomography: example from ambient-noise measurements in the AlpArray network (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-24
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: Ambient-noise records from the AlpArray network are used to measure Rayleigh wave phase velocities between more than 150,000 station pairs. From these, azimuthally anisotropic phase-velocity maps are obtained by applying the Eikonal tomography method. Several synthetic tests are shown to study the bias in the Ψ2 anisotropy. There are two main groups of bias, the first one caused by interference between refracted/reflected waves and the appearance of secondary wavefronts that affect the phase travel-time measurements. This bias can be reduced if the amplitude field can be estimated correctly. Another source of error is related to the incomplete reconstruction of the travel-time field that is only sparsely sampled due to the receiver locations. Both types of bias scale with the magnitude of the velocity heterogeneities. Most affected by the spurious Ψ2 anisotropy are areas inside and at the border of low-velocity zones. In the isotropic velocity distribution, most of the bias cancels out if the azimuthal coverage is good. Despite the lack of resolution in many parts of the surveyed area, we identify a number of anisotropic structures that are robust: in the central Alps, we find a layered anisotropic structure, arc-parallel at midcrustal depths and arc-perpendicular in the lower crust. In contrast, in the eastern Alps, the pattern is more consistently E-W oriented which we relate to the eastward extrusion. The northern Alpine forleand exhibits a preferential anisotropic orientation that is similar to SKS observations in the lowermost crust and uppermost mantle.
    Description: German Science Foundation (SPP-2017, Project Ha 2403/21-1); Swiss National Science Foundation SINERGIA Project CRSII2-154434/1 (Swiss-AlpArray); Progetto Pianeta Dinamico, finanziamento MUR-INGV, Task S2 – 2021
    Description: Published
    Description: 151–170
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Seismic anisotropy ; Seismic interferometry ; Seismic tomography ; Wave propagation ; Continental tectonics: compressional ; 04.01. Earth Interior ; 04.06. Seismology
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  • 23
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    Joint Seismic and Gravity Data Inversion to Image Intra-Crustal Structures: The Ivrea Geophysical Body Along the Val Sesia Profile (Piedmont, Italy) (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-14
    Description: We present results from a joint inversion of new seismic and recently compiled gravity data to constrain the structure of a prominent geophysical anomaly in the European Alps: the Ivrea Geophysical Body (IGB). We investigate the IGB structure along the West-East oriented Val Sesia profile at higher resolution than previous studies. We deployed 10 broadband seismic stations at 5 km spacing for 27 months, producing a new database of ∼1000 high-quality seismic receiver functions (RFs). The compiled gravity data yields 1 gravity point every 1–2 km along the profile. We set up an inversion scheme, in which RFs and gravity anomalies jointly constrain the shape and the physical properties of the IGB. We model the IGB’s top surface as a single density and shear-wave velocity discontinuity, whose geometry is defined by four, spatially variable nodes between far-field constraints. An iterative algorithm was implemented to efficiently explore the model space, directing the search toward better fitting areas. For each new candidate model, we use the velocity-model structures for both ray-tracing and observed-RFs migration, and for computation and migration of synthetic RFs: the two migrated images are then compared via cross-correlation. Similarly, forward gravity modeling for a 2D density distribution is implemented. The joint inversion performance is the product of the seismic and gravity misfits. The inversion results show the IGB protruding at shallow depths with a horizontal width of ∼30 km in the western part of the profile. Its shallowest segment reaches either 3–7 or 1–3 km depth below sea-level. The latter location fits better the outcropping lower crustal rocks at the western edge of the Ivrea-Verbano Zone. A prominent, steep eastward-deepening feature near the middle of the profile, coincident with the Pogallo Fault Zone, is interpreted as inherited crustal thickness variation. The found density and velocity contrasts of the IGB agree with physical properties of the main rock units observed in the field. Finally, by frequency-dependent analysis of RFs, we constrain the sharpness of the shallowest portion of the IGB velocity discontinuity as a vertical gradient of thickness between 0.8 km and 0.4 km.
    Description: The Swiss National Science Foundation (SNF) supported this research (grant numbers PP00P2_157627 and PP00P2_187199 of project OROG3NY), as well as the Grant Agency of the Czech Republic (No. 21-25710). The project CzechGeo/EPOS No. LM2015079 of the MEYS funded the MOBNET station pool.
    Description: Published
    Description: 671412
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: joint inversion ; seismic receiver functions ; gravity anomalies ; Ivrea Geophysical Body ; Ivrea-Verbano Zone ; continental crust ; intra-crustal structure ; 04.01. Earth Interior ; 04.06. Seismology
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  • 24
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    Campi Flegrei, Vesuvius and Ischia Seismicity in the Context of the Neapolitan Volcanic Area (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-06
    Description: Studying seismicity in a volcanic environment provides important information on the state of activity of volcanoes. The seismicity of the Neapolitan volcanoes, Campi Flegrei, Vesuvius, and Ischia, shows distinctive characteristics for each volcano, coveringwide range of patterns and types. In this study we relocated some significant volcano- tectonic earthquake swarms that occurred in Campi Flegrei and Vesuvius. Moreover, we compared the earthquake occurrence evolution, the magnitude and the seismic energy release of the three volcanoes. Also, we considered the results of seismic analysis in the light of geochemical and ground deformation data that contribute to defining the state of activity of volcanoes. In Campi Flegrei, which is experiencing a long term unrest, we identified a seismogenic structure at shallow depth in Pisciarelli zone that has been activated repeatedly. The increasing seismicity accompanies an escalation of the hydrothermal activity and a ground uplift phase. At Vesuvius a very shallow seismicity is recorded, which in recent years has shown an increase in terms of the number of events per year. Earthquakes are usually located right beneath the crater axis. They are concentrated in a volume affected by the hydrothermal system. Finally, Ischia generally shows a low level of seismicity, however, in Casamicciola area events with a moderate magnitude can occur and these are potentially capable of causing severe damage to the town and population, due to their small hypocentral depth (typically 〈 2.5 km). After the seismic crisis of August 21, 2017 (mainshock magnitude M 4), the seismicity returned to a low level in terms of occurrence rate and magnitude of earthquakes. The seismicity of these three different volcanic areas shows some common aspects that highlight a relevant role of hydrothermal processes in the seismogenesis of volcanic areas. However, while the main swarms in Campi Flegrei and most of the Vesuvian earthquakes are distributed along conduit-like structures, the seismicity of Ischia is mainly located along faults. Furthermore, the temporal evolution of seismicity in Neapolitan volcanic area suggests a concomitant increase in the occurrence of earthquakes both in Campi Flegrei and Vesuvius in recent years.
    Description: Published
    Description: 662113
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: 04.08. Volcanology
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  • 25
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    Carbon Dioxide in Lake Nyos, Cameroon, Estimated Quantitatively From Sound Speed Measurements (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-13
    Description: Dissolved gases in the deep water of lakes can pose a safety hazard when extreme concentrations are reached. A sudden release of large amounts of gas can cost the lives of humans living in the neighbourhood, as has happened at Lake Nyos in 1986. Since 2001, Lake Nyos gas risk has been mitigated by induced degassing, but the connection to the gas source is still in place and a regular survey needs to be implemented to guarantee safe conditions. Frequent sampling at the remote location of Lake Nyos requires an enormous effort and many analytical techniques are nearly impossible to run at the lake site. In this contribution, we combined a commercially available sound speed sensor with a CTD (conductivity-temperature-depth) probe to gain an indirect but quantitative estimate of carbon dioxide concentrations at fine depth resolution (decimeter scale). Dissolved carbon dioxide increases sound speed but does not contribute to electrical conductivity. Hence the difference between measured and calculated (on the base of electrical conductivity, temperature and pressure) and measured sound speed gives a quantitative indication of dissolved carbon dioxide. We highly recommend the implementation of the sound speed-CTD probe combination, at Lake Nyos, or at other gas-laden volcanic lakes, as it could safeguard the people living in the area with acceptable cost and effort for the operators, when alarming CO2 concentrations in deep lake strata will be timely detected.
    Description: Published
    Description: 645011
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
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  • 26
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    The focal mechanism of the 7 September 1920, Mw 6.5 earthquake: insights into the seismotectonics of the Lunigiana–Garfagnana area, Tuscany, Italy (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-15
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: To understand the seismotectonics and the seismic hazard of the study sector of the Northern Apennines (Italy), one of the most important earthquakes of magnitude Mw = 6.5 which struck the Lunigiana and Garfagnana areas (Tuscany) on 7 September 1920 should be studied. Given the early instrumental epoch of the event, neither geometric and kinematic information on the fault-source nor its fault-plane solution were available. Both areas were candidates for hosting the source fault and there was uncertainty between a normal fault with Apenninic direction or an anti-Apenninic strike-slip. We retrieved 11 focal parameters (including the fault-plane solution) of the 1920 earthquake. Only macroseismic intensity information (from 499 inhabited centres) through the KF-NGA inversion technique was used. This technique uses a Kinematic model of the earthquake source and speeds up the calculation by a Genetic Algorithm with Niching. The result is a pure dip-slip focal solution. The intrinsic ambiguities of the KF-NGA method (±180° on the rake angle; choice of the fault plane between the two nodal planes) were solved with field and seismotectonic evidence. The earthquake was generated by a normal fault (rake angle = 265° ± 8°) with an Apennine direction (114° ± 5°) and dipping 38° ± 6° towards SW. The likely candidate for hosting the source-fault in 1920 is the Compione-Comano fault that borders the NE edge of the Lunigiana graben. The KF-NGA algorithm proved to be invaluable for studying the kinematics of early instrumental earthquakes and allowed us to uniquely individuate, for the first time ever, the seismogenic source of the 1920 earthquake. Our findings have implications in hazard computation and seismotectonic contexts.
    Description: Published
    Description: 1465–1477
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Inverse theory ; Body waves ; Earthquake source observations ; Seismicity and tectonics ; Dynamics: seismotectonics ; Fractures, faults, and high strain deformation zones ; 04.06. Seismology
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    The Importance of Marine Research Infrastructures in Capturing Processes and Impacts of Extreme Events (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-14
    Description: Extreme events have long been underestimated in the extent to which they shape the surface of our planet, our environment, its ecological integrity, and the sustainability of human society. Extreme events are by definition rarely observed, of significant impact and, as a result of their spatiotemporal range, not always easily predicted. Extremes may be short-term catastrophic events such as tsunamis, or long-term evolving events such as those linked to climate change; both modify the environment, producing irreversible changes or regime shifts. Whatever the driver that triggers the extreme event, the damages are often due to a combination of several processes and their impacts can affect large areas with secondary events (domino effect), whose effects in turn may persist well beyond the duration of the trigger event itself. Early studies of extreme events were limited to opportunistic approaches: observations were made within the context of naturally occurring events with high societal impact. Given that climate change is now moving us out of a relatively static climate regime during the development of human civilization, extreme events are now a function of underlying climate shifts overlain by catastrophic processes. Their impacts are often due to synergistic factors, all relevant in understanding process dynamics; therefore, an integrated methodology has become essential to enhance the reliability of new assessments and to develop strategies to mitigate societal impacts. Here we summarize the current state of extreme event monitoring in the marine system, highlighting the advantages of a multidisciplinary approach using Research Infrastructures for providing the temporal and spatial resolution required to monitor Earth processes and enhance assessment of associated impacts.
    Description: Published
    Description: 626668
    Description: 3A. Geofisica marina e osservazioni multiparametriche a fondo mare
    Description: JCR Journal
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  • 28
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    Editorial: From Tsunami Science to Hazard and Risk Assessment: Methods and Models (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-23
    Description: In this Research Topic, we aimed to contribute to the ongoing scientific progress and the process of assessing and providing community-based standards, good practices, benchmarking tools and guidelines, based on the most recent observations and scientific findings. This purpose is in line with several community-based efforts like those of the “GTM—Global Tsunami Model” and “AGITHAR—Accelerating Global science In Tsunami Hazard and Risk analysis” scientific networks. We aimed to help better address the link between tsunami science and the Probabilistic Tsunami Hazard and Risk Analysis. This Topic includes numerous Original Research papers, one Brief Research Report and one Review. Overall, we gathered 20 articles contributed by more than 200 authors. We consider this a strong indication from the research community.
    Description: Published
    Description: 764922
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: 8T. Sismologia in tempo reale e Early Warning Sismico e da Tsunami
    Description: 6V. Pericolosità vulcanica e contributi alla stima del rischio
    Description: 1SR TERREMOTI - Sorveglianza Sismica e Allerta Tsunami
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 29
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    Intraplate Basalt Alkalinity Modulated by a Lithospheric Mantle Filter at the Dunedin Volcano (New Zealand) (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-22
    Description: Systematic variations in the crystal cargo and whole-rock isotopic compositions of mantle-derived basalts in the intraplate Dunedin Volcano (New Zealand) indicate the influence of a complex mantle-to-crust polybaric plumbing system. Basaltic rocks define a compositional spectrum from low-alkali basalts through mid-alkali basalts to high-alkali basalts. High-alkali basalts display clinopyroxene crystals with sector (hourglass) and oscillatory zoning (Mg#61–82) as well as Fe-rich green cores (Mg#43–69), whereas low-alkali basalts are characterized by clinopyroxenes with unzoned overgrowths (Mg#69–83) on resorbed mafic cores (Mg#78–88), coexisting with reversely zoned plagioclase crystals (An43–68 to An60–84 from core to rim). Complex magma dynamics are indicated by distinctive compositional variations in clinopyroxene phenocrysts, with Cr-rich zones (Mg#74–87) indicating continuous recharge by more mafic magmas. Crystallization of olivine, clinopyroxene and titanomagnetite occurred within a polybaric plumbing system extending from upper mantle to mid-crustal depths (485–1059 MPa and 1147–1286°C), whereas crystallization of plagioclase with subordinate clinopyroxene and titanomagnetite proceeded towards shallower crustal levels. The compositions of high-alkali basalts and mid-alkali basalts resemble those of ocean island basalts and are characterized by FOZO-HIMU isotopic signatures (87Sr/86Sri = 0.70277–0.70315, 143Nd/144Ndi = 0.51286–0.51294 and 206Pb/204Pb = 19.348–20.265), whereas low-alkali basalts have lower incompatible element abundances and isotopic compositions trending towards EMII (87Sr/86Sri = 0.70327–70397, 143Nd/144Ndi = 0.51282–0.51286 and 206Pb/204Pb = 19.278–19.793). High- and mid-alkali basalt magmas mostly crystallized in the lower crust, whereas low-alkali basalt magma recorded deeper upper mantle clinopyroxene crystallization before eruption. The variable alkaline character and isotope composition may result from interaction of low-alkaline melts derived from the asthenosphere with melts derived from lithospheric mantle, possibly initiated by asthenospheric melt percolation. The transition to more alkaline compositions was induced by variable degrees of melting of metasomatic lithologies in the lithospheric mantle, leading to eruption of predominantly small-volume, high-alkali magmas at the periphery of the volcano. Moreover, the lithosphere imposed a filtering effect on the alkalinity of these intraplate magmas. As a consequence, the eruption of low-alkali basalts with greater asthenospheric input was concentrated at the centre of the volcano, where the plumbing system was more developed.
    Description: Published
    Description: egab062
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: alkali basalts ; Dunedin Volcano ; thermobarometry ; primary magma ; lithospheric mantle filter ; Igneous Petrology ; Thermobarometry ; Mantle melting and metasomatism ; Magmatic plumbing systems
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    Water Vapor Tomography of the Lower Atmosphere from Multiparametric Inversion: the Mt. Etna Volcano Test Case (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-22
    Description: Space techniques based on GPS and SAR interferometry allow measuringmillimetric ground deformations. Achieving such accuracy means removing atmospheric anomalies that frequently affect volcanic areas by modeling the tropospheric delays. Due to the prominent orography and the high spatial and temporal variability of weather conditions, the active volcano Mt. Etna (Italy) is particularly suitableto carry out research aimed at estimating and filtering atmospheric effects on GPS and DInSAR grounddeformation measurements. The aim of this work is to improve the accuracy of the ground deformation measurements by modeling the tropospheric delays at Mt. Etna volcano. To this end, data from the monitoring network of 29 GPS permanent stations and MODIS multispectral satellite data series are used to reproduce the tropospheric delays affecting interferograms. A tomography algorithm has been developed to reproduce the wet refractivityfield over Mt. Etna in 3D, starting from the slant tropospheric delays calculated by GPS in all the stations of the network. The developed algorithm has been tested on a synthetic atmospheric anomaly. The test confirms the capability of the software to faithfully reconstruct the simulated anomaly. With the aim of applying this algorithm to real cases, we introduce the water vapor contentmeasured by the MODIS instrument on board Terra and Aqua satellites. The use of such data,although limited by cloud cover, provides a two-fold benefit: it improves the tomographic resolution and adds feedback for the GPS wet delay measurements. A cross-comparison between GPS and MODIS water vapor measurements for thefirst time shows a fair agreement between those indirect measurements on an entire year of data (2015). The tomography algorithm was applied on selected real cases to correct the Sentinel-1 DInSAR interferograms acquired over Mt. Etna during 2015. Indeed, the corrected interferograms show that the differential path delay reaches 0.1 m (i.e. 3 C-band fringes) in ground deformation, demonstrating how the atmospheric anomaly affects precision and reliability of DInSAR space-based techniques. The real cases show that the tomography is often able to capturethe atmospheric effect at the large scale and correct interferograms, although in limited areas. Furthermore, the introduction of MODIS data significantly improves by ∼80% voxel resolution at the critical layer (1,000 m). Further improvements will be suitable for monitoring active volcanoes worldwide.
    Description: Published
    Description: 510514
    Description: 5IT. Osservazioni satellitari
    Description: JCR Journal
    Keywords: tomography, GPS, etna, earth observation data, SAR, water vapor
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  • 31
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    Upward Magma Migration within the Multi-level Plumbing System of the Changbaishan Volcano (China/North Korea) Revealed by the Modeling of 2018-2020 SAR Data (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2022-02-02
    Description: Changbaishan volcano (China/North Korea border) consists of a cone with a summit caldera and last erupted in 1903. An unrest episode occurred between 2002 and 2006, followed by subsidence. The volcano was responsible for the largest eruption of the last Millennium in 946 CE and it is characterized by a multi-level plumbing system. Here, we analyze the Changbaishan 2018-2020 deformations by using remote sensing data, detecting an up to 20 mm/yr, NW-SE elongated nearly-uplift of its southeastern flank and a -20 mm/yr nearly-subsidence of the southwestern flank. Modeling results show that three active sources are responsible for the observed ground velocities: a deep tabular deflating source, a shallower inflating NW-SE elongated spheroid source, and a NW-SE striking dip-slip fault. The depth and geometry of the inferred sources are consistent with independent petrological and geophysical data. Our results reveal an upward magma migration from 14 km to 7.7 km. The modeling of the leveling data of the 2002-2005 uplift and 2009-2011 subsidence depicts sources consistent with the 2018-2020 active system retrieved. The past unrest is related to pressurization of the upper portion of the spheroid magma chamber, whereas the subsidence is due to crystallization of its floor, this latter reactivated in 2018-2020. Therefore, Changbaishan is affected by an active magma recharge controlled by a NW-SE trending fault system. Satellite data analysis is a key tool to unravel the magma dynamics at poorly monitored and crossborder volcanoes.
    Description: Published
    Description: 741287
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: active magma recharge ; Plumbing system ; Deformation modelling ; Changbaishan volcano ; InSAR ; 04.08. Volcanology
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    Editorial: Impact of Deep Oceanic Processes on Circulation and Climate Variability: Examples From the Mediterranean Sea and the Global Ocean (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-14
    Description: The ocean is a crucial component of the Earth’s climate system. Heat and CO2 are absorbed in the ocean’s surface and transported throughout the ocean depths through the overturning circulation. Exchange across the ocean’s turbulent surface boundary layer can happen rapidly, in hours or days, and significant exchange of water between the boundary layer and the stratified main thermocline occurs over timescales of years to decades. Deepwater takes many decades to millennia to return to the surface, acting as long-term storage for heat and CO2 and thereby lessening the near-term impacts of climate change. The understanding of mechanisms and rates that control the bottom flows is essential to quantify re-transfer towards the upper layers of the energy stored at the seafloor. These processes are significantly affecting the ocean system as a whole and could contribute to accelerating the rising climate trends (thermohaline circulation, sea-level rise, and ocean acidification). The Mediterranean Sea, like the ocean, has its overturning circulation and it represents a suitable lab for investigating physical mechanisms such as deepwater formation, mixing processes, strait dynamics, advective-convective feedbacks that drive the ocean variability, and the internal exchange mechanisms. Also, the scale of variability is shorter compared to other ocean basins in time and space. As mechanisms governing exchanges of heat and carbon in the ocean occur with long timescales, observational datasets over many decades are required to document, understand, and predict the climate system as a whole. This is also an essential requirement to detect and attribute changes driven by human activities and to predict how the climate system will likely behave in the future. The needs for and uses of deep ocean data extend well beyond closing the global heat budget. Deep ocean data are needed to initialize and constrain ocean models and improve their representation of mixing of heat downwards/upwards within the deep ocean. In order to understand past and future climate changes, the characterization of the still unexplored deep dynamics aims to provide crucial results to support new interpretations of the paleo circulation and of those processes that have influenced ventilation and water masses overturning. These new insights will also be essential for leading, in the near future, new tailored parameterizations able to adequately represent the dynamics below 2000m of depth. This article collection conceived in the framework of MedCliver (http://www.medclivar.eu/) community, aims to gather outcomes on deep ocean circulation and bottom mixing not only in the Mediterranean area but also through other important case studies relevant in the characterization of deep processes, considering three different points of view: 1- Theoretical (role of the bottom diffusion) 2- New assimilation and modeling 3- In situ observations of deep long time series These will contribute to improving knowledge of the impacts of key deep processes on the climate system.
    Description: Published
    Description: 801479
    Description: 4A. Oceanografia e clima
    Description: JCR Journal
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  • 33
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    Tales From Three 18th Century Eruptions to Understand Past and Present Behaviour of Etna (2021)
    Frontiers Media S.A.
    Details
    Publication Date: 2021-12-23
    Description: The structure of an active volcano is highly dependent on the interplay between the geodynamic context, the tectonic assessment as well as the magmatic processes in the plumbing system. This complex scenario, widely explored at Etna during the last 40 years, is nevertheless incomplete for the recent historical activity. In 1763 two eruptions occurred along the west flank of the volcano. There, an eruption started on 6th February and formed the scoria cone of Mt. Nuovo and a roughly 4-km-long lava flow field. Another small scoria cone, known as Mt. Mezza Luna, is not dated in historical sources. It is located just 1 km eastward of Mt. Nuovo and produced a 700mlong flow field. We focused on the activity of Mts. Nuovo and Mezza Luna for several reasons. First, the old geological maps and volcanological catalogues indicate that Mt. Mezza Luna and Mt. Nuovo cones were formed during the same eruption, while historical sources described Mt. Nuovo’s activity as producing a single scoria cone and do not give information about the formation of Mt. Mezza Luna. Second, petrologic studies highlight that the products of Mt. Mezza Luna are similar to the sub-aphyric Etna basalts; they preserve a composition relatively close to Etna primitive magma which were also erupted in 1763, during La Montagnola flank eruption, which took place along the South Rift of the volcano. Third, the two scoria cones built up along the so-called West Rift of Etna, which represents one of the main magma-ascent zones of the volcano. We applied a multidisciplinary approach that could prove useful for other volcanoes whose past activity is still to be reconstructed. Critical reviews of historical records, new field surveys, petrochemical analyses and petrologic modelling of the Mts. Nuovo and Mezza Luna eruptions have been integrated with literature data. The results allowed improving the stratigraphic record of historical eruptions reported in the Mount Etna Geological map, modelling the sub-volcanic magmatic processes responsible for magma differentiation, and evidencing recurrent mechanisms of magma transfer at Etna. Indeed, the intrusion of a deep primitive magma along the South Rift is often associated with the activation of other rift zones that erupt residual magma stored in the shallow plumbing system.
    Description: This study has been funded by the EC FP7 Mediterranean Supersite Volcanoes project (ECGA 308665) of the European Commission
    Description: Published
    Description: 774361
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Keywords: Etna volcano, historical activity, historical geological maps, stratigraphic sequence, deep magma composition, volcano rift zones ; 04.08. Volcanology
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    A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lasek-Nesselquist, E., & Johnson, M. D. A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses. Genome Biology and Evolution, 11(11), (2019): 3218–3232, doi:10.1093/gbe/evz233.
    Description: Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium—M. rubrum, M. major, and M. chamaeleon—being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination—particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate—requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.
    Description: We thank David Beaudoin and Holly V. Moeller for their assistance in collecting cells and extracting RNA. We thank the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the Marine Biological Laboratory for the generous use of their servers. This work was supported in part by a National Science Foundation grant to both authors (IOS 1354773).
    Keywords: Mesodinium ; Litostomatea ; ciliate phylogenomics ; mixed-species transcriptomes ; sequence contamination
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  • 35
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    Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Xu, X., Li, G., Li, C., Zhang, J., Wang, Q., Simmons, D. K., Chen, X., Wijesena, N., Zhu, W., Wang, Z., Wang, Z., Ju, B., Ci, W., Lu, X., Yu, D., Wang, Q., Aluru, N., Oliveri, P., Zhang, Y. E., Martindale, M. Q., & Liu, J. Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis. National Science Review, 6(5), (2019):993-1003, doi:10.1093/nsr/nwz064.
    Description: Major evolutionary transitions are enigmas, and the most notable enigma is between invertebrates and vertebrates, with numerous spectacular innovations. To search for the molecular connections involved, we asked whether global epigenetic changes may offer a clue by surveying the inheritance and reprogramming of parental DNA methylation across metazoans. We focused on gametes and early embryos, where the methylomes are known to evolve divergently between fish and mammals. Here, we find that methylome reprogramming during embryogenesis occurs neither in pre-bilaterians such as cnidarians nor in protostomes such as insects, but clearly presents in deuterostomes such as echinoderms and invertebrate chordates, and then becomes more evident in vertebrates. Functional association analysis suggests that DNA methylation reprogramming is associated with development, reproduction and adaptive immunity for vertebrates, but not for invertebrates. Interestingly, the single HOX cluster of invertebrates maintains unmethylated status in all stages examined. In contrast, the multiple HOX clusters show dramatic dynamics of DNA methylation during vertebrate embryogenesis. Notably, the methylation dynamics of HOX clusters are associated with their spatiotemporal expression in mammals. Our study reveals that DNA methylation reprogramming has evolved dramatically during animal evolution, especially after the evolutionary transitions from invertebrates to vertebrates, and then to mammals.
    Description: This work was supported by the National Key Research and Development Program of China (2018YFC1003303), the Strategic Priority Research Program of the CAS (XDB13040200), the National Natural Science Foundation of China (91519306, 31425015), the Youth Innovation Promotion Association of the CAS and the Key Research Program of Frontier Sciences, CAS (QYZDY-SSW-SMC016).
    Keywords: DNA methylation ; evolution ; development ; reprogramming
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    Spatially regulated editing of genetic information within a neuron (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Vallecillo-Viejo, I. C., Liscovitch-Brauer, N., Diaz Quiroz, J. F., Montiel-Gonzalez, Maria F., Nemes, Sonya E., Rangan, K. J., Levinson, S. R., Eisenberg, E., & Rosenthal, J. J. C. Spatially regulated editing of genetic information within a neuron. Nucleic Acids Research, (2020): gkaa172, doi: 10.1093/nar/gkaa172.
    Description: In eukaryotic cells, with the exception of the specialized genomes of mitochondria and plastids, all genetic information is sequestered within the nucleus. This arrangement imposes constraints on how the information can be tailored for different cellular regions, particularly in cells with complex morphologies like neurons. Although messenger RNAs (mRNAs), and the proteins that they encode, can be differentially sorted between cellular regions, the information itself does not change. RNA editing by adenosine deamination can alter the genome’s blueprint by recoding mRNAs; however, this process too is thought to be restricted to the nucleus. In this work, we show that ADAR2 (adenosine deaminase that acts on RNA), an RNA editing enzyme, is expressed outside of the nucleus in squid neurons. Furthermore, purified axoplasm exhibits adenosine-to-inosine activity and can specifically edit adenosines in a known substrate. Finally, a transcriptome-wide analysis of RNA editing reveals that tens of thousands of editing sites (〉70% of all sites) are edited more extensively in the squid giant axon than in its cell bodies. These results indicate that within a neuron RNA editing can recode genetic information in a region-specific manner.
    Description: National Science Foundation (NSF) [IOS1557748 to J.R.]; United States–Israel Binational Science Foundation [BSF2013094 to J.R. and E.E.]; The Grass Foundation grant in support of the Doryteuthis pealeii Genome Project, and a gift by Mr. Edward Owens. Funding for open access charge: United States–Israel Binational Science Foundation [BSF2013094].
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    A draft genome sequence of the elusive giant squid, Architeuthis dux (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, A. M., Barrio-Hernandez, I., Hoving, H. J., Tafur-Jimenez, R., Chu, C., Frazao, B., Petersen, B., Penaloza, F., Musacchia, F., Alexander, G. C., Osorio, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R., & Gilbert, M. T. P. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1), (2020): giz152. doi: 10.1093/gigascience/giz152.
    Description: Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
    Description: R.R.F. thanks the Villum Fonden for grant VKR023446 (Villum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroecology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grants from the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTA-AMB/31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.
    Keywords: Cephalopod ; Invertebrate ; Genome assembly
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    On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172 (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: Author Posting. © Oxford University Press, 2021. This article is posted here by permission of [publisher] for personal use, not for redistribution. The definitive version was published in Lund, S., Acton, G., Clement, B., Okada, M., & Keigwin, L. On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172. Geophysical Journal International, 225(2), (2021): 1129-1141, https://doi.org/10.1093/gji/ggaa564.
    Description: Palaeomagnetic secular variation (PSV) and excursion data obtained across MIS 8 (243–300 ka) from the western North Atlantic Ocean ODP (Ocean Drilling Program) sites 1060–1063 show composite high-resolution PSV records (both directions and relative palaeointensity) developed for each site and intercompared. Two methods of chronostratigraphy allow us to date these records. First, we used published results that compared the calcium carbonate records of ODP Leg 172 sediments and tuned them with Milankovich cyclicity. We also compared our palaeointensity records with the PISO-1500 global palaeointensity record that was dated with oxygen isotope stratigraphy. We prefer the PISO-1500 record to date our cores. Two excursions are preserved in our PSV records—Excursions 8α and 9α. Our revised age estimates for both excursions are 8α (236.7–239.8 ka) and 9α (283.7–286.9 ka). We have compared shipboard measurements of the two excursions with u-channel measurements of selected excursion intervals. Excursion 8α is interpreted as a ‘Class II’ excursion (local reversal) with in-phase inclination and declination changes; Excursion 9α is a ‘Class I’ excursion with 90° out-of-phase inclination and declination changes. Averaged directions (after removal of true excursional directions) and relative palaeointensity in 3 and 9 ka overlapping intervals show significant PSV directional variability over 104 yr timescales that is regionally correlatable among the four sites. A notable pattern of angular dispersion variability involves most time spent with low (∼10°) dispersion, with three shorter intervals of high (∼25°) dispersion. The relative palaeointensity variability also shows significant variability over 104 yr timescales with three notable intervals of low palaeointensity in all four records and a direct correspondence between the three low-palaeointensity intervals and the three intervals of high angular dispersion. The two magnetic field excursions occur in two of the three low-palaeointensity/high-dispersion intervals. This suggests that the geomagnetic field operates in two states between reversals, one with regular to high palaeointensity and low directional variability and one with low palaeointensity and significantly higher directional variability and excursions.
    Keywords: Geomagnetic excursions ; Palaeointensity ; Palaeomagnetic secular variation
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  • 39
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    Urban pluvial flood adaptation: Results of a household survey across four German municipalities (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-09-30
    Description: In recent years, German cities were heavily impacted by pluvial flooding and related damage is projected to increase due to climate change and urbanisation. It is important to ask how to improve urban pluvial flood risk management. To understand the current state of property level adaptation, a survey was conducted in four municipalities that had recently been impacted by pluvial flooding. A hybrid framework based on the Protection Motivation Theory (PMT) and the Protection Action Decision Model (PADM) was used to investigate drivers of adaptive behaviour through both descriptive and regression analyses. Descriptive statistics revealed that participants tended to instal more low‐ and medium‐cost measures than high‐cost measures. Regression analyses showed that coping appraisal increased protection motivation, but that the adaptive behaviour also depends on framing factors, particularly homeownership. We further found that, while threat appraisal solely affects protection motivation and responsibility appraisal affects solely maladaptive thinking, coping appraisal affects both. Our results indicate that PMT is a solid starting point to study adaptive behaviours in the context of pluvial flooding, but we need to go beyond that by, for instance, considering factors of the PADM, such as responsibility, ownership, or respondent age, to fully understand this complex decision‐making process.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:551.489 ; ddc:363.34
    Language: English
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  • 40
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    Developmental exposure to domoic acid disrupts startle response behavior and circuitry in zebrafish (2021)
    Oxford University Press
    Details
    Publication Date: 2022-06-07
    Description: Author Posting. © The Author(s), 2021. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Toxicological Sciences 182(20), (2021): 310-326, https://doi.org/10.1093/toxsci/kfab066.
    Description: Harmful algal blooms produce potent neurotoxins that accumulate in seafood and are hazardous to human health. Developmental exposure to the harmful algal bloom toxin, domoic acid (DomA), has behavioral consequences well into adulthood, but the cellular and molecular mechanisms of DomA developmental neurotoxicity are largely unknown. To assess these, we exposed zebrafish embryos to DomA during the previously identified window of susceptibility and used the well-known startle response circuit as a tool to identify specific neuronal components that are targeted by exposure to DomA. Exposure to DomA reduced startle responsiveness to both auditory/vibrational and electrical stimuli, and even at the highest stimulus intensities tested, led to a dramatic reduction of one type of startle (short-latency c-starts). Furthermore, DomA-exposed larvae had altered kinematics for both types of startle responses tested, exhibiting shallower bend angles and slower maximal angular velocities. Using vital dye staining, immunolabeling, and live imaging of transgenic lines, we determined that although the sensory inputs were intact, the reticulospinal neurons required for short-latency c-starts were absent in most DomA-exposed larvae. Furthermore, axon tracing revealed that DomA-treated larvae also showed significantly reduced primary motor neuron axon collaterals. Overall, these results show that developmental exposure to DomA targets large reticulospinal neurons and motor neuron axon collaterals, resulting in measurable deficits in startle behavior. They further provide a framework for using the startle response circuit to identify specific neural populations disrupted by toxins or toxicants and to link these disruptions to functional consequences for neural circuit function and behavior.
    Description: This research was supported by a WHOI Von Damm and Ocean Ridge Initiative Fellowships to J.M.P. and the Woods Hole Center for Oceans and Human Health (NIH: P01ES021923 and P01ES028938; NSF: OCE-1314642 and OCE-1840381).
    Description: 2022-06-07
    Keywords: domoic acid ; harmful algal blooms ; harmful algal bloom toxins ; developmental toxicity ; startle response ; escape response ; startle circuit
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 41
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    Advancing an interdisciplinary framework to study seed dispersal ecology (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beckman, N. G., Asian, C. E., Rogers, H. S., Kogan, O., Bronstein, J. L., Bullock, J. M., Hartig, F., HilleRisLambers, J., Zhou, Y., Zurell, D., Brodie, J. F., Bruna, E. M., Cantrell, R. S., Decker, R. R., Efiom, E., Fricke, E. C., Gurski, K., Hastings, A., Johnson, J. S., Loiselle, B. A., Miriti, M. N., Neubert, M. G., Pejchar, L., Poulsen, J. R., Pufal, G., Razafindratsima, O. H., Sandor, M. E., Shea, K., Schreiber, S., Schupp, E. W., Snell, R. S., Strickland, C., & Zambrano, J. Advancing an interdisciplinary framework to study seed dispersal ecology. Aob Plants, 12(2), (2020): plz048, doi:10.1093/aobpla/plz048.
    Description: Although dispersal is generally viewed as a crucial determinant for the fitness of any organism, our understanding of its role in the persistence and spread of plant populations remains incomplete. Generalizing and predicting dispersal processes are challenging due to context dependence of seed dispersal, environmental heterogeneity and interdependent processes occurring over multiple spatial and temporal scales. Current population models often use simple phenomenological descriptions of dispersal processes, limiting their ability to examine the role of population persistence and spread, especially under global change. To move seed dispersal ecology forward, we need to evaluate the impact of any single seed dispersal event within the full spatial and temporal context of a plant’s life history and environmental variability that ultimately influences a population’s ability to persist and spread. In this perspective, we provide guidance on integrating empirical and theoretical approaches that account for the context dependency of seed dispersal to improve our ability to generalize and predict the consequences of dispersal, and its anthropogenic alteration, across systems. We synthesize suitable theoretical frameworks for this work and discuss concepts, approaches and available data from diverse subdisciplines to help operationalize concepts, highlight recent breakthroughs across research areas and discuss ongoing challenges and open questions. We address knowledge gaps in the movement ecology of seeds and the integration of dispersal and demography that could benefit from such a synthesis. With an interdisciplinary perspective, we will be able to better understand how global change will impact seed dispersal processes, and potential cascading effects on plant population persistence, spread and biodiversity.
    Description: Ideas for this manuscript initiated during the Seed Dispersal Workshop held in May 2016 at the Socio-Environmental Synthesis Center in Annapolis, MD and supported by the US National Science Foundation Grant DEB-1548194 to N.G.B. and the National Socio-Environmental Synthesis Center under the US National Science Foundation Grant DBI-1052875. D.Z. received funding from the Swiss National Science Foundation (SNF, grant: PZ00P3_168136/1) and from the German Science Foundation (DFG, grant: ZU 361/1-1).
    Keywords: Analytical models ; demography ; global change ; individual-based models ; long-distance seed dispersal ; population models ; seed dispersal
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  • 42
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    Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bowen, J. L., Giblin, A. E., Murphy, A. E., Bulseco, A. N., Deegan, L. A., Johnson, D. S., Nelson, J. A., Mozdzer, T. J., & Sullivan, H. L. Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands. Bioscience, 70(12), (2020): 1108-1119, doi:10.1093/biosci/biaa140.
    Description: Excess reactive nitrogen (N) flows from agricultural, suburban, and urban systems to coasts, where it causes eutrophication. Coastal wetlands take up some of this N, thereby ameliorating the impacts on nearshore waters. Although the consequences of N on coastal wetlands have been extensively studied, the effect of the specific form of N is not often considered. Both oxidized N forms (nitrate, NO3−) and reduced forms (ammonium, NH4+) can relieve nutrient limitation and increase primary production. However, unlike NH4+, NO3− can also be used as an electron acceptor for microbial respiration. We present results demonstrating that, in salt marshes, microbes use NO3− to support organic matter decomposition and primary production is less stimulated than when enriched with reduced N. Understanding how different forms of N mediate the balance between primary production and decomposition is essential for managing coastal wetlands as N enrichment and sea level rise continue to assail our coasts.
    Description: This work was supported by the following funding sources: National Science Foundation (NSF) grant no. DEB 1902712 to LAD, JLB, DSJ, and TJM; NSF grant no. DEB 1902695 to AEG; NSF grant no. DEB 1902704 to JAN; NSF grant no. DEB 1354214 to TJM; NSF grant no. DEB 1350491 to JLB; NSF grant no. OCE 1637630 to AEG and LAD; and additional funding from the Dorr Foundation, the Department of the Interior Northeast Climate Science Center (grant no. DOI G12AC00001), and a Bullard Fellowship (Harvard University) to LAD and from the National Academies of Science, Medicine, and Engineering Gulf Research Program to JAN. Resources purchased with funds from the NSF Biological Field Stations and Marine Laboratories program (grant no. DBI 1722553, to Northeastern University) were used to generate the data for the manuscript. Initial conversations on the effects of nutrient enrichment in marshes with Scott Warren and Bruce Peterson were critical in informing the work described in the manuscript. Sam Kelsey and Jane Tucker contributed to much of the N cycling biogeochemistry; Caitlin Bauer, Frankie Leach, Paige Weber, Emily Geoghegan and Sophie Drew assisted with field work; and Joe Vineis assisted with metagenomic analysis. This is contribution 3941 from the Virginia Institute of Marine Science. The data were compiled from multiple published sources. Links to published data can be found here: https://pie-lter.ecosystems.mbl.edu/data. The sequence data used to derive figure 6 are publicly available on the MG-RAST website under project number mgp84173.
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  • 43
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    Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hirschberger, C., Sleight, V. A., Criswell, K. E., Clark, S. J., & Gillis, J. A. Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw. Molecular Biology and Evolution, (2021): msab123, https://doi.org/10.1093/molbev/msab123
    Description: The origin of the jaw is a long-standing problem in vertebrate evolutionary biology. Classical hypotheses of serial homology propose that the upper and lower jaw evolved through modifications of dorsal and ventral gill arch skeletal elements, respectively. If the jaw and gill arches are derived members of a primitive branchial series, we predict that they would share common developmental patterning mechanisms. Using candidate and RNAseq/differential gene expression analyses, we find broad conservation of dorsoventral patterning mechanisms within the developing mandibular, hyoid and gill arches of a cartilaginous fish, the skate (Leucoraja erinacea). Shared features include expression of genes encoding members of the ventralising BMP and endothelin signalling pathways and their effectors, the joint markers nkx3.2 and gdf5 and pro-chondrogenic transcription factor barx1, and the dorsal territory marker pou3f3. Additionally, we find that mesenchymal expression of eya1/six1 is an ancestral feature of the mandibular arch of jawed vertebrates, while differences in notch signalling distinguish the mandibular and gill arches in skate. Comparative transcriptomic analyses of mandibular and gill arch tissues reveal additional genes differentially expressed along the dorsoventral axis of the pharyngeal arches, including scamp5 as a novel marker of the dorsal mandibular arch, as well as distinct transcriptional features of mandibular and gill arch muscle progenitors and developing gill buds. Taken together, our findings reveal conserved patterning mechanisms in the pharyngeal arches of jawed vertebrates, consistent with serial homology of their skeletal derivatives, as well as unique transcriptional features that may underpin distinct jaw and gill arch morphologies.
    Description: This work was supported by a Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship to CH, by a Wolfson College Junior Research Fellowship and MBL Whitman Early Career Fellowship to VAS, and by a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377) and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) to JAG.
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  • 44
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    The challenges of detecting and attributing ocean acidification impacts on marine ecosystems (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Doo, S. S., Kealoha, A., Andersson, A., Cohen, A. L., Hicks, T. L., Johnson, Z., I., Long, M. H., McElhany, P., Mollica, N., Shamberger, K. E. F., Silbiger, N. J., Takeshita, Y., & Busch, D. S. The challenges of detecting and attributing ocean acidification impacts on marine ecosystems. ICES Journal of Marine Science, 77(7-8), (2020): 2411-2422, https://doi.org/10.1093/icesjms/fsaa094.
    Description: A substantial body of research now exists demonstrating sensitivities of marine organisms to ocean acidification (OA) in laboratory settings. However, corresponding in situ observations of marine species or ecosystem changes that can be unequivocally attributed to anthropogenic OA are limited. Challenges remain in detecting and attributing OA effects in nature, in part because multiple environmental changes are co-occurring with OA, all of which have the potential to influence marine ecosystem responses. Furthermore, the change in ocean pH since the industrial revolution is small relative to the natural variability within many systems, making it difficult to detect, and in some cases, has yet to cross physiological thresholds. The small number of studies that clearly document OA impacts in nature cannot be interpreted as a lack of larger-scale attributable impacts at the present time or in the future but highlights the need for innovative research approaches and analyses. We summarize the general findings in four relatively well-studied marine groups (seagrasses, pteropods, oysters, and coral reefs) and integrate overarching themes to highlight the challenges involved in detecting and attributing the effects of OA in natural environments. We then discuss four potential strategies to better evaluate and attribute OA impacts on species and ecosystems. First, we highlight the need for work quantifying the anthropogenic input of CO2 in coastal and open-ocean waters to understand how this increase in CO2 interacts with other physical and chemical factors to drive organismal conditions. Second, understanding OA-induced changes in population-level demography, potentially increased sensitivities in certain life stages, and how these effects scale to ecosystem-level processes (e.g. community metabolism) will improve our ability to attribute impacts to OA among co-varying parameters. Third, there is a great need to understand the potential modulation of OA impacts through the interplay of ecology and evolution (eco–evo dynamics). Lastly, further research efforts designed to detect, quantify, and project the effects of OA on marine organisms and ecosystems utilizing a comparative approach with long-term data sets will also provide critical information for informing the management of marine ecosystems.
    Description: SSD was funded by NSF OCE (grant # 1415268). DSB and PM were supported by the NOAA Ocean Acidification Program and Northwest Fisheries Science Center, MHL was supported by NSF OCE (grant # 1633951), ZIJ was supported by NSF OCE (grant # 1416665) and DOE EERE (grant #DE-EE008518), NJS was supported by NSF OCE (grant # 1924281), ALC was supported by NSF OCE (grant # 1737311), and AA was supported by NSF OCE (grant # 1416518). KEFS, AK, and TLH were supported by Texas A&M University. This is CSUN Marine Biology contribution (# 306).
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  • 45
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    PCB126 exposure revealed alterations in m6A RNA modifications in transcripts associated with AHR activation (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2020. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Toxicological Sciences (2020): kfaa158, doi:10.1093/toxsci/kfaa158.
    Description: Chemical modifications of proteins, DNA, and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3′ UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 h starting from 72 h post fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (false discovery rate 5%), respectively. The majority of the peaks were preferentially located around the 3′ UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (eg, ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.
    Description: National Institute of Health National Institute of Environmental Health Sciences Outstanding New Environmental Scientist (NIH R01ES024915 to N.A.); Woods Hole Center for Oceans and Human Health [National Institutes of Health (NIH) (Grant P01ES028938); National Science Foundation (Grant OCE-1840381) to M. E. Hahn, J. J. Stegeman, N.A., and S.K.].
    Description: 2021-10-16
    Keywords: dioxin-like PCBs ; development ; zebrafish ; epitranscriptomics ; m6A ; MeRIP
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  • 46
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    Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lamb, D. C., Hargrove, T. Y., Zhao, B., Wawrzak, Z., Goldstone, J. V., Nes, W. D., Kelly, S. L., Waterman, M. R., Stegeman, J. J., & Lepesheva, G. I. Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases. Molecular Biology and Evolution, (2020): msaa260, doi:10.1093/molbev/msaa260.
    Description: Sterol biosynthesis, primarily associated with eukaryotic kingdoms of life, occurs as an abbreviated pathway in the bacterium Methylococcus capsulatus. Sterol 14α-demethylation is an essential step in this pathway and is catalyzed by cytochrome P450 51 (CYP51). In M. capsulatus, the enzyme consists of the P450 domain naturally fused to a ferredoxin domain at the C-terminus (CYP51fx). The structure of M. capsulatus CYP51fx was solved to 2.7 Å resolution and is the first structure of a bacterial sterol biosynthetic enzyme. The structure contained one P450 molecule per asymmetric unit with no electron density seen for ferredoxin. We connect this with the requirement of P450 substrate binding in order to activate productive ferredoxin binding. Further, the structure of the P450 domain with bound detergent (which replaced the substrate upon crystallization) was solved to 2.4 Å resolution. Comparison of these two structures to the CYP51s from human, fungi, and protozoa reveals strict conservation of the overall protein architecture. However, the structure of an “orphan” P450 from nonsterol-producing Mycobacterium tuberculosis that also has CYP51 activity reveals marked differences, suggesting that loss of function in vivo might have led to alterations in the structural constraints. Our results are consistent with the idea that eukaryotic and bacterial CYP51s evolved from a common cenancestor and that early eukaryotes may have recruited CYP51 from a bacterial source. The idea is supported by bioinformatic analysis, revealing the presence of CYP51 genes in 〉1,000 bacteria from nine different phyla, 〉50 of them being natural CYP51fx fusion proteins.
    Description: The study was supported by National Institutes of Health (Grant No. R01 GM067871 to G.I.L.) and by a UK-USA Fulbright Scholarship and the Royal Society (to D.C.L.).
    Keywords: sterol biosynthesis ; evolution ; cytochrome P450 ; CYP51 redox partner ; crystallography
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  • 47
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    Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zemeckis, D. R., Dean, M. J., DeAngelis, A. I., Van Parijs, S. M., Hoffman, W. S., Baumgartner, M. F., Hatch, L. T., Cadrin, S. X., & McGuire, C. H. Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies. ICES Journal of Marine Science, 76(6), (2019): 1610-1625, doi: 10.1093/icesjms/fsz064.
    Description: Effective fishery management measures to protect fish spawning aggregations require reliable information on the spatio-temporal distribution of spawning. Spawning closures have been part of a suite of fishery management actions to rebuild the Gulf of Maine stock of Atlantic cod (Gadus morhua), but difficulties remain with managing rebuilding. The objective of this study was to identify the spatial and temporal distribution of cod spawning during winter in Massachusetts Bay to improve our understanding of cod spawning dynamics and inform fisheries management. Spawning was investigated in collaboration with commercial fishermen during three winter spawning seasons (October 2013–March 2016) using acoustic telemetry and passive acoustic monitoring equipment deployed in fixed-station arrays and mounted on mobile autonomous gliders. Tagged cod exhibited spawning site fidelity and spawning primarily occurred from early November through January with a mid-December peak and some inter-annual variability. The spatial distribution of spawning was generally consistent among years with multiple hotspots in areas 〉50 m depth. Current closures encompass most of spawning, but important areas are recommended for potential modifications. Utilizing multiple complementary technologies and deployment strategies in collaboration with commercial fishermen enabled a comprehensive description of spawning and provides a valuable model for future studies.
    Description: Year 1 was jointly funded by The Nature Conservancy and Massachusetts Division of Marine Fisheries. The remainder of this research was funded through the 2013–2014 NOAA Saltonstall Kennedy grant program (Award No. NA14NMF4270027) with additional support from the Nature Conservancy and Cabot Family Charitable Foundation.
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  • 48
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    Physical modeling and validation of porpoises' directional emission via hybrid metamaterials (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dong, E., Zhang, Y., Song, Z., Zhang, T., Cai, C., & Fang, N. X. Physical modeling and validation of porpoises' directional emission via hybrid metamaterials. National Science Review, 6(5), (2019): 921-928, doi:10.1093/nsr/nwz085.
    Description: In wave physics and engineering, directional emission sets a fundamental limitation on conventional simple sources as their sizes should be sufficiently larger than their wavelength. Artificial metamaterial and animal biosonar both show potential in overcoming this limitation. Existing metamaterials arranged in periodic microstructures face great challenges in realizing complex and multiphase biosonar structures. Here, we proposed a physical directional emission model to bridge the gap between porpoises’ biosonar and artificial metamaterial. Inspired by the anatomical and physical properties of the porpoise's biosonar transmission system, we fabricated a hybrid metamaterial system composed of multiple composite structures. We validated that the hybrid metamaterial significantly increased directivity and main lobe energy over a broad bandwidth both numerically and experimentally. The device displayed efficiency in detecting underwater target and suppressing false target jamming. The metamaterial-based physical model may be helpful to achieve the physical mechanisms of porpoise biosonar detection and has diverse applications in underwater acoustic sensing, ultrasound scanning, and medical ultrasonography.
    Description: E.D., Y.Z., Z.S., T.Z. and C.C. acknowledge the financial support in part by the National Key Research and Development Program of China (2018YFC1407504), the National Natural Science Foundation of China (41676023, 41276040 and 41422604). N.X.F. acknowledges the support from the MIT Energy Initiative grant. Z.S. thanks the China Scholarship Council for the financial support of his oversea study in Woods Hole Oceanographic Institution.
    Keywords: porpoise's physical model ; metamaterials ; biosonar ; directional emission
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    Mantle upwelling beneath the South China Sea and links to surrounding subduction systems (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lin, J., Xu, Y., Sun, Z., & Zhou, Z. Mantle upwelling beneath the South China Sea and links to surrounding subduction systems. National Science Review, 6(5), (2019): 877-881, doi:10.1093/nsr/nwz123.
    Description: The evolution of the South China Sea (SCS) is directly linked to the complex subduction systems of the surrounding Pacific, Philippine Sea and Indo-Australian Plates (Fig. 1a). Major advances in the last several years are providing new insights into the SCS-mantle dynamics, through regional seismic imaging of the upper mantle [1,2], unprecedented IODP drilling expeditions (349/367/368/368X) [3–5] that obtained the oceanic basement basalt samples for the first time, geochemical analyses of the SCS-mantle source compositions [6–8] and geodynamic modeling [9,10]. Furthermore, new geological mapping, seismic imaging [11,12] and IODP drilling [13,14] have revealed evidence for significantly greater magma production at the northern SCS rifted margin, in comparison to the magma-poor end-member of the Atlantic rifted margins. This paper provides a new perspective of the SCS-mantle dynamics inspired by new observations and geodynamic modeling. We first highlight new geophysical evidence for a broad region of low-seismic-velocity anomalies in the upper mantle beneath the northern SCS, abundant magmatism during continental breakup and post-seafloor spreading, and geochemical evidence for recycled oceanic components beneath the SCS. We then present new models of layered flows in the mantle beneath the SCS, revealing two modes of plate- and subduction-driven mantle upwelling, including (i) narrow centers of mantle upwelling at shallow depths induced by divergent plate motion at seafloor-spreading centers and (ii) broad zones of mantle upwelling as a result of subduction-induced mantle-return flows at greater depths. These new observations and geodynamic studies suggest strong links between mantle upwelling beneath the SCS and surrounding subducting plates.
    Description: This work was supported by the National Natural Science Foundation of China (41890813, 91628301, U1606401, 41976066, 91858207 and 41706056), the Chinese Academy of Sciences (Y4SL021001, QYZDY-SSW-DQC005 and 133244KYSB20180029), the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou, GML2019ZD0205), the National Key R&D Program of China (2018YFC0309800 and 2018YFC0310100), the State Oceanic Administration (GASI-GEOGE-02) and China Ocean Mineral Resources R&D Association (DY135-S2–1-04).
    Repository Name: Woods Hole Open Access Server
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    The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sun, Z., Lin, J., Qiu, N., Jian, Z., Wang, P., Pang, X., Zheng, J., & Zhu, B. The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling. National Science Review, 6(5), (2019): 871-876, doi:10.1093/nsr/nwz116.
    Description: Magmatism plays a key role in the process of continental margin breakup and ocean formation. Even in the extremely magma-poor Iberia and Newfoundland margin, studies of field outcrops have shown that syn-rift magmatism had participated in rifting from a very early stage and contributed directly to the rifting process. The final transition from exhumed continental mantle to the ocean formation is also triggered by the accumulation and eruption of magma [1]. Therefore, Atlantic-type passive continental margins are classified into two end-members: magma-poor (non-volcanic) and magma-rich (volcanic). The differences between them lie in whether a large amount of intrusive and extrusive magmatism from the mantle plume/hotspot is involved in the syn-rift and breakup stages. A magma-rich margin [2] should include the following characteristics: (i) a high-velocity lower crust (HVLC) caused by syn-rift mafic magma underplating; (ii) continental crust intruded by abundant sills and dikes; (iii) a large volume of seaward-dipping reflectors (SDRs) caused by flood basalt eruption or tuffs. All other margins are classified as magma-poor margins.
    Description: We thank the research team project of Guangdong Natural Science Foundation (2017A030312002), IODP-China and South China Sea Deep Project (91628301) and K.C. Wong Education Foundation (GJTD-2018-13) for providing support for the research. This research was also supported by the China National Science and Technology Major Project (2016ZX05026–003), the joint foundation of the National Natural Science Foundation of China and Guangdong province (U1301233), as well as the National Natural Science Foundation of China (41576070 and 41890813).
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    Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? (2020)
    Oxford University Press
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, W. M., Alexander, H., Bier, R. L., Miller, D. R., Muscarella, M. E., Pitz, K. J., & Smith, H. Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? FEMS Microbiology Ecology, (2020): fiaa115, doi: 10.1093/femsec/fiaa115.
    Description: Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.
    Description: This work was supported by the National Science Foundation [OCE-1356192].
    Keywords: Auxotrophy ; Microbial community stability ; Microbial interactions ; Aquatic
    Repository Name: Woods Hole Open Access Server
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    Characterizing the culturable surface microbiomes of diverse marine animals (2021)
    Oxford University Press
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keller, A. G., Apprill, A., Lebaron, P., Robbins, J., Romano, T. A., Overton, E., Rong, Y., Yuan, R., Pollara, S., & Whalen, K. E. Characterizing the culturable surface microbiomes of diverse marine animals. FEMS Microbiology Ecology, 97(4), (2021): fiab040, https://doi.org/10.1093/femsec/fiab040.
    Description: Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.
    Description: Funding was provided by the National Science Foundation (Biological Oceanography) award #1657808 and National Institutes of Health grants 1R21-AI119311–01 to K. E. Whalen, as well as funding from the Koshland Integrated Natural Science Center and Green Fund at Haverford College. This constitutes scientific manuscript #298 from the Sea Research Foundation.
    Keywords: Bacteria ; SSU rRNA ; Coral ; Whale ; Microbiome ; Skin
    Repository Name: Woods Hole Open Access Server
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  • 53
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    The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, P., Huang, C., Lin, J., Jian, Z., Sun, Z., & Zhao, M. The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting. National Science Review, 6(5), (2019): 902-913, doi:10.1093/nsr/nwz135.
    Description: The South China Sea, as ‘a non-volcanic passive margin basin’ in the Pacific, has often been considered as a small-scale analogue of the Atlantic. The recent ocean drilling in the northern South China Sea margin found, however, that the Iberian model of non-volcanic rifted margin from the Atlantic does not apply to the South China Sea. In this paper, we review a variety of rifted basins and propose to discriminate two types of rifting basins: plate-edge type such as the South China Sea and intra-plate type like the Atlantic. They not only differ from each other in structure, formation process, lifespan and geographic size, but also occur at different stages of the Wilson cycle. The intra-plate rifting occurred in the Mesozoic and gave rise to large oceans, whereas the plate-edge rifting took place mainly in the mid-Cenozoic, with three-quarters of the basins concentrated in the Western Pacific. As a member of the Western Pacific system of marginal seas, the South China Sea should be studied not in isolation on its origin and evolution, but in a systematic context to include also its neighboring counterparts.
    Description: This work was supported by the National Natural Science Foundation of China as a part of the ‘South China Sea Deep’ Project (91128000).
    Keywords: Rifting ; Marginal basin ; Passive margin ; South China Sea ; Western Pacific ; Subduction
    Repository Name: Woods Hole Open Access Server
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    Large Diversity in Nitrogen- and Sulfur-Containing Compatible Solute Profiles in Polar and Temperate Diatoms (2020)
    Oxford University Press
    In:  Integrative and Comparative Biology, 60 (6). pp. 1401-1413.
    Details
    Publication Date: 2022-01-07
    Description: Intense bottom-ice algal blooms, often dominated by diatoms, are an important source of food for grazers, organic matter for export during sea ice melt, and dissolved organic carbon. Sea-ice diatoms have a number of adaptations, including accumulation of compatible solutes, that allows them to inhabit this highly variable environment characterized by extremes in temperature, salinity, and light. In addition to protecting them from extreme conditions, these compounds present a labile, nutrient-rich source of organic matter, and include precursors to climate active compounds (e.g., dimethyl sulfide [DMS]), which are likely regulated with environmental change. Here, intracellular concentrations of 45 metabolites were quantified in three sea-ice diatom species and were compared to two temperate diatom species, with a focus on compatible solutes and free amino acid pools. There was a large diversity of metabolite concentrations between diatoms with no clear pattern identifiable for sea-ice species. Concentrations of some compatible solutes (isethionic acid, homarine) approached 1 M in the sea-ice diatoms, Fragilariopsis cylindrus and Navicula cf. perminuta, but not in the larger sea-ice diatom, Nitzschia lecointei or in the temperate diatom species. The differential use of compatible solutes in sea-ice diatoms suggests different adaptive strategies and highlights which small organic compounds may be important in polar biogeochemical cycles.
    Type: Article , PeerReviewed
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