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  • Wiley  (1,037,727)
  • Oxford University Press  (428,981)
  • American Association for the Advancement of Science  (369,592)
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  • 1
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    COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies (2022)
    Wiley
    In:  Ecology and Evolution vol. 12 no. e9549 | H2020 European Institute of Innovation and Technology, Grant/Award Number: 813360; Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Grant/ Award Number: 16.161.301
    Details
    Publication Date: 2024-06-13
    Description: Monitoring community composition of Foraminifera (single-celled marine protists) pro-vides valuable insights into environmental conditions in marine ecosystems. Despitethe efficiency of environmental DNA (eDNA) and bulk-sample DNA (bulk-DNA) me-tabarcoding to assess the presence of multiple taxa, this has not been straightforwardfor Foraminifera partially due to the high genetic variability in widely used ribosomalmarkers. Here, we test the correctness in retrieving foraminiferal communities by me-tabarcoding of mock communities, bulk-DNA from coral reef sediment samples, andeDNA from their associated ethanol preservative using the recently sequenced cy-tochrome c oxidase subunit 1 (COI) marker. To assess the detection success, we com-pared our results with large benthic foraminiferal communities previously reportedfrom the same sampling sites. Results from our mock communities demonstrate thatall species were detected in two mock communities and all but one in the remainingfour. Technical replicates were highly similar in number of reads for each assigned ASVin both the mock communities and bulk-DNA samples. Bulk-DNA showed a signifi-cantly higher species richness than their associated eDNA samples, and also detectedadditional species to what was already reported at the specific sites. Our study con-firms that metabarcoding using the foraminiferal COI marker adequately retrieves thediversity and community composition of both the mock communities and the bulk-DNA samples. With its decreased variability compared with the commonly used nu-clear 18 S rRNA, the COI marker renders bulk-DNA metabarcoding a powerful tool toassess foraminiferal community composition under the condition that the referencedatabase is adequate to the target taxa.
    Keywords: bulk-sample ; DNA ; community composition ; coral reef ; environmental DNA ; foraminifera ; metabarcoding
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 2
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    Integrative taxonomy of new neomphaloidean gastropods from deep-sea hot vents of the southwestern Pacific (2024)
    Oxford University Press
    Details
    Publication Date: 2024-06-13
    Description: Neomphaloidean gastropods are endemic to chemosynthesis-based ecosystems ranging from hot vents to organic falls, and their diversity and evolutionary history remain poorly understood. In the southwestern Pacific, deep-sea hydrothermal vents on back-arc basins and volcanic arcs are found in three geographically secluded regions: a western region around Manus Basin, an eastern region around North Fiji and Lau Basins, and the intermediate Woodlark Basin where active venting was confirmed only recently, on the 2019 R/V L’Atalante CHUBACARC expedition. Although various lineages of neomphaloidean snails have been detected, typically restricted to one of the three regions, some of these have remained without names. Here, we use integrative taxonomy to describe three of these species: the neomphalid Symmetromphalus mithril sp. nov. from Woodlark Basin and the peltospirids Symmetriapelta becki sp. nov. from the eastern region and Symmetriapelta radiata sp. nov. from Woodlark Basin. A combination of shell sculpture and radular characters allow the morphological separation of these new species from their described congeners. A molecular phylogeny reconstructed from 570 bp of the mitochondrial cytochrome c oxidase subunit I gene confirmed the placement of the three new species in their respective genera and the superfamily Neomphaloidea. The finding of these new gastropods, particularly the ones from the Woodlark Basin, provides insights and implications on the historical role of Woodlark as a dispersing centre, in addition to highlighting the uniqueness of the Woodlark faunal community.
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  • 3
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    Regional Variation in Extratropical North Atlantic Air‐Sea Interaction 1960–2020 (2024)
    AGU (American Geophysical Union) | Wiley
    Details
    Publication Date: 2024-06-13
    Description: Air-sea interaction in late boreal winter is studied over the extratropical North Atlantic (NA) during 1960–2020 by examining the relationship between sea-surface temperature (SST) and total turbulent heat flux (THF). The two quantities are positively correlated on interannual timescales over the central-midlatitude and subpolar NA, suggesting the atmosphere on average drives SST and THF variability is independent of SST. On decadal timescales and over the central-midlatitude NA the correlation is negative, suggesting ocean processes on average drive SST and THF variability is sensitive to SST. The correlation is positive over the subpolar NA. There, interannual and decadal THF variability is governed by the North Atlantic Oscillation (NAO). During the major late 20th and early 21st century SST increase in the subpolar NA diminishing oceanic heat loss associated with a weakening NAO was observed. This study suggests that the atmosphere is more sensitive to SST over the central-midlatitude than subpolar NA. Key Points: - Regional variation in the nature of air-sea interaction over the extratropical North Atlantic (NA) north of 35°N - Timescale dependence in relationship between sea-surface temperature (SST) and turbulent heat flux over the central-midlatitude NA - The atmosphere is more sensitive to SST variability over the central-midlatitude than subpolar NA
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 4
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    Reconstruction of Cenozoic δ11Bsw Using A Gaussian Process (2024)
    AGU (American Geophysical Union) | Wiley
    Details
    Publication Date: 2024-06-13
    Description: Key Points: - We reconstruct the temporal evolution of seawater isotope ratios of boron, strontium, lithium, and osmium over the last 65 million years - The evolution of seawater boron isotope ratio shows similarity to the evolution of strontium, lithium and osmium isotope ratios - Randomly drawn, smooth time series are provided for use in uncertainty propagation in calculation of palaeo pH The boron isotope ratio of seawater (δ11Bsw) is a parameter which must be known to reconstruct palaeo pH and CO2 from boron isotope measurements of marine carbonates. Beyond a few million years ago, δ11Bsw is likely to have been different to modern. Palaeo δ11Bsw can be estimated by simultaneously constraining the vertical gradients in foraminiferal δ11B (Δδ11B) and pH (ΔpH). A number of subtly different techniques have been used to estimate ΔpH in the past, all broadly based on assumptions about vertical gradients in oxygen, and/or carbon, or other carbonate system constraints. In this work we pull together existing data from previous studies, alongside a constraint on the rate of change of δ11Bsw from modeling. We combine this information in an overarching statistical framework called a Gaussian Process. The Gaussian Process technique allows us to bring together data and constraints on the rate of change in δ11Bsw to generate random plausible evolutions of δ11Bsw. We reconstruct δ11Bsw, and by extension palaeo pH, across the last 65Myr using this novel methodology. Reconstructed δ11Bsw is compared to other seawater isotope ratios, namely ,87/86 Sr, 187/188 Os , and δ7Li, which we also reconstruct with Gaussian Processes. Our method provides a template for incorporation of future δ11Bsw constraints, and a mechanism for propagation of uncertainty in δ11Bsw into future studies.
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  • 5
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    Comparing environmental impacts of deep‐seabed and land‐based mining: A defensible framework (2024)
    Wiley
    Details
    Publication Date: 2024-06-12
    Description: The crises of climate change and biodiversity loss are interlinked and must be addressed jointly. A proposed solution for reducing reliance on fossil fuels, and thus mitigating climate change, is the transition from conventional combustion-engine to electric vehicles. This transition currently requires additional mineral resources, such as nickel and cobalt used in car batteries, presently obtained from land-based mines. Most options to meet this demand are associated with some biodiversity loss. One proposal is to mine the deep seabed, a vast, relatively pristine and mostly unexplored region of our planet. Few comparisons of environmental impacts of solely expanding land-based mining versus extending mining to the deep seabed for the additional resources exist and for biodiversity only qualitative. Here, we present a framework that facilitates a holistic comparison of relative ecosystem impacts by mining, using empirical data from relevant environmental metrics. This framework (Environmental Impact Wheel) includes a suite of physicochemical and biological components, rather than a few selected metrics, surrogates, or proxies. It is modified from the “recovery wheel” presented in the International Standards for the Practice of Ecological Restoration to address impacts rather than recovery. The wheel includes six attributes (physical condition, community composition, structural diversity, ecosystem function, external exchanges and absence of threats). Each has 3–5 sub attributes, in turn measured with several indicators. The framework includes five steps: (1) identifying geographic scope; (2) identifying relevant spatiotemporal scales; (3) selecting relevant indicators for each sub-attribute; (4) aggregating changes in indicators to scores; and (5) generating Environmental Impact Wheels for targeted comparisons. To move forward comparisons of land-based with deep seabed mining, thresholds of the indicators that reflect the range in severity of environmental impacts are needed. Indicators should be based on clearly articulated environmental goals, with objectives and targets that are specific, measurable, achievable, relevant, and time bound.
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  • 6
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    Giant eggs in a deep‐sea squid (2024)
    Wiley
    Details
    Publication Date: 2024-06-12
    Description: The deep-sea water column below 200 m is a vast three-dimensional habitat with an enormous but largely unexplored biodiversity (Robison, 2009). Cephalopod mollusks are abundant in the deep sea and are important prey for many kinds of predators. Still, most deep-sea cephalopods have never been observed alive in their natural habitat and their reproductive biology remains poorly documented. In March of 2015, at a depth of 2566 m, we observed a female squid of an undescribed species but likely belonging to the Gonatidae, carrying few but exceptionally large eggs in her arms. This raises questions as to how these and other related animals reproduce in the deep sea, an environment that is generally characterized by darkness, low temperature, reduced oxygen, limited food availability, and low population densities. The authors were conducting dives with deep-sea robots (remotely operated vehicles or ROVs) equipped with cameras in the deep basins of the Gulf of California, to investigate how deep-sea fauna are distributed in relation to the extensive low-oxygen zones in the region (Gilly et al., 2013). The squid (Individual 1, Table 1) we observed with an ROV at 2566 m in the Gulf of California in 2015 was carrying 30–40 large eggs (average maximum diameter 11.2 mm, n = 5; measured eggs were 11.4, 10.4, 11.5, 11.7 and 11 mm maximum diameter) embedded in a small external egg sheet that did not extend beyond the arm tips. The size of the eggs was similar to those of two squid (Individuals 2 and 3, Table 1) that were observed close to the seafloor during earlier expeditions in the same region.
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  • 7
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    Global Climatology of Low‐Level‐Jets: Occurrence, Characteristics, and Meteorological Drivers (2024)
    AGU (American Geophysical Union) | Wiley
    Details
    Publication Date: 2024-06-12
    Description: Low-level jets (LLJs), vertical profiles with a wind speed maxima in the lowest hundred meters of the troposphere, have multiple impacts in the Earth system, but a global present-day climatology based on contemporary data does not exist. We use the spatially and temporally complete data set from ERA5 reanalysis to compile a global climatology of LLJs for studying the formation mechanisms, characteristics, and trends during the period of 1992–2021. In the global mean, LLJs are detected 21% of the time with more cases over land (32%) than over the ocean (15%). We classified the LLJs into three categories: non-polar land (LLLJ), polar land (PLLJ), and coastal (CLLJ) LLJs. For LLLJ, the averaged frequency of occurrence is 20% and 75% of them are associated with a near-surface temperature inversion as a prerequisite for an inertial oscillation. PLLJs are also associated with a temperature inversion and occur even more frequently with 59% of the time. These are also the lowest and the strongest LLJs among the three categories. CLLJs are particularly frequent in some marine hotspots, situated along the west coast of continents, with neutral to unstable stratification close to the surfaces and a stably stratified layer aloft. We found distinct regional trends in both the frequency and intensity of LLJs over the past decades, which can have implications for the emission and transport of aerosols, and the transport of atmospheric moisture. Future studies could address changes in LLJs and the associated implications in more detail, based on the here released ERA5-based LLJ data. Key Points: - First global comprehensive low-level jet (LLJ) climatology using ERA5 - Polar LLJs are the strongest and most frequent among the detected types - Distinct past trends in regional LLJ frequency and intensity
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  • 8
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    Observations of Barrier Layer Seasonal Variation in the Banda Sea (2024)
    AGU (American Geophysical Union) | Wiley
    Details
    Publication Date: 2024-06-11
    Description: The Banda Sea is of crucial importance for the circulation of the world's oceans, as it is part of the connection between the Pacific to the Indian Ocean. One peculiarity of the upper ocean hydrography in the Banda Sea is the occurrence of barrier layers. The regionality and temporal variability of barrier layer thickness (BLT) in the Banda Sea are examined in this study utilizing in-situ observations and ocean reanalysis output. It is found that a barrier layer occurs in over 90 % of the observational data profiles, and in over 72 % of those profiles, the BLT is shallower than 10 m. Furthermore, we find a seasonal cycle in BLT with a maximum thickness of about 60 m occurring during austral autumn and winter and coinciding with the presence of low saline waters fed by the regional river discharge and rainfall from the Java Sea and Makassar Strait. In addition, we identify the existence of a quasi-permanent anticyclonic circulation cell in the Banda Sea that may support the trapping of surface freshwater by retention. The anticyclonic circulation is most likely wind-driven because it coincides with the regional Ekman pumping pattern. Modulation of the anticyclone is via seasonal variability in the wind stress curl which in turn may explain the efficiency of freshwater retention and thus the BLT. The annual mean BLT distribution in the Banda Sea shows a preferential region of thickened barrier layers around 6o-8oS and 124o-126oE and resampling the pattern of the monthly mean climatology. Key Points: - First study estimating barrier layer thickness (BLT) in the Banda Sea using comprehensive observations - A quasi-permanent barrier layer exists in the Banda Sea with seasonal variation in occurrence and thickness - The intrusion of low saline waters and anticyclonic circulation are identified as the main mechanisms for creating and modulating the local BLT
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  • 9
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    Early arrival of spring‐spawning Atlantic herring Clupea harengus at their spawning ground in the Kiel Fjord, western Baltic, relates to increasing winter seawater temperature (2024)
    Wiley
    Details
    Publication Date: 2024-06-11
    Description: The disturbance of marine organism phenology due to climate change and the subsequent effects on recruitment success are still poorly understood, especially in migratory fish species, such as the Atlantic herring (Clupea harengus; Clupeidae). Here we used the commercial catch data from a local fisher over a 50-year period (1971–2020) to estimate western Baltic spring-spawning (WBSS) herring mean arrival time Q50 (i.e., the week when 50% of the total fish catches had been made) at their spawning ground within the Kiel Fjord, southwest Baltic Sea, and the duration of the spawning season for each year. The relationship between the seawater temperature in the Kiel Bight and other environmental parameters (such as water salinity, North Atlantic and Atlantic multidecadal oscillations) and Q50 was evaluated using a general linear model to test the hypothesis that fish arrived earlier after warm than cold winters. We also estimated the accumulated thermal time to Q50 during gonadal development to estimate the effects of seawater temperature on the variations of Q50. The results of this study revealed a dramatic decrease in herring catches within the Kiel Fjord since the mid-1990s, as documented for the whole southwestern Baltic Sea. Warmer winter seawater temperature was the only factor related to an earlier arrival (1 week for one January seawater temperature degree increase) of herring at their spawning ground. The relationship was found for the first time on week 52 of the year prior to spawning and was the strongest (50% of the variability explained) from the fourth week of January (8 weeks before the mean Q50 among the studied years). A thermal constant to Q50 (~316°C day) was found when temperatures were integrated from the 49th week of the year prior to spawning. These results indicate that seawater temperature enhanced the speed of gonadal maturation during the latest phases of gametogenesis, leading to an early fish arrival under warm conditions. The duration of the spawning season was elongated during warmer years, therefore potentially mitigating the effects of trophic mismatch when fish spawn early. The results of this study highlight the altering effects of climate change on the spawning activity of a migratory fish species in the Baltic Sea where fast global changes presage that in other coastal areas worldwide
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 10
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    Sizing mudsnails: Applying superpixels to scale growth detection under ocean warming (2024)
    Wiley
    Details
    Publication Date: 2024-06-11
    Description: 1. The expansion of scientific image data holds great promise to quantify individuals, size distributions and traits. Computer vision tools are especially powerful to automate data mining of images and thus have been applied widely across studies in aquatic and terrestrial ecology. Yet marine benthic communities, especially infauna, remain understudied despite their dominance of marine biomass, biodiversity and playing critical roles in ecosystem functioning. 2. Here, we disaggregated infauna from sediment cores taken throughout the spring transition (April-June) from a near-natural mesocosm setup under experimental warming (Ambient, +1.5 degrees C, +3.0 degrees C). Numerically abundant mudsnails were imaged in batches under stereomicroscopy, from which we automatically counted and sized individuals using a superpixel-based segmentation algorithm. Our segmentation approach was based on clustering superpixels, which naturally partition images by low-level properties (e.g., colour, shape and edges) and allow instance-based segmentation to extract all individuals from each image. 3. We demonstrate high accuracy and precision for counting and sizing individuals, through a procedure that is robust to the number of individuals per image (5-65) and to size ranges spanning an order of magnitude (〈750 mu m to 7.4 mm). The segmentation routine provided at least a fivefold increase in efficiency compared with manual measurements. Scaling this approach to a larger dataset tallied 〉40k individuals and revealed overall growth in response to springtime warming. 4. We illustrate that image processing and segmentation workflows can be built upon existing open-access R packages, underlining the potential for wider adoption of computer vision tools among ecologists. The image-based approach also generated reproducible data products that, alongside our scripts, we have made freely available. This work reinforces the need for next-generation monitoring of benthic communities, especially infauna, which can display differential responses to average warming.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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