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  • Other Sources  (404)
  • American Institute of Physics (AIP)
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  • 1
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    An Amphibole Perspective on the Recent Magmatic Evolution of Mount St. Helens (2024)
    Oxford University Press
    Details
    Publication Date: 2024-02-23
    Description: Compositional variations of amphibole stratigraphically recovered from multiple eruptions at a given volcano have a great potential to archive long-term magmatic processes in its crustal plumbing system. Calcic amphibole is a ubiquitous yet chemically and texturally diverse mineral at Mount St. Helens (MSH), where it occurs in dacites and in co-magmatic enclaves throughout the Spirit Lake stage (last ~4000 years of eruptive history). It forms three populations with distinct geochemical trends in key major and trace elements, which are subdivided into a high-Al (11–14.5 wt% Al2O3), a medium-Al (10–12.5 wt% Al2O3), and a low-Al (7.5–10 wt% Al2O3) amphibole population. The oldest investigated tephra record (Smith Creek period, 3900–3300 years BP) yields a bimodal amphibole distribution in which lower-crustal, high-Al amphibole cores (crystallized dominantly from basaltic andesite to andesite melts) and upper-crustal, low-Al amphibole rims (crystallized from rhyolitic melt) document occasional recharge of a shallow silicic mush by a more mafic melt from a lower-crustal reservoir. The sudden appearance of medium-Al amphiboles enriched in incompatible trace elements in eruptive periods younger than 2900 years BP is associated with a change in reservoir conditions toward hotter and drier magmas, which indicates recharge of the shallow silicic reservoir by basaltic melt enriched in incompatible elements. Deep-crystallizing, high-Al amphibole, however, appears mostly unaffected by such incompatible-element-enriched basaltic recharge, suggesting that these basalts bypass the lower crustal reservoir. This could be the result of the eastward offset position of the lower crustal reservoir relative to the upper crustal storage zone underneath the MSH edifice. Amphibole has proven to be a sensitive geochemical archive for uncovering storage conditions of magmas at MSH. In agreement with geophysical observations, storage and differentiation have occurred in two main zones: an upper crustal and lower crustal reservoir (the lower one being chemically less evolved). The upper crustal silicic reservoir, offset to the west of the lower crustal reservoir, has captured compositionally unusual mafic recharge (drier, hotter, and enriched in incompatible trace elements in comparison to the typical parental magmas in the region), resulting in an increased chemical diversity of amphiboles and their carrier intermediate magmas, in the last ~3000 years of MSH’s volcanic record.
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  • 2
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    The Impact of the Culture Regime on the Metabolome and Anti-Phytopathogenic Activity of Marine Fungal Co-Cultures (2024)
    MDPI
    Details
    Publication Date: 2024-03-15
    Description: Co-cultivation, coupled with the OSMAC approach, is considered an efficient method for expanding microbial chemical diversity through the activation of cryptic biosynthetic gene clusters (BGCs). As part of our project aiming to discover new fungal metabolites for crop protection, we previously reported five polyketides, the macrolides dendrodolides E (1) and N (2), the azaphilones spiciferinone (3) and 8α-hydroxy-spiciferinone (4), and the bis-naphtho-γ-pyrone cephalochromin (5) from the solid Potato Dextrose Agar (PDA) co-culture of two marine sediment-derived fungi, Plenodomus influorescens and Pyrenochaeta nobilis. However, some of the purified metabolites could not be tested due to their minute quantities. Here we cultivated these fungi (both axenic and co-cultures) in liquid regime using three different media, Potato Dextrose Broth (PDB), Sabouraud Dextrose Broth (SDB), and Czapek-Dox Broth (CDB), with or without shaking. The aim was to determine the most ideal co-cultivation conditions to enhance the titers of the previously isolated compounds and to produce extracts with stronger anti-phytopathogenic activity as a basis for future upscaled fermentation. Comparative metabolomics by UPLC-MS/MS-based molecular networking and manual dereplication was employed for chemical profiling and compound annotations. Liquid co-cultivation in PDB under shaking led to the strongest activity against the phytopathogen Phytophthora infestans. Except for compound 1, all target compounds were detected in the co-culture in PDB. Compounds 2 and 5 were produced in lower titers, whereas the azaphilones (3 and 4) were overexpressed in PDB compared to PDA. Notably, liquid PDB co-cultures contained meroterpenoids and depside clusters that were absent in the solid PDA co-cultures. This study demonstrates the importance of culture regime in BGC regulation and chemical diversity of fungal strains in co-culture studies.
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  • 3
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    Plankton community changes during the last 124 000 years in the subarctic Bering Sea derived from sedimentary ancient DNA (2024)
    Oxford University Press
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    Publication Date: 2024-04-05
    Description: Current global warming results in rising sea-water temperatures, and the loss of sea ice in arctic and subarctic oceans impacts the community composition of primary producers with cascading effects on the food web and potentially on carbon export rates. This study analyzes metagenomic shotgun and diatom rbcL amplicon-sequencing data from sedimentary ancient DNA (sedaDNA) of the subarctic western Bering Sea that records phyto- and zooplankton community changes over the last glacial–interglacial cycle, including the last interglacial period (Eemian). Our data show that interglacial and glacial plankton communities differ, with distinct Eemian and Holocene plankton communities. The generally warm Holocene period is dominated by pico-sized cyanobacteria and bacteria-feeding heterotrophic protists, while the Eemian period is dominated by eukaryotic pico-sized chlorophytes and Triparmaceae. In contrast, the glacial period is characterized by micro-sized phototrophic protists, including sea-ice associated diatoms in the family Bacillariaceae and co-occurring diatom-feeding crustaceous zooplankton. Our deep-time record of plankton community changes reveals a long-term decrease in phytoplankton cell size coeval with increasing temperatures, and resembling community changes in the currently warming Bering Sea. The phytoplankton community in the warmer-than-present Eemian period is distinct from modern communities and limits the use of the Eemian as an analog for future climate scenarios. However, under enhanced future warming, the expected shift towards the dominance of small-sized phytoplankton and heterotrophic protists might result in an increased productivity, whereas the community’s potential of carbon export will be decreased, thereby weakening the subarctic Bering Sea’s function as an effective carbon sink.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 4
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    Boreal (Eemian) Transgression in the Northeastern White Sea Region: Multiproxy Evidence from Bychye-2 Section (2024)
    MDPI
    Details
    Publication Date: 2024-04-09
    Description: Reconstructing interglacial marine environments helps us understand the climate change mechanisms of the past. To contribute to this body of knowledge, we studied a high-resolution 455 cm-thick sediment sequence of the Boreal (Eemian) marine beds directly overlying Moscovian (Saalian) moraine in the Bychye-2 section on the Pyoza River. We analyzed lithological and microfossil (foraminifers, ostracods, pollen, aquatic palynomorphs) variations at the studied site. Stratigraphical zonation is based on the local and well-established regional pollen zones, correlated with the western European pollen zones. The studied marine beds accumulated from the end of the Moscovian glacial (〉131 ka) until ca. 119.5 ka. We distinguished three successive phases: a seasonally sea-ice-covered, relatively deep, freshened basin in the initial rapid flooding stage (〉131–130.5 ka); a deep basin in the maximum flooding phase with less extensive sea ice cover (130.5–130.25 ka); and a shallow basin with reduced sea ice cover (130.25–119.5 ka). According to a pollen zone comparison with other sites, the regional glacioisostatic rebound started ca. 130 ka. The diverse warm-water assemblages of benthic foraminifers and ostracods containing typical Baltic Sea species occurred during the regression, mainly 128–124 ka, thus giving evidence for a relatively long-lasting connection between the White and Baltic Seas.
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  • 5
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    Screening Disinfection Byproducts in Arid-Coastal Wastewater: A Workflow Using GC×GC-TOFMS, Passive Sampling, and NMF Deconvolution Algorithm (2024)
    MDPI
    Details
    Publication Date: 2024-05-02
    Description: Disinfection during tertiary municipal wastewater treatment is a necessary step to control the spread of pathogens; unfortunately, it also gives rise to numerous disinfection byproducts (DBPs), only a few of which are regulated because of the analytical challenges associated with the vast number of potential DBPs. This study utilized polydimethylsiloxane (PDMS) passive samplers, comprehensive two-dimensional gas chromatography (GC×GC) coupled with time-of-flight mass spectrometry (TOFMS), and non-negative matrix factorization (NMF) spectral deconvolution for suspect screening of DBPs in treated wastewater. PDMS samplers were deployed upstream and downstream of the chlorination unit in a municipal wastewater treatment plant located in Abu Dhabi, and their extracts were analyzed using GC×GC-TOFMS. A workflow incorporating a multi-tiered, eight-filter screening process was developed, which successfully enabled the reliable isolation of 22 candidate DBPs from thousands of peaks. The NMF spectral deconvolution improved the match factor score of unknown mass spectra to the reference mass spectra available in the NIST library by 17% and facilitated the identification of seven additional DBPs. The close match of the first-dimension retention index data and the GC×GC elution patterns of DBPs, both predicted using the Abraham solvation model, with their respective experimental counterparts—with the measured data available in the NIST WebBook and the GC×GC elution patterns being those observed for the candidate peaks—significantly enhanced the accuracy of peak assignment. Isotopic pattern analysis revealed a close correspondence for 11 DBPs with clearly visible isotopologues in reference spectra, thereby further strengthening the confidence in the peak assignment of these DBPs. Brominated analogues were prevalent among the detected DBPs, possibly due to seawater intrusion. The fate, behavior, persistence, and toxicity of tentatively identified DBPs were assessed using EPI Suite™ and the CompTox Chemicals Dashboard. This revealed their significant toxicity to aquatic organisms, including developmental, mutagenic, and endocrine-disrupting effects in certain DBPs. Some DBPs also showed activity in various CompTox bioassays, implicating them in adverse molecular pathways. Additionally, 11 DBPs demonstrated high environmental persistence and resistance to biodegradation. This combined approach offers a powerful tool for future research and environmental monitoring, enabling accurate identification and assessment of DBPs and their potential risks.
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  • 6
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    Tracing the Origin and Magmatic Evolution of the Rejuvenated Volcanism in Santa Clara Island, Juan Fernández Ridge, SE Pacific (2024)
    MDPI
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    Publication Date: 2024-06-12
    Description: Oceanic intraplate volcanoes sometimes experience late-stage eruptive activity known as rejuvenated volcanism, and contrasting interpretations for its petrogenesis depend on the compositional characteristics. In the Juan Fernández Ridge (JFR), a volcanic chain approximately 800 km in length emplaced on the Nazca Plate, some subaerial occurrences of rejuvenated volcanism have been recognized on the Robinson Crusoe and Santa Clara Islands, both part of the same deeply eroded shield volcano complex. This study aims to understand the origin and magmatic evolution of rejuvenated volcanism on Santa Clara Island, emplaced after ~2.15 Ma of quiescence above the shield sequence, mainly via the analysis of unpublished geochemical and isotopic data. Field reconnaissance identified two nearly coeval rejuvenated sequences on Santa Clara Island: Bahía W (BW) and Morro Spartan (MS), both formed by basanitic and picro-basaltic lava flows with brecciated levels and local intercalations of sedimentary and pyroclastic deposits. In comparison to the chemical signature of the preceding shield-building stage (comprised mainly of basalts and picrites), the two rejuvenated sequences exhibit a notable enrichment in incompatible elements, but the Sr, Nd, and Pb isotopes are very similar to the FOZO mantle endmember, with an apparent additional contribution of HIMU and EM1 components. The geochemistry of lavas revealed the involvement of various processes, including contamination by ultramafic xenoliths, high-pressure fractional crystallization of olivine and clinopyroxene, and potential partial assimilation of oceanic lithospheric components. While the oceanic lithosphere has been considered as a potential source, the isotopic data from Santa Clara lies outside of the mixing curve between depleted mantle (DM, here represented by the North Chile Rise and the East Pacific Rise) and the previous shield stage, suggesting that a lithospheric mantle is not the primary source for the rejuvenated stage volcanism. Therefore, we favor an origin of the rejuvenated volcanism from the mantle plume forming the JFR, supported by similarities in isotopic signatures with the shield stage and high values of 208Pb/204Pb (only comparable to San Félix—San Ambrosio in the vicinity of JFR), implying the presence of a regional source with radiogenic 208Pb/204Pb isotope ratios. In addition, isotopic variations are subparallel to the mixing line between HIMU and EM1 components, whose participation in different proportions might explain the observed trends. In conclusion, we propose that the source of the rejuvenated volcanism on Santa Clara Island is a heterogeneous mantle plume, the same one that fed the shield stage. The rejuvenated volcanism is derived from a secondary melting zone away from the main axis of the plume.
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  • 7
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    Integrative taxonomy of new neomphaloidean gastropods from deep-sea hot vents of the southwestern Pacific (2024)
    Oxford University Press
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    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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  • 8
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    Representative Dynamic Accumulation of Hydrate-Bearing Sediments in Gas Chimney System since 30 Kyr BP in the QiongDongNan Area, Northern South China Sea (2024)
    MDPI
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    Publication Date: 2024-06-13
    Description: A stratigraphic complex composed of mass transport deposits (MTDs), where the gas occurrence allows for the formation of a gas chimney and pipe structure, is identified based on seismic interpretation in the QiongDongNan area of the northern South China Sea. During the Fifth Gas Hydrate Drilling Expedition of the Guangzhou Marine Geological Survey, this type of complex morphology that has close interaction with local gas hydrate (GH) distribution was eventually confirmed. A flow-reaction model is built to explore the spatial–temporal matching evolution process of massive GH reservoirs since 30 kyr before the present (BP). Five time snapshots, including 30, 20, 10, and 5 kyr BP, as well as the present, have been selected to exhibit key strata-evolving information. The results of in situ tensile estimation imply fracturing emergence occurs mostly at 5 kyr BP. Six other environmental scenarios and three cases of paleo-hydrate existence have been compared. The results almost coincide with field GH distribution below the bottom MTD from drilling reports, and state layer fracturing behaviors always feed and probably propagate in shallow sediments. It can be concluded that this complex system with 10% pre-existing hydrates results in the exact distribution and occurrence in local fine-grained silty clay layers adjacent to upper MTDs.
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  • 9
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    Zooplankton seasonal vertical migration in an optimality-based plankton ecosystem model (2024)
    Oxford University Press
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    Publication Date: 2024-06-24
    Description: Several species from various zooplankton taxa perform seasonal vertical migrations (SVM) of typically several hundred meters between the surface layer and overwintering depths, particularly in high-latitude regions. We use OPtimality-based PLAnkton (OPPLA) ecosystem model) to simulate SVM behavior in zooplankton in the Labrador Sea. Zooplankton in OPPLA is a generic functional group without life cycle, which facilitates analyzing SVM evolutionary stability and interactions between SVM and the plankton ecosystem. A sensitivity analysis of SVM-related parameters reveals that SVM can amplify the seasonal variations of phytoplankton and zooplankton and enhance the reduction of summer surface nutrient concentrations. SVM is often explained as a strategy to reduce exposure to visual predators during winter. We find that species doing SVM can persist and even dominate the summer-time zooplankton community, even in the presence of Stayers, which have the same traits as the migrators, but do not perform SVM. The advantage of SVM depends strongly on the timing of the seasonal migrations, particularly the day of ascent. The presence of higher (visual) predators tends to suppress the Stayers in our simulations, whereas the SVM strategy can persist in the presence of non-migrating species even without higher predators.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 10
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    What Is Missing in Offshore Explosive Ordnance Disposal Risk Assessment? (2024)
    MDPI
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    Publication Date: 2024-07-03
    Description: Offshore explosive ordnance disposal (EOD) in the marine environment is a high-risk activity. Structured risk assessment (RA) can be a helpful tool to provide EOD experts with decision-making support. This paper hypothesizes that existing RA approaches that address unexploded ordnance (UXO) in the sea do not meet the requirements of EOD RA. To test this hypothesis, the paper proposes a novel categorization tool. It uses five review criteria: study type (qualitative vs. quantitative), level of decision-making (strategic vs. applied), risk component (probability vs. consequence), spatial scale (global vs. local), and temporal scale (long-term vs. short-term). The categorization tool is used to identify the requirements of EOD RA and to test whether nine existing RA methods fulfill these requirements. The study finds that none of the investigated RAs meets the requirements and, hence, concludes that a new method should be developed. However, some aspects of the existing studies should be considered when designing a new method. This includes using risk factors (type and mass of explosive material, type and state of the fuze, and water depth) that are relevant for EOD RA. It also involves setting up a directed graph to assess the complex interdependencies between these risk factors.
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  • 11
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    Toward an adequate level of detail in flood risk assessments (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2024-01-24
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Flood risk assessments require different disciplines to understand and model the underlying components hazard, exposure, and vulnerability. Many methods and data sets have been refined considerably to cover more details of spatial, temporal, or process information. We compile case studies indicating that refined methods and data have a considerable effect on the overall assessment of flood risk. But are these improvements worth the effort? The adequate level of detail is typically unknown and prioritization of improvements in a specific component is hampered by the lack of an overarching view on flood risk. Consequently, creating the dilemma of potentially being too greedy or too wasteful with the resources available for a risk assessment. A “sweet spot” between those two would use methods and data sets that cover all relevant known processes without using resources inefficiently. We provide three key questions as a qualitative guidance toward this “sweet spot.” For quantitative decision support, more overarching case studies in various contexts are needed to reveal the sensitivity of the overall flood risk to individual components. This could also support the anticipation of unforeseen events like the flood event in Germany and Belgium in 2021 and increase the reliability of flood risk assessments.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: BMBF http://dx.doi.org/10.13039/501100002347
    Description: Federal Environment Agency http://dx.doi.org/10.13039/501100010809
    Description: http://howas21.gfz-potsdam.de/howas21/
    Description: https://www.umwelt.niedersachsen.de/startseite/themen/wasser/hochwasser_amp_kustenschutz/hochwasserrisikomanagement_richtlinie/hochwassergefahren_und_hochwasserrisikokarten/hochwasserkarten-121920.html
    Description: https://download.geofabrik.de/europe/germany.html
    Description: https://emergency.copernicus.eu/mapping/list-of-components/EMSN024
    Description: https://data.jrc.ec.europa.eu/collection/id-0054
    Description: https://oasishub.co/dataset/surface-water-flooding-footprinthurricane-harvey-august-2017-jba
    Description: https://www.wasser.sachsen.de/hochwassergefahrenkarte-11915.html
    Keywords: ddc:551.48 ; decision support ; extreme events ; integrated flood risk management ; risk assessment
    Language: English
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  • 12
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    Small lateral air pressure gradients generated by a large chamber system have a strong effect on CO2 transport in soil (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2024-02-09
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Gas transport in soils is usually assumed to be purely diffusive, although several studies have shown that non‐diffusive processes can significantly enhance soil gas transport. These processes include barometric air pressure changes, wind‐induced pressure pumping and static air pressure fields generated by wind interacting with obstacles. The associated pressure gradients in the soil can cause advective gas fluxes that are much larger than diffusive fluxes. However, the contributions of the respective transport processes are difficult to separate. We developed a large chamber system to simulate pressure fields and investigate their influence on soil gas transport. The chamber consists of four subspaces in which pressure is regulated by fans that blow air in or out of the chamber. With this setup, we conducted experiments with oscillating and static pressure fields. CO〈sub〉2〈/sub〉 concentrations were measured along two soil profiles beneath the chamber. We found a significant relationship between static lateral pressure gradients and the change in the CO〈sub〉2〈/sub〉 profiles (R〈sup〉2〈/sup〉 = 0.53; 〈italic toggle="no"〉p〈/italic〉‐value 〈2e‐16). Even small pressure gradients between −1 and 1 Pa relative to ambient pressure resulted in an increase or decrease in CO〈sub〉2〈/sub〉 concentrations of 8% on average in the upper soil, indicating advective flow of air in the pore space. Positive pressure gradients resulted in decreasing, negative pressure gradients in increasing CO〈sub〉2〈/sub〉 concentrations. The concentration changes were probably caused by an advective flow field in the soil beneath the chamber generated by the pressure gradients. No effect of oscillating pressure fields was observed in this study. The results indicate that static lateral pressure gradients have a substantial impact on soil gas transport and therefore are an important driver of gas exchange between soil and atmosphere. Lateral pressure gradients in a comparable range can be induced under windy conditions when wind interacts with terrain features. They can also be caused by chambers used for flux measurements at high wind speed or by fans used for head‐space mixing within the chambers, which yields biased flux estimates.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; advective flux ; chamber flux measurements ; static air pressure fields ; wind‐induced pressure pumping
    Language: English
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  • 13
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    Redoxtrons – An experimental system to study redox processes within the capillary fringe (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2023-11-18
    Description: Spatiotemporal characterisation of the soil redox status within the capillary fringe (CF) is a challenging task. Air‐filled porosities (ε), oxygen concentration (O〈sub〉2〈/sub〉) and soil redox potential (EH) are interrelated soil variables within active biogeochemical domains such as the CF. We investigated the impact of water table (WT) rise and drainage in an undisturbed topsoil and subsoil sample taken from a Calcaric Gleysol for a period of 46 days. We merged 1D (EH and matric potential) and 2D (O〈sub〉2〈/sub〉) systems to monitor at high spatiotemporal resolution redox dynamics within self‐constructed redoxtron housings and complemented the data set by a 3D pore network characterization using X‐ray microtomography (X‐ray μCT). Depletion of O〈sub〉2〈/sub〉 was faster in the organic matter‐ and clay‐rich aggregated topsoil and the CF extended 〉10 cm above the artificial WT. The homogeneous and less‐aggregated subsoil extended only 4 cm above the WT as indicated by ε–O〈sub〉2〈/sub〉–EH data during saturation. After drainage, 2D O〈sub〉2〈/sub〉 imaging revealed a fast aeration towards the lower depths of the topsoil, which agrees with the connected ε derived by X‐ray μCT (ε〈sub〉CT_conn〈/sub〉) of 14.9% of the total porosity. However, small‐scaled anoxic domains with O〈sub〉2〈/sub〉 saturation 〈5% were apparent even after lowering the WT (down to 0.25 cm〈sup〉2〈/sup〉 in size) for 23 days. These domains remained a nucleus for reducing soil conditions (E〈sub〉H〈/sub〉 〈 −100 mV), which made it challenging to characterise the soil redox status in the CF. In contrast, the subsoil aeration reached O〈sub〉2〈/sub〉 saturation after 8 days for the complete soil volume. Values of ε〈sub〉CT_conn〈/sub〉 around zero in the subsoil highlighted that soil aeration was independent of this parameter suggesting that other variables such as microbial activity must be considered when predicting the soil redox status from ε alone. The use of redoxtrons in combination with localised redox‐measurements and image based pore space analysis resulted in a better 2D/3D characterisation of the pore system and related O〈sub〉2〈/sub〉 transport properties. This allowed us to analyse the distribution and activity of microbiological niches highly associated with the spatiotemporal variable redox dynamics in soil environments. Highlights: The time needed to turn from reducing to oxidising (period where all platinum electrodes feature E〈sub〉H〈/sub〉 〉 300 mV) condition differ for two samples with contrasting soil structure. The subsoil with presumably low O〈sub〉2〈/sub〉 consumption rates aerated considerably faster than the topsoil and exclusively by O〈sub〉2〈/sub〉 diffusion through medium‐ and fine‐sized pores. To derive the soil redox status based upon the triplet ε–O〈sub〉2〈/sub〉–E〈sub〉H〈/sub〉 is challenging at present in heterogeneous soil domains and larger soil volumes than 250 cm〈sup〉3〈/sup〉. Undisturbed soil sampling along with 2D/3D redox measurement systems (e.g., redoxtrons) improve our understanding of redox dynamics within the capillary fringe.
    Keywords: ddc:631.4 ; environmental monitoring ; incubation experiments ; redox processes ; soil reducing conditions ; undisturbed soil ; X‐ray microtomography
    Language: English
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  • 14
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    The dilemma of analytical method changes for soil organic carbon in long‐term experiments (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-11-17
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈sec xmlns:mml="http://www.w3.org/1998/Math/MathML" id="ejss13362-sec-1003" xml:lang="en"〉 〈p xml:lang="en"〉Long‐term experiments (LTEs) have provided data to modellers and agronomists to investigate changes and dynamics of soil organic carbon (SOC) under different cropping systems. As treatment changes have occurred due to agricultural advancements, so too have analytical soil methods. This may lead to method bias over time, which could affect the robust interpretation of data and conclusions drawn. This study aims to quantify differences in SOC due to changes in dry combustion methods over time, using soil samples of a LTE established in 1963 that focuses on mineral and organic fertilizer management in the temperate zone of Northeast Germany. For this purpose, 1059 soil samples, collected between 1976 and 2008, have been analysed twice, once with their historical laboratory method right after sampling, and a second time in 2016 when all samples were analysed using the same elementary analyser. In 9 of 11 soil sampling campaigns, a paired 〈italic toggle="no"〉t〈/italic〉‐test provided evidence for significant differences in the historical SOC values when compared with the re‐analysed concentrations of the same LTE sample. In the sampling years 1988 and 2004, the historical analysis obtained about 0.9 g kg〈sup〉−1〈/sup〉 lower SOC compared with the re‐analysed one. For 1990 and 1998, this difference was about 0.4 g kg〈sup〉−1〈/sup〉. Correction factors, an approach often used to correct for different analytical techniques, could only be applied for 5 of 11 sampling campaigns to account for constant and proportional systematic method error. For this particular LTE, the interpretation of SOC changes due to agronomic management (here fertilization) deviates depending on the analytical method used, which may weaken the explanatory power of the historical data. We demonstrate that analytical method changes over time present one of many challenges in the interpretation of time series data of SOC dynamics. Therefore, LTE site managers need to ensure providing all necessary protocols and data in order to retrace method changes and if necessary recalculate SOC.〈/p〉 〈/sec〉〈sec xmlns:mml="http://www.w3.org/1998/Math/MathML" id="ejss13362-sec-0003" xml:lang="en"〉 〈title〉Highlights〈/title〉 〈p xml:lang="en"〉〈list list-type="bullet" id="ejss13362-list-0001"〉 〈list-item id="ejss13362-li-0001"〉〈p〉A total of 1059 LTE soil samples taken between 1976 and 2008 were re‐analysed for SOC in 2016〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0002"〉〈p〉Several methodological changes for SOC determination led to significant different SOC concentration in the same sample〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0003"〉〈p〉Interpretation and time series of LTE soil data suffer from consideration of analytical method changes and poor documentation of the same〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0004"〉〈p〉Soil archive establishment, thorough method protocols and diligent proficiency testing after soil method changes ameliorate the dilemma〈/p〉〈/list-item〉 〈/list〉〈/p〉 〈/sec〉
    Description: Brandenburger Staatsministerium für Wissenschaft, Forschung und Kultur http://dx.doi.org/10.13039/501100004581
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100004937
    Description: https://doi.org/10.4228/zalf-acge-b683
    Keywords: ddc:631.4 ; Bland–Altman ; carbon stocks ; data trueness ; Deming regression ; method bias ; soil archive ; soil survey
    Language: English
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  • 15
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    Optimised use of data fusion and memory‐based learning with an Austrian soil library for predictions with infrared data (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-12-12
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Infrared spectroscopy in the visible to near‐infrared (vis–NIR) and mid‐infrared (MIR) regions is a well‐established approach for the prediction of soil properties. Different data fusion and training approaches exist, and the optimal procedures are yet undefined and may depend on the heterogeneity present in the set and on the considered scale. The objectives were to test the usefulness of partial least squares regressions (PLSRs) for soil organic carbon (SOC), total carbon (C〈sub〉t〈/sub〉), total nitrogen (N〈sub〉t〈/sub〉) and pH using vis–NIR and MIR spectroscopy for an independent validation after standard calibration (use of a general PLSR model) or using memory‐based learning (MBL) with and without spiking for a national spectral database. Data fusion approaches were simple concatenation of spectra, outer product analysis (OPA) and model averaging. In total, 481 soils from an Austrian forest soil archive were measured in the vis–NIR and MIR regions, and regressions were calculated. Fivefold calibration‐validation approaches were carried out with a region‐related split of spectra to implement independent validations with n ranging from 47 to 99 soils in different folds. MIR predictions were generally superior over vis–NIR predictions. For all properties, optimal predictions were obtained with data fusion, with OPA and spectra concatenation outperforming model averaging. The greatest robustness of performance was found for OPA and MBL with spiking with 〈italic toggle="no"〉R〈/italic〉〈sup〉2〈/sup〉 ≥ 0.77 (N), 0.85 (SOC), 0.86 (pH) and 0.88 (C〈sub〉t〈/sub〉) in the validations of all folds. Overall, the results indicate that the combination of OPA for vis–NIR and MIR spectra with MBL and spiking has a high potential to accurately estimate properties when using large‐scale soil spectral libraries as reference data. However, the reduction of cost‐effectiveness using two spectrometers needs to be weighed against the potential increase in accuracy compared to a single MIR spectroscopy approach.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; data fusion ; independent validation ; infrared spectroscopy ; MBL ; nitrogen ; outer product analysis ; pH ; soil organic carbon ; spiking ; total carbon
    Language: English
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  • 16
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    Importance of catchment hydrological processes and calibration of hydrological‐hydrodynamic rainfall‐runoff models in small rural catchments (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2024-01-19
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉In recent years, many two‐dimensional (2D) hydrodynamic models have been extended to include the direct rainfall method (DRM). This allows their application as a hydrological‐hydrodynamic model for the determination of floodplains in one model system. In previous studies on DRM, the role of catchment hydrological processes (CaHyPro) and its interaction with the calibration process was not investigated in detail. In the present, case‐oriented study, the influence of the spatiotemporal distribution of the processes precipitation and runoff formation in combination with the 2D model HEC‐RAS is investigated. In a further step, a conceptual approach for event‐based interflow is integrated. The study is performed on the basis of a single storm event in a small rural catchment (low mountain range, 38 km〈sup〉2〈/sup〉) in Hesse (Germany). The model results are evaluated against six quality criteria and compared to a simplified baseline model. Finally, the calibrated improved model is contrasted with a calibrated baseline model. The results show the enhancement of the model results due to the integration of the CaHyPro and highlight its interplay with the calibrated model parameters.〈/p〉
    Keywords: ddc:551.48 ; 2D hydrodynamic modeling ; calibration ; direct rainfall modeling ; hydrological processes ; radar data ; runoff formation
    Language: English
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  • 17
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    BODIUM—A systemic approach to model the dynamics of soil functions (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2024-01-26
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The increasing demand for biomass for food, animal feed, fibre and bioenergy requires optimization of soil productivity, while at the same time, protecting other soil functions such as nutrient cycling and buffering, carbon storage, habitat for biological activity and water filter and storage. Therefore, one of the main challenges for sustainable agriculture is to produce high yields while maintaining all the other soil functions. Mechanistic simulation models are an essential tool to fully understand and predict the complex interactions between physical, biological and chemical processes of soils that generate those functions. We developed a soil model to simulate the impact of various agricultural management options and climate change on soil functions by integrating the relevant processes mechanistically and in a systemic way. As a special feature, we include the dynamics of soil structure induced by tillage and biological activity, which is especially relevant in arable soils. The model operates on a 1D soil profile consisting of a number of discrete layers with dynamic thickness. We demonstrate the model performance by simulating crop growth, root growth, nutrient and water uptake, nitrogen cycling, soil organic matter turnover, microbial activity, water distribution and soil structure dynamics in a long‐term field experiment including different crops and different types and levels of fertilization. The model is able to capture essential features that are measured regularly including crop yield, soil organic carbon, and soil nitrogen. In this way, the plausibility of the implemented processes and their interactions is confirmed. Furthermore, we present the results of explorative simulations comparing scenarios with and without tillage events to analyse the effect of soil structure on soil functions. Since the model is process‐based, we are confident that the model can also be used to predict quantities that have not been measured or to estimate the effect of management measures and climate states not yet been observed. The model thus has the potential to predict the site‐specific impact of management decisions on soil functions, which is of great importance for the development of a sustainable agriculture that is currently also on the agenda of the ‘Green Deal’ at the European level.〈/p〉
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Description: https://git.ufz.de/bodium/bodium_v1.0
    Keywords: ddc:631.4 ; agriculture ; computational model ; simulation ; soil microbiology ; soil structure ; sustainable soil
    Language: English
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  • 18
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    Temperature and soil moisture change microbial allocation of pesticide‐derived carbon (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2024-03-18
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Temperature and soil moisture are known to control pesticide mineralization. Half‐life times (DT〈sub〉50〈/sub〉) derived from pesticide mineralization curves generally indicate longer residence times at low soil temperature and moisture but do not consider potential changes in the microbial allocation of pesticide‐derived carbon (C). We aimed to determine carbon use efficiency (CUE, formation of new biomass relative to total C uptake) to better understand microbial utilization of pesticide‐derived C under different environmental conditions and to support the conventional description of degradation dynamics based on mineralization. We performed a microcosm experiment at two MCPA (2‐methyl‐4‐chlorophenoxyacetic acid) concentrations (1 and 20 mg kg〈sup〉−1〈/sup〉) and defined 20°C/pF 1.8 as optimal and 10°C/pF 3.5 as limiting environmental conditions. After 4 weeks, 70% of the initially applied MCPA was mineralized under optimal conditions but MCPA mineralization reached less than 25% under limiting conditions. However, under limiting conditions, an increase in CUE was observed, indicating a shift towards anabolic utilization of MCPA‐derived C. In this case, increased C assimilation implied C storage or the formation of precursor compounds to support resistance mechanisms, rather than actual growth since we did not find an increase in the 〈italic toggle="no"〉tfdA〈/italic〉 gene relevant to MCPA degradation. We were able to confirm the assumption that under limiting conditions, C assimilation increases relative to mineralization and that C redistribution, may serve as an explanation for the difference between mineralization and MCPA dissipation‐derived degradation dynamics. In addition, by introducing CUE to the temperature‐ and moisture‐dependent degradation of pesticides, we can capture the underlying microbial constraints and adaptive mechanisms to changing environmental conditions.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Changing environmental conditions alter the MCPA degradation dynamics and the allocation of pesticide‐derived carbon to anabolic or catabolic metabolism.〈boxed-text position="anchor" content-type="graphic" id="ejss13417-blkfxd-0001" xml:lang="en"〉 〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:13510754:media:ejss13417:ejss13417-toc-0001"〉 〈/graphic〉 〈/boxed-text〉〈/p〉
    Description: Collaborative Research Center 1253 CAMPOS (DFG)
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: DFG Priority Program 2322 “Soil System”
    Description: Ellrichshausen Foundation
    Description: Research Training Group “Integrated Hydrosystem modeling”
    Description: https://doi.org/10.5281/zenodo.5081655
    Keywords: ddc:631.4 ; anabolism ; carbon use efficiency ; catabolism ; effect of soil moisture and temperature ; gene‐centric process model ; MCPA biodegradation
    Language: English
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  • 19
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    Fifty years after deep‐ploughing: Effects on yield, roots, nutrient stocks and soil structure (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2024-05-30
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Deep‐ploughing far beyond the common depth of 30 cm was used more than 50 years ago in Northern Germany with the aim to break root‐restricting layers and thereby improve access to subsoil water and nutrient resources. We hypothesized that effects of this earlier intervention on soil properties and yields prevailed after 50 years. Hence, we sampled two sandy soils and one silty soil (Cambisols and a Luvisol) of which half of the field had been deep‐ploughed 50 years ago (soils then re‐classified as Treposols). The adjacent other half was not deep‐ploughed and thus served as the control. At all the three sites, both deep‐ploughed and control parts were then conventionally managed over the last 50 years. We assessed yields during the dry year 2019 and additionally in 2020, and rooting intensity at the year of sampling (2019), as well as changes in soil structure, carbon and nutrient stocks in that year. We found that deep‐ploughing improved yields in the dry spell of 2019 at the sandy sites, which was supported by a more general pattern of higher NDVI indices in deep‐ploughed parts for the period from 2016 to 2021 across varying weather conditions. Subsoil stocks of soil organic carbon and total plant‐available phosphorus were enhanced by 21%–199% in the different sites. Root biomass in the subsoil was reduced due to deep‐ploughing at the silty site and was increased or unaffected at the sandy sites. Overall, the effects of deep‐ploughing were site‐specific, with reduced bulk density in the buried topsoil stripes in the subsoil of the sandy sites, but with elevated subsoil density in the silty site. Hence, even 50 years after deep‐ploughing, changes in soil properties are still detectable, although effect size differed among sites.〈/p〉
    Description: BonaRes http://dx.doi.org/10.13039/501100022576
    Keywords: ddc:631.4 ; aggregates ; carbon sequestration ; deep‐ploughing ; macronutrients ; subsoil ; Treposol
    Language: English
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  • 20
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    Calcium isotope ratios in serum are the strongest predictor of bone calcium balance in patients on dialysis (2023)
    Oxford University Press
    Details
    Publication Date: 2024-01-17
    Description: Background and Aims Dysregulated mineral homeostasis is common in chronic kidney disease (CKD) and associated with bone demineralization and vascular calcification. The balance between bone formation and resorption, which reflect the bone calcium (Ca) balance (BCaB), cannot be determined without bone biopsy which is invasive and not easily repeatable. Recently, we have shown that stable (i.e. non-radioactive) Ca isotopes, 42Ca and 44Ca, can be measured in serum and their ratio (δ44/42Caserum) quantitatively determines net bone gain or loss of Ca. Thus, when bone formation exceeds bone resorption, the net BCaB is positive and δ44/42Caserum is high, and when bone resorption is the predominant process δ44/42Caserum is low compared to age-matched controls. In this study we compared δ44/42Caserum against δ44/42Cabone and arterial biopsy samples (δ44/42Caartery) and the sensitivity of δ44/42Ca in predicting changes in bone histology.
    Type: Article , NonPeerReviewed
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  • 21
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    Test of P-wave receiver functions for a seismic velocity and gravity model across the Baikal Rift Zone (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: The seismic receiver function (RF) technique is widely used as an economic method to image earth's deep interior in a large number of seismic experiments. P-wave receiver functions (RFs) constrain crustal thickness and average Vp/Vs in the crust by analysis of the Ps phase and multiples (reflected/converted waves) from the Moho. Regional studies often show significant differences between the Moho depth constrained by RF and by reflection/refraction methods. We compare the results from RF and controlled source seismology for the Baikal Rift Zone by calculating 1480 synthetic RFs for a seismic refraction/reflection velocity model and processing them with two common RF techniques [H–κ and Common Conversion Point (CCP) stacking]. We compare the resulting synthetic RF structure with the velocity model, a density model (derived from gravity and the velocity model), and with observed RFs. Our results demonstrate that the use of different frequency filters, the presence of complex phases from sediments and gradual changes in the properties of crustal layers can lead to erroneous interpretation of RFs and incorrect geological interpretations. We suggest that the interpretation of RFs should be combined with other geophysical methods, in particular in complex tectonic regions and that the long-wavelength Bouguer gravity anomaly signal may provide effective calibration for the determination of the correct Moho depth from RF results. We propose and validate a new automated, efficient method for this calibration.
    Type: Article , PeerReviewed
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  • 22
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    Enhanced Molecular Networking Shows Microbacterium sp. V1 as a Factory of Antioxidant Proline-Rich Peptides (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Two linear proline-rich peptides (1–2), bearing an N-terminal pyroglutamate, were isolated from the marine bacterium Microbacterium sp. V1, associated with the marine sponge Petrosia ficiformis, collected in the volcanic CO2 vents in Ischia Island (South Italy). Peptide production was triggered at low temperature following the one strain many compounds (OSMAC) method. Both peptides were detected together with other peptides (3–8) via an integrated, untargeted MS/MS-based molecular networking and cheminformatic approach. The planar structure of the peptides was determined by extensive 1D and 2D NMR and HR-MS analysis, and the stereochemistry of the aminoacyl residues was inferred by Marfey’s analysis. Peptides 1–8 are likely to arise from Microbacterium V1 tailor-made proteolysis of tryptone. Peptides 1 and 2 were shown to display antioxidant properties in the ferric-reducing antioxidant power (FRAP) assay.
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  • 23
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    Ectothiorhodospira lacustris sp. nov., a New Purple Sulfur Bacterium from Low-Mineralized Soda Lakes That Contains a Unique Pathway for Nitric Oxide Reduction (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Several strains of a Gram-negative, anaerobic photoautotrophic, motile, rod-shaped bacterium, designated as B14B, A-7R, and A-7Y were isolated from biofilms of low-mineralized soda lakes in central Mongolia and Russia (southeast Siberia). They had lamellar stacks as photosynthetic structures and bacteriochlorophyll a as the major photosynthetic pigment. The strains were found to grow at 25–35 °C, pH 7.5–10.2 (optimum, pH 9.0), and with 0–8% (w/v) NaCl (optimum, 0%). In the presence of sulfide and bicarbonate, acetate, butyrate, yeast extract, lactate, malate, pyruvate, succinate, and fumarate promoted growth. The DNA G + C content was 62.9–63.0 mol%. While the 16S rRNA gene sequences confirmed that the new strains belonged to the genus Ectothiorhodospira of the Ectothiorhodospiraceae, comparison of the genome nucleotide sequences of strains B14B, A-7R, and A-7Y revealed that the new isolates were remote from all described Ectothiorhodospira species both in dDDH (19.7–38.8%) and in ANI (75.0–89.4%). The new strains are also genetically differentiated by the presence of a nitric oxide reduction pathway that is lacking from all other Ectiothiorhodospiraceae. We propose to assign the isolates to the new species, Ectothiorhodospira lacustris sp. nov., with the type strain B14BT (=DSM 116064T = KCTC 25542T = UQM 41491T).
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  • 24
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    Artificial Intelligence Forecasting of Marine Heatwaves in the South China Sea Using a Combined U-Net and ConvLSTM System (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Marine heatwaves (MHWs) are extreme events characterized by abnormally high sea surface temperatures, and they have significant impacts on marine ecosystems and human society. The rapid and accurate forecasting of MHWs is crucial for preventing and responding to the impacts they can lead to. However, the research on relevant forecasting methods is limited, and a dedicated forecasting system specifically tailored for the South China Sea (SCS) region has yet to be reported. This study proposes a novel forecasting system utilizing U-Net and ConvLSTM models to predict MHWs in the SCS. Specifically, the U-Net model is used to forecast the intensity of MHWs, while the ConvLSTM model is employed to predict the probability of their occurrence. The indication of an MHW relies on both the intensity forecasted by the U-Net model exceeding threshold T and the occurrence probability predicted by the ConvLSTM model surpassing threshold P. Incorporating sensitivity analysis, optimal thresholds for T are determined as 0.9 °C, 0.8 °C, 1.0 °C, and 1.0 °C for 1-, 3-, 5-, and 7-day forecast lead times, respectively. Similarly, optimal thresholds for P are identified as 0.29, 0.30, 0.20, and 0.28. Employing these thresholds yields the highest forecast accuracy rates of 0.92, 0.89, 0.88, and 0.87 for the corresponding forecast lead times. This innovative approach gives better predictions of MHWs in the SCS, providing invaluable reference information for marine management authorities to make well-informed decisions and issue timely MHW warnings.
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  • 25
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    Integrated statolith and genomic analysis reveals high connectivity in the nektonic squid Illex argentinus: implications for management of an international cephalopod fishery (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: The neritic-oceanic squid Illex argentinus supports one of the largest fisheries in the Southwest Atlantic. It is characterized by extensive migrations across the Patagonian Shelf and complex population structure comprising distinct seasonal spawning groups. To address uncertainty as to the demographic independence of these groups that may compromise sustainable management, a multidisciplinary approach was applied integrating statolith ageing with genome-wide single-nucleotide polymorphism (SNP) analysis. To obtain complete coverage of the spawning groups, sampling was carried out at multiple times during the 2020 fishing season and covered a large proportion of the species' range across the Patagonian Shelf. Statolith and microstructure analysis revealed three distinct seasonal spawning groups of winter-, spring-, and summer-hatched individuals. Subgroups were identified within each seasonal group, with statolith microstructure indicating differences in environmental conditions during ontogeny. Analysis of 〉10 000 SNPs reported no evidence of neutral or non-neutral genetic structure among the various groups. These findings indicate that I. argentinus across the Patagonian Shelf belong to one genetic population and a collaborative management strategy involving international stakeholders is required. The connectivity among spawning groups may represent a "bet-hedging" mechanism important for population resilience.
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    Analysis of Mesoscale Eddy Merging in the Subtropical Northwest Pacific Using Satellite Remote Sensing Data (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Mesoscale eddies are ubiquitous in the ocean, yet our understanding of their evolutions, particularly eddy merging processes, remains enigmatic. In this study, the merging processes of two cyclonic–cyclonic and two anticyclonic–anticyclonic eddies are analyzed in the Subtropical Northwest Pacific using satellite remote sensing altimetry data. The results reveal that, as eddies approach each other, their contours become connected, leading to the formation of multi-core eddies. Simultaneously, the merging process prompts substantial exchanges of energy and vorticity, resulting in the dissipation of one eddy and the emergence of a more extensive merged eddy. Throughout the merging process, the eddy contours elongate upwards along the centerline (the line connecting eddy centers) and there are distinct changes in both the horizontal and vertical morphology of the eddies. Notably, after the merging, the eddies distinctly exhibit intensified signals of sea surface temperature and vertical temperature anomaly, an outcome of their transformative fusion. The findings of this study significantly enhance our understanding of mesoscale eddy dynamics, particularly in the intricate eddy merging process. However, it is important to note that, due to limitations in vertical observational data, this study does not provide a quantitative portrayal of the vertical mechanisms of eddy merging, which also underscores a pivotal avenue for future research in the field.
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  • 27
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    Integrating human dimensions in decadal-scale prediction for marine social–ecological systems: lighting the grey zone (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: The dynamics of marine systems at decadal scales are notoriously hard to predict—hence references to this timescale as the “grey zone” for ocean prediction. Nevertheless, decadal-scale prediction is a rapidly developing field with an increasing number of applications to help guide ocean stewardship and sustainable use of marine environments. Such predictions can provide industry and managers with information more suited to support planning and management over strategic timeframes, as compared to seasonal forecasts or long-term (century-scale) predictions. The most significant advances in capability for decadal-scale prediction over recent years have been for ocean physics and biogeochemistry, with some notable advances in ecological prediction skill. In this paper, we argue that the process of “lighting the grey zone” by providing improved predictions at decadal scales should also focus on including human dimensions in prediction systems to better meet the needs and priorities of end users. Our paper reviews information needs for decision-making at decadal scales and assesses current capabilities for meeting these needs. We identify key gaps in current capabilities, including the particular challenge of integrating human elements into decadal prediction systems. We then suggest approaches for overcoming these challenges and gaps, highlighting the important role of co-production of tools and scenarios, to build trust and ensure uptake with end users of decadal prediction systems. We also highlight opportunities for combining narratives and quantitative predictions to better incorporate the human dimension in future efforts to light the grey zone of decadal-scale prediction.
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  • 28
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    Middle-Late Miocene to Pleistocene Post-Collisional Magmatism in the Arabia-Eurasia Collision Zone, an Example from Northwest Iran (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: Post-collisional volcanism contains important clues for understanding the processes that prevail in orogenic belts, including those in the mantle and the uplift and collapse of continents. Here we report new geochronological and geochemical data for a suite of post-collisional Miocene to Pleistocene volcanic rocks from northwest Iran. Four groups of volcanic rocks can be distinguished according to their geochemical and isotopic signatures, including: (1) Miocene depleted lavas with high Nd and Hf but low Pb and Sr isotopic ratios, (2) less depleted lavas with quite variable Pb isotopic composition, (3) lavas with non-radiogenic Nd and Hf isotopic values, but highly radiogenic Sr and Pb isotopic composition, and (4) Pleistocene adakitic rocks with depleted isotopic signatures. The isotopic data reveal that the Miocene rocks are derived from asthenospheric and highly heterogeneous sub-continental lithospheric mantle sources. Evidence suggests that the lithospheric mantle contains recycled upper continental material and is isotopically similar to the enriched mantle two (EMII) end-member. Analysis of Sr-Nd-Pb-Hf-O isotopes in both mineral and rock groundmass, in conjunction with energy-constrained assimilation and fractional crystallization (EC-AFC) numerical modeling, demonstrates that the incorporation of continental crust during magma fractionation via AFC had an insignificant impact on the isotopic composition of the Miocene lavas. Moreover, adakites are the youngest rocks and show a geochemical signature consistent with the partial melting of a young and mafic continental lower crust. Both seismological data and geochemical signatures on these Miocene to Pleistocene volcanic rocks indicate the initiation of asthenospheric upwelling and orogen uplift in the Arabia-Eurasia collision zone, which occurred after slab break-off, following the Neotethyan closure.
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    The Use of Bi-Potentiostat as a Simple and Accurate Electrochemical Approach for the Determination of Orthophosphate in Seawater (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Autonomous on-site monitoring of orthophosphate (PO43−), an important nutrient for primary production in natural waters, is urgently needed. Here, we report on the development and validation of an on-site autonomous electrochemical analyzer for PO43− in seawater. The approach is based on the use of flow injection analysis in conjunction with a dual electrochemical cell (i.e., a bi-potentiostat detector (FIA-DECD) that uses two working electrodes sharing the same reference and counter electrode. The two working electrodes are used (molybdate/carbon paste electrode (CPE) and CPE) to correct for matrix effects. Optimization of squarewave voltammetry parameters (including step potential, amplitude, and frequency) was undertaken to enhance analytical sensitivity. Possible interferences from non-ionic surfactants and humic acid were investigated. The limit of quantification in artificial seawater (30 g/L NaCl, pH 0.8) was 0.014 µM for a linear concentration range of 0.02–3 µM. The system used a Python script for operation and data processing. The analyzer was tested for ship-board PO43- determination during a four-day research cruise in the North Sea. The analyzer successfully measured 34 samples and achieved a good correlation (Pearson’ R = 0.91) with discretely collected water samples analyzed using a laboratory-based colorimetric reference analyzer.
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    Magnesian Andesites from Kibblewhite Volcano in the Kermadec Arc, New Zealand (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: Primary andesitic magmas could be an important component of arc magma genesis and might have played a key role in the advent of continents. Recent studies hypothesized that primary andesitic magmas occur in the oceanic arc, where the crust is thin. The Kermadec arc has the thinnest crust among all the studied oceanic arcs (〈15 km in thickness); however, there are no studies that corroborate the formation of primary andesitic magmas in the arc. The aim of this study is to develop a better understanding of primary andesites in oceanic arcs through the petrology of the Kermadec arc. Here, we present the petrology of volcanic rocks dredged from the Kibblewhite Volcano in the Kermadec arc during the R/V SONNE SO-255 expedition in 2017. Magma types range from andesite to rhyolite at the Kibblewhite Volcano, but basalts dominate at the neighboring cones. This study focuses on magnesian andesites from the northeastern flank of this volcano. The magnesian andesites are nearly aphyric and plagioclase free but contain microphenocrysts of olivine (Fo84–86) and clinopyroxene (Mg# = 81–87). Using olivine addition models, the primary magmas were estimated to contain 55–56 wt % SiO2 and 10–12 wt % MgO, similar to the high-Mg andesites observed in other convergent plate margins, indicating the generation of primary andesitic magma beneath the Kibblewhite Volcano. The trace element and isotopic characteristics of the magnesian andesites are typical of volcanic rocks from the Kermadec arc. This indicates that the subduction of a young plate or melting of a pyroxenitic source is not necessary to produce magnesian andesites. Instead, we propose that the magnesian andesites were produced by the direct melting of the uppermost mantle of the Kermadec arc. The thin crust of the Kermadec arc should yield low-pressure conditions in the uppermost mantle, allowing the sub-arc mantle to generate primary andesitic melts. This study supports the hypothesis that primary andesitic magmas generate in the arc where the crust is thin and provides a new insight into the magma genesis of the Kermadec arc.
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    Elevated Temperature-Induced Epimicrobiome Shifts in an Invasive Seaweed Gracilaria vermiculophylla (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Epibacterial communities on seaweeds are affected by several abiotic factors such as temperature and acidification. Due to global warming, surface seawater temperatures are expected to increase by 0.5–5 °C in the next century. However, how epibacterial communities associated with seaweeds will respond to global warming remains unknown. In this study, we investigated the response of epibacterial communities associated with the invasive Gracilaria vermiculophylla exposed to 3 °C above ambient temperature for 4 months using a benthocosm system in Kiel, Germany, and 16S rRNA gene amplicon sequencing. The results showed that elevated temperature affected the beta-diversity of the epibacterial communities. Some potential seaweed pathogens such as Pseudoalteromonas, Vibrio, Thalassotalea, and Acinetobacter were identified as indicator genera at the elevated temperature level. Thirteen core raw amplicon sequence variants in the elevated temperature group were the same as the populations distributed over a wide geographical range, indicating that these core ASVs may play an important role in the invasive G. vermicullophylla. Overall, this study not only contributes to a better understanding of how epibacterial communities associated with G. vermiculophylla may adapt to ocean warming, but also lays the foundation for further exploration of the interactions between G. vermiculophylla and its epimicrobiota.
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    Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuration of metabolites with stereogenic centers. This review comprehensively focuses on recent technological and instrumental advances, highlighting the development of methods that alleviate these obstacles, paving the way for accelerating NP discovery towards biotechnological applications. Herein, we emphasize the most innovative high-throughput tools and methods for advancing bioactivity screening, NP chemical analysis, dereplication, metabolite profiling, metabolomics, genome sequencing and/or genomics approaches, databases, bioinformatics, chemoinformatics, and three-dimensional NP structure elucidation.
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  • 33
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    Metabolic Regulation of Copper Toxicity during Marine Mussel Embryogenesis (2023)
    MDPI
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    Publication Date: 2024-02-07
    Description: The development of new tools for assessing the health of cultured shellfish larvae is crucial for aquaculture industries to develop and refine hatchery methodologies. We established a large-volume ecotoxicology/health stressor trial, exposing mussel (Perna canaliculus) embryos to copper in the presence of ethylenediaminetetraacetic acid (EDTA). GC/MS-based metabolomics was applied to identify potential biomarkers for monitoring embryonic/larval health and to characterise mechanisms of metal toxicity. Cellular viability, developmental abnormalities, larval behaviour, mortality, and a targeted analysis of proteins involved in the regulation of reactive oxygen species were simultaneously evaluated to provide a complementary framework for interpretative purposes and authenticate the metabolomics data. Trace metal analysis and speciation modelling verified EDTA as an effective copper chelator. Toxicity thresholds for P. canaliculus were low, with 10% developmental abnormalities in D-stage larvae being recorded upon exposure to 1.10 μg·L−1 bioavailable copper for 66 h. Sublethal levels of bioavailable copper (0.04 and 1.10 μg·L−1) caused coordinated fluctuations in metabolite profiles, which were dependent on development stage, treatment level, and exposure duration. Larvae appeared to successfully employ various mechanisms involving the biosynthesis of antioxidants and a restructuring of energy-related metabolism to alleviate the toxic effects of copper on cells and developing tissues. These results suggest that regulation of trace metal-induced toxicity is tightly linked with metabolism during the early ontogenic development of marine mussels. Lethal-level bioavailable copper (50.3 μg·L−1) caused severe metabolic dysregulation after 3 h of exposure, which worsened with time, substantially delayed embryonic development, induced critical oxidative damage, initiated the apoptotic pathway, and resulted in cell/organism death shortly after 18 h of exposure. Metabolite profiling is a useful approach to (1) assess the health status of marine invertebrate embryos and larvae, (2) detect early warning biomarkers for trace metal contamination, and (3) identify novel regulatory mechanisms of copper-induced toxicity.
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  • 34
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    Wanted Dead or Alive: Skeletal Structure Alteration of Cold-Water Coral Desmophyllum pertusum (Lophelia pertusa) from Anthropogenic Stressors (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Ocean acidification (OA) has provoked changes in the carbonate saturation state that may alter the formation and structural biomineralisation of calcium carbonate exoskeletons for marine organisms. Biomineral production in organisms such as cold-water corals (CWC) rely on available carbonate in the water column and the ability of the organism to sequester ions from seawater or nutrients for the formation and growth of a skeletal structure. As an important habitat structuring species, it is essential to examine the impact that anthropogenic stressors (i.e., OA and rising seawater temperatures) have on living corals and the structural properties of dead coral skeletons; these are important contributors to the entire reef structure and the stability of CWC mounds. In this study, dead coral skeletons in seawater were exposed to various levels of pCO2 and different temperatures over a 12-month period. Nanoindentation was subsequently conducted to assess the structural properties of coral samples’ elasticity (E) and hardness (H), whereas the amount of dissolution was assessed through scanning electron microscopy. Overall, CWC samples exposed to elevated pCO2 and temperature show changes in properties which leave them more susceptible to breakage and may in turn negatively impact the formation and stability of CWC mound development.
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    Total Mass Flux in the Northern Humboldt Current System: Rates and Contribution Sources from Central Peru (12° S) (2023)
    MDPI
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    Publication Date: 2024-02-07
    Description: The total mass flux (TMF) of particulate organic matter (POM) is key for understanding the energetic transfer within the “biological pump” (i.e., involving the carbon cycle), reflecting a critical connection between the surface and the bottom. A fixed multi-sediment trap was installed at 30 m depth in Callao Bay, central Peru from March to December 2020. After recovery, samples were dried and weighed to calculate the TMF and pellet flux. The average TMF was 601.9 mg·m−2·day−1, with 70.2 and 860 mg·m−2·day−1 as the lowest and highest values during “normal conditions”. Zooplankton fecal pellets (ZFP) were found in ovoid (e.g., larvae) and cylindrical (e.g., adult copepods) shapes and their flux contribution to TMF was low, ranging from 0.17 to 85.59 mg·m−2·day−1. In contrast with ZFP, fish fecal pellets (FFP) were found in fragments with a cylindrical shape, and their contribution to the TMF was higher than ZFP, ranging from 1 to 92.56 mg·m−2·day−1. Mean sinking velocities were 4.63 ± 3.47 m·day−1 (ZFP) and 432.27 ± 294.26 m·day−1 (FFP). There is a considerable difference between the ZFP and FFP contributions to TMFs. We discuss the implications of these results regarding a still poorly understood process controlling the POM flux off the Peruvian coast.
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  • 36
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    Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitogenome composition of the seagrass Zostera marina is conserved among worldwide populations that diverged ca. 350,000 years ago. Using long-read sequencing, we characterized the Z. marina mitochondrial genome and inferred the repertoire of recombination-induced configurations. To characterize the mitochondrial genome architecture worldwide and study its evolution, we examined the mitogenome in Z. marina meristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the isoform relative copy number, indicating a high conservation of the mitogenome composition among distantly related populations and within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.
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    Identifying Probable Submarine Hydrothermal Spots in North Santorini Caldera Using the Generalized Moments Method (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: The presence of active hydrothermal vent fields near residential areas and their possible link to volcanic activity poses a potential hazard to the environment, society, and the economy. By capitalizing on Autonomous Underwater Vehicle sampling methodologies and applying the Generalized Moments Method model for geological and physical processes in these environments, we shed light on the underlying dynamics shaping the physicochemical characteristics of the vents. In this study, we focus on the Northern Caldera of Santorini and, more specifically, on the recorded CTD data (Conductivity, Temperature, Depth). The data sets were collected in 2017 in Santorini using an Autonomous Underwater Vehicle during the GEOMAR POS510 mission. Our research shows that the active vent field within the caldera probably follows a multifractal behavior and exhibits a weak memory effect. Depth Profiles and Time Series show similar behavior among conductivity and temperature. The variance and moments of both parameters underline the existence of two different mechanisms governing the behavior of the vent field. Finally, the structure function shows that changes in the time series are described by a Cauchy–Lorentz distribution.
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  • 38
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    Phosphate limitation responses in marine green algae are linked to reprogramming of the tRNA epitranscriptome and codon usage bias (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: Marine algae are central to global carbon fixation and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change, however there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate (P) availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA (tRNA) modification enzymes and biased codon usage of transcripts more abundant during P-limiting versus P-replete conditions, consistent with the role of tRNA modifications in regulating codon recognition. To associate the observed shift in expression of the tRNA modification enzyme complement with the tRNAs encoded by M. commoda, we also determined the tRNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing P-limitation and photosystem-associated proteins that have ill-characterized putative functions in “light stress”. The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in tRNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation, that extends beyond the catalog of up- or down-regulated protein-encoding genes, to the cell biological controls that underpin acclimation to changing environmental conditions.
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  • 39
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    Indications from C:N:P Ratios in Surface Sediments along Land-to-Sea Gradients to Support Coastal Nutrient Management (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Shallow, semi-enclosed coastal systems are particularly prone to eutrophication. Depending on local site conditions and historical nutrient legacies, sea-based measures might be necessary in addition to land-based nutrient removal. In this study, C:N:P ratios were combined with open-source bathymetric information and linked with the prevailing geomorphological and sedimentological regimes to gain insights into nutrient hotspots and understand their sources and fate in coastal waters. Land-based sediment samples were taken behind outlets at three sites in Eckernförde Bay (Baltic Sea), and complemented with ship-based sampling at locations approximately 8 m and 12 m water depth. The total carbon, nitrogen and phosphorus concentrations in surface sediments increased at deeper sites. This suggests that an increased downslope particle transport and deposition regime, based on local geomorphology, might influence nutrient hotspots to a larger extent than proximity to sources (e.g., outlets). Overall, the recorded C:N ratios (mean = 28.12) were closer to the ratio of terrestrial plants than those of marine phytoplankton, indicating allochthonous sources of organic matter.
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  • 40
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    Chemical and Biological Evaluation of Amazonian Medicinal Plant Vouacapoua americana Aubl (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Vouacapoua americana (Fabaceae) is an economically important tree in the Amazon region and used for its highly resistant heartwood as well as for medicinal purposes. Despite its frequent use, phytochemical investigations have been limited and rather focused on ecological properties than on its pharmacological potential. In this study, we investigated the phytochemistry and bioactivity of V. americana stem bark extract and its constituents to identify eventual lead structures for further drug development. Applying hydrodistillation and subsequent GC-MS analysis, we investigated the composition of the essential oil and identified the 15 most abundant components. Moreover, the diterpenoids deacetylchagresnone (1), cassa-13(14),15-dien-oic acid (2), isoneocaesalpin H (3), (+)-vouacapenic acid (4), and (+)-methyl vouacapenate (5) were isolated from the stem bark, with compounds 2 and 4 showing pronounced effects on Methicillin-resistant Staphylococcus aureus and Enterococcus faecium, respectively. During the structure elucidation of deacetylchagresnone (1), which was isolated from a natural source for the first time, we detected inconsistencies regarding the configuration of the cyclopropane ring. Thus, the structure was revised for both deacetylchagresnone (1) and the previously isolated chagresnone. Following our works on Copaifera reticulata and Vatairea guianensis, the results of this study further contribute to the knowledge of Amazonian medicinal plants.
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  • 41
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    A Deep-Learning Based Pipeline for Estimating the Abundance and Size of Aquatic Organisms in an Unconstrained Underwater Environment from Continuously Captured Stereo Video (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: The utilization of stationary underwater cameras is a modern and well-adapted approach to provide a continuous and cost-effective long-term solution to monitor underwater habitats of particular interest. A common goal of such monitoring systems is to gain better insight into the dynamics and condition of populations of various marine organisms, such as migratory or commercially relevant fish taxa. This paper describes a complete processing pipeline to automatically determine the abundance, type and estimate the size of biological taxa from stereoscopic video data captured by the stereo camera of a stationary Underwater Fish Observatory (UFO). A calibration of the recording system was carried out in situ and, afterward, validated using the synchronously recorded sonar data. The video data were recorded continuously for nearly one year in the Kiel Fjord, an inlet of the Baltic Sea in northern Germany. It shows underwater organisms in their natural behavior, as passive low-light cameras were used instead of active lighting to dampen attraction effects and allow for the least invasive recording possible. The recorded raw data are pre-filtered by an adaptive background estimation to extract sequences with activity, which are then processed by a deep detection network, i.e., Yolov5. This provides the location and type of organisms detected in each video frame of both cameras, which are used to calculate stereo correspondences following a basic matching scheme. In a subsequent step, the size and distance of the depicted organisms are approximated using the corner coordinates of the matched bounding boxes. The Yolov5 model employed in this study was trained on a novel dataset comprising 73,144 images and 92,899 bounding box annotations for 10 categories of marine animals. The model achieved a mean detection accuracy of 92.4%, a mean average precision (mAP) of 94.8% and an F1 score of 93%.
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    The founding charter of the Omic Biodiversity Observation Network (Omic BON) (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.
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    Links between Ikaite Morphology, Recrystallised Ikaite Petrography and Glendonite Pseudomorphs Determined from Polar and Deep-Sea Ikaite (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Petrography of recrystallised ikaite from Ocean Drilling Program material has been presented previously from Nankai Trough and Congo (ex-Zaire) deep-sea fan. This paper expands on the Nankai Trough ikaite observations, drawing on evidence from Laptev Sea, South Georgia, Okhotsk Sea, and coastal lagoon Point Barrow. However, even though many ikaite and glendonite sites occur at high latitudes, it cannot be that ikaite forms exclusively in polar environments, as demonstrated by the occurrences in the low latitude low temperature deep sea sediments offshore Gulf of Guinea (Angola Congo) and mid-latitude deep-sea trenches offshore Japan. Recrystallised ikaite occurs as mm large, zoned calcite crystals in all samples, along with secondary phases of calcite. Our data set is unique in that the origin, storage, and recrystallisation process of natural formed ikaite is recorded in detail and confirms that glendonite petrographic characteristics are a consequence of the structure and chemistry of recrystallising ikaite and not the physical or geochemical environment. The transformation of man-made ikaite to calcite as recorded in laboratory studies, is a process very similar to the one we have observed for natural ikaite. Most significant is that there is variation in the order of the calcite types within a single sample, leading to the conclusion that the variation is a consequence of impurities and geochemical variability in the ikaite, not the external environment. Morphological observations reveal similarities in ikaite and glendonite, this and the similarity in internal textures in glendonite and recrystallised ikaite confirms that glendonite may be used as an indicator of past presence of ikaite.
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    Opportunistic bacteria of grapevine crown galls are equipped with the genomic repertoire for opine utilization (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: Young grapevines (Vitis vinifera) suffer and eventually can die from the crown gall disease caused by the plant pathogen Allorhizobium vitis (Rhizobiaceae). Virulent members of A. vitis harbor a tumor-inducing plasmid and induce formation of crown galls due to the oncogenes encoded on the transfer DNA. The expression of oncogenes in transformed host cells induces unregulated cell proliferation and metabolic and physiological changes. The crown gall produces opines uncommon to plants, which provide an important nutrient source for A. vitis harboring opine catabolism enzymes. Crown galls host a distinct bacterial community, and the mechanisms establishing a crown gall–specific bacterial community are currently unknown. Thus, we were interested in whether genes homologous to those of the tumor-inducing plasmid coexist in the genomes of the microbial species coexisting in crown galls. We isolated 8 bacterial strains from grapevine crown galls, sequenced their genomes, and tested their virulence and opine utilization ability in bioassays. In addition, the 8 genome sequences were compared with 34 published bacterial genomes, including closely related plant-associated bacteria not from crown galls. Homologous genes for virulence and opine anabolism were only present in the virulent Rhizobiaceae. In contrast, homologs of the opine catabolism genes were present in all strains including the nonvirulent members of the Rhizobiaceae and non-Rhizobiaceae. Gene neighborhood and sequence identity of the opine degradation cluster of virulent and nonvirulent strains together with the results of the opine utilization assay support the important role of opine utilization for cocolonization in crown galls, thereby shaping the crown gall community.
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    Should we reconsider how to assess eutrophication? (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: Eutrophication in marine waters is traditionally assessed by checking if nutrients, algal biomass and oxygen are below/above a given threshold. However, increased biomass, nutrient concentrations and oxygen demand do not lead to undesirable environmental effects if the flow of carbon/energy from primary producers toward high trophic levels is consistently preserved. Consequently, traditional indicators might provide a misleading assessment of the eutrophication risk. To avoid this, we propose to evaluate eutrophication by using a new index based on plankton trophic fluxes instead of biogeochemical concentrations. A preliminary, model-based, assessment suggests that this approach might give a substantially different picture of the eutrophication status of our seas, with potential consequences on marine ecosystem management. Given the difficulties to measure trophic fluxes in the field, the use of numerical simulations is recommended although the uncertainty associated with biogeochemical models inevitably affects the reliability of the index. However, given the effort currently in place to develop refined numerical tools describing the marine environment (Ocean Digital Twins), a reliable, model-based, eutrophication index could be operational in the near future.
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    Reproductive Biology of the Golden Cuttlefish Sepia esculenta (Cephalopoda, Sepiida) (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: The golden cuttlefish Sepia esculenta is the one of most abundant cuttlefish species around south-east Asia and has a high commercial value. Despite its wide distribution and high commercial value, its reproductive biology is still poorly understood. This study was based on 25 males and 6 females. The potential fecundity (PF) of females was 1701–3719 oocytes, which was an increase, as compared to the previously known values. The oocyte resorption reached up to 13.2% of fecundity. The ovulation pattern was group-synchronous, with a predominance of previtellogenic oocytes. The pre-meiotic and primary growth oocyte phases were absent in mature females. The number of spermatophores carried by an individual male was 146–1698 (length 9–20 mm). The spermatophores were characterised by a cement body consisting of conical oral and cylindrical aboral parts. The ontogenetic changes in the spermatophores and their parts were recorded for the first time in the order of Sepiida. Their sperm content and their adhesive abilities also increased during ontogenesis. The data obtained in the present study significantly increased and corrected the existing knowledge of S. esculenta biology. Moreover, these data help to explain the general patterns of reproductive biology in cuttlefish, as well as in Cephalopoda as a whole.
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    Bioactivity and Metabolome Mining of Deep-Sea Sediment-Derived Microorganisms Reveal New Hybrid PKS-NRPS Macrolactone from Aspergillus versicolor PS108-62 (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Despite low temperatures, poor nutrient levels and high pressure, microorganisms thrive in deep-sea environments of polar regions. The adaptability to such extreme environments renders deep-sea microorganisms an encouraging source of novel, bioactive secondary metabolites. In this study, we isolated 77 microorganisms collected by a remotely operated vehicle from the seafloor in the Fram Strait, Arctic Ocean (depth of 2454 m). Thirty-two bacteria and six fungal strains that represented the phylogenetic diversity of the isolates were cultured using an One-Strain-Many-Compounds (OSMAC) approach. The crude EtOAc extracts were tested for antimicrobial and anticancer activities. While antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium was common for many isolates, only two bacteria displayed anticancer activity, and two fungi inhibited the pathogenic yeast Candida albicans. Due to bioactivity against C. albicans and rich chemical diversity based on molecular network-based untargeted metabolomics, Aspergillus versicolor PS108-62 was selected for an in-depth chemical investigation. A chemical work-up of the SPE-fractions of its dichloromethane subextract led to the isolation of a new PKS-NRPS hybrid macrolactone, versicolide A (1), a new quinazoline (−)-isoversicomide A (3), as well as three known compounds, burnettramic acid A (2), cyclopenol (4) and cyclopenin (5). Their structures were elucidated by a combination of HRMS, NMR, [α]D, FT-IR spectroscopy and computational approaches. Due to the low amounts obtained, only compounds 2 and 4 could be tested for bioactivity, with 2 inhibiting the growth of C. albicans (IC50 7.2 µg/mL). These findings highlight, on the one hand, the vast potential of the genus Aspergillus to produce novel chemistry, particularly from underexplored ecological niches such as the Arctic deep sea, and on the other, the importance of untargeted metabolomics for selection of marine extracts for downstream chemical investigations.
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    Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla Periphylla (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: The marine mesopelagic zone extends from water depths of 200 m to 1000 m and is home to a vast number and diversity of species. It is one of the least understood regions of the marine environment with untapped resources of pharmaceutical relevance. The mesopelagic jellyfish Periphylla periphylla is a well-known and widely distributed species in the mesopelagic zone; however, the diversity or the pharmaceutical potential of its cultivable microbiota has not been explored. In this study, we isolated microorganisms associated with the inner and outer umbrella of P. periphylla collected in Irminger Sea by a culture-dependent approach, and profiled their chemical composition and biological activities. Sixteen mostly gram-negative bacterial isolates were selected and subjected to an OSMAC cultivation regime approach using liquid and solid marine broth (MB) and glucose–yeast–malt (GYM) media. Their ethyl acetate (EtOAc) extracts were assessed for cytotoxicity and antimicrobial activity against fish and human pathogens. All, except one extract, displayed diverse levels of antimicrobial activities. Based on low IC50 values, four most bioactive gram-negative strains; Polaribacter sp. SU124, Shewanella sp. SU126, Psychrobacter sp. SU143 and Psychrobacter sp. SU137, were prioritized for an in-depth comparative and untargeted metabolomics analysis using feature-based molecular networking. Various chemical classes such as diketopiperazines, polyhydroxybutyrates (PHBs), bile acids and other lipids were putatively annotated, highlighting the biotechnological potential in P. periphylla-associated microbiota as well as gram-negative bacteria. This is the first study providing an insight into the cultivable bacterial community associated with the mesopelagic jellyfish P. periphylla and, indeed, the first to mine the metabolome and antimicrobial activities of these microorganisms.
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    Combining an Eddy Detection Algorithm with In-Situ Measurements to Study North Brazil Current Rings (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: North Brazil Current (NBC) rings are believed to play a key role in the Atlantic Ocean circulation and climate. Here, we use a new collection of high-resolution in-situ observations acquired during the EUREC4A-OA field experiment together with satellite altimetry to define, with unprecedented detail, the structure and evolution of these eddies. In-situ observations reveal a more complex structure than previously documented. In particular, we highlight a measurable impact of the Amazon outflow in creating a barrier layer over a large portion of the eddies. We show that this unprecedented data set allows us to estimate the accuracy of satellite altimetry gridded fields. The geostrophic velocities derived from satellite altimetry turn out to be considerably lower (up to 50% in amplitude) than the values measured by current meters. However, eddy properties as detected by TOEddies, a newly developed algorithm show to be relatively precise. For example, the eddy center and maximum azimuthal velocity contour fall within 25 ± 5 km and 16 ± 9 km, respectively, from the in-situ observed values. We apply TOEddies to 27 years of satellite altimetry to investigate the generic NBC rings behavior. We found a mean generation rate of 4.5 ± 1.1 rings per year, and a strong seasonal cycle in all eddy properties.
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    The Rhodoexplorer Platform for Red Algal Genomics and Whole Genome Assemblies for Several Gracilaria Species (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: Macroalgal (seaweed) genomic resources are generally lacking as compared to other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole genome assemblies for two species (G. chilensis and G. gracilis), a draft genome assembly of G. caudata, and genome annotation of the previously published G. vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.
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    Impact of Enzymatically Extracted High Molecular Weight Fucoidan on Lipopolysaccharide-Induced Endothelial Activation and Leukocyte Adhesion (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: The endothelial cell lining creates an interface between circulating blood and adjoining tissue and forms one of the most critical barriers and targets for therapeutical intervention. Recent studies suggest that fucoidans, sulfated and fucose-rich polysaccharides from brown seaweed, show multiple promising biological effects, including anti-inflammatory properties. However, their biological activity is determined by chemical characteristics such as molecular weight, sulfation degree, and molecular structure, which vary depending on the source, species, and harvesting and isolation method. In this study, we investigated the impact of high molecular weight (HMW) fucoidan extract on endothelial cell activation and interaction with primary monocytes (MNCs) in lipopolysaccharide (LPS)-induced inflammation. Gentle enzyme-assisted extraction combined with fractionation by ion exchange chromatography resulted in well-defined and pure fucoidan fractions. FE_F3, with a molecular weight ranging from 110 to 800 kDa and a sulfate content of 39%, was chosen for further investigation of its anti-inflammatory potential. We observed that along with higher purity of fucoidan fractions, the inflammatory response in endothelial mono- and co-cultures with MNCs was reduced in a dose-dependent manner when testing two different concentrations. This was demonstrated by a decrease in IL-6 and ICAM-1 on gene and protein levels and a reduced gene expression of TLR-4, GSK3β and NF-kB. Expression of selectins and, consequently, the adhesion of monocytes to the endothelial monolayer was reduced after fucoidan treatment. These data indicate that the anti-inflammatory effect of fucoidans increases with their purity and suggest that fucoidans might be useful in limiting the inflammatory response of endothelial cells in cases of LPS-induced bacterial infection.
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    Phytoplankton Diversity and Co-Dependency in a Stratified Oligotrophic Ecosystem in the South Adriatic Sea (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: The oligotrophy of the southern Adriatic Sea is characterized by seasonal stratification which enables nutrient supply to the euphotic layer. A set of interdisciplinary methods was used to elucidate the diversity and co-dependency of bacterio- and phytoplankton of the water column during the stratification period of July 2021. A total of 95 taxa were determined by microscopy: 58 diatoms, 27 dinoflagellates, 6 coccolithophores, and 4 other autotrophs, which included Chlorophyceae, Chrysophyceae, and Cryptophytes. Nanophytoplankton abundances were higher in comparison to microphytoplankton. The prokaryotic plankton community as revealed by HTS was dominated by Proteobacteria (41–73%), Bacteroidota (9.5–27%), and cyanobacteria (1–10%), while the eukaryotic plankton community was composed of parasitic Syndiniales (45–80%), Ochrophyta (2–18%), Ciliophora (2–21%), Chlorophytes (2–4%), Haptophytes (1–4%), Bacillariophyta (1–13%), Pelagophyta (0.5–12%) and Chrysophyta (0.5–3%). Flow cytometry analysis has recorded Prochlorococcus and photosynthetic picoeukaryotes as more abundant in deep chlorophyll maximum (DCM), and Synechococcus and heterotrophic bacteria as most abundant in surface and thermocline layers. Surface, thermocline, and DCM layers were distinct considering community diversity, temperature, and nutrient correlations, while extreme nutrient values at the beginning of the investigating period indicated a possible nutrient flux. Nutrient and temperature were recognized as the main environmental drivers of phytoplankton and bacterioplankton community abundance.
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    Recent advances in availability and synthesis of the economic costs of biological invasions (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: Biological invasions are a global challenge that has received insufficient attention. Recently available cost syntheses have provided policy- and decision makers with reliable and up-to-date information on the economic impacts of biological invasions, aiming to motivate effective management. The resultant InvaCost database is now publicly and freely accessible and enables rapid extraction of monetary cost information. This has facilitated knowledge sharing, developed a more integrated and multidisciplinary network of researchers, and forged multidisciplinary collaborations among diverse organizations and stakeholders. Over 50 scientific publications so far have used the database and have provided detailed assessments of invasion costs across geographic, taxonomic, and spatiotemporal scales. These studies have provided important information that can guide future policy and legislative decisions on the management of biological invasions while simultaneously attracting public and media attention. We provide an overview of the improved availability, reliability, standardization, and defragmentation of monetary costs; discuss how this has enhanced invasion science as a discipline; and outline directions for future development.
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  • 54
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    Smaller herring larval size-at-stage in response to environmental changes is associated with ontogenic processes and stress response (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: The development and physiology of herring larvae were monitored for individuals reared in control and combined warming-acidification crossed with different food quality treatments. The experiment revealed that warming and acidification triggers a stress response at the molecular level and decrease herring larvae size-at-stage. Global change puts coastal systems under pressure, affecting the ecology and physiology of marine organisms. In particular, fish larvae are sensitive to environmental conditions, and their fitness is an important determinant of fish stock recruitment and fluctuations. To assess the combined effects of warming, acidification and change in food quality, herring larvae were reared in a control scenario (11 & DEG;C*pH 8.0) and a scenario predicted for 2100 (14 & DEG;C*pH 7.6) crossed with two feeding treatments (enriched in phosphorus and docosahexaenoic acid or not). The experiment lasted from hatching to the beginning of the post-flexion stage (i.e. all fins present) corresponding to 47 days post-hatch (dph) at 14 & DEG;C and 60 dph at 11 & DEG;C. Length and stage development were monitored throughout the experiment and the expression of genes involved in growth, metabolic pathways and stress responses were analysed for stage 3 larvae (flexion of the notochord). Although the growth rate was unaffected by acidification and temperature changes, the development was accelerated in the 2100 scenario, where larvae reached the last developmental stage at a smaller size (-8%). We observed no mortality related to treatments and no effect of food quality on the development of herring larvae. However, gene expression analyses revealed that heat shock transcripts expression was higher in the warmer and more acidic treatment. Our findings suggest that the predicted warming and acidification environment are stressful for herring larvae, inducing a decrease in size-at-stage at a precise period of ontogeny. This could either negatively affect survival and recruitment via the extension of the predation window or positively increase the survival by reducing the larval stage duration.
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    Metabolomics and Microbiomics Insights into Differential Surface Fouling of Three Macroalgal Species of Fucus (Fucales, Phaeophyceae) That Co-Exist in the German Baltic Sea (2023)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: The brown algal genus Fucus provides essential ecosystem services crucial for marine environments. Macroalgae (seaweeds) release dissolved organic matter, hence, are under strong settlement pressure from micro- and macrofoulers. Seaweeds are able to control surface epibionts directly by releasing antimicrobial compounds onto their surfaces, and indirectly by recruiting beneficial microorganisms that produce antimicrobial/antifouling metabolites. In the Kiel Fjord, in the German Baltic Sea, three distinct Fucus species coexist: F. vesiculosus, F. serratus, and F. distichus subsp. evanescens. Despite sharing the same habitat, they show varying fouling levels; F. distichus subsp. evanescens is the least fouled, while F. vesiculosus is the most fouled. The present study explored the surface metabolomes and epiphytic microbiota of these three Fucus spp., aiming to uncover the factors that contribute to the differences in the fouling intensity on their surfaces. Towards this aim, algal surface metabolomes were analyzed using comparative untargeted LC-MS/MS-based metabolomics, to identify the marker metabolites influencing surface fouling. Their epiphytic microbial communities were also comparatively characterized using high-throughput amplicon sequencing, to pinpoint the differences in the surface microbiomes of the algae. Our results show that the surface of the least fouling species, F. distichus subsp. evanescens, is enriched with bioactive compounds, such as betaine lipids MGTA, 4-pyridoxic acid, and ulvaline, which are absent from the other species. Additionally, it exhibits a high abundance of the fungal genera Mucor and Alternaria, along with the bacterial genus Yoonia-Loktanella. These taxa are known for producing antimicrobial/antifouling compounds, suggesting their potential role in the observed fouling resistance on the surface of the F. distichus subsp. evanescens compared to F. serratus and F. vesiculosus. These findings provide valuable clues on the differential surface fouling intensity of Fucus spp., and their importance in marine chemical defense and fouling dynamics.
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    Machine learning in marine ecology: an overview of techniques and applications (2023)
    Oxford University Press
    Details
    Publication Date: 2024-02-14
    Description: Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of & SIM;1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets.
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    Inspecting the Reliability of Geochemical Facies Identified for the Waterworks' Capture Zone in Germany (2022)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publication Date: 2022-09-27
    Description: Little research attention has been given to validating clusters obtained from the groundwater geochemistry of the waterworks' capture zone with a prevailing lake‐groundwater exchange. To address this knowledge gap, we proposed a new scheme whereby Gaussian finite mixture modeling (GFMM) and Spike‐and‐Slab Bayesian (SSB) algorithms were utilized to cluster the groundwater geochemistry while quantifying the probability of the resulting cluster membership against each other. We applied GFMM and SSB to 13 geochemical parameters collected during different sampling periods at 13 observation points across the Barnim Highlands plateau located in the northeast of Berlin, Germany; this included 10 observation wells, two lakes, and a gallery of drinking production wells. The cluster analysis of GFMM yielded nine clusters, either with a probability ≥0.8, while the SSB produced three hierarchical clusters with a probability of cluster membership varying from 〈0.2 to 〉0.8. The findings demonstrated that the clustering results of GFMM were in good agreement with the classification as per the principal component analysis and Piper diagram. By superimposing the parameter clustering onto the observation clustering, we could identify discrepancies that exist among the parameters of a certain cluster. This enables the identification of different factors that may control the geochemistry of a certain cluster, although parameters of that cluster share a strong similarity. The GFMM results have shown that from 2002, there has been active groundwater inflow from the lakes towards the capture zone. This means that it is necessary to adopt appropriate measures to reverse the inflow towards the lakes.
    Description: Article impact statement: The probability of cluster membership quantified using an algorithm should be validated against another probabilistic‐based classifier.
    Description: Federal Ministry of Education and Research http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:551.9 ; ddc:551.49
    Language: English
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    Application of mixed‐effects modelling and rule‐based models to explain copper variation in soil profiles of southern Germany (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-10-01
    Description: Copper (Cu) is an essential element for plants and microorganisms and at larger concentrations a toxic pollutant. A number of factors controlling Cu dynamics have been reported, but information on quantitative relationships is scarce. We aimed to (i) quantitatively describe and predict soil Cu concentrations (CuAR) in aqua regia considering site‐specific effects and effects of pH, soil organic carbon (SOC) and cation exchange capacity (CEC), and (ii) study the suitability of mixed‐effects modelling and rule‐based models for the analysis of long‐term soil monitoring data. Thirteen uncontaminated long‐term monitoring soil profiles in southern Germany were analysed. Since there was no measurable trend of increasing CuAR concentrations with time in the respective depth ranges of the sites, data from different sampling dates were combined and horizon‐specific regression analyses including model simplifications were carried out for 10 horizons. Fixed‐ and mixed‐effects models with the site as a random effect were useful for the different horizons and significant contributions (either of main effects or interactions) of SOC, CEC and pH were present for 9, 8 and 7 horizons, respectively. Horizon‐specific rule‐based cubist models described the CuAR data similarly well. Validations of cubist models and mixed‐effects models for the CuAR concentrations in A horizons were successful for the given population after random splitting into calibration and validation samples, but not after independent validations with random splitting according to sites. Overall, site, CEC, SOC and pH provide important information for a description of CuAR concentrations using the different regression approaches. Highlights: Information on quantitative relationships for factors controlling Cu dynamics is scarce. Site, CEC, SOC and pH provide important information for a description of Cu concentrations. Validations of cubist models and mixed‐effects models for A horizons were successful for a closed population of sites.
    Description: Bavarian State Ministry of the Environment and Consumer Protection http://dx.doi.org/10.13039/501100010219
    Description: Ministry of Agriculture and Environment Mecklenburg‐Western Pomerania
    Keywords: ddc:631.4
    Language: English
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    Millimetre scale aeration of the rhizosphere and drilosphere (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-10-04
    Description: Soil aeration is a critical factor for oxygen‐limited subsoil processes, as transport by diffusion and advection is restricted by the long distance to the free atmosphere. Oxygen transport into the soil matrix is highly dependent on its connectivity to larger pore channels like earthworm and root colonised biopores. Here we hypothesize that the soil matrix around biopores represents different connectivity depending on biopore genesis and actual coloniser. We analysed the soil pore system of undisturbed soil core samples around biopores generated or colonised by roots and earthworms and compared them with the pore system of soil, not in the immediacy of a biopore. Oxygen partial pressure profiles and gas relative diffusion was measured in the rhizosphere and drilosphere from the biopore wall into the bulk soil with microelectrodes. The measurements were linked with structural features such as porosity and connectivity obtained from X‐ray tomography and image analysis. Aeration was enhanced in the soil matrix surrounding biopores in comparison to the bulk soil, shown by higher oxygen concentrations and higher relative diffusion coefficients. Biopores colonised by roots presented more connected lateral pores than earthworm colonised ones, which resulted in enhanced aeration of the rhizosphere compared to the drilosphere. This has influenced biotic processes (microbial turnover/mineralization or root respiration) at biopore interfaces and highlights the importance of microstructural features for soil processes and their dependency on the biopore's coloniser.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4
    Language: English
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    Response of subsoil organic matter contents and physical properties to long‐term, high‐rate farmyard manure application (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-07-26
    Description: Application of farmyard manure (FYM) is common practice to improve physical and chemical properties of arable soil and crop yields. However, studies on effects of FYM application mainly focussed on topsoils, whereas subsoils have rarely been addressed so far. We, therefore, investigated the effects of 36‐year FYM application with different rates of annual organic carbon (OC) addition (0, 469, 938 and 1875 g C m−2 a−1) on OC contents of a Chernozem in 0–30 cm (topsoil) and 35–45 cm (subsoil) depth. We also investigated its effects on soil structure and hydraulic properties in subsoil. X‐ray computed tomography was used to analyse the response of the subsoil macropore system (≥19 μm) and the distribution of particulate organic matter (POM) to different FYM applications, which were related to contents in total OC (TOC) and water‐extractable OC (WEOC). We show that FYM‐C application of 469 g C m−2 a−1 caused increases in TOC and WEOC contents only in the topsoil, whereas rates of ≥938 g C m−2 a−1 were necessary for TOC enrichment also in the subsoil. At this depth, the subdivision of TOC into different OC sources shows that most of the increase was due to fresh POM, likely by the stimulation of root growth and bioturbation. The increase in subsoil TOC went along with increases in macroporosity and macropore connectivity. We neither observed increases in plant‐available water capacity nor in unsaturated hydraulic conductivity. In conclusion, only very high application of FYM over long periods can increase OC content of subsoil at our study site, but this increase is largely based on fresh, easily degradable POM and likely accompanied by high C losses when considering the discrepancy between OC addition rate by FYM and TOC response in soil. Highlights A new image processing procedure to distinguish fresh and decomposed POM. The increase of subsoil C stock based to a large extend on fresh, labile POM. Potential of arable subsoils for long‐term C storage by large FYM application rates is limited. The increase in TOC has no effect on hydraulic properties of the subsoil.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4
    Language: English
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    Non‐exchangeable stable hydrogen isotope ratios in clay minerals and soil clay fractions: A method test (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-01-20
    Description: Stable hydrogen isotope ratios (δ2H values) in structural hydroxyl groups of pedogenic clay minerals are inherited from the surrounding water at the time of their formation. Only non‐exchangeable H preserves the environmental forensic and paleoclimate information (δ2Hn value). To measure δ2Hn values in structural H of clay minerals and soil clay fractions, we adapted a steam equilibration method by accounting for high hygroscopicity. Our δ2Hn values for USGS57 biotite (−95.3 ± SD 0.9‰) and USGS58 muscovite (30.7 ± 1.4‰) differed slightly but significantly from the reported δ2H values (−91.5 ± 2.4‰ and −28.4 ± 1.6‰), because the minerals contained 1.1%–4.4% of exchangeable H. The low SD of replicate measurements (n = 3) confirmed a high precision. The clay separation method including destruction of Fe oxides, carbonates and soil organic matter, and dispersion did not significantly change the δ2Hn values of five different clay minerals. However, we were unable to remove all organic matter from the soil clay fractions resulting in an estimated bias of 1‰ in two samples and 15‰ in the carbon‐richest sample. Our results demonstrate that δ2Hn values of structural H of clay minerals and soil clay fractions can be reliably measured without interference from atmospheric water and the method used to separate the soil clay fraction. Highlights We tested steam equilibration to determine stable isotope ratios of structural H in clay. Gas‐tight capsule sealing in Ar atmosphere was necessary to avoid remoistening. Our steam equilibration method showed a high accuracy and precision. The clay separation method did not change stable isotope ratios of structural H in clay.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:549 ; controlled isotope exchange technique ; deuterium ; montmorillonite ; soil clay separation ; soil organic matter removal ; steam equilibration ; structural H ; USGS57 biotite ; vermiculite ; δ2H
    Language: English
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    Potential erodibility of semi‐arid steppe soils derived from aggregate stability tests (2022)
    Koza, Moritz ; Pöhlitz, Julia ; Prays, Aleksey ; [et al.]
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-01-26
    Description: Erosion is a severe threat to the sustainable use of agricultural soils. However, the structural resistance of soil against the disruptive forces steppe soils experience under field conditions has not been investigated. Therefore, 132 topsoils under grass‐ and cropland covering a large range of physico‐chemical soil properties (sand: 2–76%, silt: 18–80%, clay: 6–30%, organic carbon: 7.3–64.2 g kg−1, inorganic carbon: 0.0–8.5 g kg−1, pH: 4.8–9.5, electrical conductivity: 32–946 μS cm−1) from northern Kazakhstan were assessed for their potential erodibility using several tests. An adjusted drop‐shatter method (low energy input of 60 Joule on a 250‐cm3 soil block) was used to estimate the stability of dry soil against weak mechanical forces, such as saltating particles striking the surface causing wind erosion. Three wetting treatments with various conditions and energies (fast wetting, slow wetting, and wet shaking) were applied to simulate different disruptive effects of water. Results indicate that aggregate stability was higher for grassland than cropland soils and declined with decreasing soil organic carbon content. The results of the drop‐shatter test suggested that 29% of the soils under cropland were at risk of wind erosion, but only 6% were at high risk (i.e. erodible fraction 〉60%). In contrast, the fast wetting treatment revealed that 54% of the samples were prone to become “very unstable” and 44% “unstable” during heavy rain or snowmelt events. Even under conditions comparable to light rain events or raindrop impact, 53–59% of the samples were “unstable.” Overall, cropland soils under semi‐arid conditions seem much more susceptible to water than wind erosion. Considering future projections of increasing precipitation in Kazakhstan, we conclude that the risk of water erosion is potentially underestimated and needs to be taken into account when developing sustainable land use strategies. Highlights Organic matter is the important binding agent enhancing aggregation in steppe topsoils. Tillage always declines aggregate stability even without soil organic carbon changes. All croplands soil are prone to wind or water erosion independent of their soil properties. Despite the semi‐arid conditions, erosion risk by water seems higher than by wind.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:631.4 ; climate change ; land use ; soil organic carbon ; soil texture ; water erosion ; wind erosion
    Language: English
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    Vertical SOC distribution and aromatic carbon in centuries old charcoal‐rich Technosols (2022)
    Bonhage, Alexander ; Raab, Thomas ; Schneider, Anna ; [et al.]
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-01-21
    Description: Charcoal‐rich Technosols on century‐old relict charcoal hearths (RCHs) are the subject of ongoing research regarding potential legacy effects that result from historic charcoal production and subsequent charcoal amendments on forest soil properties and forest ecosystems today. RCHs consist mostly of Auh horizons that are substantially enriched in soil organic carbon (SOC), of which the largest part seems to be of pyrogenic origin (PyC). However, the reported range of SOC and PyC contents in RCH soil also suggests that they are enriched in nonpyrogenic SOC. RCH soils are discussed as potential benchmarks for the long‐term influence of biochar amendment and the post‐wildfire influences on soil properties. In this study, we utilised a large soil sample dataset (n = 1245) from 52 RCH sites in north‐western Connecticut, USA, to quantify SOC contents by total element analysis. The contents of condensed highly aromatic carbon as a proxy for black carbon (BC) were predicted by using a modified benzene polycarboxylated acid (BPCA) marker method in combination with diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy‐based partial least square regression (r2 = 0.89). A high vertical spatial sampling resolution allowed the identification of soil organic matter (SOM) enrichment and translocation processes. The results show an average 75% and 1862% increase in TOC and BPCA‐derived carbon, respectively, for technogenic Auh horizons compared to reference soils. In addition to an increase in aromatic properties, increased carboxylic properties of the RCH SOC suggest self‐humification effects of degrading charcoal and thereby the continuing formation of leachable aromatic carbon compounds, which could have effects on pedogenic processes in buried soils. Indeed, we show BPCA‐derived carbon concentrations in intermediate technogenic Cu horizons and buried top/subsoils that suggest vertical translocation of highly aromatic carbon originating in RCH Auh horizons. Topmost Auh horizons showed a gradual decrease in total organic carbon (TOC) contents with increasing depth, suggesting accumulation of recent, non‐pyrogenic SOM. Lower aliphatic absorptions in RCH soil spectra suggest different SOM turnover dynamics compared to reference soils. Furthermore, studied RCH soils featured additional TOC enrichment, which cannot be fully explained now. Highlights BC to TOC ratio and high resolution vertical SOC distribution in 52 RCH sites were studied. RCH soils non‐BC pool was potentially different to reference soils. RCH soils feature TOC accumulation in the topmost horizon. There is BC translocation into buried soils on RCH sites.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; benzene polycarboxylated acid marker (BPCA) ; black carbon ; charcoal degradation ; charcoal kiln ; pyrogenic carbon ; relict charcoal hearth ; biochar
    Language: English
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    Defining Hydrogeological Site Similarity with Hierarchical Agglomerative Clustering (2022)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publication Date: 2024-02-28
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Hydrogeological information about an aquifer is difficult and costly to obtain, yet essential for the efficient management of groundwater resources. Transferring information from sampled sites to a specific site of interest can provide information when site‐specific data is lacking. Central to this approach is the notion of site similarity, which is necessary for determining relevant sites to include in the data transfer process. In this paper, we present a data‐driven method for defining site similarity. We apply this method to selecting groups of similar sites from which to derive prior distributions for the Bayesian estimation of hydraulic conductivity measurements at sites of interest. We conclude that there is now a unique opportunity to combine hydrogeological expertise with data‐driven methods to improve the predictive ability of stochastic hydrogeological models.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉〈italic〉Article impact statement〈/italic〉: This article introduces hierarchical clustering as a method for defining a notion of site similarity; the aim of this method is to improve the derivation of prior distributions in Bayesian methods in hydrogeology.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: https://github.com/GeoStat-Bayesian/geostatDB
    Description: https://github.com/GeoStat-Bayesian/exPrior
    Description: https://github.com/GeoStat-Bayesian/siteSimilarity
    Keywords: ddc:551.49 ; hydrogeological sites ; hydrogeological modeling
    Language: English
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    Reducing tillage intensity benefits the soil micro‐ and mesofauna in a global meta‐analysis (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2024-03-22
    Description: Soil fauna drives crucial processes of energy and nutrient cycling in agricultural systems, and influences the quality of crops and pest incidence. Soil tillage is the most influential agricultural manipulation of soil structure, and has a profound influence on soil biology and its provision of ecosystem services. The objective of this study was to quantify through meta‐analyses the effects of reducing tillage intensity on density and diversity of soil micro‐ and mesofaunal communities, and how these effects vary among different pedoclimatic conditions and interact with concurrent management practices. We present the results of a global meta‐analysis of available literature data on the effects of different tillage intensities on taxonomic and functional groups of soil micro‐ and mesofauna. We collected paired observations (conventional vs. reduced forms of tillage/no‐tillage) from 133 studies across 33 countries. Our results show that reduced tillage intensity or no‐tillage increases the total density of springtails (+35%), mites (+23%), and enchytraeids (+37%) compared to more intense tillage methods. The meta‐analyses for different nematode feeding groups, life‐forms of springtails, and taxonomic mite groups showed higher densities under reduced forms of tillage compared to conventional tillage on omnivorous nematodes (+53%), epedaphic (+81%) and hemiedaphic (+84%) springtails, oribatid (+43%) and mesostigmatid (+57%) mites. Furthermore, the effects of reduced forms of tillage on soil micro‐ and mesofauna varied with depth, climate and soil texture, as well as with tillage method, tillage frequency, concurrent fertilisation, and herbicide application. Our findings suggest that reducing tillage intensity can have positive effects on the density of micro‐ and mesofaunal communities in areas subjected to long‐term intensive cultivation practices. Our results will be useful to support decision making on the management of soil faunal communities and will facilitate modelling efforts of soil biology in global agroecosystems. HIGHLIGHTS Global meta‐analysis to estimate the effect of reducing tillage intensity on micro‐ and mesofauna Reduced tillage or no‐tillage has positive effects on springtail, mite and enchytraeid density Effects vary among nematode feeding groups, springtail life forms and mite suborders Effects vary with texture, climate and depth and depend on the tillage method and frequency
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Description: https://doi.org/10.20387/bonares-eh0f-hj28
    Keywords: ddc:631.4 ; agricultural land use ; conservation agriculture ; conventional agriculture ; soil biodiversity ; soil cultivation
    Language: English
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    PISM parameter ensemble analysis of Antarctic Ice Sheet glacial cycle simulations - additional data (2022)
    PANGAEA
    Details
    Publication Date: 2022-09-22
    Description: This dataset contains PISM simulation results of the Antarctic Ice Sheet based on code release v1.0-paleo-ensemble (https://doi.org/10.5281/zenodo.3574033). PISM is the open-source Parallel Ice Sheet Model developed mainly at UAF, USA and PIK, Germany. See documentation in https://www.pism.io. These are additional netCDF data from the same ensemble simulations already stored in doi:10.1594/PANGAEA.909728. 1) 1000-year snapshots since 125000 years before present, of ice thickness, bed topography, change in bed topography, floating/grounded mask, surface elevation, basal melt rate and vertically averaged velocity magnitude (SIA+SSA) (16GB) 2) 5000-year snapshots since 125000 years before present, SSA velocity components in x and y direction (8GB)
    Type: info:eu-repo/semantics/workingPaper
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    Influence of the Atlantic Multidecadal Oscillation on South American Atmosphere Dynamics and Precipitation (2022)
    MDPI
    Details
    Publication Date: 2024-01-08
    Description: The Atlantic Multidecadal Oscillation (AMO) is coherently linked to climate variations over many parts of the globe. Despite recent achievements, the mechanism by which the AMO influences regional precipitation over South America is not well understood. In this study, we isolate the atmospheric response to the AMO using a water isotope-enabled version of the Community Earth System Model version 1.2 (iCESM1.2) and determine its influence on (sub)tropical South American regional precipitation and atmospheric circulation. The results suggest an interhemispheric seesaw in Hadley circulation strength and that the section of the Atlantic Hadley cell is marked by a stronger upward air component south of the equator during the cold AMO phase. We also find that the precipitation anomalies over (sub)tropical South America during AMO phases are mainly related to changes in the Atlantic Intertropical Convergence Zone (ITCZ) core strength, where in the cold (warm) AMO phase the core region strengthens (weakens) from February to July, while from July to November the core region weakens (strengthens). Our results stress the importance of acknowledging the dynamics of season- and regional-dependent ITCZ responses, as they are sufficient to produce observed AMO-related signals even in the absence of marked changes in the ITCZ position.
    Type: Article , PeerReviewed
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    Geomorphological Data from Detonation Craters in the Fehmarn Belt, German Baltic Sea (2022)
    MDPI
    Details
    Publication Date: 2024-01-08
    Description: Military munitions from World War I and II dumped at the seafloor are a threat to the marine environment and its users. Decades of saltwater exposure make the explosives fragile and difficult to dispose of. If required, the munition is blast-in-place. In August 2019, 42 ground mines were detonated in a controlled manner underwater during a NATO maneuver in the German Natura2000 Special Area of Conservation Fehmarn Belt, the Baltic Sea. In June 2020, four detonation craters were investigated with a multibeam echosounder for the first time. This dataset is represented here as maps of bathymetry, slope angle, and height difference to the surrounding. The circular craters were still clearly visible a year after the detonation. The diameter and depth of the structures were between 7.5–12.6 m and 0.7–2.2 m, respectively. In total, about 321 m2 of the seafloor was destroyed along the track line.
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    AUV navigation correction based on automated Multibeam Tile Matching (2022)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Ocean science and hydroacoustic seafloor mapping rely on accurate navigation underwater. By exploiting terrain information provided by a multibeam echosounder system, it is possible to significantly improve map quality. This article presents an algorithm capable of improving map quality and accuracy by aligning consecutive pings to tiles that are matched pairwise. A globally consistent solution is calculated from these matches. The proposed method has the potential to be used online in addition to other navigation solutions, but is mainly targeted for post processing. The algorithm was tested using different parameter settings on an AUV and a ship-based dataset. The ship-based dataset is publicly available as a benchmark. The original accurate navigation serving as a ground truth, alongside trajectories that include an artificial drift, are available. This allows quantitative comparisons between algorithms and parameter settings.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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    Functional Responses and Additive Multiple Predator Effects of Two Common Wetland Fish (2022)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Understanding trophic interactions is essential for the prediction and measurement of structure and function in aquatic environments. Communities in these ecosystems may be shaped by variables such as predator diversity, prey density and emergent multiple predator effects (MPEs), which are likely to influence trophic dynamics. In this study, we examined the effect of key predatory fish in floodplain wetlands, namely Oreochromis mossambicus and Enteromius paludinosus, towards Chironomidae prey, using a comparative functional response (FR) approach. We used single predator species as well as intra- and interspecific paired species to contrast FRs under multiple predator scenarios. Attack rate and handling time estimates from single predator FRs were used to predict multiple predators’ feeding rates, which were compared to observe multiple predators’ feeding rates to quantify potential MPEs. From single fish trials, each species displayed a significant Type II FR, characterized by high feeding rates at low prey densities. Oreochromis mossambicus had a steeper (initial slope, i.e., higher attack rate) and higher (asymptote of curve, i.e., shorter handling time and higher maximum feeding rate) FR, whereas E. paludinosus exhibited lower-magnitude FRs (i.e., lower attack rate, longer handling time and lower feeding rate). In multiple predator scenarios, feeding rates were well-predicted by those of single predators, both in conspecific and interspecific pairs, and thus we did not find evidence for antagonistic or synergistic MPEs. Predator–prey interactions in wetland systems can have significant consequences on the structure and dynamics of ecological communities. In turn, this could have destabilizing effects on resources in tropical wetlands. These results, although experimental, help us understand how trophic interaction among conspecific or interspecific fish species in Austral tropical wetlands might influence their aquatic prey species. This will help us to understand food web dynamics better.
    Type: Article , PeerReviewed
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    Application of Feature-Based Molecular Networking for Comparative Metabolomics and Targeted Isolation of Stereoisomers from Algicolous Fungi (2022)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Seaweed endophytic (algicolous) fungi are talented producers of bioactive natural products. We have previously isolated two strains of the endophytic fungus, Pyrenochaetopsis sp. FVE-001 and FVE-087, from the thalli of the brown alga Fucus vesiculosus. Initial chemical studies yielded four new decalinoylspirotetramic acid derivatives with antimelanoma activity, namely pyrenosetins A–C (1–3) from Pyrenochaetopsis sp. strain FVE-001, and pyrenosetin D (4) from strain FVE-087. In this study, we applied a comparative metabolomics study employing HRMS/MS based feature-based molecular networking (FB MN) on both Pyrenochaetopsis strains. A higher chemical capacity in production of decalin derivatives was observed in Pyrenochaetopsis sp. FVE-087. Notably, several decalins showed different retention times despite the same MS data and MS/MS fragmentation pattern with the previously isolated pyrenosetins, indicating they may be their stereoisomers. FB MN-based targeted isolation studies coupled with antimelanoma activity testing on the strain FVE-087 afforded two new stereoisomers, pyrenosetins E (5) and F (6). Extensive NMR spectroscopy including DFT computational studies, HR-ESIMS, and Mosher’s ester method were used in the structure elucidation of compounds 5 and 6. The 3′R,5′R stereochemistry determined for compound 6 was identical to that previously reported for pyrenosetin C (3), whose stereochemistry was revised as 3′S,5′R in this study. Pyrenosetin E (5) inhibited the growth of human malignant melanoma cells (A-375) with an IC50 value of 40.9 μM, while 6 was inactive. This study points out significant variations in the chemical repertoire of two closely related fungal strains and the versatility of FB MN in identification and targeted isolation of stereoisomers. It also confirms that the little-known fungal genus Pyrenochaetopsis is a prolific source of complex decalinoylspirotetramic acid derivatives.
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    Nutritional Calcium Supply Dependent Calcium Balance, Bone Calcification and Calcium Isotope Ratios in Rats (2022)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Serum calcium isotopes (δ44/42Ca) have been suggested as a non-invasive and sensitive Ca balance marker. Quantitative δ44/42Ca changes associated with Ca flux across body compartment barriers relative to the dietary Ca and the correlation of δ44/42CaSerum with bone histology are unknown. We analyzed Ca and δ44/42Ca by mass-spectrometry in rats after two weeks of standard-Ca-diet (0.5%) and after four subsequent weeks of standard- and of low-Ca-diet (0.25%). In animals on a low-Ca-diet net Ca gain was 61 ± 3% and femur Ca content 68 ± 41% of standard-Ca-diet, bone mineralized area per section area was 68 ± 15% compared to standard-Ca-diet. δ44/42Ca was similar in the diets, and decreased in feces and urine and increased in serum in animals on low-Ca-diet. δ44/42CaBone was higher in animals on low-Ca-diet, lower in the diaphysis than the metaphysis and epiphysis, and unaffected by gender. Independent of diet, δ44/42CaBone was similar in the femora and ribs. At the time of sacrifice, δ44/42CaSerum inversely correlated with intestinal Ca uptake and histological bone mineralization markers, but not with Ca content and bone mineral density by µCT. In conclusion, δ44/42CaBone was bone site specific, but mechanical stress and gender independent. Low-Ca-diet induced marked changes in feces, serum and urine δ44/42Ca in growing rats. δ44/42CaSerum inversely correlated with markers of bone mineralization.
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    Impacts of Warming and Acidification on Coral Calcification Linked to Photosymbiont Loss and Deregulation of Calcifying Fluid pH (2022)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Corals are globally important calcifiers that exhibit complex responses to anthropogenic warming and acidification. Although coral calcification is supported by high seawater pH, photosynthesis by the algal symbionts of zooxanthellate corals can be promoted by elevated pCO2. To investigate the mechanisms underlying corals’ complex responses to global change, three species of tropical zooxanthellate corals (Stylophora pistillata, Pocillopora damicornis, and Seriatopora hystrix) and one species of asymbiotic cold-water coral (Desmophyllum pertusum, syn. Lophelia pertusa) were cultured under a range of ocean acidification and warming scenarios. Under control temperatures, all tropical species exhibited increased calcification rates in response to increasing pCO2. However, the tropical species’ response to increasing pCO2 flattened when they lost symbionts (i.e., bleached) under the high-temperature treatments—suggesting that the loss of symbionts neutralized the benefit of increased pCO2 on calcification rate. Notably, the cold-water species that lacks symbionts exhibited a negative calcification response to increasing pCO2, although this negative response was partially ameliorated under elevated temperature. All four species elevated their calcifying fluid pH relative to seawater pH under all pCO2 treatments, and the magnitude of this offset (Δ[H+]) increased with increasing pCO2. Furthermore, calcifying fluid pH decreased along with symbiont abundance under thermal stress for the one species in which calcifying fluid pH was measured under both temperature treatments. This observation suggests a mechanistic link between photosymbiont loss (‘bleaching’) and impairment of zooxanthellate corals’ ability to elevate calcifying fluid pH in support of calcification under heat stress. This study supports the assertion that thermally induced loss of photosymbionts impairs tropical zooxanthellate corals’ ability to cope with CO2-induced ocean acidification.
    Type: Article , PeerReviewed
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    Induction of Isochromanones by Co-Cultivation of the Marine Fungus Cosmospora sp. and the Phytopathogen Magnaporthe oryzae (2022)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Microbial co-cultivation is a promising approach for the activation of biosynthetic gene clusters (BGCs) that remain transcriptionally silent under artificial culture conditions. As part of our project aiming at the discovery of marine-derived fungal agrochemicals, we previously used four phytopathogens as model competitors in the co-cultivation of 21 marine fungal strains. Based on comparative untargeted metabolomics analyses and anti-phytopathogenic activities of the co-cultures, we selected the co-culture of marine Cosmospora sp. with the phytopathogen Magnaporthe oryzae for in-depth chemical studies. UPLC-MS/MS-based molecular networking (MN) of the co-culture extract revealed an enhanced diversity of compounds in several molecular families, including isochromanones, specifically induced in the co-culture. Large scale co-cultivation of Cosmospora sp. and M. oryzae resulted in the isolation of five isochromanones from the whole co-culture extract, namely the known soudanones A, E, D (1-3) and their two new derivatives, soudanones H-I (4-5), the known isochromans, pseudoanguillosporins A and B (6, 7), naphtho-γ-pyrones, cephalochromin and ustilaginoidin G (8, 9), and ergosterol (10). Their structures were established by NMR, HR-ESIMS, FT-IR, electronic circular dichroism (ECD) spectroscopy, polarimetry ([α]D), and Mosher’s ester reaction. Bioactivity assays revealed antimicrobial activity of compounds 2 and 3 against the phytopathogens M. oryzae and Phytophthora infestans, while pseudoanguillosporin A (6) showed the broadest and strongest anti-phytopathogenic activity against Pseudomonas syringae, Xanthomonas campestris, M. oryzae and P. infestans. This is the first study assessing the anti-phytopathogenic activities of soudanones.
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    Error estimates for seismic body wave delay times in the ISC-EHB Bulletin (2022)
    Oxford University Press
    Details
    Publication Date: 2024-02-07
    Description: We analyse the consistency of the delay time data in the most recent version of the ISC-EHB bulletin published by the International Seismological Centre covering the years 1964–2018. Considering that the delays are influenced by the lateral heterogeneity in the Earth’s mantle, we construct a tomographic matrix. We use singular value decomposition of the tomographic matrix for 19 707 dense clusters of earthquakes to compute objective estimates of the standard error from data that project into the null space and should be zero if there were no errors. Using a robust initial estimate of the standard deviation of the clustered delay times, we remove a small fraction of outliers before calculating the ultimate errors. We found that the errors depend on the type of body wave, depth of the earthquake (crust or mantle) and the number of decimals with which the arrival time was reported. Using these parameters, we distinguish 45 different classes of delay times for 11 different types of body waves. The errors of each class so divided generally follow a distribution that is approximately normal with a mean that ranges from 0.32 s for PKPbc waves from mantle earthquakes, to 2.82 s for S waves from shallow earthquakes bottoming in the upper mantle. The widths of the distributions of the errors themselves are small enough to serve in formal statistical quantification of the quality of fit in tomographic experiments.
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    Improvement of On-Site Sensor for Simultaneous Determination of Phosphate, Silicic acid, Nitrate plus Nitrite in Seawater (2022)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Accurate, on-site determinations of macronutrients (phosphate (PO43−), nitrate (NO3−), and silicic acid (H4SiO4)) in seawater in real time are essential to obtain information on their distribution, flux, and role in marine biogeochemical cycles. The development of robust sensors for long-term on-site analysis of macronutrients in seawater is a great challenge. Here, we present improvements of a commercial automated sensor for nutrients (including PO43−, H4SiO4, and NO2− plus NO3−), suitable for a variety of aquatic environments. The sensor uses the phosphomolybdate blue method for PO43−, the silicomolybdate blue method for H4SiO4 and the Griess reagent method for NO2−, modified with vanadium chloride as reducing agent for the determination of NO3−. Here, we report the optimization of analytical conditions, including reaction time for PO43− analysis, complexation time for H4SiO4 analysis, and analyte to reagent ratio for NO3− analysis. The instrument showed wide linear ranges, from 0.2 to 100 μM PO43−, between 0.2 and 100 μM H4SiO4, from 0.5 to 100 μM NO3−, and between 0.4 and 100 μM NO2−, with detection limits of 0.18 μM, 0.15 μM, 0.45 μM, and 0.35 μM for PO43−, H4SiO4, NO3−, and NO2−, respectively. The analyzer showed good precision with a relative standard deviation of 8.9% for PO43−, 4.8% for H4SiO4, and 7.4% for NO2− plus NO3− during routine analysis of certified reference materials (KANSO, Japan). The analyzer performed well in the field during a 46-day deployment on a pontoon in the Kiel Fjord (located in the southwestern Baltic Sea), with a water supply from a depth of 1 m. The system successfully collected 443, 440, and 409 on-site data points for PO43−, Σ(NO3− + NO2−), and H4SiO4, respectively. Time series data agreed well with data obtained from the analysis of discretely collected samples using standard reference laboratory procedures and showed clear correlations with key hydrographic parameters throughout the deployment period.
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    Phytoplankton Surveys in the Arctic Fram Strait Demonstrate the Tiny Eukaryotic Alga Micromonas and Other Picoprasinophytes Contribute to Deep Sea Export (2022)
    MDPI
    Details
    Publication Date: 2024-02-07
    Description: Critical questions exist regarding the abundance and, especially, the export of picophytoplankton (≤2 µm diameter) in the Arctic. These organisms can dominate chlorophyll concentrations in Arctic regions, which are subject to rapid change. The picoeukaryotic prasinophyte Micromonas grows in polar environments and appears to constitute a large, but variable, proportion of the phytoplankton in these waters. Here, we analyze 81 samples from the upper 100 m of the water column from the Fram Strait collected over multiple years (2009–2015). We also analyze sediment trap samples to examine picophytoplankton contributions to export, using both 18S rRNA gene qPCR and V1-V2 16S rRNA Illumina amplicon sequencing to assess the Micromonas abundance within the broader diversity of photosynthetic eukaryotes based on the phylogenetic placement of plastid-derived 16S amplicons. The material sequenced from the sediment traps in July and September 2010 showed that 11.2 ± 12.4% of plastid-derived amplicons are from picoplanktonic prasinophyte algae and other green lineage (Viridiplantae) members. In the traps, Micromonas dominated (83.6% ± 21.3%) in terms of the overall relative abundance of Viridiplantae amplicons, specifically the species Micromonas polaris. Temporal variations in Micromonas abundances quantified by qPCR were also observed, with higher abundances in the late-July traps and deeper traps. In the photic zone samples, four prasinophyte classes were detected in the amplicon data, with Micromonas again being the dominant prasinophyte, based on the relative abundance (89.4% ± 8.0%), but with two species (M. polaris and M. commoda-like) present. The quantitative PCR assessments showed that the photic zone samples with higher Micromonas abundances (〉1000 gene copies per mL) had significantly lower standing stocks of phosphate and nitrate, and a shallower average depth (20 m) than those with fewer Micromonas. This study shows that despite their size, prasinophyte picophytoplankton are exported to the deep sea, and that Micromonas is particularly important within this size fraction in Arctic marine ecosystems.
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  • 78
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    A Winter-to-Summer Transition of Bacterial and Archaeal Communities in Arctic Sea Ice (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: The Arctic is warming 2–3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community.
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  • 79
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    A Vision on a UNESCO Global Geopark at the Southeastern Dead Sea in Jordan - Geosites and Conceptual Approach (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: A vision for the establishment of a Geopark in Jordan is given in this work, with a subsequent application to the UNESCO Global Geopark programme. The Dead Sea area and its surroundings have suffered strong changes in the last decades, accompanied by a variety of natural hazards related to enhanced erosional processes. The aspiring Geopark will thematically encompass the influence that these changes and related natural hazards, including flash floods and subsidence, have had on the local population, from geological, over historical up to recent times. The hydrogeology and geomorphology, i.e., the connection between erosion by water, dissolution of minerals, and landscape evolution, will be the main guiding theme that connects the Eastern Rim Highlands with the Dead Sea rift valley through ephemeral wadis, vegetated springs areas, and traditionally communities. The creation of the Geopark is aimed at holistic, sustainable development and management of the area by eco-tourism, and includes education on water resource management, hazard awareness and resilience, as well as international research. We here present the conceptual approach to the initial development of a Geopark network in Jordan. In a narrative discourse, we highlight realised and further implementation steps, with an evaluation of the expected timeline, potential partner institutions, regional involvement and the chances for realisation.
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  • 80
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    Assessing Representation Learning and Clustering Algorithms for Computer-Assisted Image Annotation - Simulating and Benchmarking MorphoCluster (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: Image annotation is a time-consuming and costly task. Previously, we published MorphoCluster as a novel image annotation tool to address problems of conventional, classifier-based image annotation approaches: their limited efficiency, training set bias and lack of novelty detection. MorphoCluster uses clustering and similarity search to enable efficient, computer-assisted image annotation. In this work, we provide a deeper analysis of this approach. We simulate the actions of a MorphoCluster user to avoid extensive manual annotation runs. This simulation is used to test supervised, unsupervised and transfer representation learning approaches. Furthermore, shrunken k-means and partially labeled k-means, two new clustering algorithms that are tailored specifically for the MorphoCluster approach, are compared to the previously used HDBSCAN*. We find that labeled training data improve the image representations, that unsupervised learning beats transfer learning and that all three clustering algorithms are viable options, depending on whether completeness, efficiency or runtime is the priority. The simulation results support our earlier finding that MorphoCluster is very efficient and precise. Within the simulation, more than five objects per simulated click are being annotated with 95% precision.
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  • 81
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    Maintenance of Intraspecific Diversity in Response to Species Competition and Nutrient Fluctuations (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: Intraspecific diversity is a substantial part of biodiversity, yet little is known about its maintenance. Understanding mechanisms of intraspecific diversity shifts provides realistic detail about how phytoplankton communities evolve to new environmental conditions, a process especially important in times of climate change. Here, we aimed to identify factors that maintain genotype diversity and link the observed diversity change to measured phytoplankton morpho-functional traits Vmax and cell size of the species and genotypes. In an experimental setup, the two phytoplankton species Emiliania huxleyi and Chaetoceros affinis, each consisting of nine genotypes, were cultivated separately and together under different fluctuation and nutrient regimes. Their genotype composition was assessed after 49 and 91 days, and Shannon’s diversity index was calculated on the genotype level. We found that a higher intraspecific diversity can be maintained in the presence of a competitor, provided it has a substantial proportion to total biovolume. Both fluctuation and nutrient regime showed species-specific effects and especially structured genotype sorting of C. affinis. While we could relate species sorting with the measured traits, genotype diversity shifts could only be partly explained. The observed context dependency of genotype maintenance suggests that the evolutionary potential could be better understood, if studied in more natural settings including fluctuations and competition.
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  • 82
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    A Vision on a UNESCO Global Geopark at the Southeastern Dead Sea in Jordan — How Natural Hazards May Offer Geotourism Opportunities (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: This paper aims to identify and discuss the chances, solutions, and possible drawbacks related to the establishment of safe geotourism sites in subsidence-affected areas, exemplarily applied to the Ghor Al-Haditha sinkhole site at the southeastern shore of the Dead Sea. Such safe areas shall be established in the territory of the proposed future UNESCO Global Geopark (UGGp) in Jordan. The highlights of the geopark and the basis of its creation are the subsidence features and stream channels found along the SE shoreline of the Dead Sea, which form both a natural hazard and geological heritage of high international significance and have attracted many researchers so far. This recent and ongoing formation is related to the sharp regression of the lake, the specific geomechanical conditions, and the hydrogeologic and climatic background of the surroundings. Nearby communities have suffered in economic terms from these natural phenomena, including flash floods and droughts in this semi-arid to arid region. We here present a concept on how to integrate geoscientific research for hazard monitoring and early warning to maintain safety for inhabitants and visitors on the one hand and reach sustainable economic development through the establishment of geotourism sites on the other hand. This highlight area of the proposed UGGp serves as a starting example for delineating safe zones for walkways and infrastructure. This involves two-way knowledge transfer between spatial planning and hydrogeophysical monitoring, a network of community-supported geophysical surveillance, and regular maintenance and adaptation. The cross-cutting benefits for the territory involve the delineation of safe areas for agriculture and geotourism, the increase of sustainable tourism in the region with a shift towards alternative ways of income, more investment in infrastructure, a growth of international visibility of the region, enhanced environmental education with focus on responsible water usage, and involvement in international research and education projects.
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  • 83
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    Polymetallic Sulfide–Quartz Vein System in the Koudiat Aïcha Massive Sulfide Deposit, Jebilet Massif, Morocco: Microanalytical and Fluid Inclusion Approaches (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: The Koudiat Aïcha Zn-Cu-Pb deposit (3–Mt ore @ 3 wt.% Zn, 1 wt.% Pb, 0.6 wt.% Cu) in the Jebilet massif (Morocco) comprises stratabound lenticular orebodies and crosscutting sulfide-bearing quartz ± carbonate veins in the lower Carboniferous Sarhlef volcano sedimentary succession. The veins are characterized by abundant pyrrhotite, sphalerite, subordinate chalcopyrite and galena and rare Ag and Au minerals. The stratabound massive sulfide ores are attributed to a “VMS” type, whereas the origin of the sulfide–quartz ± carbonate veins remains poorly understood. New mineralogical and microanalytical data (SEM, EPMA and LA-ICP-MS) combined with fluid inclusion results point to two-stage vein formation. The early stage involved C–H–O–N Variscan metamorphic fluids which percolated through fractures and shear zones and deposited pyrite at 〉400 °C, followed by the formation of pyrrhotite and sphalerite (300 ± 20 °C) in quartz veins and in banded and breccia ores. The pyrrhotite–sphalerite mineralization was overprinted by aqueous brines (34 to 38 wt% eq. NaCl + CaCl2) that precipitated carbonate and Cu-Pb sulfides (±Ag-Au) at ~180–210 °C through mixing with low-salinity fluids during tectonic reworking of early-formed structures and in late extension fractures. The latter ore fluids were similar to widspread post-Variscan evaporitic brines that circulated in the Central Jebilet. Overlapping or successive pulses of different ore fluids, i.e., metamorphic fluids and basinal brines, led to metal enrichment in the quartz–carbonate veins compared to the massive sulfide ores. These results underscore that even a single deposit may record several distinct mineralizing styles, such that the ultimate metal endowment may be cumulative over multiple stages.
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  • 84
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    Comparative Genome Analysis of the Photosynthetic Betaproteobacteria of the Genus Rhodocyclus: Heterogeneity within Strains Assigned to Rhodocyclus tenuis and Description of Rhodocyclus gracilis sp. nov. as a New Species (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: The genome sequences for Rhodocyclus purpureus DSM 168T and four strains assigned to Rhodocyclus tenuis (DSM 110, DSM 111, DSM 112, and IM 230) have been determined. One of the strains studied (IM 230) has an average nucleotide identity (ANI) of 97% to the recently reported genome of the type strain DSM 109 of Rcy. tenuis and is regarded as virtually identical at the species level. The ANI of 80% for three other strains (DSM 110, DSM 111, DSM 112) to the type strain of Rcy. tenuis points to a differentiation of these at the species level. Rcy. purpureus is equidistant from Rcy. tenuis and the new species, based on both ANI (78–80%) and complete proteome comparisons (70% AAI). Strains DSM 110, DSM 111, and DSM 112 are very closely related to each other based on ANI, whole genome, and proteome comparisons but clearly distinct from the Rcy. tenuis type strain DSM 109. In addition to the whole genome differentiation, these three strains also contain unique genetic differences in cytochrome genes and contain genes for an anaerobic cobalamin synthesis pathway that is lacking from both Rcy. tenuis and Rcy. purpureus. Based on genomic and genetic differences, these three strains should be considered to represent a new species, which is distinctly different from both Rcy. purpureus and Rcy. tenuis, for which the new name Rhodocyclus gracilis sp. nov. is proposed.
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  • 85
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    The Diversity, Metabolomics Profiling, and the Pharmacological Potential of Actinomycetes Isolated from the Estremadura Spur Pockmarks (Portugal) (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: The Estremadura Spur pockmarks are a unique and unexplored ecosystem located in the North Atlantic, off the coast of Portugal. A total of 85 marine-derived actinomycetes were isolated and cultured from sediments collected from this ecosystem at a depth of 200 to 350 m. Nine genera, Streptomyces, Micromonospora, Saccharopolyspora, Actinomadura, Actinopolymorpha, Nocardiopsis, Saccharomonospora, Stackebrandtia, and Verrucosispora were identified by 16S rRNA gene sequencing analyses, from which the first two were the most predominant. Non-targeted LC-MS/MS, in combination with molecular networking, revealed high metabolite diversity, including several known metabolites, such as surugamide, antimycin, etamycin, physostigmine, desferrioxamine, ikarugamycin, piericidine, and rakicidin derivatives, as well as numerous unidentified metabolites. Taxonomy was the strongest parameter influencing the metabolite production, highlighting the different biosynthetic potentials of phylogenetically related actinomycetes; the majority of the chemical classes can be used as chemotaxonomic markers, as the metabolite distribution was mostly genera-specific. The EtOAc extracts of the actinomycete isolates demonstrated antimicrobial and antioxidant activity. Altogether, this study demonstrates that the Estremadura Spur is a source of actinomycetes with potential applications for biotechnology. It highlights the importance of investigating actinomycetes from unique ecosystems, such as pockmarks, as the metabolite production reflects their adaptation to this habitat.
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  • 86
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    Gut and Gill-Associated Microbiota of the Flatfish European Plaice (Pleuronectes platessa): Diversity, Metabolome and Bioactivity against Human and Aquaculture Pathogens (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: Similar to other marine holobionts, fish are colonized by complex microbial communities that promote their health and growth. Fish-associated microbiota is emerging as a promising source of bioactive metabolites. Pleuronectes platessa (European plaice, plaice), a flatfish with commercial importance, is common in the Baltic Sea. Here we used a culture-dependent survey followed by molecular identification to identify microbiota associated with the gills and the gastrointestinal tract (GIT) of P. platessa, then profiled their antimicrobial activity and metabolome. Altogether, 66 strains (59 bacteria and 7 fungi) were isolated, with Proteobacteria being the most abundant phylum. Gill-associated microbiota accounted for higher number of isolates and were dominated by the Proteobacteria (family Moraxellaceae) and Actinobacteria (family Nocardiaceae), whereas Gram-negative bacterial families Vibrionaceae and Shewanellaceae represented the largest group associated with the GIT. The EtOAc extracts of the solid and liquid media cultures of 21 bacteria and 2 fungi representing the diversity of cultivable plaice-associated microbiota was profiled for their antimicrobial activity against three fish pathogens, human bacterial pathogen panel (ESKAPE) and two human fungal pathogens. More than half of all tested microorganisms, particularly those originating from the GIT epithelium, exhibited antagonistic effect against fish pathogens (Lactococcus garvieae, Vibrio ichthyoenteri) and/or human pathogens (Enterococcus faecium, methicillin-resistant Staphylococcus aureus). Proteobacteria represented the most active isolates. Notably, the solid media extracts displayed higher activity against fish pathogens, while liquid culture extracts were more active against human pathogens. Untargeted metabolomics approach using feature-based molecular networking showed the high chemical diversity of the liquid extracts that contained undescribed clusters. This study highlights plaice-associated microbiota as a potential source of antimicrobials for the control of human and the aquaculture-associated infections. This is the first study reporting diversity, bioactivity and chemical profile of culture-dependent microbiota of plaice.
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  • 87
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    Classification Ensembles for Beach Cast and Drifting Vegetation Mapping with Sentinel-2 and PlanetScope (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: Along the Baltic coastline of Germany, drifting vegetation and beach cast create overlays at the otherwise sandy or stony beaches. These overlays influence the morphodynamics and structures of the beaches. To better understand the influence of these patchy habitats on coastal environments, regular monitoring is necessary. Most studies, however, have been conducted on spatially larger and temporally more stable occurrences of aquatic vegetation such as floating fields of Sargassum. Nevertheless, drifting vegetation and beach cast pose a particular challenge, as they exhibit high temporal dynamics and sometimes small spatial extent. Regular surveys and mappings are the traditional methods to record their habitats, but they are time-consuming and cost-intensive. Spaceborne remote sensing can provide frequent recordings of the coastal zone at lower cost. Our study therefore aims at the monitoring of drifting vegetation and beach cast on spatial scales between 3 and 10 m. We developed an automated coastline masking algorithm and tested six supervised classification methods and various classification ensembles for their suitability to detect small-scale assemblages of drifting vegetation and beach cast in a study area at the coastline of the Western Baltic Sea using multispectral data of the sensors Sentinel-2 MSI and PlanetScope. The shoreline masking algorithm shows high accuracies in masking the land area while preserving the sand-covered shoreline. We could achieve best classification results using PlanetScope data with an ensemble of a random forest classifier, cart classifier, support vector machine classifier, naïve bayes classifier and stochastic gradient boosting classifier. This ensemble accomplished a combined f1-score of 0.95. The accuracy of the Sentinel-2 classifications was lower but still achieved a combined f1-score of 0.86 for the same ensemble. The results of this study can be considered as a starting point for the development of time series analysis of the vegetation dynamics along Baltic beaches
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  • 88
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    Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov. (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: The Ectothiorhodospiraceae family represents purple sulfur bacteria of the Gammaproteobacteria found primarily in alkaline soda lakes of moderate to extremely high salinity. The main microscopi-cally visible characteristic separating them from the Chromatiaceae is the excretion of the intermediate elemental sulfur formed during oxidation of sulfide prior to complete oxidation to sulfate rather than storing it in the periplasm. We present a comparative study of 38 genomes of all species of phototrophic Ectothiorhodospiraceae. We also include a comparison with those chemotrophic bacteria that have been assigned to the family previously and critically reevaluate this assignment. The data demonstrate the separation of Halorhodospira species in a major phylogenetic branch distant from other Ectothiorhodospiraceae and support their separation into a new family, for which the name Halorho-dospiraceae fam. nov. is proposed. In addition, the green-colored, bacteriochlorophyll-containing species Halorhodospira halochloris and Halorhodospira abdelmalekii were transferred to the new genus Halochlorospira gen. nov. of this family. The data also enable classification of several so far unclassified isolates and support the separation of Ectothiorhodospira shaposhnikovii and Ect. vacuolata as well as Ect. mobilis and Ect. marismortui as distinct species.
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  • 89
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    Experimental and Numerical Modelling of Deep-Sea-Mining-Generated Turbidity Currents (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: Renewable energy installations and energy storage solutions require significant quantities of critical raw materials such as nickel, cobalt and rare earth metals. The supply chains of these raw materials face many difficulties, such as the continuous decrease of mineral ore grades on land. In view of these complications, the motivation to search for new resources has grown, with the deep sea being seen as a potential source of these minerals. Polymetallic nodule mining generates turbidity currents, which could negatively impact the deep-sea environment. For that reason, we investigate this type of current experimentally and numerically in order to characterize the generated turbidity current. Various non-cohesive sediment types, i.e., different particle sizes, and different concentrations are tested using a lock-exchange set-up. Three sediment types (glass beads, silica sand and a 50/50 blend of glass beads and silica sand) with seven initial sediment concentrations are examined. Additionally, for the numerical work, a drift–flux modelling approach is used to simulate the performed lock-exchange experiments. The results show that the front velocities of the currents resulting from the three sediment types increases with increasing initial concentrations inside the lock regardless. Moreover, using the same initial concentration, the difference in front velocities between the generated currents of the three sediment types decreases as the initial concentration increases. When using an initial volumetric concentration of 2.5% and 3%, the difference in front velocities between the generated current of the three sediment types vanishes. Finally, by comparing the numerical and experimental results, the drift–flux model is proven to be a reliable numerical model for predicting the current.
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  • 90
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    Behavioural Responses and Mortality of Mozambique Tilapia Oreochromis mossambicus to Three Commonly Used Macadamia Plantation Pesticides (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: The use of pesticides in agricultural systems may have deleterious effects on surrounding environments. Aquatic systems are no exception and are increasingly polluted through the leaching of pesticides from agricultural activities. However, the pesticide pollution effects on key aquatic species have not been studied in many regions. In southern Africa, increasing pesticide use associated with macadamia tree Macadamia integrifolia farming presents a growing risk to surrounding aquatic ecosystems. This study assessed behavioural responses of an important and widely-distributed freshwater fish, Mozambique tilapia Oreochromis mossambicus, following exposure to three commonly used macadamia pesticides (i.e., Karate Zeon 10 CS, Mulan 20 SP, Pyrinex 250 CS) at different concentrations (0.7–200 µL, 0.3–1000 mg, and 0.7–8750 µL, respectively) over 24 h. Behavioural responses, i.e., swimming erratically, surfacing, vertical positioning, loss of equilibrium, being motionless and mortality were observed after pesticides exposure. Lethal dose 50 (LD50) values of Karate Zeon 10 CS, Mulan 20 SP and Pyrinex 250 CS were 2.1 µL (per water litre dilution—WLD), 5.2 mg (WLD) and 21.5 µL (WLD), respectively. These concentrations are therefore expressed as a maximal threshold usage in the environment around macadamia farms and a minimum distance of the plantations to water systems should be considered. Further studies should examine effects on other fish species and aquatic invertebrates to inform on pesticide pollution threats and mitigation plans for the region.
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  • 91
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    Calcium Carbonate Hexahydrate (Ikaite): History of Mineral Formation as Recorded by Stable Isotopes (2022)
    MDPI
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    Publication Date: 2024-02-07
    Description: Calcium carbonate hexahydrate (ikaite) is a rare mineral that forms as metastable species in the organic-carbon-rich sediments of the King George Basin, Bransfield Strait, Antarctica, as a consequence of early diagenetic decomposition of organic matter under cold water (−1.4 °C) and high pressure (200 bar) conditions. Large crystals grow in the sediment immediately below the diagenetic transition between microbial sulfate reduction and methanogenesis at ~320 cm below sea floor (bsf). This process is reflected in the dissolved sulfate, total carbon dioxide, and methane concentrations, as well as in the carbon, hydrogen, and oxygen isotope chemistries of the interstitial fluids and dissolved gases of the host sediment. The ikaite crystal faithfully records in its zonal structure the changing carbon isotope ratio of the total dissolved carbon dioxide pool as it gradually diminishes during methanogenesis (δ13Cikaite = −17.5 to −21.4‰). These changes in the crystal’s host environment follow general Rayleigh carbon isotope fractionation. The oxygen isotopes of the ikaite carbonate (δ18Oikaite = 1.46 to 4.45‰) also show a strong zonal distribution, unrelated to temperature of formation, but perhaps controlled by the degree of recrystallization of ikaite to calcite. The crystal water of the ikaite is depleted 11‰ in 2H/1H (VSMOW) relative to the coexisting interstitial water, which is in excellent agreement with the isotope fractionation of other hydrated minerals. In addition to the in situ temperature and pressure, nucleation of the ikaite crystals in the Bransfield Basin sediments may be induced by the high alkalinity, high phosphate concentrations, and dissolved organic compounds. Intense microbial metabolism generates such compounds; of these, aspartic acid and glutamic acid may play an important role, as they do in biological and extracellular carbonate mineral precipitation. All indications are that low temperatures (such as of polar environments), high calcium carbonate supersaturation caused by interstitial methanogenesis, and a sufficiently large supply of dissolved phosphate and amino acids favor metastable ikaite formation. These conditions, modified by recrystallization, may be preserved in calcite glendonites, thinolites, and other calcitic pseudomorphs derived from ikaite and found throughout the ancient sedimentary record.
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  • 92
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    The Hiccup of Villarrica volcano (Chile) during the 2015 eruption and its expression in LP activity and VLP ground motion (2022)
    Oxford University Press
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    Publication Date: 2024-02-23
    Description: Volcano seismology is an essential tool for monitoring volcanic processes in the advent and during eruptions. A variety of seismic signals can be recorded at volcanoes, of which some are thought to be related to the migration of fluids which is of primary importance for the anticipation of imminent eruptions. We investigate the volcanic crises at Villarrica volcano in 2015 and report on a newly discovered very-long-period (VLP) signal that accompanies phases of periodic long period (LP) signal burst. Despite their low amplitude emergent character, we can locate the source region of the 1 Hz LP signals to the close vicinity of the volcano using a network-based correlation method. The source of the VLP signal with a period of about 30–100 s appears to locate in the vicinity of two stations a few kilometres from the summit. Both stations record very similar VLP waveforms that are correlated with the envelope of the LP bursts. A shallow magma reservoir was inferred by Contreras from surface deformation as the source of inflation following the eruption in 2015. Cyclic volume changes of 6 m3 in this reservoir at 3 km depth can explain the observed amplitudes of the vertical VLP signal. We propose that the LP signal is generated by the migration of gas or gas-rich magma that is periodically released from the inflating reservoir through a non-linear valve structure which modulates the flux, and thereby causes bursts of flow-related LP signals and pressure changes observed as VLP deformation. Our model predicts that the correlated occurrence of LP bursts and VLP surface motion depends on the intensity of the fluid flux. A weaker flux of fluids may not exceed the opening pressure of valve structure, and higher rates might maintain pressure above the closing pressure. In both cases, the VLP signal vanishes. Our observation provides constrains for models of fluid transport inside volcanoes. At Villarrica the VLP signal, and its relation to the LP activity, reveal additional information about fluxes in the magmatic reservoir that might aide forecasting of volcanic activity.
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  • 93
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    Life History of the Arctic Squid Gonatus fabricii (Cephalopoda: Oegopsida) Reconstructed by Analysis of Individual Ontogenetic Stable Isotopic Trajectories (2022)
    MDPI
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    Publication Date: 2024-04-18
    Description: Cephalopods are important in Arctic marine ecosystems as predators and prey, but knowledge of their life cycles is poor. Consequently, they are under-represented in the Arctic ecosystems assessment models. One important parameter is the change in ecological role (habitat and diet) associated with individual ontogenies. Here, the life history of Gonatus fabricii, the most abundant Arctic cephalopod, is reconstructed by the analysis of individual ontogenetic trajectories of stable isotopes (δ13C and δ15N) in archival hard body structures. This approach allows the prediction of the exact mantle length (ML) and mass when the species changes its ecological role. Our results show that the life history of G. fabricii is divided into four stages, each having a distinct ecology: (1) epipelagic squid (ML 〈 20 mm), preying mostly on copepods; (2) epi- and occasionally mesopelagic squid (ML 20–50 mm), preying on larger crustaceans, fish, and cephalopods; (3) meso- and bathypelagic squid (ML 〉 50 mm), preying mainly on fish and cephalopods; and (4) non-feeding bathypelagic gelatinous females (ML 〉 200 mm). Existing Arctic ecosystem models do not reflect the different ecological roles of G. fabricii correctly, and the novel data provided here are a necessary baseline for Arctic ecosystem modelling and forecasting.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 94
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    Evaluating learning spaces in flood risk management in Germany: Lessons for governance research (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2021-06-28
    Description: Efforts to collaboratively manage the risk of flooding are ultimately based on individuals learning about risks, the decision process, and the effectiveness of decisions made in prior situations. This article argues that much can be learned about a governance setting by explicitly evaluating the relationships through which influential individuals and their immediate contacts receive and send information to one another. We define these individuals as “brokers,” and the networks that emerge from their interactions as “learning spaces.” The aim of this article is to develop strategies to identify and evaluate the properties of a broker's learning space that are indicative of a collaborative flood risk management arrangement. The first part of this article introduces a set of indicators, and presents strategies to employ this list so as to systematically identify brokers, and compare their learning spaces. The second part outlines the lessons from an evaluation that explored cases in two distinct flood risk management settings in Germany. The results show differences in the observed brokers' learning spaces. The contacts and interactions of the broker in Baden‐Württemberg imply a collaborative setting. In contrast, learning space of the broker in North Rhine‐Westphalia lacks the same level of diversity and polycentricity.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: MWK Baden‐Württemberg
    Keywords: 333.91 ; brokerage ; collaborative water governance ; comanagement ; comparative analysis ; social networks
    Type: article
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    Synthetic resampling strategies and machine learning for digital soil mapping in Iran (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2021-07-04
    Description: Most common machine learning (ML) algorithms usually work well on balanced training sets, that is, datasets in which all classes are approximately represented equally. Otherwise, the accuracy estimates may be unreliable and classes with only a few values are often misclassified or neglected. This is known as a class imbalance problem in machine learning and datasets that do not meet this criterion are referred to as imbalanced data. Most datasets of soil classes are, therefore, imbalanced data. One of our main objectives is to compare eight resampling strategies that have been developed to counteract the imbalanced data problem. We compared the performance of five of the most common ML algorithms with the resampling approaches. The highest increase in prediction accuracy was achieved with SMOTE (the synthetic minority oversampling technique). In comparison to the baseline prediction on the original dataset, we achieved an increase of about 10, 20 and 10% in the overall accuracy, kappa index and F‐score, respectively. Regarding the ML approaches, random forest (RF) showed the best performance with an overall accuracy, kappa index and F‐score of 66, 60 and 57%, respectively. Moreover, the combination of RF and SMOTE improved the accuracy of the individual soil classes, compared to RF trained on the original dataset and allowed better prediction of soil classes with a low number of samples in the corresponding soil profile database, in our case for Chernozems. Our results show that balancing existing soil legacy data using synthetic sampling strategies can significantly improve the prediction accuracy in digital soil mapping (DSM). Highlights Spatial distribution of soil classes in Iran can be predicted using machine learning (ML) algorithms. The synthetic minority oversampling technique overcomes the drawback of imbalanced and highly biased soil legacy data. When combining a random forest model with synthetic sampling strategies the prediction accuracy of the soil model improves significantly. The resulting new soil map of Iran has a much higher spatial resolution compared to existing maps and displays new soil classes that have not yet been mapped in Iran.
    Description: Alexander von Humboldt‐Stiftung http://dx.doi.org/10.13039/100005156
    Description: German Research Foundation http://dx.doi.org/10.13039/501100001659
    Description: Soil and Water Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
    Keywords: 631.4 ; covariates ; imbalanced data ; machine learning ; random forest ; soil legacy data
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    Impact of biochar on nutrient supply, crop yield and microbial respiration on sandy soils of northern Germany (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2021-06-16
    Description: The application of biochar to agricultural soils to increase nutrient availability, crop production and carbon sequestration has gained increasing interest but data from field experiments on temperate, marginal soils are still under‐represented. In the current study, biochar, produced from organic residues (digestates) from a biogas plant, was applied with and without digestates at low (3.4 t ha−1) and intermediate (17.1 t ha−1) rates to two acidic and sandy soils in northern Germany that are used for corn (Zea mays L.) production. Soil nutrient availability, crop yields, microbial biomass and carbon dioxide (CO2) emissions from heterotrophic respiration were measured over two consecutive years. The effects of biochar application depended on the intrinsic properties of the two tested soils and the biochar application rates. Although the soils at the fallow site, with initially low nutrient concentrations, showed a significant increase in pH, soil nutrients and crop yield after low biochar application rates, a similar response was found at the cornfield site only after application of substantially larger amounts of biochar. The effect of a single dose of biochar at the beginning of the experiment diminished over time but was still detectable after 2 years. Whereas plant available nutrient concentrations increased after biochar application, the availability of potentially phytotoxic trace elements (Zn, Pb, Cd, Cr) decreased significantly, and although slight increases in microbial biomass carbon and heterotrophic CO2 fluxes were observed after biochar application, they were mostly not significant. The results indicate that the application of relatively small amounts of biochar could have positive effects on plant available nutrients and crop yields of marginal arable soils and may decrease the need for mineral fertilizers while simultaneously increasing the sequestration of soil organic carbon. Highlights A low rate of biochar increased plant available nutrients and crop yield on marginal soils. Biochar application reduced the availability of potentially harmful trace elements. Heterotrophic respiration showed no clear response to biochar application. Biochar application may reduce fertilizer need and increase carbon sequestration on marginal soils.
    Description: German Academic Exchange Service http://dx.doi.org/10.13039/501100001655
    Description: Institute Strategic Programme grants, “Soils to Nutrition”
    Keywords: 631.4 ; black carbon ; carbon sequestration ; corn ; digestate ; heterotrophic respiration ; marginal soils ; microbial biomass
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    Self‐stated recovery from flooding: Empirical results from a survey in Central Vietnam (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2021-06-27
    Description: Social inequalities lead to flood resilience inequalities across social groups, a topic that requires improved documentation and understanding. The objective of this paper is to attend to these differences by investigating self‐stated flood recovery across genders in Vietnam as a conceptual replication of earlier results from Germany. This study employs a regression‐based analysis of 1,010 respondents divided between a rural coastal and an urban community in Thua Thien‐Hue province. The results highlight an important set of recovery process‐related variables. The set of relevant variables is similar across genders in terms of inclusion and influence, and includes age, social capital, internal and external support after a flood, perceived severity of previous flood impacts, and the perception of stress‐resilience. However, women were affected more heavily by flooding in terms of longer recovery times, which should be accounted for in risk management. Overall, the studied variables perform similarly in Vietnam and Germany. This study, therefore, conceptually replicates previous results suggesting that women display slightly slower recovery levels as well as that psychological variables influence recovery rates more than adverse flood impacts. This provides an indication of the results' potentially robust nature due to the different socio‐environmental contexts in Germany and Vietnam.
    Keywords: 333.7 ; flood recovery ; resilience ; societal equity ; vulnerability
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    The potential of ryegrass as cover crop to reduce soil N2O emissions and increase the population size of denitrifying bacteria (2021)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2021-07-05
    Description: Nitrogen (N) fertilization is the major contributor to nitrous oxide (N2O) emissions from agricultural soil, especially in post‐harvest seasons. This study was carried out to investigate whether ryegrass serving as cover crop affects soil N2O emissions and denitrifier community size. A microcosm experiment was conducted with soil planted with perennial ryegrass (Lolium perenne L.) and bare soil, each with four levels of N fertilizer (0, 5, 10 and 20 g N m−2; applied as calcium ammonium nitrate). The closed‐chamber approach was used to measure soil N2O fluxes. Real‐time PCR was used to estimate the biomass of bacteria and fungi and the abundance of genes involved in denitrification in soil. The results showed that the presence of ryegrass decreased the nitrate content in soil. Cumulative N2O emissions of soil with grass were lower than in bare soil at 5 and 10 g N m−2. Fertilization levels did not affect the abundance of soil bacteria and fungi. Soil with grass showed greater abundances of bacteria and fungi, as well as microorganisms carrying narG, napA, nirK, nirS and nosZ clade I genes. It is concluded that ryegrass serving as a cover crop holds the potential to mitigate soil N2O emissions in soils with moderate or high NO3− concentrations. This highlights the importance of cover crops for the reduction of N2O emissions from soil, particularly following N fertilization. Future research should explore the full potential of ryegrass to reduce soil N2O emissions under field conditions as well as in different soils. Highlights This study was to investigate whether ryegrass serving as cover crop affects soil N2O emissions and denitrifier community size; Plant reduced soil N substrates on one side, but their root exudates stimulated denitrification on the other side; N2O emissions were lower in soil with grass than bare soil at medium fertilizer levels, and growing grass stimulated the proliferation of almost all the denitrifying bacteria except nosZ clade II; Ryegrass serving as a cover crop holds the potential to mitigate soil N2O emissions.
    Description: China Scholarship Council http://dx.doi.org/10.13039/501100004543
    Description: The National Science Project for University of Anhui Province
    Keywords: 551.9 ; 631.4 ; denitrification ; perennial ryegrass (Lolium perenne L.) ; soil bacteria ; soil CO2 emissions ; soil N2O emissions
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    ogs5py: A Python‐API for the OpenGeoSys 5 Scientific Modeling Package (2021)
    Blackwell Publishing Ltd | Malden, US
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    Publication Date: 2021-07-04
    Description: High‐performance numerical codes are an indispensable tool for hydrogeologists when modeling subsurface flow and transport systems. But as they are written in compiled languages, like C/C++ or Fortran, established software packages are rarely user‐friendly, limiting a wider adoption of such tools. OpenGeoSys (OGS), an open‐source, finite‐element solver for thermo‐hydro‐mechanical–chemical processes in porous and fractured media, is no exception. Graphical user interfaces may increase usability, but do so at a dramatic reduction of flexibility and are difficult or impossible to integrate into a larger workflow. Python offers an optimal trade‐off between these goals by providing a highly flexible, yet comparatively user‐friendly environment for software applications. Hence, we introduce ogs5py, a Python‐API for the OpenGeoSys 5 scientific modeling package. It provides a fully Python‐based representation of an OGS project, a large array of convenience functions for users to interact with OGS and connects OGS to the scientific and computational environment of Python.
    Description: German Federal Environmental Foundation http://dx.doi.org/10.13039/100007636
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: 551.49 ; hydrogeology ; subsurface flow ; modeling ; software
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    High‐Resolution Integrated Transport Model for Studying Surface Water–Groundwater Interaction (2021)
    Blackwell Publishing Ltd | Malden, US
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    Publication Date: 2021-06-27
    Description: Transport processes that lead to exchange of mass between surface water and groundwater play a significant role for the ecological functioning of aquatic systems, for hydrological processes and for biogeochemical transformations. In this study, we present a novel integral modeling approach for flow and transport at the sediment–water interface. The model allows us to simultaneously simulate turbulent surface and subsurface flow and transport with the same conceptual approach. For this purpose, a conservative transport equation was implemented to an existing approach that uses an extended version of the Navier–Stokes equations. Based on previous flume studies which investigated the spreading of a dye tracer under neutral, losing and gaining flow conditions the new solver is validated. Tracer distributions of the experiments are in close agreement with the simulations. The simulated flow paths are significantly affected by in‐ and outflowing groundwater flow. The highest velocities within the sediment are found for losing condition, which leads to shorter residence times compared to neutral and gaining conditions. The largest extent of the hyporheic exchange flow is observed under neutral condition. The new solver can be used for further examinations of cases that are not suitable for the conventional coupled models, for example, if Reynolds numbers are larger than 10. Moreover, results gained with the integral solver provide high‐resolution information on pressure and velocity distributions at the rippled streambed, which can be used to improve flow predictions. This includes the extent of hyporheic exchange under varying ambient groundwater flow conditions.
    Description: Technische Universität Berlin, Germany
    Description: German Research Foundation http://dx.doi.org/10.13039/501100001659
    Keywords: 551.4 ; aquatic systems ; sediment-water interface ; transport model
    Type: article
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