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  • Blackwell Publishing Ltd  (182,057)
  • National Academy of Sciences
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  • 1
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    Dynamics of Aggregates and Sinking Carbon Fluxes in a Turbulent Ocean (2024)
    National Academy of Sciences
    Details
    Publication Date: 2024-04-26
    Description: The sinking of particulate matter from the upper ocean dominates the export and sequestration of organic carbon by the biological pump, a critical component of the Earth's carbon cycle. Controls on carbon export are thought to be driven by ecological processes that produce and repackage sinking biogenic particles. Here, we present observations during the demise of the Northeast Atlantic Ocean spring bloom illustrating the importance of storm-induced turbulence on the dynamics of sinking particles. A sequence of four large storms caused upper layer mean turbulence levels to vary by more than three orders of magnitude. Large particle (>0.1 to 10 mm) abundance and size changed accordingly: increasing via shear coagulation when turbulence was moderate and decreasing rapidly when turbulence was intense due to shear disaggregation. Particle export was also tied to storm forcing as large particles were mixed to depth during mixed layer deepening. After the mixed layer shoaled, these particles, now isolated from intense surface mixing, grew larger and subsequently sank. This sequence of events matched the timing of sinking particle flux observations. Particle export was influenced by increases in aggregate abundance and porosity, which appeared to be enhanced by the repeated creation and destruction of aggregates. Last, particle transit efficiency through the mesopelagic zone was reduced by presumably biotic processes that created small particles (〈0.5 mm) from larger ones. Our results demonstrate that ocean turbulence significantly impacts the nature and dynamics of sinking particles, strongly influencing particle export and the efficiency of the biological pump.
    Type: Article , NonPeerReviewed
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  • 2
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    A Late Pleistocene coastal ecosystem in French Guiana was hyperdiverse relative to today (2024)
    National Academy of Sciences
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    Publication Date: 2024-05-13
    Description: Warmer temperatures and higher sea level than today characterized the Last Interglacial interval [Pleistocene, 128 to 116 thousand years ago (ka)]. This period is a remarkable deep-time analog for temperature and sea-level conditions as projected for 2100 AD, yet there has been no evidence of fossil assemblages in the equatorial Atlantic. Here, we report foraminifer, metazoan (mollusks, bony fish, bryozoans, decapods, and sharks among others), and plant communities of coastal tropical marine and mangrove affinities, dating precisely from a ca. 130 to 115 ka time interval near the Equator, at Kourou, in French Guiana. These communities include ca. 230 recent species, some being endangered today and/or first recorded as fossils. The hyperdiverse Kourou mollusk assemblage suggests stronger affinities between Guianese and Caribbean coastal waters by the Last Interglacial than today, questioning the structuring role of the Amazon Plume on tropical Western Atlantic communities at the time. Grassland-dominated pollen, phytoliths, and charcoals from younger deposits in the same sections attest to a marine retreat and dryer conditions during the onset of the last glacial (ca. 110 to 50 ka), with a savanna-dominated landscape and episodes of fire. Charcoals from the last millennia suggest human presence in a mosaic of modern-like continental habitats. Our results provide key information about the ecology and biogeography of pristine Pleistocene tropical coastal ecosystems, especially relevant regarding the—widely anthropogenic—ongoing global warming.
    Type: Article , PeerReviewed
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  • 3
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    The strength of the Earth's magnetic field from Pre-Pottery to Pottery Neolithic, Jordan (2023)
    National Academy of Sciences
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    Publication Date: 2023-10-26
    Description: Constraining secular variation of the Earth's magnetic field strength in the past is fundamental to understanding short-term processes of the geodynamo. Such records also constitute a powerful and independent dating tool for archaeological sites and geological formations. In this study, we present 11 robust archaeointensity results from Pre-Pottery to Pottery Neolithic Jordan that are based on both clay and flint (chert) artifacts. Two of these results constitute the oldest archaeointensity data for the entire Levant, ancient Egypt, Turkey, and Mesopotamia, extending the archaeomagnetic reference curve for the Holocene. Virtual Axial Dipole Moments (VADMs) show that the Earth's magnetic field in the Southern Levant was weak (about two-thirds the present field) at around 7600 BCE, recovering its strength to greater than the present field around 7000 BCE, and gradually weakening again around 5200 BCE. In addition, successful results obtained from burnt flint demonstrate the potential of this very common, and yet rarely used, material in archaeomagnetic research, in particular for prehistoric periods from the first use of fire to the invention of pottery.
    Description: Published
    Description: e2100995118
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Keywords: Jordan ; Neolithic ; Pre-Pottery Neolithic ; archaeointensity
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean (2023)
    National Academy of Sciences
    Details
    Publication Date: 2023-03-08
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Saunders, J. K., McIlvin, M. R., Dupont, C. L., Kaul, D., Moran, D. M., Horner, T., Laperriere, S. M., Webb, E. A., Bosak, T., Santoro, A. E., & Saito, M. A. Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proceedings of the National Academy of Sciences of the United States of America, 119(37),(2022): e2200014119, https://doi.org/10.1073/pnas.2200014119.
    Description: Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.
    Description: Funding for this research was provided by the Gordon and Betty Moore Foundation (grants 3782 and 8453), the US NSF (NSF grants OCE-1924554, 2123055, 2125063, 2048774, and 2026933), the Center for Chemical Currencies on a Microbial Planet (NSF grant OCE-2019589), and the US NIH General Medicine (grant GM135709-01A1). J.K.S. was supported by a NASA Postdoctoral Program Fellowship with the NASA Astrobiology Program, administered by Universities Space Research Association under contract with NASA. A.E.S. was supported by the Sloan Foundation, the Simons Foundation, and NSF grant OCE-1437310. A portion of this research used resources at the US Department of Energy JGI sponsored by the Office of Biological and Environmental Research and operated under contract DE-AC02-05CH11231 (JGI). C.L.D. and D.K. were supported by NSF grants OCE-1558453 and OCE-2049299. T.H. was supported by NSF grant OCE-2023456.
    Keywords: Marine microbial ecology ; Metaproteomics ; Mesopelagic ; Nitrification ; Methylotrophy
    Repository Name: Woods Hole Open Access Server
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  • 5
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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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  • 6
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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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  • 7
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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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  • 8
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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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  • 9
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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
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    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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  • 10
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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
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    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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  • 11
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    BODIUM—A systemic approach to model the dynamics of soil functions (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    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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  • 12
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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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  • 13
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    A metabologenomics approach to unlock the metabolome of the novel Antarctic deep-sea isolate Lacinutrix shetlandiensis sp. nov. WUR7 (2023)
    National Academy of Sciences
    Details
    Publication Date: 2024-01-08
    Description: The South Shetland Trough, Antarctica, is an underexplored region for microbiological and biotechnological exploitation. Herein, we describe the isolation and characterization of the novel bacterium Lacinutrix shetlandiensis sp. nov. WUR7 from a deep-sea environment. We explored its chemical diversity via a metabologenomics approach, wherein the OSMAC strategy was strategically employed to upregulate cryptic genes for secondary metabolite production. Based on hybrid de novo whole genome sequencing and digital DNA–DNA hybridization, isolate WUR7 was identified as a novel species from the Gram-negative genus Lacinutrix. Its genome was mined for the presence of biosynthetic gene clusters with limited results. However, extensive investigation of its metabolism uncovered an unusual tryptophan decarboxylase with high sequence homology and conserved structure of the active site as compared to ZP_02040762, a highly specific tryptophan decarboxylase from Ruminococcus gnavus. Therefore, WUR7's metabolism was directed toward indole-based alkaloid biosynthesis by feeding it with L-tryptophan. As expected, its metabolome profile changed dramatically, by triggering the extracellular accumulation of a massive array of metabolites unexpressed in the absence of tryptophan. Untargeted LC-MS/MS coupled with molecular networking, followed along with chemoinformatic dereplication, allowed for the annotation of 10 indole alkaloids, belonging to β-carboline, bisindole, and monoindole classes, alongside several unknown alkaloids. These findings guided us to the isolation of a new natural bisindole alkaloid 8,9-dihydrocoscinamide B (1), as the first alkaloid from the genus Lacinutrix, whose structure was elucidated on the basis of extensive 1D and 2D NMR and HR-ESIMS experiments. This comprehensive strategy allowed us to unlock the previously unexploited metabolome of L. shetlandiensis sp. nov. WUR7.
    Type: Article , PeerReviewed
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  • 14
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    Long-term stability in the circumpolar foraging range of a Southern Ocean predator between the eras of whaling and rapid climate change (2023)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance Assessing change in Southern Ocean ecosystems is challenging due to its remoteness. Large-scale datasets that allow comparison between present-day conditions and those prior to large-scale ecosystem disturbances caused by humans (e.g., fishing/whaling) are rare. We infer the contemporary offshore foraging distribution of a marine predator, southern right whales (n = 1,002), using a customized stable isotope-based assignment approach based on biogeochemical models of the Southern Ocean. We then compare the contemporary distributions during the late austral summer and autumn to whaling catch data representing historical distributions during the same seasons. We show remarkable consistency of mid-latitude distribution across four centuries but shifts in foraging grounds in the past 30 y, particularly in the high latitudes that are likely driven by climate-associated alterations in prey availability. Abstract Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis), that forages on copepods and krill from ~30°S to the Antarctic ice edge (〉60°S). We analyzed carbon and nitrogen isotope values of 1,002 skin samples from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude (〉60°S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 15
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    Choanoflagellates alongside diverse uncultured predatory protists consume the abundant open-ocean cyanobacterium Prochlorococcus (2023)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Prochlorococcus is a key member of open-ocean primary producer communities. Despite its importance, little is known about the predators that consume this cyanobacterium and make its biomass available to higher trophic levels. We identify potential predators along a gradient wherein Prochlorococcus abundance increased from near detection limits (coastal California) to 〉200,000 cells mL-1 (subtropical North Pacific Gyre). A replicated RNA-Stable Isotope Probing experiment involving the in situ community, and labeled Prochlorococcus as prey, revealed choanoflagellates as the most active predators of Prochlorococcus, alongside a radiolarian, chrysophytes, dictyochophytes, and specific MAST lineages. These predators were not appropriately highlighted in multiyear conventional 18S rRNA gene amplicon surveys where dinoflagellates and other taxa had highest relative amplicon abundances across the gradient. In identifying direct consumers of Prochlorococcus, we reveal food-web linkages of individual protistan taxa and resolve routes of carbon transfer from the base of marine food webs.
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  • 16
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    Evidence of nitrate-based nighttime atmospheric nucleation driven by marine microorganisms in the South Pacific (2023)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-23
    Description: Significance Oceans represent 70% of our planet’s surface, housing a large spectrum of microorganisms that interact with the above atmosphere. Ocean microorganisms were proposed in the late 80’s to be at the center of a climate feedback loop involving dimethyl sulfide (DMS) that would form aerosols and modify cloud properties (CLAW hypothesis). In the present paper, we report observational evidence from semicontrolled experiments in the South Pacific that nitrate ions, yet hitherto not considered, is a key species involved in aerosol nucleation in the pristine marine atmosphere and which precursors are coemitted with DMS. Our results further indicate that nitrate ion formation would be related to short-term microbial processes, sensitive to environmental stressors, therefore potentially “closing the loop”. Abstract Our understanding of ocean–cloud interactions and their effect on climate lacks insight into a key pathway: do biogenic marine emissions form new particles in the open ocean atmosphere? Using measurements collected in ship-borne air–sea interface tanks deployed in the Southwestern Pacific Ocean, we identified new particle formation (NPF) during nighttime that was related to plankton community composition. We show that nitrate ions are the only species for which abundance could support NPF rates in our semicontrolled experiments. Nitrate ions also prevailed in the natural pristine marine atmosphere and were elevated under higher sub-10 nm particle concentrations. We hypothesize that these nucleation events were fueled by complex, short-term biogeochemical cycling involving the microbial loop. These findings suggest a new perspective with a previously unidentified role of nitrate of marine biogeochemical origin in aerosol nucleation.
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  • 17
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    Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Criswell, K. E., Roberts, L. E., Koo, E. T., Head, J. J., & Gillis, J. A. Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences of the United States of America, 118(51), (2021): e2114563118, https://doi.org/10.1073/pnas.2114563118.
    Description: The axial skeleton of tetrapods is organized into distinct anteroposterior regions of the vertebral column (cervical, trunk, sacral, and caudal), and transitions between these regions are determined by colinear anterior expression boundaries of Hox5/6, -9, -10, and -11 paralogy group genes within embryonic paraxial mesoderm. Fishes, conversely, exhibit little in the way of discrete axial regionalization, and this has led to scenarios of an origin of Hox-mediated axial skeletal complexity with the evolutionary transition to land in tetrapods. Here, combining geometric morphometric analysis of vertebral column morphology with cell lineage tracing of hox gene expression boundaries in developing embryos, we recover evidence of at least five distinct regions in the vertebral skeleton of a cartilaginous fish, the little skate (Leucoraja erinacea). We find that skate embryos exhibit tetrapod-like anteroposterior nesting of hox gene expression in their paraxial mesoderm, and we show that anterior expression boundaries of hox5/6, hox9, hox10, and hox11 paralogy group genes predict regional transitions in the differentiated skate axial skeleton. Our findings suggest that hox-based axial skeletal regionalization did not originate with tetrapods but rather has a much deeper evolutionary history than was previously appreciated.
    Description: This research was funded by a Natural Environment Research Council Grant (to J.J.H., J.A.G., and K.E.C.: NE/S000739/1) and a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377), and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) (to J.A.G.).
    Keywords: Hox genes ; Regionalization ; Chondrichthyan ; Vertebral column
    Repository Name: Woods Hole Open Access Server
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  • 18
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    Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dommain, R., Riedl, S., Olaka, L. A., deMenocal, P., Deino, A. L., Owen, R. B., Muiruri, V., Müller, J., Potts, R., & Strecker, M. R. Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients. Proceedings of the National Academy of Sciences of the United States of America, 119(28),(2022): e2121388119, https://doi.org/10.1073/pnas.2121388119.
    Description: East Africa is a global biodiversity hotspot and exhibits distinct longitudinal diversity gradients from west to east in freshwater fishes and forest mammals. The assembly of this exceptional biodiversity and the drivers behind diversity gradients remain poorly understood, with diversification often studied at local scales and less attention paid to biotic exchange between Afrotropical regions. Here, we reconstruct a river system that existed for several millennia along the now semiarid Kenya Rift Valley during the humid early Holocene and show how this river system influenced postglacial dispersal of fishes and mammals due to its dual role as a dispersal corridor and barrier. Using geomorphological, geochronological, isotopic, and fossil analyses and a synthesis of radiocarbon dates, we find that the overflow of Kenyan rift lakes between 12 and 8 ka before present formed a bidirectional river system consisting of a “Northern River” connected to the Nile Basin and a “Southern River,” a closed basin. The drainage divide between these rivers represented the only viable terrestrial dispersal corridor across the rift. The degree and duration of past hydrological connectivity between adjacent river basins determined spatial diversity gradients for East African fishes. Our reconstruction explains the isolated distribution of Nilotic fish species in modern Kenyan rift lakes, Guineo-Congolian mammal species in forests east of the Kenya Rift, and recent incipient vertebrate speciation and local endemism in this region. Climate-driven rearrangements of drainage networks unrelated to tectonic activity contributed significantly to the assembly of species diversity and modern faunas in the East African biodiversity hotspot.
    Description: R.D. was funded by a Smithsonian Human Origins Postdoctoral Fellowship and by Geo.X—the Research Network for Geosciences in Berlin and Potsdam. Fig. 1 D, E, and G and SI Appendix, Figs. S1 and S3 are based on the TanDEM-X Science DEM granted to L.A.O. and S.R. by the German Aerospace Center (DLR) in 2017. L.A.O. acknowledges the Volkswagen Foundation for funding this study with Grant No. 89369. M.R.S. and S.R. were supported by funds from Potsdam University and the Geothermal Development Company of Kenya, and R.B.O. and V.M. were supported by the Hong Kong General Research Fund. We acknowledge support from the National Museums of Kenya and the Kenya Government permission granted by the Ministry of Sports, Culture and the Arts, and by the National Commission for Science, Technology and Innovation (NACOSTI) Permits P/14/7709/683 (to R.P.) and P/16/11924/11448 (to L.A.O.). This work is a contribution of the Olorgesailie Drilling Project, for which support from the National Museums of Kenya, the Oldonyo Nyokie Group Ranch, the Peter Buck Fund for Human Origins Research (Smithsonian Institution), the William H. Donner Foundation, the Ruth and Vernon Taylor Foundation, Whitney and Betty MacMillan, and the Smithsonian Human Origins Program is gratefully acknowledged. LacCore is acknowledged for support in drilling and core storage.
    Keywords: East Africa ; Biogeography ; Biodiversity ; Hydrological connectivity ; Holocene
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  • 19
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    Nutrient availability and senescence spatially structure the dynamics of a foundation species (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bell, T. W., & Siegel, D. A. Nutrient availability and senescence spatially structure the dynamics of a foundation species. Proceedings of the National Academy of Sciences of the United States of America, 119(1), (2021): e2105135118, https://doi.org/10.1073/pnas.2105135118.
    Description: Disentangling the roles of the external environment and internal biotic drivers of plant population dynamics is challenging due to the absence of relevant physiological and abundance information over appropriate space and time scales. Remote observations of giant kelp biomass and photosynthetic pigment concentrations are used to show that spatiotemporal patterns of physiological condition, and thus growth and production, are regulated by different processes depending on the scale of observation. Nutrient supply was linked to regional scale (〉1 km) physiological condition dynamics, and kelp forest stands were more persistent where nutrient levels were consistently high. However, on local scales (〈1 km), internal senescence processes related to canopy age demographics determined patterns of biomass loss across individual kelp forests despite uniform nutrient conditions. Repeat measurements of physiology over continuous spatial fields can provide insights into complex dynamics that are unexplained by the environmental drivers thought to regulate abundance. Emerging remote sensing technologies that provide simultaneous estimates of abundance and physiology can quantify the roles of environmental change and demographics governing plant population dynamics for a wide range of aquatic and terrestrial ecosystems.
    Description: This work was supported by the US NSF (Grants OCE 1232779 and 1831937), by the US Department of Energy (Cooperative Agreement DE-AR0000922), and by NASA (Grant NNX14AR62A) and the NASA Earth and Space Sciences Fellowship program in support of T.W.B.
    Keywords: Physiology ; Population ; Biomass ; Hyperspectral ; Giant kelp
    Repository Name: Woods Hole Open Access Server
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  • 20
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    Trivalent chromium isotopes in the eastern tropical North Pacific oxygen-deficient zone (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2021. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 118(8), (2021): e1918605118, https://doi.org/10.1073/pnas.1918605118.
    Description: Changes in chromium (Cr) isotope ratios due to fractionation between trivalent [Cr(III)] and hexavalent [Cr(VI)] are being utilized by geologists to infer oxygen conditions in past environments. However, there is little information available on Cr in the modern ocean to ground-truth these inferences. Transformations between the two chromium species are important processes in oceanic Cr cycling. Here we present profiles of hexavalent and trivalent Cr concentrations and stable isotope ratios from the eastern tropical North Pacific (ETNP) oxygen-deficient zone (ODZ) which support theoretical and experimental studies that predict that lighter Cr is preferentially reduced in low-oxygen environments and that residual dissolved Cr becomes heavier due to removal of particle-reactive Cr(III) on sinking particles. The Cr(III) maximum dominantly occurs in the upper portion of the ODZ, implying that microbial activity (dependent on the sinking flux of organic matter) may be the dominant mechanism for this transformation, rather than a simple inorganic chemical conversion between the species depending on the redox potential.
    Description: We thank chief scientist Gabrielle Rocap for accommodating us on cruises Roger Revelle 1804-5 and Kilo Moana 19-20 (sponsored by NSF Grant DEB-1542240 to G. Rocap, A. Devol, R. Kiel, and C. Deutch), Jim Moffett for helping with sampling on these cruises, and Mark Altabet and Frank Stewart for collecting the samples from station 2T on cruise New Horizon 1410. This research was supported by NSF Grant OCE-1736996 (to E.A.B.) and by a fellowship from the Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program in Oceanography.
    Keywords: Chromium isotopes ; Oxygen-deficient zones ; Trace elements ; Trivalent chromium ; Hexavalent ; Chromium
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  • 21
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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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  • 22
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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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  • 23
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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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  • 24
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    Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-08-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Womersley, F. C., Humphries, N. E., Queiroz, N., Vedor, M., da Costa, I., Furtado, M., Tyminski, J. P., Abrantes, K., Araujo, G., Bach, S. S., Barnett, A., Berumen, M. L., Bessudo Lion, S., Braun, C. D., Clingham, E., Cochran, J. E. M., de la Parra, R., Diamant, S., Dove, A. D. M., Dudgeon, C. L., Erdmann, M. V., Espinoza, E., Fitzpatrick, R., González Cano, J., Green, J. R., Guzman, H. M., Hardenstine, R., Hasan, A., Hazin, F. H. V., Hearn, A. R., Hueter, R. E., Jaidah, M. Y., Labaja, J., Ladinol, F., Macena, B. C. L., Morris Jr., J. J., Norman, B. M., Peñaherrera-Palmav, C., Pierce, S. J., Quintero, L. M., Ramırez-Macías, D., Reynolds, S. D., Richardson, A. J., Robinson, D. P., Rohner, C. A., Rowat, D. R. L., Sheaves, M., Shivji, M. S., Sianipar, A. B., Skomal, G. B., Soler, G., Syakurachman, I., Thorrold, S. R., Webb, D. H., Wetherbee, B. M., White, T. D., Clavelle, T., Kroodsma, D. A., Thums, M., Ferreira, L. C., Meekan, M. G., Arrowsmith, L. M., Lester, E. K., Meyers, M. M., Peel, L. R., Sequeira, A. M. M., Eguıluz, V. M., Duarte, C. M., & Sims, D. W. Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark. Proceedings of the National Academy of Sciences of the United States of America, 119(20), (2022): e2117440119, https://doi.org/10.1073/pnas.2117440119.
    Description: Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (〉300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.
    Description: Funding for data analysis was provided by the UK Natural Environment Research Council (NERC) through a University of Southampton INSPIRE DTP PhD Studentship to F.C.W. Additional funding for data analysis was provided by NERC Discovery Science (NE/R00997/X/1) and the European Research Council (ERC-AdG-2019 883583 OCEAN DEOXYFISH) to D.W.S., Fundação para a Ciência e a Tecnologia (FCT) under PTDC/BIA/28855/2017 and COMPETE POCI-01–0145-FEDER-028855, and MARINFO–NORTE-01–0145-FEDER-000031 (funded by Norte Portugal Regional Operational Program [NORTE2020] under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund–ERDF) to N.Q. FCT also supported N.Q. (CEECIND/02857/2018) and M.V. (PTDC/BIA-COM/28855/2017). D.W.S. was supported by a Marine Biological Association Senior Research Fellowship. All tagging procedures were approved by institutional ethical review bodies and complied with all relevant ethical regulations in the jurisdictions in which they were performed. Details for individual research teams are given in SI Appendix, section 8. Full acknowledgments for tagging and field research are given in SI Appendix, section 7. This research is part of the Global Shark Movement Project (https://www.globalsharkmovement.org).
    Keywords: ship strike ; marine megafauna ; conservation ; movement ecology ; human impact
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  • 25
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    Phosphonate production by marine microbes: exploring new sources and potential function (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-06-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Acker, M., Hogle, S. L., Berube, P. M., Hackl, T., Coe, A., Stepanauskas, R., Chisholm, S. W., & Repeta, D. J. Phosphonate production by marine microbes: exploring new sources and potential function. Proceedings of the National Academy of Sciences of the United States of America, 119(11), (2022): e2113386119, https://doi.org/10.1073/pnas.2113386119.
    Description: Phosphonates are organophosphorus metabolites with a characteristic C-P bond. They are ubiquitous in the marine environment, their degradation broadly supports ecosystem productivity, and they are key components of the marine phosphorus (P) cycle. However, the microbial producers that sustain the large oceanic inventory of phosphonates as well as the physiological and ecological roles of phosphonates are enigmatic. Here, we show that phosphonate synthesis genes are rare but widely distributed among diverse bacteria and archaea, including Prochlorococcus and SAR11, the two major groups of bacteria in the ocean. In addition, we show that Prochlorococcus can allocate over 40% of its total cellular P-quota toward phosphonate production. However, we find no evidence that Prochlorococcus uses phosphonates for surplus P storage, and nearly all producer genomes lack the genes necessary to degrade and assimilate phosphonates. Instead, we postulate that phosphonates are associated with cell-surface glycoproteins, suggesting that phosphonates mediate ecological interactions between the cell and its surrounding environment. Our findings indicate that the oligotrophic surface ocean phosphonate pool is sustained by a relatively small fraction of the bacterioplankton cells allocating a significant portion of their P quotas toward secondary metabolism and away from growth and reproduction.
    Description: This work was supported in part by grants from the NSF (OCE-1153588 and DBI-0424599 to S.W.C.; OCE-1335810 and OIA-1826734 to R.S.; and OCE-1634080 to D.J.R.), the Gordon and Betty Moore Foundation (no. 6000 to D.J.R.), and the Simons Foundation (Life Sciences Project Award IDs 337262 and 647135 to S.W.C.; 510023 to R.S.; and Simons Collaboration on Ocean Processes and Ecology [SCOPE] Award ID 329108 to S.W.C. and D.J.R.).
    Keywords: phosphonate ; Prochlorococcus ; marine ; biogeochemistry ; phosphorus
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  • 26
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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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  • 27
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    The Earth BioGenome Project 2020: starting the clock (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, Mark L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S-M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. Thomas P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J-H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O’Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. The Earth BioGenome Project 2020: starting the clock. Proceedings of the National Academy of Sciences of the United States of America, 119(4), (2022): e2115635118, https://doi.org/10.1073/pnas.2115635118.
    Description: November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP’s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP.
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  • 28
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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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  • 29
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    High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bekaert, D. V., Gazel, E., Turner, S., Behn, M. D., de Moor, J. M., Zahirovic, S., Manea, V. C., Hoernle, K., Fischer, T. P., Hammerstrom, A., Seltzer, A. M., Kulongoski, J. T., Patel, B. S., Schrenk, M. O., Halldórsson, S. A., Nakagawa, M., Ramírez, C. J., Krantz, J. A., Yücel, M., Ballentine, C. J., Giovannelli, D., Lloyd, K. G., Barry, P. H. High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume. Proceedings of the National Academy of Sciences of the United States of America, 118(47), (2021): e2110997118, https://doi.org/10.1073/pnas.2110997118.
    Description: It is well established that mantle plumes are the main conduits for upwelling geochemically enriched material from Earth's deep interior. The fashion and extent to which lateral flow processes at shallow depths may disperse enriched mantle material far (〉1,000 km) from vertical plume conduits, however, remain poorly constrained. Here, we report He and C isotope data from 65 hydrothermal fluids from the southern Central America Margin (CAM) which reveal strikingly high 3He/4He (up to 8.9RA) in low-temperature (≤50 °C) geothermal springs of central Panama that are not associated with active volcanism. Following radiogenic correction, these data imply a mantle source 3He/4He 〉10.3RA (and potentially up to 26RA, similar to Galápagos hotspot lavas) markedly greater than the upper mantle range (8 ± 1RA). Lava geochemistry (Pb isotopes, Nb/U, and Ce/Pb) and geophysical constraints show that high 3He/4He values in central Panama are likely derived from the infiltration of a Galápagos plume–like mantle through a slab window that opened ∼8 Mya. Two potential transport mechanisms can explain the connection between the Galápagos plume and the slab window: 1) sublithospheric transport of Galápagos plume material channeled by lithosphere thinning along the Panama Fracture Zone or 2) active upwelling of Galápagos plume material blown by a “mantle wind” toward the CAM. We present a model of global mantle flow that supports the second mechanism, whereby most of the eastward transport of Galápagos plume material occurs in the shallow asthenosphere. These findings underscore the potential for lateral mantle flow to transport mantle geochemical heterogeneities thousands of kilometers away from plume conduits.
    Description: This work was principally supported by Grant G-2016-7206 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to P.H.B. We also acknowledge the NSF awards (1144559, 1923915, and 2015789) to P.H.B., which partially supported this work. S.Z. was supported by the Australian Research Council Grant DE210100084 and a University of Sydney Robinson Fellowship. D.G. was partially supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program Grant Agreement No. 948972—COEVOLVE—ERC-2020-STG. This study was also supported in part by NSF award No. EAR 1826673 to E.G. Folkmar Hauff is acknowledged for contributing to the analysis of the La Providencia samples at GEOMAR.
    Keywords: Helium ; Mantle plume ; Slab window ; Mantle flow ; Geochemistry
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  • 30
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    The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Orvis, J., Albertin, C., Shrestha, P., Chen, S., Zheng, M., Rodriguez, C., Tallon, L., Mahurkar, A., Zimin, A., Kim, M., Liu, K., Kandel, E., Fraser, C., Sossin, W., & Abrams, T. The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia. Proceedings of the National Academy of Sciences of the United States of America, 119(28), (2022): e2122301119, https://doi.org/10.1073/pnas.2122301119.
    Description: The gastropod mollusk Aplysia is an important model for cellular and molecular neurobiological studies, particularly for investigations of molecular mechanisms of learning and memory. We developed an optimized assembly pipeline to generate an improved Aplysia nervous system transcriptome. This improved transcriptome enabled us to explore the evolution of cognitive capacity at the molecular level. Were there evolutionary expansions of neuronal genes between this relatively simple gastropod Aplysia (20,000 neurons) and Octopus (500 million neurons), the invertebrate with the most elaborate neuronal circuitry and greatest behavioral complexity? Are the tremendous advances in cognitive power in vertebrates explained by expansion of the synaptic proteome that resulted from multiple rounds of whole genome duplication in this clade? Overall, the complement of genes linked to neuronal function is similar between Octopus and Aplysia. As expected, a number of synaptic scaffold proteins have more isoforms in humans than in Aplysia or Octopus. However, several scaffold families present in mollusks and other protostomes are absent in vertebrates, including the Fifes, Lev10s, SOLs, and a NETO family. Thus, whereas vertebrates have more scaffold isoforms from select families, invertebrates have additional scaffold protein families not found in vertebrates. This analysis provides insights into the evolution of the synaptic proteome. Both synaptic proteins and synaptic plasticity evolved gradually, yet the last deuterostome-protostome common ancestor already possessed an elaborate suite of genes associated with synaptic function, and critical for synaptic plasticity.
    Description: This work was supported by NSF EAGER Award IOS-1255695 and NIH grant R01 MH 55880 grant to T.W.A.; by a Natural Sciences and Engineering Research Council of Canada Discovery grant and Canadian Institutes of Health Research project grant 340328 to W.S.; by funding from the HHMI to E.R.K.; and by a Hibbitt Early Career Fellowship to C.A. W.S. is James McGill Professor at McGill University.
    Keywords: Neural plasticity ; Synaptic plasticity ; Evolution ; Neuromodulation ; Aplysia
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  • 31
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    Discovery of active off-axis hydrothermal vents at 9° 54’N East Pacific Rise (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McDermott, J. M., Parnell-Turner, R., Barreyre, T., Herrera, S., Downing, C. C., Pittoors, N. C., Pehr, K., Vohsen, S. A., Dowd, W. S., Wu, J.-N., Marjanović, M., & Fornari, D. J. Discovery of active off-axis hydrothermal vents at 9° 54’N East Pacific Rise. Proceedings of the National Academy of Sciences of the United States of America, 119(30), (2022): e2205602119, https://doi.org/10.1073/pnas.2205602119.
    Description: Comprehensive knowledge of the distribution of active hydrothermal vent fields along midocean ridges is essential to understanding global chemical and heat fluxes and endemic faunal distributions. However, current knowledge is biased by a historical preference for on-axis surveys. A scarcity of high-resolution bathymetric surveys in off-axis regions limits vent identification, which implies that the number of vents may be underestimated. Here, we present the discovery of an active, high-temperature, off-axis hydrothermal field on a fast-spreading ridge. The vent field is located 750 m east of the East Pacific Rise axis and ∼7 km north of on-axis vents at 9° 50′N, which are situated in a 50- to 100-m-wide trough. This site is currently the largest vent field known on the East Pacific Rise between 9 and 10° N. Its proximity to a normal fault suggests that hydrothermal fluid pathways are tectonically controlled. Geochemical evidence reveals deep fluid circulation to depths only 160 m above the axial magma lens. Relative to on-axis vents at 9° 50′N, these off-axis fluids attain higher temperatures and pressures. This tectonically controlled vent field may therefore exhibit greater stability in fluid composition, in contrast to more dynamic, dike-controlled, on-axis vents. The location of this site indicates that high-temperature convective circulation cells extend to greater distances off axis than previously realized. Thorough high-resolution mapping is necessary to understand the distribution, frequency, and physical controls on active off-axis vent fields so that their contribution to global heat and chemical fluxes and role in metacommunity dynamics can be determined.
    Description: Financial support was provided by the NSF Awards OCE-1949938 (to J.M.M.), OCE-1948936 (to R.P.-T.), and OCE-1949485 (to D.J.F. and T.B.).
    Keywords: Hydrothermal activity ; Midocean ridge ; Ocean chemistry ; Chemosynthetic ecosystem ; East Pacific Rise
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  • 32
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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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  • 33
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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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    Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows (2022)
    National Academy of Sciences
    Details
    Publication Date: 2023-03-08
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schorn, S., Ahmerkamp, S., Bullock, E., Weber, M., Lott, C., Liebeke, M., Lavik, G., Kuypers, M. M. M., Graf, J. S., & Milucka, J. Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows. Proceedings of the National Academy of Sciences of the United States of America, 119(9), (2022): e2106628119, https://doi.org/10.1073/pnas.2106628119.
    Description: Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of Posidonia oceanica in the Mediterranean Sea. The underlying sediments exhibited median net fluxes of methane into the water column of ca. 106 µmol CH4 ⋅ m−2 ⋅ d−1. Our data show that this methane production was sustained by methylated compounds produced by the plant, rather than by fermentation of buried organic carbon. Interestingly, methane production was maintained long after the living plant died off, likely due to the persistence of methylated compounds, such as choline, betaines, and dimethylsulfoniopropionate, in detached plant leaves and rhizomes. We recovered multiple mcrA gene sequences, encoding for methyl-coenzyme M reductase (Mcr), the key methanogenic enzyme, from the seagrass sediments. Most retrieved mcrA gene sequences were affiliated with a clade of divergent Mcr and belonged to the uncultured Candidatus Helarchaeota of the Asgard superphylum, suggesting a possible involvement of these divergent Mcr in methane metabolism. Taken together, our findings identify the mechanisms controlling methane emissions from these important blue carbon ecosystems.
    Description: This project was funded by theMax Planck Society.
    Repository Name: Woods Hole Open Access Server
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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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    Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria (2022)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance A substantial component of the global nitrogen cycle is the production of biologically inaccessible dinitrogen attributed to anaerobic denitrification by prokaryotes. Recent evidence identified a eukaryote, foraminifera, as new key players in this “loss” of bioavailable nitrogen. The evolution of denitrification in eukaryotes is a rare event, and the genetic mechanisms of the denitrification pathway in foraminifera are just starting to be elucidated. We present large-scale sequencing analyses of 10 denitrifying foraminiferal species, which reveals the high conservation of the foraminiferal denitrification pathway. We further find evidence for a complementation of denitrification by the foraminiferal microbiome. Together, these findings provide insights into the early evolution of a previously overlooked component in the marine nitrogen cycle. Abstract: Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.
    Type: Article , PeerReviewed
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    Rapid radiation in a highly diverse marine environment (2022)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance: Adaptive radiation, the evolutionary process whereby a lineage diversifies over a short period of time, often occurs in geographically isolated or newly formed habitats where colonizing species encounter unoccupied niches and reduced selective pressures. Rapid radiations may also occur in diverse and complex environments, but these cases are less well documented. Here, we show that the hamlets, a group of Caribbean reef fishes, radiated within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. Genomic analysis suggests that color pattern diversity is generated by different combinations of alleles at a few genes with large effect. Such a modular genomic architecture of diversification is emerging as a common denominator to a variety of radiations. Abstract: Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth’s diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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    Experimental evolution reveals the synergistic genomic mechanisms of adaptation to ocean warming and acidification in a marine copepod (2022)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance Resilience to global change will require adaptation to multiple concurrent environmental changes. However, it is unclear if adaptations to multiple stressors can be predicted from the sum of single-stressor adaptation. To answer this question, we experimentally evolved a marine copepod to warming, acidification, and their combination, finding that copepods were able to adapt to all conditions over 25 generations. Warming was a much stronger selective pressure than acidification alone and under multiple-stressor conditions. Nevertheless, the multiple-stressor response to selection was synergistic and unique from either single stressor. Thus, adaptation to single stressors may not reveal adaptive potential or mechanisms of adaptation under multiple stressors, demonstrating the complexity of predicting adaptive responses under multifaceted environmental change. Abstract Metazoan adaptation to global change relies on selection of standing genetic variation. Determining the extent to which this variation exists in natural populations, particularly for responses to simultaneous stressors, is essential to make accurate predictions for persistence in future conditions. Here, we identified the genetic variation enabling the copepod Acartia tonsa to adapt to experimental ocean warming, acidification, and combined ocean warming and acidification (OWA) over 25 generations of continual selection. Replicate populations showed a consistent polygenic response to each condition, targeting an array of adaptive mechanisms including cellular homeostasis, development, and stress response. We used a genome-wide covariance approach to partition the allelic changes into three categories: selection, drift and replicate-specific selection, and laboratory adaptation responses. The majority of allele frequency change in warming (57%) and OWA (63%) was driven by shared selection pressures across replicates, but this effect was weaker under acidification alone (20%). OWA and warming shared 37% of their response to selection but OWA and acidification shared just 1%, indicating that warming is the dominant driver of selection in OWA. Despite the dominance of warming, the interaction with acidification was still critical as the OWA selection response was highly synergistic with 47% of the allelic selection response unique from either individual treatment. These results disentangle how genomic targets of selection differ between single and multiple stressors and demonstrate the complexity that nonadditive multiple stressors will contribute to predictions of adaptation to complex environmental shifts caused by global change.
    Type: Article , PeerReviewed
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    Modes of Pangean lake level cyclicity driven by astronomical climate pacing modulated by continental position and p CO2 (2022)
    National Academy of Sciences
    Details
    Publication Date: 2024-05-22
    Description: Orbital cyclicity is a fundamental pacemaker of Earth’s climate system. The Newark–Hartford Basin (NHB) lake sediment record of eastern North America contains compelling geologic expressions of this cyclicity, reflecting variations of climatic conditions in tropical Pangea during the Late Triassic and earliest Jurassic (~233 to 199 Ma). Climate modeling enables a deeper mechanistic understanding of Earth system modulation during this unique greenhouse and supercontinent period. We link major features of the NHB record to the combined climatic effects of orbital forcing, paleogeographic changes, and atmospheric p CO 2 variations. An ensemble of transient, orbitally driven climate simulations is assessed for nine time slices, three atmospheric p CO 2 values, and two paleogeographic reconstructions. Climatic transitions from tropical humid to more seasonal and ultimately semiarid are associated with tectonic drift of the NHB from ~ 5 ° N to 20 ° N . The modeled orbital modulation of the precipitation–evaporation balance is most pronounced during the 220 to 200 Ma interval, whereas it is limited by weak seasonality and increasing aridity before and after this interval. Lower p CO 2 at around 205 Ma contributes to drier climates and could have led to the observed damping of sediment cyclicity. Eccentricity-modulated precession dominates the orbitally driven climate response in the NHB region. High obliquity further amplifies summer precipitation through the seasonal shifts in the tropical rainfall belt. Regions with other proxy records are also assessed, providing guidance toward an integrated picture of global astronomical climate forcing in the Late Triassic and ultimately of other periods in Earth history.
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    Evaluating learning spaces in flood risk management in Germany: Lessons for governance research (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    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
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    Synthetic resampling strategies and machine learning for digital soil mapping in Iran (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    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
    Details
    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
    Details
    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
    Details
    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
    Details
    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
    Details
    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
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    Iron isotope fractionation in soil and graminaceous crops after 100 years of liming in the long‐term agricultural experimental site at Berlin‐Dahlem, Germany (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2021-07-05
    Description: Sustainable arable cropping relies on repeated liming. Yet, the associated increase in soil pH can reduce the availability of iron (Fe) to plants. We hypothesized that repeated liming, but not pedogenic processes such as lessivage (i.e., translocation of clay particles), alters the Fe cycle in Luvisol soil, thereby affecting Fe isotope composition in soils and crops. Hence, we analysed Fe concentrations and isotope compositions in soil profiles and winter rye from the long‐term agricultural experimental site in Berlin‐Dahlem, Germany, where a controlled liming trial with three field replicates per treatment has been conducted on Albic Luvisols since 1923. Heterogeneity in subsoil was observed at this site for Fe concentration but not for Fe isotope composition. Lessivage had not affected Fe isotope composition in the soil profiles. The results also showed that almost 100 years of liming lowered the concentration of the HCl‐extractable Fe that was potentially available for plant uptake in the surface soil (0–15 cm) from 1.03 (standard error (SE) 0.03) to 0.94 (SE 0.01) g kg−1. This HCl‐extractable Fe pool contained isotopically lighter Fe (δ56Fe = −0.05 to −0.29‰) than the bulk soil (δ56Fe = −0.08 to 0.08‰). However, its Fe isotope composition was not altered by the long‐term lime application. Liming resulted in relatively lower Fe concentrations in the roots of winter rye. In addition, liming led to a heavier Fe isotope composition of the whole plants compared with those grown in the non‐limed plots (δ56FeWholePlant_ + Lime = −0.12‰, SE 0.03 vs. δ56FeWholePlant_‐Lime = −0.21‰, SE 0.01). This suggests that the elevated soil pH (increased by one unit due to liming) promoted the Fe uptake strategy through complexation of Fe(III) from the rhizosphere, which favoured heavier Fe isotopes. Overall, the present study showed that liming and a related increase in pH did not affect the Fe isotope compositions of the soil, but may influence the Fe isotope composition of plants grown in the soil if they alter their Fe uptake strategy upon the change of Fe availability. Highlights Fe concentrations and stocks, but not Fe isotope compositions, were more heterogeneous in subsoil than in topsoil. Translocation of clay minerals did not result in Fe isotope fractionation in the soil profile of a Luvisol. Liming decreased Fe availability in topsoil, but did not affect its δ56Fe values. Uptake of heavier Fe isotopes by graminaceous crops was more pronounced at elevated pH.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Keywords: 551.9 ; liming ; plant‐available Fe pool in soil ; winter rye ; δ56Fe
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    How to Find Aquifer Statistics Utilizing Pumping Tests? Two Field Studies Using welltestpy (2021)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publication Date: 2022-04-01
    Description: We present a workflow to estimate geostatistical aquifer parameters from pumping test data using the Python package welltestpy. The procedure of pumping test analysis is exemplified for two data sets from the Horkheimer Insel site and from the Lauswiesen site, Germany. The analysis is based on a semi‐analytical drawdown solution from the upscaling approach Radial Coarse Graining, which enables to infer log‐transmissivity variance and horizontal correlation length, beside mean transmissivity, and storativity, from pumping test data. We estimate these parameters of aquifer heterogeneity from type‐curve analysis and determine their sensitivity. This procedure, implemented in welltestpy, is a template for analyzing any pumping test. It goes beyond the possibilities of standard methods, for example, based on Theis' equation, which are limited to mean transmissivity and storativity. A sensitivity study showed the impact of observation well positions on the parameter estimation quality. The insights of this study help to optimize future test setups for geostatistical aquifer analysis and provides guidance for investigating pumping tests with regard to aquifer statistics using the open‐source software package welltestpy.
    Description: Article impact statement: We present a workflow to infer parameters of subsurface heterogeneity from pumping test data exemplified at two sites using welltestpy.
    Description: German Federal Environmental Foundation (DBU) http://dx.doi.org/10.13039/100007636
    Keywords: ddc:551.49
    Language: English
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    Importance of sources of variability, scales and experimental design: A case study about the effects of biochar and slurry application on soil properties in agricultural silty loam soils (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-04-01
    Description: In designed experiments, different sources of variability and an adequate scale of measurement need to be considered, but not all approaches in common usage are equally valid. In order to elucidate the importance of sources of variability and choice of scale, we conducted an experiment where the effects of biochar and slurry applications on soil properties related to soil fertility were studied for different designs: (a) for a field‐scale sampling design with either a model soil (without natural variability) as an internal control or with composited soils, (b) for a design with a focus on amendment variabilities, and (c) for three individual field‐scale designs with true field replication and a combined analysis representative of the population of loess‐derived soils. Three silty loam sites in Germany were sampled and the soil macroaggregates were crushed. For each design, six treatments (0, 0.15 and 0.30 g slurry‐N kg−1 with and without 30 g biochar kg−1) were applied before incubating the units under constant soil moisture conditions for 78 days. CO2 fluxes were monitored and soils were analysed for macroaggregate yields and associated organic carbon (C). Mixed‐effects models were used to describe the effects. For all soil properties, results for the loess sites differed with respect to significant contributions of fixed effects for at least one site, suggesting the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils to be made and showed that site:slurry:biochar and site:slurry interactions were not negligible for macroaggregate yields. The use of a model soil as an internal control enabled observation of variabilities other than those related to soils or amendments. Experiments incorporating natural variability in soils or amendments resulted in partially different outcomes, indicating the need to include all important sources of variability. Highlights Effects of biochar and slurry applications were studied for different designs and mixed‐effects models were used to describe the effects. Including an internal control allowed observation of, e.g., methodological and analytical variabilities. The results suggested the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils. The results indicated the need to include all important sources of variability.
    Keywords: ddc:631.4
    Language: English
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    Do tree species affect decadal changes in soil organic carbon and total nitrogen stocks in Danish common garden experiments? (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-04-01
    Description: Temperate forest soils are often considered as an important sink for atmospheric carbon (C), thereby buffering anthropogenic CO2 emissions. However, the effect of tree species composition on the magnitude of this sink is unclear. We resampled a tree species common garden experiment (six sites) a decade after initial sampling to evaluate whether forest floor (FF) and topsoil organic carbon (Corg) and total nitrogen (Nt) stocks changed in dependence of tree species (Norway spruce—Picea abies L., European beech—Fagus sylvatica L., pedunculate oak—Quercus robur L., sycamore maple—Acer pseudoplatanus L., European ash—Fraxinus excelsior L. and small‐leaved lime—Tilia cordata L.). Two groups of species were identified in terms of Corg and Nt distribution: (1) Spruce with high Corg and Nt stocks in the FF developed as a mor humus layer which tended to have smaller Corg and Nt stocks and a wider Corg:Nt ratio in the mineral topsoil, and (2) the broadleaved species, of which ash and maple distinguished most clearly from spruce by very low Corg and Nt stocks in the FF developed as mull humus layer, had greater Corg and Nt stocks, and narrow Corg:Nt ratios in the mineral topsoil. Over 11 years, FF Corg and Nt stocks increased most under spruce, while small decreases in bulk mineral soil (esp. in 0–15 cm and 0–30 cm depth) Corg and Nt stocks dominated irrespective of species. Observed decadal changes were associated with site‐related and tree species‐mediated soil properties in a way that hinted towards short‐term accumulation and mineralisation dynamics of easily available organic substances. We found no indication for Corg stabilisation. However, results indicated increasing Nt stabilisation with increasing biomass of burrowing earthworms, which were highest under ash, lime and maple and lowest under spruce. Highlights We studied if tree species differences in topsoil Corg and Nt stocks substantiate after a decade. The study is unique in its repeated soil sampling in a multisite common garden experiment. Forest floors increased under spruce, but topsoil stocks decreased irrespective of species. Changes were of short‐term nature. Nitrogen was most stable under arbuscular mycorrhizal species.
    Description: Deutsche Forschungsgemeinschaff (DFG)
    Keywords: ddc:551.9 ; ddc:631.41
    Language: English
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    The ‘Flood Resilience Rose’: A management tool to promote transformation towards flood resilience (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2021-09-29
    Description: Coping with the growing impacts of flooding in EU countries, a paradigm shift in flood management can be observed, moving from safety‐based towards risk‐based approaches and holistic perspectives. Flood resilience is a common denominator of most of the approaches. In this article, we present the ‘Flood Resilience Rose’ (FRR), a management tool to promote harmonised action towards flood resilience in European regions and beyond. The FRR is a result of a two‐step process. First, based on scientific concepts as well as analysis of relevant policy documents, we identified three ‘levels of operation’. The first level refers to the EU Floods Directive and an extended multi‐layer safety approach, comprising the four different layers of protection, prevention, preparedness and recovery, and related measures to be taken. This level is not independent but depends both on the institutional (second level) and the wider (third level) context. Second, we used surveys, semi‐structured interviews and group discussions during workshops with experts from Belgium, Denmark, Germany, the Netherlands and the United Kingdom to validate the definitions and the FRR's practical relevance. The presented FRR is thus the result of rigorous theoretical and practical consideration and provides a tool capable to strengthen flood risk management practice.
    Description: European Regional Development Fund http://dx.doi.org/10.13039/501100008530
    Keywords: 551.48 ; flood defence measures ; governance and institutions ; integrated flood risk management ; resilience
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    Neuromechanical wave resonance in jellyfish swimming (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-27
    Description: Author Posting. © National Academy of Sciences, 2021. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 118(11), (2021): e2020025118, https://doi.org/10.1073/pnas.2020025118.
    Description: For organisms to have robust locomotion, their neuromuscular organization must adapt to constantly changing environments. In jellyfish, swimming robustness emerges when marginal pacemakers fire action potentials throughout the bell’s motor nerve net, which signals the musculature to contract. The speed of the muscle activation wave is dictated by the passage times of the action potentials. However, passive elastic material properties also influence the emergent kinematics, with time scales independent of neuromuscular organization. In this multimodal study, we examine the interplay between these two time scales during turning. A three-dimensional computational fluid–structure interaction model of a jellyfish was developed to determine the resulting emergent kinematics, using bidirectional muscular activation waves to actuate the bell rim. Activation wave speeds near the material wave speed yielded successful turns, with a 76-fold difference in turning rate between the best and worst performers. Hyperextension of the margin occurred only at activation wave speeds near the material wave speed, suggesting resonance. This hyperextension resulted in a 34-fold asymmetry in the circulation of the vortex ring between the inside and outside of the turn. Experimental recording of the activation speed confirmed that jellyfish actuate within this range, and flow visualization using particle image velocimetry validated the corresponding fluid dynamics of the numerical model. This suggests that neuromechanical wave resonance plays an important role in the robustness of an organism’s locomotory system and presents an undiscovered constraint on the evolution of flexible organisms. Understanding these dynamics is essential for developing actuators in soft body robotics and bioengineered pumps.
    Description: This research was funded by the NSF Division of Mathematical Sciences, under Faculty Early Career Development Program Grant 1151478 (to L.A.M.).
    Description: 2021-09-16
    Keywords: Jellyfish ; Propulsion ; Neuromechanics ; Fluid-structure interaction ; Maneuverability
    Repository Name: Woods Hole Open Access Server
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    Teamwork in the viscous oceanic microscale (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kanso, E. A., Lopes, R. M., Strickler, J. R., Dabiri, J. O., & Costello, J. H. Teamwork in the viscous oceanic microscale. Proceedings of the National Academy of Sciences of the United States of America, 118(29), (2021): e2018193118, https://doi.org/10.1073/pnas.2018193118.
    Description: Nutrient acquisition is crucial for oceanic microbes, and competitive solutions to solve this challenge have evolved among a range of unicellular protists. However, solitary solutions are not the only approach found in natural populations. A diverse array of oceanic protists form temporary or even long-lasting attachments to other protists and marine aggregates. Do these planktonic consortia provide benefits to their members? Here, we use empirical and modeling approaches to evaluate whether the relationship between a large centric diatom, Coscinodiscus wailesii, and a ciliate epibiont, Pseudovorticella coscinodisci, provides nutrient flux benefits to the host diatom. We find that fluid flows generated by ciliary beating can increase nutrient flux to a diatom cell surface four to 10 times that of a still cell without ciliate epibionts. This cosmopolitan species of diatom does not form consortia in all environments but frequently joins such consortia in nutrient-depleted waters. Our results demonstrate that symbiotic consortia provide a cooperative alternative of comparable or greater magnitude to sinking for enhancement of nutrient acquisition in challenging environments.
    Description: We are grateful to Y. Garcia for help with organism sampling and sorting. E.A.K. is funded by NSF-2100209, NSF RAISE IOS-2034043 and NIH R01 HL 153622-01A1. R.M.L. is a CNPq research fellow (grant # 310642/2017-5). J.H.C. and J.O.D. are funded by Grant NSF-2100705.
    Keywords: Phytoplankton ; Nutrient limitation ; Symbiosis ; Diffusion limitation ; Cell size
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    Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Reysenbach, A. L., St John, E., Meneghin, J., Flores, G. E., Podar, M., Dombrowski, N., Spang, A., L'Haridon, S., Humphris, S. E., de Ronde, C. E. J., Caratori Tontini, F., Tivey, M., Stucker, V. K., Stewart, L. C., Diehl, A., & Bach, W. Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities. Proceedings of the National Academy of Sciences of the United States of America, 117(51), (2020): 202019021, doi:10.1073/pnas.2019021117.
    Description: Hydrothermally active submarine volcanoes are mineral-rich biological oases contributing significantly to chemical fluxes in the deep sea, yet little is known about the microbial communities inhabiting these systems. Here we investigate the diversity of microbial life in hydrothermal deposits and their metagenomics-inferred physiology in light of the geological history and resulting hydrothermal fluid paths in the subsurface of Brothers submarine volcano north of New Zealand on the southern Kermadec arc. From metagenome-assembled genomes we identified over 90 putative bacterial and archaeal genomic families and nearly 300 previously unknown genera, many potentially endemic to this submarine volcanic environment. While magmatically influenced hydrothermal systems on the volcanic resurgent cones of Brothers volcano harbor communities of thermoacidophiles and diverse members of the superphylum “DPANN,” two distinct communities are associated with the caldera wall, likely shaped by two different types of hydrothermal circulation. The communities whose phylogenetic diversity primarily aligns with that of the cone sites and magmatically influenced hydrothermal systems elsewhere are characterized predominately by anaerobic metabolisms. These populations are probably maintained by fluids with greater magmatic inputs that have interacted with different (deeper) previously altered mineral assemblages. However, proximal (a few meters distant) communities with gene-inferred aerobic, microaerophilic, and anaerobic metabolisms are likely supported by shallower seawater-dominated circulation. Furthermore, mixing of fluids from these two distinct hydrothermal circulation systems may have an underlying imprint on the high microbial phylogenomic diversity. Collectively our results highlight the importance of considering geologic evolution and history of subsurface processes in studying microbial colonization and community dynamics in volcanic environments.
    Description: We thank the captain and crew of the R/V Thompson and the engineers from Woods Hole Oceanographic Institution for the successful operation of ROV Jason. The project was funded by NSF grants OCE‐1558356 (Principal Investigator S.E.H.) and OCE-1558795 (Principal Investigator A.-L.R.). S.L. received a grant from the University of Brest to work in the A.-L.R. laboratory. A travel fund from Interridge enabled A.D. to participate on the R/V Thompson cruise. Funding for this work for C.E.J.d.R., F.C.T., V.K.S., and L.C.S. was provided by the New Zealand government. A.S. was supported by the Swedish Research Council (Vetenskapsrådet starting grant 2016-03559 to A.S.) and the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Dutch Research Council) Foundation of the Netherlands Organization for Scientific Research (Women In Science Excel [WISE] fellowship to A.S.). A.-L.R. and E.S.J. thank Rika Anderson for helpful methodological discussions and Sean Sylva for assistance in shipboard geochemical analysis.
    Keywords: Metagenomics ; Deep-sea hydrothermal ; Thermophiles ; Archaea ; Volcanics
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    Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coesel, S. N., Durham, B. P., Groussman, R. D., Hu, S. K., Caron, D. A., Morales, R. L., Ribalet, F., & Armbrust, E. V. Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proceedings of the National Academy of Sciences of the United States of America, 118(6), (2021): e2011038118, https://doi.org/10.1073./pnas.2011038118.
    Description: The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
    Description: This work was supported by a grant from the Simons Foundation (SCOPE Award 329108 [to E.V.A.]) and XSEDE Grant Allocation OCE160019 (to R.D.G.).
    Keywords: Photoreceptors ; Microbial eukaryotes ; Oligotrophic gyre ; Diel cycles ; Metatranscriptomics
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    Evidence for massive and recurrent toxic blooms of Alexandrium catenella in the Alaskan Arctic (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Anderson, D. M., Fachon, E., Pickart, R. S., Lin, P., Fischer, A. D., Richlen, M. L., Uva, V., Brosnahan, M. L., McRaven, L., Bahr, F., Lefebvre, K., Grebmeier, J. M., Danielson, S. L., Lyu, Y., & Fukai, Y. Evidence for massive and recurrent toxic blooms of Alexandrium catenella in the Alaskan Arctic. Proceedings of the National Academy of Sciences of the United States of America, 118(41) (2021): e2107387118, https://doi.org/10.1073/pnas.2107387118.
    Description: Among the organisms that spread into and flourish in Arctic waters with rising temperatures and sea ice loss are toxic algae, a group of harmful algal bloom species that produce potent biotoxins. Alexandrium catenella, a cyst-forming dinoflagellate that causes paralytic shellfish poisoning worldwide, has been a significant threat to human health in southeastern Alaska for centuries. It is known to be transported into Arctic regions in waters transiting northward through the Bering Strait, yet there is little recognition of this organism as a human health concern north of the Strait. Here, we describe an exceptionally large A. catenella benthic cyst bed and hydrographic conditions across the Chukchi Sea that support germination and development of recurrent, locally originating and self-seeding blooms. Two prominent cyst accumulation zones result from deposition promoted by weak circulation. Cyst concentrations are among the highest reported globally for this species, and the cyst bed is at least 6× larger in area than any other. These extraordinary accumulations are attributed to repeated inputs from advected southern blooms and to localized cyst formation and deposition. Over the past two decades, warming has likely increased the magnitude of the germination flux twofold and advanced the timing of cell inoculation into the euphotic zone by 20 d. Conditions are also now favorable for bloom development in surface waters. The region is poised to support annually recurrent A. catenella blooms that are massive in scale, posing a significant and worrisome threat to public and ecosystem health in Alaskan Arctic communities where economies are subsistence based.
    Description: Funding for D.M.A., R.S.P., E.F., P.L., A.D.F., V.U., M.L.B., L.M., F.B., and M.L.R. was provided by grants from the NSF Office of Polar Programs (Grants OPP-1823002 and OPP-1733564) and the National Ocanic and Atmospheric Administration (NOAA) Arctic Research program (through the Cooperative Institute for the North Atlantic Region [CINAR; Grants NA14OAR4320158 and NA19OAR4320074]), for J.M.G. through CINAR 22309.07 UMCES (University of Maryland Center for Environmental Science), and for D.M.A. and K.L. through NOAA’s Center for Coastal and Ocean Studies Ecology and Oceanography of Harmful Algal Blooms (ECOHAB) Program (NA20NOS4780195). Funding for D.M.A., M.L.R., M.L.B., E.F., V.U., and A.D.F. was also provided by NSF (Grant OCE-1840381) and NIH (Grant 1P01-ES028938-01) through the Woods Hole Center for Oceans and Human Health. S.L.D. was supported by North Pacific Research Board IERP Grants A91-99a and A91-00a. This is IERP publication ArcticIERP-41 and ECOHAB Contribution No. ECO983.
    Keywords: Harmful algal bloom ; HAB ; Alexandrium ; Alaskan Arctic ; Climate
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    Urban pluvial flood adaptation: Results of a household survey across four German municipalities (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-09-30
    Description: In recent years, German cities were heavily impacted by pluvial flooding and related damage is projected to increase due to climate change and urbanisation. It is important to ask how to improve urban pluvial flood risk management. To understand the current state of property level adaptation, a survey was conducted in four municipalities that had recently been impacted by pluvial flooding. A hybrid framework based on the Protection Motivation Theory (PMT) and the Protection Action Decision Model (PADM) was used to investigate drivers of adaptive behaviour through both descriptive and regression analyses. Descriptive statistics revealed that participants tended to instal more low‐ and medium‐cost measures than high‐cost measures. Regression analyses showed that coping appraisal increased protection motivation, but that the adaptive behaviour also depends on framing factors, particularly homeownership. We further found that, while threat appraisal solely affects protection motivation and responsibility appraisal affects solely maladaptive thinking, coping appraisal affects both. Our results indicate that PMT is a solid starting point to study adaptive behaviours in the context of pluvial flooding, but we need to go beyond that by, for instance, considering factors of the PADM, such as responsibility, ownership, or respondent age, to fully understand this complex decision‐making process.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:551.489 ; ddc:363.34
    Language: English
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    Unifying chemical and biological perspectives of carbon accumulation in the environment (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Repeta, D. J. Unifying chemical and biological perspectives of carbon accumulation in the environment. Proceedings of the National Academy of Sciences of the United States of America, 118(11), (2021); e2100935118, https://doi.org/10.1073/pnas.2100935118.
    Description: Heterotrophic microorganisms are fiendishly clever at degrading all shapes and sizes of organic compounds to extract the energy they need to build biomass. Every year marine phytoplankton fix ∼50 billion tons of carbon dioxide into organic matter, and every year marine heterotrophs respire nearly all of this organic matter back to carbon dioxide (1). Nearly all, but not all. With each spin of this carbon cycle, a small amount of organic matter escapes respiration and becomes sequestered in seawater, sediments, and soils. Over time, this small “leak” in the system leads to the accumulation of a vast reservoir of carbon; some 5 × 1019 kg of organic matter are thought to be sequestered in sedimentary rocks (2). This carbon sequestration has immense consequences for life on Earth, as illustrated by the change in climate we are now experiencing due in part to the transfer of a minute portion of this inventory from geologic reservoirs into the atmosphere.
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    Climate control on terrestrial biospheric carbon turnover (2021)
    National Academy of Sciences
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Eglinton, T. I., Galy, V. V., Hemingway, J. D., Feng, X., Bao, H., Blattmann, T. M., Dickens, A. F., Gies, H., Giosan, L., Haghipour, N., Hou, P., Lupker, M., McIntyre, C. P., Montluçon, D. B., Peucker-Ehrenbrink, B., Ponton, C., Schefuß, E., Schwab, M. S., Voss, B. M., Wacker, L., Wu, Y., & Zhao, M. Climate control on terrestrial biospheric carbon turnover. Proceedings of the National Academy of Sciences of the United States of America, 118(8), (2021): e2011585118, htps://doi.org/ 10.1073/pnas.2011585118.
    Description: Terrestrial vegetation and soils hold three times more carbon than the atmosphere. Much debate concerns how anthropogenic activity will perturb these surface reservoirs, potentially exacerbating ongoing changes to the climate system. Uncertainties specifically persist in extrapolating point-source observations to ecosystem-scale budgets and fluxes, which require consideration of vertical and lateral processes on multiple temporal and spatial scales. To explore controls on organic carbon (OC) turnover at the river basin scale, we present radiocarbon (14C) ages on two groups of molecular tracers of plant-derived carbon—leaf-wax lipids and lignin phenols—from a globally distributed suite of rivers. We find significant negative relationships between the 14C age of these biomarkers and mean annual temperature and precipitation. Moreover, riverine biospheric-carbon ages scale proportionally with basin-wide soil carbon turnover times and soil 14C ages, implicating OC cycling within soils as a primary control on exported biomarker ages and revealing a broad distribution of soil OC reactivities. The ubiquitous occurrence of a long-lived soil OC pool suggests soil OC is globally vulnerable to perturbations by future temperature and precipitation increase. Scaling of riverine biospheric-carbon ages with soil OC turnover shows the former can constrain the sensitivity of carbon dynamics to environmental controls on broad spatial scales. Extracting this information from fluvially dominated sedimentary sequences may inform past variations in soil OC turnover in response to anthropogenic and/or climate perturbations. In turn, monitoring riverine OC composition may help detect future climate-change–induced perturbations of soil OC turnover and stocks.
    Description: This work was supported by grants from the US NSF (OCE-0928582 to T.I.E. and V.V.G.; OCE-0851015 to B.P.-E., T.I.E., and V.V.G.; and EAR-1226818 to B.P.-E.), Swiss National Science Foundation (200021_140850, 200020_163162, and 200020_184865 to T.I.E.), and National Natural Science Foundation of China (41520104009 to M.Z.).
    Keywords: Radiocarbon ; Plant biomarkers ; Carbon turnover times ; Fluvial carbon ; Carbon cycle
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    Human arrival and landscape dynamics in the northern Bahamas (2021)
    National Academy of Sciences
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fall, P. L., van Hengstum, P. J., Lavold-Foote, L., Donnelly, J. P., Albury, N. A., & Tamalavage, A. E. Human arrival and landscape dynamics in the northern Bahamas. Proceedings of the National Academy of Sciences of the United States of America, 118(10), (2021): e2015764118, https://doi.org/10.1073/pnas.2015764118.
    Description: The first Caribbean settlers were Amerindians from South America. Great Abaco and Grand Bahama, the final islands colonized in the northernmost Bahamas, were inhabited by the Lucayans when Europeans arrived. The timing of Lucayan arrival in the northern Bahamas has been uncertain because direct archaeological evidence is limited. We document Lucayan arrival on Great Abaco Island through a detailed record of vegetation, fire, and landscape dynamics based on proxy data from Blackwood Sinkhole. From about 3,000 to 1,000 y ago, forests dominated by hardwoods and palms were resilient to the effects of hurricanes and cooling sea surface temperatures. The arrival of Lucayans by about 830 CE (2σ range: 720 to 920 CE) is demarcated by increased burning and followed by landscape disturbance and a time-transgressive shift from hardwoods and palms to the modern pine forest. Considering that Lucayan settlements in the southern Bahamian archipelago are dated to about 750 CE (2σ range: 600 to 900 CE), these results demonstrate that Lucayans spread rapidly through the archipelago in less than 100 y. Although precontact landscapes would have been influenced by storms and climatic trends, the most pronounced changes follow more directly from landscape burning and ecosystem shifts after Lucayan arrival. The pine forests of Abaco declined substantially between 1500 and 1670 CE, a period of increased regional hurricane activity, coupled with fires on an already human-impacted landscape. Any future intensification of hurricane activity in the tropical North Atlantic Ocean threatens the sustainability of modern pine forests in the northern Bahamas.
    Description: This research was supported by NSF Awards GSS-1118340 (P.L.F.), OCE-1356509 (P.J.v.H.), OCE-1703087 (P.J.v.H.), and OCE-1356708 (J.P.D.).
    Keywords: Anthropogenic burning ; Lucayan ; Caribbean ; Pollen ; Vegetation change
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    Thermodynamic feasibility of shipboard conversion of marine plastics to blue diesel for self-powered ocean cleanup (2021)
    National Academy of Sciences
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Belden, E. R., Kazantzis, N. K., Reddy, C. M., Kite-Powell, H., Timko, M. T., Italiani, E., & Herschbach, D. R. Thermodynamic feasibility of shipboard conversion of marine plastics to blue diesel for self-powered ocean cleanup. Proceedings of the National Academy of Sciences of the United States of America, 118(46),(2021): e2107250118, https://doi.org/10.1073/pnas.2107250118.
    Description: Collecting and removing ocean plastics can mitigate their environmental impacts; however, ocean cleanup will be a complex and energy-intensive operation that has not been fully evaluated. This work examines the thermodynamic feasibility and subsequent implications of hydrothermally converting this waste into a fuel to enable self-powered cleanup. A comprehensive probabilistic exergy analysis demonstrates that hydrothermal liquefaction has potential to generate sufficient energy to power both the process and the ship performing the cleanup. Self-powered cleanup reduces the number of roundtrips to port of a waste-laden ship, eliminating the need for fossil fuel use for most plastic concentrations. Several cleanup scenarios are modeled for the Great Pacific Garbage Patch (GPGP), corresponding to 230 t to 11,500 t of plastic removed yearly; the range corresponds to uncertainty in the surface concentration of plastics in the GPGP. Estimated cleanup times depends mainly on the number of booms that can be deployed in the GPGP without sacrificing collection efficiency. Self-powered cleanup may be a viable approach for removal of plastics from the ocean, and gaps in our understanding of GPGP characteristics should be addressed to reduce uncertainty.
    Description: The US NSF supported this work as part of its 2026 Idea Machine initiative (Chemical, Bioengineering, Environmental, and Transport Systems, EArly-concept Grants for Exploratory Research Award #2032621). E.R.B.’s contribution was funded, in part, by the NSF Graduate Research Fellowship Program under Grant No. 2038257.
    Keywords: Ocean plastic ; Hydrothermal liquefaction ; Exergy analysis ; Monte Carlo simulation
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    Electrochemical implications of modulating the solvation shell around redox active organic species in aqueous organic redox flow batteries (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Organic and organometallic reactants in aqueous electrolytes, being composed of earth-abundant elements, are promising redox active candidates for cost-effective organic redox flow batteries (ORFBs). Various compounds of ferrocene and methyl viologen have been examined as promising redox actives for this application. Herein, we examined the influence of the electrolyte pH and the salt anion on model redox active organic cations, bis((3-trimethylammonio) propyl)- ferrocene dichloride (BTMAP-Fc) and bis(3-trimethylammonio) propyl viologen tetrachloride (BTMAP-Vi), which have exhibited excellent cycling stability and capacity retention at ≥1.00 M concentration [E. S. Beh, et al. ACS Energy Lett. 2, 639–644 (2017)]. We examined the solvation shell around BTMAP-Fc and BTMAP-Vi at acidic and neutral pH with SO42-, Cl−, and CH3SO3− counterions and elucidated their impact on cation diffusion coefficient, first electron transfer rate constant, and thereby the electrochemical Thiele modulus. The electrochemical Thiele modulus was found to be exponentially correlated with the solvent reorganizational energy (λ) in both neutral and acidic pH. Thus, λ is proposed as a universal descriptor and selection criteria for organic redox flow battery electrolyte compositions. In the specific case of the BTMAP-Fc/BTMAP-Vi ORFB, low pH electrolytes with methanesulfonate or chloride counterions were identified as offering the best balance of transport and kinetic requirements.
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    An in vivo selection-derived d-peptide for engineering erythrocyte-binding antigens that promote immune tolerance (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: When displayed on erythrocytes, peptides and proteins can drive antigen-specific immune tolerance. Here, we investigated a straightforward approach based on erythrocyte binding to promote antigen-specific tolerance to both peptides and proteins. We first identified a robust erythrocyte-binding ligand. A pool of one million fully d-chiral peptides was injected into mice, blood cells were isolated, and ligands enriched on these cells were identified using nano-liquid chromatography–tandem mass spectrometry. One round of selection yielded a murine erythrocyte-binding ligand with an 80 nM apparent dissociation constant, Kd. We modified an 83-kDa bacterial protein and a peptide antigen derived from ovalbumin (OVA) with the identified erythrocyte-binding ligand. An administration of the engineered bacterial protein led to decreased protein-specific antibodies in mice. Similarly, mice given the engineered OVA-derived peptide had decreased inflammatory anti-OVA CD8+ T cell responses. These findings suggest that our tolerance-induction strategy is applicable to both peptide and protein antigens and that our in vivo selection strategy can be used for de novo discovery of robust erythrocyte-binding ligands.
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    The trisulfur radical ion S3•− controls platinum transport by hydrothermal fluids (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Platinum group elements (PGE) are considered to be very poorly soluble in aqueous fluids in most natural hydrothermal–magmatic contexts and industrial processes. Here, we combined in situ X-ray absorption spectroscopy and solubility experiments with atomistic and thermodynamic simulations to demonstrate that the trisulfur radical ion S3•− forms very stable and soluble complexes with both PtII and PtIV in sulfur-bearing aqueous solution at elevated temperatures (∼300 °C). These Pt-bearing species enable (re)mobilization, transfer, and focused precipitation of platinum up to 10,000 times more efficiently than any other common inorganic ligand, such as hydroxide, chloride, sulfate, or sulfide. Our results imply a far more important contribution of sulfur-bearing hydrothermal fluids to PGE transfer and accumulation in the Earth’s crust than believed previously. This discovery challenges traditional models of PGE economic concentration from silicate and sulfide melts and provides new possibilities for resource prospecting in hydrothermal shallow crust settings. The exceptionally high capacity of the S3•− ion to bind platinum may also offer new routes for PGE selective extraction from ore and hydrothermal synthesis of noble metal nanomaterials.
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    Structural insights into a novel family of integral membrane siderophore reductases (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Gram-negative bacteria take up the essential ion Fe3+ as ferric-siderophore complexes through their outer membrane using TonB-dependent transporters. However, the subsequent route through the inner membrane differs across many bacterial species and siderophore chemistries and is not understood in detail. Here, we report the crystal structure of the inner membrane protein FoxB (from Pseudomonas aeruginosa) that is involved in Fe-siderophore uptake. The structure revealed a fold with two tightly bound heme molecules. In combination with in vitro reduction assays and in vivo iron uptake studies, these results establish FoxB as an inner membrane reductase involved in the release of iron from ferrioxamine during Fe-siderophore uptake.
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    Counting equilibria of large complex systems by instability index (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: We consider a nonlinear autonomous system of N≫1 degrees of freedom randomly coupled by both relaxational (“gradient”) and nonrelaxational (“solenoidal”) random interactions. We show that with increased interaction strength, such systems generically undergo an abrupt transition from a trivial phase portrait with a single stable equilibrium into a topologically nontrivial regime of “absolute instability” where equilibria are on average exponentially abundant, but typically, all of them are unstable, unless the dynamics is purely gradient. When interactions increase even further, the stable equilibria eventually become on average exponentially abundant unless the interaction is purely solenoidal. We further calculate the mean proportion of equilibria that have a fixed fraction of unstable directions.
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    On randomly changing conformity bias in cultural transmission (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Humans and nonhuman animals display conformist as well as anticonformist biases in cultural transmission. Whereas many previous mathematical models have incorporated constant conformity coefficients, empirical research suggests that the extent of (anti)conformity in populations can change over time. We incorporate stochastic time-varying conformity coefficients into a widely used conformity model, which assumes a fixed number n of “role models” sampled by each individual. We also allow the number of role models to vary over time (nt). Under anticonformity, nonconvergence can occur in deterministic and stochastic models with different parameter values. Even if strong anticonformity may occur, if conformity or random copying (i.e., neither conformity nor anticonformity) is expected, there is convergence to one of the three equilibria seen in previous deterministic models of conformity. Moreover, this result is robust to stochastic variation in nt. However, dynamic properties of these equilibria may be different from those in deterministic models. For example, with random conformity coefficients, all equilibria can be stochastically locally stable simultaneously. Finally, we study the effect of randomly changing weak selection. Allowing the level of conformity, the number of role models, and selection to vary stochastically may produce a more realistic representation of the wide range of group-level properties that can emerge under (anti)conformist biases. This promises to make interpretation of the effect of conformity on differences between populations, for example those connected by migration, rather difficult. Future research incorporating finite population sizes and migration would contribute added realism to these models.
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    Structure of Usutu virus SAAR-1776 displays fusion loop asymmetry (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Usutu virus (USUV) is an emerging arbovirus in Europe that has been increasingly identified in asymptomatic humans and donated blood samples and is a cause of increased incidents of neuroinvasive human disease. Treatment or prevention options for USUV disease are currently nonexistent, the result of a lack of understanding of the fundamental elements of USUV pathogenesis. Here, we report two structures of the mature USUV virus, determined at a resolution of 2.4 Å, using single-particle cryogenic electron microscopy. Mature USUV is an icosahedral shell of 180 copies of envelope (E) and membrane (M) proteins arranged in the classic herringbone pattern. However, unlike previous reports of flavivirus structures, we observe virus subpopulations and differences in the fusion loop disulfide bond. Presence of a second, unique E glycosylation site could elucidate host interactions, contributing to the broad USUV tissue tropism. The structures provide a basis for exploring USUV interactions with glycosaminoglycans and lectins, the role of the RGD motif as a receptor, and the inability of West Nile virus therapeutic antibody E16 to neutralize the mature USUV strain SAAR-1776. Finally, we identify three lipid binding sites and predict key residues that likely participate in virus stability and flexibility during membrane fusion. Our findings provide a framework for the development of USUV therapeutics and expand the current knowledge base of flavivirus biology.
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    A dynamic electrically driven soft valve for control of soft hydraulic actuators (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Regulation systems for fluid-driven soft robots predominantly consist of inflexible and bulky components. These rigid structures considerably limit the adaptability and mobility of these robots. Soft valves in various forms for fluidic actuators have been developed, primarily fluidically or electrically driven. However, fluidic soft valves require external pressure sources that limit robot locomotion. State-of-the-art electrostatic valves are unable to modulate pressure beyond 3.5 kPa with a sufficient flow rate (〉6 mL⋅min−1). In this work, we present an electrically powered soft valve for hydraulic actuators with mesoscale channels based on a different class of ultrahigh-power density dynamic dielectric elastomer actuators. The dynamic dielectric elastomer actuators (DEAs) are actuated at 500 Hz or above. These DEAs generate 300% higher blocked force compared with the dynamic DEAs in previous works and their loaded power density reaches 290 W⋅kg−1 at operating conditions. The soft valves are developed with compact (7 mm tall) and lightweight (0.35 g) dynamic DEAs, and they allow effective control of up to 51 kPa of pressure and a 40 mL⋅min−1 flow rate with a response time less than 0.1 s. The valves can also tune flow rates based on their driving voltages. Using the DEA soft valves, we demonstrate control of hydraulic actuators of different volumes and achieve independent control of multiple actuators powered by a single pressure source. This compact and lightweight DEA valve is capable of unprecedented electrical control of hydraulic actuators, showing the potential for future onboard motion control of soft fluid-driven robots.
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    Metapopulation capacity determines food chain length in fragmented landscapes (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Metapopulation capacity provides an analytic tool to quantify the impact of landscape configuration on metapopulation persistence, which has proven powerful in biological conservation. Yet surprisingly few efforts have been made to apply this approach to multispecies systems. Here, we extend metapopulation capacity theory to predict the persistence of trophically interacting species. Our results demonstrate that metapopulation capacity could be used to predict the persistence of trophic systems such as prey–predator pairs and food chains in fragmented landscapes. In particular, we derive explicit predictions for food chain length as a function of metapopulation capacity, top-down control, and population dynamical parameters. Under certain assumptions, we show that the fraction of empty patches for the basal species provides a useful indicator to predict the length of food chains that a fragmented landscape can support and confirm this prediction for a host–parasitoid interaction. We further show that the impact of habitat changes on biodiversity can be predicted from changes in metapopulation capacity or approximately by changes in the fraction of empty patches. Our study provides an important step toward a spatially explicit theory of trophic metacommunities and a useful tool for predicting their responses to habitat changes.
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    Topological braiding and virtual particles on the cell membrane (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Braiding of topological structures in complex matter fields provides a robust framework for encoding and processing information, and it has been extensively studied in the context of topological quantum computation. In living systems, topological defects are crucial for the localization and organization of biochemical signaling waves, but their braiding dynamics remain unexplored. Here, we show that the spiral wave cores, which organize the Rho-GTP protein signaling dynamics and force generation on the membrane of starfish egg cells, undergo spontaneous braiding dynamics. Experimentally measured world line braiding exponents and topological entropy correlate with cellular activity and agree with predictions from a generic field theory. Our analysis further reveals the creation and annihilation of virtual quasi-particle excitations during defect scattering events, suggesting phenomenological parallels between quantum and living matter.
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    Synergistic dispersal of plant pathogen spores by jumping-droplet condensation and wind (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Plant pathogens are responsible for the annual yield loss of crops worldwide and pose a significant threat to global food security. A necessary prelude to many plant disease epidemics is the short-range dispersal of spores, which may generate several disease foci within a field. New information is needed on the mechanisms of plant pathogen spread within and among susceptible plants. Here, we show that self-propelled jumping dew droplets, working synergistically with low wind flow, can propel spores of a fungal plant pathogen (wheat leaf rust) beyond the quiescent boundary layer and disperse them onto neighboring leaves downwind. An array of horizontal water-sensitive papers was used to mimic healthy wheat leaves and showed that up to 25 spores/h may be deposited on a single leaf downwind of the infected leaf during a single dew cycle. These findings reveal that a single dew cycle can disperse copious numbers of fungal spores to other wheat plants, even in the absence of rain splash or strong gusts of wind.
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    Replication across space and time must be weak in the social and environmental sciences (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Replicability takes on special meaning when researching phenomena that are embedded in space and time, including phenomena distributed on the surface and near surface of the Earth. Two principles, spatial dependence and spatial heterogeneity, are generally characteristic of such phenomena. Various practices have evolved in dealing with spatial heterogeneity, including the use of place-based models. We review the rapidly emerging applications of artificial intelligence to phenomena distributed in space and time and speculate on how the principle of spatial heterogeneity might be addressed. We introduce a concept of weak replicability and discuss possible approaches to its measurement.
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    Stephen T. Warren: Human geneticist who advanced understanding of mutational mechanisms and developmental disorders (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
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    Mitochondrial fatty acid utilization increases chromatin oxidative stress in cardiomyocytes (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: The inability of adult mammalian cardiomyocytes to proliferate underpins the development of heart failure following myocardial injury. Although the newborn mammalian heart can spontaneously regenerate for a short period of time after birth, this ability is lost within the first week after birth in mice, partly due to increased mitochondrial reactive oxygen species (ROS) production which results in oxidative DNA damage and activation of DNA damage response. This increase in ROS levels coincides with a postnatal switch from anaerobic glycolysis to fatty acid (FA) oxidation by cardiac mitochondria. However, to date, a direct link between mitochondrial substrate utilization and oxidative DNA damage is lacking. Here, we generated ROS-sensitive fluorescent sensors targeted to different subnuclear compartments (chromatin, heterochromatin, telomeres, and nuclear lamin) in neonatal rat ventricular cardiomyocytes, which allowed us to determine the spatial localization of ROS in cardiomyocyte nuclei upon manipulation of mitochondrial respiration. Our results demonstrate that FA utilization by the mitochondria induces a significant increase in ROS detection at the chromatin level compared to other nuclear compartments. These results indicate that mitochondrial metabolic perturbations directly alter the nuclear redox status and that the chromatin appears to be particularly sensitive to the prooxidant effect of FA utilization by the mitochondria.
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    Two-dimensional electronic–vibrational sum frequency spectroscopy for interactions of electronic and nuclear motions at interfaces (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Interactions of electronic and vibrational degrees of freedom are essential for understanding excited-states relaxation pathways of molecular systems at interfaces and surfaces. Here, we present the development of interface-specific two-dimensional electronic–vibrational sum frequency generation (2D-EVSFG) spectroscopy for electronic–vibrational couplings for excited states at interfaces and surfaces. We demonstrate this 2D-EVSFG technique by investigating photoexcited interface-active (E)-4-((4-(dihexylamino) phenyl)diazinyl)-1-methylpyridin-1- lum (AP3) molecules at the air–water interface as an example. Our 2D-EVSFG experiments show strong vibronic couplings of interfacial AP3 molecules upon photoexcitation and subsequent relaxation of a locally excited (LE) state. Time-dependent 2D-EVSFG experiments indicate that the relaxation of the LE state, S2, is strongly coupled with two high-frequency modes of 1,529.1 and 1,568.1 cm−1. Quantum chemistry calculations further verify that the strong vibronic couplings of the two vibrations promote the transition from the S2 state to the lower excited state S1. We believe that this development of 2D-EVSFG opens up an avenue of understanding excited-state dynamics related to interfaces and surfaces.
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    Inactivation of Hedgehog signal transduction in adult astrocytes results in region-specific blood–brain barrier defects (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: In this study, we use molecular genetic approaches to clarify the role of the Hedgehog (Hh) pathway in regulating the blood–brain/spinal cord barrier (BBB) in the adult mouse central nervous system (CNS). Our work confirms and extends prior studies to demonstrate that astrocytes are the predominant cell type in the adult CNS that transduce Hh signaling, revealed by the expression of Gli1, a target gene of the canonical pathway that is activated in cells receiving Hh, and other key pathway transduction components. Gli1+ (Hh-responsive) astrocytes are distributed in specific regions of the CNS parenchyma, including layers 4/5/6 of the neocortex, hypothalamus, thalamus, and spinal cord, among others. Notably, although BBB properties in endothelial cells are normally regulated by both paracellular and transcellular mechanisms, conditional inactivation of Hh signaling in astrocytes results in transient, region-specific BBB defects that affect transcytosis but not paracellular diffusion. These findings stand in contrast to prior studies that implicated astrocytes as a source of Sonic hedgehog that limited extravasation via both mechanisms [J. I. Alvarez et al., Science 334, 1727–1731 (2011)]. Furthermore, using three distinct Cre driver lines as well as pharmacological approaches to inactivate Hh-pathway transduction globally in CNS astrocytes, we find that these specific BBB defects are only detected in the rostral hypothalamus and spinal cord but not the cortex or other regions where Gli1+ astrocytes are found. Together, our data show that Gli1+ Hh-responsive astrocytes have regionally distinct molecular and functional properties and that the pathway is required to maintain BBB properties in specific regions of the adult mammalian CNS.
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    Droplet tilings for rapid exploration of spatially constrained many-body systems (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Geometry in materials is a key concept which can determine material behavior in ordering, frustration, and fragmentation. More specifically, the behavior of interacting degrees of freedom subject to arbitrary geometric constraints has the potential to be used for engineering materials with exotic phase behavior. While advances in lithography have allowed for an experimental exploration of geometry on ordering that has no precedent in nature, many of these methods are low throughput or the underlying dynamics remain difficult to observe directly. Here, we introduce an experimental system that enables the study of interacting many-body dynamics by exploiting the physics of multidroplet evaporation subject to two-dimensional spatial constraints. We find that a high-energy initial state of this system settles into frustrated, metastable states with relaxation on two timescales. We understand this process using a minimal dynamical model that simulates the overdamped dynamics of motile droplets by identifying the force exerted on a given droplet as being proportional to the two-dimensional vapor gradients established by its neighbors. Finally, we demonstrate the flexibility of this platform by presenting experimental realizations of droplet−lattice systems representing different spin degrees of freedom and lattice geometries. Our platform enables a rapid and low-cost means to directly visualize dynamics associated with complex many-body systems interacting via long-range interactions. More generally, this platform opens up the rich design space between geometry and interactions for rapid exploration with minimal resources.
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    Assisted assembly of bacteriophage T7 core components for genome translocation across the bacterial envelope (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: In most bacteriophages, genome transport across bacterial envelopes is carried out by the tail machinery. In viruses of the Podoviridae family, in which the tail is not long enough to traverse the bacterial wall, it has been postulated that viral core proteins assembled inside the viral head are translocated and reassembled into a tube within the periplasm that extends the tail channel. Bacteriophage T7 infects Escherichia coli, and despite extensive studies, the precise mechanism by which its genome is translocated remains unknown. Using cryo-electron microscopy, we have resolved the structure of two different assemblies of the T7 DNA translocation complex composed of the core proteins gp15 and gp16. Gp15 alone forms a partially folded hexamer, which is further assembled upon interaction with gp16 into a tubular structure, forming a channel that could allow DNA passage. The structure of the gp15–gp16 complex also shows the location within gp16 of a canonical transglycosylase motif involved in the degradation of the bacterial peptidoglycan layer. This complex docks well in the tail extension structure found in the periplasm of T7-infected bacteria and matches the sixfold symmetry of the phage tail. In such cases, gp15 and gp16 that are initially present in the T7 capsid eightfold-symmetric core would change their oligomeric state upon reassembly in the periplasm. Altogether, these results allow us to propose a model for the assembly of the core translocation complex in the periplasm, which furthers understanding of the molecular mechanism involved in the release of T7 viral DNA into the bacterial cytoplasm.
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    A recombinant herpes virus expressing influenza hemagglutinin confers protection and induces antibody-dependent cellular cytotoxicity (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Despite widespread yearly vaccination, influenza leads to significant morbidity and mortality across the globe. To make a more broadly protective influenza vaccine, it may be necessary to elicit antibodies that can activate effector functions in immune cells, such as antibody-dependent cellular cytotoxicity (ADCC). There is growing evidence supporting the necessity for ADCC in protection against influenza and herpes simplex virus (HSV), among other infectious diseases. An HSV-2 strain lacking the essential glycoprotein D (gD), was used to create ΔgD-2, which is a highly protective vaccine against lethal HSV-1 and HSV-2 infection in mice. It also elicits high levels of IgG2c antibodies that bind FcγRIV, a receptor that activates ADCC. To make an ADCC-eliciting influenza vaccine, we cloned the hemagglutinin (HA) gene from an H1N1 influenza A strain into the ΔgD-2 HSV vector. Vaccination with ΔgD-2::HAPR8 was protective against homologous influenza challenge and elicited an antibody response against HA that inhibits hemagglutination (HAI+), is predominantly IgG2c, strongly activates FcγRIV, and protects against influenza challenge following passive immunization of naïve mice. Prior exposure of mice to HSV-1, HSV-2, or a replication-defective HSV-2 vaccine (dl5-29) does not reduce protection against influenza by ΔgD-2::HAPR8. This vaccine also continues to elicit protection against both HSV-1 and HSV-2, including high levels of IgG2c antibodies against HSV-2. Mice lacking the interferon-α/β receptor and mice lacking the interferon-γ receptor were also protected against influenza challenge by ΔgD-2::HAPR8. Our results suggest that ΔgD-2 can be used as a vaccine vector against other pathogens, while also eliciting protective anti-HSV immunity.
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    Metabolism drives demography in an experimental field test (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Metabolism should drive demography by determining the rates of both biological work and resource demand. Long-standing “rules” for how metabolism should covary with demography permeate biology, from predicting the impacts of climate change to managing fisheries. Evidence for these rules is almost exclusively indirect and in the form of among-species comparisons, while direct evidence is exceptionally rare. In a manipulative field experiment on a sessile marine invertebrate, we created experimental populations that varied in population size (density) and metabolic rate, but not body size. We then tested key theoretical predictions regarding relationships between metabolism and demography by parameterizing population models with lifetime performance data from our field experiment. We found that populations with higher metabolisms had greater intrinsic rates of increase and lower carrying capacities, in qualitative accordance with classic theory. We also found important departures from theory—in particular, carrying capacity declined less steeply than predicted, such that energy use at equilibrium increased with metabolic rate, violating the long-standing axiom of energy equivalence. Theory holds that energy equivalence emerges because resource supply is assumed to be independent of metabolic rate. We find this assumption to be violated under real-world conditions, with potentially far-reaching consequences for the management of biological systems.
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    Regulation of metamorphosis in neopteran insects is conserved in the paleopteran Cloeon dipterum (Ephemeroptera) (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: In the Paleozoic era, more than 400 Ma, a number of insect groups continued molting after forming functional wings. Today, however, flying insects stop molting after metamorphosis when they become fully winged. The only exception is the mayflies (Paleoptera, Ephemeroptera), which molt in the subimago, a flying stage between the nymph and the adult. However, the identity and homology of the subimago still is underexplored. Debate remains regarding whether this stage represents a modified nymph, an adult, or a pupa like that of butterflies. Another relevant question is why mayflies have the subimago stage despite the risk of molting fragile membranous wings. These questions have intrigued numerous authors, but nonetheless, clear answers have not yet been found. By combining morphological studies, hormonal treatments, and molecular analysis in the mayfly Cloeon dipterum, we found answers to these old questions. We observed that treatment with a juvenile hormone analog in the last nymphal instar stimulated the expression of the Kr-h1 gene and reduced that of E93, which suppress and trigger metamorphosis, respectively. The regulation of metamorphosis thus follows the MEKRE93 pathway, as in neopteran insects. Moreover, the treatment prevented the formation of the subimago. These findings suggest that the subimago must be considered an instar of the adult mayfly. We also observed that the forelegs dramatically grow between the last nymphal instar, the subimago, and the adult. This necessary growth spread over the last two stages could explain, at least in part, the adaptive sense of the subimago.
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    Correction for Kim et al., The mechanics and dynamics of cancer cells sensing noisy 3D contact guidance (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
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    Pro-inflammatory T helper 17 directly harms oligodendrocytes in neuroinflammation (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: T helper (Th)17 cells are considered to contribute to inflammatory mechanisms in diseases such as multiple sclerosis (MS). However, the discussion persists regarding their true role in patients. Here, we visualized central nervous system (CNS) inflammatory processes in models of MS live in vivo and in MS brains and discovered that CNS-infiltrating Th17 cells form prolonged stable contact with oligodendrocytes. Strikingly, compared to Th2 cells, direct contact with Th17 worsened experimental demyelination, caused damage to human oligodendrocyte processes, and increased cell death. Importantly, we found that in comparison to Th2 cells, both human and murine Th17 cells express higher levels of the integrin CD29, which is linked to glutamate release pathways. Of note, contact of human Th17 cells with oligodendrocytes triggered release of glutamate, which induced cell stress and changes in biosynthesis of cholesterol and lipids, as revealed by single-cell RNA-sequencing analysis. Finally, exposure to glutamate decreased myelination, whereas blockade of CD29 preserved oligodendrocyte processes from Th17-mediated injury. Our data provide evidence for the direct and deleterious attack of Th17 cells on the myelin compartment and show the potential for therapeutic opportunities in MS.
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    Oculo-retinal dynamics can explain the perception of minimal recognizable configurations (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Natural vision is a dynamic and continuous process. Under natural conditions, visual object recognition typically involves continuous interactions between ocular motion and visual contrasts, resulting in dynamic retinal activations. In order to identify the dynamic variables that participate in this process and are relevant for image recognition, we used a set of images that are just above and below the human recognition threshold and whose recognition typically requires 〉2 s of viewing. We recorded eye movements of participants while attempting to recognize these images within trials lasting 3 s. We then assessed the activation dynamics of retinal ganglion cells resulting from ocular dynamics using a computational model. We found that while the saccadic rate was similar between recognized and unrecognized trials, the fixational ocular speed was significantly larger for unrecognized trials. Interestingly, however, retinal activation level was significantly lower during these unrecognized trials. We used retinal activation patterns and oculomotor parameters of each fixation to train a binary classifier, classifying recognized from unrecognized trials. Only retinal activation patterns could predict recognition, reaching 80% correct classifications on the fourth fixation (on average, ∼2.5 s from trial onset). We thus conclude that the information that is relevant for visual perception is embedded in the dynamic interactions between the oculomotor sequence and the image. Hence, our results suggest that ocular dynamics play an important role in recognition and that understanding the dynamics of retinal activation is crucial for understanding natural vision.
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    Cryo-EM structures of Escherichia coli cytochrome bo3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Two independent structures of the proton-pumping, respiratory cytochrome bo3 ubiquinol oxidase (cyt bo3) have been determined by cryogenic electron microscopy (cryo-EM) in styrene–maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme b, heme o3, and CuB), the redox-active cross-linked histidine–tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75I and R71I. In both structures, residue H98I occupies two conformations. In conformation 1, H98I forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98I has flipped to form a hydrogen bond with E14I at the N-terminal end of TM0. We propose that H98I dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98I.
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    Wnt signaling recruits KIF2A to the spindle to ensure chromosome congression and alignment during mitosis (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Canonical Wnt signaling plays critical roles in development and tissue renewal by regulating β-catenin target genes. Recent evidence showed that β-catenin–independent Wnt signaling is also required for faithful execution of mitosis. However, the targets and specific functions of mitotic Wnt signaling still remain uncharacterized. Using phosphoproteomics, we identified that Wnt signaling regulates the microtubule depolymerase KIF2A during mitosis. We found that Dishevelled recruits KIF2A via its N-terminal and motor domains, which is further promoted upon LRP6 signalosome formation during cell division. We show that Wnt signaling modulates KIF2A interaction with PLK1, which is critical for KIF2A localization at the spindle. Accordingly, inhibition of basal Wnt signaling leads to chromosome misalignment in somatic cells and pluripotent stem cells. We propose that Wnt signaling monitors KIF2A activity at the spindle poles during mitosis to ensure timely chromosome alignment. Our findings highlight a function of Wnt signaling during cell division, which could have important implications for genome maintenance, notably in stem cells.
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    Dynamic localization of a helper NLR at the plant–pathogen interface underpins pathogen recognition (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Plants employ sensor–helper pairs of NLR immune receptors to recognize pathogen effectors and activate immune responses. Yet, the subcellular localization of NLRs pre- and postactivation during pathogen infection remains poorly understood. Here, we show that NRC4, from the “NRC” solanaceous helper NLR family, undergoes dynamic changes in subcellular localization by shuttling to and from the plant–pathogen haustorium interface established during infection by the Irish potato famine pathogen Phytophthora infestans. Specifically, prior to activation, NRC4 accumulates at the extrahaustorial membrane (EHM), presumably to mediate response to perihaustorial effectors that are recognized by NRC4-dependent sensor NLRs. However, not all NLRs accumulate at the EHM, as the closely related helper NRC2 and the distantly related ZAR1 did not accumulate at the EHM. NRC4 required an intact N-terminal coiled-coil domain to accumulate at the EHM, whereas the functionally conserved MADA motif implicated in cell death activation and membrane insertion was dispensable for this process. Strikingly, a constitutively autoactive NRC4 mutant did not accumulate at the EHM and showed punctate distribution that mainly associated with the plasma membrane, suggesting that postactivation, NRC4 may undergo a conformation switch to form clusters that do not preferentially associate with the EHM. When NRC4 is activated by a sensor NLR during infection, however, NRC4 forms puncta mainly at the EHM and, to a lesser extent, at the plasma membrane. We conclude that following activation at the EHM, NRC4 may spread to other cellular membranes from its primary site of activation to trigger immune responses.
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    SAMD9L autoinflammatory or ataxia pancytopenia disease mutations activate cell-autonomous translational repression (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Sterile α motif domain-containing protein 9-like (SAMD9L) is encoded by a hallmark interferon-induced gene with a role in controlling virus replication that is not well understood. Here, we analyze SAMD9L function from the perspective of human mutations causing neonatal-onset severe autoinflammatory disease. Whole-genome sequencing of two children with leukocytoclastic panniculitis, basal ganglia calcifications, raised blood inflammatory markers, neutrophilia, anemia, thrombocytopaenia, and almost no B cells revealed heterozygous de novo SAMD9L mutations, p.Asn885Thrfs*6 and p.Lys878Serfs*13. These frameshift mutations truncate the SAMD9L protein within a domain a region of homology to the nucleotide-binding and oligomerization domain (NOD) of APAF1, ∼80 amino acids C-terminal to the Walker B motif. Single-cell analysis of human cells expressing green fluorescent protein (GFP)-SAMD9L fusion proteins revealed that enforced expression of wild-type SAMD9L repressed translation of red fluorescent protein messenger RNA and globally repressed endogenous protein translation, cell autonomously and in proportion to the level of GFP-SAMD9L in each cell. The children’s truncating mutations dramatically exaggerated translational repression even at low levels of GFP-SAMD9L per cell, as did a missense Arg986Cys mutation reported recurrently as causing ataxia pancytopenia syndrome. Autoinflammatory disease associated with SAMD9L truncating mutations appears to result from an interferon-induced translational repressor whose activity goes unchecked by the loss of C-terminal domains that may normally sense virus infection.
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    Benzofuran sulfonates and small self-lipid antigens activate type II NKT cells via CD1d (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Natural killer T (NKT) cells detect lipids presented by CD1d. Most studies focus on type I NKT cells that express semi-invariant αβ T cell receptors (TCR) and recognize α-galactosylceramides. However, CD1d also presents structurally distinct lipids to NKT cells expressing diverse TCRs (type II NKT cells), but our knowledge of the antigens for type II NKT cells is limited. An early study identified a nonlipidic NKT cell agonist, phenyl pentamethyldihydrobenzofuransulfonate (PPBF), which is notable for its similarity to common sulfa drugs, but its mechanism of NKT cell activation remained unknown. Here, we demonstrate that a range of pentamethylbenzofuransulfonates (PBFs), including PPBF, activate polyclonal type II NKT cells from human donors. Whereas these sulfa drug–like molecules might have acted pharmacologically on cells, here we demonstrate direct contact between TCRs and PBF-treated CD1d complexes. Further, PBF-treated CD1d tetramers identified type II NKT cell populations expressing αβTCRs and γδTCRs, including those with variable and joining region gene usage (TRAV12-1–TRAJ6) that was conserved across donors. By trapping a CD1d–type II NKT TCR complex for direct mass-spectrometric analysis, we detected molecules that allow the binding of CD1d to TCRs, finding that both selected PBF family members and short-chain sphingomyelin lipids are present in these complexes. Furthermore, the combination of PPBF and short-chain sphingomyelin enhances CD1d tetramer staining of PPBF-reactive T cell lines over either molecule alone. This study demonstrates that nonlipidic small molecules, which resemble sulfa drugs implicated in systemic hypersensitivity and drug allergy reactions, are targeted by a polyclonal population of type II NKT cells in a CD1d-restricted manner.
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    Band gaps of crystalline solids from Wannier-localization–based optimal tuning of a screened range-separated hybrid functional (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Accurate prediction of fundamental band gaps of crystalline solid-state systems entirely within density functional theory is a long-standing challenge. Here, we present a simple and inexpensive method that achieves this by means of nonempirical optimal tuning of the parameters of a screened range-separated hybrid functional. The tuning involves the enforcement of an ansatz that generalizes the ionization potential theorem to the removal of an electron from an occupied state described by a localized Wannier function in a modestly sized supercell calculation. The method is benchmarked against experiment for a set of systems ranging from narrow band-gap semiconductors to large band-gap insulators, spanning a range of fundamental band gaps from 0.2 to 14.2 electronvolts (eV), and is found to yield quantitative accuracy across the board, with a mean absolute error of ∼0.1 eV and a maximal error of ∼0.2 eV.
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    Measuring the scientific effectiveness of contact tracing: Evidence from a natural experiment (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-12
    Description: Contact tracing has for decades been a cornerstone of the public health approach to epidemics, including Ebola, severe acute respiratory syndrome, and now COVID-19. It has not yet been possible, however, to causally assess the method’s effectiveness using a randomized controlled trial of the sort familiar throughout other areas of science. This study provides evidence that comes close to that ideal. It exploits a large-scale natural experiment that occurred by accident in England in late September 2020. Because of a coding error involving spreadsheet data used by the health authorities, a total of 15,841 COVID-19 cases (around 20% of all cases) failed to have timely contact tracing. By chance, some areas of England were much more severely affected than others. This study finds that the random breakdown of contact tracing led to more illness and death. Conservative causal estimates imply that, relative to cases that were initially missed by the contact tracing system, cases subject to proper contact tracing were associated with a reduction in subsequent new infections of 63% and a reduction insubsequent COVID-19–related deaths of 66% across the 6 wk following the data glitch.
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    Vaccinating the oldest against COVID-19 saves both the most lives and most years of life (2021)
    National Academy of Sciences
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    Publication Date: 2021-02-25
    Description: Many competing criteria are under consideration for prioritizing COVID-19 vaccination. Two criteria based on age are demographic: lives saved and years of future life saved. Vaccinating the very old against COVID-19 saves the most lives, but, since older age is accompanied by falling life expectancy, it is widely supposed that these two goals are in conflict. We show this to be mistaken. The age patterns of COVID-19 mortality are such that vaccinating the oldest first saves the most lives and, surprisingly, also maximizes years of remaining life expectancy. We demonstrate this relationship empirically in the United States, Germany, and South Korea and with mathematical analysis of life tables. Our age-risk results, under usual conditions, also apply to health risks.
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    Effects of fluorinated solvents on electrolyte solvation structures and electrode/electrolyte interphases for lithium metal batteries (2021)
    National Academy of Sciences
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    Publication Date: 2021-02-25
    Description: Electrolyte is very critical to the performance of the high-voltage lithium (Li) metal battery (LMB), which is one of the most attractive candidates for the next-generation high-density energy-storage systems. Electrolyte formulation and structure determine the physical properties of the electrolytes and their interfacial chemistries on the electrode surfaces. Localized high-concentration electrolytes (LHCEs) outperform state-of-the-art carbonate electrolytes in many aspects in LMBs due to their unique solvation structures. Types of fluorinated cosolvents used in LHCEs are investigated here in searching for the most suitable diluent for high-concentration electrolytes (HCEs). Nonsolvating solvents (including fluorinated ethers, fluorinated borate, and fluorinated orthoformate) added in HCEs enable the formation of LHCEs with high-concentration solvation structures. However, low-solvating fluorinated carbonate will coordinate with Li+ ions and form a second solvation shell or a pseudo-LHCE which diminishes the benefits of LHCE. In addition, it is evident that the diluent has significant influence on the electrode/electrolyte interphases (EEIs) beyond retaining the high-concentration solvation structures. Diluent molecules surrounding the high-concentration clusters could accelerate or decelerate the anion decomposition through coparticipation of diluent decomposition in the EEI formation. The varied interphase features lead to significantly different battery performance. This study points out the importance of diluents and their synergetic effects with the conductive salt and the solvating solvent in designing LHCEs. These systematic comparisons and fundamental insights into LHCEs using different types of fluorinated solvents can guide further development of advanced electrolytes for high-voltage LMBs.
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    Transcriptional regulation of intermolecular Ca2+ signaling in hibernating ground squirrel cardiomyocytes: The myocardin–junctophilin axis (2021)
    National Academy of Sciences
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    Publication Date: 2021-03-30
    Description: The contraction of heart cells is controlled by the intermolecular signaling between L-type Ca2+ channels (LCCs) and ryanodine receptors (RyRs), and the nanodistance between them depends on the interaction between junctophilin-2 (JPH2) in the sarcoplasmic reticulum (SR) and caveolin-3 (CAV3) in the transversal tubule (TT). In heart failure, decreased expression of JPH2 compromises LCC–RyR communication leading to deficient blood-pumping power. In the present study, we found that JPH2 and CAV3 transcription was concurrently regulated by serum response factor (SRF) and myocardin. In cardiomyocytes from torpid ground squirrels, compared with those from euthermic counterparts, myocardin expression was up-regulated, which boosted both JPH2 and CAV3 expression. Transmission electron microscopic imaging showed that the physical coupling between TTs and SRs was tightened during hibernation and after myocardin overexpression. Confocal Ca2+ imaging under the whole-cell patch clamp condition revealed that these changes enhanced the efficiency of LCC–RyR intermolecular signaling and fully compensated the adaptive down-regulation of LCCs, maintaining the power of heart contraction while avoiding the risk of calcium overload during hibernation. Our finding not only revealed an essential molecular mechanism underlying the survival of hibernating mammals, but also demonstrated a “reverse model of heart failure” at the molecular level, suggesting a strategy for treating heart diseases.
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    A unique Malpighian tubule architecture in Tribolium castaneum informs the evolutionary origins of systemic osmoregulation in beetles (2021)
    National Academy of Sciences
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    Publication Date: 2021-03-30
    Description: Maintaining internal salt and water balance in response to fluctuating external conditions is essential for animal survival. This is particularly true for insects as their high surface-to-volume ratio makes them highly susceptible to osmotic stress. However, the cellular and hormonal mechanisms that mediate the systemic control of osmotic homeostasis in beetles (Coleoptera), the largest group of insects, remain largely unidentified. Here, we demonstrate that eight neurons in the brain of the red flour beetle Tribolium castaneum respond to internal changes in osmolality by releasing diuretic hormone (DH) 37 and DH47—homologs of vertebrate corticotropin-releasing factor (CRF) hormones—to control systemic water balance. Knockdown of the gene encoding the two hormones (Urinate, Urn8) reduces Malpighian tubule secretion and restricts organismal fluid loss, whereas injection of DH37 or DH47 reverses these phenotypes. We further identify a CRF-like receptor, Urinate receptor (Urn8R), which is exclusively expressed in a functionally unique secondary cell in the beetle tubules, as underlying this response. Activation of Urn8R increases K+ secretion, creating a lumen-positive transepithelial potential that drives fluid secretion. Together, these data show that beetle Malpighian tubules operate by a fundamentally different mechanism than those of other insects. Finally, we adopt a fluorescent labeling strategy to identify the evolutionary origin of this unusual tubule architecture, revealing that it evolved in the last common ancestor of the higher beetle families. Our work thus uncovers an important homeostatic program that is key to maintaining osmotic control in beetles, which evolved parallel to the radiation of the “advanced” beetle lineages.
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    Topics: Biology , Medicine , Natural Sciences in General
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    Signal transduction through Cys-loop receptors is mediated by the nonspecific bumping of closely apposed domains (2021)
    National Academy of Sciences
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    Publication Date: 2021-03-30
    Description: One of the most fundamental questions in the field of Cys-loop receptors (pentameric ligand-gated ion channels, pLGICs) is how the affinity for neurotransmitters and the conductive/nonconductive state of the transmembrane pore are correlated despite the ∼60-Å distance between the corresponding domains. Proposed mechanisms differ, but they all converge into the idea that interactions between wild-type side chains across the extracellular–transmembrane-domain (ECD–TMD) interface are crucial for this phenomenon. Indeed, the successful design of fully functional chimeras that combine intact ECD and TMD modules from different wild-type pLGICs has commonly been ascribed to the residual conservation of sequence that exists at the level of the interfacial loops even between evolutionarily distant parent channels. Here, using mutagenesis, patch-clamp electrophysiology, and radiolabeled-ligand binding experiments, we studied the effect of eliminating this residual conservation of sequence on ion-channel function and cell-surface expression. From our results, we conclude that proper state interconversion (“gating”) does not require conservation of sequence—or even physicochemical properties—across the ECD–TMD interface. Wild-type ECD and TMD side chains undoubtedly interact with their surroundings, but the interactions between them—straddling the interface—do not seem to be more important for gating than those occurring elsewhere in the protein. We propose that gating of pLGICs requires, instead, that the overall structure of the interfacial loops be conserved, and that their relative orientation and distance be the appropriate ones for changes in one side to result in changes in the other, in a phenomenon akin to the nonspecific “bumping” of closely apposed domains.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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    Structural analyses of an RNA stability element interacting with poly(A) (2021)
    National Academy of Sciences
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    Publication Date: 2021-03-30
    Description: Cis-acting RNA elements are crucial for the regulation of polyadenylated RNA stability. The element for nuclear expression (ENE) contains a U-rich internal loop flanked by short helices. An ENE stabilizes RNA by sequestering the poly(A) tail via formation of a triplex structure that inhibits a rapid deadenylation-dependent decay pathway. Structure-based bioinformatic studies identified numerous ENE-like elements in evolutionarily diverse genomes, including a subclass containing two ENE motifs separated by a short double-helical region (double ENEs [dENEs]). Here, the structure of a dENE derived from a rice transposable element (TWIFB1) before and after poly(A) binding (∼24 kDa and ∼33 kDa, respectively) is investigated. We combine biochemical structure probing, small angle X-ray scattering (SAXS), and cryo‐electron microscopy (cryo-EM) to investigate the dENE structure and its local and global structural changes upon poly(A) binding. Our data reveal 1) the directionality of poly(A) binding to the dENE, and 2) that the dENE-poly(A) interaction involves a motif that protects the 3ʹ-most seven adenylates of the poly(A). Furthermore, we demonstrate that the dENE does not undergo a dramatic global conformational change upon poly(A) binding. These findings are consistent with the recently solved crystal structure of a dENE+poly(A) complex [S.-F. Torabi et al., Science 371, eabe6523 (2021)]. Identification of additional modes of poly(A)–RNA interaction opens new venues for better understanding of poly(A) tail biology.
    Print ISSN: 0027-8424
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    Selective autophagy of AKAP11 activates cAMP/PKA to fuel mitochondrial metabolism and tumor cell growth (2021)
    National Academy of Sciences
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    Publication Date: 2021-03-30
    Description: Autophagy is a catabolic pathway that provides self-nourishment and maintenance of cellular homeostasis. Autophagy is a fundamental cell protection pathway through metabolic recycling of various intracellular cargos and supplying the breakdown products. Here, we report an autophagy function in governing cell protection during cellular response to energy crisis through cell metabolic rewiring. We observe a role of selective type of autophagy in direct activation of cyclic AMP protein kinase A (PKA) and rejuvenation of mitochondrial function. Mechanistically, autophagy selectively degrades the inhibitory subunit RI of PKA holoenzyme through A-kinase–anchoring protein (AKAP) 11. AKAP11 acts as an autophagy receptor that recruits RI to autophagosomes via LC3. Glucose starvation induces AKAP11-dependent degradation of RI, resulting in PKA activation that potentiates PKA-cAMP response element-binding signaling, mitochondria respiration, and ATP production in accordance with mitochondrial elongation. AKAP11 deficiency inhibits PKA activation and impairs cell survival upon glucose starvation. Our results thus expand the view of autophagy cytoprotection mechanism by demonstrating selective autophagy in RI degradation and PKA activation that fuels the mitochondrial metabolism and confers cell resistance to glucose deprivation implicated in tumor growth.
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    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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