ALBERT

Description: TR17-08, a marine sedimentary core (14.6 m), was collected during 2017 from the Edisto Inlet (Ross Sea, Antarctica), a small fjord near Cape Hallett. The core is characterized by expanded laminated sedimentary sequences making it suitable for studying submillennial processes during the Early Holocene. By studying different well-known foraminifera species (Globocassidulina biora, G. subglobosa, Trifarina angulosa, Nonionella iridea, Epistominella exigua, Stainforthia feylingi, Miliammina arenacea, Paratrochammina bartrami and Portatrochammina antarctica), we were able to identify five different foraminiferal assemblages over the last ∼ 2000 years BP. Comparison with diatom assemblages and other geochemical proxies retrieved from nearby sediment cores in the Edisto Inlet (BAY05-20 and HLF17-1) made it possible to distinguish three different phases characterized by different environmental settings: (1) a seasonal phase (from 2012 to 1486 years BP) characterized by the dominance of calcareous species, indicating a seasonal opening of the inlet by more frequent events of melting of the sea-ice cover during the austral summer and, in general, a higher-productivity, more open and energetic environment; (2) a transitional phase (from 1486 to 696 years BP) during which the fjord experienced less extensive sea-ice melting, enhanced oxygen-poor conditions and carbonate dissolution conditions, indicated by the shifts from calcareous-dominated association to agglutinated-dominated association probably due to a freshwater input from the retreat of three local glaciers at the start of this period; and (3) a cooler phase (from 696 years BP to present) during which the sedimentation rate decreased and few to no foraminiferal specimens were present, indicating ephemeral openings or a more prolonged cover of the sea ice during the austral summer, affecting the nutrient supply and the sedimentation regime.

Description: Published

Description: 95–115

Description: OSA2: Evoluzione climatica: effetti e loro mitigazione

Description: JCR Journal

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

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.

Description: Abstract. Clouds are assumed to play an important role in the Arctic amplification process. This motivated a detailed investigation of cloud processes, including radiative and turbulent fluxes. Data from the aircraft campaign ACLOUD were analyzed with a focus on the mean and turbulent structure of the cloudy boundary layer over the Fram Strait marginal sea ice zone in late spring and early summer 2017. Vertical profiles of turbulence moments are presented from contrasting atmospheric boundary layers (ABLs) from 4 d. They differ by the magnitude of wind speed, boundary-layer height, stability, the strength of the cloud-top radiative cooling and the number of cloud layers. Turbulence statistics up to third-order moments are presented, which were obtained from horizontal-level flights and from slanted profiles. It is shown that both of these flight patterns complement each other and form a data set that resolves the vertical structure of the ABL turbulence well. The comparison of the 4 d shows that especially during weak wind, even in shallow Arctic ABLs with mixing ratios below 3 g kg-1, cloud-top cooling can serve as a main source of turbulent kinetic energy (TKE).Well-mixed ABLs are generated where TKE is increased and vertical velocity variance shows pronounced maxima in the cloud layer. Negative vertical velocity skewness points then to upside-down convection. Turbulent heat fluxes are directed upward in the cloud layer as a result of cold downdrafts. In two cases with single-layer stratocumulus, turbulent transport of heat flux and of temperature variance are both negative in the cloud layer, suggesting an important role of large eddies. In contrast, in a case with weak cloud-top cooling, these quantities are positive in the ABL due to the heating from the surface. Based on observations and results of a mixed-layer model it is shown that the maxima of turbulent fluxes are, however, smaller than the jump of the net terrestrial radiation flux across the upper part of a cloud due to the (i) shallowness of the mixed layer and (ii) the presence of a downward entrainment heat flux. The mixed-layer model also shows that the buoyancy production of TKE is substantially smaller in stratocumulus over the Arctic sea ice compared to subtropics due to a smaller surface moisture flux and smaller decrease in specific humidity (or even humidity inversions) right above the cloud top. In a case of strong wind, wind shear shapes the ABL turbulent structure, especially over rough sea ice, despite the presence of a strong cloud-top cooling. In the presence of mid-level clouds, cloud-top radiative cooling and thus also TKE in the lowermost cloud layer are strongly reduced, and the ABL turbulent structure becomes governed by stability, i.e., by the surface–air temperature difference and wind speed. A comparison of slightly unstable and weakly stable cases shows a strong reduction of TKE due to increased stability even though the absolute value of wind speed was similar. In summary, the presented study documents vertical profiles of the ABL turbulence with a high resolution in a wide range of conditions. It can serve as a basis for turbulence closure evaluation and process studies in Arctic clouds.

Description: Springtime Arctic mixed-phase convection over open water in the Fram Strait as observed during the recent ACLOUD (Arctic CLoud Observations Using airborne measurements during polar Day) field campaign is simulated at turbulence-resolving resolutions. The first objective is to assess the skill of large-eddy simulation (LES) in reproducing the observed mixed-phase convection. The second goal is to then use the model to investigate how aerosol modulates the way in which turbulent mixing and clouds transform the low-level air mass. The focus lies on the low-level thermal structure and lapse rate, the heating efficiency of turbulent entrainment, and the low-level energy budget. A composite case is constructed based on data collected by two research aircraft on 18 June 2017. Simulations are evaluated against independent datasets, showing that the observed thermodynamic, cloudy, and turbulent states are well reproduced. Sensitivity tests on cloud condensation nuclei (CCN) concentration are then performed, covering a broad range between pristine polar and polluted continental values. We find a significant response in the resolved mixed-phase convection, which is in line with previous LES studies. An increased CCN substantially enhances the depth of convection and liquid cloud amount, accompanied by reduced surface precipitation. Initializing with the in situ CCN data yields the best agreement with the cloud and turbulence observations, a result that prioritizes its measurement during field campaigns for supporting high-resolution modeling efforts. A deeper analysis reveals that CCN significantly increases the efficiency of radiatively driven entrainment in warming the boundary layer. The marked strengthening of the thermal inversion plays a key role in this effect. The low-level heat budget shifts from surface driven to radiatively driven. This response is accompanied by a substantial reduction in the surface energy budget, featuring a weakened flow of solar radiation into the ocean. Results are interpreted in the context of air–sea interactions, air mass transformations, and climate feedbacks at high latitudes.

Description: The presence of reactive bromine in polar regions is a widespread phenomenon that plays an important role in the photochemistry of the Arctic and Antarctic lower troposphere, including the destruction of ozone, the disturbance of radical cycles, and the oxidation of gaseous elemental mercury. The chemical mechanisms leading to the heterogeneous release of gaseous bromine compounds from saline surfaces are in principle well understood. There are, however, substantial uncertainties about the contribution of different potential sources to the release of reactive bromine, such as sea ice, brine, aerosols, and the snow surface, as well as about the seasonal and diurnal variation and the vertical distribution of reactive bromine. Here we use continuous long-term measurements of the vertical distribution of bromine monoxide (BrO) and aerosols at the two Antarctic sites Neumayer (NM) and Arrival Heights (AH), covering the periods of 2003–2021 and 2012–2021, respectively, to investigate how chemical and physical parameters affect the abundance of BrO. We find the strongest correlation between BrO and aerosol extinction (R=0.56 for NM and R=0.28 for AH during spring), suggesting that the heterogeneous release of Br2 from saline airborne particles (blowing snow and aerosols) is a dominant source for reactive bromine. Positive correlations between BrO and contact time of air masses, both with sea ice and the Antarctic ice sheet, suggest that reactive bromine is not only emitted by the sea ice surface but by the snowpack on the ice shelf and in the coastal regions of Antarctica. In addition, the open ocean appears to represent a source for reactive bromine during late summer and autumn when the sea ice extent is at its minimum. A source–receptor analysis based on back trajectories and sea ice maps shows that main source regions for BrO at NM are the Weddell Sea and the Filchner–Ronne Ice Shelf, as well as coastal polynyas where sea ice is newly formed. A strong morning peak in BrO frequently occurring during summer and that is particularly strong during autumn suggests a night-time build-up of Br2 by heterogeneous reaction of ozone on the saline snowpack in the vicinity of the measurement sites. We furthermore show that BrO can be sustained for at least 3 d while travelling across the Antarctic continent in the absence of any saline surfaces that could serve as a source for reactive bromine.

Description: Stable water isotopologues of snow, firn and ice cores provide valuable information on past climate variations. Yet single profiles are generally not suitable for robust climate reconstructions. Stratigraphic noise, introduced by the irregular deposition, wind-driven erosion and redistribution of snow, impacts the utility of high-resolution isotope records, especially in low-Accumulation areas. However, it is currently unknown how stratigraphic noise differs across the East Antarctic Plateau and how it is affected by local environmental conditions. Here, we assess the amount and structure of stratigraphic noise at seven sites along a 120 km transect on the plateau of Dronning Maud Land, East Antarctica. Replicated oxygen isotope records of 1 m length were used to estimate signal-To-noise ratios as a measure of stratigraphic noise at sites characterised by different accumulation rates (43-64 mm w.e. a-1), snow surface roughnesses and slope inclinations. While we found a high level of stratigraphic noise at all sites, there was also considerable variation between sites. At sastrugi-dominated sites, greater stratigraphic noise coincided with stronger surface roughnesses, steeper slopes and lower accumulation rates, probably related to increased wind speeds. These results provide a first step to modelling stratigraphic noise and might guide site selection and sampling strategies for future expeditions to improve high-resolution climate reconstructions from low-Accumulation regions.

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.

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.

Description: Changes in Southern Ocean export production have broad biogeochemical and climatic implications. Specifically, iron fertilization likely increased subantarctic nutrient utilization and enhanced the efficiency of the biological pump during glacials. However, past export production in the subantarctic Southeast Pacific is poorly documented, and its connection to Fe fertilization, potentially related to Patagonian Ice Sheet dynamics is unknown. We report on biological productivity changes over the past 400 ka, based on a combination of 230Thxs-normalized and stratigraphy-based mass accumulation rates of biogenic barium, organic carbon, biogenic opal, and calcium carbonate as indicators of paleo-export production in a sediment core upstream of the Drake Passage. In addition, we use fluxes of iron and lithogenic material as proxies for terrigenous matter, and thus potential micronutrient supply. Stratigraphy-based mass accumulation rates are strongly influenced by bottom-current dynamics, which result in variable sediment focussing or winnowing at our site. Carbonate is virtually absent in the core, except during peak interglacial intervals of the Holocene, and Marine Isotope Stages (MIS) 5 and 11, likely caused by transient decreases in carbonate dissolution. All other proxies suggest that export production increased during most glacial periods, coinciding with high iron fluxes. Such augmented glacial iron fluxes at the core site were most likely derived from glaciogenic input from the Patagonian Ice Sheet promoting the growth of phytoplankton. Additionally, glacial export production peaks are also consistent with northward shifts of the Subantarctic and Polar Fronts, which positioned our site south of the Subantarctic Front and closer to silicic acid-rich waters of the Polar Frontal Zone, as well as a with a decrease in the diatom utilization of Si relative to nitrate under Fe-replete conditions. However, glacial export production near the Drake Passage was lower than in the Atlantic and Indian sectors of the Southern Ocean, which may relate to complete consumption of silicic acid in the study area. Our results underline the importance of micro-nutrient fertilization through lateral terrigenous input from South America rather than aeolian transport, and exemplify the role of frontal shifts and nutrient limitation for past productivity changes in the Pacific entrance to the Drake Passage.

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.

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.).

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.).

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.

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.

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.

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).

Description: We developed a new version of the Alfred Wegener Institute Climate Model (AWI-CM3), which has higher skills in representing the observed climatology and better computational efficiency than its predecessors. Its ocean component FESOM2 has the multi-resolution functionality typical for unstructured-mesh models while still featuring a scalability and efficiency similar to regular-grid models. The atmospheric component OpenIFS (CY43R3) enables the use of latest developments in the numerical weather prediction community in climate sciences. In this paper we describe the coupling of the model components and evaluate the model performance on a variable resolution (25–125 km) ocean mesh and a 61 km atmosphere grid, which serves as a reference and starting point for other on-going research activities with AWI-CM3. This includes the exploration of high and variable resolution, the development of a full Earth System Model as well as the creation of a new sea ice prediction system. At this early development stage and with the given coarse to medium resolutions, the model already features above CMIP6-average skills in representing the climatology and competitive model throughput. Finally we identify remaining biases and suggest further improvements to be made to the model.

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.).

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.

Description: Arctic river deltas and deltaic near-shore zones represent important land–ocean transition zones influencing sediment dynamics and nutrient fluxes from permafrost-affected terrestrial ecosystems into the coastal Arctic Ocean. To accurately model fluvial carbon and freshwater export from rapidly changing river catchments as well as assess impacts of future change on the Arctic shelf and coastal ecosystems, we need to understand the sea floor characteristics and topographic variety of the coastal zones. To date, digital bathymetrical data from the poorly accessible, shallow, and large areas of the eastern Siberian Arctic shelves are sparse. We have digitized bathymetrical information for nearly 75 000 locations from large-scale (1:25 000–1:500 000) current and historical nautical maps of the Lena Delta and the Kolyma Gulf region in northeastern Siberia. We present the first detailed and seamless digital models of coastal zone bathymetry for both delta and gulf regions in 50 and 200 m spatial resolution. We validated the resulting bathymetry layers using a combination of our own water depth measurements and a collection of available depth measurements, which showed a strong correlation (r〉0.9). Our bathymetrical models will serve as an input for a high-resolution coupled hydrodynamic–ecosystem model to better quantify fluvial and coastal carbon fluxes to the Arctic Ocean, but they may be useful for a range of other studies related to Arctic delta and near-shore dynamics such as modeling of submarine permafrost, near-shore sea ice, or shelf sediment transport. The new digital high-resolution bathymetry products are available on the PANGAEA data set repository for the Lena Delta (https://doi.org/10.1594/PANGAEA.934045; Fuchs et al., 2021a) and Kolyma Gulf region (https://doi.org/10.1594/PANGAEA.934049; Fuchs et al., 2021b), respectively. Likewise, the depth validation data are available on PANGAEA as well (https://doi.org/10.1594/PANGAEA.933187; Fuchs et al., 2021c).

Description: The diagnosis of the conservation state of monumental structures from constraints to the spatial distribution of their physical properties on shallow and inner materials represents one of the key objectives in the application of non-invasive techniques. In situ, CRP and 3D ultrasonic tomography can provide an effective coverage of stone materials in space and time. The intrinsic characteristics of the materials that make up a monumental structure and affect the two properties (i.e., reflectivity, longitudinal velocity) through the above methods substantially differ. Consequently, the content of their information is mainly complementary rather than redundant. In this study we present the integrated application of different non-destructive techniques i.e., Close Range Photogrammetry (CRP), and low frequency (24 KHz) ultrasonic tomography complemented by petrographycal analysis based essentially on Optical Microscopy (OM). This integrated methodology has been applied to a Carrara marble column of the Basilica of San Saturnino, in Byzantine-Proto-Romanesque style, which is part of the Paleo Christian complex of the V-VI century. This complex also includes the adjacent Christian necropolis in the square of San Cosimo in the city of Cagliari, Sardinia, Italy. The column under study is made of bare material dating back probably to the first century A.D., it was subjected to various traumas due to disassembly and transport to the site, including damage caused by the close blast of a WWII fragmentation bomb. High resolution 3D modelling of the studied artifact was computed starting from the integration of proximal sensing techniques such as CRP based on Structure from Motion (SfM), with which information about the geometrical anomalies and reflectivity of the investigated marble column surface was obtained. On the other hand, the inner parts of the studied body were successfully inspected in a non-invasive way by computing the velocity pattern of the ultrasonic signal through the investigated materials using 3D ultrasonic tomography. This technique gives information on the elastic properties of the material related with mechanical properties and a number of factors, such as presence of fractures, voids, and flaws. Extracting information on such factors from the elastic wave velocity using 3D tomography provides a non-invasive approach to analyse the property changes of the inner material of the ancient column. The integrated application of in situ CRP and ultrasonic techniques provides a full 3D high resolution model of the investigated artifact. This model enhanced by the knowledge of the petrographic characteristics of the materials, improves the diagnostic process and affords reliable information on the state of conservation of the materials used in the construction processes of the studied monumental structure. The integrated use of the non-destructive techniques described above also provides suitable data for a possible restoration and future preservation.

Description: Copernicus

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Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica

Description: Originating from the boreal forest and often transported over large distances, driftwood characterises many Arctic coastlines. Here we present a combined assessment of radiocarbon (14C) and dendrochronological (ring width) age estimates of driftwood samples to constrain the progradation of two Holocene beach-ridge systems near the Lena Delta in the Siberian Arctic (Laptev Sea). Our data show that the 14C ages obtained on syndepositional driftwood from beach deposits yield surprisingly coherent chronologies for the coastal evolution of the field sites. The dendrochronological analysis of wood from modern driftlines revealed the origin and recent delivery of the wood from the Lena River catchments. This finding suggests that the duration transport lies within the uncertainty of state-of-the-art 14C dating and thus substantiates the validity of age indication obtained from driftwood. This observation will help to better understand changes in similar coastal environments, and to improve our knowledge about the response of coastal systems to past climate and sea-level changes.

Description: Earth system and climate modelling involves the simulation of processes on a wide range of scales and within and across various compartments of the Earth system. In practice, component models are often developed independently by different research groups, adapted by others to their special interests and then combined using a dedicated coupling software. This procedure not only leads to a strongly growing number of available versions of model components and coupled setups but also to model- and high-performance computing (HPC)-system-dependent ways of obtaining, configuring, building and operating them. Therefore, implementing these Earth system models (ESMs) can be challenging and extremely time consuming, especially for less experienced modellers or scientists aiming to use different ESMs as in the case of intercomparison projects. To assist researchers and modellers by reducing avoidable complexity, we developed the ESM-Tools software, which provides a standard way for downloading, configuring, compiling, running and monitoring different models on a variety of HPC systems. It should be noted that ESM-Tools is not a coupling software itself but a workflow and infrastructure management tool to provide access to increase usability of already existing components and coupled setups. As coupled ESMs are technically the more challenging tasks, we will focus on coupled setups, always implying that stand-alone models can benefit in the same way. With ESM-Tools, the user is only required to provide a short script consisting of only the experiment-specific definitions, while the software executes all the phases of a simulation in the correct order. The software, which is well documented and easy to install and use, currently supports four ocean models, three atmosphere models, two biogeochemistry models, an ice sheet model, an isostatic adjustment model, a hydrology model and a land-surface model. Compared to previous versions, ESM-Tools has lately been entirely recoded in a high-level programming language (Python) and provides researchers with an even more user-friendly interface for Earth system modelling. ESM-Tools was developed within the framework of the Advanced Earth System Model Capacity project, supported by the Helmholtz Association.

Description: Numerous studies have addressed the possible existence of large floating ice sheets in the glacial Arctic Ocean from theoretical, modelling, or seafloor morphology perspectives. Here, we add evidence from the sediment record that support the existence of such freshwater ice caps in certain intervals, and we discuss their implications for possible non-linear and rapid behaviour of such a system in the high latitudes. We present sedimentary activities of 230Th together with 234U/238U ratios, the concentrations of manganese, sulphur and calcium in the context of lithological information and records of microfossils and their isotope composition. New analyses (PS51/038, PS72/396) and a re-analysis of existing marine sediment records (PS1533, PS1235, PS2185, PS2200, amongst others) in view of the naturally occurring radionuclide 230Thex and, where available, 10Be from the Arctic Ocean and the Nordic Seas reveal the widespread occurrence of intervals with a specific geochemical signature. The pattern of these parameters in a pan-Arctic view can best be explained when assuming the repeated presence of freshwater in frozen and liquid form across large parts of the Arctic Ocean and the Nordic Seas. Based on the sedimentary evidence and known environmental constraints at the time, we develop a glacial scenario that explains how these ice sheets, together with eustatic sea-level changes, may have affected the past oceanography of the Arctic Ocean in a fundamental way that must have led to a drastic and non-linear response to external forcing. This concept offers a possibility to explain and to some extent reconcile contrasting age models for the Late Pleistocene in the Arctic Ocean. Our view, if adopted, offers a coherent dating approach across the Arctic Ocean and the Nordic Seas, linked to events outside the Arctic.

Description: The modeling of paleoclimate, using physically based tools, is increasingly seen as a strong out-of-sample test of the models that are used for the projection of future climate changes. New to the Coupled Model Intercomparison Project (CMIP6) is the Tier 1 Last Interglacial experiment for 127 000 years ago (lig127k), designed to address the climate responses to stronger orbital forcing than the midHolocene experiment, using the same state-of-the-art models as for the future and following a common experimental protocol. Here we present a first analysis of a multi-model ensemble of 17 climate models, all of which have completed the CMIP6 DECK (Diagnostic, Evaluation and Characterization of Klima) experiments. The equilibrium climate sensitivity (ECS) of these models varies from 1.8 to 5.6 ∘C. The seasonal character of the insolation anomalies results in strong summer warming over the Northern Hemisphere continents in the lig127k ensemble as compared to the CMIP6 piControl and much-reduced minimum sea ice in the Arctic. The multi-model results indicate enhanced summer monsoonal precipitation in the Northern Hemisphere and reductions in the Southern Hemisphere. These responses are greater in the lig127k than the CMIP6 midHolocene simulations as expected from the larger insolation anomalies at 127 than 6 ka. New synthesis for surface temperature and precipitation, targeted for 127 ka, have been developed for comparison to the multi-model ensemble. The lig127k model ensemble and data reconstructions are in good agreement for summer temperature anomalies over Canada, Scandinavia, and the North Atlantic and for precipitation over the Northern Hemisphere continents. The model–data comparisons and mismatches point to further study of the sensitivity of the simulations to uncertainties in the boundary conditions and of the uncertainties and sparse coverage in current proxy reconstructions. The CMIP6–Paleoclimate Modeling Intercomparison Project (PMIP4) lig127k simulations, in combination with the proxy record, improve our confidence in future projections of monsoons, surface temperature, and Arctic sea ice, thus providing a key target for model evaluation and optimization.

Description: In order to investigate the impact of spatial resolution on the discrepancy between simulated δ18O and observed δ18O in Greenland ice cores, regional climate simulations are performed with the isotope-enabled regional climate model (RCM) COSMO_iso. For this purpose, isotope-enabled general circulation model (GCM) simulations with the ECHAM5-wiso general circulation model (GCM) under present-day conditions and the MPI-ESM-wiso GCM under mid-Holocene conditions are dynamically downscaled with COSMO_iso for the Arctic region. The capability of COSMO_iso to reproduce observed isotopic ratios in Greenland ice cores for these two periods is investigated by comparing the simulation results to measured δ18O ratios from snow pit samples, Global Network of Isotopes in Precipitation (GNIP) stations and ice cores. To our knowledge, this is the first time that a mid-Holocene isotope-enabled RCM simulation is performed for the Arctic region. Under present-day conditions, a dynamical downscaling of ECHAM5-wiso (1.1◦ × 1.1◦) with COSMO_iso to a spatial resolution of 50km improves the agreement with the measured δ18O ratios for 14 of 19 observational data sets. A further increase in the spatial resolution to 7km does not yield substantial improvements except for the coastal areas with its complex terrain. For the mid-Holocene, a fully coupled MPI-ESM-wiso time slice simulation is downscaled with COSMO_iso to a spatial resolution of 50km. In the mid-Holocene, MPI-ESM-wiso already agrees well with observations in Greenland and a downscaling with COSMO_iso does not further improve the model–data agreement. Despite this lack of improvement in model biases, the study shows that in both periods, observed δ18O values at measurement sites constitute isotope ratios which are mainly within the subgrid-scale variability of the global ECHAM5-wiso and MPI-ESM-wiso simulation results. The correct δ18O ratios are consequently not resolved in the GCM simulation results and need to be extracted by a refinement with an RCM. In this context, the RCM simulations provide a spatial δ18O distribution by which the effects of local uncertainties can be taken into account in the comparison between point measurements and model outputs. Thus, an isotope-enabled GCM–RCM model chain with realistically implemented fractionating processes constitutes a useful supplement to reconstruct regional paleo-climate conditions during the mid-Holocene in Greenland. Such model chains might also be applied to reveal the full potential of GCMs in other regions and climate periods, in which large deviations relative to observed isotope ratios are simulated.

Description: Proxy climate records are an invaluable source of information about the earth’s climate prior to the instrumental record. The temporal- and spatial-coverage of records continues to increase, however, these records of past climate are associated with significant uncertainties due to non-climate processes that influence the recorded and measured proxy values. Generally, these uncertainties are timescale-dependent and correlated in time. Accounting for structure in the errors is essential to providing realistic error estimates for smoothed or stacked records, detection of anomalies and identifying trends, but this structure is seldom accounted for. In the first of these companion articles we outlined a theoretical framework for handling proxy uncertainties by deriving the power spectrum of proxy error components from which it is possible to obtain timescale-dependent error estimates. Here in part II, we demonstrate the practical application of this theoretical framework using the example of marine sediment cores. We consider how to obtain estimates for the required parameters and give examples of the application of this approach for typical marine sediment proxy records. Our new approach of estimating and providing timescale-dependent proxy errors overcomes the limitations of simplistic single value error estimates. We aim to provide the conceptual basis for a more quantitative use of paleo-records for applications such as model-data comparison, regional and global synthesis of past climate states and data assimilation.

Description: The mid-Pliocene warm period (mPWP; ∼3.2 million years ago) is seen as the most recent time period characterized by a warm climate state, with similar to modern geography and ∼400 ppmv atmospheric CO2 concentration, and is therefore often considered an interesting analogue for near-future climate projections. Paleoenvironmental reconstructions indicate higher surface temperatures, decreasing tropical deserts, and a more humid climate in West Africa characterized by a strengthened West African Monsoon (WAM). Using model results from the second phase of the Pliocene Modelling Intercomparison Project (PlioMIP2) ensemble, we analyse changes of the WAM rainfall during the mPWP by comparing them with the control simulations for the pre-industrial period. The ensemble shows a robust increase in the summer rainfall over West Africa and the Sahara region, with an average increase of 2.5 mm/d, contrasted by a rainfall decrease over the equatorial Atlantic. An anomalous warming of the Sahara and deepening of the Saharan Heat Low, seen in 〉90 % of the models, leads to a strengthening of the WAM and an increased monsoonal flow into the continent. A similar warming of the Sahara is seen in future projections using both phase 3 and 5 of the Coupled Model Intercomparison Project (CMIP3 and CMIP5). Though previous studies of future projections indicate a west–east drying–wetting contrast over the Sahel, PlioMIP2 simulations indicate a uniform rainfall increase in that region in warm climates characterized by increasing greenhouse gas forcing. We note that this effect will further depend on the long-term response of the vegetation to the CO2 forcing.

Description: The mid-Pliocene warm period (3.264–3.025 Ma) is the most recent geological period during which atmospheric CO2 levels were similar to recent historical values (∼400 ppm). Several proxy reconstructions for the mid-Pliocene show highly reduced zonal sea surface temperature (SST) gradients in the tropical Pacific Ocean, indicating an El Niño-like mean state. However, past modelling studies do not show these highly reduced gradients. Efforts to understand mid-Pliocene climate dynamics have led to the Pliocene Model Intercomparison Project (PlioMIP). Results from the first phase (PlioMIP1) showed clear El Niño variability (albeit significantly reduced) and did not show the greatly reduced time-mean zonal SST gradient suggested by some of the proxies. In this work, we study El Niño–Southern Oscillation (ENSO) variability in the PlioMIP2 ensemble, which consists of additional global coupled climate models and updated boundary conditions compared to PlioMIP1. We quantify ENSO amplitude, period, spatial structure and “flavour”, as well as the tropical Pacific annual mean state in mid-Pliocene and pre-industrial simulations. Results show a reduced ENSO amplitude in the model-ensemble mean (−24 %) with respect to the pre-industrial, with 15 out of 17 individual models showing such a reduction. Furthermore, the spectral power of this variability considerably decreases in the 3–4-year band. The spatial structure of the dominant empirical orthogonal function shows no particular change in the patterns of tropical Pacific variability in the model-ensemble mean, compared to the pre-industrial. Although the time-mean zonal SST gradient in the equatorial Pacific decreases for 14 out of 17 models (0.2 ∘C reduction in the ensemble mean), there does not seem to be a correlation with the decrease in ENSO amplitude. The models showing the most “El Niño-like” mean state changes show a similar ENSO amplitude to that in the pre-industrial reference, while models showing more “La Niña-like” mean state changes generally show a large reduction in ENSO variability. The PlioMIP2 results show a reasonable agreement with both time-mean proxies indicating a reduced zonal SST gradient and reconstructions indicating a reduced, or similar, ENSO variability.

Description: The mid-Pliocene (∼3 Ma) is one of the most recent warm periods with high CO2 concentrations in the atmosphere and resulting high temperatures, and it is often cited as an analog for near-term future climate change. Here, we apply a moisture budget analysis to investigate the response of the large-scale hydrological cycle at low latitudes within a 13-model ensemble from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2). The results show that increased atmospheric moisture content within the mid-Pliocene ensemble (due to the thermodynamic effect) results in wetter conditions over the deep tropics, i.e., the Pacific intertropical convergence zone (ITCZ) and the Maritime Continent, and drier conditions over the subtropics. Note that the dynamic effect plays a more important role than the thermodynamic effect in regional precipitation minus evaporation (PmE) changes (i.e., northward ITCZ shift and wetter northern Indian Ocean). The thermodynamic effect is offset to some extent by a dynamic effect involving a northward shift of the Hadley circulation that dries the deep tropics and moistens the subtropics in the Northern Hemisphere (i.e., the subtropical Pacific). From the perspective of Earth's energy budget, the enhanced southward cross-equatorial atmospheric transport (0.22 PW), induced by the hemispheric asymmetries of the atmospheric energy, favors an approximately 1∘ northward shift of the ITCZ. The shift of the ITCZ reorganizes atmospheric circulation, favoring a northward shift of the Hadley circulation. In addition, the Walker circulation consistently shifts westward within PlioMIP2 models, leading to wetter conditions over the northern Indian Ocean. The PlioMIP2 ensemble highlights that an imbalance of interhemispheric atmospheric energy during the mid-Pliocene could have led to changes in the dynamic effect, offsetting the thermodynamic effect and, hence, altering mid-Pliocene hydroclimate.

Description: Due to its dryness, the subtropical free troposphere plays a critical role in the radiative balance of the Earth's climate system. But the complex interactions of the dynamical and physical processes controlling the variability in the moisture budget of this sensitive region of the subtropical atmosphere are still not fully understood. Stable water isotopes can provide important information about several of the latter processes, namely subsidence drying, turbulent mixing, and dry and moist convective moistening. In this study, we use high-resolution simulations of the isotope-enabled version of the regional weather and climate prediction model of the Consortium for Small-Scale Modelling (COSMOiso) to investigate predominant moisture transport pathways in the Canary Islands region in the eastern subtropical North Atlantic. Comparison of the simulated isotope signals with multi-platform isotope observations (aircraft, ground- and space-based remote sensing) from a field campaign in summer 2013 shows that COSMOiso can reproduce the observed variability of stable water vapour isotopes on timescales of hours to days, thus allowing us to study the mechanisms that control the subtropical free-tropospheric humidity. Changes in isotopic signals along backward trajectories from the Canary Islands region reveal the physical processes behind the synoptic-scale isotope variability. We identify four predominant moisture transport pathways of mid-tropospheric air, each with distinct isotopic signatures: - air parcels originating from the convective boundary layer of the Saharan heat low (SHL) – these are characterised by a homogeneous isotopic composition with a particularly high δD (median mid-tropospheric δD=−122‰), which results from dry convective mixing of low-level moisture of diverse origin advected into the SHL; - air parcels originating from the free troposphere above the SHL – although experiencing the largest changes in humidity and δD during their subsidence over West Africa, these air parcels typically have lower δD values (median δD=−148‰) than air parcels originating from the boundary layer of the SHL; - air parcels originating from outside the SHL region, typically descending from tropical upper levels south of the SHL, which are often affected by moist convective injections from mesoscale convective systems in the Sahel – their isotopic composition is much less enriched in heavy isotopes (median δD=−175‰) than those from the SHL region; - air parcels subsiding from the upper-level extratropical North Atlantic – this pathway leads to the driest and most depleted conditions (median δD=−255‰) in the middle troposphere near the Canary Islands. The alternation of these transport pathways explains the observed high variability in humidity and δD on synoptic timescales to a large degree. We further show that the four different transport pathways are related to specific large-scale flow conditions. In particular, distinct differences in the location of the North African mid-level anticyclone and of extratropical Rossby wave patterns occur between the four transport pathways. Overall, this study demonstrates that the adopted Lagrangian isotope perspective enhances our understanding of air mass transport and mixing and offers a sound interpretation of the free-tropospheric variability of specific humidity and isotope composition on timescales of hours to days in contrasting atmospheric conditions over the eastern subtropical North Atlantic.

Description: The Italian earthquake waveform data are collected here in a dataset suited for machine learning analysis (ML) applications. The dataset consists of nearly 1.2 million three-component (3C) waveform traces from about 50 000 earthquakes and more than 130 000 noise 3C waveform traces, for a total of about 43 000 h of data and an average of 21 3C traces provided per event. The earthquake list is based on the Italian Seismic Bulletin (http://terremoti.ingv.it/bsi, last access: 15 February 2020​​​​​​​) of the Istituto Nazionale di Geofisica e Vulcanologia between January 2005 and January 2020, and it includes events in the magnitude range between 0.0 and 6.5. The waveform data have been recorded primarily by the Italian National Seismic Network (network code IV) and include both weak- (HH, EH channels) and strong-motion (HN channels) recordings. All the waveform traces have a length of 120 s, are sampled at 100 Hz, and are provided both in counts and ground motion physical units after deconvolution of the instrument transfer functions. The waveform dataset is accompanied by metadata consisting of more than 100 parameters providing comprehensive information on the earthquake source, the recording stations, the trace features, and other derived quantities. This rich set of metadata allows the users to target the data selection for their own purposes. Much of these metadata can be used as labels in ML analysis or for other studies. The dataset, assembled in HDF5 format, is available at http://doi.org/10.13127/instance (Michelini et al., 2021).

Description: Published

Description: 5509–5544

Description: 4T. Sismicità dell'Italia

Description: JCR Journal

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.).

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.).

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.

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

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.

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.

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.).

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.

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.

Description: The thermokarst lakes of permafrost regions play a major role in the global carbon cycle. These lakes are sources of methane to the atmosphere although the methane flux is restricted by an ice cover for most of the year. How methane concentrations and fluxes in these waters are affected by the presence of an ice cover is poorly understood. To relate water body morphology, ice formation and methane to each other, we studied the ice of three different water bodies in locations typical of the transition of permafrost from land to ocean in a continuous permafrost coastal region in Siberia. In total, 11 ice cores were analyzed as records of the freezing process and methane composition during the winter season. The three water bodies differed in terms of connectivity to the sea, which affected fall freezing. The first was a bay underlain by submarine permafrost (Tiksi Bay, BY), the second a shallow thermokarst lagoon cut off from the sea in winter (Polar Fox Lagoon, LG) and the third a land-locked freshwater thermokarst lake (Goltsovoye Lake, LK). Ice on all water bodies was mostly methane-supersaturated with respect to atmospheric equilibrium concentration, except for three cores from the isolated lake. In the isolated thermokarst lake, ebullition from actively thawing basin slopes resulted in the localized integration of methane into winter ice. Stable δ13C-CH4 isotope signatures indicated that methane in the lagoon ice was oxidized to concentrations close to or below the calculated atmospheric equilibrium concentration. Increasing salinity during winter freezing led to a micro-environment on the lower ice surface where methane oxidation occurred and the lagoon ice functioned as a methane sink. In contrast, the ice of the coastal marine environment was slightly supersaturated with methane, consistent with the brackish water below. Our interdisciplinary process study shows how water body morphology affects ice formation which mitigates methane fluxes to the atmosphere.

Description: Methane emissions from boreal and arctic wetlands, lakes, and rivers are expected to increase in response to warming and associated permafrost thaw. However, the lack of appropriate land cover datasets for scaling field-measured methane emissions to circumpolar scales has contributed to a large uncertainty for our understanding of present-day and future methane emissions. Here we present the Boreal–Arctic Wetland and Lake Dataset (BAWLD), a land cover dataset based on an expert assessment, extrapolated using random forest modelling from available spatial datasets of climate, topography, soils, permafrost conditions, vegetation, wetlands, and surface water extents and dynamics. In BAWLD, we estimate the fractional coverage of five wetland, seven lake, and three river classes within 0.5 × 0.5∘ grid cells that cover the northern boreal and tundra biomes (17 % of the global land surface). Land cover classes were defined using criteria that ensured distinct methane emissions among classes, as indicated by a co-developed comprehensive dataset of methane flux observations. In BAWLD, wetlands occupied 3.2 × 106 km2 (14 % of domain) with a 95 % confidence interval between 2.8 and 3.8 × 106 km2. Bog, fen, and permafrost bog were the most abundant wetland classes, covering ∼ 28 % each of the total wetland area, while the highest-methane-emitting marsh and tundra wetland classes occupied 5 % and 12 %, respectively. Lakes, defined to include all lentic open-water ecosystems regardless of size, covered 1.4 × 106 km2 (6 % of domain). Low-methane-emitting large lakes (〉10 km2) and glacial lakes jointly represented 78 % of the total lake area, while high-emitting peatland and yedoma lakes covered 18 % and 4 %, respectively. Small (〈0.1 km2) glacial, peatland, and yedoma lakes combined covered 17 % of the total lake area but contributed disproportionally to the overall spatial uncertainty in lake area with a 95 % confidence interval between 0.15 and 0.38 × 106 km2. Rivers and streams were estimated to cover 0.12  × 106 km2 (0.5 % of domain), of which 8 % was associated with high-methane-emitting headwaters that drain organic-rich landscapes. Distinct combinations of spatially co-occurring wetland and lake classes were identified across the BAWLD domain, allowing for the mapping of “wetscapes” that have characteristic methane emission magnitudes and sensitivities to climate change at regional scales. With BAWLD, we provide a dataset which avoids double-accounting of wetland, lake, and river extents and which includes confidence intervals for each land cover class. As such, BAWLD will be suitable for many hydrological and biogeochemical modelling and upscaling efforts for the northern boreal and arctic region, in particular those aimed at improving assessments of current and future methane emissions. Data are freely available at https://doi.org/10.18739/A2C824F9X (Olefeldt et al., 2021).

Description: Lakes in permafrost regions are dynamiclandscape components and play an important role for climatechange feedbacks. Lake processes such as mineralizationand flocculation of dissolved organic carbon (DOC), oneof the main carbon fractions in lakes, contribute to thegreenhouse effect and are part of the global carbon cycle.These processes are in the focus of climate research, butstudies so far are limited to specific study regions. Inour synthesis, we analyzed 2167 water samples from 1833lakes across the Arctic in permafrost regions of Alaska,Canada, Greenland, and Siberia to provide first pan-Arcticinsights for linkages between DOC concentrations andthe environment. Using published data and unpublisheddatasets from the author team, we report regional DOCdifferences linked to latitude, permafrost zones, ecoregions,geology, near-surface soil organic carbon contents, andground ice classification of each lake region. The lakeDOC concentrations in our dataset range from 0 to1130 mg L−1(10.8 mg L−1median DOC concentration).Regarding the permafrost regions of our synthesis, wefound median lake DOC concentrations of 12.4 mg L−1(Siberia), 12.3 mg L−1(Alaska), 10.3 mg L−1(Greenland),and 4.5 mg L−1(Canada). Our synthesis shows a significantrelationship between lake DOC concentration and lakeecoregion. We found higher lake DOC concentrationsat boreal permafrost sites compared to tundra sites. Wefound significantly higher DOC concentrations in lakesin regions with ice-rich syngenetic permafrost deposits(yedoma) compared to non-yedoma lakes and a weak butsignificant relationship between soil organic carbon contentand lake DOC concentration as well as between ground icecontent and lake DOC. Our pan-Arctic dataset shows that theDOC concentration of a lake depends on its environmentalproperties, especially on permafrost extent and ecoregion, aswell as vegetation, which is the most important driver of lakeDOC in this study. This new dataset will be fundamental toquantify a pan-Arctic lake DOC pool for estimations of theimpact of lake DOC on the global carbon cycle and climatechange.

Description: 〈jats:p〉Abstract. The risk of carbon emissions from permafrost ground is linked to ground temperature and thus in particular to thermal insulation by vegetation and organic soil layers in summer and snow cover in winter. This ground insulation is strongly influenced by the presence of large herbivorous animals browsing for food. In this study, we examine the potential impact of large herbivore presence on the ground carbon storage in thermokarst landscapes of northeastern Siberia. Our aim is to understand how intensive animal grazing may affect permafrost thaw and hence organic matter decomposition, leading to different ground carbon storage, which is significant in the active layer. Therefore, we analysed sites with differing large herbivore grazing intensity in the Pleistocene Park near Chersky and measured maximum thaw depth, total organic carbon content and decomposition state by δ13C isotope analysis. In addition, we determined sediment grain size composition as well as ice and water content. We found the thaw depth to be shallower and carbon storage to be higher in intensively grazed areas compared to extensively and non-grazed sites in the same thermokarst basin. The intensive grazing presumably leads to a more stable thermal ground regime and thus to increased carbon storage in the thermokarst deposits and active layer. However, the high carbon content found within the upper 20 cm on intensively grazed sites could also indicate higher carbon input rather than reduced decomposition, which requires further studies. We connect our findings to more animal trampling in winter, which causes snow disturbance and cooler winter ground temperatures during the average annual 225 days below freezing. This winter cooling overcompensates ground warming due to the lower insulation associated with shorter heavily grazed vegetation during the average annual 140 thaw days. We conclude that intensive grazing influences the carbon storage capacities of permafrost areas and hence might be an actively manageable instrument to reduce net carbon emission from these sites. 〈/jats:p〉

Description: 〈jats:p〉Abstract. The combined effect of hot and dry extremes can have disastrous consequences for the society, economy, and the environment. While a significant number of studies have been conducted regarding the variability of the individual hot or dry extremes in Romania, the evaluation of the combined effect of these extremes (e.g. compound effect) is still lacking for this region. Thus, in this study we have assessed the spatio-temporal variability and trends of hot and dry summers in the eastern part of Europe, focusing on Romania, between 1950 and 2020 and we have analyzed the relationship between the frequency of hot summers and the prevailing large-scale atmospheric circulation. The length, spatial extent and frequency of HWs in Romania has increased significantly over the last 70 years, while for the drought conditions no significant changes have been observed. The rate of increase in the frequency and spatial extent of HWs has accelerated significantly after the 1990’s, while the smallest number of HWs was observed between 1970 and 1985. The hottest years, in terms of heatwave duration and frequency, were 2007, 2012, 2015, and 2019. One of the key drivers of hot summers, over our analyzed region, is the prevailing large-scale circulation, featuring an anticyclonic circulation over the central and eastern parts of Europe and enhanced atmospheric blocking activity associated with positive temperature anomalies underneath. We conclude that our study can help improve our understanding of the spatio-temporal variability of hot and dry summers, especially at the regional scale, as well as their driving mechanisms which might lead to a better predictability of these extreme events. 〈/jats:p〉

Description: We combine satellite data products to provide a first and general overview of the physical sea ice conditions along the drift of the international Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition and a comparison with previous years (2005–2006 to 2018–2019). We find that the MOSAiC drift was around 20 % faster than the climatological mean drift, as a consequence of large-scale low-pressure anomalies prevailing around the Barents–Kara–Laptev sea region between January and March. In winter (October–April), satellite observations show that the sea ice in the vicinity of the Central Observatory (CO; 50 km radius) was rather thin compared to the previous years along the same trajectory. Unlike ice thickness, satellite-derived sea ice concentration, lead frequency and snow thickness during winter months were close to the long-term mean with little variability. With the onset of spring and decreasing distance to the Fram Strait, variability in ice concentration and lead activity increased. In addition, the frequency and strength of deformation events (divergence, convergence and shear) were higher during summer than during winter. Overall, we find that sea ice conditions observed within 5 km distance of the CO are representative for the wider (50 and 100 km) surroundings. An exception is the ice thickness; here we find that sea ice within 50 km radius of the CO was thinner than sea ice within a 100 km radius by a small but consistent factor (4 %) for successive monthly averages. Moreover, satellite acquisitions indicate that the formation of large melt ponds began earlier on the MOSAiC floe than on neighbouring floes.

Description: In this study, the first fully continuous monitoring of water vapour isotopic composition at Neumayer Station III, Antarctica, during the 2-year period from February 2017 to January 2019 is presented. Seasonal and synoptic-scale variations in both stable water isotopes H182O and HDO are reported, and their links to variations in key meteorological variables are analysed. In addition, the diurnal cycle of isotope variations during the summer months (December and January 2017/18 and 2018/19) has been examined. Changes in local temperature and specific humidity are the main drivers for the variability in δ18O and δD in vapour at Neumayer Station III, on both seasonal and shorter timescales. In contrast to the measured δ18O and δD variations, no seasonal cycle in the Deuterium excess signal (d) in vapour is detected. However, a rather high uncertainty in measured d values especially in austral winter limits the confidence of this finding. Overall, the d signal shows a stronger inverse correlation with specific humidity than with temperature, and this inverse correlation between d and specific humidity is stronger for the cloudy-sky conditions than for clear-sky conditions during summertime. Back-trajectory simulations performed with the FLEXPART model show that seasonal and synoptic variations in δ18O and δD in vapour coincide with changes in the main sources of water vapour transported to Neumayer Station III. In general, moisture transport pathways from the east lead to higher temperatures and more enriched δ18O values in vapour, while weather situations with southerly winds lead to lower temperatures and more depleted δ18O values. However, on several occasions, δ18O variations linked to wind direction changes were observed, which were not accompanied by a corresponding temperature change. Comparing isotopic compositions of water vapour at Neumayer Station III and snow samples taken in the vicinity of the station reveals almost identical slopes, both for the δ18O–δD relation and for the temperature–δ18O relation.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Description: Hyrrokkin sarcophaga is a parasitic foraminifera that is commonly found in cold-water coral reefs where it infests the file clam Acesta excavata and the scleractinian coral Desmophyllum pertusum (formerly known as Lophelia pertusa). Here, we present measurements of the trace element and isotopic composition of these parasitic foraminifera, analyzed by inductively coupled optical emission spectrometry (ICP-OES), electron probe microanalysis (EPMA) and mass spectrometry (gas-source MS and inductively-coupled-plasma MS). Our results reveal that the geochemical signature of H. sarcophaga depends on the host organism it infests. Sr / Ca ratios are 1.1 mmol mol−1 higher in H. sarcophaga that infest D. pertusum, which could be an indication that dissolved host carbonate material is utilized in shell calcification, given that the aragonite of D. pertusum has a naturally higher Sr concentration compared to the calcite of A. excavata. Similarly, we measure 3.1 ‰ lower δ13C and 0.25 ‰ lower δ18O values in H. sarcophaga that lived on D. pertusum, which might be caused by the direct uptake of the host's carbonate material with a more negative isotopic composition or different pH regimes in these foraminifera (pH can exert a control on the extent of CO2 hydration/hydroxylation) due to the uptake of body fluids of the host. We also observe higher Mn / Ca ratios in foraminifera that lived on A. excavata but did not penetrate the host shell compared to specimen that penetrated the shell, which could be interpreted as a change in food source, changes in the calcification rate, Rayleigh fractionation or changing oxygen conditions. While our measurements provide an interesting insight into the calcification process of this unusual foraminifera, these data also indicate that the geochemistry of this parasitic foraminifera is unlikely to be a reliable indicator of paleoenvironmental conditions using Sr / Ca, Mn / Ca, δ18O or δ13C unless the host organism is known and its geochemical composition can be accounted for.

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.

Description: In this work we have performed a detailed study of vectors to ore to a representative volcanic-rock-hosted replacive volcanogenic massive sulfide (VMS) deposit located in the northern Iberian Pyrite Belt (Spain), the Aguas Teñidas deposit. The investigated vectors include the following: (1) mineralogical zoning, (2) host sequence characterization and mineralized unit identification based on whole rock geochemistry discrimination diagrams, (3) study of the characteristics and behaviour of whole rock geochemical anomalies around the ore (e.g. alteration-related compositional changes, characteristics and extent of geochemical halos of indicative elements such as Cu, Zn, Pb, Sb, Tl, and Ba around the deposit), and (4) application of portable X-ray fluorescence (p-XRF) analysis to the detection of the previous vectors. In the footwall, a concentric cone-shaped hydrothermal alteration zone bearing the stockwork passes laterally, from core to edge, from quartz (only local) to chlorite–quartz, sericite–chlorite–quartz, and sericite–quartz alteration zones. The hydrothermal alteration is also found in the hanging wall despite being tectonically allochthonous to the orebody: a proximal sericite alteration zone is followed by a more distal albite-rich one. Whole rock major elements show an increase in alteration indexes (e.g. AI, CCPI) towards the mineralization, a general SiO2 enrichment, and FeO enrichment as well as K2O and Na2O depletion towards the centre of the hydrothermal system, with MgO showing a less systematic behaviour. K2O and Na2O leached from the centre of the system are transported and deposited in more external areas. Copper, Pb, and Zn produce proximal anomalies around mineralized areas, with the more mobile Sb, Tl, and Ba generating wider halos. Whereas Sb and Tl halos form around all mineralized areas, Ba anomalies are restricted to areas around the massive sulfide body. Our results show that proposed vectors, or adaptations designed to overcome p-XRF limitations, can be confidently used by analysing unprepared hand specimens, including the external rough curved surface of drill cores. The data presented in this work are not only applicable to VMS exploration in the Iberian Pyrite Belt, but on a broader scale they will also contribute to improving our general understanding of vectors to ore in replacive-type VMS deposits.

Description: We combine satellite data products to provide a first and general overview of the physical sea ice conditions along the drift of the international Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition and a comparison with previous years (2005–2006 to 2018–2019). We find that the MOSAiC drift was around 20 % faster than the climatological mean drift, as a consequence of large-scale low-pressure anomalies prevailing around the Barents–Kara–Laptev sea region between January and March. In winter (October–April), satellite observations show that the sea ice in the vicinity of the Central Observatory (CO; 50 km radius) was rather thin compared to the previous years along the same trajectory. Unlike ice thickness, satellite-derived sea ice concentration, lead frequency and snow thickness during winter months were close to the long-term mean with little variability. With the onset of spring and decreasing distance to the Fram Strait, variability in ice concentration and lead activity increased. In addition, the frequency and strength of deformation events (divergence, convergence and shear) were higher during summer than during winter. Overall, we find that sea ice conditions observed within 5 km distance of the CO are representative for the wider (50 and 100 km) surroundings. An exception is the ice thickness; here we find that sea ice within 50 km radius of the CO was thinner than sea ice within a 100 km radius by a small but consistent factor (4 %) for successive monthly averages. Moreover, satellite acquisitions indicate that the formation of large melt ponds began earlier on the MOSAiC floe than on neighbouring floes.

Description: Across the Qinghai–Tibet Plateau (QTP) there is a narrow engineering corridor with widely distributed slopes called the Qinghai–Tibet Engineering Corridor (QTEC), where a variety of important infrastructures are concentrated. These facilities are transportation routes for people, materials, energy, etc. from inland China to the Tibet Autonomous Region. From Golmud to Lhasa, the engineering corridor covers 632 km of permafrost containing the densely developed Qinghai–Tibet Railway and Qinghai–Tibet Highway, as well as power and communication towers. Slope failure in permafrost regions, caused by permafrost degradation, ground ice melting, etc., affects the engineering construction and permafrost environments in the QTEC. We implement a variety of sensors to monitor the hydrological and thermal deformation between permafrost slopes and permafrost engineering projects in the corridor. In addition to soil temperature and moisture sensors, the global navigation satellite system (GNSS), terrestrial laser scanning (TLS), and unmanned aerial vehicles (UAVs) were adopted to monitor the spatial distribution and changes in thermal deformation. An integrated dataset of hydrological and thermal deformation in permafrost engineering and slopes in the QTEC from the 1950s to 2020, including meteorological and ground observations, TLS point cloud data, and RGB and thermal infrared (TIR) images, can be of great value for estimating the hydrological and thermal impact and stability between engineering and slopes under the influence of climate change and engineering disturbance. The dataset and code were uploaded to the Zenodo repository and can be accessed through https://zenodo.org/communities/qtec (last access: 23 June 2021), including meteorological and ground observations at https://doi.org/10.5281/zenodo.5009871 (Luo et al., 2020d), TLS measurements at https://doi.org/10.5281/zenodo.5009558 (Luo et al., 2020a), UAV RGB and TIR images at https://doi.org/10.5281/zenodo.5016192 (Luo et al., 2020b), and R code for permafrost indices and visualisation at https://doi.org/10.5281/zenodo.5002981 (Luo et al., 2020c).

Description: We present the first incorporation of the Common Representative Intermediates version 2.2 tropospheric chemistry mechanism, CRI v2.2, combined with stratospheric chemistry, into the global chemistry–climate United Kingdom Chemistry and Aerosols (UKCA) model to give the CRI-Strat 2 mechanism. A rigorous comparison of CRI-Strat 2 with the earlier version, CRI-Strat, is performed in UKCA in addition to an evaluation of three mechanisms, CRI-Strat 2, CRI-Strat and the standard UKCA chemical mechanism, StratTrop v1.0, against a wide array of surface and airborne chemical data. CRI-Strat 2 comprises a state-of-the-art isoprene scheme, optimized against the Master Chemical Mechanism v3.3.1, which includes isoprene peroxy radical isomerization, HOx recycling through the addition of photolabile hydroperoxy aldehydes (HPALDs), and isoprene epoxy diol (IEPOX) formation. CRI-Strat 2 also features updates to several rate constants for the inorganic chemistry, including the reactions of inorganic nitrogen and O(1D). The update to the isoprene chemistry in CRI-Strat 2 increases OH over the lowest 500 m in tropical forested regions by 30 %–50 % relative to CRI-Strat, leading to an improvement in model–observation comparisons for surface OH and isoprene relative to CRI-Strat and StratTrop. Enhanced oxidants also cause a 25 % reduction in isoprene burden and an increase in oxidation fluxes of isoprene and other biogenic volatile organic compounds (BVOCs) at low altitudes with likely impacts on subsequent aerosol formation, atmospheric lifetime, and climate. By contrast, updates to the rate constants of O(1D) with its main reactants relative to CRI-Strat reduces OH in much of the free troposphere, producing a 2 % increase in the methane lifetime, and increases the tropospheric ozone burden by 8 %, primarily from reduced loss via O(1D)+H2O. The changes to inorganic nitrogen reaction rate constants increase the NOx burden by 4 % and shift the distribution of nitrated species closer to that simulated by StratTrop. CRI-Strat 2 is suitable for multi-decadal model integrations and the improved representation of isoprene chemistry provides an opportunity to explore the consequences of HOx recycling in the United Kingdom Earth System Model (UKESM1). This new mechanism will enable a re-evaluation of the impact of BVOCs on the chemical composition of the atmosphere and further probe the feedback between the biosphere and the climate.

Description: The use of mass flow simulations in volcanic hazard zonation and mapping is often limited by model complexity (i.e. uncertainty in correct values of model parameters), a lack of model uncertainty quantification, and limited approaches to incorporate this uncertainty into hazard maps. When quantified, mass flow simulation errors are typically evaluated on a pixel-pair basis, using the difference between simulated and observed (“actual”) map-cell values to evaluate the performance of a model. However, these comparisons conflate location and quantification errors, neglecting possible spatial autocorrelation of evaluated errors. As a result, model performance assessments typically yield moderate accuracy values. In this paper, similarly moderate accuracy values were found in a performance assessment of three depth-averaged numerical models using the 2012 debris avalanche from the Upper Te Maari crater, Tongariro Volcano, as a benchmark. To provide a fairer assessment of performance and evaluate spatial covariance of errors, we use a fuzzy set approach to indicate the proximity of similarly valued map cells. This “fuzzification” of simulated results yields improvements in targeted performance metrics relative to a length scale parameter at the expense of decreases in opposing metrics (e.g. fewer false negatives result in more false positives) and a reduction in resolution. The use of this approach to generate hazard zones incorporating the identified uncertainty and associated trade-offs is demonstrated and indicates a potential use for informed stakeholders by reducing the complexity of uncertainty estimation and supporting decision-making from simulated data.

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.

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.

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.

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.

Description: In this study, we analyse the climatology of ionosphere over Nepal based on GPS-derived vertical total electron content (VTEC) observed from four stations as defined in Table 1: KKN4 (27.80∘ N, 85.27∘ E), GRHI (27.95∘ N, 82.49∘ E), JMSM (28.80∘ N, 83.74∘ E) and DLPA (28.98∘ N, 82.81∘ E) during the years 2008 to 2018. The study illustrates the diurnal, monthly, annual, seasonal and solar cycle variations in VTEC during all times of solar cycle 24. The results clearly reveal the presence of equinoctial asymmetry in TEC, which is more pronounced in maximum phases of solar cycle in the year 2014 at KKN4 station, followed by descending, ascending and minimum phases. Diurnal variations in VTEC showed the short-lived day minimum which occurs between 05:00 to 06:00 LT (local time) at all the stations considered, with diurnal peaks between 12:00 and 15:00 LT. The maximum value of TEC is observed more often during the spring equinox than the autumn equinox, with a few asymmetries. Seasonal variation in TEC is observed to be a manifestation of variations in solar flux, particularly regarding the level of solar flux in consecutive solstices.

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.

Description: We report on applications of the ultraviolet-light-emitting-diode-based incoherent broadband cavity-enhanced absorption spectroscopy (UV-LED-IBBCEAS) technique for optical monitoring of HONO, NO2 and CH2O in a simulation chamber. Performance intercomparison of UV-LED-IBBCEAS with a wet chemistry-based NitroMAC sensor and a Fourier transform infrared (FTIR) spectrometer has been carried out on real-time simultaneous measurement of HONO, NO2 and CH2O concentrations during the reaction of NO2 with H2O vapour in CESAM (French acronym for Experimental Multiphasic Atmospheric Simulation Chamber). The 1σ (signal-to-noise ratio (SNR) = 1) detection limits of 112 pptv for NO2, 56 pptv for HONO and 41 ppbv for CH2O over 120 s were found for the UV-LED-IBBCEAS measurement. On the contrary to many set-ups where cavities are installed outside the simulation chamber, we describe here an original in situ permanent installation. The intercomparison results demonstrate that IBBCEAS is a very well suitable technique for in situ simultaneous measurements of multiple chemically reactive species with high sensitivity and high precision even if the absorption bands of these species are overlapped. It offers excellent capacity for non-invasive optical monitoring of chemical reactions without any perturbation. For the application to simulation chambers, it has the advantage to provide a spatially integrated measurement across the reactor and hence to avoid point-sampling-related artefacts.

Description: Assimilation of weather radar measurements including radar reflectivity and radial wind data has been operational at the Deutscher Wetterdienst, with a diagonal observation error (OE) covariance matrix. For an implementation of a full OE covariance matrix, the statistics of the OE have to be a priori estimated, for which the Desroziers method has been often used. However, the resulted statistics consists of contributions from different error sources and are difficult to interpret. In this work, we use an approach that is based on samples for truncation error in radar observation space to approximate the representation error due to unresolved scales and processes (RE) and compare its statistics with the OE statistics estimated by the Desroziers method. It is found that the statistics of the RE help the understanding of several important features in the variances and correlation length scales of the OE for both reflectivity and radial wind data and the other error sources from the microphysical scheme, radar observation operator and the superobbing technique may also contribute, for instance, to differences among different elevations and observation types. The statistics presented here can serve as a guideline for selecting which observations are assimilated and for assignment of the OE covariance matrix that can be diagonal or full and correlated.

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.

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.

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.

Description: Determining controls on the temperature sensitivity of heterotrophic soil respiration remains critical to incorporating soil–climate feedbacks into climate models. Most information on soil respiratory responses to temperature comes from laboratory incubations of isolated soils and typically subsamples of individual horizons. Inconsistencies between field and laboratory results may be explained by microbial priming supported by cross-horizon exchange of labile C or N. Such exchange is feasible in intact soil profiles but is absent when soils are isolated from surrounding depths. Here we assess the role of soil horizon connectivity, by which we mean the degree to which horizons remain layered and associated with each other as they are in situ, on microbial C and N substrate use and its relationship to the temperature sensitivity of respiration. We accomplished this by exploring changes in C : N, soil organic matter composition (via C : N, amino acid composition and concentration, and nuclear magnetic resonance spectroscopy), and the δ13C of respiratory CO2 during incubations of organic horizons collected across boreal forests in different climate regions where soil C and N compositions differ. The experiments consisted of two treatments: soil incubated (1) with each organic horizon separately and (2) as a whole organic profile, permitting cross-horizon exchange of substrates during the incubation. The soils were incubated at 5 and 15 ∘C for over 430 d. Enhanced microbial use of labile C-rich, but not N-rich, substrates were responsible for enhanced, whole-horizon respiratory responses to temperature relative to individual soil horizons. This impact of a labile C priming mechanism was most emergent in soils from the warmer region, consistent with these soils' lower C bioreactivity relative to soils from the colder region. Specifically, cross-horizon exchange within whole soil profiles prompted increases in mineralization of carbohydrates and more 13C-enriched substrates and increased soil respiratory responses to warming relative to soil horizons incubated in isolation. These findings highlight that soil horizon connectivity can impact microbial substrate use in ways that affect how soil effluxes of CO2 are controlled by temperature. The degree to which this mechanism exerts itself in other soils remains unknown, but these results highlight the importance of understanding mechanisms that operate in intact soil profiles – only rarely studied – in regulating a key soil–climate feedback.

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.

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.

Description: Plumes from the boreal spring biomass burning (BB) in northern peninsular Southeast Asia (nPSEA) are lifted into the subtropical jet stream and transported and deposited across nPSEA, South China, Taiwan and even the western North Pacific Ocean. This paper as part of the Seven SouthEast Asian Studies (7-SEAS) project effort attempts to improve the chemical weather prediction capability of the Weather Research and Forecasting coupled with the Community Multiscale for Air Quality (WRF–CMAQ) model over a vast region, from the mountainous near-source burning sites at nPSEA to its downwind region. Several sensitivity analyses of plume rise are compared in the paper, and it is discovered that the initial vertical allocation profile of BB plumes and the plume rise module (PLMRIM) are the main reasons causing the inaccuracies of the WRF–CMAQ simulations. The smoldering emission from the Western Regional Air Partnership (WRAP) empirical algorithm included has improved the accuracies of PM10, O3 and CO at the source. The best performance at the downwind sites is achieved with the inline PLMRIM, which accounts for the atmospheric stratification at the mountainous source region with the FINN burning emission dataset. Such a setup greatly improves not only the BB aerosol concentration prediction over near-source and receptor ground-based measurement sites but also the aerosol vertical distribution and column aerosol optical depth of the BB aerosol along the transport route. The BB aerosols from nPSEA are carried by the subtropical westerlies in the free troposphere to the western North Pacific, while BB aerosol has been found to interact with the local pollutants in the Taiwan region through three conditions: (a) overpassing western Taiwan and entering the central mountain area, (b) mixing down to western Taiwan, (c) transport of local pollutants upwards and mixing with a BB plume on higher ground. The second condition, which involves the prevailing high-pressure system from Asian cold surge, is able to impact most of the population in Taiwan.

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.

Description: The German Bight located within the central North Sea is a hydro- and morphodynamically highly complex system of estuaries, barrier islands, and part of the world's largest coherent tidal flats, the Wadden Sea. To identify and understand challenges faced by coastal stakeholders, such as harbor operators or governmental agencies, to maintain waterways and employ numerical models for further analyses, it is imperative to have a consistent database for both bathymetry and surface sedimentology. Current commercial and public data products are insufficient in spatial and temporal resolution and coverage for recent analysis methods. Thus, this first part of a two-part publication series of the German joint project EasyGSH-DB describes annual bathymetric digital terrain models at a 10 m gridded resolution for the German North Sea coast and German Bight from 1996 to 2016 (Sievers et al., 2020a, https://doi.org/10.48437/02.2020.K2.7000.0001), as well as surface sedimentological models of discretized cumulative grain size distribution functions for 1996, 2006, and 2016 on 100 m grids (Sievers et al., 2020b, https://doi.org/10.48437/02.2020.K2.7000.0005). Furthermore, basic morphodynamic and sedimentological processing analyses, such as the estimation of, for example, bathymetric stability or surface maps of sedimentological parameters, are provided (Sievers et al., 2020a, b, see respective download links).

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.