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  • American Physical Society  (663,490)
  • Public Library of Science  (275,023)
  • Blackwell Publishers Ltd
  • National Academy of Sciences
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  • 1
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    Linking the Langevin equation to scaling properties of space plasma turbulence at sub-ion scales (2024)
    American Physical Society
    Details
    Publication Date: 2024-04-30
    Description: Current understanding of the kinetic-scale turbulence in weakly collisional plasmas still remains elusive. We employ a general framework in which the turbulent energy transfer is envisioned as a scale-to-scale Langevin process. Fluctuations in the sub-ion range show a global scale invariance, thus suggesting a homogeneous energy repartition. In this Letter, we interpret such a feature by linking the drift term of the Langevin equation to scaling properties of fluctuations. Theoretical expectations are verified on solar wind observations and numerical simulations, thus giving relevance to the proposed framework for understanding kinetic-scale turbulence in space plasmas.
    Description: Published
    Description: L042014
    Description: OSA3: Climatologia e meteorologia spaziale
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Dynamics of Aggregates and Sinking Carbon Fluxes in a Turbulent Ocean (2024)
    National Academy of Sciences
    Details
    Publication Date: 2024-04-26
    Description: The sinking of particulate matter from the upper ocean dominates the export and sequestration of organic carbon by the biological pump, a critical component of the Earth's carbon cycle. Controls on carbon export are thought to be driven by ecological processes that produce and repackage sinking biogenic particles. Here, we present observations during the demise of the Northeast Atlantic Ocean spring bloom illustrating the importance of storm-induced turbulence on the dynamics of sinking particles. A sequence of four large storms caused upper layer mean turbulence levels to vary by more than three orders of magnitude. Large particle (>0.1 to 10 mm) abundance and size changed accordingly: increasing via shear coagulation when turbulence was moderate and decreasing rapidly when turbulence was intense due to shear disaggregation. Particle export was also tied to storm forcing as large particles were mixed to depth during mixed layer deepening. After the mixed layer shoaled, these particles, now isolated from intense surface mixing, grew larger and subsequently sank. This sequence of events matched the timing of sinking particle flux observations. Particle export was influenced by increases in aggregate abundance and porosity, which appeared to be enhanced by the repeated creation and destruction of aggregates. Last, particle transit efficiency through the mesopelagic zone was reduced by presumably biotic processes that created small particles (〈0.5 mm) from larger ones. Our results demonstrate that ocean turbulence significantly impacts the nature and dynamics of sinking particles, strongly influencing particle export and the efficiency of the biological pump.
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  • 3
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    A Late Pleistocene coastal ecosystem in French Guiana was hyperdiverse relative to today (2024)
    National Academy of Sciences
    Details
    Publication Date: 2024-05-13
    Description: Warmer temperatures and higher sea level than today characterized the Last Interglacial interval [Pleistocene, 128 to 116 thousand years ago (ka)]. This period is a remarkable deep-time analog for temperature and sea-level conditions as projected for 2100 AD, yet there has been no evidence of fossil assemblages in the equatorial Atlantic. Here, we report foraminifer, metazoan (mollusks, bony fish, bryozoans, decapods, and sharks among others), and plant communities of coastal tropical marine and mangrove affinities, dating precisely from a ca. 130 to 115 ka time interval near the Equator, at Kourou, in French Guiana. These communities include ca. 230 recent species, some being endangered today and/or first recorded as fossils. The hyperdiverse Kourou mollusk assemblage suggests stronger affinities between Guianese and Caribbean coastal waters by the Last Interglacial than today, questioning the structuring role of the Amazon Plume on tropical Western Atlantic communities at the time. Grassland-dominated pollen, phytoliths, and charcoals from younger deposits in the same sections attest to a marine retreat and dryer conditions during the onset of the last glacial (ca. 110 to 50 ka), with a savanna-dominated landscape and episodes of fire. Charcoals from the last millennia suggest human presence in a mosaic of modern-like continental habitats. Our results provide key information about the ecology and biogeography of pristine Pleistocene tropical coastal ecosystems, especially relevant regarding the—widely anthropogenic—ongoing global warming.
    Type: Article , PeerReviewed
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  • 4
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    3D intrusions transport active surface microbial assemblages to the dark ocean (2024)
    National Academy of Sciences
    Details
    Publication Date: 2024-06-05
    Description: Significance Particulate organic carbon (POC) formed by photosynthesis in the sunlit surface ocean fuels the ecosystems in the dark ocean below. We show that mesoscale fronts and eddies, which are ubiquitous physical features in subtropical oceans, generate three-dimensional intrusions connecting the surface to deep ocean. Intrusions are enriched in total POC due to enhancement of small, nonsinking photosynthetic plankton and free-living bacteria that resemble surface microbial communities. Flow-driven export of POC, estimated using an approximation of eddy physics, is the same order of magnitude as export by sinking POC, which was previously thought to dominate export. These observations reveal coupling of surface and deep ocean productivity and biodiversity and give insight into mechanisms by which the ocean transports carbon to depth. Abstract Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.
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  • 5
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    The strength of the Earth's magnetic field from Pre-Pottery to Pottery Neolithic, Jordan (2023)
    National Academy of Sciences
    Details
    Publication Date: 2023-10-26
    Description: Constraining secular variation of the Earth's magnetic field strength in the past is fundamental to understanding short-term processes of the geodynamo. Such records also constitute a powerful and independent dating tool for archaeological sites and geological formations. In this study, we present 11 robust archaeointensity results from Pre-Pottery to Pottery Neolithic Jordan that are based on both clay and flint (chert) artifacts. Two of these results constitute the oldest archaeointensity data for the entire Levant, ancient Egypt, Turkey, and Mesopotamia, extending the archaeomagnetic reference curve for the Holocene. Virtual Axial Dipole Moments (VADMs) show that the Earth's magnetic field in the Southern Levant was weak (about two-thirds the present field) at around 7600 BCE, recovering its strength to greater than the present field around 7000 BCE, and gradually weakening again around 5200 BCE. In addition, successful results obtained from burnt flint demonstrate the potential of this very common, and yet rarely used, material in archaeomagnetic research, in particular for prehistoric periods from the first use of fire to the invention of pottery.
    Description: Published
    Description: e2100995118
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Keywords: Jordan ; Neolithic ; Pre-Pottery Neolithic ; archaeointensity
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Spintronics-compatible approach to solving maximum satisfiability problems with probabilistic computing, invertible logic and parallel tempering (2023)
    American Physical Society
    Details
    Publication Date: 2023-02-22
    Description: 7 Figures, 20 pages
    Description: The search of hardware-compatible strategies for solving NP-hard combinatorial optimization problems (COPs) is an important challenge of today s computing research because of their wide range of applications in real world optimization problems. Here, we introduce an unconventional scalable approach to face maximum satisfiability problems (Max-SAT) which combines probabilistic computing with p-bits, parallel tempering, and the concept of invertible logic gates. We theoretically show the spintronic implementation of this approach based on a coupled set of Landau-Lifshitz-Gilbert equations, showing a potential path for energy efficient and very fast (p-bits exhibiting ns time scale switching) architecture for the solution of COPs. The algorithm is benchmarked with hard Max-SAT instances from the 2016 Max-SAT competition (e.g., HG-4SAT-V150-C1350-1.cnf which can be described with 2851 p-bits), including weighted Max-SAT and Max-Cut problems.
    Description: Published
    Description: 024052
    Description: 3IT. Calcolo scientifico
    Description: JCR Journal
    Keywords: Physics - Mesoscopic Systems and Quantum Hall Effect; Physics - Mesoscopic Systems and Quantum Hall Effect
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    La Sassa cave: Isotopic evidence for Copper Age and Bronze Age population dynamics in Central Italy (2023)
    Public Library of Science
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    Publication Date: 2023-08-29
    Description: This study focuses on the changes in diet and mobility of people buried in the La Sassa cave (Latium, Central Italy) during the Copper and Bronze Ages to contribute to the understanding of the complex contemporary population dynamics in Central Italy. To that purpose, carbon and nitrogen stable isotope analyses, strontium isotope analyses, and FT-IR evaluations were performed on human and faunal remains from this cave. The stable isotope analyses evidence a slight shift in diet between Copper and Bronze Age individuals, which becomes prominent in an individual, dating from a late phase, when the cave was mainly used as a cultic shelter. This diachronic study documents an increased dietary variability due to the introduction of novel resources in these protohistoric societies, possibly related to the southward spread of northern human groups into Central Italy. This contact between different cultures is also testified by the pottery typology found in the cave. The latter shows an increase in cultural intermingling starting during the beginning of the middle Bronze Age. The local mobility during this phase likely involved multiple communities scattered throughout an area of a few kilometers around the cave, which used the latter as a burial site both in the Copper and Bronze ages.
    Description: Published
    Description: e0288637
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: 6SR VULCANI – Servizi e ricerca per la società
    Description: 7SR AMBIENTE – Servizi e ricerca per la società
    Description: JCR Journal
    Keywords: La Sassa cave (Central Italy) ; population dynamics ; nitrogen isotope ; strontium isotope
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean (2023)
    National Academy of Sciences
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    Publication Date: 2023-03-08
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Saunders, J. K., McIlvin, M. R., Dupont, C. L., Kaul, D., Moran, D. M., Horner, T., Laperriere, S. M., Webb, E. A., Bosak, T., Santoro, A. E., & Saito, M. A. Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean. Proceedings of the National Academy of Sciences of the United States of America, 119(37),(2022): e2200014119, https://doi.org/10.1073/pnas.2200014119.
    Description: Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.
    Description: Funding for this research was provided by the Gordon and Betty Moore Foundation (grants 3782 and 8453), the US NSF (NSF grants OCE-1924554, 2123055, 2125063, 2048774, and 2026933), the Center for Chemical Currencies on a Microbial Planet (NSF grant OCE-2019589), and the US NIH General Medicine (grant GM135709-01A1). J.K.S. was supported by a NASA Postdoctoral Program Fellowship with the NASA Astrobiology Program, administered by Universities Space Research Association under contract with NASA. A.E.S. was supported by the Sloan Foundation, the Simons Foundation, and NSF grant OCE-1437310. A portion of this research used resources at the US Department of Energy JGI sponsored by the Office of Biological and Environmental Research and operated under contract DE-AC02-05CH11231 (JGI). C.L.D. and D.K. were supported by NSF grants OCE-1558453 and OCE-2049299. T.H. was supported by NSF grant OCE-2023456.
    Keywords: Marine microbial ecology ; Metaproteomics ; Mesopelagic ; Nitrification ; Methylotrophy
    Repository Name: Woods Hole Open Access Server
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  • 9
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    A metabologenomics approach to unlock the metabolome of the novel Antarctic deep-sea isolate Lacinutrix shetlandiensis sp. nov. WUR7 (2023)
    National Academy of Sciences
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    Publication Date: 2024-01-08
    Description: The South Shetland Trough, Antarctica, is an underexplored region for microbiological and biotechnological exploitation. Herein, we describe the isolation and characterization of the novel bacterium Lacinutrix shetlandiensis sp. nov. WUR7 from a deep-sea environment. We explored its chemical diversity via a metabologenomics approach, wherein the OSMAC strategy was strategically employed to upregulate cryptic genes for secondary metabolite production. Based on hybrid de novo whole genome sequencing and digital DNA–DNA hybridization, isolate WUR7 was identified as a novel species from the Gram-negative genus Lacinutrix. Its genome was mined for the presence of biosynthetic gene clusters with limited results. However, extensive investigation of its metabolism uncovered an unusual tryptophan decarboxylase with high sequence homology and conserved structure of the active site as compared to ZP_02040762, a highly specific tryptophan decarboxylase from Ruminococcus gnavus. Therefore, WUR7's metabolism was directed toward indole-based alkaloid biosynthesis by feeding it with L-tryptophan. As expected, its metabolome profile changed dramatically, by triggering the extracellular accumulation of a massive array of metabolites unexpressed in the absence of tryptophan. Untargeted LC-MS/MS coupled with molecular networking, followed along with chemoinformatic dereplication, allowed for the annotation of 10 indole alkaloids, belonging to β-carboline, bisindole, and monoindole classes, alongside several unknown alkaloids. These findings guided us to the isolation of a new natural bisindole alkaloid 8,9-dihydrocoscinamide B (1), as the first alkaloid from the genus Lacinutrix, whose structure was elucidated on the basis of extensive 1D and 2D NMR and HR-ESIMS experiments. This comprehensive strategy allowed us to unlock the previously unexploited metabolome of L. shetlandiensis sp. nov. WUR7.
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  • 10
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    Respiration rate scales inversely with sinking speed of settling marine aggregates (2023)
    Public Library of Science
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    Publication Date: 2024-02-07
    Description: Sinking marine aggregates have been studied for a long time to understand their role in carbon sequestration. Traditionally, sinking speed and respiration rates have been treated as independent variables, but two recent papers suggest that there is a connection albeit in contrasting directions. Here we collected recently formed (〈2 days old) aggregates from sediment traps mounted underneath mesocosms during two different experiments. The mesocosms were moored off Gran Canaria, Spain (~ 27.9 N; 15.4 E) in a coastal, sub-tropical and oligotrophic ecosystem. We determined the respiration rates of organisms (mainly heterotrophic prokaryotes) attached to aggregates sinking at different velocities. The average respiration rate of fast sinking aggregates (〉100 m d-1) was 0.12 d-1 ± 0.08 d-1 (SD). Slower sinking aggregates (〈50 m d-1) had on average higher (p 〈0.001) and more variable respiration rates (average 0.31 d-1 ± 0.16 d-1, SD). There was evidence that slower sinking aggregates had higher porosity than fast sinking aggregates, and we hypothesize that higher porosity increase the settlement area for bacteria and the respiration rate. These findings provide insights into the efficiency of the biological carbon pump and help resolve the apparent discrepancy in the recent studies of the correlation between respiration and sinking speed. © 2023 Spilling et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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  • 11
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    Were climatic forcings the main driver for mid-holocene changes in settlement dynamics on the Varamin Plain (Central Iranian Plateau)? (2023)
    Public Library of Science
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    Publication Date: 2024-02-07
    Description: Settlement crises in ancient cultures of Western Asia are commonly thought to be caused by climatic events such as severe droughts. However, the insufficient climate proxy situation in this region challenges the inference of clear relationships between climate and settlement dynamics. We investigate the Holocene climatic changes on the Varamin Plain in the context of the climatic history of Western Central Asia by using a transient comprehensive Earth System Model simulation (8 ka BP to pre-industrial), a high-resolution regional snapshot simulation and a synthesis of pollen-based climate reconstructions. In line with the reconstructions, the models reveal only slightly varying mean climatic conditions on the Varamin Plain but indicate substantial changes in seasonality during the Holocene. Increased precipitation during spring, combined with lower temperature and potentially stronger snow accumulation on the upstream Alborz mountains may have led to an increased water supply on the alluvial fan during the vegetation period and thus to more favourable conditions for agricultural production during the Mid-Holocene compared to modern times. According to the model, dry periods on the Central Iranian Plateau are related to particularly weak Westerly winds, fostering the subsidence in the mid-troposphere and hampering precipitation over the region. The model reveals that dry periods have spatially heterogenous manifestations, thus explaining why they do not appear in all proxy records in the wider study region. In fact, the climatic signal may depend on local environmental conditions. The interaction of the topography with the atmospheric circulation leads to additional spatial heterogeneity. Although our results provide several indications for a connection between climate and settlement dynamics, the small overall changes in moisture call into question whether climate is the main driver for settlement discontinuities on the Central Iranian Plateau. To shed further light on this issue, more high-resolution long-term proxy records are needed.
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  • 12
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    Long-term stability in the circumpolar foraging range of a Southern Ocean predator between the eras of whaling and rapid climate change (2023)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance Assessing change in Southern Ocean ecosystems is challenging due to its remoteness. Large-scale datasets that allow comparison between present-day conditions and those prior to large-scale ecosystem disturbances caused by humans (e.g., fishing/whaling) are rare. We infer the contemporary offshore foraging distribution of a marine predator, southern right whales (n = 1,002), using a customized stable isotope-based assignment approach based on biogeochemical models of the Southern Ocean. We then compare the contemporary distributions during the late austral summer and autumn to whaling catch data representing historical distributions during the same seasons. We show remarkable consistency of mid-latitude distribution across four centuries but shifts in foraging grounds in the past 30 y, particularly in the high latitudes that are likely driven by climate-associated alterations in prey availability. Abstract Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis), that forages on copepods and krill from ~30°S to the Antarctic ice edge (〉60°S). We analyzed carbon and nitrogen isotope values of 1,002 skin samples from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude (〉60°S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.
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  • 13
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    Choanoflagellates alongside diverse uncultured predatory protists consume the abundant open-ocean cyanobacterium Prochlorococcus (2023)
    National Academy of Sciences
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    Publication Date: 2024-02-07
    Description: Prochlorococcus is a key member of open-ocean primary producer communities. Despite its importance, little is known about the predators that consume this cyanobacterium and make its biomass available to higher trophic levels. We identify potential predators along a gradient wherein Prochlorococcus abundance increased from near detection limits (coastal California) to 〉200,000 cells mL-1 (subtropical North Pacific Gyre). A replicated RNA-Stable Isotope Probing experiment involving the in situ community, and labeled Prochlorococcus as prey, revealed choanoflagellates as the most active predators of Prochlorococcus, alongside a radiolarian, chrysophytes, dictyochophytes, and specific MAST lineages. These predators were not appropriately highlighted in multiyear conventional 18S rRNA gene amplicon surveys where dinoflagellates and other taxa had highest relative amplicon abundances across the gradient. In identifying direct consumers of Prochlorococcus, we reveal food-web linkages of individual protistan taxa and resolve routes of carbon transfer from the base of marine food webs.
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  • 14
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    Evidence of nitrate-based nighttime atmospheric nucleation driven by marine microorganisms in the South Pacific (2023)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-23
    Description: Significance Oceans represent 70% of our planet’s surface, housing a large spectrum of microorganisms that interact with the above atmosphere. Ocean microorganisms were proposed in the late 80’s to be at the center of a climate feedback loop involving dimethyl sulfide (DMS) that would form aerosols and modify cloud properties (CLAW hypothesis). In the present paper, we report observational evidence from semicontrolled experiments in the South Pacific that nitrate ions, yet hitherto not considered, is a key species involved in aerosol nucleation in the pristine marine atmosphere and which precursors are coemitted with DMS. Our results further indicate that nitrate ion formation would be related to short-term microbial processes, sensitive to environmental stressors, therefore potentially “closing the loop”. Abstract Our understanding of ocean–cloud interactions and their effect on climate lacks insight into a key pathway: do biogenic marine emissions form new particles in the open ocean atmosphere? Using measurements collected in ship-borne air–sea interface tanks deployed in the Southwestern Pacific Ocean, we identified new particle formation (NPF) during nighttime that was related to plankton community composition. We show that nitrate ions are the only species for which abundance could support NPF rates in our semicontrolled experiments. Nitrate ions also prevailed in the natural pristine marine atmosphere and were elevated under higher sub-10 nm particle concentrations. We hypothesize that these nucleation events were fueled by complex, short-term biogeochemical cycling involving the microbial loop. These findings suggest a new perspective with a previously unidentified role of nitrate of marine biogeochemical origin in aerosol nucleation.
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  • 15
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    Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea (2022)
    National Academy of Sciences
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Criswell, K. E., Roberts, L. E., Koo, E. T., Head, J. J., & Gillis, J. A. Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences of the United States of America, 118(51), (2021): e2114563118, https://doi.org/10.1073/pnas.2114563118.
    Description: The axial skeleton of tetrapods is organized into distinct anteroposterior regions of the vertebral column (cervical, trunk, sacral, and caudal), and transitions between these regions are determined by colinear anterior expression boundaries of Hox5/6, -9, -10, and -11 paralogy group genes within embryonic paraxial mesoderm. Fishes, conversely, exhibit little in the way of discrete axial regionalization, and this has led to scenarios of an origin of Hox-mediated axial skeletal complexity with the evolutionary transition to land in tetrapods. Here, combining geometric morphometric analysis of vertebral column morphology with cell lineage tracing of hox gene expression boundaries in developing embryos, we recover evidence of at least five distinct regions in the vertebral skeleton of a cartilaginous fish, the little skate (Leucoraja erinacea). We find that skate embryos exhibit tetrapod-like anteroposterior nesting of hox gene expression in their paraxial mesoderm, and we show that anterior expression boundaries of hox5/6, hox9, hox10, and hox11 paralogy group genes predict regional transitions in the differentiated skate axial skeleton. Our findings suggest that hox-based axial skeletal regionalization did not originate with tetrapods but rather has a much deeper evolutionary history than was previously appreciated.
    Description: This research was funded by a Natural Environment Research Council Grant (to J.J.H., J.A.G., and K.E.C.: NE/S000739/1) and a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377), and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) (to J.A.G.).
    Keywords: Hox genes ; Regionalization ; Chondrichthyan ; Vertebral column
    Repository Name: Woods Hole Open Access Server
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  • 16
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    Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dommain, R., Riedl, S., Olaka, L. A., deMenocal, P., Deino, A. L., Owen, R. B., Muiruri, V., Müller, J., Potts, R., & Strecker, M. R. Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients. Proceedings of the National Academy of Sciences of the United States of America, 119(28),(2022): e2121388119, https://doi.org/10.1073/pnas.2121388119.
    Description: East Africa is a global biodiversity hotspot and exhibits distinct longitudinal diversity gradients from west to east in freshwater fishes and forest mammals. The assembly of this exceptional biodiversity and the drivers behind diversity gradients remain poorly understood, with diversification often studied at local scales and less attention paid to biotic exchange between Afrotropical regions. Here, we reconstruct a river system that existed for several millennia along the now semiarid Kenya Rift Valley during the humid early Holocene and show how this river system influenced postglacial dispersal of fishes and mammals due to its dual role as a dispersal corridor and barrier. Using geomorphological, geochronological, isotopic, and fossil analyses and a synthesis of radiocarbon dates, we find that the overflow of Kenyan rift lakes between 12 and 8 ka before present formed a bidirectional river system consisting of a “Northern River” connected to the Nile Basin and a “Southern River,” a closed basin. The drainage divide between these rivers represented the only viable terrestrial dispersal corridor across the rift. The degree and duration of past hydrological connectivity between adjacent river basins determined spatial diversity gradients for East African fishes. Our reconstruction explains the isolated distribution of Nilotic fish species in modern Kenyan rift lakes, Guineo-Congolian mammal species in forests east of the Kenya Rift, and recent incipient vertebrate speciation and local endemism in this region. Climate-driven rearrangements of drainage networks unrelated to tectonic activity contributed significantly to the assembly of species diversity and modern faunas in the East African biodiversity hotspot.
    Description: R.D. was funded by a Smithsonian Human Origins Postdoctoral Fellowship and by Geo.X—the Research Network for Geosciences in Berlin and Potsdam. Fig. 1 D, E, and G and SI Appendix, Figs. S1 and S3 are based on the TanDEM-X Science DEM granted to L.A.O. and S.R. by the German Aerospace Center (DLR) in 2017. L.A.O. acknowledges the Volkswagen Foundation for funding this study with Grant No. 89369. M.R.S. and S.R. were supported by funds from Potsdam University and the Geothermal Development Company of Kenya, and R.B.O. and V.M. were supported by the Hong Kong General Research Fund. We acknowledge support from the National Museums of Kenya and the Kenya Government permission granted by the Ministry of Sports, Culture and the Arts, and by the National Commission for Science, Technology and Innovation (NACOSTI) Permits P/14/7709/683 (to R.P.) and P/16/11924/11448 (to L.A.O.). This work is a contribution of the Olorgesailie Drilling Project, for which support from the National Museums of Kenya, the Oldonyo Nyokie Group Ranch, the Peter Buck Fund for Human Origins Research (Smithsonian Institution), the William H. Donner Foundation, the Ruth and Vernon Taylor Foundation, Whitney and Betty MacMillan, and the Smithsonian Human Origins Program is gratefully acknowledged. LacCore is acknowledged for support in drilling and core storage.
    Keywords: East Africa ; Biogeography ; Biodiversity ; Hydrological connectivity ; Holocene
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  • 17
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    Automated satellite remote sensing of giant kelp at the Falkland Islands (Islas Malvinas) (2022)
    Public Library of Science
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    Publication Date: 2022-10-14
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Houskeeper, H. F., Rosenthal, I. S., Cavanaugh, K. C., Pawlak, C., Trouille, L., Byrnes, J. E. K., Bell, T. W., & Cavanaugh, K. C. Automated satellite remote sensing of giant kelp at the Falkland Islands (Islas Malvinas). Plos One, 17(1), (2022): e0257933, https://doi.org/10.1371/journal.pone.0257933.
    Description: Giant kelp populations that support productive and diverse coastal ecosystems at temperate and subpolar latitudes of both hemispheres are vulnerable to changing climate conditions as well as direct human impacts. Observations of giant kelp forests are spatially and temporally uneven, with disproportionate coverage in the northern hemisphere, despite the size and comparable density of southern hemisphere kelp forests. Satellite imagery enables the mapping of existing and historical giant kelp populations in understudied regions, but automating the detection of giant kelp using satellite imagery requires approaches that are robust to the optical complexity of the shallow, nearshore environment. We present and compare two approaches for automating the detection of giant kelp in satellite datasets: one based on crowd sourcing of satellite imagery classifications and another based on a decision tree paired with a spectral unmixing algorithm (automated using Google Earth Engine). Both approaches are applied to satellite imagery (Landsat) of the Falkland Islands or Islas Malvinas (FLK), an archipelago in the southern Atlantic Ocean that supports expansive giant kelp ecosystems. The performance of each method is evaluated by comparing the automated classifications with a subset of expert-annotated imagery (8 images spanning the majority of our continuous timeseries, cumulatively covering over 2,700 km of coastline, and including all relevant sensors). Using the remote sensing approaches evaluated herein, we present the first continuous timeseries of giant kelp observations in the FLK region using Landsat imagery spanning over three decades. We do not detect evidence of long-term change in the FLK region, although we observe a recent decline in total canopy area from 2017–2021. Using a nitrate model based on nearby ocean state measurements obtained from ships and incorporating satellite sea surface temperature products, we find that the area of giant kelp forests in the FLK region is positively correlated with the nitrate content observed during the prior year. Our results indicate that giant kelp classifications using citizen science are approximately consistent with classifications based on a state-of-the-art automated spectral approach. Despite differences in accuracy and sensitivity, both approaches find high interannual variability that impedes the detection of potential long-term changes in giant kelp canopy area, although recent canopy area declines are notable and should continue to be monitored carefully.
    Description: This work was funded by the National Aeronautics and Space Administration as part of the Citizen Science for Earth Systems Program (https://earthdata.nasa.gov/esds/competitive-programs/csesp) with grant #80NSSC18M0103 (awarded to JEKB), which also provided salary to HFH, and by the National Science Foundation through the Santa Barbara Coastal Long-Term Environmental Research (https://sbclter.msi.ucsb.edu) program with grants #OCE 0620276 and 1232779. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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  • 18
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    Nutrient availability and senescence spatially structure the dynamics of a foundation species (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bell, T. W., & Siegel, D. A. Nutrient availability and senescence spatially structure the dynamics of a foundation species. Proceedings of the National Academy of Sciences of the United States of America, 119(1), (2021): e2105135118, https://doi.org/10.1073/pnas.2105135118.
    Description: Disentangling the roles of the external environment and internal biotic drivers of plant population dynamics is challenging due to the absence of relevant physiological and abundance information over appropriate space and time scales. Remote observations of giant kelp biomass and photosynthetic pigment concentrations are used to show that spatiotemporal patterns of physiological condition, and thus growth and production, are regulated by different processes depending on the scale of observation. Nutrient supply was linked to regional scale (〉1 km) physiological condition dynamics, and kelp forest stands were more persistent where nutrient levels were consistently high. However, on local scales (〈1 km), internal senescence processes related to canopy age demographics determined patterns of biomass loss across individual kelp forests despite uniform nutrient conditions. Repeat measurements of physiology over continuous spatial fields can provide insights into complex dynamics that are unexplained by the environmental drivers thought to regulate abundance. Emerging remote sensing technologies that provide simultaneous estimates of abundance and physiology can quantify the roles of environmental change and demographics governing plant population dynamics for a wide range of aquatic and terrestrial ecosystems.
    Description: This work was supported by the US NSF (Grants OCE 1232779 and 1831937), by the US Department of Energy (Cooperative Agreement DE-AR0000922), and by NASA (Grant NNX14AR62A) and the NASA Earth and Space Sciences Fellowship program in support of T.W.B.
    Keywords: Physiology ; Population ; Biomass ; Hyperspectral ; Giant kelp
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  • 19
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    Trivalent chromium isotopes in the eastern tropical North Pacific oxygen-deficient zone (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2021. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 118(8), (2021): e1918605118, https://doi.org/10.1073/pnas.1918605118.
    Description: Changes in chromium (Cr) isotope ratios due to fractionation between trivalent [Cr(III)] and hexavalent [Cr(VI)] are being utilized by geologists to infer oxygen conditions in past environments. However, there is little information available on Cr in the modern ocean to ground-truth these inferences. Transformations between the two chromium species are important processes in oceanic Cr cycling. Here we present profiles of hexavalent and trivalent Cr concentrations and stable isotope ratios from the eastern tropical North Pacific (ETNP) oxygen-deficient zone (ODZ) which support theoretical and experimental studies that predict that lighter Cr is preferentially reduced in low-oxygen environments and that residual dissolved Cr becomes heavier due to removal of particle-reactive Cr(III) on sinking particles. The Cr(III) maximum dominantly occurs in the upper portion of the ODZ, implying that microbial activity (dependent on the sinking flux of organic matter) may be the dominant mechanism for this transformation, rather than a simple inorganic chemical conversion between the species depending on the redox potential.
    Description: We thank chief scientist Gabrielle Rocap for accommodating us on cruises Roger Revelle 1804-5 and Kilo Moana 19-20 (sponsored by NSF Grant DEB-1542240 to G. Rocap, A. Devol, R. Kiel, and C. Deutch), Jim Moffett for helping with sampling on these cruises, and Mark Altabet and Frank Stewart for collecting the samples from station 2T on cruise New Horizon 1410. This research was supported by NSF Grant OCE-1736996 (to E.A.B.) and by a fellowship from the Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program in Oceanography.
    Keywords: Chromium isotopes ; Oxygen-deficient zones ; Trace elements ; Trivalent chromium ; Hexavalent ; Chromium
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  • 20
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    Beluga whale (Delphinapterus leucas) acoustic foraging behavior and applications for long term monitoring (2022)
    Public Library of Science
    Details
    Publication Date: 2022-05-27
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Castellote, M., Mooney, A., Andrews, R., Deruiter, S., Lee, W.-J., Ferguson, M., & Wade, P. Beluga whale (Delphinapterus leucas) acoustic foraging behavior and applications for long term monitoring. Plos One, 16(11), (2021): e0260485, https://doi.org/10.1371/journal.pone.0260485.
    Description: Cook Inlet, Alaska, is home to an endangered and declining population of 279 belugas (Delphinapterus leucas). Recovery efforts highlight a paucity of basic ecological knowledge, impeding the correct assessment of threats and the development of recovery actions. In particular, information on diet and foraging habitat is very limited for this population. Passive acoustic monitoring has proven to be an efficient approach to monitor beluga distribution and seasonal occurrence. Identifying acoustic foraging behavior could help address the current gap in information on diet and foraging habitat. To address this conservation challenge, eight belugas from a comparative, healthy population in Bristol Bay, Alaska, were instrumented with a multi-sensor tag (DTAG), a satellite tag, and a stomach temperature transmitter in August 2014 and May 2016. DTAG deployments provided 129.6 hours of data including foraging and social behavioral states. A total of 68 echolocation click trains ending in terminal buzzes were identified during successful prey chasing and capture, as well as during social interactions. Of these, 37 click trains were successfully processed to measure inter-click intervals (ICI) and ICI trend in their buzzing section. Terminal buzzes with short ICI (minimum ICI 〈8.98 ms) and consistently decreasing ICI trend (ICI increment range 〈1.49 ms) were exclusively associated with feeding behavior. This dual metric was applied to acoustic data from one acoustic mooring within the Cook Inlet beluga critical habitat as an example of the application of detecting feeding in long-term passive acoustic monitoring data. This approach allowed description of the relationship between beluga presence, feeding occurrence, and the timing of spawning runs by different species of anadromous fish. Results reflected a clear preference for the Susitna River delta during eulachon (Thaleichthys pacificus), Chinook (Oncorhynchus tshawytscha), pink (Oncorhynchus gorbuscha), and coho (Oncorhynchus kisutch) salmon spawning run periods, with increased feeding occurrence at the peak of the Chinook and pink salmon runs.
    Description: Project funding was provided by Georgia Aquarium, the Marine Mammal Laboratory of the Alaska Fisheries Science Center (MML/AFSC). Tagging was funded by the NOAA Fisheries Office of Science and Technology’s Ocean Acoustics Program. DTAG data analysis was funded by the U.S. Marine Mammal Commission grant #16-239. Funding for collecting and analyzing Cook Inlet beluga acoustic data in Susitna Delta was provided by the National Marine Fisheries Service Section 6 Office to the Alaska Department of Fish and Game. This publication is partially funded by the Cooperative Institute for Climate, Ocean, and Ecosystem Studies (CICOES), University of Washington, under NOAA Cooperative Agreement NA15OAR4320063, Contribution No. 2021-1145.
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  • 21
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    Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-08-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Womersley, F. C., Humphries, N. E., Queiroz, N., Vedor, M., da Costa, I., Furtado, M., Tyminski, J. P., Abrantes, K., Araujo, G., Bach, S. S., Barnett, A., Berumen, M. L., Bessudo Lion, S., Braun, C. D., Clingham, E., Cochran, J. E. M., de la Parra, R., Diamant, S., Dove, A. D. M., Dudgeon, C. L., Erdmann, M. V., Espinoza, E., Fitzpatrick, R., González Cano, J., Green, J. R., Guzman, H. M., Hardenstine, R., Hasan, A., Hazin, F. H. V., Hearn, A. R., Hueter, R. E., Jaidah, M. Y., Labaja, J., Ladinol, F., Macena, B. C. L., Morris Jr., J. J., Norman, B. M., Peñaherrera-Palmav, C., Pierce, S. J., Quintero, L. M., Ramırez-Macías, D., Reynolds, S. D., Richardson, A. J., Robinson, D. P., Rohner, C. A., Rowat, D. R. L., Sheaves, M., Shivji, M. S., Sianipar, A. B., Skomal, G. B., Soler, G., Syakurachman, I., Thorrold, S. R., Webb, D. H., Wetherbee, B. M., White, T. D., Clavelle, T., Kroodsma, D. A., Thums, M., Ferreira, L. C., Meekan, M. G., Arrowsmith, L. M., Lester, E. K., Meyers, M. M., Peel, L. R., Sequeira, A. M. M., Eguıluz, V. M., Duarte, C. M., & Sims, D. W. Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark. Proceedings of the National Academy of Sciences of the United States of America, 119(20), (2022): e2117440119, https://doi.org/10.1073/pnas.2117440119.
    Description: Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (〉300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.
    Description: Funding for data analysis was provided by the UK Natural Environment Research Council (NERC) through a University of Southampton INSPIRE DTP PhD Studentship to F.C.W. Additional funding for data analysis was provided by NERC Discovery Science (NE/R00997/X/1) and the European Research Council (ERC-AdG-2019 883583 OCEAN DEOXYFISH) to D.W.S., Fundação para a Ciência e a Tecnologia (FCT) under PTDC/BIA/28855/2017 and COMPETE POCI-01–0145-FEDER-028855, and MARINFO–NORTE-01–0145-FEDER-000031 (funded by Norte Portugal Regional Operational Program [NORTE2020] under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund–ERDF) to N.Q. FCT also supported N.Q. (CEECIND/02857/2018) and M.V. (PTDC/BIA-COM/28855/2017). D.W.S. was supported by a Marine Biological Association Senior Research Fellowship. All tagging procedures were approved by institutional ethical review bodies and complied with all relevant ethical regulations in the jurisdictions in which they were performed. Details for individual research teams are given in SI Appendix, section 8. Full acknowledgments for tagging and field research are given in SI Appendix, section 7. This research is part of the Global Shark Movement Project (https://www.globalsharkmovement.org).
    Keywords: ship strike ; marine megafauna ; conservation ; movement ecology ; human impact
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    Environmental factors shaping bacterial, archaeal and fungal community structure in hydrothermal sediments of Guaymas Basin, Gulf of California (2022)
    Public Library of Science
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    Publication Date: 2022-06-06
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ramirez, G. A., Mara, P., Sehein, T., Wegener, G., Chambers, C. R., Joye, S. B., Peterson, R. N., Philippe, A., Burgaud, G., Edgcomb, V. P., & Teske, A. P. Environmental factors shaping bacterial, archaeal and fungal community structure in hydrothermal sediments of Guaymas Basin, Gulf of California. Plos One, 16(9), (2021): e0256321, https://doi.org/10.1371/journal.pone.0256321.
    Description: The flanking regions of Guaymas Basin, a young marginal rift basin located in the Gulf of California, are covered with thick sediment layers that are hydrothermally altered due to magmatic intrusions. To explore environmental controls on microbial community structure in this complex environment, we analyzed site- and depth-related patterns of microbial community composition (bacteria, archaea, and fungi) in hydrothermally influenced sediments with different thermal conditions, geochemical regimes, and extent of microbial mats. We compared communities in hot hydrothermal sediments (75-100°C at ~40 cm depth) covered by orange-pigmented Beggiatoaceae mats in the Cathedral Hill area, temperate sediments (25-30°C at ~40 cm depth) covered by yellow sulfur precipitates and filamentous sulfur oxidizers at the Aceto Balsamico location, hot sediments (〉115°C at ~40 cm depth) with orange-pigmented mats surrounded by yellow and white mats at the Marker 14 location, and background, non-hydrothermal sediments (3.8°C at ~45 cm depth) overlain with ambient seawater. Whereas bacterial and archaeal communities are clearly structured by site-specific in-situ thermal gradients and geochemical conditions, fungal communities are generally structured by sediment depth. Unexpectedly, chytrid sequence biosignatures are ubiquitous in surficial sediments whereas deeper sediments contain diverse yeasts and filamentous fungi. In correlation analyses across different sites and sediment depths, fungal phylotypes correlate to each other to a much greater degree than Bacteria and Archaea do to each other or to fungi, further substantiating that site-specific in-situ thermal gradients and geochemical conditions that control bacteria and archaea do not extend to fungi.
    Description: This project was supported by collaborative NSF Biological Oceanography grants 1829903 and 1829680 “Hydrothermal fungi in the Guaymas Basin Hydrocarbon Ecosystem” to V. Edgcomb and A. Teske, respectively. Postdoc G. Ramirez and Graduate student C.R. Chambers were supported by NSF Molecular and Cellular Biology grant 1817381 “Next Generation Physiology” and by ARPA-E grant “Mining the Deep Sea for Microbial Ethano- and Propanogenesis”. Sampling in Guaymas Basin was supported by collaborative NSF Biological Oceanography grants 1357238 and 1357360 “Collaborative Research: Microbial carbon cycling and its interaction with sulfur and nitrogen transformations in Guaymas Basin hydrothermal sediments” to A. Teske and S. B. Joye, respectively.
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  • 23
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    Phosphonate production by marine microbes: exploring new sources and potential function (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-06-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Acker, M., Hogle, S. L., Berube, P. M., Hackl, T., Coe, A., Stepanauskas, R., Chisholm, S. W., & Repeta, D. J. Phosphonate production by marine microbes: exploring new sources and potential function. Proceedings of the National Academy of Sciences of the United States of America, 119(11), (2022): e2113386119, https://doi.org/10.1073/pnas.2113386119.
    Description: Phosphonates are organophosphorus metabolites with a characteristic C-P bond. They are ubiquitous in the marine environment, their degradation broadly supports ecosystem productivity, and they are key components of the marine phosphorus (P) cycle. However, the microbial producers that sustain the large oceanic inventory of phosphonates as well as the physiological and ecological roles of phosphonates are enigmatic. Here, we show that phosphonate synthesis genes are rare but widely distributed among diverse bacteria and archaea, including Prochlorococcus and SAR11, the two major groups of bacteria in the ocean. In addition, we show that Prochlorococcus can allocate over 40% of its total cellular P-quota toward phosphonate production. However, we find no evidence that Prochlorococcus uses phosphonates for surplus P storage, and nearly all producer genomes lack the genes necessary to degrade and assimilate phosphonates. Instead, we postulate that phosphonates are associated with cell-surface glycoproteins, suggesting that phosphonates mediate ecological interactions between the cell and its surrounding environment. Our findings indicate that the oligotrophic surface ocean phosphonate pool is sustained by a relatively small fraction of the bacterioplankton cells allocating a significant portion of their P quotas toward secondary metabolism and away from growth and reproduction.
    Description: This work was supported in part by grants from the NSF (OCE-1153588 and DBI-0424599 to S.W.C.; OCE-1335810 and OIA-1826734 to R.S.; and OCE-1634080 to D.J.R.), the Gordon and Betty Moore Foundation (no. 6000 to D.J.R.), and the Simons Foundation (Life Sciences Project Award IDs 337262 and 647135 to S.W.C.; 510023 to R.S.; and Simons Collaboration on Ocean Processes and Ecology [SCOPE] Award ID 329108 to S.W.C. and D.J.R.).
    Keywords: phosphonate ; Prochlorococcus ; marine ; biogeochemistry ; phosphorus
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  • 24
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    Biologging of emperor penguins-attachment techniques and associated deployment performance (2022)
    Public Library of Science
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    Publication Date: 2022-12-06
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Houstin, A., Zitterbart, D., Winterl, A., Richter, S., Planas-Bielsa, V., Chevallier, D., Ancel, A., Fournier, J., Fabry, B., & Le Bohec, C. Biologging of emperor penguins-attachment techniques and associated deployment performance. PLoS One, 17(8), (2022): e0265849, https://doi.org/10.1371/journal.pone.0265849.
    Description: An increasing number of marine animals are equipped with biologgers, to study their physiology, behaviour and ecology, often for conservation purposes. To minimise the impacts of biologgers on the animals’ welfare, the Refinement principle from the Three Rs framework (Replacement, Reduction, Refinement) urges to continuously test and evaluate new and updated biologging protocols. Here, we propose alternative and promising techniques for emperor penguin (Aptenodytes forsteri) capture and on-site logger deployment that aim to mitigate the potential negative impacts of logger deployment on these birds. We equipped adult emperor penguins for short-term (GPS, Time-Depth Recorder (TDR)) and long-term (i.e. planned for one year) deployments (ARGOS platforms, TDR), as well as juvenile emperor penguins for long-term deployments (ARGOS platforms) in the Weddell Sea area where they had not yet been studied. We describe and qualitatively evaluate our protocols for the attachment of biologgers on-site at the colony, the capture of the animals and the recovery of the devices after deployment. We report unprecedented recaptures of long-term equipped adult emperor penguins (50% of equipped individuals recaptured after 290 days). Our data demonstrate that the traditional technique of long-term attachment by gluing the biologgers directly to the back feathers causes excessive feather breakage and the loss of the devices after a few months. We therefore propose an alternative method of attachment for back-mounted devices. This technique led to successful year-round deployments on 37.5% of the equipped juveniles. Finally, we also disclose the first deployments of leg-bracelet mounted TDRs on emperor penguins. Our findings highlight the importance of monitoring potential impacts of biologger deployments on the animals and the need to continue to improve methods to minimize disturbance and enhance performance and results.
    Description: This study was funded by the Centre Scientifique de Monaco with additional support from the LIA-647 and RTPI-NUTRESS (CSM/CNRS¬-University of Strasbourg), by The Penzance Endowed Fund and The Grayce B. Kerr Fund in Support of Assistant Scientists and by the Deutsche Forschungsgemeinschaft (DFG) grants ZI1525/3-1 in the framework of the priority program “Antarctic research with comparative investigations in Arctic ice areas”. Logistics and field efforts were supported by the Alfred Wegener Institute (AWI) within the framework of the program MARE.
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  • 25
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    The Earth BioGenome Project 2020: starting the clock (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, Mark L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S-M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. Thomas P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J-H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O’Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. The Earth BioGenome Project 2020: starting the clock. Proceedings of the National Academy of Sciences of the United States of America, 119(4), (2022): e2115635118, https://doi.org/10.1073/pnas.2115635118.
    Description: November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP’s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP.
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  • 26
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    Tracking calcium dynamics from individual neurons in behaving animals (2022)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lagache, T., Hanson, A., Perez-Ortega, J. E., Fairhall, A., & Yuste, R. Tracking calcium dynamics from individual neurons in behaving animals. Plos Computational Biology, 17(10), (2021): e1009432, https://doi.org/10.1371/journal.pcbi.1009432.
    Description: Measuring the activity of neuronal populations with calcium imaging can capture emergent functional properties of neuronal circuits with single cell resolution. However, the motion of freely behaving animals, together with the intermittent detectability of calcium sensors, can hinder automatic monitoring of neuronal activity and their subsequent functional characterization. We report the development and open-source implementation of a multi-step cellular tracking algorithm (Elastic Motion Correction and Concatenation or EMC2) that compensates for the intermittent disappearance of moving neurons by integrating local deformation information from detectable neurons. We demonstrate the accuracy and versatility of our algorithm using calcium imaging data from two-photon volumetric microscopy in visual cortex of awake mice, and from confocal microscopy in behaving Hydra, which experiences major body deformation during its contractions. We quantify the performance of our algorithm using ground truth manual tracking of neurons, along with synthetic time-lapse sequences, covering a wide range of particle motions and detectability parameters. As a demonstration of the utility of the algorithm, we monitor for several days calcium activity of the same neurons in layer 2/3 of mouse visual cortex in vivo, finding significant turnover within the active neurons across days, with only few neurons that remained active across days. Also, combining automatic tracking of single neuron activity with statistical clustering, we characterize and map neuronal ensembles in behaving Hydra, finding three major non-overlapping ensembles of neurons (CB, RP1 and RP2) whose activity correlates with contractions and elongations. Our results show that the EMC2 algorithm can be used as a robust and versatile platform for neuronal tracking in behaving animals.
    Description: R.Y. was supported by the NSF (CRCNS 1822550), the NEI (R01EY011787), the NIMH (R01MH115900), and Vannevar Bush Faculty Award (ONR N000142012828). T.L. was supported by the Fondation pour la Recherche Médicale (https://www.frm.org/) and the Philippe Foundation (https://www.philippefoundation.org/). A.H. was supported by the NIMH (T32MH018870). J.P.-O. was supported by the CONACYT (CVU365863). ALF was supported by NSF (CRCNS 1822550), the Simons Foundation Collaboration for the Global Brain (542975SPI) and the Weill NeuroHub (https://www.weillneurohub.org/).
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    High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bekaert, D. V., Gazel, E., Turner, S., Behn, M. D., de Moor, J. M., Zahirovic, S., Manea, V. C., Hoernle, K., Fischer, T. P., Hammerstrom, A., Seltzer, A. M., Kulongoski, J. T., Patel, B. S., Schrenk, M. O., Halldórsson, S. A., Nakagawa, M., Ramírez, C. J., Krantz, J. A., Yücel, M., Ballentine, C. J., Giovannelli, D., Lloyd, K. G., Barry, P. H. High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume. Proceedings of the National Academy of Sciences of the United States of America, 118(47), (2021): e2110997118, https://doi.org/10.1073/pnas.2110997118.
    Description: It is well established that mantle plumes are the main conduits for upwelling geochemically enriched material from Earth's deep interior. The fashion and extent to which lateral flow processes at shallow depths may disperse enriched mantle material far (〉1,000 km) from vertical plume conduits, however, remain poorly constrained. Here, we report He and C isotope data from 65 hydrothermal fluids from the southern Central America Margin (CAM) which reveal strikingly high 3He/4He (up to 8.9RA) in low-temperature (≤50 °C) geothermal springs of central Panama that are not associated with active volcanism. Following radiogenic correction, these data imply a mantle source 3He/4He 〉10.3RA (and potentially up to 26RA, similar to Galápagos hotspot lavas) markedly greater than the upper mantle range (8 ± 1RA). Lava geochemistry (Pb isotopes, Nb/U, and Ce/Pb) and geophysical constraints show that high 3He/4He values in central Panama are likely derived from the infiltration of a Galápagos plume–like mantle through a slab window that opened ∼8 Mya. Two potential transport mechanisms can explain the connection between the Galápagos plume and the slab window: 1) sublithospheric transport of Galápagos plume material channeled by lithosphere thinning along the Panama Fracture Zone or 2) active upwelling of Galápagos plume material blown by a “mantle wind” toward the CAM. We present a model of global mantle flow that supports the second mechanism, whereby most of the eastward transport of Galápagos plume material occurs in the shallow asthenosphere. These findings underscore the potential for lateral mantle flow to transport mantle geochemical heterogeneities thousands of kilometers away from plume conduits.
    Description: This work was principally supported by Grant G-2016-7206 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to P.H.B. We also acknowledge the NSF awards (1144559, 1923915, and 2015789) to P.H.B., which partially supported this work. S.Z. was supported by the Australian Research Council Grant DE210100084 and a University of Sydney Robinson Fellowship. D.G. was partially supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program Grant Agreement No. 948972—COEVOLVE—ERC-2020-STG. This study was also supported in part by NSF award No. EAR 1826673 to E.G. Folkmar Hauff is acknowledged for contributing to the analysis of the La Providencia samples at GEOMAR.
    Keywords: Helium ; Mantle plume ; Slab window ; Mantle flow ; Geochemistry
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    The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Orvis, J., Albertin, C., Shrestha, P., Chen, S., Zheng, M., Rodriguez, C., Tallon, L., Mahurkar, A., Zimin, A., Kim, M., Liu, K., Kandel, E., Fraser, C., Sossin, W., & Abrams, T. The evolution of synaptic and cognitive capacity: insights from the nervous system transcriptome of Aplysia. Proceedings of the National Academy of Sciences of the United States of America, 119(28), (2022): e2122301119, https://doi.org/10.1073/pnas.2122301119.
    Description: The gastropod mollusk Aplysia is an important model for cellular and molecular neurobiological studies, particularly for investigations of molecular mechanisms of learning and memory. We developed an optimized assembly pipeline to generate an improved Aplysia nervous system transcriptome. This improved transcriptome enabled us to explore the evolution of cognitive capacity at the molecular level. Were there evolutionary expansions of neuronal genes between this relatively simple gastropod Aplysia (20,000 neurons) and Octopus (500 million neurons), the invertebrate with the most elaborate neuronal circuitry and greatest behavioral complexity? Are the tremendous advances in cognitive power in vertebrates explained by expansion of the synaptic proteome that resulted from multiple rounds of whole genome duplication in this clade? Overall, the complement of genes linked to neuronal function is similar between Octopus and Aplysia. As expected, a number of synaptic scaffold proteins have more isoforms in humans than in Aplysia or Octopus. However, several scaffold families present in mollusks and other protostomes are absent in vertebrates, including the Fifes, Lev10s, SOLs, and a NETO family. Thus, whereas vertebrates have more scaffold isoforms from select families, invertebrates have additional scaffold protein families not found in vertebrates. This analysis provides insights into the evolution of the synaptic proteome. Both synaptic proteins and synaptic plasticity evolved gradually, yet the last deuterostome-protostome common ancestor already possessed an elaborate suite of genes associated with synaptic function, and critical for synaptic plasticity.
    Description: This work was supported by NSF EAGER Award IOS-1255695 and NIH grant R01 MH 55880 grant to T.W.A.; by a Natural Sciences and Engineering Research Council of Canada Discovery grant and Canadian Institutes of Health Research project grant 340328 to W.S.; by funding from the HHMI to E.R.K.; and by a Hibbitt Early Career Fellowship to C.A. W.S. is James McGill Professor at McGill University.
    Keywords: Neural plasticity ; Synaptic plasticity ; Evolution ; Neuromodulation ; Aplysia
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    Discovery of active off-axis hydrothermal vents at 9° 54’N East Pacific Rise (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McDermott, J. M., Parnell-Turner, R., Barreyre, T., Herrera, S., Downing, C. C., Pittoors, N. C., Pehr, K., Vohsen, S. A., Dowd, W. S., Wu, J.-N., Marjanović, M., & Fornari, D. J. Discovery of active off-axis hydrothermal vents at 9° 54’N East Pacific Rise. Proceedings of the National Academy of Sciences of the United States of America, 119(30), (2022): e2205602119, https://doi.org/10.1073/pnas.2205602119.
    Description: Comprehensive knowledge of the distribution of active hydrothermal vent fields along midocean ridges is essential to understanding global chemical and heat fluxes and endemic faunal distributions. However, current knowledge is biased by a historical preference for on-axis surveys. A scarcity of high-resolution bathymetric surveys in off-axis regions limits vent identification, which implies that the number of vents may be underestimated. Here, we present the discovery of an active, high-temperature, off-axis hydrothermal field on a fast-spreading ridge. The vent field is located 750 m east of the East Pacific Rise axis and ∼7 km north of on-axis vents at 9° 50′N, which are situated in a 50- to 100-m-wide trough. This site is currently the largest vent field known on the East Pacific Rise between 9 and 10° N. Its proximity to a normal fault suggests that hydrothermal fluid pathways are tectonically controlled. Geochemical evidence reveals deep fluid circulation to depths only 160 m above the axial magma lens. Relative to on-axis vents at 9° 50′N, these off-axis fluids attain higher temperatures and pressures. This tectonically controlled vent field may therefore exhibit greater stability in fluid composition, in contrast to more dynamic, dike-controlled, on-axis vents. The location of this site indicates that high-temperature convective circulation cells extend to greater distances off axis than previously realized. Thorough high-resolution mapping is necessary to understand the distribution, frequency, and physical controls on active off-axis vent fields so that their contribution to global heat and chemical fluxes and role in metacommunity dynamics can be determined.
    Description: Financial support was provided by the NSF Awards OCE-1949938 (to J.M.M.), OCE-1948936 (to R.P.-T.), and OCE-1949485 (to D.J.F. and T.B.).
    Keywords: Hydrothermal activity ; Midocean ridge ; Ocean chemistry ; Chemosynthetic ecosystem ; East Pacific Rise
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    Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows (2022)
    National Academy of Sciences
    Details
    Publication Date: 2023-03-08
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Schorn, S., Ahmerkamp, S., Bullock, E., Weber, M., Lott, C., Liebeke, M., Lavik, G., Kuypers, M. M. M., Graf, J. S., & Milucka, J. Diverse methylotrophic methanogenic archaea cause high methane emissions from seagrass meadows. Proceedings of the National Academy of Sciences of the United States of America, 119(9), (2022): e2106628119, https://doi.org/10.1073/pnas.2106628119.
    Description: Marine coastlines colonized by seagrasses are a net source of methane to the atmosphere. However, methane emissions from these environments are still poorly constrained, and the underlying processes and responsible microorganisms remain largely unknown. Here, we investigated methane turnover in seagrass meadows of Posidonia oceanica in the Mediterranean Sea. The underlying sediments exhibited median net fluxes of methane into the water column of ca. 106 µmol CH4 ⋅ m−2 ⋅ d−1. Our data show that this methane production was sustained by methylated compounds produced by the plant, rather than by fermentation of buried organic carbon. Interestingly, methane production was maintained long after the living plant died off, likely due to the persistence of methylated compounds, such as choline, betaines, and dimethylsulfoniopropionate, in detached plant leaves and rhizomes. We recovered multiple mcrA gene sequences, encoding for methyl-coenzyme M reductase (Mcr), the key methanogenic enzyme, from the seagrass sediments. Most retrieved mcrA gene sequences were affiliated with a clade of divergent Mcr and belonged to the uncultured Candidatus Helarchaeota of the Asgard superphylum, suggesting a possible involvement of these divergent Mcr in methane metabolism. Taken together, our findings identify the mechanisms controlling methane emissions from these important blue carbon ecosystems.
    Description: This project was funded by theMax Planck Society.
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    Physical mechanisms of the linear stabilization of convection by rotation (2022)
    American Physical Society
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    Publication Date: 2023-01-04
    Description: Despite the well-known limitations of linear stability theory in describing nonlinear and turbulent flows, it has been found to accurately capture the transitions between certain nonlinear flow behavior. Specifically, the transition in heat flux scaling in rotating convective flows can be well predicted by applying a linear stability analysis to simple profiles of a convective boundary layer. This fact motivates the present study of the linear mechanisms involved in the stability properties of simple convective setups subject to rotation. We look at an idealized two-layer setup and gradually add complexity by including rotation, a bounded domain, and viscosity. The two-layer setup has the advantage of allowing for the use of wave interaction theory, traditionally applied to understand stratified and homogeneous shear flow instabilities, in order to quantify the various physical mechanisms leading to the growth of convective instabilities. We quantitatively show that the physical mechanisms involved in the stabilization of convection by rotation take two different forms acting within the stratified interfacial region, and in the homogeneous mixed layers. The latter of these we associate with the tendency of a rotating flow to develop Taylor columns (TCs). This TC mechanism can lead to both a stabilization or destabilization of the instability and varies depending on the parameters of the problem. A simple criterion is found for classifying the influence of these physical mechanisms.
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    Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria (2022)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance A substantial component of the global nitrogen cycle is the production of biologically inaccessible dinitrogen attributed to anaerobic denitrification by prokaryotes. Recent evidence identified a eukaryote, foraminifera, as new key players in this “loss” of bioavailable nitrogen. The evolution of denitrification in eukaryotes is a rare event, and the genetic mechanisms of the denitrification pathway in foraminifera are just starting to be elucidated. We present large-scale sequencing analyses of 10 denitrifying foraminiferal species, which reveals the high conservation of the foraminiferal denitrification pathway. We further find evidence for a complementation of denitrification by the foraminiferal microbiome. Together, these findings provide insights into the early evolution of a previously overlooked component in the marine nitrogen cycle. Abstract: Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.
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    Living apart together: Long-term coexistence of Baltic cod stocks associated with depth-specific habitat use (2022)
    Public Library of Science
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    Publication Date: 2024-02-07
    Description: Coexistence of fish populations (= stocks) of the same species is a common phenomenon. In the Baltic Sea, two genetically divergent stocks of Atlantic cod (Gadus morhua), Western Baltic cod (WBC) and Eastern Baltic cod (EBC), coexist in the Arkona Sea. Although the relative proportions of WBC and EBC in this area are considered in the current stock assessments, the mixing dynamics and ecological mechanisms underlying coexistence are not well understood. In this study, a genetically validated otolith shape analysis was used to develop the most comprehensive time series of annual stock mixing data (1977–2019) for WBC and EBC. Spatio-temporal mixing analysis confirmed that the two stocks coexist in the Arkona Sea, albeit with fluctuating mixing proportions over the 43-year observation period. Depth-stratified analysis revealed a strong correlation between capture depth and stock mixing patterns, with high proportions of WBC in shallower waters (48–61% in 〈20m) and increasing proportions of EBC in deeper waters (50–86% in 40-70m). Consistent depth-specific mixing patterns indicate stable differences in depth distribution and habitat use of WBC and EBC that may thus underlie the long-term coexistence of the two stocks in the Arkona Sea. These differences were also reflected in significantly different proportions of WBC and EBC in fisheries applying passive gears in shallower waters (more WBC) and active gears in deeper waters (more EBC). This highlights the potential for fishing gear-specific exploitation of different stocks, and calls for stronger consideration of capture depth and gear type in stock assessments. This novel evidence provides the basis for improved approaches to research, monitoring and management of Baltic cod stocks.
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    Rapid radiation in a highly diverse marine environment (2022)
    National Academy of Sciences
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    Publication Date: 2024-02-07
    Description: Significance: Adaptive radiation, the evolutionary process whereby a lineage diversifies over a short period of time, often occurs in geographically isolated or newly formed habitats where colonizing species encounter unoccupied niches and reduced selective pressures. Rapid radiations may also occur in diverse and complex environments, but these cases are less well documented. Here, we show that the hamlets, a group of Caribbean reef fishes, radiated within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. Genomic analysis suggests that color pattern diversity is generated by different combinations of alleles at a few genes with large effect. Such a modular genomic architecture of diversification is emerging as a common denominator to a variety of radiations. Abstract: Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth’s diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.
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    Impact of paleoclimate on present and future evolution of the Greenland Ice Sheet (2022)
    Public Library of Science
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    Publication Date: 2024-02-07
    Description: Using transient climate forcing based on simulations from the Alfred Wegener Institute Earth System Model (AWI-ESM), we simulate the evolution of the Greenland Ice Sheet (GrIS) from the last interglacial (125 ka, kiloyear before present) to 2100 AD with the Parallel Ice Sheet Model (PISM). The impact of paleoclimate, especially Holocene climate, on the present and future evolution of the GrIS is explored. Our simulations of the past show close agreement with reconstructions with respect to the recent timing of the peaks in ice volume and the climate of Greenland. The maximum and minimum ice volume at around 18–17 ka and 6–5 ka lag the respective extremes in climate by several thousand years, implying that the ice volume response of the GrIS strongly lags climatic changes. Given that Greenland’s climate was getting colder from the Holocene Thermal Maximum (i.e., 8 ka) to the Pre-Industrial era, our simulation implies that the GrIS experienced growth from the mid-Holocene to the industrial era. Due to this background trend, the GrIS still gains mass until the second half of the 20th century, even though anthropogenic warming begins around 1850 AD. This is also in agreement with observational evidence showing mass loss of the GrIS does not begin earlier than the late 20th century. Our results highlight that the present evolution of the GrIS is not only controlled by the recent climate changes, but is also affected by paleoclimate, especially the relatively warm Holocene climate. We propose that the GrIS was not in equilibrium throughout the entire Holocene and that the slow response to Holocene climate needs to be represented in ice sheet simulations in order to predict ice mass loss, and therefore sea level rise, accurately.
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    Experimental evolution reveals the synergistic genomic mechanisms of adaptation to ocean warming and acidification in a marine copepod (2022)
    National Academy of Sciences
    Details
    Publication Date: 2024-02-07
    Description: Significance Resilience to global change will require adaptation to multiple concurrent environmental changes. However, it is unclear if adaptations to multiple stressors can be predicted from the sum of single-stressor adaptation. To answer this question, we experimentally evolved a marine copepod to warming, acidification, and their combination, finding that copepods were able to adapt to all conditions over 25 generations. Warming was a much stronger selective pressure than acidification alone and under multiple-stressor conditions. Nevertheless, the multiple-stressor response to selection was synergistic and unique from either single stressor. Thus, adaptation to single stressors may not reveal adaptive potential or mechanisms of adaptation under multiple stressors, demonstrating the complexity of predicting adaptive responses under multifaceted environmental change. Abstract Metazoan adaptation to global change relies on selection of standing genetic variation. Determining the extent to which this variation exists in natural populations, particularly for responses to simultaneous stressors, is essential to make accurate predictions for persistence in future conditions. Here, we identified the genetic variation enabling the copepod Acartia tonsa to adapt to experimental ocean warming, acidification, and combined ocean warming and acidification (OWA) over 25 generations of continual selection. Replicate populations showed a consistent polygenic response to each condition, targeting an array of adaptive mechanisms including cellular homeostasis, development, and stress response. We used a genome-wide covariance approach to partition the allelic changes into three categories: selection, drift and replicate-specific selection, and laboratory adaptation responses. The majority of allele frequency change in warming (57%) and OWA (63%) was driven by shared selection pressures across replicates, but this effect was weaker under acidification alone (20%). OWA and warming shared 37% of their response to selection but OWA and acidification shared just 1%, indicating that warming is the dominant driver of selection in OWA. Despite the dominance of warming, the interaction with acidification was still critical as the OWA selection response was highly synergistic with 47% of the allelic selection response unique from either individual treatment. These results disentangle how genomic targets of selection differ between single and multiple stressors and demonstrate the complexity that nonadditive multiple stressors will contribute to predictions of adaptation to complex environmental shifts caused by global change.
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    Modes of Pangean lake level cyclicity driven by astronomical climate pacing modulated by continental position and p CO2 (2022)
    National Academy of Sciences
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    Publication Date: 2024-05-22
    Description: Orbital cyclicity is a fundamental pacemaker of Earth’s climate system. The Newark–Hartford Basin (NHB) lake sediment record of eastern North America contains compelling geologic expressions of this cyclicity, reflecting variations of climatic conditions in tropical Pangea during the Late Triassic and earliest Jurassic (~233 to 199 Ma). Climate modeling enables a deeper mechanistic understanding of Earth system modulation during this unique greenhouse and supercontinent period. We link major features of the NHB record to the combined climatic effects of orbital forcing, paleogeographic changes, and atmospheric p CO 2 variations. An ensemble of transient, orbitally driven climate simulations is assessed for nine time slices, three atmospheric p CO 2 values, and two paleogeographic reconstructions. Climatic transitions from tropical humid to more seasonal and ultimately semiarid are associated with tectonic drift of the NHB from ~ 5 ° N to 20 ° N . The modeled orbital modulation of the precipitation–evaporation balance is most pronounced during the 220 to 200 Ma interval, whereas it is limited by weak seasonality and increasing aridity before and after this interval. Lower p CO 2 at around 205 Ma contributes to drier climates and could have led to the observed damping of sediment cyclicity. Eccentricity-modulated precession dominates the orbitally driven climate response in the NHB region. High obliquity further amplifies summer precipitation through the seasonal shifts in the tropical rainfall belt. Regions with other proxy records are also assessed, providing guidance toward an integrated picture of global astronomical climate forcing in the Late Triassic and ultimately of other periods in Earth history.
    Type: Article , PeerReviewed
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    Neuromechanical wave resonance in jellyfish swimming (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-27
    Description: Author Posting. © National Academy of Sciences, 2021. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 118(11), (2021): e2020025118, https://doi.org/10.1073/pnas.2020025118.
    Description: For organisms to have robust locomotion, their neuromuscular organization must adapt to constantly changing environments. In jellyfish, swimming robustness emerges when marginal pacemakers fire action potentials throughout the bell’s motor nerve net, which signals the musculature to contract. The speed of the muscle activation wave is dictated by the passage times of the action potentials. However, passive elastic material properties also influence the emergent kinematics, with time scales independent of neuromuscular organization. In this multimodal study, we examine the interplay between these two time scales during turning. A three-dimensional computational fluid–structure interaction model of a jellyfish was developed to determine the resulting emergent kinematics, using bidirectional muscular activation waves to actuate the bell rim. Activation wave speeds near the material wave speed yielded successful turns, with a 76-fold difference in turning rate between the best and worst performers. Hyperextension of the margin occurred only at activation wave speeds near the material wave speed, suggesting resonance. This hyperextension resulted in a 34-fold asymmetry in the circulation of the vortex ring between the inside and outside of the turn. Experimental recording of the activation speed confirmed that jellyfish actuate within this range, and flow visualization using particle image velocimetry validated the corresponding fluid dynamics of the numerical model. This suggests that neuromechanical wave resonance plays an important role in the robustness of an organism’s locomotory system and presents an undiscovered constraint on the evolution of flexible organisms. Understanding these dynamics is essential for developing actuators in soft body robotics and bioengineered pumps.
    Description: This research was funded by the NSF Division of Mathematical Sciences, under Faculty Early Career Development Program Grant 1151478 (to L.A.M.).
    Description: 2021-09-16
    Keywords: Jellyfish ; Propulsion ; Neuromechanics ; Fluid-structure interaction ; Maneuverability
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  • 39
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    Teamwork in the viscous oceanic microscale (2021)
    National Academy of Sciences
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kanso, E. A., Lopes, R. M., Strickler, J. R., Dabiri, J. O., & Costello, J. H. Teamwork in the viscous oceanic microscale. Proceedings of the National Academy of Sciences of the United States of America, 118(29), (2021): e2018193118, https://doi.org/10.1073/pnas.2018193118.
    Description: Nutrient acquisition is crucial for oceanic microbes, and competitive solutions to solve this challenge have evolved among a range of unicellular protists. However, solitary solutions are not the only approach found in natural populations. A diverse array of oceanic protists form temporary or even long-lasting attachments to other protists and marine aggregates. Do these planktonic consortia provide benefits to their members? Here, we use empirical and modeling approaches to evaluate whether the relationship between a large centric diatom, Coscinodiscus wailesii, and a ciliate epibiont, Pseudovorticella coscinodisci, provides nutrient flux benefits to the host diatom. We find that fluid flows generated by ciliary beating can increase nutrient flux to a diatom cell surface four to 10 times that of a still cell without ciliate epibionts. This cosmopolitan species of diatom does not form consortia in all environments but frequently joins such consortia in nutrient-depleted waters. Our results demonstrate that symbiotic consortia provide a cooperative alternative of comparable or greater magnitude to sinking for enhancement of nutrient acquisition in challenging environments.
    Description: We are grateful to Y. Garcia for help with organism sampling and sorting. E.A.K. is funded by NSF-2100209, NSF RAISE IOS-2034043 and NIH R01 HL 153622-01A1. R.M.L. is a CNPq research fellow (grant # 310642/2017-5). J.H.C. and J.O.D. are funded by Grant NSF-2100705.
    Keywords: Phytoplankton ; Nutrient limitation ; Symbiosis ; Diffusion limitation ; Cell size
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    Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Reysenbach, A. L., St John, E., Meneghin, J., Flores, G. E., Podar, M., Dombrowski, N., Spang, A., L'Haridon, S., Humphris, S. E., de Ronde, C. E. J., Caratori Tontini, F., Tivey, M., Stucker, V. K., Stewart, L. C., Diehl, A., & Bach, W. Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities. Proceedings of the National Academy of Sciences of the United States of America, 117(51), (2020): 202019021, doi:10.1073/pnas.2019021117.
    Description: Hydrothermally active submarine volcanoes are mineral-rich biological oases contributing significantly to chemical fluxes in the deep sea, yet little is known about the microbial communities inhabiting these systems. Here we investigate the diversity of microbial life in hydrothermal deposits and their metagenomics-inferred physiology in light of the geological history and resulting hydrothermal fluid paths in the subsurface of Brothers submarine volcano north of New Zealand on the southern Kermadec arc. From metagenome-assembled genomes we identified over 90 putative bacterial and archaeal genomic families and nearly 300 previously unknown genera, many potentially endemic to this submarine volcanic environment. While magmatically influenced hydrothermal systems on the volcanic resurgent cones of Brothers volcano harbor communities of thermoacidophiles and diverse members of the superphylum “DPANN,” two distinct communities are associated with the caldera wall, likely shaped by two different types of hydrothermal circulation. The communities whose phylogenetic diversity primarily aligns with that of the cone sites and magmatically influenced hydrothermal systems elsewhere are characterized predominately by anaerobic metabolisms. These populations are probably maintained by fluids with greater magmatic inputs that have interacted with different (deeper) previously altered mineral assemblages. However, proximal (a few meters distant) communities with gene-inferred aerobic, microaerophilic, and anaerobic metabolisms are likely supported by shallower seawater-dominated circulation. Furthermore, mixing of fluids from these two distinct hydrothermal circulation systems may have an underlying imprint on the high microbial phylogenomic diversity. Collectively our results highlight the importance of considering geologic evolution and history of subsurface processes in studying microbial colonization and community dynamics in volcanic environments.
    Description: We thank the captain and crew of the R/V Thompson and the engineers from Woods Hole Oceanographic Institution for the successful operation of ROV Jason. The project was funded by NSF grants OCE‐1558356 (Principal Investigator S.E.H.) and OCE-1558795 (Principal Investigator A.-L.R.). S.L. received a grant from the University of Brest to work in the A.-L.R. laboratory. A travel fund from Interridge enabled A.D. to participate on the R/V Thompson cruise. Funding for this work for C.E.J.d.R., F.C.T., V.K.S., and L.C.S. was provided by the New Zealand government. A.S. was supported by the Swedish Research Council (Vetenskapsrådet starting grant 2016-03559 to A.S.) and the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Dutch Research Council) Foundation of the Netherlands Organization for Scientific Research (Women In Science Excel [WISE] fellowship to A.S.). A.-L.R. and E.S.J. thank Rika Anderson for helpful methodological discussions and Sean Sylva for assistance in shipboard geochemical analysis.
    Keywords: Metagenomics ; Deep-sea hydrothermal ; Thermophiles ; Archaea ; Volcanics
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    Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coesel, S. N., Durham, B. P., Groussman, R. D., Hu, S. K., Caron, D. A., Morales, R. L., Ribalet, F., & Armbrust, E. V. Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proceedings of the National Academy of Sciences of the United States of America, 118(6), (2021): e2011038118, https://doi.org/10.1073./pnas.2011038118.
    Description: The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
    Description: This work was supported by a grant from the Simons Foundation (SCOPE Award 329108 [to E.V.A.]) and XSEDE Grant Allocation OCE160019 (to R.D.G.).
    Keywords: Photoreceptors ; Microbial eukaryotes ; Oligotrophic gyre ; Diel cycles ; Metatranscriptomics
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    Evidence for massive and recurrent toxic blooms of Alexandrium catenella in the Alaskan Arctic (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Anderson, D. M., Fachon, E., Pickart, R. S., Lin, P., Fischer, A. D., Richlen, M. L., Uva, V., Brosnahan, M. L., McRaven, L., Bahr, F., Lefebvre, K., Grebmeier, J. M., Danielson, S. L., Lyu, Y., & Fukai, Y. Evidence for massive and recurrent toxic blooms of Alexandrium catenella in the Alaskan Arctic. Proceedings of the National Academy of Sciences of the United States of America, 118(41) (2021): e2107387118, https://doi.org/10.1073/pnas.2107387118.
    Description: Among the organisms that spread into and flourish in Arctic waters with rising temperatures and sea ice loss are toxic algae, a group of harmful algal bloom species that produce potent biotoxins. Alexandrium catenella, a cyst-forming dinoflagellate that causes paralytic shellfish poisoning worldwide, has been a significant threat to human health in southeastern Alaska for centuries. It is known to be transported into Arctic regions in waters transiting northward through the Bering Strait, yet there is little recognition of this organism as a human health concern north of the Strait. Here, we describe an exceptionally large A. catenella benthic cyst bed and hydrographic conditions across the Chukchi Sea that support germination and development of recurrent, locally originating and self-seeding blooms. Two prominent cyst accumulation zones result from deposition promoted by weak circulation. Cyst concentrations are among the highest reported globally for this species, and the cyst bed is at least 6× larger in area than any other. These extraordinary accumulations are attributed to repeated inputs from advected southern blooms and to localized cyst formation and deposition. Over the past two decades, warming has likely increased the magnitude of the germination flux twofold and advanced the timing of cell inoculation into the euphotic zone by 20 d. Conditions are also now favorable for bloom development in surface waters. The region is poised to support annually recurrent A. catenella blooms that are massive in scale, posing a significant and worrisome threat to public and ecosystem health in Alaskan Arctic communities where economies are subsistence based.
    Description: Funding for D.M.A., R.S.P., E.F., P.L., A.D.F., V.U., M.L.B., L.M., F.B., and M.L.R. was provided by grants from the NSF Office of Polar Programs (Grants OPP-1823002 and OPP-1733564) and the National Ocanic and Atmospheric Administration (NOAA) Arctic Research program (through the Cooperative Institute for the North Atlantic Region [CINAR; Grants NA14OAR4320158 and NA19OAR4320074]), for J.M.G. through CINAR 22309.07 UMCES (University of Maryland Center for Environmental Science), and for D.M.A. and K.L. through NOAA’s Center for Coastal and Ocean Studies Ecology and Oceanography of Harmful Algal Blooms (ECOHAB) Program (NA20NOS4780195). Funding for D.M.A., M.L.R., M.L.B., E.F., V.U., and A.D.F. was also provided by NSF (Grant OCE-1840381) and NIH (Grant 1P01-ES028938-01) through the Woods Hole Center for Oceans and Human Health. S.L.D. was supported by North Pacific Research Board IERP Grants A91-99a and A91-00a. This is IERP publication ArcticIERP-41 and ECOHAB Contribution No. ECO983.
    Keywords: Harmful algal bloom ; HAB ; Alexandrium ; Alaskan Arctic ; Climate
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    A cross-institutional analysis of the effects of broadening trainee professional development on research productivity (2021)
    Public Library of Science
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Brandt, P. D., Sturzenegger Varvayanis, S., Baas, T., Bolgioni, A. F., Alder, J., Petrie, K. A., Dominguez, I., Brown, A. M., Stayart, C. A., Singh, H., Van Wart, A., Chow, C. S., Mathur, A., Schreiber, B. M., Fruman, D. A., Bowden, B., Wiesen, C. A., Golightly, Y. M., Holmquist, C. E., Arneman, D., Hall, J. D., Hyman, L. E., Gould, K. L., Chalkley, R., Brennwald, P. J., Layton, R. L. A cross-institutional analysis of the effects of broadening trainee professional development on research productivity. Plos Biology, 19(7), (2021): e3000956, https://doi.org/10.1371/journal.pbio.3000956.
    Description: PhD-trained scientists are essential contributors to the workforce in diverse employment sectors that include academia, industry, government, and nonprofit organizations. Hence, best practices for training the future biomedical workforce are of national concern. Complementing coursework and laboratory research training, many institutions now offer professional training that enables career exploration and develops a broad set of skills critical to various career paths. The National Institutes of Health (NIH) funded academic institutions to design innovative programming to enable this professional development through a mechanism known as Broadening Experiences in Scientific Training (BEST). Programming at the NIH BEST awardee institutions included career panels, skill-building workshops, job search workshops, site visits, and internships. Because doctoral training is lengthy and requires focused attention on dissertation research, an initial concern was that students participating in additional complementary training activities might exhibit an increased time to degree or diminished research productivity. Metrics were analyzed from 10 NIH BEST awardee institutions to address this concern, using time to degree and publication records as measures of efficiency and productivity. Comparing doctoral students who participated to those who did not, results revealed that across these diverse academic institutions, there were no differences in time to degree or manuscript output. Our findings support the policy that doctoral students should participate in career and professional development opportunities that are intended to prepare them for a variety of diverse and important careers in the workforce.
    Description: Funding sources included the Common Fund NIH Director’s Biomedical Research Workforce Innovation Broadening Experiences in Scientific Training (BEST) Award. The following institutional NIH BEST awards (alphabetical by institution) included: DP7OD020322 (Boston University; AFB, ID, BMS, LEH); DP7OD020316 (University of Chicago; CAS); DP7OD018425 (Cornell University; SSV); DP7OD018428 (Virginia Polytechnic Institute; AVW, BB); DP7OD020314 (Rutgers University; JA); DP7OD020315 (University of Rochester; TB); DP7OD018423 (Vanderbilt University; KAP, AMB, KLG, RC); DP7OD020321 (University of California, Irvine; HS, DAF); DP7OD020317 (University of North Carolina, Chapel Hill; PDB, PJB, RLL); DP7 OD018427 (Wayne State University; CSC, AM). National Institutes of Health (NIH) General Medical Sciences - Science of Science Policy Approach to Analyzing and Innovating the Biomedical Research Enterprise (SCISIPBIO) Award (GM-19-011) - 1R01GM140282-01 (University of North Carolina at Chapel Hill; RLL, PDB, PJB).
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    Lingering Chukchi Sea sea ice and Chukchi Sea mean winds influence population age structure of euphausiids (krill) found in the bowhead whale feeding hotspot near Pt. Barrow, Alaska (2021)
    Public Library of Science
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ashjian, C. J., Okkonen, S. R., Campbell, R. G., & Alatalo, P. Lingering Chukchi Sea sea ice and Chukchi Sea mean winds influence population age structure of euphausiids (krill) found in the bowhead whale feeding hotspot near Pt. Barrow, Alaska. Plos One, 16(7), (2021): e0254418, https://doi.org/10.1371/journal.pone.0254418.
    Description: Interannual variability in euphausiid (krill) abundance and population structure and associations of those measures with environmental drivers were investigated in an 11-year study conducted in late August–early September 2005–2015 in offshelf waters (bottom depth 〉 40 m) in Barrow Canyon and the Beaufort Sea just downstream of Distributed Biological Observatory site 5 (DBO5) near Pt. Barrow, Alaska. Statistically-significant positive correlations were observed among krill population structure (proportion of juveniles and adults), the volume of Late Season Melt Water (LMW), and late-spring Chukchi Sea sea ice extent. High proportions of juvenile and adult krill were seen in years with larger volumes of LMW and greater spring sea ice extents (2006, 2009, 2012–2014) while the converse, high proportions of furcilia, were seen in years with smaller volumes of LMW and lower spring sea ice extent (2005, 2007, 2010, 2011, 2015). These different life stage, sea ice and water mass regimes represent integrated advective responses to mean fall and/or spring Chukchi Sea winds, driven by prevailing atmospheric pressure distributions in the two sets of years. In years with high proportions of juveniles and adults, late-spring and preceding-fall winds were weak and variable while in years with high proportions of furcilia, late-spring and preceding-fall winds were strong, easterly and consistent. The interaction of krill life history with yearly differences in the northward transports of krill and water masses along with sea ice retreat determines the population structure of late-summer krill populations in the DBO5 region near Pt. Barrow. Years with higher proportions of mature krill may provide larger prey to the Pt. Barrow area bowhead whale prey hotspot. The characteristics of prey near Pt. Barrow is dependent on krill abundance and size, large-scale environmental forcing, and interannual variability in recruitment success of krill in the Bering Sea.
    Description: This research was supported by the National Science Foundation through grants PLR-1023331 (CJA), OPP-0436131 (CJA), PLR-1022139 (RGC), OPP-0436110 (RGC), PLR-1023446 (SRO), and OPP-043166 (SRO), the National Oceanic and Atmospheric Administration (NOAA) under cooperative agreement NA08OAR4320751 with the University of Alaska (SRO) and cooperative agreements NA17RJ1223 and NA09OAR4320129 with the Woods Hole Oceanographic Institution (CJA), the Bureau of Ocean Energy Management through Interagency Agreement 0106RU39923/M08PG20021 between the National Marine Fisheries Service and MMS/BOEM (CJA, RGC, SRO) and through the National Oceanographic Partnership Program award number N00014-08-1-0311 from the Office of Naval Research to the Woods Hole Oceanographic Institution (CJA, SRO, RGC). Additional support was provided by the Coastal Marine Institute at the University of Alaska (SRO, RGC) and the James M. and Ruth P. Clark Arctic Research Initiative Fund at the Woods Hole Oceanographic Institution (CJA). The participation of the K-12 teachers was supported by the National Science Foundation through the ARMADA program at the University of Rhode Island (2005, 2006) and through the POLARTrec program at the Arctic Research Consortium of the United States (2012).
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    Quantitative PCR assays to detect whales, rockfish, and common murre environmental DNA in marine water samples of the Northeastern Pacific (2021)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Andruszkiewicz, E. A., Yamahara, K. M., Closek, C. J., & Boehm, A. B. Quantitative PCR assays to detect whales, rockfish, and common murre environmental DNA in marine water samples of the Northeastern Pacific. Plos One, 15(12), (2020): e0242689, doi:10.1371/journal.pone.0242689.
    Description: Monitoring aquatic species by identification of environmental DNA (eDNA) is becoming more common. To obtain quantitative eDNA datasets for individual species, organism-specific quantitative PCR (qPCR) assays are required. Here, we present detailed methodology of qPCR assay design and testing, including in silico, in vitro, and in vivo testing, and comment on the challenges associated with assay design and performance. We use the presented methodology to design assays for three important marine organisms common in the California Current Ecosystem (CCE): humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge). All three assays have excellent sensitivity and high efficiencies ranging from 92% to 99%. However, specificities of the assays varied from species-specific in the case of common murre, genus-specific for the shortbelly rockfish assay, and broadly whale-specific for the humpback whale assay, which cross-amplified with other two other whale species, including one in a different family. All assays detected their associated targets in complex environmental water samples.
    Description: This work is a contribution to the Marine Biodiversity Observation Network (MBON). The MBON project was supported by NASA grant NNX14AP62A ‘National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)’ funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM, and NASA), and the U.S. Integrated Ocean Observing System (IOOS) Program Office.
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    Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum "Campylobacterota". (2021)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shiotani, T., Mino, S., Sato, W., Nishikawa, S., Yonezawa, M., Sievert, S. M., & Sawabe, T. Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum "Campylobacterota". Plos One, 15(12), (2020): e0241366, doi:10.1371/journal.pone.0241366.
    Description: A novel bacterium, strain EPR55-1T, was isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The cells were motile rods. Growth was observed at temperatures between 50 and 60°C (optimum, 60°C), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4–3.2% (w/v) NaCl (optimum, 2.4%). The isolate used molecular hydrogen as its sole electron donor, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and thiosulfate, sulfite (0.01 to 0.001%, w/v) or elemental sulfur as its sole sulfur source. Nitrate, nitrous oxide (33%, v/v), thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur could serve as the sole electron acceptor to support growth. Phylogenetic analyses based on both 16S rRNA gene sequences and whole genome sequences indicated that strain EPR55-1T belonged to the family Nitratiruptoraceae of the class “Campylobacteria”, but it had the distinct phylogenetic relationship with the genus Nitratiruptor. On the basis of the physiological and molecular characteristics of the isolate, the name Nitrosophilus alvini gen. nov. sp. nov. is proposed, with EPR55-1T as the type strain (= JCM 32893T = KCTC 15925T). In addition, it is shown that “Nitratiruptor labii” should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JCM 34002T = DSM 111345T) is proposed for this organism. Furthermore, 16S rRNA gene-based and genome-based analyses showed that Cetia pacifica is phylogenetically associated with Caminibacter species. We therefore propose the reclassification of Cetia pacifica as Caminibacter pacificus comb. nov. (DSM 27783T = JCM 19563T). Additionally, AAI thresholds for genus classification and the reclassification of subordinate taxa within “Campylobacteria” are also evaluated, based on the analyses using publicly available genomes of all the campylobacterial species.
    Description: This study was partially supported by the JSPS KAKENHI (No. 12J03037 and No. 15H05991), the Takahashi Industrial and Economic Research Foundation, and US National Science Foundation grant OCE-1559198 and the WHOI Investment in Science Fund to S.M.S. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    An assessment of temporal, spatial and taxonomic trends in harmful algal toxin exposure in stranded marine mammals from the US New England coast (2021)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fire, S. E., Bogomolni, A., DiGiovanni, R. A., Jr., Early, G., Leighfield, T. A., Matassa, K., Miller, G. A., Moore, K. M. T., Moore, M., Niemeyer, M., Pugliares, K., Wang, Z., & Wenzel, F. W. An assessment of temporal, spatial and taxonomic trends in harmful algal toxin exposure in stranded marine mammals from the US New England coast. Plos One, 16(1),(2021): e0243570, https://doi.org/10.1371/journal.pone.0243570.
    Description: Despite a long-documented history of severe harmful algal blooms (HABs) in New England coastal waters, corresponding HAB-associated marine mammal mortality events in this region are far less frequent or severe relative to other regions where HABs are common. This long-term survey of the HAB toxins saxitoxin (STX) and domoic acid (DA) demonstrates significant and widespread exposure of these toxins in New England marine mammals, across multiple geographic, temporal and taxonomic groups. Overall, 19% of the 458 animals tested positive for one or more toxins, with 15% and 7% testing positive for STX and DA, respectively. 74% of the 23 different species analyzed demonstrated evidence of toxin exposure. STX was most prevalent in Maine coastal waters, most frequently detected in common dolphins (Delphinus delphis), and most often detected during July and October. DA was most prevalent in animals sampled in offshore locations and in bycaught animals, and most frequently detected in mysticetes, with humpback whales (Megaptera novaeangliae) testing positive at the highest rates. Feces and urine appeared to be the sample matrices most useful for determining the presence of toxins in an exposed animal, with feces samples having the highest concentrations of STX or DA. No relationship was found between the bloom season of toxin-producing phytoplankton and toxin detection rates, however STX was more likely to be present in July and October. No relationship between marine mammal dietary preference and frequency of toxin detection was observed. These findings are an important part of a framework for assessing future marine mammal morbidity and mortality events, as well as monitoring ecosystem health using marine mammals as sentinel organisms for predicting coastal ocean changes.
    Description: S.F. - NOAA John H. Prescott Marine Mammal Rescue Assistance Grant Program #NA16NMF4390151 S.F. - NOAA John H. Prescott Marine Mammal Rescue Assistance Grant Program #NA17NMF4390082 S.F. - Florida Tech Department of Biological Sciences S.F. - Florida Tech John H. Evans Library Open Access Subvention Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    Unifying chemical and biological perspectives of carbon accumulation in the environment (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Repeta, D. J. Unifying chemical and biological perspectives of carbon accumulation in the environment. Proceedings of the National Academy of Sciences of the United States of America, 118(11), (2021); e2100935118, https://doi.org/10.1073/pnas.2100935118.
    Description: Heterotrophic microorganisms are fiendishly clever at degrading all shapes and sizes of organic compounds to extract the energy they need to build biomass. Every year marine phytoplankton fix ∼50 billion tons of carbon dioxide into organic matter, and every year marine heterotrophs respire nearly all of this organic matter back to carbon dioxide (1). Nearly all, but not all. With each spin of this carbon cycle, a small amount of organic matter escapes respiration and becomes sequestered in seawater, sediments, and soils. Over time, this small “leak” in the system leads to the accumulation of a vast reservoir of carbon; some 5 × 1019 kg of organic matter are thought to be sequestered in sedimentary rocks (2). This carbon sequestration has immense consequences for life on Earth, as illustrated by the change in climate we are now experiencing due in part to the transfer of a minute portion of this inventory from geologic reservoirs into the atmosphere.
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    Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution (2021)
    Public Library of Science
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Leray, M., Wilkins, L. G. E., Apprill, A., Bik, H. M., Clever, F., Connolly, S. R., De Leon, M. E., Duffy, J. E., Ezzat, L., Gignoux-Wolfsohn, S., Herre, E. A., Kaye, J. Z., Kline, D. I., Kueneman, J. G., McCormick, M. K., McMillan, W. O., O’Dea, A., Pereira, T. J., Petersen, J. M., Petticord, D. F., Torchin, M. E., Thurber, R. V., Videvall, E., Wcislo, W. T., Yuen, B., Eisen, J. A. . Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution. Plos Biology, 19(8), (2021): e3001322, https://doi.org/10.1371/journal.pbio.3001322.
    Description: Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.
    Description: Financial support for the workshop was provided by grant GBMF5603 (https://doi.org/10.37807/GBMF5603) from the Gordon and Betty Moore Foundation (W.T. Wcislo, J.A. Eisen, co-PIs), and additional funding from the Smithsonian Tropical Research Institute and the Office of the Provost of the Smithsonian Institution (W.T. Wcislo, J.P. Meganigal, and R.C. Fleischer, co-PIs). JP was supported by a WWTF VRG Grant and the ERC Starting Grant 'EvoLucin'. LGEW has received funding from the European Union’s Framework Programme for Research and Innovation Horizon 2020 (2014-2020) under the Marie Sklodowska-Curie Grant Agreement No. 101025649. AO was supported by the Sistema Nacional de Investigadores (SENACYT, Panamá). A. Apprill was supported by NSF award OCE-1938147. D.I. Kline, M. Leray, S.R. Connolly, and M.E. Torchin were supported by a Rohr Family Foundation grant for the Rohr Reef Resilience Project, for which this is contribution #2. This is contribution #85 from the Smithsonian’s MarineGEO and Tennenbaum Marine Observatories Network. T
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    Climate control on terrestrial biospheric carbon turnover (2021)
    National Academy of Sciences
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Eglinton, T. I., Galy, V. V., Hemingway, J. D., Feng, X., Bao, H., Blattmann, T. M., Dickens, A. F., Gies, H., Giosan, L., Haghipour, N., Hou, P., Lupker, M., McIntyre, C. P., Montluçon, D. B., Peucker-Ehrenbrink, B., Ponton, C., Schefuß, E., Schwab, M. S., Voss, B. M., Wacker, L., Wu, Y., & Zhao, M. Climate control on terrestrial biospheric carbon turnover. Proceedings of the National Academy of Sciences of the United States of America, 118(8), (2021): e2011585118, htps://doi.org/ 10.1073/pnas.2011585118.
    Description: Terrestrial vegetation and soils hold three times more carbon than the atmosphere. Much debate concerns how anthropogenic activity will perturb these surface reservoirs, potentially exacerbating ongoing changes to the climate system. Uncertainties specifically persist in extrapolating point-source observations to ecosystem-scale budgets and fluxes, which require consideration of vertical and lateral processes on multiple temporal and spatial scales. To explore controls on organic carbon (OC) turnover at the river basin scale, we present radiocarbon (14C) ages on two groups of molecular tracers of plant-derived carbon—leaf-wax lipids and lignin phenols—from a globally distributed suite of rivers. We find significant negative relationships between the 14C age of these biomarkers and mean annual temperature and precipitation. Moreover, riverine biospheric-carbon ages scale proportionally with basin-wide soil carbon turnover times and soil 14C ages, implicating OC cycling within soils as a primary control on exported biomarker ages and revealing a broad distribution of soil OC reactivities. The ubiquitous occurrence of a long-lived soil OC pool suggests soil OC is globally vulnerable to perturbations by future temperature and precipitation increase. Scaling of riverine biospheric-carbon ages with soil OC turnover shows the former can constrain the sensitivity of carbon dynamics to environmental controls on broad spatial scales. Extracting this information from fluvially dominated sedimentary sequences may inform past variations in soil OC turnover in response to anthropogenic and/or climate perturbations. In turn, monitoring riverine OC composition may help detect future climate-change–induced perturbations of soil OC turnover and stocks.
    Description: This work was supported by grants from the US NSF (OCE-0928582 to T.I.E. and V.V.G.; OCE-0851015 to B.P.-E., T.I.E., and V.V.G.; and EAR-1226818 to B.P.-E.), Swiss National Science Foundation (200021_140850, 200020_163162, and 200020_184865 to T.I.E.), and National Natural Science Foundation of China (41520104009 to M.Z.).
    Keywords: Radiocarbon ; Plant biomarkers ; Carbon turnover times ; Fluvial carbon ; Carbon cycle
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    Human arrival and landscape dynamics in the northern Bahamas (2021)
    National Academy of Sciences
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fall, P. L., van Hengstum, P. J., Lavold-Foote, L., Donnelly, J. P., Albury, N. A., & Tamalavage, A. E. Human arrival and landscape dynamics in the northern Bahamas. Proceedings of the National Academy of Sciences of the United States of America, 118(10), (2021): e2015764118, https://doi.org/10.1073/pnas.2015764118.
    Description: The first Caribbean settlers were Amerindians from South America. Great Abaco and Grand Bahama, the final islands colonized in the northernmost Bahamas, were inhabited by the Lucayans when Europeans arrived. The timing of Lucayan arrival in the northern Bahamas has been uncertain because direct archaeological evidence is limited. We document Lucayan arrival on Great Abaco Island through a detailed record of vegetation, fire, and landscape dynamics based on proxy data from Blackwood Sinkhole. From about 3,000 to 1,000 y ago, forests dominated by hardwoods and palms were resilient to the effects of hurricanes and cooling sea surface temperatures. The arrival of Lucayans by about 830 CE (2σ range: 720 to 920 CE) is demarcated by increased burning and followed by landscape disturbance and a time-transgressive shift from hardwoods and palms to the modern pine forest. Considering that Lucayan settlements in the southern Bahamian archipelago are dated to about 750 CE (2σ range: 600 to 900 CE), these results demonstrate that Lucayans spread rapidly through the archipelago in less than 100 y. Although precontact landscapes would have been influenced by storms and climatic trends, the most pronounced changes follow more directly from landscape burning and ecosystem shifts after Lucayan arrival. The pine forests of Abaco declined substantially between 1500 and 1670 CE, a period of increased regional hurricane activity, coupled with fires on an already human-impacted landscape. Any future intensification of hurricane activity in the tropical North Atlantic Ocean threatens the sustainability of modern pine forests in the northern Bahamas.
    Description: This research was supported by NSF Awards GSS-1118340 (P.L.F.), OCE-1356509 (P.J.v.H.), OCE-1703087 (P.J.v.H.), and OCE-1356708 (J.P.D.).
    Keywords: Anthropogenic burning ; Lucayan ; Caribbean ; Pollen ; Vegetation change
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    Thermodynamic feasibility of shipboard conversion of marine plastics to blue diesel for self-powered ocean cleanup (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Belden, E. R., Kazantzis, N. K., Reddy, C. M., Kite-Powell, H., Timko, M. T., Italiani, E., & Herschbach, D. R. Thermodynamic feasibility of shipboard conversion of marine plastics to blue diesel for self-powered ocean cleanup. Proceedings of the National Academy of Sciences of the United States of America, 118(46),(2021): e2107250118, https://doi.org/10.1073/pnas.2107250118.
    Description: Collecting and removing ocean plastics can mitigate their environmental impacts; however, ocean cleanup will be a complex and energy-intensive operation that has not been fully evaluated. This work examines the thermodynamic feasibility and subsequent implications of hydrothermally converting this waste into a fuel to enable self-powered cleanup. A comprehensive probabilistic exergy analysis demonstrates that hydrothermal liquefaction has potential to generate sufficient energy to power both the process and the ship performing the cleanup. Self-powered cleanup reduces the number of roundtrips to port of a waste-laden ship, eliminating the need for fossil fuel use for most plastic concentrations. Several cleanup scenarios are modeled for the Great Pacific Garbage Patch (GPGP), corresponding to 230 t to 11,500 t of plastic removed yearly; the range corresponds to uncertainty in the surface concentration of plastics in the GPGP. Estimated cleanup times depends mainly on the number of booms that can be deployed in the GPGP without sacrificing collection efficiency. Self-powered cleanup may be a viable approach for removal of plastics from the ocean, and gaps in our understanding of GPGP characteristics should be addressed to reduce uncertainty.
    Description: The US NSF supported this work as part of its 2026 Idea Machine initiative (Chemical, Bioengineering, Environmental, and Transport Systems, EArly-concept Grants for Exploratory Research Award #2032621). E.R.B.’s contribution was funded, in part, by the NSF Graduate Research Fellowship Program under Grant No. 2038257.
    Keywords: Ocean plastic ; Hydrothermal liquefaction ; Exergy analysis ; Monte Carlo simulation
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    Electrochemical implications of modulating the solvation shell around redox active organic species in aqueous organic redox flow batteries (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Organic and organometallic reactants in aqueous electrolytes, being composed of earth-abundant elements, are promising redox active candidates for cost-effective organic redox flow batteries (ORFBs). Various compounds of ferrocene and methyl viologen have been examined as promising redox actives for this application. Herein, we examined the influence of the electrolyte pH and the salt anion on model redox active organic cations, bis((3-trimethylammonio) propyl)- ferrocene dichloride (BTMAP-Fc) and bis(3-trimethylammonio) propyl viologen tetrachloride (BTMAP-Vi), which have exhibited excellent cycling stability and capacity retention at ≥1.00 M concentration [E. S. Beh, et al. ACS Energy Lett. 2, 639–644 (2017)]. We examined the solvation shell around BTMAP-Fc and BTMAP-Vi at acidic and neutral pH with SO42-, Cl−, and CH3SO3− counterions and elucidated their impact on cation diffusion coefficient, first electron transfer rate constant, and thereby the electrochemical Thiele modulus. The electrochemical Thiele modulus was found to be exponentially correlated with the solvent reorganizational energy (λ) in both neutral and acidic pH. Thus, λ is proposed as a universal descriptor and selection criteria for organic redox flow battery electrolyte compositions. In the specific case of the BTMAP-Fc/BTMAP-Vi ORFB, low pH electrolytes with methanesulfonate or chloride counterions were identified as offering the best balance of transport and kinetic requirements.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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    Origin of anomalous band-gap bowing in two-dimensional tin-lead mixed perovskite alloys (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2469-9950
    Electronic ISSN: 2469-9969
    Topics: Physics
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  • 55
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    An in vivo selection-derived d-peptide for engineering erythrocyte-binding antigens that promote immune tolerance (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: When displayed on erythrocytes, peptides and proteins can drive antigen-specific immune tolerance. Here, we investigated a straightforward approach based on erythrocyte binding to promote antigen-specific tolerance to both peptides and proteins. We first identified a robust erythrocyte-binding ligand. A pool of one million fully d-chiral peptides was injected into mice, blood cells were isolated, and ligands enriched on these cells were identified using nano-liquid chromatography–tandem mass spectrometry. One round of selection yielded a murine erythrocyte-binding ligand with an 80 nM apparent dissociation constant, Kd. We modified an 83-kDa bacterial protein and a peptide antigen derived from ovalbumin (OVA) with the identified erythrocyte-binding ligand. An administration of the engineered bacterial protein led to decreased protein-specific antibodies in mice. Similarly, mice given the engineered OVA-derived peptide had decreased inflammatory anti-OVA CD8+ T cell responses. These findings suggest that our tolerance-induction strategy is applicable to both peptide and protein antigens and that our in vivo selection strategy can be used for de novo discovery of robust erythrocyte-binding ligands.
    Print ISSN: 0027-8424
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    Topics: Biology , Medicine , Natural Sciences in General
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    The trisulfur radical ion S3•− controls platinum transport by hydrothermal fluids (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Platinum group elements (PGE) are considered to be very poorly soluble in aqueous fluids in most natural hydrothermal–magmatic contexts and industrial processes. Here, we combined in situ X-ray absorption spectroscopy and solubility experiments with atomistic and thermodynamic simulations to demonstrate that the trisulfur radical ion S3•− forms very stable and soluble complexes with both PtII and PtIV in sulfur-bearing aqueous solution at elevated temperatures (∼300 °C). These Pt-bearing species enable (re)mobilization, transfer, and focused precipitation of platinum up to 10,000 times more efficiently than any other common inorganic ligand, such as hydroxide, chloride, sulfate, or sulfide. Our results imply a far more important contribution of sulfur-bearing hydrothermal fluids to PGE transfer and accumulation in the Earth’s crust than believed previously. This discovery challenges traditional models of PGE economic concentration from silicate and sulfide melts and provides new possibilities for resource prospecting in hydrothermal shallow crust settings. The exceptionally high capacity of the S3•− ion to bind platinum may also offer new routes for PGE selective extraction from ore and hydrothermal synthesis of noble metal nanomaterials.
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    Unidirectional magnetotransport of linearly dispersing topological edge states (2021)
    American Physical Society
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    Publication Date: 2021-08-20
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  • 58
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    Perturbation theory of nearly spherical dielectric optical resonators (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2469-9926
    Electronic ISSN: 2469-9934
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 59
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    Wilson loops and area laws in lattice gauge theory tensor networks (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2643-1564
    Topics: Physics
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    Electroluminescence and thermal radiation from metallic armchair carbon nanotubes with defects (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2469-9950
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    Socioeconomic position is associated with N-terminal pro-brain natriuretic peptide (NT-proBNP)—Results of the population-based Heinz Nixdorf Recall study (2021)
    Public Library of Science
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    Publication Date: 2021-08-20
    Description: Objectives N-Terminal pro Brain Natriuretic Peptide (NT-proBNP) is a diagnostic marker for heart failure and a prognostic factor for cardiovascular disease (CVD). The aim of this study was to examine the association of socioeconomic position (SEP) with NT-proBNP while assessing sex-differences and the impact of CVD risk factors and prevalent CVD on the association. Methods Baseline data of 4598 participants aged 45–75 years of the Heinz Nixdorf Recall Study were used. Income and education were used as SEP indicators. Age- and sex-adjusted linear regression models were fitted to calculate effect size estimates and 95% confidence intervals (95%-CIs) for the total effect of SEP indicators on NT-proBNP, while potential mediation was assessed by additionally accounting for traditional CVD risk factors (i.e., systolic blood pressure, HDL cholesterol, LDL cholesterol, diabetes, anti-hypertensive medication, lipid-lowering medication, BMI, current smoking). Education and income were included separately in the models. Results With an age- and sex-adjusted average change in NT-proBNP of -6.47% (95%-CI: -9.91; -2.91) per 1000€, the association between income and NT-proBNP was more pronounced compared to using education as a SEP indicator (-0.80% [95%-CI: -1.92; 0.32] per year of education). Sex-stratified results indicated stronger associations in men (-8.43% [95%-CI: -13.21; -3.38] per 1000€; -1.63% [95%-CI: -3.23; -0.001] per year of education) compared to women (-5.10% [95%-CI: -9.82; -0.01] per 1000€; -1.04% [95%-CI: -2.59; 0.50] per year of education). After adjusting for CVD risk factors some of the observed effect size estimates were attenuated, while the overall association between SEP indicators and NT-proBNP was still indicated. The exclusion of participants with prevalent coronary heart disease or stroke did not lead to a substantial change in the observed associations. Conclusions In the present study associations of education and income with NT-proBNP were observed in a population-based study sample. Only parts of the association were explained by traditional CVD risk factors, while there were substantial sex-differences in the strength of the observed association. Overt coronary heart disease or stroke did not seem to trigger the associations.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Differential expression of urinary volatile organic compounds by sex, male reproductive status, and pairing status in the maned wolf (Chrysocyon brachyurus) (2021)
    Public Library of Science
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    Publication Date: 2021-08-20
    Description: The maned wolf (Chrysocyon brachyurus) is an induced ovulator. Though the mechanism of ovulation induction remains unknown, it is suspected to be urinary chemical signals excreted by males. This study assessed volatile organic compounds (VOCs) in weekly urine samples across 5 months from 13 maned wolves (6 intact males, 1 neutered male, 6 females) with the goal of identifying VOCs that are differentially expressed across sex, reproductive status, and pairing status. Solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS) were used to extract and separate VOCs that were identified via spectral matching with authentic standards, with spectral libraries, or with new software that further matches molecular fragment structures with mass spectral peaks. Two VOCs were present across all 317 urine samples: 2,5-dimethyl pyrazine and 2-methyl-6-(1-propenyl)-pyrazine. Fifteen VOCs differed significantly (Adj. P 〈 0.001 and |log2 fold change| 〉2.0) between intact males and females. Using partial least squares-discriminant analysis, the compounds with the highest importance to the sex classification were delta-decalactone, delta-dodecalactone, and bis(prenyl) sulfide. Sixty-two VOCs differed between intact males and the neutered male. Important classifier compounds were 3-ethyl 2,5-dimethyl pyrazine, 2-methyl-6-(1-propenyl)-pyrazine, and tetrahydro-2-isopentyl-5-propyl furan. Several VOCs established as important here have been implicated in reproductive communication in other mammals. This study is the most robust examination of differential expression in the maned wolf thus far and provides the most comprehensive analysis of maned wolf urinary VOCs to date, increasing the sample size substantially over previous chemical communication studies in this species. New data analysis software allowed for the identification of compounds in the hormone-producing mevalonate pathway which were previously unreported in maned wolf urine. Several putative semiochemicals were identified as good candidates for behavioral bioassays to determine their role in maned wolf reproduction, and specifically in ovulation induction.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Remote Generation of Magnon Schrödinger Cat State via Magnon-Photon Entanglement (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 64
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    Quantum process inference for a single-qubit Maxwell demon (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2469-9926
    Electronic ISSN: 2469-9934
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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    Simulating the dynamics of braiding of Majorana zero modes using an IBM quantum computer (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2643-1564
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    Searches for beyond-Riemann gravity (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2470-0010
    Electronic ISSN: 2470-0029
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    Modified quantum delayed-choice experiment without quantum control or entanglement assistance (2021)
    American Physical Society
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    Publication Date: 2021-08-20
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    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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    Impact of informal physics programs on university student development: Creating a physicist (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2469-9896
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    Optimal resource cost for error mitigation (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2643-1564
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    Triggering on emerging jets (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2470-0010
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  • 71
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    Dark Matter Detection with Bound Nuclear Targets: The Poisson Phonon Tail (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
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  • 72
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    Relativistic modified Bessel-Gaussian beam generated from plasma-based beam braiding (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2469-9926
    Electronic ISSN: 2469-9934
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 73
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    Characterization of soft x-ray echo-enabled harmonic generation free-electron laser pulses in the presence of incoherent electron beam energy modulations (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2469-9888
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  • 74
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    Averaging Local Structure to Predict the Dynamic Propensity in Supercooled Liquids (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 0031-9007
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  • 75
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    Consistent Treatment of Axions in the Weak Chiral Lagrangian (2021)
    American Physical Society
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    Publication Date: 2021-08-20
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  • 76
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    Controlling the RKKY interaction and heat transport in a Kitaev spin liquid via Z2 flux walls (2021)
    American Physical Society
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    Publication Date: 2021-08-20
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  • 77
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    Interplay of charge noise and coupling to phonons in adiabatic electron transfer between quantum dots (2021)
    American Physical Society
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    Publication Date: 2021-08-20
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  • 78
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    A national survey in United Arab Emirates on practice of passive range of motion by physiotherapists in intensive care unit (2021)
    Public Library of Science
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    Publication Date: 2021-08-20
    Description: Background Patients admitted to intensive care units (ICU) are at an increased risk of developing immobility related complications. Physiotherapists are challenged to employ preventive and rehabilitative strategies to combat these effects. Passive limb range of motion (PROM) exercises- a part of early mobilization-aid in maintaining joint range of motion and functional muscle strength and forms a part of treatment for patients in ICU. However, there is a lack of evidence on practice of PROM exercises on patients admitted to ICU in the United Arab Emirates (UAE). This study aimed at exploring practices regarding the same in UAE. Methods This survey, conducted from January 2021 to February 2021 in College of Physiotherapy, Sharjah University studied practice of physiotherapists in the intensive care units. Physiotherapists currently working in ICU completed an online questionnaire composed of forty-two questions about physiotherapy service provision, assessment and intervention in the intensive care units. Results 33 physiotherapists completed the survey. 66.6% of respondents routinely assessed PROM for all the patients in ICU referred for physiotherapy. 84.8% of them assessed all the joints. More than half of the respondents (57.8%) reported that they administered PROM regularly to all the patients. According to 63.6% respondents, maintaining joint range of motion was the main reason for performing PROM. Responses pertaining to sets and repetitions of PROM were variable ranging from 1–6 sets and from 3 to 30 repetitions. Personal experience, resources/financial consideration and research findings were found to have influence on the practice. Conclusions PROM was found to be one of the frequently used mobilization techniques administered by physiotherapists in the intensive care units and was mostly performed after assessment. Maintaining joint range of motion was the main aim for performing PROM. Variability was found in the sets and repetitions of PROM administered. Various factors influenced the practice of PROM.
    Electronic ISSN: 1932-6203
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  • 79
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    Laguerre reconstruction of the correlation function on baryon acoustic oscillation scales (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2470-0010
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  • 80
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    Excitons and carriers in transient absorption and time-resolved ARPES spectroscopy: An ab initio approach (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2475-9953
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 81
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    Core circadian clock transcription factor BMAL1 regulates mammary epithelial cell growth, differentiation, and milk component synthesis (2021)
    Public Library of Science
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    Publication Date: 2021-08-20
    Description: The role the mammary epithelial circadian clock plays in gland development and lactation is unknown. We hypothesized that mammary epithelial clocks function to regulate mammogenesis and lactogenesis, and propose the core clock transcription factor BMAL1:CLOCK regulates genes that control mammary epithelial development and milk synthesis. Our objective was to identify transcriptional targets of BMAL1 in undifferentiated (UNDIFF) and lactogen differentiated (DIFF) mammary epithelial cells (HC11) using ChIP-seq. Ensembl gene IDs with the nearest transcriptional start site to ChIP-seq peaks were explored as potential targets, and represented 846 protein coding genes common to UNDIFF and DIFF cells and 2773 unique to DIFF samples. Genes with overlapping peaks between samples (1343) enriched cell-cell adhesion, membrane transporters and lipid metabolism categories. To functionally verify targets, an HC11 line with Bmal1 gene knocked out (BMAL1-KO) using CRISPR-CAS was created. BMAL1-KO cultures had lower cell densities over an eight-day growth curve, which was associated with increased (p
    Electronic ISSN: 1932-6203
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    Evaluation of the ability of the trypsin-like peptidase activity assay to detect severe periodontitis (2021)
    Public Library of Science
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    Publication Date: 2021-08-20
    Description: Objectives N-benzoyl-DL-arginine peptidase (trypsin-like peptidase) is specifically produced by certain strains of periodontitis-associated bacteria. We aimed to examine the effectiveness of an objectively quantified trypsin-like peptidase activity assay (TLP-AA) for detecting severe periodontitis. Methods The study population included 347 adults (108 men and 239 women; average age, 43.3 years) who underwent a full-mouth periodontal examination. Specimens for the TLP-AA were obtained using tongue swabs. Using a color reader, the TLP-AA results were obtained as a* values, with higher positive a* values indicating an increased intense enzymatic activity. The predictive validity of the TLP-AA results for severe periodontitis was assessed using receiver operating characteristic curve analysis and the periodontitis case definition provided by the Centers for Disease Control and Prevention/American Academy of Periodontology as the gold standard. Furthermore, multivariable logistic regression analyses were performed to predict severe periodontitis using the TLP-AA results and health characteristics, as the exposure variables. Results Severe periodontitis was observed in 5.2% of the participants. TLP-AA had high diagnostic accuracy for severe periodontitis, with an area under the curve of 0.83 (95% confidence interval [CI]: 0.75–0.92). The cut-off score for the a* value that best differentiated individuals with severe periodontitis was 0.09, with a sensitivity of 83% and specificity of 77%. Multivariable logistic regression analyses revealed that the TLP-AA results were significantly associated with severe periodontitis after adjusting for health characteristics (adjusted odds ratios: 1.90 [95% CI: 1.37–2.62] for the a* value). Conclusions Objectively quantified TLP-AA results are potentially useful for detecting severe periodontitis in epidemiological surveillance.
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    Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regulation within the liver (2021)
    Public Library of Science
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    Publication Date: 2021-08-10
    Description: Ultradian glucocorticoid rhythms are highly conserved across mammalian species, however, their functional significance is not yet fully understood. Here we demonstrate that pulsatile corticosterone replacement in adrenalectomised rats induces a dynamic pattern of glucocorticoid receptor (GR) binding at ~3,000 genomic sites in liver at the pulse peak, subsequently not found during the pulse nadir. In contrast, constant corticosterone replacement induced prolonged binding at the majority of these sites. Additionally, each pattern further induced markedly different transcriptional responses. During pulsatile treatment, intragenic occupancy by active RNA polymerase II exhibited pulsatile dynamics with transient changes in enrichment, either decreased or increased depending on the gene, which mostly returned to baseline during the inter-pulse interval. In contrast, constant corticosterone exposure induced prolonged effects on RNA polymerase II occupancy at the majority of gene targets, thus acting as a sustained regulatory signal for both transactivation and repression of glucocorticoid target genes. The nett effect of these differences were consequently seen in the liver transcriptome as RNA-seq analysis indicated that despite the same overall amount of corticosterone infused, twice the number of transcripts were regulated by constant corticosterone infusion, when compared to pulsatile. Target genes that were found to be differentially regulated in a pattern-dependent manner were enriched in functional pathways including carbohydrate, cholesterol, glucose and fat metabolism as well as inflammation, suggesting a functional role for dysregulated glucocorticoid rhythms in the development of metabolic dysfunction.
    Print ISSN: 1553-7390
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    Topics: Biology
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    Effect of suicidality on clinical and behavioural outcomes in HIV positive adults in Uganda (2021)
    Public Library of Science
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    Publication Date: 2021-08-20
    Description: Introduction Suicidality is a risk of a person committing suicide often characterized by suicidal ideation, intent or attempts. Despite the high burden of suicidality among individuals living with HIV and HAIDS, there is paucity of data on the impact of suicidality on clinical (such as CD4 counts and HIV disease progression) and behavioural outcomes (such as adherence to HIV Medications). Cross-sectional investigations of these associations are often complicated by bidirectional causal relationships and hence the need for longitudinal study designs. We conducted a cohort study to determine the impact of suicidality on clinical and behavioural outcomes among adults living with HIV/AIDS in Uganda. Materials and methods We conducted the study among 1099 ART naïve adults living with HIV/AIDS in Uganda. Data were collected at three time points: baseline, 6 and 12 months. Multiple regression and discrete time survival models were used to determine the relationship between suicidality and indices of HIV outcomes. Results Majority of the participants were female and the participant mean age was 35 years. Most of them (73%) had primary or no formal education. The proportion of participants with suicidality decreased from 2.9% at baseline to roughly 1% both at month 6 and month 12. Of the investigated clinical and behavioural outcomes, baseline suicidality only had a negative impact on missing a dose of ART where the odds of missing a dose of ART were 8.25 (95% CI 2.45–27.71, p〉0.01) times higher for participants with suicidality compared to those without suicidality. The following outcomes were not significantly impacted by baseline suicidality: HIV clinical stage, CD4 count and risky sexual behaviour. Conclusions The fact that baseline suicidality significantly negatively impacted ART adherence calls for the incorporation of psychosocial interventions to target indices of psychological distress such as suicidality to improve HIV related outcomes.
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    Natural 2HDMs without FCNCs (2021)
    American Physical Society
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  • 86
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    Resonant Measurement of Nonreorientable Spin-Orbit Torque from a Ferromagnetic Source Layer Accounting for Dynamic Spin Pumping (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2331-7019
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  • 87
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    Rydberg excitons in synthetic cuprous oxide Cu2O (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2475-9953
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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    Dephasing-induced growth of discrete time-crystalline order in spin networks (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2469-9950
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  • 89
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    Deterministic quantum one-time pad via Fibonacci anyons (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2469-9926
    Electronic ISSN: 2469-9934
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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    Structural insights into a novel family of integral membrane siderophore reductases (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: Gram-negative bacteria take up the essential ion Fe3+ as ferric-siderophore complexes through their outer membrane using TonB-dependent transporters. However, the subsequent route through the inner membrane differs across many bacterial species and siderophore chemistries and is not understood in detail. Here, we report the crystal structure of the inner membrane protein FoxB (from Pseudomonas aeruginosa) that is involved in Fe-siderophore uptake. The structure revealed a fold with two tightly bound heme molecules. In combination with in vitro reduction assays and in vivo iron uptake studies, these results establish FoxB as an inner membrane reductase involved in the release of iron from ferrioxamine during Fe-siderophore uptake.
    Print ISSN: 0027-8424
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    Preferences for COVID-19 vaccine distribution strategies in the US: A discrete choice survey (2021)
    Public Library of Science
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    Publication Date: 2021-08-20
    Description: Background The COVID-19 vaccination campaign in the US has been immensely successful in vaccinating those who are receptive, further increases in vaccination rates however will require more innovative approaches to reach those who remain hesitant. Developing vaccination strategies that are modelled on what people want could further increase uptake. Methods and findings To inform COVID-19 vaccine distribution strategies that are aligned with public preferences we conducted a discrete choice experiment among the US public (N = 2,895) between March 15 to March 22, 2021. We applied sampling weights, evaluated mean preferences using mixed logit models, and identified latent class preference subgroups. On average, the public prioritized ease, preferring single to two dose vaccinations (mean preference: -0.29; 95%CI: -0.37 to -0.20), vaccinating once rather than annually (mean preference: -0.79; 95%CI: -0.89 to -0.70) and reducing waiting times at vaccination sites. Vaccine enforcement reduced overall vaccine acceptance (mean preference -0.20; 95%CI: -0.30 to -0.10), with a trend of increasing resistance to enforcement with increasing vaccine hesitancy. Latent class analysis identified four distinct preference phenotypes: the first prioritized inherent “vaccine features” (46.1%), the second were concerned about vaccine “service delivery” (8.8%), a third group desired “social proof” of vaccine safety and were susceptible to enforcement (13.2%), and the fourth group were “indifferent” to vaccine and service delivery features and resisted enforcement (31.9%). Conclusions This study identifies several critical insights for the COVID-19 public health response. First, identifying preference segments is essential to ensure that vaccination services meet the needs of diverse population subgroups. Second, making vaccination easy and promoting autonomy by simplifying services and offering the public choices (where feasible) may increase uptake in those who remain deliberative. And, third vaccine mandates have the potential to increase vaccination rates in susceptible groups but may simultaneously promote control aversion and resistance in those who are most hesitant.
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  • 92
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    Generalized angular momentum transfer to up-converted photons via four-wave mixing in atomic gases (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2643-1564
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    Quantum chaos of the Bose-Fermi Kondo model at intermediate temperature (2021)
    American Physical Society
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    Publication Date: 2021-08-20
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  • 94
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    Ordering of Oxygen Vacancies and Related Ferroelectric Properties in HfO2−δ (2021)
    American Physical Society
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    Publication Date: 2021-08-20
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  • 95
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    Relativistic plasma aperture for laser intensity enhancement (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2643-1564
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  • 96
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    Topological magnetic textures in magnetic topological insulators (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2643-1564
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  • 97
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    Erratum: Nonadiabatic dynamics of superfluid spin-orbit-coupled degenerate Fermi gas [Phys. Rev. A 92 , 053626 (2015)] (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Print ISSN: 2469-9926
    Electronic ISSN: 2469-9934
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 98
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    The single-leg heel raise does not predict maximal plantar flexion strength in healthy males and females (2021)
    Public Library of Science
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    Publication Date: 2021-08-20
    Description: Introduction The single-leg heel raise test (SLHR) is commonly used in clinical settings to approximate plantar flexor strength, yet this is neither validated nor supported physiologically. The purposes of this study were to: determine (1) associations between SLHR repetitions, maximal plantar flexor strength, and reductions in strength; and (2) whether sex differences exist in performance of the SLHR. Methods Twenty-eight young, healthy participants (14 males,14 females, 19–30 years) performed repeated single-leg heel raises to task failure. Pre- and post-task measures included maximal voluntary isometric contractions (MVIC), and voluntary activation and contractile properties of the plantar flexor muscles, assessed using peripheral electrical stimulation of the tibial nerve. Surface electromyography was recorded for the medial and lateral gastrocnemius, soleus, and anterior tibialis muscles. Results The SLHR resulted in 20.5% reductions in MVIC torque (p
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    Remote advanced lab course: A case study analysis of open-ended projects (2021)
    American Physical Society
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    Publication Date: 2021-08-20
    Electronic ISSN: 2469-9896
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  • 100
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    Counting equilibria of large complex systems by instability index (2021)
    National Academy of Sciences
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    Publication Date: 2021-08-20
    Description: We consider a nonlinear autonomous system of N≫1 degrees of freedom randomly coupled by both relaxational (“gradient”) and nonrelaxational (“solenoidal”) random interactions. We show that with increased interaction strength, such systems generically undergo an abrupt transition from a trivial phase portrait with a single stable equilibrium into a topologically nontrivial regime of “absolute instability” where equilibria are on average exponentially abundant, but typically, all of them are unstable, unless the dynamics is purely gradient. When interactions increase even further, the stable equilibria eventually become on average exponentially abundant unless the interaction is purely solenoidal. We further calculate the mean proportion of equilibria that have a fixed fraction of unstable directions.
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