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  • National Academy of Sciences  (15,026)
  • American Society of Hematology  (13,387)
  • American Physical Society (APS)
  • MDPI Publishing
  • Public Library of Science
  • 2020-2023  (56)
  • 2000-2004  (28,954)
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  • 1
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    Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae (2020)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Peredo, E. L., & Cardon, Z. G. Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. Proceedings of the National Academy of Sciences of the United States of America, 117(29), 1(2020): 7438-17445, doi:10.1073/pnas.1906904117.
    Description: Among green plants, desiccation tolerance is common in seeds and spores but rare in leaves and other vegetative green tissues. Over the last two decades, genes have been identified whose expression is induced by desiccation in diverse, desiccation-tolerant (DT) taxa, including, e.g., late embryogenesis abundant proteins (LEA) and reactive oxygen species scavengers. This up-regulation is observed in DT resurrection plants, mosses, and green algae most closely related to these Embryophytes. Here we test whether this same suite of protective genes is up-regulated during desiccation in even more distantly related DT green algae, and, importantly, whether that up-regulation is unique to DT algae or also occurs in a desiccation-intolerant relative. We used three closely related aquatic and desert-derived green microalgae in the family Scenedesmaceae and capitalized on extraordinary desiccation tolerance in two of the species, contrasting with desiccation intolerance in the third. We found that during desiccation, all three species increased expression of common protective genes. The feature distinguishing gene expression in DT algae, however, was extensive down-regulation of gene expression associated with diverse metabolic processes during the desiccation time course, suggesting a switch from active growth to energy-saving metabolism. This widespread downshift did not occur in the desiccation-intolerant taxon. These results show that desiccation-induced up-regulation of expression of protective genes may be necessary but is not sufficient to confer desiccation tolerance. The data also suggest that desiccation tolerance may require induced protective mechanisms operating in concert with massive down-regulation of gene expression controlling numerous other aspects of metabolism.
    Description: Dr. Louise Lewis (University of Connecticut) provided F. rotunda and A. deserticola. Suzanne Thomas and Jordan Stark provided expert technical assistance. This work was supported by the NSF, Division of Integrative Organismal Systems (1355085 to Z.G.C.), and an anonymous donor (to Z.G.C.).
    Keywords: Aquatic green algae ; Desert-evolved green algae ; Extremophiles ; Microbiotic ; Crusts ; Scenedesmaceae
    Repository Name: Woods Hole Open Access Server
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  • 2
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    Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Criswell, K. E., Roberts, L. E., Koo, E. T., Head, J. J., & Gillis, J. A. Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences of the United States of America, 118(51), (2021): e2114563118, https://doi.org/10.1073/pnas.2114563118.
    Description: The axial skeleton of tetrapods is organized into distinct anteroposterior regions of the vertebral column (cervical, trunk, sacral, and caudal), and transitions between these regions are determined by colinear anterior expression boundaries of Hox5/6, -9, -10, and -11 paralogy group genes within embryonic paraxial mesoderm. Fishes, conversely, exhibit little in the way of discrete axial regionalization, and this has led to scenarios of an origin of Hox-mediated axial skeletal complexity with the evolutionary transition to land in tetrapods. Here, combining geometric morphometric analysis of vertebral column morphology with cell lineage tracing of hox gene expression boundaries in developing embryos, we recover evidence of at least five distinct regions in the vertebral skeleton of a cartilaginous fish, the little skate (Leucoraja erinacea). We find that skate embryos exhibit tetrapod-like anteroposterior nesting of hox gene expression in their paraxial mesoderm, and we show that anterior expression boundaries of hox5/6, hox9, hox10, and hox11 paralogy group genes predict regional transitions in the differentiated skate axial skeleton. Our findings suggest that hox-based axial skeletal regionalization did not originate with tetrapods but rather has a much deeper evolutionary history than was previously appreciated.
    Description: This research was funded by a Natural Environment Research Council Grant (to J.J.H., J.A.G., and K.E.C.: NE/S000739/1) and a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377), and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) (to J.A.G.).
    Keywords: Hox genes ; Regionalization ; Chondrichthyan ; Vertebral column
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  • 3
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    Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis (2020)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-31
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Northcutt, A. J., Kick, D. R., Otopalik, A. G., Goetz, B. M., Harris, R. M., Santin, J. M., Hofmann, H. A., Marder, E., & Schulz, D. J. Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis. Proceedings of the National Academy of Sciences of the United States of America, 116 (52) (2019): 26980-26990, doi: 10.1073/pnas.1911413116.
    Description: Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling—RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.
    Description: We thank members of the D.J.S., H.A.H., and E.M. laboratories for helpful discussions. We thank the Genomic Sequencing and Analysis Facility (The University of Texas [UT] at Austin) for library preparation and sequencing and the bioinformatics consulting team at the UT Austin Center for Computational Biology and Bioinformatics for helpful advice. This work was supported by National Institutes of Health grant R01MH046742-29 (to E.M. and D.J.S.) and the National Institute of General Medical Sciences T32GM008396 (support for A.J.N.) and National Institute of Mental Health grant 5R25MH059472-18 and the Grass Foundation (support for Neural Systems and Behavior Course at the Marine Biological Laboratory).
    Keywords: qPCR ; RNA-seq ; Stomatogastric ; Expression profiling
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  • 4
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    Chromatin dynamics enable transcriptional rhythms in the cnidarian Nematostella vectensis (2020)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Weizman, E. N., Tannenbaum, M., Tarrant, A. M., Hakim, O., & Levy, O. Chromatin dynamics enable transcriptional rhythms in the cnidarian Nematostella vectensis. Plos Genetics, 15(11), (2019): e1008397, doi: 10.1371/journal.pgen.1008397.
    Description: In animals, circadian rhythms are driven by oscillations in transcription, translation, and proteasomal degradation of highly conserved genes, resulting in diel cycles in the expression of numerous clock-regulated genes. Transcription is largely regulated through the binding of transcription factors to cis-regulatory elements within accessible regions of the chromatin. Chromatin remodeling is linked to circadian regulation in mammals, but it is unknown whether cycles in chromatin accessibility are a general feature of clock-regulated genes throughout evolution. To assess this, we applied an ATAC-seq approach using Nematostella vectensis, grown under two separate light regimes (light:dark (LD) and constant darkness (DD)). Based on previously identified N. vectensis circadian genes, our results show the coupling of chromatin accessibility and circadian transcription rhythmicity under LD conditions. Out of 180 known circadian genes, we were able to list 139 gene promoters that were highly accessible compared to common promoters. Furthermore, under LD conditions, we identified 259 active enhancers as opposed to 333 active enhancers under DD conditions, with 171 enhancers shared between the two treatments. The development of a highly reproducible ATAC-seq protocol integrated with published RNA-seq and ChIP-seq databases revealed the enrichment of transcription factor binding sites (such as C/EBP, homeobox, and MYB), which have not been previously associated with circadian signaling in cnidarians. These results provide new insight into the regulation of cnidarian circadian machinery. Broadly speaking, this supports the notion that the association between chromatin remodeling and circadian regulation arose early in animal evolution as reflected in this non-bilaterian lineage.
    Description: The research leading for this paper was funded by the Moore Foundation (https://www.moore.org), “Unwinding the Circadian Clock in a Sea Anemone” (Grant #4598) to A.T and O.L. The founders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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  • 5
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    The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean (2020)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Planes, S., Allemand, D., Agostini, S., Banaigs, B., Boissin, E., Boss, E., Bourdin, G., Bowler, C., Douville, E., Flores, J. M., Forcioli, D., Furla, P., Galand, P. E., Ghiglione, J. F., Gilson, E., Lombard, F., Moulin, C., Pesant, S., Poulain, J., Reynaud, S., Romac, S., Sullivan, M. B., Sunagawa, S., Thomas, O. P., Trouble, R., de Vargas, C., Thurber, R. V., Voolstra, C. R., Wincker, P., Zoccola, D., the Tara Pacific Consortium. The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean. Plos Biology, 17(9),(2019): e3000483, doi: 10.1371/journal.pbio.3000483.
    Description: Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects—in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the “-omics” complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016–2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east–west transect from Panama to Papua New Guinea and a south–north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.
    Description: We are keen to thank the commitment of the people and the following institutions for their financial and scientific support that made this singular expedition possible: CNRS, PSL, CSM, EPHE, Genoscope/CEA, Inserm, Université Cote d’Azur, ANR, agnès b., UNESCO-IOC, the Veolia Environment Foundation, Région Bretagne, Serge Ferrari, Billerudkorsnas, Amerisource Bergen Company, Lorient Agglomeration, Oceans by Disney, the Prince Albert II de Monaco Foundation, L’Oréal, Biotherm, France Collectivités, Kankyo Station, Fonds Français pour l’Environnement Mondial (FFEM), Etienne BOURGOIS, and the Tara Ocean Foundation teams and crew. Tara Pacific would not exist without the continuous support of the participating institutes. This study has been conducted using E.U. Copernicus Marine Service Information and Mercator Ocean products. We acknowledged funding from the Investissement d’avenir projects France Génomique (ANR-10-INBS-09) and OCEANOMICS (ANR-11-BTBR-0008). RVT was funded by a Dimensions of Biodiversity NSF grant (#1442306) for this work. SS is supported by the ETH Zurich and Helmut Horten Foundation. FL is supported by Sorbonne Université, Institut Universitaire de France, and the Fondation CA-PCA. Finally, we thank the ANR for funding the project CORALGENE, which will support the work the Tara Pacific program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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  • 6
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    Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks (2020)
    Public Library of Science
    Details
    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 Hopkinson, B. M., King, A. C., Owen, D. P., Johnson-Roberson, M., Long, M. H., & Bhandarkar, S. M. Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks. PLoS One, 15(3), (2020): e0230671, doi: 10.1371/journal.pone.0230671.
    Description: Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structure-from-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of ~96% and 〉90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.
    Description: This study was funded by grants from the Alfred P. Sloan Foundation (BMH, BR2014-049; https://sloan.org), and the National Science Foundation (MHL, OCE-1657727; https://www.nsf.gov). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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  • 7
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    Diel, daily, and spatial variation of coral reef seawater microbial communities (2020)
    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 inWeber, L., & Apprill, A. Diel, daily, and spatial variation of coral reef seawater microbial communities. PLoS One, 15(3), (2020): e0229442, doi: 10.1371/journal.pone.0229442.
    Description: Reef organisms influence microorganisms within the surrounding seawater, yet the spatial and temporal dynamics of seawater microbial communities located in proximity to corals are rarely investigated. To better understand reef seawater microbial community dynamics over time and space, we collected small-volume seawater samples during the day and night over a 72 hour period from three locations that differed in spatial distance from 5 Porites astreoides coral colonies on a shallow reef in St. John, U.S. Virgin Islands: near-coral (sampled 5 cm horizontally from each colony), reef-depth (sampled 2 m above each colony) and surface seawater (sampled 1 m from the seawater surface). At all time points and locations, we quantified abundances of microbial cells, sequenced small subunit rRNA genes of bacterial and archaeal communities, and measured inorganic nutrient concentrations. Prochlorococcus and Synechococcus cells were consistently elevated at night compared to day and these abundances changed over time, corresponding with temperature, nitrite, and silicate concentrations. During the day, bacterial and archaeal alpha diversity was significantly higher in reef-depth and near-coral seawater compared to the surface seawater, signifying that the reef influences the diversity of the seawater microorganisms. At night, alpha diversity decreased across all samples, suggesting that photosynthesis may favor a more taxonomically diverse community. While Prochlorococcus exhibited consistent temporal rhythmicity, additional taxa were enriched in reef seawater at night compared to day or in reef-depth compared to surface seawater based on their normalized sequence counts. There were some significant differences in nutrient concentrations and cell abundances between reef-depth and near-coral seawater but no clear trends. This study demonstrates that temporal variation supersedes small-scale spatial variation in proximity to corals in reef seawater microbial communities. As coral reefs continue to change in benthic composition worldwide, monitoring microbial composition in response to temporal changes and environmental fluctuations will help discern normal variability from longer lasting changes attributed to anthropogenic stressors and global climate change.
    Description: This work was supported by a National Science Foundation (NSF; https://www.nsf.gov/) Graduate Research Fellowship award to L.Weber. This research was also supported by NSF award OCE-1536782 to A. Mooney, J. Llopiz, and A. Apprill and NSF award OCE-1736288 to A. Apprill. Additionally, this work was supported by the NOAA Cooperative Institutes award NA19OAR4320074 to A.A. and E. Kujawinski and the Andrew W. Mellon Foundation Endowed Fund for Innovative Research to A.A.
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  • 8
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    Radial alignment of microtubules through tubulin polymerization in an evaporating droplet (2020)
    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 Keya, J. J., Kudoh, H., Kabir, A. M. R., Inoue, D., Miyamoto, N., Tani, T., Kakugo, A., & Shikinaka, K. Radial alignment of microtubules through tubulin polymerization in an evaporating droplet. Plos One, 15(4), (2020): e0231352, doi:10.1371/journal.pone.0231352.
    Description: We report the formation of spherulites from droplets of highly concentrated tubulin solution via nucleation and subsequent polymerization to microtubules (MTs) under water evaporation by heating. Radial alignment of MTs in the spherulites was confirmed by the optical properties of the spherulites observed using polarized optical microscopy and fluorescence microscopy. Temperature and concentration of tubulins were found as important parameters to control the spherulite pattern formation of MTs where evaporation plays a significant role. The alignment of MTs was regulated reversibly by temperature induced polymerization and depolymerization of tubulins. The formation of the MTs patterns was also confirmed at the molecular level from the small angle X-ray measurements. This work provides a simple method for obtaining radially aligned arrays of MTs.
    Description: Fund receiver: Akira Kakugo Grant-in-Aid for Scientific Research on Innovative Areas (Grant Nos. JP24104004 and 18H05423) and a Grant-in-Aid for Scientific Research (A) (Grant No. 18H03673) from kaken. NO - The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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  • 9
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    Global variability in seawater Mg:Ca and Sr:Ca ratios in the modern ocean (2020)
    National Academy of Sciences
    Details
    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 Lebrato, M., Garbe-Schönberg, D., Müller, M. N., Blanco-Ameijeiras, S., Feely, R. A., Lorenzoni, L., Molinero, J. C., Bremer, K., Jones, D. O. B., Iglesias-Rodriguez, D., Greeley, D., Lamare, M. D., Paulmier, A., Graco, M., Cartes, J., Barcelos E Ramos, J., de Lara, A., Sanchez-Leal, R., Jimenez, P., Paparazzo, F. E., Hartman, S. E., Westernströer, U., Küter, M., Benavides, R., da Silva, A. F., Bell, S., Payne, C., Olafsdottir, S., Robinson, K., Jantunen, L. M., Korablev, A., Webster, R. J., Jones, E. M., Gilg, O., Bailly du Bois, P., Beldowski, J., Ashjian, C., Yahia, N. D., Twining, B., Chen, X. G., Tseng, L. C., Hwang, J. S., Dahms, H. U., & Oschlies, A. Global variability in seawater Mg:Ca and Sr:Ca ratios in the modern ocean. Proceedings of the National Academy of Sciences of the United States of America, 117(36), (2020): 22281-22292, doi:10.1073/pnas.1918943117.
    Description: Seawater Mg:Ca and Sr:Ca ratios are biogeochemical parameters reflecting the Earth–ocean–atmosphere dynamic exchange of elements. The ratios’ dependence on the environment and organisms' biology facilitates their application in marine sciences. Here, we present a measured single-laboratory dataset, combined with previous data, to test the assumption of limited seawater Mg:Ca and Sr:Ca variability across marine environments globally. High variability was found in open-ocean upwelling and polar regions, shelves/neritic and river-influenced areas, where seawater Mg:Ca and Sr:Ca ratios range from ∼4.40 to 6.40 mmol:mol and ∼6.95 to 9.80 mmol:mol, respectively. Open-ocean seawater Mg:Ca is semiconservative (∼4.90 to 5.30 mol:mol), while Sr:Ca is more variable and nonconservative (∼7.70 to 8.80 mmol:mol); both ratios are nonconservative in coastal seas. Further, the Ca, Mg, and Sr elemental fluxes are connected to large total alkalinity deviations from International Association for the Physical Sciences of the Oceans (IAPSO) standard values. Because there is significant modern seawater Mg:Ca and Sr:Ca ratios variability across marine environments we cannot absolutely assume that fossil archives using taxa-specific proxies reflect true global seawater chemistry but rather taxa- and process-specific ecosystem variations, reflecting regional conditions. This variability could reconcile secular seawater Mg:Ca and Sr:Ca ratio reconstructions using different taxa and techniques by assuming an error of 1 to 1.50 mol:mol, and 1 to 1.90 mmol:mol, respectively. The modern ratios’ variability is similar to the reconstructed rise over 20 Ma (Neogene Period), nurturing the question of seminonconservative behavior of Ca, Mg, and Sr over modern Earth geological history with an overlooked environmental effect.
    Description: We thank the researchers, staff, students, and volunteers in all the expeditions around the world for their contributions. One anonymous referee and Bernhard Peucker-Ehenbrink, Woods Hole Oceanographic Institution, contributed significantly to the final version of the manuscript. This study was developed under a grant from the Federal Ministry of Education and Research to D.G.-S. under contract 03F0722A, by the Kiel Cluster of Excellence “The Future Ocean” (D1067/87) to A.O. and M.L., and by the “European project on Ocean Acidification” (European Community’s Seventh Framework Programme FP7/2007-2013, grant agreement 211384) to A.O. and M.L. Additional funding was provided from project DOSMARES CTM2010-21810-C03-02, by the UK Natural Environment Research Council, to the National Oceanography Centre. This is Pacific Marine Environmental Laboratory contribution number 5046.
    Keywords: global ; seawater ; Mg:Ca ; Sr:Ca ; biogeochemistry
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  • 10
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    Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres (2020)
    National Academy of Sciences
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chakraborty, A., Ruff, S. E., Dong, X., Ellefson, E. D., Li, C., Brooks, J. M., McBee, J., Bernard, B. B., & Hubert, C. R. J. Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. Proceedings of the National Academy of Sciences of the United States of America, 117(20), (2020): 11029-11037, doi: 10.1073/pnas.2002289117.
    Description: Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.
    Description: We wish to thank Jody Sandel as well as the crew of R/V GeoExplorer for collection of piston cores, onboard core processing, sample preservation, and shipment. Cynthia Kwan and Oliver Horanszky are thanked for assistance with amplicon library preparation. We also wish to thank Jayne Rattray, Daniel Gittins, and Marc Strous for valuable discussions and suggestions, and Rhonda Clark for research support. Collaborations with Andy Mort from the Geological Survey of Canada, and Richard Hatton from Geoscience Wales are also gratefully acknowledged. This work was financially supported by a Mitacs Elevate Postdoctoral Fellowship awarded to A.C.; an Alberta Innovates-Technology Futures/Eyes High Postdoctoral Fellowship to S.E.R.; and a Natural Sciences and Engineering Research Council Strategic Project Grant, a Genome Canada Genomics Applications Partnership Program grant, a Canada Foundation for Innovation grant (CFI-JELF 33752) for instrumentation, and Campus Alberta Innovates Program Chair funding to C.R.J.H.
    Keywords: Deep biosphere ; Microbiome ; Dispersal
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  • 11
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    A demographic and evolutionary analysis of maternal effect senescence (2020)
    National Academy of Sciences
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    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in MBL Hernandez, C. M., van Daalen, S. F., Caswell, H., Neubert, M. G., & Gribble, K. E. A demographic and evolutionary analysis of maternal effect senescence. Proceedings of the National Academy of Sciences of the United States of America, 17(28), (2020):16431-16437, doi: 10.1073/pnas.1919988117.
    Description: Maternal effect senescence—a decline in offspring survival or fertility with maternal age—has been demonstrated in many taxa, including humans. Despite decades of phenotypic studies, questions remain about how maternal effect senescence impacts evolutionary fitness. To understand the influence of maternal effect senescence on population dynamics, fitness, and selection, we developed matrix population models in which individuals are jointly classified by age and maternal age. We fit these models to data from individual-based culture experiments on the aquatic invertebrate, Brachionus manjavacas (Rotifera). By comparing models with and without maternal effects, we found that maternal effect senescence significantly reduces fitness for B. manjavacas and that this decrease arises primarily through reduced fertility, particularly at maternal ages corresponding to peak reproductive output. We also used the models to estimate selection gradients, which measure the strength of selection, in both high growth rate (laboratory) and two simulated low growth rate environments. In all environments, selection gradients on survival and fertility decrease with increasing age. They also decrease with increasing maternal age for late maternal ages, implying that maternal effect senescence can evolve through the same process as in Hamilton’s theory of the evolution of age-related senescence. The models we developed are widely applicable to evaluate the fitness consequences of maternal effect senescence across species with diverse aging and fertility schedule phenotypes.
    Description: K.E.G. was supported by Grant 5K01AG049049 from the National Institute on Aging and by the Bay and Paul Foundations. H.C. and S.F.v.D. were supported by the European Research Council through Advanced Grants 322829 and 788195 and by the Dutch Research Council through Grant ALWOP.2015.100. C.M.H. was supported by a National Science Foundation Graduate Research Fellowship. M.G.N. received funding from The Paul MacDonald Fye Chair for Excellence in Oceanography at the Woods Hole Oceanographic Institution.
    Keywords: Aging ; Demography ; Fitness ; Maternal effects ; Selection gradients
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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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  • 13
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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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  • 14
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    Dynamics and functional diversity of the smallest phytoplankton on the Northeast US shelf (2020)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2020. 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 117(22), (2020): 12215-12221, doi: 10.1073/pnas.1918439117.
    Description: Picophytoplankton are the most abundant primary producers in the ocean. Knowledge of their community dynamics is key to understanding their role in marine food webs and global biogeochemical cycles. To this end, we analyzed a 16-y time series of observations of a phytoplankton community at a nearshore site on the Northeast US Shelf. We used a size-structured population model to estimate in situ division rates for the picoeukaryote assemblage and compared the dynamics with those of the picocyanobacteria Synechococcus at the same location. We found that the picoeukaryotes divide at roughly twice the rate of the more abundant Synechococcus and are subject to greater loss rates (likely from viral lysis and zooplankton grazing). We describe the dynamics of these groups across short and long timescales and conclude that, despite their taxonomic differences, their populations respond similarly to changes in the biotic and abiotic environment. Both groups appear to be temperature limited in the spring and light limited in the fall and to experience greater mortality during the day than at night. Compared with Synechococcus, the picoeukaryotes are subject to greater top-down control and contribute more to the region’s primary productivity than their standing stocks suggest.
    Description: We thank E. T. Crockford, E. E. Peacock, J. Fredericks, Z. Sandwith, the MVCO Operations Team, and divers of the Woods Hole Oceanographic Institution diving program. This work was supported by NSF Grants OCE-0119915 (to R.J.O. and H.M.S.) and OCE-1655686 (to M.G.N., R.J.O., A.R.S., and H.M.O.); NASA Grants NNX11AF07G (to H.M.S.) and NNX13AC98G (to H.M.S.); Gordon and Betty Moore Foundation Grant GGA#934 (to H.M.S.); and Simons Foundation Grant 561126 (to H.M.S.).
    Description: 2020-11-15
    Keywords: Picoeukaryotes ; Flow cytometry ; Matrix model ; Primary productivity
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  • 15
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    Abiotic redox reactions in hydrothermal mixing zones: decreased energy availability for the subsurface biosphere (2020)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 202. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McDermott, J. M., Sylva, S. P., Ono, S., German, C. R., & Seewald, J. S. Abiotic redox reactions in hydrothermal mixing zones: decreased energy availability for the subsurface biosphere. Proceedings of the National Academy of Sciences of the United States of America, 117(34), (2020): 20453-20461, doi:10.1073/pnas.2003108117.
    Description: Subseafloor mixing of high-temperature hot-spring fluids with cold seawater creates intermediate-temperature diffuse fluids that are replete with potential chemical energy. This energy can be harnessed by a chemosynthetic biosphere that permeates hydrothermal regions on Earth. Shifts in the abundance of redox-reactive species in diffuse fluids are often interpreted to reflect the direct influence of subseafloor microbial activity on fluid geochemical budgets. Here, we examine hydrothermal fluids venting at 44 to 149 °C at the Piccard hydrothermal field that span the canonical 122 °C limit to life, and thus provide a rare opportunity to study the transition between habitable and uninhabitable environments. In contrast with previous studies, we show that hydrocarbons are contributed by biomass pyrolysis, while abiotic sulfate (SO42−) reduction produces large depletions in H2. The latter process consumes energy that could otherwise support key metabolic strategies employed by the subseafloor biosphere. Available Gibbs free energy is reduced by 71 to 86% across the habitable temperature range for both hydrogenotrophic SO42− reduction to hydrogen sulfide (H2S) and carbon dioxide (CO2) reduction to methane (CH4). The abiotic H2 sink we identify has implications for the productivity of subseafloor microbial ecosystems and is an important process to consider within models of H2 production and consumption in young oceanic crust.
    Description: Financial support was provided by the National Aeronautics and Space Administration (NASA) Astrobiology program (Awards NNX09AB75G and 80NSSC19K1427 to C.R.G. and J.S.S.) and the NSF (Award OCE-1061863 to C.R.G. and J.S.S.). Ship and vehicle time for cruise FK008 was provided by the Schmidt Ocean Institute. We thank the ROV Jason II and HROV Nereus groups, and the captain, officers, and crew of R/V Atlantis (AT18-16) and R/V Falkor (FK008) for their dedication to skillful operations at sea. We thank our scientific colleagues from both cruises, as well as Meg Tivey, Frieder Klein, and Scott Wankel for insightful discussions. We are grateful to the editor and two anonymous reviewers for providing helpful comments and suggestions.
    Keywords: Hydrothermal vent ; Subsurface biosphere ; Bioenergetics ; Biogeochemistry
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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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    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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    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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  • 20
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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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  • 21
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    Aseismic transient slip on the Gofar transform fault, East Pacific Rise (2020)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2020. 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 (2020): 201913625, doi: 10.1073/pnas.1913625117.
    Description: Oceanic transform faults display a unique combination of seismic and aseismic slip behavior, including a large globally averaged seismic deficit, and the local occurrence of repeating magnitude (M) ∼6 earthquakes with abundant foreshocks and seismic swarms, as on the Gofar transform of the East Pacific Rise and the Blanco Ridge in the northeast Pacific Ocean. However, the underlying mechanisms that govern the partitioning between seismic and aseismic slip and their interaction remain unclear. Here we present a numerical modeling study of earthquake sequences and aseismic transient slip on oceanic transform faults. In the model, strong dilatancy strengthening, supported by seismic imaging that indicates enhanced fluid-filled porosity and possible hydrothermal circulation down to the brittle–ductile transition, effectively stabilizes along-strike seismic rupture propagation and results in rupture barriers where aseismic transients arise episodically. The modeled slow slip migrates along the barrier zones at speeds ∼10 to 600 m/h, spatiotemporally correlated with the observed migration of seismic swarms on the Gofar transform. Our model thus suggests the possible prevalence of episodic aseismic transients in M ∼6 rupture barrier zones that host active swarms on oceanic transform faults and provides candidates for future seafloor geodesy experiments to verify the relation between aseismic fault slip, earthquake swarms, and fault zone hydromechanical properties.
    Description: We thank Joan Gomberg, Ruth Harris, Steve Hickman, Shane Detweiler, Mike Diggles, and two anonymous external reviewers for their thoughtful comments that helped to improve the manuscript. This study was supported by Natural Sciences and Engineering Research Council of Canada Discovery Grants RGPIN/418338-2012 and RGPIN-2018-05389; and NSF Grants OCE-10-61203 and OCE-18-33279.
    Description: 2020-10-28
    Keywords: Oceanic transform faults ; Earthquake rupture segmentation ; Aseismic transients ; Seismic swarms
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  • 22
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    Metrics that matter for assessing the ocean biological carbon pump (2020)
    National Academy of Sciences
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    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 Buesseler, K. O., Boyd, P. W., Black, E. E., & Siegel, D. A. Metrics that matter for assessing the ocean biological carbon pump. Proceedings of the National Academy of Sciences of the United States of America, (2020): 201918114, doi: 10.1073/pnas.1918114117.
    Description: The biological carbon pump (BCP) comprises wide-ranging processes that set carbon supply, consumption, and storage in the oceans’ interior. It is becoming increasingly evident that small changes in the efficiency of the BCP can significantly alter ocean carbon sequestration and, thus, atmospheric CO2 and climate, as well as the functioning of midwater ecosystems. Earth system models, including those used by the United Nation’s Intergovernmental Panel on Climate Change, most often assess POC (particulate organic carbon) flux into the ocean interior at a fixed reference depth. The extrapolation of these fluxes to other depths, which defines the BCP efficiencies, is often executed using an idealized and empirically based flux-vs.-depth relationship, often referred to as the “Martin curve.” We use a new compilation of POC fluxes in the upper ocean to reveal very different patterns in BCP efficiencies depending upon whether the fluxes are assessed at a fixed reference depth or relative to the depth of the sunlit euphotic zone (Ez). We find that the fixed-depth approach underestimates BCP efficiencies when the Ez is shallow, and vice versa. This adjustment alters regional assessments of BCP efficiencies as well as global carbon budgets and the interpretation of prior BCP studies. With several international studies recently underway to study the ocean BCP, there are new and unique opportunities to improve our understanding of the mechanistic controls on BCP efficiencies. However, we will only be able to compare results between studies if we use a common set of Ez-based metrics.
    Description: We thank the many scientists whose ideas and contributions over the years are the foundation of this paper. This includes A. Martin, who led the organization of the BIARRITZ group (now JETZON) workshop in July 2019, discussions at which helped to motivate this article. We thank D. Karl for pointing us in the right direction for this paper format at PNAS and two thoughtful reviewers who through their comments helped to improve this manuscript. Support for writing this piece is acknowledged from several sources, including the Woods Hole Oceanographic Institution’s Ocean Twilight Zone project (K.O.B.); NASA as part of the EXport Processes in the global Ocean from RemoTe Sensing (EXPORTS) program (K.O.B. and D.A.S.). E.E.B. was supported by a postdoctoral fellowship through the Ocean Frontier Institute at Dalhousie University. P.W.B. was supported by the Australian Research Council through a Laureate (FL160100131).
    Keywords: Biological carbon pump ; Twilight zone ; Particle flux
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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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    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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    A cross-institutional analysis of the effects of broadening trainee professional development on research productivity (2021)
    Public Library of Science
    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 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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    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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    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
    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 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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    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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    Inflammasome activation in neutrophils of patients with severe COVID-19 (2022)
    American Society of Hematology
    Details
    Publication Date: 2022-08-22
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aymonnier, K., Ng, J., Fredenburgh, L. E., Zambrano-Vera, K., Muenzer, P., Gutch, S., Fukui, S., Desjardins, M., Subramaniam, M., Baron, R. M., Raby, B. A., Perrella, M. A., Lederer, J. A., & Wagner, D. D. Inflammasome activation in neutrophils of patients with severe COVID-19. Blood Advances, 6(7), (2022): 2001–2013, https://doi.org/10.1182/bloodadvances.2021005949.
    Description: Infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) engages the inflammasome in monocytes and macrophages and leads to the cytokine storm in COVID-19. Neutrophils, the most abundant leukocytes, release neutrophil extracellular traps (NETs), which have been implicated in the pathogenesis of COVID-19. Our recent study shows that activation of the NLRP3 inflammasome is important for NET release in sterile inflammation. However, the role of neutrophil inflammasome formation in human disease is unknown. We hypothesized that SARS-CoV-2 infection may induce inflammasome activation in neutrophils. We also aimed to assess the localization of inflammasome formation (ie, apoptosis-associated speck-like protein containing a CARD [ASC] speck assembly) and timing relative to NETosis in stimulated neutrophils by real-time video microscopy. Neutrophils isolated from severe COVID-19 patients demonstrated that ∼2% of neutrophils in both the peripheral blood and tracheal aspirates presented ASC speck. ASC speck was observed in neutrophils with an intact poly-lobulated nucleus, suggesting early formation during neutrophil activation. Additionally, 40% of nuclei were positive for citrullinated histone H3, and there was a significant correlation between speck formation and nuclear histone citrullination. Time-lapse microscopy in lipopolysaccharide -stimulated neutrophils from fluorescent ASC reporter mice showed that ASC speck formed transiently and at the microtubule organizing center long before NET release. Our study shows that ASC speck is present in neutrophils from COVID-19 patients with respiratory failure and that it forms early in NETosis. Our findings suggest that inhibition of neutrophil inflammasomes may be beneficial in COVID-19.
    Description: P.M. received an Individual Marie Skłodowska-Curie Actions fellowship by the European Commission (796365 - COAGULANT). This work was supported by the National Institutes of Health (NIH)/Research Program Award grant R35 HL135765 (D.W.), by the NIH/National Heart, Lung, and Blood Institute grant T32 HL007633-35 (J.N.), and by the NIH/National Institute of Allergy and Infectious Diseases grant U01AI138318 (J.L and M.P); by the Massachusetts Consortium on Pathogen Readiness (MassCPR) Evergrande COVID‐19 Response Fund Award to B.R.; and by a generous gift to D.W. from the Steven Berzin family.
    Keywords: Phagocytes ; Granulocytes ; Myelopoiesis
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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
    Details
    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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    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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    Inflammasome expression is higher in ovarian tumors than in normal ovary (2020)
    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 Luborsky, J., Barua, A., Edassery, S., Bahr, J. M., & Edassery, S. L. Inflammasome expression is higher in ovarian tumors than in normal ovary. Plos One, 15(1), (2020): e0227081, doi:10.1371/journal.pone.0227081.
    Description: Chronic inflammation fundamentally influences cancer risk and development. A mechanism of chronic inflammation is the formation of inflammasome complexes which results in the sustained secretion of the pro-inflammatory cytokines IL1β and IL18. Inflammasome expression and actions vary among cancers. There is no information on inflammasome expression in ovarian cancer (OvCa). To determine if ovarian tumors express inflammasome components, mRNA and protein expression of NLRP3 (nucleotide-binding domain, leucine-rich repeat family, pyrin domain containing 3), caspase-1, IL1β, and IL18 expression in hen and human OvCa was assessed. Chicken (hen) OvCa a valid model of spontaneous human OvCa. Hens were selected into study groups with or without tumors using ultrasonography; tumors were confirmed by histology, increased cellular proliferation, and expression of immune cell marker mRNA. mRNA expression was higher for hallmarks of inflammasome activity (caspase-1, 5.9x increase, p = 0.04; IL1β, 4x increase, p = 0.04; and IL18, 7.8x increase, p = 0.0003) in hen OvCa compared to normal ovary. NLRP3, caspase-8 and caspase-11 mRNA did not differ significantly between tumor and non-tumor containing ovaries. Similar results occurred for human OvCa. Protein expression by immunohistochemistry paralleled mRNA expression and was qualitatively higher in tumors. Increased protein expression of caspase-1, IL1β, and IL18 occurred in surface epithelium, tumor cells, and immune cells. The aryl hydrocarbon receptor (AHR), a potential tumor suppressor and NLRP3 regulator, was higher in hen (2.4x increase, p = 0.002) and human tumors (1.8x increase, p = 0.038), suggesting a role in OvCa. Collectively, the results indicate that inflammasome expression is associated with hen and human OvCa, although the NLR sensor type remains to be determined.
    Description: This research was made possible by NIH grant NCI R03CA182120 (JL), DOD grant W81XWH-08-1-0203 (JL) and Swim Across America (AB). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    A geospatially resolved wetland vulnerability index: synthesis of physical drivers (2020)
    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 Defne, Z., Aretxabaleta, A. L., Ganju, N. K., Kalra, T. S., Jones, D. K., & Smith, K. E. L. A geospatially resolved wetland vulnerability index: synthesis of physical drivers. Plos One, 15(1), (2020): e0228504, doi:10.1371/journal.pone.0228504.
    Description: Assessing wetland vulnerability to chronic and episodic physical drivers is fundamental for establishing restoration priorities. We synthesized multiple data sets from E.B. Forsythe National Wildlife Refuge, New Jersey, to establish a wetland vulnerability metric that integrates a range of physical processes, anthropogenic impact and physical/biophysical features. The geospatial data are based on aerial imagery, remote sensing, regulatory information, and hydrodynamic modeling; and include elevation, tidal range, unvegetated to vegetated marsh ratio (UVVR), shoreline erosion, potential exposure to contaminants, residence time, marsh condition change, change in salinity, salinity exposure and sediment concentration. First, we delineated the wetland complex into individual marsh units based on surface contours, and then defined a wetland vulnerability index that combined contributions from all parameters. We applied principal component and cluster analyses to explore the interrelations between the data layers, and separate regions that exhibited common characteristics. Our analysis shows that the spatial variation of vulnerability in this domain cannot be explained satisfactorily by a smaller subset of the variables. The most influential factor on the vulnerability index was the combined effect of elevation, tide range, residence time, and UVVR. Tide range and residence time had the highest correlation, and similar bay-wide spatial variation. Some variables (e.g., shoreline erosion) had no significant correlation with the rest of the variables. The aggregated index based on the complete dataset allows us to assess the overall state of a given marsh unit and quickly locate the most vulnerable units in a larger marsh complex. The application of geospatially complete datasets and consideration of chronic and episodic physical drivers represents an advance over traditional point-based methods for wetland assessment.
    Description: This study was part of the Estuarine Physical Response to Storms project (GS2-2D awarded to NKG), supported by the Department of the Interior Hurricane Sandy Recovery program. Support was also provided by the U.S. Geological Survey, Coastal and Marine Hazards/Resources Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    The effect of bacteria on planula-larvae settlement and metamorphosis in the octocoral Rhytisma fulvum fulvum (2020)
    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 Freire, I., Gutner-Hoch, E., Muras, A., Benayahu, Y., & Otero, A. The effect of bacteria on planula-larvae settlement and metamorphosis in the octocoral Rhytisma fulvum fulvum. Plos One, 14(9), (2019): e0223214, doi:10.1371/journal.pone.0223214.
    Description: While increasing evidence supports a key role of bacteria in coral larvae settlement and development, the relative importance of environmentally-acquired versus vertically-transferred bacterial population is not clear. Here we have attempted to elucidate the role of post-brooding-acquired bacteria on the development of planula-larvae of the octocoral Rhytisma f. fulvum, in an in vitro cultivation system employing different types of filtered (FSW) and autoclaved (ASW) seawater and with the addition of native bacteria. A good development of larvae was obtained in polystyrene 6-well cell culture plates in the absence of natural reef substrata, achieving a 60–80% of larvae entering metamorphosis after 32 days, even in bacteria-free seawater, indicating that the bacteria acquired during the brooding period are sufficient to support planulae development. No significant difference in planulae attachment and development was observed when using 0.45 μm or 0.22 μm FSW, although autoclaving the 0.45 μm FSW negatively affected larval development, indicating the presence of beneficial bacteria. Autoclaving the different FSW homogenized the development of the larvae among the different treatments. The addition of bacterial strains isolated from the different FSW did not cause any significant effect on planulae development, although some specific strains of the genus Alteromonas seem to be beneficial for larvae development. Light was beneficial for planulae development after day 20, although no Symbiodinium cells could be observed, indicating either that light acts as a positive cue for larval development or the presence of beneficial phototrophic bacteria in the coral microbiome. The feasibility of obtaining advanced metamorphosed larvae in sterilized water provides an invaluable tool for studying the physiological role of the bacterial symbionts in the coral holobiont and the specificity of bacteria-coral interactions.
    Description: This work was supported by: EU FP7-Research Infrastructure Initiative Assemble (Association of European marine biological laboratories); EU FP7 Project Byefouling (grant agreement no 612717); Xunta de Galicia, Consellería de Cultura, Educación e Ordenación Universitaria (grant number ED431D 2017/22). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    Opinion: we need better data about the environmental persistence of plastic goods (2020)
    National Academy of Sciences
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    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2020. 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 117(26), (2020): 14618-14621, doi:10.1073/pnas.2008009117.
    Description: Plastic pollution is one of the most visible and complex environmental issues today. Interested and concerned parties include researchers, governmental agencies, nongovernmental organizations, industry, media, and the general public. One key assumption behind the issue and the public outcry is that plastics last indefinitely in the environment, resulting in chronic exposure that harms animals and humans. But the data supporting this assumption are scant.
    Description: We thank Briana Prado, Cassia Armstrong, and Anna Walsh for their help with the review, Kenneth Kostel, Katie Linehan, Daniel Ward, and Rose Cory for feedback on an earlier version of this piece, John Furfey for assistance with tracking down the original sources of the environmental lifetime estimates, and Natalie Reiner for help with Fig. 1. We acknowledge financial support from Woods Hole Oceanographic Institution (Woods Hole, MA) and the Seaver Institute (Los Angeles, CA).
    Description: 2020-12-10
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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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    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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    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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    A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome (2020)
    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 Furman, B. L. S., Cauret, C. M. S., Knytl, M., Song, X. Y., Premachandra, T., Ofori-Boateng, C., Jordan, D. C., Horb, M. E., & Evans, B. J. (2020). A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome. PLoS Genetics, 16(11), e1009121, doi:10.1371/journal.pgen.1009121.
    Description: In many species, sexual differentiation is a vital prelude to reproduction, and disruption of this process can have severe fitness effects, including sterility. It is thus interesting that genetic systems governing sexual differentiation vary among—and even within—species. To understand these systems more, we investigated a rare example of a frog with three sex chromosomes: the Western clawed frog, Xenopus tropicalis. We demonstrate that natural populations from the western and eastern edges of Ghana have a young Y chromosome, and that a male-determining factor on this Y chromosome is in a very similar genomic location as a previously known female-determining factor on the W chromosome. Nucleotide polymorphism of expressed transcripts suggests genetic degeneration on the W chromosome, emergence of a new Y chromosome from an ancestral Z chromosome, and natural co-mingling of the W, Z, and Y chromosomes in the same population. Compared to the rest of the genome, a small sex-associated portion of the sex chromosomes has a 50-fold enrichment of transcripts with male-biased expression during early gonadal differentiation. Additionally, X. tropicalis has sex-differences in the rates and genomic locations of recombination events during gametogenesis that are similar to at least two other Xenopus species, which suggests that sex differences in recombination are genus-wide. These findings are consistent with theoretical expectations associated with recombination suppression on sex chromosomes, demonstrate that several characteristics of old and established sex chromosomes (e.g., nucleotide divergence, sex biased expression) can arise well before sex chromosomes become cytogenetically distinguished, and show how these characteristics can have lingering consequences that are carried forward through sex chromosome turnovers.
    Description: This work was supported by the Natural Science and Engineering Research Council of Canada (RGPIN-2017-05770) (BJE), Resource Allocation Competition awards from Compute Canada (BJE), the Whitman Center Fellowship Program at the Marine Biological Laboratory (BJE), the Museum of Comparative Zoology at Harvard University (BJE), and National Institutes of Health grants R01-HD084409 (MEH) and P40-OD010997 (MEH). 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
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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 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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    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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    Tracking calcium dynamics from individual neurons in behaving animals (2022)
    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 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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    A scalable culturing system for the marine annelid Platynereis dumerilii (2020)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kuehn, E., Stockinger, A. W., Girard, J., Raible, F., & Özpolat, B. D. A scalable culturing system for the marine annelid Platynereis dumerilii. Plos One, 14(12), (2019): e0226156, doi: 10.1371/journal.pone.0226156.
    Description: Platynereis dumerilii is a marine segmented worm (annelid) with externally fertilized embryos and it can be cultured for the full life cycle in the laboratory. The accessibility of embryos and larvae combined with the breadth of the established molecular and functional techniques has made P. dumerilii an attractive model for studying development, cell lineages, cell type evolution, reproduction, regeneration, the nervous system, and behavior. Traditionally, these worms have been kept in rooms dedicated for their culture. This allows for the regulation of temperature and light cycles, which is critical to synchronizing sexual maturation. However, regulating the conditions of a whole room has limitations, especially if experiments require being able to change culturing conditions. Here we present scalable and flexible culture methods that provide ability to control the environmental conditions, and have a multi-purpose culture space. We provide a closed setup shelving design with proper light conditions necessary for P. dumerilii to mature. We also implemented a standardized method of feeding P. dumerilii cultures with powdered spirulina which relieves the ambiguity associated with using frozen spinach, and helps standardize nutrition conditions across experiments and across different labs. By using these methods, we were able to raise mature P. dumerilii, capable of spawning and producing viable embryos for experimentation and replenishing culture populations. These methods will allow for the further accessibility of P. dumerilii as a model system, and they can be adapted for other aquatic organisms.
    Description: BDO received funding from Hibbitt Startup Funds. FR received funding from projects P30035, and I2972, by Austrian Science Fund (FWF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    12-h clock regulation of genetic information flow by XBP1s (2020)
    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 Pan, Y., Ballance, H., Meng, H., Gonzalez, N., Kim, S., Abdurehman, L., York, B., Chen, X., Schnytzer, Y., Levy, O., Dacso, C. C., McClung, C. A., O'Malley, B. W., Liu, S., & Zhu, B. 12-h clock regulation of genetic information flow by XBP1s. Plos Biology, 18(1), (2020): e3000580, doi:10.1371/journal.pbio.3000580.
    Description: Our group recently characterized a cell-autonomous mammalian 12-h clock independent from the circadian clock, but its function and mechanism of regulation remain poorly understood. Here, we show that in mouse liver, transcriptional regulation significantly contributes to the establishment of 12-h rhythms of mRNA expression in a manner dependent on Spliced Form of X-box Binding Protein 1 (XBP1s). Mechanistically, the motif stringency of XBP1s promoter binding sites dictates XBP1s’s ability to drive 12-h rhythms of nascent mRNA transcription at dawn and dusk, which are enriched for basal transcription regulation, mRNA processing and export, ribosome biogenesis, translation initiation, and protein processing/sorting in the Endoplasmic Reticulum (ER)-Golgi in a temporal order consistent with the progressive molecular processing sequence described by the central dogma information flow (CEDIF). We further identified GA-binding proteins (GABPs) as putative novel transcriptional regulators driving 12-h rhythms of gene expression with more diverse phases. These 12-h rhythms of gene expression are cell autonomous and evolutionarily conserved in marine animals possessing a circatidal clock. Our results demonstrate an evolutionarily conserved, intricate network of transcriptional control of the mammalian 12-h clock that mediates diverse biological pathways. We speculate that the 12-h clock is coopted to accommodate elevated gene expression and processing in mammals at the two rush hours, with the particular genes processed at each rush hour regulated by the circadian and/or tissue-specific pathways.
    Description: This study was supported by the American Diabetes Association junior faculty development award 1-18-JDF-025 to B.Z., by funding from National Institute of Health HD07879 and 1P01DK113954 to B.W.O, by funding from National Science Foundation award 1703170 to C.C.D. and B.Z., and by funding from Brockman Foundation to C.C.D and B.W.O. This work was further supported by the UPMC Genome Center with funding from UPMC’s Immunotherapy and Transplant Center. This research was supported in part by the University of Pittsburgh Center for Research Computing through the resources provided. Research reported in this publication was further supported by the National Institute of Diabetes And Digestive And Kidney Diseases of the National Institutes of Health under award number P30DK120531 to Pittsburgh Liver Research Center, in which both S.L. and B.Z. are members. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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    Ecophysiology of coral reef primary producers across an upwelling gradient in the tropical central Pacific (2020)
    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 Johnson, M. D., Fox, M. D., Kelly, E. L. A., Zgliczynski, B. J., Sandin, S. A., & Smith, J. E. Ecophysiology of coral reef primary producers across an upwelling gradient in the tropical central Pacific. Plos One, 15(2), (2020): e0228448, doi:10.1371/journal.pone.0228448.
    Description: Upwelling is an important source of inorganic nutrients in marine systems, yet little is known about how gradients in upwelling affect primary producers on coral reefs. The Southern Line Islands span a natural gradient of inorganic nutrient concentrations across the equatorial upwelling region in the central Pacific. We used this gradient to test the hypothesis that benthic autotroph ecophysiology is enhanced on nutrient-enriched reefs. We measured metabolism and photophysiology of common benthic taxa, including the algae Porolithon, Avrainvillea, and Halimeda, and the corals Pocillopora and Montipora. We found that temperature (27.2–28.7°C) was inversely related to dissolved inorganic nitrogen (0.46–4.63 μM) and surface chlorophyll a concentrations (0.108–0.147 mg m-3), which increased near the equator. Contrary to our prediction, ecophysiology did not consistently track these patterns in all taxa. Though metabolic rates were generally variable, Porolithon and Avrainvillea photosynthesis was highest at the most productive and equatorial island (northernmost). Porolithon photosynthetic rates also generally increased with proximity to the equator. Photophysiology (maximum quantum yield) increased near the equator and was highest at northern islands in all taxa. Photosynthetic pigments also were variable, but chlorophyll a and carotenoids in Avrainvillea and Montipora were highest at the northern islands. Phycobilin pigments of Porolithon responded most consistently across the upwelling gradient, with higher phycoerythrin concentrations closer to the equator. Our findings demonstrate that the effects of in situ nutrient enrichment on benthic autotrophs may be more complex than laboratory experiments indicate. While upwelling is an important feature in some reef ecosystems, ancillary factors may regulate the associated consequences of nutrient enrichment on benthic reef organisms.
    Description: This work was supported by funding from the Moore Family Foundation, the Gordon and Betty Moore Foundation, the Scripps family, and anonymous donors. The funders had no role in study design, data collection and analysis, or preparation of the manuscript.
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    Origin of interannual variability in global mean sea level (2020)
    National Academy of Sciences
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    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2020. 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 117(25), (2020): 13983-13990, doi: 10.1073/pnas.1922190117.
    Description: The two dominant drivers of the global mean sea level (GMSL) variability at interannual timescales are steric changes due to changes in ocean heat content and barystatic changes due to the exchange of water mass between land and ocean. With Gravity Recovery and Climate Experiment (GRACE) satellites and Argo profiling floats, it has been possible to measure the relative steric and barystatic contributions to GMSL since 2004. While efforts to “close the GMSL budget” with satellite altimetry and other observing systems have been largely successful with regards to trends, the short time period covered by these records prohibits a full understanding of the drivers of interannual to decadal variability in GMSL. One particular area of focus is the link between variations in the El Niño−Southern Oscillation (ENSO) and GMSL. Recent literature disagrees on the relative importance of steric and barystatic contributions to interannual to decadal variability in GMSL. Here, we use a multivariate data analysis technique to estimate variability in barystatic and steric contributions to GMSL back to 1982. These independent estimates explain most of the observed interannual variability in satellite altimeter-measured GMSL. Both processes, which are highly correlated with ENSO variations, contribute about equally to observed interannual GMSL variability. A theoretical scaling analysis corroborates the observational results. The improved understanding of the origins of interannual variability in GMSL has important implications for our understanding of long-term trends in sea level, the hydrological cycle, and the planet’s radiation imbalance.
    Description: The research was carried out at JPL, California Institute of Technology, under a contract with NASA. This study was funded by NASA Grants NNX17AH35G (Ocean Surface Topography Science Team), 80NSSC17K0564, and 80NSSC17K0565 (NASA Sea Level Change Team). The efforts of J.T.F. in this work were also supported by NSF Award AGS-1419571, and by the Regional and Global Model Analysis component of the Earth and Environmental System Modeling Program of the US Department of Energy's Office of Biological & Environmental Research via National Science Foundation Grant IA 1844590. C.G.P. was supported by the J. Lamar Worzel Assistant Scientist Fund and the Penzance Endowed Fund in Support of Assistant Scientists at the Woods Hole Oceanographic Institution.
    Description: 2020-12-08
    Keywords: Sea level ; Climate variability ; Global mean sea level ; Satellite altimetry
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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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    Identification of chondritic krypton and xenon in Yellowstone gases and the timing of terrestrial volatile accretion (2020)
    National Academy of Sciences
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    Publication Date: 2022-10-26
    Description: © The Author(s), [year]. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Broadley, M. W., Barry, P. H., Bekaert, D. V., Byrne, D. J., Caracausi, A., Ballentine, C. J., & Marty, B. Identification of chondritic krypton and xenon in Yellowstone gases and the timing of terrestrial volatile accretion. Proceedings of the National Academy of Sciences of the United States of America, 117 (25), (2020): 13997-14004, doi: 10.1073/pnas.2003907117.
    Description: Identifying the origin of noble gases in Earth’s mantle can provide crucial constraints on the source and timing of volatile (C, N, H2O, noble gases, etc.) delivery to Earth. It remains unclear whether the early Earth was able to directly capture and retain volatiles throughout accretion or whether it accreted anhydrously and subsequently acquired volatiles through later additions of chondritic material. Here, we report high-precision noble gas isotopic data from volcanic gases emanating from, in and around, the Yellowstone caldera (Wyoming, United States). We show that the He and Ne isotopic and elemental signatures of the Yellowstone gas requires an input from an undegassed mantle plume. Coupled with the distinct ratio of 129Xe to primordial Xe isotopes in Yellowstone compared with mid-ocean ridge basalt (MORB) samples, this confirms that the deep plume and shallow MORB mantles have remained distinct from one another for the majority of Earth’s history. Krypton and xenon isotopes in the Yellowstone mantle plume are found to be chondritic in origin, similar to the MORB source mantle. This is in contrast with the origin of neon in the mantle, which exhibits an isotopic dichotomy between solar plume and chondritic MORB mantle sources. The co-occurrence of solar and chondritic noble gases in the deep mantle is thought to reflect the heterogeneous nature of Earth’s volatile accretion during the lifetime of the protosolar nebula. It notably implies that the Earth was able to retain its chondritic volatiles since its earliest stages of accretion, and not only through late additions.
    Description: Samples were collected as part of Study YELL-08056: Xenon Anomalies in the Yellowstone Hotspot. We thank Annie Carlson and all of the rangers at the Yellowstone National Park for providing invaluable advice and help when collecting the samples. M.W.B., D.V.B., D.J.B., and B.M. were supported by the European Research Council (PHOTONIS Project Grant 695618). This work was partially supported by Grants G-2016-7206 and G-2017-9696 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory (to P.H.B.) and UK National Environment Research Council Deep Volatile Grant NE/M000427/1 (to C.J.B.). We also thank Laurent Zimmerman for providing help with the analysis. Finally, we thank the editor for efficient handling of our manuscript and the two anonymous reviewers for their insightful comments. This is CRPG contribution 2998.
    Keywords: Origin of Earth’s volatiles ; Accretion ; Mantle plume ; Noble gases ; Yellowstone
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    Dark biological superoxide production as a significant flux and sink of marine dissolved oxygen (2020)
    National Academy of Sciences
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    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 Sutherland, K. M., Wankel, S. D., & Hansel, C. M. Dark biological superoxide production as a significant flux and sink of marine dissolved oxygen. Proceedings of the National Academy of Sciences of the United States of America, 117(7), (2020): 3433-3439, doi:10.1073/pnas.1912313117.
    Description: The balance between sources and sinks of molecular oxygen in the oceans has greatly impacted the composition of Earth’s atmosphere since the evolution of oxygenic photosynthesis, thereby exerting key influence on Earth’s climate and the redox state of (sub)surface Earth. The canonical source and sink terms of the marine oxygen budget include photosynthesis, respiration, photorespiration, the Mehler reaction, and other smaller terms. However, recent advances in understanding cryptic oxygen cycling, namely the ubiquitous one-electron reduction of O2 to superoxide by microorganisms outside the cell, remains unexplored as a potential player in global oxygen dynamics. Here we show that dark extracellular superoxide production by marine microbes represents a previously unconsidered global oxygen flux and sink comparable in magnitude to other key terms. We estimate that extracellular superoxide production represents a gross oxygen sink comprising about a third of marine gross oxygen production, and a net oxygen sink amounting to 15 to 50% of that. We further demonstrate that this total marine dark extracellular superoxide flux is consistent with concentrations of superoxide in marine environments. These findings underscore prolific marine sources of reactive oxygen species and a complex and dynamic oxygen cycle in which oxygen consumption and corresponding carbon oxidation are not necessarily confined to cell membranes or exclusively related to respiration. This revised model of the marine oxygen cycle will ultimately allow for greater reconciliation among estimates of primary production and respiration and a greater mechanistic understanding of redox cycling in the ocean.
    Description: This work was supported by NASA Earth and Space Science Fellowship NNX15AR62H to K.M.S., NASA Exobiology grant NNX15AM04G to S.D.W. and C.M.H., and NSF Division of Ocean Sciences grant 1355720 to C.M.H. This research was further supported in part by Hanse-Wissenschaftskolleg Institute of Advanced Study fellowships to C.M.H. and S.D.W. We thank Danielle Hicks for assistance with figures and Community Earth Systems Model (CESM) Large Ensemble Project for the availability and use of its data product. The CESM project is primarily supported by the NSF.
    Keywords: Microbial superoxide ; Reactive oxygen species ; Marine dissolved oxygen
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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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    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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    Growth retardation and abnormal maternal behavior in mice lacking testicular orphan nuclear receptor 4 (2004)
    National Academy of Sciences
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    Publication Date: 2004-10-11
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    The mouse juvenile spermatogonial depletion (jsd) phenotype is due to a mutation in the X-derived retrogene, mUtp14b (2004)
    National Academy of Sciences
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    Publication Date: 2004-08-02
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  • 59
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    Ghrelin cells replace insulin-producing   cells in two mouse models of pancreas development (2004)
    National Academy of Sciences
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    Publication Date: 2004-02-17
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  • 60
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    Luteinizing hormone induction of ovarian tumors: Oligogenic differences between mouse strains dictates tumor disposition (2000)
    National Academy of Sciences
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    Publication Date: 2000-01-04
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  • 61
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    Neurotrophin secretion from hippocampal neurons evoked by long-term-potentiation-inducing electrical stimulation patterns (2002)
    National Academy of Sciences
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    Publication Date: 2002-04-30
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  • 62
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    Interactions that determine the assembly of a retinoid X receptor/corepressor complex (2002)
    National Academy of Sciences
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    Publication Date: 2002-04-23
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  • 63
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    Akt suppresses androgen-induced apoptosis by phosphorylating and inhibiting androgen receptor (2001)
    National Academy of Sciences
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    Publication Date: 2001-06-12
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  • 64
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    Alternate surfaces of transcriptional coregulator GRIP1 function in different glucocorticoid receptor activation and repression contexts (2002)
    National Academy of Sciences
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    Publication Date: 2002-12-12
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  • 65
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    Rapid modulation of osteoblast ion channel responses by 1 ,25(OH)2-vitamin D3 requires the presence of a functional vitamin D nuclear receptor (2004)
    National Academy of Sciences
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    Publication Date: 2004-02-02
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  • 66
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    Female preproenkephalin-knockout mice display altered emotional responses (2001)
    National Academy of Sciences
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    Publication Date: 2001-02-13
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  • 67
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    From The Cover: Chromatin immunoprecipitation (ChIP) scanning identifies primary glucocorticoid receptor target genes (2004)
    National Academy of Sciences
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    Publication Date: 2004-10-22
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  • 68
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    Constitutive arrestin-mediated desensitization of a human vasopressin receptor mutant associated with nephrogenic diabetes insipidus (2001)
    National Academy of Sciences
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    Publication Date: 2001-01-02
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  • 69
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    An agonist-induced switch in G protein coupling of the gonadotropin-releasing hormone receptor regulates pulsatile neuropeptide secretion (2003)
    National Academy of Sciences
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    Publication Date: 2003-02-18
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  • 70
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    Mutations in the small heterodimer partner gene are associated with mild obesity in Japanese subjects (2001)
    National Academy of Sciences
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    Publication Date: 2001-01-16
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  • 71
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    From The Cover: 11 -Hydroxysteroid dehydrogenase inhibition improves cognitive function in healthy elderly men and type 2 diabetics (2004)
    National Academy of Sciences
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    Publication Date: 2004-04-07
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  • 72
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    Identification of the human cytochrome P450, P450RAI-2, which is predominantly expressed in the adult cerebellum and is responsible for all-trans-retinoic acid metabolism (2000)
    National Academy of Sciences
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    Publication Date: 2000-05-23
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  • 73
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    Loss of BETA2/NeuroD leads to malformation of the dentate gyrus and epilepsy (2000)
    National Academy of Sciences
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    Publication Date: 2000-01-18
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  • 74
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    A role for estrogen receptor   in the regulation of growth of the ventral prostate (2001)
    National Academy of Sciences
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    Publication Date: 2001-05-22
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  • 75
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    A newborn lethal defect due to inactivation of retinaldehyde dehydrogenase type 3 is prevented by maternal retinoic acid treatment (2003)
    National Academy of Sciences
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    Publication Date: 2003-11-17
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  • 76
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    Lack of tissue glucocorticoid reactivation in 11 -hydroxysteroid dehydrogenase type 1 knockout mice ameliorates age-related learning impairments (2001)
    National Academy of Sciences
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    Publication Date: 2001-03-27
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  • 77
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    A dynamic shift of VEGF isoforms with a transient and selective progesterone-induced expression of VEGF189 regulates angiogenesis and vascular permeability in human uterus (2002)
    National Academy of Sciences
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    Publication Date: 2002-04-23
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  • 78
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    Comparative PRKAR1A genotype-phenotype analyses in humans with Carney complex and prkar1a haploinsufficient mice (2004)
    National Academy of Sciences
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    Publication Date: 2004-09-15
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  • 79
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    Coactivator/corepressor ratios modulate PR-mediated transcription by the selective receptor modulator RU486 (2002)
    National Academy of Sciences
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    Publication Date: 2002-06-04
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  • 80
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    Expression of a nonmyristylated variant of the catalytic subunit of protein kinase A during male germ-cell development (2000)
    National Academy of Sciences
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    Publication Date: 2000-06-06
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  • 81
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    Contrasting patterns of expression of transcription factors in pancreatic   and   cells (2003)
    National Academy of Sciences
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    Publication Date: 2003-10-13
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  • 82
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    Genetic disruption of PPAR  decreases the tumorigenicity of human colon cancer cells (2001)
    National Academy of Sciences
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    Publication Date: 2001-02-27
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  • 83
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    Filamin-A fragment localizes to the nucleus to regulate androgen receptor and coactivator functions (2003)
    National Academy of Sciences
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    Publication Date: 2003-04-07
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  • 84
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    The role of Shc and insulin-like growth factor 1 receptor in mediating the translocation of estrogen receptor α to the plasma membrane (2004)
    National Academy of Sciences
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    Publication Date: 2004-02-05
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  • 85
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    Allosteric activation of the CaR by L-amino acids (2000)
    National Academy of Sciences
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    Publication Date: 2000-04-25
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  • 86
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    3D structure of human FK506-binding protein 52: Implications for the assembly of the glucocorticoid receptor/Hsp90/immunophilin heterocomplex (2004)
    National Academy of Sciences
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    Publication Date: 2004-05-24
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  • 87
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    Nongenomic actions of estrogens and xenoestrogens by binding at a plasma membrane receptor unrelated to estrogen receptor alpha and estrogen receptor beta (2000)
    National Academy of Sciences
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    Publication Date: 2000-10-10
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  • 88
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    Tonic inhibition in mouse hippocampal CA1 pyramidal neurons is mediated by  5 subunit-containing  -aminobutyric acid type A receptors (2004)
    National Academy of Sciences
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    Publication Date: 2004-03-01
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  • 89
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    Ordered recruitment of histone acetyltransferases and the TRAP/Mediator complex to thyroid hormone-responsive promoters in vivo (2002)
    National Academy of Sciences
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    Publication Date: 2002-05-28
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  • 90
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    Molecular cloning and spatio-temporal expression of the prostaglandin transporter: A basis for the action of prostaglandins in the bovine reproductive system (2003)
    National Academy of Sciences
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    Publication Date: 2003-09-16
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  • 91
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    The further redefining of steroid-mediated signaling (2003)
    National Academy of Sciences
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    Publication Date: 2003-02-26
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  • 92
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    Prostatic intraepithelial neoplasia in mice expressing an androgen receptor transgene in prostate epithelium (2001)
    National Academy of Sciences
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    Publication Date: 2001-09-04
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  • 93
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    Corticotropin-releasing factor receptor 2 is a tonic suppressor of vascularization (2002)
    National Academy of Sciences
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    Publication Date: 2002-05-21
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  • 94
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    Microfluidic glucose stimulation reveals limited coordination of intracellular Ca2+ activity oscillations in pancreatic islets (2004)
    National Academy of Sciences
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    Publication Date: 2004-08-18
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  • 95
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    Linking osteopetrosis and pycnodysostosis: Regulation of cathepsin K expression by the microphthalmia transcription factor family (2001)
    National Academy of Sciences
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    Publication Date: 2001-05-01
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  • 96
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    Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice (2001)
    National Academy of Sciences
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    Publication Date: 2001-09-04
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  • 97
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    Identification of bile acid precursors as endogenous ligands for the nuclear xenobiotic pregnane X receptor (2002)
    National Academy of Sciences
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    Publication Date: 2002-12-30
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  • 98
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    Reduced glucose tolerance is associated with poor memory performance and hippocampal atrophy among normal elderly (2003)
    National Academy of Sciences
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    Publication Date: 2003-02-05
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  • 99
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    Unknown
    Serum leptin level is a regulator of bone mass (2004)
    National Academy of Sciences
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    Publication Date: 2004-02-20
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  • 100
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    Semaphorin 3B (SEMA3B) induces apoptosis in lung and breast cancer, whereas VEGF165 antagonizes this effect (2004)
    National Academy of Sciences
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    Publication Date: 2004-07-23
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