Presentations and Papers

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This collection represents presentations made by members of the staff of the MBLWHOI Library or at the behest of the Library, and articles authored by members of the Library staff.

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  • Article
    Rice’s whale occurrence in the western Gulf of Mexico from passive acoustic recordings
    (Wiley, 2024-02-13) Soldevilla, Melissa S. ; Debich, Amanda J. ; Perez-Carballo, Itzel ; Jarriel, Sierra ; Frasier, Kaitlin E. ; Garrison, Lance P. ; Gracia, Adolfo ; Hildebrand, John A. ; Rosel, Patricia E. ; Serrano, Arturo
    Rice's whales (Balaenoptera ricei) are one of the most endangered marine mammal species in the world. Their known distribution is restricted to the Gulf of Mexico (GoMx) and basic knowledge of their ecology is limited. In their core distribution area along the northeastern GoMx shelf break (Rosel & Garrison, 2021), their abundance was estimated at 51 individuals, 95% CI [20, 130], based on line transect surveys conducted during 2017 and 2018 (Garrison et al., 2020). Most Rice's whale sightings and acoustic detections during the last 30 years occur in this area off the northwestern coast of Florida (Rice et al., 2014; Rosel et al., 2021; Širović et al., 2014; Soldevilla et al., 2017; Soldevilla, Ternus, et al., 2022). While visual sightings are rare (e.g., Rosel et al., 2021), recent passive acoustic detections during one year of recordings (Soldevilla, Debich, et al., 2022) establish that they routinely occur along the shelf break of the northwestern GoMx off Louisiana as well. Currently, Rice's whales are only known to occur within U.S. waters of the northern GoMx, although whaling records (Reeves et al., 2011) suggest they were distributed more broadly across the GoMx historically. Understanding their range and distribution is important for evaluating the impacts of human activities, including climate change, that threaten their long-term survival. Considering the high levels of anthropogenic activity throughout the GoMx (e.g., oil and gas exploration and extraction, fisheries, shipping, and oil spills), a comprehensive knowledge of the current distribution of Rice's whales is needed to understand the risk of these activities to the whales and to develop effective recovery and conservation strategies for this endangered species (Rosel et al., 2016).
  • Article
    Recent advances in vertical temperature profiler instrumentation and flux estimation methods facilitate groundwater – Surface water exchange studies in environments with strong discharge zones
    (Elsevier, 2024-06-23) Sohn, Robert A. ; Briggs, Martin A. ; Rey, David M.
    Groundwater fluxes to many surface water systems are spatially heterogeneous with discharge focused into discrete, high-flux zones. Quantifying fluxes in these preferential discharge zones is critical to a range of surface water habitat and water quality processes, but characterization can be difficult due to short-scale spatial and temporal variability. Passive heat-as-a-tracer methods employing vertical temperature profiler (VTP) data can provide the necessary spatial and temporal resolution, but upward fluid flow strongly attenuates the thermal signals used for estimating fluxes. In preferential discharge zones it becomes difficult to measure the signals in the subsurface and the flux parameter can become insensitive in the analysis models, leading to large uncertainties. We use data from a high-flux site of contaminant-loaded groundwater discharge to the Quashnet River on Cape Cod, Massachusetts, USA, to demonstrate how recent advances in VTP instrumentation that allow for the acquisition of high-resolution (0.001 °C) temperature data at short (1 cm) offsets near the ground surface, combined with advances in flux estimation methods that exploit the information content of the high-resolution data, facilitate heat-as-a-tracer approaches for characterizing groundwater-surface water exchanges and make it possible to obtain accurate and statistically robust results in a preferential discharge zone with a specific discharge of ∼1 m/d.
  • Article
    Non-equilibrium scour evolution around an emerged structure exposed to a transient wave
    (MDPI, 2024-06-05) Sogut, Deniz Velioglu ; Sogut, Erdinc ; Farhadzadeh, Ali ; Hsu, Tian-Jian
    The present study evaluates the performance of two numerical approaches in estimating non-equilibrium scour patterns around a non-slender square structure subjected to a transient wave, by comparing numerical findings with experimental data. This study also investigates the impact of the structure’s positioning on bed evolution, analyzing configurations where the structure is either attached to the sidewall or positioned at the centerline of the wave flume. The first numerical method treats sediment particles as a distinct continuum phase, directly solving the continuity and momentum equations for both sediment and fluid phases. The second method estimates sediment transport using the quadratic law of bottom shear stress, yielding robust predictions of bed evolution through meticulous calibration and validation. The findings reveal that both methods underestimate vortex-induced near-bed vertical velocities. Deposits formed along vortex trajectories are overestimated by the first method, while the second method satisfactorily predicts the bed evolution beneath these paths. Scour holes caused by wave impingement tend to backfill as the flow intensity diminishes. The second method cannot sufficiently capture this backfilling, whereas the first method adequately reflects the phenomenon. Overall, this study highlights significant variations in the predictive capabilities of both methods in regard to the evolution of non-equilibrium scour at low Keulegan–Carpenter numbers.
  • Article
    Fiber-optic seismic sensing of vadose zone soil moisture dynamics
    (Nature Research, 2024-08-05) Shen, Zhichao ; Yang, Yan ; Fu, Xiaojing ; Adams, Kyra H. ; Biondi, Ettore ; Zhan, Zhongwen
    Vadose zone soil moisture is often considered a pivotal intermediary water reservoir between surface and groundwater in semi-arid regions. Understanding its dynamics in response to changes in meteorologic forcing patterns is essential to enhance the climate resiliency of our ecological and agricultural system. However, the inability to observe high-resolution vadose zone soil moisture dynamics over large spatiotemporal scales hinders quantitative characterization. Here, utilizing pre-existing fiber-optic cables as seismic sensors, we demonstrate a fiber-optic seismic sensing principle to robustly capture vadose zone soil moisture dynamics. Our observations in Ridgecrest, California reveal sub-seasonal precipitation replenishments and a prolonged drought in the vadose zone, consistent with a zero-dimensional hydrological model. Our results suggest a significant water loss of 0.25 m/year through evapotranspiration at our field side, validated by nearby eddy-covariance based measurements. Yet, detailed discrepancies between our observations and modeling highlight the necessity for complementary in-situ validations. Given the escalated regional drought risk under climate change, our findings underscore the promise of fiber-optic seismic sensing to facilitate water resource management in semi-arid regions.
  • Article
    Surface latent and sensible heat fluxes over the Pacific Sub-Arctic Ocean from saildrone observations and three global reanalysis products
    (Frontiers Media, 2024-07-12) Sivam, Subhatra ; Zhang, Chidong ; Zhang, Dongxiao ; Yu, Lisan ; Dressel, Isabella
    Sea surface latent and sensible heat fluxes are crucial components of the air-sea energy exchanges that influence the upper-ocean heat content and the marine atmospheric boundary layer. Due to the limited availability of in situ observations, assessing their impact on Arctic weather and climate has mainly been done using data assimilation products and numerical model simulations. The accuracy of the surface fluxes in numerical models are, however, largely unvalidated. Recent deployments of saildrones, remotely piloted uncrewed surface vehicles, can help bridge this data gap of in situ observations. This study represents an initial effort to validate sea surface latent and sensible heat fluxes over the Pacific sub-Arctic open ocean from three commonly used global reanalysis products (NASA MERRA2, ECMWF ERA5, NOAA CFSR2) against observations by saildrones. In general, fluxes from these reanalysis products and saildrone observations agree well, except for CFSR2 sensible heat fluxes, which exhibit systematic negative biases. Sporadic, very large (greater than two observed standard deviations) discrepancies between fluxes from the reanalysis products and observations do occur. These substantial discrepancies in the reanalysis products primarily result from errors in temperature for sensible heat fluxes and errors in both humidity and wind speed for latent heat fluxes. The results from this study suggest that the sea surface latent and sensible heat fluxes from MERRA2 and ERA5 are reliable in representing the mean features of air-sea exchanges in the sub-Arctic region. Nonetheless, their reliability is limited when used for studies of high-frequency variability, such as synoptic weather events.
  • Article
    Meltwater orientations modify seismic anisotropy in temperate ice
    (American Geophysical Union, 2024-07-04) Seltzer, Cassandra ; Llorens, Maria-Gema ; Cross, Andrew J.
    Seismology is increasingly used to infer the magnitude and direction of glacial ice flow. However, the effects of interstitial meltwater on seismic properties remain poorly constrained. Here, we extend previous studies on seismic anisotropy in temperate ices to consider the role of melt preferred orientation (MPO). We used the ELLE numerical toolbox to simulate microstructural shear deformation of temperate ice with variable MPO strength and orientation, and calculated the effective seismic properties of these numerical ice-melt aggregates. Our models demonstrate that even 3.5% melt volume is sufficient to rotate fast directions by up to 90°, to increase Vp anisotropy by up to +110%, and to modify Vs anisotropy by −9 to +36%. These effects are especially prominent at strain rates ≥3.17 × 10−12 s−1. MPO may thus obscure the geophysical signatures of temperate ice flow in regions of rapid ice discharge, and is therefore pivotal for understanding ice mass loss.
  • Article
    On the role of small estuaries in retaining buoyant particles
    (National Academy of Sciences, 2024-08-19) Bo, Tong ; Ralston, David K. ; Geyer, W. Rockwell ; McWilliams, James C.
    Estuaries, as connectors between land and ocean, have complex interactions of river and tidal flows that affect the transport of buoyant materials like floating plastics, oil spills, organic matter, and larvae. This study investigates surface-trapped buoyant particle transport in estuaries by using idealized and realistic numerical simulations along with a theoretical model. While river discharge and estuarine exchange flow are usually expected to export buoyant particles to the ocean over subtidal timescales, this study reveals a ubiquitous physical transport mechanism that causes retention of buoyant particles in estuaries. Tidally varying surface convergence fronts affect the aggregation of buoyant particles, and the coupling between particle aggregation and oscillatory tidal currents leads to landward transport at subtidal timescales. Landward transport and retention of buoyant particles is greater in small estuaries, while large estuaries tend to export buoyant particles to the ocean. A dimensionless width parameter incorporating the tidal radian frequency and lateral velocity distinguishes small and large estuaries at a transitional value of around 1. Additionally, higher river flow tends to shift estuaries toward seaward transport and export of buoyant particles. These findings provide insights into understanding the distribution of buoyant materials in estuaries and predicting their fate in the land–sea exchange processes.
  • Article
    Mobilization of isotopically heavy sulfur during serpentinite subduction
    (American Association for the Advancement of Science, 2024-08-07) Schwarzenbach, Esther M. ; Dragovic, Besim ; Codillo, Emmanuel A. ; Streicher, Linus ; Scicchitano, Maria Rosa ; Wiechert, Uwe ; Klein, Frieder ; Marschall, Horst R. ; Scambelluri, Marco
    Primitive arc magmas are more oxidized and enriched in sulfur-34 (34S) compared to mid-ocean ridge basalts. These findings have been linked to the addition of slab-derived volatiles, particularly sulfate, to arc magmas. However, the oxidation state of sulfur in slab fluids and the mechanisms of sulfur transfer in the slab remain inconclusive. Juxtaposed serpentinite and eclogitic metagabbro from the Voltri Massif (Italy) provide evidence for sulfur mobilization and associated redox processes during infiltration of fluids. Using bulk rock and in situ δ34S measurements, combined with thermodynamic calculations, we document the transfer of bisulfide-dominated, 34S-enriched fluids in equilibrium with serpentinite into adjacent metagabbro. We argue that the process documented in this study is pervasive along the subduction interface and infer that subsequent melting of these reacted slab-mantle interface rocks could produce melts that display the characteristic oxygen fugacity and sulfur isotope signatures of arc magmas worldwide.
  • Article
    The Eurasian Arctic Ocean along the MOSAiC drift in 2019-2020: An interdisciplinary perspective on physical properties and processes
    (University of California Press, 2024-07-05) Schulz, Kirstin ; Koenig, Zoe ; Muilwijk, Morven ; Bauch, Dorothea ; Hoppe, Clara J. M. ; Droste, Elise S. ; Hoppmann, Mario ; Chamberlain, Emelia J. ; Laukert, Georgi ; Stanton, Tim ; Quintanilla-Zurita, Alejandra ; Fer, Ilker ; Heuze, Celine ; Karam, Salar ; Mieruch-Schnülle, Sebastian ; Baumann, Till M. ; Vredenborg, Myriel ; Tippenhauer, Sandra ; Granskog, Mats A.
    The Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC, 2019–2020), a year-long drift with the Arctic sea ice, has provided the scientific community with an unprecedented, multidisciplinary dataset from the Eurasian Arctic Ocean, covering high atmosphere to deep ocean across all seasons. However, the heterogeneity of data and the superposition of spatial and temporal variability, intrinsic to a drift campaign, complicate the interpretation of observations. In this study, we have compiled a quality-controlled physical hydrographic dataset with best spatio-temporal coverage and derived core parameters, including the mixed layer depth, heat fluxes over key layers, and friction velocity. We provide a comprehensive and accessible overview of the ocean conditions encountered along the MOSAiC drift, discuss their interdisciplinary implications, and compare common ocean climatologies to these new data. Our results indicate that, for the most part, ocean variability was dominated by regional rather than seasonal signals, carrying potentially strong implications for ocean biogeochemistry, ecology, sea ice, and even atmospheric conditions. Near-surface ocean properties were strongly influenced by the relative position of sampling, within or outside the river-water influenced Transpolar Drift, and seasonal warming and meltwater input. Ventilation down to the Atlantic Water layer in the Nansen Basin allowed for a stronger connectivity between subsurface heat and the sea ice and surface ocean via elevated upward heat fluxes. The Yermak Plateau and Fram Strait regions were characterized by heterogeneous water mass distributions, energetic ocean currents, and stronger lateral gradients in surface water properties in frontal regions. Together with the presented results and core parameters, we offer context for interdisciplinary research, fostering an improved understanding of the complex, coupled Arctic System.
  • Article
    Insights into the diet and feeding behavior of immature polar cod (Boreogadus saida) from the under-ice habitat of the central Arctic Ocean
    (Wiley, 2024-06-24) Schaafsma, Fokje L. ; Flores, Hauke ; David, Carmen L. ; Castellani, Giulia ; Sakinan, Serdar ; Meijboom, Andre ; Niehoff, Barbara ; Cornils, Astrid ; Hildebrandt, Nicole ; Schmidt, Katrin ; Snoeijs-Leijonmalm, Pauline ; Ehrlich, Julia ; Ashjian, Carin J. ; The MOSAiC team ECO
    Polar cod (Boreogadus saida) is an endemic key species of the Arctic Ocean ecosystem. The ecology of this forage fish is well studied in Arctic shelf habitats where a large part of its population lives. However, knowledge about its ecology in the central Arctic Ocean (CAO), including its use of the sea-ice habitat, is hitherto very limited. To increase this knowledge, samples were collected at the under-ice surface during several expeditions to the CAO between 2012 and 2020, including the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition. The diet of immature B. saida and the taxonomic composition of their potential prey were analysed, showing that both sympagic and pelagic species were important prey items. Stomach contents included expected prey such as copepods and amphipods. Surprisingly, more rarely observed prey such as appendicularians, chaetognaths, and euphausiids were also found to be important. Comparisons of the fish stomach contents with prey distribution data suggests opportunistic feeding. However, relative prey density and catchability are important factors that determine which type of prey is ingested. Prey that ensures limited energy expenditure on hunting and feeding is often found in the stomach contents even though it is not the dominant species present in the environment. To investigate the importance of prey quality and quantity for the growth of B. saida in this area, we measured energy content of dominant prey species and used a bioenergetic model to quantify the effect of variations in diet on growth rate potential. The modeling results suggest that diet variability was largely explained by stomach fullness and, to a lesser degree, the energetic content of the prey. Our results suggest that under climate change, immature B. saida may be at least equally sensitive to a loss in the number of efficiently hunted prey than to a reduction in the prey's energy content. Consequences for the growth and survival of B. saida will not depend on prey presence alone, but also on prey catchability, digestibility, and energy content.
  • Article
    Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells
    (Public Library of Science, 2024-07-11) Schaible, George A. ; Jay, Zackary J. ; Cliff, John ; Schulz, Frederik ; Gauvin, Colin ; Goudeau, Danielle ; Malmstrom, Rex R. ; Ruff, S. Emil ; Edgcomb, Virginia P. ; Hatzenpichler, Roland
    Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.
  • Article
    Models of the sea-surface height expression of the internal-wave continuum
    (American Meteorological Society, 2024-09-25) Samelson, Roger M. ; Farrar, J. Thomas
    Several models are presented for the sea surface height (SSH) signature of the interior-ocean internal-wave continuum. Most are based on the Garrett–Munk internal-wave model. One is derived from the frequency spectrum of dynamic height from mooring observations. The different models are all plausibly consistent with accepted dynamical and semiempirical spectral descriptions of the climatological interval-wave field in the interior ocean, but they result in different proportionalities between interior and SSH spectral energy levels. The differences arise in part from differences in the treatment of near-surface stratification, and a major source of uncertainty for all the models comes from inadequately constrained assumptions about the energy in the low-vertical-mode internal-wave field. Most of these models suggest that the SSH signature of the internal-wave continuum will be visible in SSH measurements from the Surface Water and Ocean Topography (SWOT) wide-swath satellite altimeter. Temporal variability of internal-wave energy levels and the internal-wave directional spectrum are less well characterized but will also be consequential for the observability of internal-wave signals in SWOT data.
  • Article
    Methane seeps on the US Atlantic margin: An updated inventory and interpretative framework
    (Elsevier, 2024-04-09) Ruppel, Carolyn D. ; Skarke, Adam D. ; Miller, Nathaniel C. ; Kidiwela, Maleen Wijeratna ; Kluesner, Jared W. ; Baldwin, Wayne E.
    Since the discovery of >570 methane flares on the northern U.S. Atlantic margin between Cape Hatteras and Georges Bank in the last decade, the acquisition of thousands of kilometers of additional water column imaging data has provided greater coverage at water depths between the outer continental shelf and the lower continental slope. The additional high-resolution data reveal >1400 gas flares, but the removal of probable duplicates from the combined database of new flares and those recognized in 2014 yields ∼1139 unique sites. Most of these sites occur in clusters of 5 or more seeps, leaving about 275 unique locations (including 47 clusters) for seepage along the margin. As a function of depth, seep distribution is heavily skewed toward the upper continental slope at water depths shallower than 400 m on the southern New England margin and ∼ 550 m in the Mid-Atlantic Bight, with additional seeps clustered at ∼1100 m and just deeper than ∼1400 m in both sectors. Despite little ongoing tectonic deformation or active faulting on this passive margin, a variety of processes driven from below the seafloor (e.g., migration of fluids along faults or through permeable strata, seepage above diapirs or other pre-existing structures) and from above (e.g., erosion, sapping, unroofing) contribute to the development of seeps in different settings along the margin. In addition, the prevalence of seeps on promontories overlooking shelf-breaking canyons may be directly related to the three-dimensional nature of the hydrate stability zone in these locations. As a function of depth, the parts of the slope at the contemporary landward limit of gas hydrate stability are devoid of seeps, and the upper slope zones with the most concentrated seepage were not within the gas hydrate stability zone even during the Last Glacial Maximum. Thus, if the large number of upper slope seeps is at least partially sourced in gas hydrate degradation, the gas emitted at these seeps must have migrated there from greater depths on the continental slope.
  • Article
    Narrowband noise induces frequency-specific underwater temporary threshold shifts in freshwater turtles
    (Acoustical Society of America, 2024-08-21) Salas, Andria K. ; Sims, Michele A. ; Harms, Craig A. ; Piniak, Wendy E. D. ; Mooney, T. Aran
    Freshwater turtles exhibit temporary threshold shifts (TTS) when exposed to broadband sound, but whether frequency-restricted narrowband noise induces TTS was unknown. Underwater TTS was investigated in two freshwater turtle species (Emydidae) following exposures to 1/6 -octave narrowband noise (155–172 dB re 1 μPa2 s). While shifts occurred in all turtles at the noise center frequency (400 Hz), there were more instances of TTS and greater shift magnitudes at 1/2 octave above the center frequency, despite considerably lower received levels. These frequency-specific data provide new insight into how TTS manifests in turtles and expand empirical models to predict freshwater turtle TTS.
  • Article
    Depth-partitioning of particulate organic carbon composition in the rising and falling stages of the Amazon River
    (American Geophysical Union, 2024-06-25) Rosengard, Sarah Z. ; Moura, Jose Mauro S. ; Spencer, Robert G. M. ; Johnson, Carl G. ; McNichol, Ann P. ; Steen, Andrew D. ; Galy, Valier
    The Amazon River mobilizes organic carbon across one of the world's largest terrestrial carbon reservoirs. Quantifying the sources of particulate organic carbon (POC) to this flux is typically challenging in large systems such as the Amazon River due to hydrodynamic sorting of sediments. Here, we analyze the composition of POC collected from multiple total suspended sediment (TSS) profiles in the mainstem at Óbidos, and surface samples from the Madeira, Solimões and Tapajós Rivers. As hypothesized, TSS and POC concentrations in the mainstem increased with depth and fit well to Rouse models for sediment sorting by grain size. Coupling these profiles with Acoustic Doppler Current Profiler discharge data, we estimate a large decrease in POC flux (from 540 to 370 kg per second) between the rising and falling stages of the Amazon River mainstem. The C/N ratio and stable and radiocarbon signatures of bulk POC are less variable within the cross-section at Óbidos and suggest that riverine POC in the Amazon River is predominantly soil-derived. However, smaller shifts in these compositional metrics with depth, including leaf wax n-alkanes and fatty acids, are consistent with the perspective that deeper and larger particles carry fresher, less degraded organic matter sources (i.e., vegetation debris) through the mainstem. Overall, our cross-sectional surveys at Óbidos highlight the importance of depth-specific sampling for estimating riverine export fluxes. At the same time, they imply that this approach to sampling is perhaps less essential with respect to characterizing the composition of POC sources exported by the river.
  • Article
    Inhabitation of bathyal hydrocarbon seeps by early-branching benthic foraminifera: Implications for Neo-Proterozoic ecosystem functioning
    (Cushman Foundation for Foraminiferal Research, 2024-07-26) Rohret, Shari M. ; Bernhard, Joan M.
    Little is known about mechanisms allowing agglutinated and thecate (i.e., organic-walled) foraminifera associated with extreme environments to survive. Here, we present cytological observations of organic-walled and agglutinated monothalamid and milioline tubothalamids collected from sulfur-oxidizing microbial mats of Gulf of Mexico hydrocarbon seeps. This is the first ultrastructural analysis of allogromids, a basal group of organic-walled thecate foraminifera, from seeps. We show most allogromids contained numerous ingested bacteria of various forms; organelle abundance and distribution varied among their morphotypes. Saccaminids (agglutinated monothalamids) had abundant phagocytosed bacteria, including putative methanotrophic and sulfur-oxidizing bacteria, indicating foraminiferal activity in seeps. A porcelaneous tubothalamid morphotype contained phagocytosed bacteria of one morphology, suggesting food selectivity. Increasing our knowledge of the cytology and ecology of these modern representatives of early-evolving foraminifera could help elucidate their evolutionary history. Thus, we augment understanding of extremophile foraminifera, adding to our burgeoning understanding of microeukaryote protists and microfossil adaptations.
  • Article
    Genomic sequences of Mycobacterium smegmatis a cluster phages LBerry, Pembroke, and Zolita
    (American Society for Microbiology, 2024-07-09) Berry, Nathan E. ; Cassford, Marly S. ; Agostino, Colby J. ; Dionne, Ethan N. ; Schmitt, Olivia J. ; Butela, Kristen A. ; Jacobs-Sera, Deborah ; DeGiorgis, Joseph A. ; Cornely, Kathleen
    LBerry, Pembroke, and Zolita are newly isolated bacteriophages that infect Mycobacterium smegmatis mc²155. Based on gene content similarity, LBerry and Pembroke are assigned to cluster A3, and Zolita is assigned to cluster A5. LBerry and Pembroke are 99% identical to Anaysia and Caviar, and Zolita is 99% identical to SydNat.
  • Article
    North Atlantic right whale density surface model for the US Atlantic evaluated with passive acoustic monitoring
    (Inter-Research Science Publisher, 2024-03-20) Roberts, Jason J. ; Yack, Tina M. ; Fujioka, Ei ; Halpin, Patrick N. ; Baumgartner, Mark F. ; Boisseau, Oliver ; Chavez-Rosales, Samuel ; Cole, Timothy V. N. ; Cotter, Mark P. ; Davis, Genevieve E. ; DiGiovanni, Robert A., Jr. ; Ganley, Laura C. ; Garrison, Lance P. ; Good, Caroline P. ; Gowan, Timothy A. ; Jackson, Katharine A. ; Kenney, Robert D. ; Khan, Christin B. ; Knowlton, Amy R. ; Kraus, Scott D. ; Lockhart, Gwen G. ; Lomac-MacNair, Kate S. ; Mayo, Charles A. ; McKenna, Brigid E. ; McLellan, William A. ; Nowacek, Douglas P. ; O’Brien, Orfhlaith ; Pabst, D. Ann ; Palka, Debra L. ; Patterson, Eric M. ; Pendleton, Daniel E. ; Quintana-Rizzo, Ester ; Record, Nicholas R. ; Redfern, Jessica V. ; Rickard, Meghan E. ; White, Melanie ; Whitt, Amy D. ; Zoidis, Ann M.
    The Critically Endangered North Atlantic right whale Eubalaena glacialis entered a population decline around 2011. To save this species without closing the ocean to human activities requires detailed information about its intra-annual density patterns that can be used to assess and mitigate human-caused risks. Using 2.9 million km of visual line-transect survey effort from the US Atlantic and Canadian Maritimes conducted in 2003-2020 by 11 institutions, we modeled the absolute density (ind. km-2) of the species using spatial, temporal, and environmental covariates at a monthly time step. We accounted for detectability differences between survey platforms, teams, and conditions, and corrected all data for perception and availability biases, accounting for platform differences, whale dive behavior, group composition, and group size. We produced maps of predicted density and evaluated our results using independently collected passive acoustic monitoring (PAM) data. Densities correlated positively (r = 0.46, ρ = 0.58, τ = 0.46) with acoustic detection rates obtained at 492 stationary PAM recorders deployed across the study area (mean recorder duration = 138 d). This is the first study to quantify the concurrence of visual and acoustic observations of the species in US waters. We summarized predictions into mean monthly density and uncertainty maps for the 2003-2009 and 2010-2020 eras, based on the significant changes in the species’ spatial distribution that began around 2010. The results quantify the striking distribution shifts and provide effort- and bias-corrected density surfaces to inform risk assessments, estimations of take, and marine spatial planning.
  • Article
    Downscaling the ocean response to the Madden–Julian Oscillation in the Northwest Atlantic and adjacent shelf seas
    (Springer, 2024-05-06) Renkl, Christoph ; Oliver, Eric C. J. ; Thompson, Keith R.
    Subseasonal-to-seasonal (S2S) prediction is a global effort to forecast the state of the atmosphere and ocean with lead times between two weeks and a season. This study explores the feasibility of S2S prediction of the ocean using a variety of tools including statistical analysis, a statistical-dynamical mixed layer model, and a regional, high-resolution ocean circulation model based on physical principles. Ocean predictability on S2S timescales is analyzed by compositing winter sea surface temperature (SST) anomalies in the North Atlantic with respect to the state of the Madden–Julian Oscillation (MJO). It is found that statistically significant, large-scale SST changes, particularly along the eastern seaboard of North America, can be related to the MJO. This signal is shown to be driven by anomalous air–sea heat fluxes caused by atmospheric perturbations in response to the MJO. The high-resolution model of the Gulf of Maine and Scotian Shelf is used to downscale the mean ocean response to the MJO. The model is able to capture the observed relationship between the MJO and SST in the northwest Atlantic. It is also shown that the anomalous atmospheric circulation in response to the MJO leads to anomalous upwelling on the Scotian Shelf. Overall, this study demonstrates that it is feasible, and of value, to use regional ocean models for S2S prediction.
  • Article
    Acute introduction of phosphoserine-129 α-synuclein induces severe swelling of mitochondria at lamprey synapses
    (Caltech Library, 2024-05-23) Rivera, Caroline V. Casiano ; Wallace, Jaqulin N. ; Fisher, Gia E. ; Morgan, Jennifer R.
    Abnormal synaptic aggregation of α-synuclein is linked to cognitive deficits in Parkinson’s disease (PD). While the impacts of excess α-synuclein on synaptic function are well established, comparatively less is known about the effects on local mitochondria. Here, we examined morphological features of synaptic mitochondria treated with wild type (WT) or phosphoserine 129 (pS129) α-synuclein, a variant with prominent synaptic accumulation in PD. Acute introduction of pS129 α-synuclein to lamprey synapses caused an activity-dependent swelling and bursting of mitochondria, which did not occur with WT α-synuclein. These pS129-induced effects on mitochondria likely contribute to the synaptic deficits observed in PD.