Biology

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WHOI biological oceanographers study the biology of individual marine organisms, their spatial and temporal distributions, and how they interact both with their surrounding environment and with each other.

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  • Article
    Mixoplankton and mixotrophy: future research priorities
    (Oxford University Press, 2023-06-09) Millette, Nicole C. ; Gast, Rebecca J. ; Luo, Jessica Y. ; Moeller, Holly V. ; Stamieszkin, Karen ; Andersen, Ken H. ; Brownlee, Emily F. ; Cohen, Natalie R. ; Duhamel, Solange ; Dutkiewicz, Stephanie ; Glibert, Patricia M. ; Johnson, Matthew D. ; Leles, Suzana G. ; Maloney, Ashley E. ; Mcmanus, George B. ; Poulton, Nicole ; Princiotta, Sarah D. ; Sanders, Robert W. ; Wilken, Susanne
    Phago-mixotrophy, the combination of photoautotrophy and phagotrophy in mixoplankton, organisms that can combine both trophic strategies, have gained increasing attention over the past decade. It is now recognized that a substantial number of protistan plankton species engage in phago-mixotrophy to obtain nutrients for growth and reproduction under a range of environmental conditions. Unfortunately, our current understanding of mixoplankton in aquatic systems significantly lags behind our understanding of zooplankton and phytoplankton, limiting our ability to fully comprehend the role of mixoplankton (and phago-mixotrophy) in the plankton food web and biogeochemical cycling. Here, we put forward five research directions that we believe will lead to major advancement in the field: (i) evolution: understanding mixotrophy in the context of the evolutionary transition from phagotrophy to photoautotrophy; (ii) traits and trade-offs: identifying the key traits and trade-offs constraining mixotrophic metabolisms; (iii) biogeography: large-scale patterns of mixoplankton distribution; (iv) biogeochemistry and trophic transfer: understanding mixoplankton as conduits of nutrients and energy; and (v) in situ methods: improving the identification of in situ mixoplankton and their phago-mixotrophic activity.
  • Article
    Parasite diversity at isolated, disturbed hydrothermal vents
    (The Royal Society, 2023-06-14) Dykman Lauren ; Tepolt, Carolyn K. ; Kuris, Armand M. ; Solow, Andrew R. ; Mullineaux, Lauren S.
    Habitat isolation and disturbance are important regulators of biodiversity, yet it remains unclear how these environmental features drive differences in parasite diversity between ecosystems. We test whether the biological communities in an isolated, frequently disturbed marine ecosystem (deep-sea hydrothermal vents) have reduced parasite richness and relatively fewer parasite species with indirect life cycles (ILCs) compared to ecosystems that are less isolated and less disturbed. We surveyed the parasite fauna of the biological community at the 9°50′N hydrothermal vent field on the East Pacific Rise and compared it to similar datasets from a well-connected and moderately disturbed ecosystem (kelp forest) and an isolated and undisturbed ecosystem (atoll sandflat). Parasite richness within host species did not differ significantly between ecosystems, yet total parasite richness in the vent community was much lower due to the low number of predatory fish species. Contrary to expectation, the proportion of ILC parasite species was not lower at vents due to a high richness of trematodes, while other ILC parasite taxa were scarce (nematodes) or absent (cestodes). These results demonstrate the success of diverse parasite taxa in an extreme environment and reinforce the importance of host diversity and food web complexity in governing parasite diversity.
  • Article
    Assessing the potential of backscattering as a proxy for phytoplankton carbon biomass
    (American Geophysical Union, 2023-04-28) Serra‐Pompei, Camila ; Hickman, Anna ; Britten, Gregory L. ; Dutkiewicz, Stephanie
    Despite phytoplankton contributing roughly half of the photosynthesis on earth and fueling marine food‐webs, field measurements of phytoplankton biomass remain scarce. The particulate backscattering coefficient (bbp) has often been used as an optical proxy to estimate phytoplankton carbon biomass (Cphyto). However, total observed bbp is impacted by phytoplankton size, cell composition, and non‐algal particles. The lack of phytoplankton field data has prevented the quantification of uncertainties driven by these factors. Here, we first review and discuss existing bbp algorithms by applying them to bbp data from the BGC‐Argo array in surface waters (<10 m). We find a bbp threshold where estimated Cphyto differs by more than an order of magnitude. Next, we use a global ocean circulation model (the MITgcm Biogeochemical and Optical model) that simulates plankton dynamics and associated inherent optical properties to quantify and understand uncertainties from bbp‐based algorithms in surface waters. We do so by developing and calibrating an algorithm to the model. Simulated error‐estimations show that bbp‐based algorithms overestimate/underestimate Cphyto between 5% and 100% in surface waters, depending on the location and time. This is achieved in the ideal scenario where Cphyto and bbp are known precisely. This is not the case for algorithms derived from observations, where the largest source of uncertainty is the scarcity of phytoplankton biomass data and related methodological inconsistencies. If these other uncertainties are reduced, the model shows that bbp could be a relatively good proxy for phytoplankton carbon biomass, with errors close to 20% in most regions.Key PointsPhytoplankton carbon bbp‐based algorithms can differ up to an order of magnitude at low bbp valuesAn algorithm fitted to a global model output shows biases ranging between 15% and 40% in most regionsMost uncertainties are due to the relative contribution of phytoplankton to total bbp
  • Article
    Acropora cervicornis Data Coordination Hub, an open access database for evaluating genet performance
    (Rosenstiel School of Marine and Atmospheric Science, 2023-03-24) Kiel, Patrick M. ; Formel, Nathan ; Jankulak, Mike ; Baker, Andrew C. ; Cunning, Ross ; Gilliam, David S. ; Kenkel, Carly ; Langdon, Chris ; Lirman, Diego ; Lustic, Caitlin ; Maxwell, Kerry ; Moulding, Alison L. ; Moura, Amelia ; Muller, Erinn M. ; Schopmeyer, Stephanie ; Winters, R. Scott ; Enochs, Ian C.
    Once one of the predominant reef-building corals in the region, Acropora cervicornis is now a focal species of coral restoration efforts in Florida and the western Caribbean. Scientists and restoration practitioners have been independently collecting phenotypic data on genets of A. cervicornis grown in restoration nurseries. While these data are important for understanding the intraspecific response to varying environmental conditions, and thus the potential genetic contribution to phenotypic variation, in isolation these observations are of limited use for large-scale, multi- institution restoration efforts that are becoming increasingly necessary. Here, we present the Acropora cervicornis Data Coordination Hub, a web-accessible relational database to align disparate datasets to compare genet-specific performance. In this data descriptor, we release data for 248 genets evaluated across 38 separate traits. We present a framework to align datasets with the ultimate goal of facilitating informed, data-driven restoration throughout the Caribbean.
  • Article
    Deconstructing the Lomagundi-Jatuli Carbon Isotope Excursion
    (Annual Reviews, 2023-05-31) Hodgskiss, Malcolm S. W. ; Crockford, Peter W. ; Turchyn, Alexandra V.
    The early to mid-Paleoproterozoic Lomagundi-Jatuli Excursion (LJE) is ostensibly the largest magnitude (approximately +5 to +30‰), longest duration (ca. 130-250 million years) positive carbon isotope excursion measured in carbonate rocks in Earth history. The LJE has been attributed to large nutrient fluxes, an increase in the size of the biosphere, a reorganization of the global carbon cycle, and oxygenation of the atmosphere. However, significant debate remains about its genesis, synchroneity, global-versus-local extent, and role in atmospheric oxygenation. Here we review existing models and mechanisms suggested for the LJE and analyze a compilation of ∼9,400 δ13 Ccarb and associated contextual data. These data call into question the interpretation of the LJE as a globally synchronous carbon isotope excursion and suggest that any model for the LJE must account for both the absence of a clearly defined initiation and termination of the excursion and a facies-dependent expression of 13C-enrichment.The Lomagundi-Jatuli Excursion (LJE) continues to challenge current understandings of the carbon cycle.Understanding this excursion is critical for reconstructing biogeochemical cycles and atmospheric oxygenation through Earth history.Some evidence indicates local rather than global changes in δ13CDIC and raises the possibility of asynchronous, local excursions.Resolving whether the LJE was globally synchronous or asynchronous is essential for discriminating between different models.
  • Article
    Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein
    (Oxford University Press, 2023-05-27) Butkovic, Anamarija ; Kraberger, Simona ; Smeele, Zoe ; Martin, Darren P. ; Schmidlin, Kara ; Fontenele, Rafaela S. ; Shero, Michelle R. ; Beltran, Roxanne S. ; Kirkham, Amy L. ; Aleamotu'a, Maketalena ; Burns, Jennifer M. ; Koonin, Eugene V. ; Varsani, Arvind ; Krupovic, Mart
    Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the 'healthy virome'. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, 'Commensaviricota', and including it into the kingdom(realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.
  • Presentation
    FAIR Data Training for Deep Ocean Early Career Researchers: Syllabus and slide presentations
    (Woods Hole Oceanographic Institution, 2024-02-09) Beaulieu, Stace E. ; Stocks, Karen ; Smith, Leslie M.
    It is essential for our next generation of leaders in deep ocean observing to gain knowledge and skills in research data management, including how to make data FAIR - Findable, Accessible, Interoperable, and Reusable. This educational package was developed as a virtual workshop series for Deep Ocean Early career Researchers (DOERs) with content tailored for the Deep Ocean Observing Strategy (DOOS), an international network of deep ocean observing, mapping, exploration, and modeling programs endorsed as a UN Ocean Decade Programme. Modules step through the research data lifecycle, starting with 1 “Foundational Practices for FAIR Data,” 2 “Collaborating in the Research Data Lifecycle,” 3 “Best Practices in the Ocean Sciences,” and concluding with 4 “The “R” in FAIR data lifecycle: Reusable data.” This package includes the syllabus which shows the schedule for delivery of the workshop series as well as an overview of content and learning objectives. There are no prerequisites to participate in this course. The training was delivered in English; recordings were provided ahead of the virtual sessions and a live transcript was implemented during the sessions to improve accessibility.
  • Article
    Sex as a biological variable in tissue engineering and regenerative medicine
    (Annual Reviews, 2023-04-27) Allen, Josephine B. ; Ludtka, Christopher ; James, Bryan D.
    Although sex differences have been noted in cellular function and behavior, therapy efficacy, and disease incidence and outcomes, the adoption of sex as a biological variable in tissue engineering and regenerative medicine remains limited. Furthering the development of personalized, precision medicine requires considering biological sex at the bench and in the clinic. This review provides the basis for considering biological sex when designing tissue-engineered constructs and regenerative therapies by contextualizing sex as a biological variable within the tissue engineering triad of cells, matrices, and signals. To achieve equity in biological sex within medicine requires a cultural shift in science and engineering research, with active engagement by researchers, clinicians, companies, policymakers, and funding agencies.
  • Article
    Ecotrophic perspective in fisheries management: a review of Ecopath with Ecosim models in European marine ecosystems
    (Frontiers Media, 2023-05-02) Keramidas, Ioannis ; Dimarchopoulou, Donna ; Ofir, Eyal ; Scotti, Marco ; Tsikliras, Athanassios C. ; Gal, Gideon
    The aim of this work is to present the food web models developed using the Ecopath with Ecosim (EwE) software tool to describe structure and functioning of various European marine ecosystems (eastern, central and western Mediterranean Sea; Black Sea; Bay of Biscay, Celtic Sea and Iberian coast; Baltic Sea; North Sea; English Channel, Irish Sea and west Scottish Sea; and Norwegian and Barents Seas). A total of 195 Ecopath models based on 168 scientific publications, which report original, updated and modified versions, were reviewed. Seventy models included Ecosim temporal simulations while 28 implemented Ecospace spatiotemporal dynamics. Most of the models and publications referred to the western Mediterranean Sea followed by the English Channel, Irish Sea and west Scottish Sea sub-regions. In the Mediterranean Sea, the western region had the largest number of models and publications, followed by the central and eastern regions; similar trends were observed in previous literature reviews. Most models addressed ecosystem functioning and fisheries-related hypotheses while several investigated the impact of climate change, the presence of alien species, aquaculture, chemical pollution, infrastructure, and energy production. Model complexity (i.e., number of functional groups) increased over time. Main forcing factors considered to run spatial and temporal simulations were trophic interactions, fishery, and primary production. Average scores of ecosystem indicators derived from the Ecopath summary statistics were compared. Uncertainty was also investigated based on the use of the Ecosampler plug-in and the Monte Carlo routine; only one third of the reviewed publications incorporated uncertainty analysis. Only a limited number of the models included the use of the ECOIND plug-in which provides the user with quantitative output of ecological indicators. We assert that the EwE modelling approach is a successful tool which provides a quantitative framework to analyse the structure and dynamics of ecosystems, and to evaluate the potential impacts of different management scenarios.
  • Article
    Amphipoda from depths exceeding 6,000 meters revisited 60 years on
    (Oxford University Press, 2023-05-15) Jamieson, Alan J. ; Weston, Johanna N. J.
    In the 1950s, the Danish Galathea Expedition undertook one of the first and most comprehensive explorations of our ocean’s hadal zone, depths extending from 6,000 to nearly 11,000 m, and presented a rich collection of the diversity of Amphipoda. The subsequent papers, however, concluded that these established ‘nothing essentially new’ to the existing knowledge of amphipod biology. Since Dahl’s foundational paper in 1959, amphipods, primarily from the superfamilies Lysianassoidea and Alicelloidea, emerged as one of the best-sampled hadal fauna, as these mobile invertebrates are readily recovered by different sampling techniques. Importantly, amphipods have become the model taxon, helping us to unlock knowledge about life in the hadal zone. In this review, we collate the knowledge gained since the Galathea Expedition and summarise the current understanding of how amphipods that appear during hadal exploration survive the trench environments. We discuss population structures across depth, inter-trench distribution and connectivity, applications in hadal microbiology, and, critically, how the hadal zone is being impacted by anthropogenic activity.
  • Article
    Five reasons to take the precautionary approach to deep sea exploitation
    (Nature Research, 2023-05-05) Bisson, Kelsey ; McMonagle, Helena ; Iglesias, Ilysa ; Halfter, Svenja ; Gallo, Natalya
    Extractive activities in the deep sea are poised to advance faster than the science needed to evaluate risks. Here, we call for a strong precautionary approach in developing these industries. Food and energy insecurity have been exacerbated by climate change, conflict, and disease, with global energy demands only expected to grow. Seabed mining and deep-sea fishing have been suggested as ways to support shifting to renewable energy and increasing food supply. These industries are likely to impact one of the largest habitats on Earth, our ocean’s mesopelagic zone, at depths between ~200 and 1000 m. Once assumed to be lifeless, we now know the mesopelagic zone is rich with life and a vital component of the global ecosystem. Recently, industries have begun exploratory extractive activities, while our scientific understanding of the impacts of these activities on the mesopelagic zone is trailing behind (Fig. 1). Here, we outline five reasons why we advocate for a precautionary approach to deep-sea exploitation in order to make evidence-based decisions.
  • Article
    Challenges and opportunities in connecting gene count observations with ocean biogeochemical models: Reply to Zehr and Riemann (2023)
    (Association for the Sciences of Limnology and Oceanography, 2023-05-08) Meiler, Simona ; Britten, Gregory L. ; Dutkiewicz, Stephanie ; Moisander, Pia H. ; Follows, Michael J.
    As authors of Meiler et al. (2022), we welcome Zehr and Riemann's (2023) comment and discussion. We agree, of course, with the general statement that “quantification of gene copy numbers is valuable in marine microbial ecology” and wish to clarify that one of the purposes of Meiler et al. (2022) was to address the specific challenge of using a compilation of quantitative polymerase chain reaction (qPCR) nifH data to evaluate the skill of biogeochemical models. In that particular case, the data were most helpful in constraining the range of diazotrophs, but several sources of uncertainty limited more detailed quantitative evaluations. This was not intended to imply a lack of value or promise for such applications of qPCR data: we believe that testing and constraining biogeochemical and ecological models will be an important application of qPCR data, yet the quantitative interface between molecular data and biogeochemical models remains at its infancy. In the following, we first provide a background perspective for the Meiler et al. (2022) study, pointing out why observations and simulations are rooted in different currencies. We then discuss in more detail some of the specific points raised by Zehr and Riemann (2023) and highlight why further efforts toward intercalibration of currencies used to measure and simulate marine microbial populations is particularly significant if we are to fully exploit the data in biogeochemical and climate modeling applications. We end by summarizing some potentially fruitful avenues for future effort stimulated by this dialog.
  • Article
    Genetic rescue from protected areas is modulated by migration, hunting rate, and timing of harvest
    (Wiley Open Access, 2023-05-12) Lassis, Roxane ; Festa‐Bianchet, Marco ; Van de Walle, Joanie ; Pelletier, Fanie
    In terrestrial and marine ecosystems, migrants from protected areas may buffer the risk of harvest‐induced evolutionary changes in exploited populations that face strong selective harvest pressures. Understanding the mechanisms favoring genetic rescue through migration could help ensure evolutionarily sustainable harvest outside protected areas and conserve genetic diversity inside those areas. We developed a stochastic individual‐based metapopulation model to evaluate the potential for migration from protected areas to mitigate the evolutionary consequences of selective harvest. We parameterized the model with detailed data from individual monitoring of two populations of bighorn sheep subjected to trophy hunting. We tracked horn length through time in a large protected and a trophy‐hunted populations connected through male breeding migrations. We quantified and compared declines in horn length and rescue potential under various combinations of migration rate, hunting rate in hunted areas and temporal overlap in timing of harvest and migrations, which affects the migrants' survival and chances to breed within exploited areas. Our simulations suggest that the effects of size‐selective harvest on male horn length in hunted populations can be dampened or avoided if harvest pressure is low, migration rate is substantial, and migrants leaving protected areas have a low risk of being shot. Intense size‐selective harvest impacts the phenotypic and genetic diversity in horn length, and population structure through changes in proportions of large‐horned males, sex ratio and age structure. When hunting pressure is high and overlaps with male migrations, effects of selective removal also emerge in the protected population, so that instead of a genetic rescue of hunted populations, our model predicts undesirable effects inside protected areas. Our results stress the importance of a landscape approach to management, to promote genetic rescue from protected areas and limit ecological and evolutionary impacts of harvest on both harvested and protected populations.
  • Article
    Broadband backscattering from scyphozoan jellyfish
    (Acoustical Society of America, 2023-05-24) Kahn, Rachel E. ; Lavery, Andone C. ; Govindarajan, Annette F.
    As the ecological importance of gelatinous organisms becomes increasingly appreciated, so has the need for improved knowledge of their abundance and distribution. Acoustic backscattering measurements are routine for fisheries assessments but are not yet widely used to survey populations of gelatinous zooplankton. The use of acoustic backscattering techniques to understand the distribution and abundance of organisms requires an understanding of their target strength (TS). This study presents a framework for a sound scattering model for jellyfish based on the Distorted Wave Born Approximation that incorporates size, shape, and material properties of individual organisms. This model, with a full three-dimensional shape rendition, is applied to a common species of scyphomedusa (Chrysaora chesapeakei) and verified experimentally with broadband (52-90 and 93-161 kHz) laboratory TS measurements of live individuals. Cyclical changes in the organism's shape due to swimming kinematics were examined, as well as averages over swimming position and comparisons with scattering from simpler shapes. The model predicts overall backscattering levels and broad spectral behavior within <2 dB. Measured TS exhibits greater variability than is predicted by scaling the size of the organism in the scattering model, showing that density and sound speed vary among individuals.
  • Article
    Shared and distinct patterns of genetic structure in two sympatric large decapods
    (Wiley, 2023-05-02) Ellis, Charlie D. ; MacLeod, Kirsty L. ; Jenkins, Tom L. ; Rato, Lénia D. ; Jézéquel, Youenn ; Pavičić, Mišo ; Díaz, David ; Stevens, Jamie R.
    Aim Comparing genetic structure in species with shared spatial ranges and ecological niches can help identify how dissimilar aspects of biology can shape differences in population connectivity. Similarly, where species are widely distributed across heterogeneous environments and major topographic barriers, knowledge of the structuring of populations can help reveal the impacts of factors which limit dispersal and/or drive divergence, aiding conservation management. Location European seas of the northeast Atlantic and Mediterranean. Taxa European clawed lobster (Homarus gammarus) and European crawfish (Palinurus elephas), two sympatric, heavily fished decapods with extensive dispersal potential. Methods By RAD‐sequencing 214 H. gammarus from 32 locations and 349 P. elephas from 15 locations, we isolated 6340 and 7681 SNP loci, respectively. Using these data to characterise contemporary population structuring, we investigate potential spatial and environmental drivers of genomic heterogeneity. Results We found higher levels of differentiation among clawed lobsters than crawfish, both globally and within basins, and demonstrate where known hydrographic and topographic barriers generate shared patterns of divergence, such as a genetic break between the Atlantic and Mediterranean basins. Genetic structure not common to both species is principally apparent in the Atlantic portions of their range, where clawed lobster exhibits a genetic cline and increased differentiation towards range margins, while crawfish appear effectively panmictic throughout this region. Main Conclusions We attribute the comparative lack of crawfish population structuring to their greater dispersal tendencies via a longer pelagic larval duration and sporadic adult movements. In contrast, genetic connectivity in clawed lobster is relatively restricted, with the correlation of site of origin and temperature to geographical heterogeneity at many divergent loci indicative of both neutral and adaptive processes. Our results help inform how contemporary management can account for likely demographic connectivity and marry the conservation of genomic variation with sustainable fisheries in these ecologically and economically important crustaceans.
  • Article
    Predator switching strength controls stability in diamond-shaped food web models
    (Elsevier, 2023-05-25) Archibald, Kevin M. ; Sosik, Heidi M. ; Moeller, Holly V. ; Neubert, Michael G.
    In food web models that include more than one prey type for a single predator, it is common for the predator’s functional response to include some form of switching—preferential consumption of more abundant prey types. Predator switching promotes coexistence among competing prey types and increases diversity in the prey community. Here, we show how the dynamics of a diamond-shaped food web model of a marine plankton community are sensitive to a parameter that sets the strength of predator switching. Stronger switching destabilizes the model’s coexistence equilibrium and leads to the appearance of limit cycles. Stronger switching also increases the evenness of the asymptotic prey community and promotes synchrony in the dynamics of disparate prey types. Given the dependence of model behavior on the strength of predator switching, it is important that modelers carefully consider the parameterization of functional responses that include switching.•Predators that exhibit switching promote coexistence between prey types.•However, strong switching may destabilize this coexistence and produce limit cycles.•In communities with many prey, evenness increases with the strength of switching.
  • Article
    Temperature regulates Synechococcus population dynamics seasonally and across the continental shelf
    (Association for the Sciences of Limnology and Oceanography, 2023-05-12) Stevens, Bethany L. F. ; Crockford, E. Taylor ; Peacock, Emily E. ; Neubert, Michael G. ; Sosik, Heidi M.
    Hourly, year‐round flow cytometry has made it possible to relate seasonal environmental variability to the population dynamics of the smallest, most abundant phytoplankton on the Northeast US Shelf. To evaluate whether the insights from these data extend to Synechococcus farther from shore, we analyze flow cytometry measurements made continuously from the underway systems on 21 cruises traveling between the Martha's Vineyard Coastal Observatory (MVCO) and the continental shelf break. We describe how seasonal patterns in Synechococcus , which have been documented in detail at MVCO, occur across the region with subtle variation. We find that the underlying relationship between temperature and division rate is consistent across the shelf and can explain much of the observed spatial variability in concentration. Connecting individual cell properties to annual and regional patterns in environmental conditions, these results demonstrate the value of autonomous monitoring and create an improved picture of picophytoplankton dynamics within an economically important ecosystem.
  • Article
    Spatio-temporal transferability of environmentally-dependent population models: Insights from the intrinsic predictabilities of Adélie penguin abundance time series
    (Elsevier, 2023-04-19) Şen, Bilgecan ; Che-Castaldo, Christian ; Krumhardt, Kristen M. ; Landrum, Laura ; Holland, Marika M. ; LaRue, Michelle A. ; Long, Matthew C. ; Jenouvrier, Stéphanie ; Lynch, Heather J.
    Ecological predictions are necessary for testing whether processes hypothesized to regulate species population dynamics are generalizable across time and space. In order to demonstrate generalizability, model predictions should be transferable in one or more dimensions, where transferability is the successful prediction of responses outside of the model data bounds. While much is known as to what makes spatially-oriented models transferable, there is no general consensus as to the spatio-temporal transferability of ecological time series models. Here, we examine whether the intrinsic predictability of a time series, as measured by its complexity, could limit such transferability using an exceptional long-term dataset of Adélie penguin breeding abundance time series collected at 24 colonies around Antarctica. For each colony, we select a suite of environmental variables from the Community Earth System Model, version 2 to predict population growth rates, before assessing how well these environmentally-dependent population models transfer temporally and how reliably temporal signals replicate through space. We show that weighted permutation entropy (WPE), a model-free measure of intrinsic predictability recently introduced to ecology, varies spatially across Adélie penguin populations, perhaps in response to stochastic environmental events. We demonstrate that WPE can strongly limit temporal predictive performance, although this relationship could be weakened if intrinsic predictability is not constant over time. Lastly, we show that WPE can also limit spatial forecast horizon, which we define as the decay in spatial predictive performance with respect to the physical distance between focal colony and predicted colony. Irrespective of intrinsic predictability, spatial forecast horizons for all Adélie penguin breeding colonies included in this study are surprisingly short and our population models often have similar temporal and spatial predictive performance compared to null models based on long-term average growth rates. For cases where time series are complex, as measured by WPE, and the transferability of biologically-motivated mechanistic models are poor, we advise that null models should instead be used for prediction. These models are likely better at capturing more generalizable relationships between average growth rates and long-term environmental conditions. Lastly, we recommend that WPE can provide valuable insights when evaluating model performance, designing sampling or monitoring programs, or assessing the appropriateness of preexisting datasets for making conservation management decisions in response to environmental change.
  • Article
    Coral persistence despite marginal conditions in the Port of Miami
    (Nature Research, 2023-04-25) Enochs, Ian C. ; Studivan, Michael S. ; Kolodziej, Graham ; Foord, Colin ; Basden, Isabelle ; Boyd, Albert ; Formel, Nathan ; Kirkland, Amanda ; Rubin, Ewelina ; Jankulak, Mike ; Smith, Ian ; Kelble, Christopher R. ; Manzello, Derek P.
    Coral cover has declined worldwide due to anthropogenic stressors that manifest on both global and local scales. Coral communities that exist in extreme conditions can provide information on how these stressors influence ecosystem structure, with implications for their persistence under future conditions. The Port of Miami is located within an urbanized environment, with active coastal development, as well as commercial shipping and recreational boating activity. Monitoring of sites throughout the Port since 2018 has revealed periodic extremes in temperature, seawater pH, and salinity, far in excess of what have been measured in most coral reef environments. Despite conditions that would kill many reef species, we have documented diverse coral communities growing on artificial substrates at these sites-reflecting remarkable tolerance to environmental stressors. Furthermore, many of the more prevalent species within these communities are now conspicuously absent or in low abundance on nearby reefs, owing to their susceptibility and exposure to stony coral tissue loss disease. Natural reef frameworks, however, are largely absent at the urban sites and while diverse fish communities are documented, it is unlikely that these communities provide the same goods and services as natural reef habitats. Regardless, the existence of these communities indicates unlikely persistence and highlights the potential for coexistence of threatened species in anthropogenic environments, provided that suitable stewardship strategies are in place.
  • Article
    Effects of warming and fishing on Atlantic sea scallop (Placopecten magellanicus) size structure in the Mid-Atlantic rotationally closed areas
    (Oxford University Press, 2023-04-17) Zang, Zhengchen ; Ji, Rubao ; Hart, Deborah R. ; Jin, Di ; Chen, Changsheng ; Liu, Yonggang ; Davis, Cabell S.
    The Atlantic sea scallop supports one of the most lucrative fisheries on the Northeast U.S. shelf. Understanding the interannual variability of sea scallop size structure and associated drivers is critically important for projecting the response of population dynamics to climate change and designing coherent fishery management strategies. In this study, we constructed time series of sea scallop size structures in three rotationally closed areas in the Mid-Atlantic Bight (MAB) and decomposed their total variances using the variance partitioning method. The results suggested that the interannual variances in sea scallop size structures were associated more with thermal stress in regions shallower than 60 m but more with fishing mortality in regions deeper than 60 m. The percentages of small (large) size groups increased (decreased) with elevated thermal stress and fishing pressure. We adopted a scope for growth model to build a mechanistic link between temperature and sea scallop size. Model results suggested a gradual decrease in maximum shell height and habitat contraction under warming. This study quantified the relative contributions of thermal stress and fishing mortality to the variance of scallop size structure and discussed the need for adaptive management plans to mitigate potential socioeconomic impacts caused by size structure changes.