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Open access publications by faculty, postdocs, and graduate students in the School of Marine Science & Policy

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Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon
(Applied and Environmental Microbiology, 2024-08-12) Tothero, Gracee K.; Hoover, Rene L.; Farag, Ibrahim F.; Kaplan, Daniel I.; Weisenhorn, Pamela; Emerson, David; Chan, Clara S.
Leptothrix ochracea creates distinctive iron-mineralized mats that carpet streams and wetlands. Easily recognized by its iron-mineralized sheaths, L. ochracea was one of the first microorganisms described in the 1800s. Yet it has never been isolated and does not have a complete genome sequence available, so key questions about its physiology remain unresolved. It is debated whether iron oxidation can be used for energy or growth and if L. ochracea is an autotroph, heterotroph, or mixotroph. To address these issues, we sampled L. ochracea-rich mats from three of its typical environments (a stream, wetlands, and a drainage channel) and reconstructed nine high-quality genomes of L. ochracea from metagenomes. These genomes contain iron oxidase genes cyc2 and mtoA, showing that L. ochracea has the potential to conserve energy from iron oxidation. Sox genes confer potential to oxidize sulfur for energy. There are genes for both carbon fixation (RuBisCO) and utilization of sugars and organic acids (acetate, lactate, and formate). In silico stoichiometric metabolic models further demonstrated the potential for growth using sugars and organic acids. Metatranscriptomes showed a high expression of genes for iron oxidation; aerobic respiration; and utilization of lactate, acetate, and sugars, as well as RuBisCO, supporting mixotrophic growth in the environment. In summary, our results suggest that L. ochracea has substantial metabolic flexibility. It is adapted to iron-rich, organic carbon-containing wetland niches, where it can thrive as a mixotrophic iron oxidizer by utilizing both iron oxidation and organics for energy generation and both inorganic and organic carbon for cell and sheath production. IMPORTANCE Winogradsky's observations of L. ochracea led him to propose autotrophic iron oxidation as a new microbial metabolism, following his work on autotrophic sulfur-oxidizers. While much culture-based research has ensued, isolation proved elusive, so most work on L. ochracea has been based in the environment and in microcosms. Meanwhile, the autotrophic Gallionella became the model for freshwater microbial iron oxidation, while heterotrophic and mixotrophic iron oxidation is not well-studied. Ecological studies have shown that Leptothrix overtakes Gallionella when dissolved organic carbon content increases, demonstrating distinct niches. This study presents the first near-complete genomes of L. ochracea, which share some features with autotrophic iron oxidizers, while also incorporating heterotrophic metabolisms. These genome, metabolic modeling, and transcriptome results give us a detailed metabolic picture of how the organism may combine lithoautotrophy with organoheterotrophy to promote Fe oxidation and C cycling and drive many biogeochemical processes resulting from microbial growth and iron oxyhydroxide formation in wetlands.
Hypoxia Triggered by Expanding River Plume on the East China Sea Inner Shelf During Flood Years
(Journal of Geophysical Research: Oceans, 2024-07-31) Li, Dewang; Chen, Jianfang; Wang, Bin; Jin, Haiyan; Shou, Lu; Lin, Hua; Miao, Yanyi; Sun, Qianwen; Jiang, Zhibing; Meng, Qicheng; Zeng, Jiangning; Zhou, Feng; Cai, Wei-Jun
The frequency of riverine floods is predicted to increase in East Asia. However, the response of coastal hypoxia (<63 μmol L−1) to floods has not been well understood. In the summer of 2020, characterized by one of the most significant Changjiang water fluxes in three decades, we conducted a cruise during the flood period on the East China Sea inner shelf. Our observations revealed severe bottom hypoxia with a maximum spatial coverage of ∼11,600 km2 and a minimum dissolved oxygen concentration (DO) of 21 μmol L−1. In the surface layer, the relationships between salinity and nitrate, dissolved inorganic carbon (DIC) indicated significant organic matter production, validated by a high-Chlorophyll-a (Chl a) patch (>5 μg L−1). Furthermore, the significant relationship between apparent oxygen utilization and DIC of deep waters reveals that the organic matter decomposition primarily drove the hypoxia during the flood period. Episodic wind events also influenced bottom DO and DIC, by transporting surface waters to the deep. Multiple-years data set shows that the average Changjiang nitrate flux during flood years is about 1.4 times that during non-flood years. The flood waters mix with estuarine waters, forming the high-nutrient plume waters, which expanded farther offshore during the flood period. While high turbidity remained confined to the inner estuary. Consequently, the high-Chl a area significantly expanded, which significantly exacerbated the hypoxia. Key Points - We observed a maximum hypoxia area of ∼11,600 km2, and a minimum dissolved oxygen of 21 μmol L−1 during the flood period in 2020 - Significant nitrate removal and surface Chlorophyll a exceeding 29 μg L−1 suggested intense biological production during the flood period - The expansion of high-Chl a plume area during flood periods surpasses that of non-flood periods, contributing to hypoxia area increase Plain Language Summary Coastal waters are severely threatened by hypoxia, which impacts the growth, reproduction, and migration of marine organisms. Nutrient inputs from river basins are one of the major controlling factors of hypoxia in coastal oceans. The frequency and intensity of floods in river basins are projected to increase in the context of global warming in East Asia. However, the relationship between floods and coastal hypoxia is not well documented. The year 2020 witnessed lots of riverine flood events across Asian countries, which provided us with an excellent opportunity to reveal the influences of flood on hypoxia development on the shelf. In 2020, the August nitrate flux of Changjiang was 1.5 times higher compared to that in non-flood years. We observed maximum hypoxic waters covering 11,600 km2 with a minimum DO of 21 μmol L−1 on the East China Sea inner shelf. Historical data showed that the floods led to the expansion of the high-nutrient plume area, resulting in high biological production in the plume, and a nearly doubling of the hypoxia extent in the bottom waters. With the growing risk of intensive floods, hypoxia is likely to aggravate in coastal waters.
The source and accumulation of anthropogenic carbon in the U.S. East Coast
(Science Advances, 2024-08-09) Li, Xinyu; Wu, Zelun; Ouyang, Zhangxian; Cai, Wei-Jun
The ocean has absorbed anthropogenic carbon dioxide (Canthro) from the atmosphere and played an important role in mitigating global warming. However, how much Canthro is accumulated in coastal oceans and where it comes from have rarely been addressed with observational data. Here, we use a high-quality carbonate dataset (1996–2018) in the U.S. East Coast to address these questions. Our work shows that the offshore slope waters have the highest Canthro accumulation changes (ΔCanthro) consistent with water mass age and properties. From offshore to nearshore, ΔCanthro decreases with salinity to near zero in the subsurface, indicating no net increase in the export of Canthro from estuaries and wetlands. Excesses over the conservative mixing baseline also reveal an uptake of Canthro from the atmosphere within the shelf. Our analysis suggests that the continental shelf exports most of its absorbed Canthro from the atmosphere to the open ocean and acts as an essential pathway for global ocean Canthro storage and acidification.
Development of an efficient, effective, and economical technology for proteome analysis
(Cell Reports: Methods, 2024-06-11) Martin, Katherine R.; Le, Ha T.; Abdelgawad, Ahmed; Yang, Canyuan; Lu, Guotao; Keffer, Jessica L.; Zhang, Xiaohui; Zhuang, Zhihao; Asare-Okai, Papa Nii; Chan, Clara S.; Batish, Mona; Yu, Yanbao
Highlights • Rapid, robust, and cost-effective alternative to proteomics sample preparation • Versatile filter devices can meet a wide range of proteomics analysis needs • On-filter in-cell digestion facilitates low-input proteomics • Ready-to-go E3 and E4 filter devices are available Motivation Conventional proteomics sample processing methods often have high technical barriers to broad biomedical scientists, leading to difficulties for quick adoption and standardization. Existing protocols are also typically associated with costly reagents and accessories, making them less feasible for resource-limited settings as well as for clinical proteomics and/or core facilities where large numbers of samples are usually processed. Thus, there is a strong unmet need for an easy-to-use, reliable, and low-cost approach for general proteomics sample preparation. Summary We present an efficient, effective, and economical approach, named E3technology, for proteomics sample preparation. By immobilizing silica microparticles into the polytetrafluoroethylene matrix, we develop a robust membrane medium, which could serve as a reliable platform to generate proteomics-friendly samples in a rapid and low-cost fashion. We benchmark its performance using different formats and demonstrate them with a variety of sample types of varied complexity, quantity, and volume. Our data suggest that E3technology provides proteome-wide identification and quantitation performance equivalent or superior to many existing methods. We further propose an enhanced single-vessel approach, named E4technology, which performs on-filter in-cell digestion with minimal sample loss and high sensitivity, enabling low-input and low-cell proteomics. Lastly, we utilized the above technologies to investigate RNA-binding proteins and profile the intact bacterial cell proteome. Graphical abstract available at: https://doi.org/10.1016/j.crmeth.2024.100796
Novel CTD tag establishes shark fins as ocean observing platforms
(Scientific Reports, 2024-06-15) Pagniello, Camille M. L. S.; Castleton, Michael R.; Carlisle, Aaron B.; Chapple, Taylor K.; Schallert, Robert J.; Fedak, Michael; Block, Barbara A.
Animal-borne tags are effective instruments for collecting ocean data and can be used to fill spatial gaps in the observing network. We deployed the first conductivity, temperature, and depth (CTD) satellite tags on the dorsal fin of salmon sharks (Lamna ditropis) to demonstrate the potential of sharks to monitor essential ocean variables and oceanographic features in the Gulf of Alaska. Over 1360 km and 36 days in the summer of 2015, the salmon shark collected 56 geolocated, temperature-salinity profiles. The shark swam through a plume of anomalously salty water that originated from the “Blob” and encountered several mesoscale eddies, whose subsurface properties were altered by the marine heatwave. We demonstrate that salmon sharks have the potential to serve as submesoscale-resolving oceanographic platforms and substantially increase the spatial coverage of observations in the Gulf of Alaska.
Obliquity Dominance in Early Pleistocene Sediments From the Antarctic Zone of the Southern Ocean (Indian Ocean Sector)
(Paleoceanography and Paleoclimatology, 2024-05-26) Billups, K.; Münch, B.; Garrioch, I.; Bradtmiller, L.
We constructed a record of percent biogenic silica (opal) accumulation at Ocean Drilling Program Site 745B located in the Indian Ocean sector of the Antarctic Zone of the Southern Ocean. The record spans the majority of the early Pleistocene (1.1–2.6 Ma). Orbital-scale sampling affords a look at the relative importance of obliquity versus precession variability through a time interval that is characterized by obliquity pacing in early Pleistocene δ18O records. Variations in the site's magnetic susceptibility record closely resemble those in the benthic foraminiferal δ18O stack (Lisiecki & Raymo, 2005, https://doi.org/10.1029/2004pa001071) and provide orbital-scale age control. Between 1.1 and 1.8 Ma, obliquity-related 41 kyr spectral peaks dominate with relatively little power at precession periods (23–19 kyr) in all records. Between 1.8 and 2.6 Ma, only the δ18O and magnetic susceptibility data display a distinct 41 kyr peak, while the opal lacks spectral power at any of the orbital periodicities. The lack of more pronounced precession-scale variations in the two proxy records is consistent with observations in foraminiferal δ18O records. A low or absent response to precession in these records appears to be due to environmental control. Lack of orbital forcing in the opal record before 1.8 Ma may reflect both a more southerly location of the polar frontal zone with respect to the site, and thus the site's position outside the region of wind-driven upwelling, and/or upwelling waters undersaturated with respect to silica prior to the establishment of the opal belt at about 2 Ma.
Geolocated fish spawning habitats
(Scientific Data, 2024-05-22) Oremus, Kimberly L.; Rising, James; Ramesh, Nandini; Ostroski, Audrey J.
Fish spawning locations are a crucial input into fisheries management and conservation plans, and many stocks are especially sensitive to the environmental conditions within these localized zones. Globally collated data on spawning locations across many species has been unavailable, hindering global stock assessments and analyses of sustainable development and global environmental change. To address this, we created a geocoded fish spawning dataset using qualitative spawning information from FishBase and Science and Conservation of Fish Aggregations (SCRFA). We cleaned and geocoded the spawning locations of 1,045 marine fish species into 2,931 regions. Each spawning region is defined by one or more polygons, and most spawning regions are associated with spawning months. The resulting dataset covers oceans globally. This dataset will be useful to scientists studying marine fish population dynamics and their interactions with the physical environment on regional to large scales.
Historical climate drivers and species’ ecological niche in the Beaufort Sea food web
(ICES Journal of Marine Science, 2024-05-14) Sora, Kristen J.; Wabnitz, Colette C. C.; Steiner, Nadja S.; Sumaila, U. Rashid; Hoover, Carie; Niemi, Andrea; Loseto, Lisa L.; Li, Mi-Ling; Giang, Amanda; Gillies, Emma; Cheung, William W. L.
Climate change impacts have been particularly acute and rapid in the Arctic, raising concerns about the conservation of key ecologically and culturally significant species (e.g. beluga whales, Arctic cod), with consequences for the Indigenous community groups in the region. Here, we build on an Ecopath with Ecosim model for the Canadian Beaufort Sea Shelf and Slope to examine historical (1970–2021) changes in the ecological dynamics of the food web and key species under climate change. We compare the individual and cumulative effects of (i) increased sea surface temperature; (ii) reduced sea ice extent; (iii) ocean deoxygenation; and (iv) changing ocean salinity in the ecosystem models. We found that including salinity time series in our ecosystem models reduced the diversity found within the ecosystem, and altered the trophic levels, biomass, and consumption rates of some marine mammal and fish functional groups, including the key species: beluga whales, as well as Arctic and polar cods. Inclusion of the dissolved oxygen time series showed no difference to ecosystem indicators. The model findings reveal valuable insights into the attribution of temperature and salinity on Arctic ecosystems and highlight important factors to be considered to ensure that existing conservation measures can support climate adaptation.
Comparisons of Underwater Light From Atmospheric and Mechanically Stimulated Bioluminescence Sources in High Arctic Polar Night
(Journal of Geophysical Research: Oceans, 2024-04-29) Shulman, Igor; Cohen, Jonathan H.; Anderson, Stephanie; Penta, Bradley; Moline, Mark A.
At high latitudes, polar night is a prolonged period of seasonal darkness with the sun remaining below the horizon throughout the diel cycle for up to 177 days at the North Pole. Along with diffuse atmospheric light from the sun and the moon, bioluminescence is an in-water light source that can facilitate ecological interactions in an otherwise dim-light environment. At high latitudes during polar night, bioluminescence rather than sunlight represents a significant portion of the photons available in the pelagic. We investigated depths of transition zones (called the bioluminescence transition depth) in the pelagic light field during polar night, defining the transition of a light field dominated by atmospheric irradiance, to one dominated by bioluminescent point sources. We derived relationships between values of the transition depth, bioluminescence potential, surface irradiance due to atmospheric light and the diffuse attenuation coefficient. We conducted studies for two Svalbard, Norway fjords, as well as for offshore areas located in the shelf-break, shelf-slope and in the Arctic basin. Based on our results for two polar nights, the transition from underwater light dominated by atmospheric sources to that dominated by bioluminescence occurs between 10 and 40 m in two Svalbard fjords, and between 18 and 60 m for offshore areas. These transition depths may be of particular importance to understanding how bioluminescence structures planktonic communities both in polar regions and at lower latitudes. Key Points - We investigated depths of transition zones from one dominated by atmospheric irradiance to one dominated by bioluminescent sources - We derived relationships between transition depth, bioluminescence potential, surface irradiance and diffuse attenuation coefficient - At high latitudes during polar night, bioluminescence represents a significant portion of the photons available in the pelagic Plain Language Summary The polar night is a period of continuous winter darkness north of ∼72.5°N latitude, and this period presents challenging light conditions for Arctic pelagic organisms. With the sun remaining below the horizon from one day at the Arctic Circle to 6 months at the North Pole, prolonged darkness limits light-mediated predator prey interactions in the plankton. Bioluminescence is light produced by a photochemical reaction in organisms, and it is an in-water light source that can facilitate ecological interactions in an otherwise dim-light environment. We investigated depths of transition zones from a light field dominated by atmospheric irradiance, to one dominated by bioluminescent point sources, across a gradient from Svalbard fjords to the Arctic basin. Based on our results, the transition from underwater light dominated by atmospheric sources to that dominated by bioluminescence occurs between 10 and 40 m in two Svalbard fjords, and between 18 and 60 m for offshore areas. The light gradient occurring in these transition zones has ecological implications, including depth selection and predator-prey interactions. This work provides another step in the difficult task of untangling the complex relationships among marine organisms and natural light.
Archaeal blooms and busts in an estuarine time series
(Environmental Microbiology, 2024-02-07) Guider, Justin T.; Yoshimura, Kristin M.; Block, Kaleigh R.; Biddle, Jennifer F.; Shah Walter. Sunita R.
Coastal bays, such as Delaware Bay, are highly productive, ecologically important transitions between rivers and the coastal ocean. They offer opportunities to investigate archaeal assemblages across seasons, with the exchange of water masses that occurs with tidal cycles, and in the context of variable organic matter quality. For a year-long estuarine, size-fractionated time series, we used amplicon sequencing, chemical measurements, and qPCR to follow archaeal groups through the seasons. We detected seasonally high abundances of Marine Group II archaea in summer months which correlate with indicators of phytoplankton production, although not phytoplankton biomass. Although previous studies have reported associations between Marine Group II archaea and particles, here they are almost entirely found in very small particles (0.22–0.7 μm), suggesting they are free-living cells. Populations of Nitrososphaeria did not vary with particle size or environmental conditions. Methanogens were significant fractions of archaeal sequences in large particles at low tide during winter months. Contrary to expectations, Nanoarchaeia were found predominantly in the free-living fraction despite the previous observation that they require an association with hosts. These results underscore the utility of time series studies in shallow, tidally mixed estuarine environments that capture variable conditions for understanding the ecology and biogeochemistry of planktic archaea.
A recreation demand model for warmwater fishing in Delaware with welfare effects for improvements in catch rates, species diversity, and water clarity
(Agricultural and Resource Economics Review, 2024-03-18) Dalvand, Kaveh; Parsons, George
We estimate a recreation demand model for warmwater fishing in Delaware and then use it to measure welfare gains associated with improved fishing quality as measured by catch rate of fish, diversity of species, and clarity of water. We use a “linked” site choice – trip frequency model with data gathered by the Delaware Division of Fish and Wildlife. Our site choice model includes 118 rivers and lakes in the state with detailed characteristics of each. We develop hypothetical scenarios of fishing quality improvement involving combinations of fish catch, fish diversity, and water clarity and apply it to individual water bodies, water basins, selected water body groupings, and statewide. Values are reported in seasonal per angler and aggregate terms.
Environmental drivers of biogeography and community structure in a Mid-Atlantic estuary
(Oecologia, 2024-02-14) Oleynik, Haley A.; Bizzarro, Joseph J.; Hale, Edward A.; Carlisle, Aaron B.
Estuaries include some of the most productive yet anthropogenically impacted marine ecosystems on the planet, and provide critical habitat to many ecologically and economically important marine species. In order to elucidate ecological function in estuaries, we must understand what factors drive community dynamics. Delaware Bay is the third largest estuary in the United States and hosts over 200 species of migrant and resident fishes and invertebrates. The Delaware Division of Fish and Wildlife has conducted two long-term trawl surveys at monthly intervals in Delaware Bay since 1966. The two surveys collect data on environmental conditions, species composition, and number of fishes and macroinvertebrates across different size classes and life histories. Using a suite of multivariate approaches including hierarchical cluster analysis, canonical correlation analysis, and permutational multivariate analysis of variance, we characterized the fish and macroinvertebrate community in Delaware Bay and found that community composition and environmental conditions varied across spatial and seasonal scales. We identified four distinct biogeographic regions, based on environmental conditions and community composition, which were consistent across surveys. We found that the community was driven primarily by gradients in temperature and salinity and that abundant, frequently occurring species in the Bay have well-defined environmental associations. Our work represents the first attempt to use an existing historical survey to better understand how environmental parameters influence diversity and distribution of macrofauna within Delaware Bay, providing insight into how abiotic variables, influenced by climate, may impact the Delaware Bay ecosystem and similar estuarine ecosystems worldwide.
Counterfactual Modeling of Multispecies Fisheries Outcomes under Market-Based Regulation
(Journal of the Association of Environmental and Resource Economists, 2024-04-04) Birkenbach, Anna M.; Lee, Min-Yang; Smith, Martin D.
Much of the recent work evaluating economic impacts of rights-based management (“catch shares”) in fisheries relies on treatment effects models, which typically identify net effects of the policy change but not underlying causal mechanisms. We develop a structural discrete choice model of individual vessel behavior to elucidate how catch shares—and the policies that they replace—influence species targets, timing of fishing activity, and the value generated from the resource. We estimate our model using trip-level data on 286 New England groundfish vessels before and after catch-share implementation. Controlling for weather, costs, and prices, we recover structural parameters characterizing microlevel targeting decisions and simulate the effects of removing input controls and replacing them with catch shares. We find that, under catch shares, the fleet experienced longer and more even fishing seasons, somewhat higher groundfish revenues, fewer closures, and a more balanced portfolio of target stocks than in the counterfactual. Dataverse data: https://doi.org/10.7910/DVN/PJ4YZZ
Sea-ice loss accelerates carbon cycling and enhances seasonal extremes of acidification in the Arctic Chukchi Sea
(Limnology and Oceanography Letters, 2024-02-05) Zhang, Yixing; Wu, Yingxu; Cai, Wei-Jun; Yi, Xiangqi; Gao, Xiang; Bi, Haibo; Zhuang, Yanpei; Chen, Liqi; Qi, Di
The Chukchi Sea shelf (CSS) is a highly productive region in the Arctic Ocean and it is highly efficient for absorbing atmospheric carbon dioxide and exporting and retaining carbon in the deep sea. However, with global warming, the carbon retention time in CSS may decrease, leading to less efficient carbon export. Here, we investigate the seasonal variability of carbonate chemistry in CSS using three sets of late- vs. early-summer reoccupations of the same transect. Our findings demonstrate substantially increased and rapid degradation of biologically produced organic matter and therefore acidification over time in the southern CSS due to earlier sea-ice retreat, resulting in significantly shorter carbon retention time. In sharp contrast, no increased degradation has been observed in the northern CSS where photosynthesis has just commenced. In the future, climate change would further diminish the carbon export capacity and exacerbate seasonal acidification not only within CSS but also across other polar coastal oceans. Scientific Significance Statement The Arctic Chukchi Sea shelf (CSS) is a prominent site for the biological drawdown of atmospheric carbon dioxide, which can subsequently be transported to the deep sea in the Arctic Ocean. The efficiency of carbon export is influenced by seasonal sea-ice formation and retreat: longer period of sea-ice opening results in shorter carbon retention time and reduced carbon export due to rapid recycling of organic matter. However, this process is poorly understood due to lack of observations. Here, we present three sets of late- vs. early-summer reoccupations along the same transect in the CSS. We unveil distinct spatial patterns of carbonate chemistry and subsurface acidification between the southern CSS and northern CSS. In the sCSS, degradation of biologically produced organic matter has occurred rapidly and caused subsurface acidification since early summer due to earlier sea-ice retreat; however, no such phenomenon is observed in the northern region. As Arctic warming continues in the future, these conditions are expected to persist, further diminishing carbon export capacity and exacerbating seasonal acidification.
Dynamics of carbon substrate competition among heterotrophic microorganisms
(The ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2024-01-29) McNichol, Samuel M.; Sanchez-Quete, Fernando; Loeb, Stephanie K.; Teske, Andreas P.; Walter, Sunita R Shah; Mahmoudi, Nagissa
Growing evidence suggests that interactions among heterotrophic microorganisms influence the efficiency and rate of organic matter turnover. These interactions are dynamic and shaped by the composition and availability of resources in their surrounding environment. Heterotrophic microorganisms inhabiting marine environments often encounter fluctuations in the quality and quantity of carbon inputs, ranging from simple sugars to large, complex compounds. Here, we experimentally tested how the chemical complexity of carbon substrates affects competition and growth dynamics between two heterotrophic marine isolates. We tracked cell density using species-specific polymerase chain reaction (PCR) assays and measured rates of microbial CO2 production along with associated isotopic signatures (13C and 14C) to quantify the impact of these interactions on organic matter remineralization. The observed cell densities revealed substrate-driven interactions: one species exhibited a competitive advantage and quickly outgrew the other when incubated with a labile compound whereas both species seemed to coexist harmoniously in the presence of more complex organic matter. Rates of CO2 respiration revealed that coincubation of these isolates enhanced organic matter turnover, sometimes by nearly 2-fold, compared to their incubation as mono-cultures. Isotopic signatures of respired CO2 indicated that coincubation resulted in a greater remineralization of macromolecular organic matter. These results demonstrate that simple substrates promote competition whereas high substrate complexity reduces competitiveness and promotes the partitioning of degradative activities into distinct niches, facilitating coordinated utilization of the carbon pool. Taken together, this study yields new insight into how the quality of organic matter plays a pivotal role in determining microbial interactions within marine environments.
A machine learning model for reconstructing skin-friction drag over ocean surface waves
(Journal of Fluid Mechanics, 2024-03-25) Yousefi, Kianoosh; Hora, Gurpreet Singh; Yang, Hongshuo; Veron, Fabrice; Giometto, Marco G.
In order to improve the predictive abilities of weather and climate models, it is essential to understand the behaviour of wind stress at the ocean surface. Wind stress is contingent on small-scale interfacial dynamics typically not directly resolved in numerical models. Although skin friction contributes considerably to the total stress up to moderate wind speeds, it is notoriously challenging to measure and predict using physics-based approaches. This work proposes a supervised machine learning (ML) model that estimates the spatial distribution of the skin-friction drag over wind waves using solely wave elevation and wave age, which are relatively easy to acquire. The input–output pairs are high-resolution wave profiles and their corresponding surface viscous stresses collected from laboratory experiments. The ML model is built upon a convolutional neural network architecture that incorporates the Mish nonlinearity as its activation function. Results show that the model can accurately predict the overall distribution of viscous stresses; it captures the peak of viscous stress at/near the crest and its dramatic drop to almost null just past the crest in cases of intermittent airflow separation. The predicted area-aggregate skin friction is also in excellent agreement with the corresponding measurements. The proposed method offers a practical pathway for estimating both local and area-aggregate skin friction and can be easily integrated into existing numerical models for the study of air–sea interactions.
The impact of sea ice melt on the evolution of surface pCO2 in a polar ocean basin
(Frontiers in Marine Science, 2024-02-07) Yang, Wei; Zhao, Yu; Wu, Yingxu; Chen, Zijie; Gao, Xiang; Lin, Hongmei; Ouyang, Zhangxian; Cai, Weijun; Chen, Liqi; Qi, Di
The strong CO2 sink in Arctic Ocean plays a significant role in the global carbon budget. As a high-latitude oceanic ecosystem, the features of sea surface pCO2 and air-sea CO2 flux are significantly influenced by sea ice melt; however, our understanding of pCO2 evolution during sea ice melt remains limited. In this study, we investigate the dynamics of pCO2 during the progression of sea ice melt in the western Arctic Ocean based on data from two cruises conducted in 2010 and 2012. Our findings reveal substantial spatiotemporal variability in surface pCO2 on the Chukchi Sea shelf and Canada Basin, with a boundary along the shelf breaks at depths of 250-500 m isobaths. On the Chukchi Sea shelf, strong biological consumption dominates pCO2 variability. Moreover, in Canada Basin, the pCO2 dynamics are modulated by various processes. During the active sea ice melt stage before sea ice concentration decreases to 15%, biological production through photosynthetic processes and dilution of ice melt water lead to a reduction in DIC concentration and subsequent decline in pCO2. Further, these effects are counteracted by the air-sea CO2 exchange at the sea surface which tends to increase seawater DIC and subsequently elevate surface pCO2. Compared to the pCO2 reduction resulting from biological production and dilution effects, the contribution of air-sea CO2 exchange is significantly lower. The combined effects of these factors have a significant impact on reducing pCO2 during this stage. Conversely, during the post sea ice melt stage, an increase in pCO2 resulting from high temperatures and air-sea CO2 exchange outweighs its decrease caused by biological production. Their combined effects result in a prevailing increase in sea surface pCO2. We argue that enhanced air-sea CO2 uptake under high wind speeds also contributes to the high sea surface pCO2 observed in 2012, during both active sea ice melt stage and post sea ice melt stage. The present study reports, for the first time, the carbonate dynamics and pCO2 controlling processes during the active sea ice melt stage. These findings have implications for accurate estimation of air-sea CO2 fluxes and improved modeling simulations within the Arctic Ocean. Highlights ● The decrease in DIC resulting from biological production and dilution of ice melt water tends to reduce pCO2 during the active sea ice melt stage in Canada Basin, although it is counteracted by CO2 uptake at the air-sea interface. ● The increase in pCO2 resulting from high temperatures and air-sea CO2 exchange outweighs its decrease caused by biological production, leading to elevated sea surface pCO2 during the post sea ice melt stage in Canada Basin. ● The enhanced air-sea CO2 uptake under high wind speeds also contributes to the high sea surface pCO2 observed in 2012, during both active sea ice melt stage and post sea ice melt stage.
Rapid Sea Level Rise in the Tropical Southwest Indian Ocean in the Recent Two Decades
(Geophysical Research Letters, 2023-12-27) Huang, Lei; Zhuang, Wei; Lu, Wenfang; Zhang, Yang; Edwing, Deanna; Yan, Xiao-Hai
It has been reported that the sea level falls in the tropical Southwest Indian Ocean (SWIO) from the 1960s to the early 2000s. However, a rising trend of 4.05 ± 0.56 cm/decade has occurred during the recent two decades with our analysis showing that manometric sea level contributes 41% to this sea level rise. 30% of this rise is due to steric sea level (SSL) change in the upper 2,000 m with SSL rise in the upper 300 m of secondary importance. Conversely, thermal expansion below the thermocline (300–2,000 m), likely caused by water mass spread from the Southern Ocean, induces major contribution to SSL changes. Compared to existing studies demonstrating the contribution of thermal variations above the thermocline to sea level variability in the tropical SWIO, this study emphasizes the importance of ocean mass and deeper ocean changes in a warming climate. Key Points - Rapid sea level rise occurs in the tropical Southwest Indian Ocean (SWIO) since the early 2000s - The ocean mass addition and the upper 2,000 m ocean warming contribute significantly to the total sea level rise - The upper 2,000 m ocean warming is primarily attributed to thermal expansion below the thermocline associated with the spread of water masses Plain Language Summary Global ocean sea level change is spatially and temporally nonuniform due to oceanic and atmospheric dynamics. The tropical Southwest Indian Ocean (SWIO) experienced a sea level fall from the 1960s to the early 2000s. However, a rapid sea level rise has occurred over the last two decades in the tropical SWIO that is faster than the global average. The ocean mass increase due to extra water input leads to an essential impact on sea level rise in the tropical SWIO. Compared to previous studies demonstrating the effect of thermal expansion in the upper 300 m, this study shows larger contributions from deeper ocean (300–2,000 m) warming over the past two decades. Overall, this study highlights the importance of ocean mass and deeper water thermal structure in regulating tropical SWIO sea level rise in a changing climate, as well as the need for observations and direct assessment of the abyssal ocean beneath 2,000 m.
Network Analysis Reveals Species-Specific Organization of Microbial Communities in Four Co-Occurring Elasmobranch Species along the Georgia Coast
(Fishes, 2024-01-15) Lyons, Kady; Bedore, Christine N.; Carlisle, Aaron B.; Moniz, Lauren; Odom, Timothy L.; Ahmed, Rokeya; Greiman, Stephen E.; Freedman, Ryan M.
Comparing co-occurring species may provide insights into how aspects of ecology may play a role in influencing their microbial communities. During the 2019 commercial shrimp trawl season off coastal Georgia, swabs of skin, gills, cloaca, and gut were taken for three species of batoids (Butterfly Ray, Bluntnose Stingray, and Atlantic Stingray) and one shark species (Atlantic Sharpnose) for high-throughput sequencing of the V4 region of the bacterial 16S rRNA gene. White muscle was analyzed for stable isotopes (δ13C and δ15N) to evaluate potential niche overlap in these four sympatric mesopredators. Significant differences were found in both δ13C and δ15N signatures across species, suggesting a degree of resource partitioning. When examined within tissue type, the host species had a weak effect on β-diversity for cloaca and skin, with no differences found for gill and gut samples. However, network analysis metrics demonstrated a stronger species-specific effect and distinct microbial community relationships were apparent between the shark and batoids, with the former having tighter networks for both internally- and externally-influenced tissues (gut/cloaca and skin/gills, respectively). Despite overlapping habitat use, species’ microbiomes differed in their organizational structuring that paralleled differences in stable isotope results, suggesting a mediating role of species-specific ecology on bacterial microbiomes.
The Role of Coastal Yedoma Deposits and Continental Shelf Sediments in the Arctic Ocean Silicon Cycle
(Global Biogeochemical Cycles, 2024-01-09) Ray, Nicholas E.; Martens, Jannik; Ajmar, Marco; Tesi, Tommaso; Yakushev, Evgeniy; Gangnus, Ivan; Strauss, Jens; Schirrmeister, Lutz; Semiletov, Igor; Wild, Birgit
The availability of silicon (Si) in the ocean plays an important role in regulating biogeochemical and ecological processes. The Si budget of the Arctic Ocean appears balanced, with inputs equivalent to outputs, though it is unclear how a changing climate might aggravate this balance. In this study, we focus on Si cycling in Arctic coastal areas and continental shelf sediments to better constrain the Arctic Ocean Si budget. We provide the first estimate of amorphous Si (ASi) loading from erosion of coastal Yedoma deposits (30–90 Gmol yr−1), demonstrating comparable rates to particulate Si loading from rivers (10–90 Gmol yr−1). We found a positive relationship between surface sediment ASi and organic matter content on continental shelves. Combining these values with published Arctic shelf sediment properties and burial rates we estimate 70 Gmol Si yr−1 is buried on Arctic continental shelves, equivalent to 4.5% of all Si inputs to the Arctic Ocean. Sediment dissolved Si fluxes increased with distance from river mouths along cruise transects of shelf regions influenced by major rivers in the Laptev and East Siberian seas. On an annual basis, we estimate that Arctic shelf sediments recycle approximately up to twice as much DSi (680 Gmol Si) as is loaded from rivers (340–500 Gmol Si). Key Points - Coastal erosion loads 30–90 Gmol Si yr−1 to the Arctic Ocean in the form of amorphous silicon - Continental shelf sediments in the Arctic Ocean recycle more silicon than is loaded from rivers - Approximately 4.5% of silicon loaded on the Arctic Ocean is buried in continental shelf sediments

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