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Open access publications by faculty, postdocs, and graduate students in the Department of Earth Sciences.

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Genome editing in ubiquitous freshwater Actinobacteria
(Applied and Environmental Microbiology, 2024-10-16) Bairagi, Nachiketa; Keffer, Jessica L.; Heydt, Jordan C.; Maresca, Julia A.
Development of genome-editing tools in diverse microbial species is an important step both in understanding the roles of those microbes in different environments, and in engineering microbes for a variety of applications. Freshwater-specific clades of Actinobacteria are ubiquitous and abundant in surface freshwaters worldwide. Here, we show that Rhodoluna lacicola and Aurantimicrobium photophilum, which represent widespread clades of freshwater Actinobacteria, are naturally transformable. We also show that gene inactivation via double homologous recombination and replacement of the target gene with antibiotic selection markers can be used in both strains, making them convenient and broadly accessible model organisms for freshwater systems. We further show that in both strains, the predicted phytoene synthase is the only phytoene synthase, and its inactivation prevents the synthesis of all pigments. The tools developed here enable targeted modification of the genomes of some of the most abundant microbes in freshwater communities. These genome-editing tools will enable hypothesis testing about the genetics and (eco)physiology of freshwater Actinobacteria and broaden the available model systems for engineering freshwater microbial communities. IMPORTANCE To advance bioproduction or bioremediation in large, unsupervised environmental systems such as ponds, wastewater lagoons, or groundwater systems, it will be necessary to develop diverse genetically amenable microbial model organisms. Although we already genetically modify a few key species, tools for engineering more microbial taxa, with different natural phenotypes, will enable us to genetically engineer multispecies consortia or even complex communities. Developing genetic tools for modifying freshwater bacteria is particularly important, as wastewater, production ponds or raceways, and contaminated surface water are all freshwater systems where microbial communities are already deployed to do work, and the outputs could potentially be enhanced by genetic modifications. Here, we demonstrate that common tools for genome editing can be used to inactivate specific genes in two representatives of a very widespread, environmentally relevant group of Actinobacteria. These Actinobacteria are found in almost all tested surface freshwater environments, where they co-occur with primary producers, and genome-editing tools in these species are thus a step on the way to engineering microbial consortia in freshwater environments.
Beyond the Wedge: Impact of Tidal Streams on Salinization of Groundwater in a Coastal Aquifer Stressed by Pumping and Sea-Level Rise
(Water Resources Research, 2024-09-27) Hingst, M. C.; Housego, R. M.; He, C.; Minsley, B. J.; Ball, L. B.; Michael, H. A.
Saltwater intrusion (SWI) is a well-studied phenomenon that threatens the freshwater supplies of coastal communities around the world. The development and advancement of numerical models has led to improved assessment of the risk of salinization. However, these studies often fail to include the impact of surface waters as potential sources of aquifer salinity and how they may impact SWI. Based on field-collected data, we developed a regional, variable-density groundwater model using SEAWAT for east Dover, Delaware. In this location, major users of groundwater from the surficial aquifer are the City of Dover and irrigation for agriculture. Our model includes salinized marshland and tidal streams, along with irrigation and municipal pumping wells. Model scenarios were run for 100 years and included changes in pumping rates and sea-level rise (SLR). We examined how these drivers of SWI affect the extent and location of salinization in the surficial aquifer by evaluating differences in chloride concentration near surface waters and the subsurface freshwater-saltwater interface. We found the presence of the marsh inverts the typical freshwater-saltwater wedge interface and that the edge of the interface did not migrate farther inland. Additionally, we found that tidal streams are the dominant pathways of SWI at our site with salinization from streams being exacerbated by SLR. Our results also show that spatial distribution of pumping affects both the magnitude and extent of salinization, with an increase in concentrated pumping leading to more intensive salinization than a more widely distributed increase of the same total pumping volume. Key Points - Presence of a saltmarsh inverts the freshwater-saltwater interface in our study location - Tidal streams contribute substantially to salinization of inland groundwater - Concentrated pumping led to more intensive salinization than widespread pumping
Clues on the Australasian impact crater site inferred from detailed mineralogical study of a monazite inclusion in a Muong Nong tektite
(Geology, 2024-09-04) Seydoux-Guillaume, A.-M.; Rochette, P.; Gardés, E.; Zanetta, P.-M.; Sao-Joao, S.; de Parseval, Ph.; Glass, B.P.
Tektites are terrestrial impact-generated glasses distributed over regions of Earth’s surface with ejection distances up to 10,000 km. The Australasian tektite strewn field is the largest and the youngest discovered so far (788 ka). However, the location of the source crater remains unsolved. The present work is the first to investigate the only monazite ever found as an inclusion in a Muong Nong tektite (MNT) from Indochina. In-depth observations down to the nanoscale revealed that the monazite experienced very high temperature, with silicate melt injection sometimes trapped within porosity at the grain boundaries, followed by a recovery mechanism responsible for dislocation migration and subgrain formation. The absence of radiation damage confirms that this recovery episode occurred recently, in line with the age of the tektite. The preservation of a primary zonation (Th component) and the absence of detectable diffusion profiles indicate that the monazite did not reach the melting point (∼2050 °C) before initial rapid cooling (∼1000 °C/s). The U-Th−total Pb dates of the monazite thus remained unchanged during the impact: 73 ± 6 Ma in a Th-rich domain and 156 ± 15 Ma in a Th-poor domain. This allows the source of the MNT to be constrained. Comparison with a detailed database of monazite ages and Th/U ratios in SE Asia indicates that the Australasian crater should be sought for in the triangle made up of the Philippines, coastal south China, and northern Vietnam, though the latter appears less probable.
Size-dependent effects of dams on river ecosystems and implications for dam removal outcomes
(Ecological Applications, 2024-08-13) Brown, Rebecca L.; Charles, Don; Horwitz, Richard J.; Pizzuto, James E.; Skalak, Katherine; Velinsky, David J.; Hart, David D.
Understanding the relationship between a dam's size and its ecological effects is important for prioritization of river restoration efforts based on dam removal. Although much is known about the effects of large storage dams, this information may not be applicable to small dams, which represent the vast majority of dams being considered for removal. To better understand how dam effects vary with size, we conducted a multidisciplinary study of the downstream effect of dams on a range of ecological characteristics including geomorphology, water chemistry, periphyton, riparian vegetation, benthic macroinvertebrates, and fish. We related dam size variables to the downstream–upstream fractional difference in measured ecological characteristics for 16 dams in the mid-Atlantic region ranging from 0.9 to 57 m high, with hydraulic residence times (HRTs) ranging from 30 min to 1.5 years. For a range of physical attributes, larger dams had larger effects. For example, the water surface width below dams was greater below large dams. By contrast, there was no effect of dam size on sediment grain size, though the fraction of fine-grained bed material was lower below dams independently of dam size. Larger dams tended to reduce water quality more, with decreased downstream dissolved oxygen and increased temperature. Larger dams decreased inorganic nutrients (N, P, Si), but increased particulate nutrients (N, P) in downstream reaches. Aquatic organisms tended to have greater dissimilarity in species composition below larger dams (for fish and periphyton), lower taxonomic diversity (for macroinvertebrates), and greater pollution tolerance (for periphyton and macroinvertebrates). Plants responded differently below large and small dams, with fewer invasive species below large dams, but more below small dams. Overall, these results demonstrate that larger dams have much greater impact on the ecosystem components we measured, and hence their removal has the greatest potential for restoring river ecosystems.
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.
Insight into the Evolution of the Eastern Margin of the Wyoming Craton from Complex, Laterally Variable Shear Wave Splitting
(Lithosphere, 2024-07-12) Birkey, Andrew; Ford, Heather A.; Anderson, Megan; Byrnes, Joseph S.; Bezada, Maximiliano J.; Shapovalov, Maxim
Dense seismic arrays such as EarthScope’s Transportable Array (TA) have enabled high-resolution seismic observations that show the structure of cratonic lithosphere is more heterogeneous and complex than previously assumed. In this study, we pair TA data with data from the Bighorn Arch Seismic Experiment and the Crust and lithosphere Investigation of the Easternmost expression of the Laramide Orogeny (CIELO) to provide unprecedented detail on the seismic anisotropic structure of the eastern margin of the Wyoming Craton, where several orogens emerged from nominally strong cratonic lithosphere during the Laramide Orogeny. In this study, we use the splitting of teleseismic shear waves to characterize fabrics associated with deformation in the Earth’s crust and mantle. We constrain distinct anisotropic domains in the study area, and forward modeling shows that each of these domains can be explained by a single layer of anisotropy. Most significantly, we find a fast direction in the southern part of the Powder River Basin, which we refer to as the Thunder Basin Block (TBB), that deviates from absolute plate motion (APM). This change in splitting behavior coincides with changes in other modeled geophysical observations, such as active source P-wave velocity models, potential field modeling, and seismic attenuation analysis, which all show a significant change moving from the Bighorn Mountains to the TBB. We argue that these results correspond to structure predating the Laramide Orogeny, and most likely indicate a Neoarchean boundary preserved within the lithosphere.
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
Incorporating flowpaths as an explicit measure of river-floodplain connectivity to improve estimates of floodplain sediment deposition
(Geomorphica, 2024-05-28) Sumaiya, Sumaiya; Schubert, John T.; Czuba, Jonathan A.; Pizzuto, James E.
Variation in floodplain topography can lead to gradual flooding and increase river-floodplain connectivity. We show that incorporating flowpaths as an explicit measure of river-floodplain connectivity can improve estimates of floodplain sediment deposition. We focus on the floodplain of the South River, downstream of Waynesboro, Virginia, where measurements of mercury accumulation have been used to estimate decadal-scale sedimentation rates. We developed a two-dimensional Hydrologic Engineering Center's River Analysis System (2D HEC-RAS) hydrodynamic model and used simulated model results with sediment deposition data to create regression models describing sedimentation across the floodplain. All of our statistical models incorporated a flowpath length from the location on the floodplain downstream to the riverbank as an explicit measure of river-floodplain connectivity that improved our estimates of floodplain sediment deposition (r2 = 0.514). We applied our best regression model to our hydrodynamic model results to create a map of floodplain sedimentation rate and discuss differences of three separate sections of floodplain. We found that floodplains with variable topography had wider, bimodal probability distribution functions (PDFs) of sedimentation rate (aggregated spatially) than floodplains without this topographic relief (with narrower log-normal PDFs). Our work highlights how floodplain topography and river-floodplain connectivity affect sedimentation rates and can help inform the development of floodplain sediment budgets.
Magmatic conditions aiding synconvergent extension above the Peruvian flat slab
(Geosphere, 2024-05-17) Grambling, Tyler A.; Jessup, Micah J.; Newell, Dennis L.; Grambling, Nadine L.; Hiett, Coleman D.
The Cordillera Blanca and Cordillera Huayhuash contain some of the highest topography in the Andes and provide insight into tectonomagmatic processes associated with the onset of flat-slab subduction. These adjacent ranges shared a similar history of deformation and exhumation prior to the late Miocene, when synconvergent extension began in the Cordillera Blanca. Magmatism in the Cordillera Huayhuash has been inferred as coeval with magmatism in the Cordillera Blanca. Yet, extension, which has been correlated with magmatic heat flow, is limited to the Cordillera Blanca. New zircon U-Pb dates and trace and rare earth element concentrations from the Cordillera Blanca batholith and the Huayllapa pluton in the Cordillera Huayhuash and reassessment of existing zircon data help to characterize regional magmatic processes prior to the establishment of flat-slab subduction. Two compositionally distinct samples of the Huayllapa pluton yielded mean ages of 24.8 ± 0.4 Ma and 25.4 ± 0.8 Ma. In contrast, the Cordillera Blanca batholith has a protracted crystallization history postdating that of the Cordillera Huayhuash by up to 20 m.y. Miocene magmatism in the Cordillera Blanca began at 19 Ma and ended with injection of large volumes of geochemically distinct, mantle-derived magma from 10 to 5 Ma. We suggest that 6–5 Ma magmatism in the Cordillera Blanca promoted elevated heat flow and reduced shear strength, which facilitated extensional shearing along the western slopes of the range, whereas colder amagmatic crust in the Cordillera Huayhuash inhibited southward propagation of faulting. Our data demonstrate that the linkages between magmatism and elevated heat flow identified in the Cordillera Blanca are important driving processes in initiating extension in cordilleran-style orogenies.
Saltwater Intrusion Into a Confined Island Aquifer Driven by Erosion, Changing Recharge, Sea-Level Rise, and Coastal Flooding
(Water Resources Research, 2024-01-08) Stanic, S.; LeRoux, N. K.; Paldor, A.; Mohammed, A. A.; Michael, H. A.; Kurylyk, B. L.
Aquifers on small islands are at risk of salinization due to low elevations and limited adaptive capacity, and present risks will be exacerbated by climate change. Most studies addressing small-island saltwater intrusion (SWI) have focused on homogeneous sandy islands and one or two hydraulic disturbances. We herein investigate SWI dynamics in a layered, confined island aquifer in response to multiple environmental perturbations related to climate change, with two considered in tandem. Our field and modeling work is based on an island aquifer that provides the drinking water supply for an Indigenous community in Atlantic Canada. Observation well data and electrical resistivity profiles were used to calibrate a numerical model (HydroGeoSphere) of coupled groundwater flow and salt transport. The calibrated model was used to simulate the impacts of climate change including sea-level rise (SLR), storm surge overtopping, changing aquifer recharge, and erosion. Simulated aquifer conditions were resilient to surges because the confining layer prevented deeper saltwater leaching. However, reduced recharge and erosion resulted in saltwater wedge migration of 170 and 110 m, respectively when considered individually, and up to 295 m (i.e., into the wellfield) when considered together. Despite the confining conditions, SLR resulted in wedge migration up to 55 m as the confining pressures were not sufficient to resist wedge movement. This is the first study to harness an integrated, surface-subsurface hydrologic model to assess effects of coastal erosion and other hydroclimatic stressors on island aquifers, highlighting that climate change can drive extensive salinization of critical groundwater resources. Key Points - A surface-subsurface numerical model is used to investigate climate change impacts on island groundwater resources used for water supply - The confined aquifer is resilient to storm surges which only salinize the unpumped surficial aquifer before being flushed - Coastal erosion and recharge reductions result in the most saltwater intrusion and can work in tandem to threaten future water supply Plain Language Summary Due to their limited resources and adaptive capacity, small islands are highly vulnerable to climate change impacts, including saltwater intrusion. Freshwater needs on small islands are often sourced from small aquifers that are in delicate balance between conditions in the ocean, atmosphere, and land. In this study, we investigate the movement of saltwater into the freshwater aquifer of a small island that provides drinking water resources for an Indigenous First Nation. We consider climatic changes in the ocean (sea-level rise (SLR), storm surges, and related coastal erosion) and atmosphere (changes to net precipitation) and associated impacts to the island's fresh groundwater resources. We use field data paired with a mathematical model and demonstrate that the pressurized conditions of the layered island aquifer make it more resilient to SLR than unconfined aquifers in sandy islands are. However, the aquifer's freshwater volume is susceptible to coastal erosion and reduced precipitation, particularly when these happen at the same time. Results point to coastal erosion as a potential widespread driver of freshwater loss along eroding portions of the global coastline.
Trace elements in abyssal peridotite olivine record melting, thermal evolution, and melt refertilization in the oceanic upper mantle
(Contributions to Mineralogy and Petrology, 2023-09-06) Lin, Kuan-Yu; Warren, Jessica M.; Davis, Fred A.
Trace element concentrations in abyssal peridotite olivine provide insights into the formation and evolution of the oceanic lithosphere. We present olivine trace element compositions (Al, Ca, Ti, V, Cr, Mn, Co, Ni, Zn, Y, Yb) from abyssal peridotites to investigate partial melting, melt–rock interaction, and subsolidus cooling at mid-ocean ridges and intra-oceanic forearcs. We targeted 44 peridotites from fast (Hess Deep, East Pacific Rise) and ultraslow (Gakkel and Southwest Indian Ridges) spreading ridges and the Tonga trench, including 5 peridotites that contain melt veins. We found that the abundances of Ti, Mn, Co, and Zn increase, while Ni decreases in melt-veined samples relative to unveined samples, suggesting that these elements are useful tracers of melt infiltration. The abundances of Al, Ca, Cr, and V in olivine are temperature sensitive. Thermometers utilizing Al and Ca in olivine indicate temperatures of 650–1000 °C, with variations corresponding to the contrasting cooling rates the peridotites experienced in different tectonic environments. Finally, we demonstrate with a two-stage model that olivine Y and Yb abundances reflect both partial melting and subsolidus re-equilibration. Samples that record lower Al- and Ca-in-olivine temperatures experienced higher extents of diffusive Y and Yb loss during cooling. Altogether, we demonstrate that olivine trace elements document both high-temperature melting and melt–rock interaction events, as well as subsolidus cooling related to their exhumation and emplacement onto the seafloor. This makes them useful tools to study processes associated with seafloor spreading and mid-ocean ridge tectonics.
Pre- and postsettlement depositional processes and environments of the 3rd- to 5th-order White Clay Creek watershed, Piedmont Province, Pennsylvania and Delaware, USA
(GSA Bulletin, 2023-08-23) Pizzuto, J.E.; Huffman, M. E.; Symes, E.
We extend two hypotheses based on studies of 1st- to 3rd-order Piedmont watersheds of southeastern Pennsylvania, USA, by collecting data in a larger 3rd- to 5th-order watershed nearby. One hypothesis posits that presettlement river corridors were dominated by wetlands, and the other suggests that river valleys were filled by millpond sedimentation following European settlement. Both hypotheses support new river restoration practices, so their generality is important to assess. Ten lithofacies indicate depositional environments, while pedostratigraphic criteria and 14C dating define presettlement and postsettlement stratigraphic units. Basal gravels similar to modern stream bed sediments represent presettlement channels with active bedload transport. Wedge-shaped gravel deposits resembling modern bars further document presettlement bedload transport by channelized flows. Extensive presettlement and postsettlement units of massive, organic-poor, fine-grained sediment formed when overbank flows inundated floodplains. Peat deposits, exposed at a single site (but absent elsewhere), represent a presettlement wetland. Decimeter-thick, discontinuous, massive carbonaceous fine-grained sediments occasionally overlie basal gravels; these may represent localized wetlands adjacent to presettlement channels or hydraulic backwater environments. Laminated sand and mud accumulated behind one 3-m-high mill dam, but these millpond deposits are absent at other sites. Instead of being dominated by wetlands, presettlement river corridors are better described as a complex mosaic of riparian environments including older colluvial landforms, floodplains (some of which may have been seasonally inundated wetlands), primary (and possibly secondary) channels, and depending on geomorphic setting, either localized or valley-spanning wetlands. After European settlement, millponds were important locally, but their deposits represent a minor component of the stratigraphic record.
Physiochemical Controls on the Horizontal Exchange of Blue Carbon Across the Salt Marsh-Tidal Channel Interface
(Journal of Geophysical Research: Biogeosciences, 2023-06-06) Fettrow, Sean; Jeppi, Virginia; Wozniak, Andrew; Vargas, Rodrigo; Michael, Holly; Seyfferth, Angelia L.
Tidal channels are biogeochemical hotspots that horizontally exchange carbon (C) with marsh platforms, but the physiochemical drivers controlling these dynamics are poorly understood. We hypothesized that C-bearing iron (Fe) oxides precipitate and immobilize dissolved organic carbon (DOC) during ebb tide as the soils oxygenate, and dissolve into the porewater during flood tide, promoting transport to the channel. The hydraulic gradient physically controls how these solutes are horizontally exchanged across the marsh platform-tidal channel interface; we hypothesized that this gradient alters the concentration and source of C being exchanged. We further hypothesized that trace soil gases (i.e., CO2, CH4, dimethyl sulfide) are pushed out of the channel bank as the groundwater rises. To test these hypotheses, we measured porewater, surface water, and soil trace gases over two 24-hr monitoring campaigns (i.e., summer and spring) in a mesohaline tidal marsh. We found that Fe2+ and DOC were positively related during flood tide but not during ebb tide in spring when soils were more oxidized. This finding shows evidence for the formation and dissolution of C-bearing Fe oxides across a tidal cycle. In addition, the tidal channel contained significantly (p < 0.05) more terrestrial-like DOC when the hydraulic gradient was driving flow toward the channel. In comparison, the channel water was saltier and contained significantly (p < 0.05) more marine-like DOC when the hydraulic gradient reversed direction. Trace gas fluxes increased with rising groundwater levels, particularly dimethyl sulfide. These findings suggest multiple physiochemical mechanisms controlling the horizontal exchange of C at the marsh platform-tidal channel interface. Plain Language Summary Tidal salt marshes store large amounts of carbon belowground in soils, but there is also a significant amount of carbon flowing into and out of these ecosystems via tidal channels. We investigated the carbon flowing between the channel bank and surface water in a salt marsh in Delaware. We found that soil minerals (i.e., iron oxides) control the mobility of carbon as iron oxides retain carbon during ebb tides and release carbon during flood tides as the minerals dissolve. The gradient between the groundwater and surface water elevation (i.e., hydraulic gradient) controls the flow direction for dissolved carbon, altering the concentration and source of carbon found in the tidal channel across tidal cycles. In addition, gases trapped in channel banks are pushed out of the soils as the tide rises. These findings will improve our understanding of carbon cycles in these critical carbon sinks. Key Points - Physiochemical mechanisms control horizontal exchange of carbon across marsh-tidal channel interfaces, affecting lateral carbon flux - Dissolution and reprecipitation of carbon-bearing Fe oxides during flood and ebb tides control the horizontal mobility of carbon - Hydraulic gradients control the carbon character in the tidal channel, and rising tides push greenhouse gases out of the channel bank
Predicting Subsurface Architecture From Surface Channel Networks in the Bengal Delta
(Journal of Geophysical Research: Earth Surface, 2023-03-19) Xu, Zhongyuan; Khan, Mahfuzur R.; Ahmed, Kazi Matin; Zahid, Anwar; Hariharan, Jayaram; Passalacqua, Paola; Steel, Elisabeth; Chadwick, Austin; Paola, Chris; Goodbred, Steven L. Jr.; Paldor, Anner; Michael, Holly A.
Groundwater is the primary source of water in the Bengal Delta but contamination threatens this vital resource. In deltaic environments, heterogeneous sedimentary architecture controls groundwater flow; therefore, characterizing subsurface structure is a critical step in predicting groundwater contamination. Here, we show that surface information can improve the characterization of the nature and geometry of subsurface features, thus improving the predictions of groundwater flow. We selected three locations in the Bengal Delta with distinct surface river network characteristics—the lower delta with straighter tidal channels, the mid-delta with meandering and braided channels, and the inactive delta with transitional sinuous channels. We used surface information, including channel widths, depths, and sinuosity, to create models of the subsurface with object-based geostatistical simulations. We collected an extensive set of lithologic data and filled in gaps with newly drilled boreholes. Our results show that densely distributed lithologic data from active lower and mid-delta are consistent with the object-based models generated from surface information. In the inactive delta, metrics from object-based models derived from surface geometries are not consistent with subsurface data. We further simulated groundwater flow and solute transport through the object-based models and compared these with simulated flow through lithologic models based only on variograms. Substantial differences in flow and transport through the different geologic models show that geometric structure derived from surface information strongly influences groundwater flow and solute transport. Land surface features in active deltas are therefore a valuable source of information for improving the evaluation of groundwater vulnerability to contamination. Key Points: - We demonstrate a novel approach that harnesses land surface characteristics to inform groundwater modeling in deltas - The subsurface lithologic data of an active delta is more consistent with surface features than that of an inactive delta - Incorporation of surface information can improve the prediction of contaminant transport in aquifers Plain Language Summary: The structure of groundwater aquifers affects how groundwater and contaminants move through them. In deltas, dynamic river networks are responsible for depositing sediments that ultimately form subsurface aquifers. Therefore, the characteristics of the surface river channel network should provide information about the structure of the subsurface. We tested this idea using a large set of sedimentary data from the Bengal Basin. We created models of the subsurface based on the surface network and showed that the subsurface data reflect the model characteristics in deltas that are actively depositing sediment. Using these subsurface models as input for groundwater flow models, we showed that incorporating this surface information is important for being able to predict how contaminants move in groundwater.
The role of iron in the formation of Ediacaran ‘death masks’
(Geobiology, 2023-02-26) Gibson, Brandt M.; Schiffbauer, James D.; Wallace, Adam F.; Darroch, Simon A. F.
The Ediacara biota are an enigmatic group of Neoproterozoic soft-bodied fossils that mark the first major radiation of complex eukaryotic and macroscopic life. These fossils are thought to have been preserved via pyritic “death masks” mediated by seafloor microbial mats, though little about the chemical constraints of this preservational pathway is known, in particular surrounding the role of bioavailable iron in death mask formation and preservational fidelity. In this study, we perform decay experiments on both diploblastic and triploblastic animals under a range of simulated sedimentary iron concentrations, in order to characterize the role of iron in the preservation of Ediacaran organisms. After 28 days of decay, we demonstrate the first convincing “death masks” produced under experimental laboratory conditions composed of iron sulfide and probable oxide veneers. Moreover, our results demonstrate that the abundance of iron in experiments is not the sole control on death mask formation, but also tissue histology and the availability of nucleation sites. This illustrates that Ediacaran preservation via microbial death masks need not be a “perfect storm” of paleoenvironmental porewater and sediment chemistry, but instead can occur under a range of conditions.
Aqueous Geochemical Controls on the Sestonic Microbial Community in Lakes Michigan and Superior
(Microorganisms, 2023-02-17) Rani, Asha; Ranjan, Ravi; Bonina, Solidea M. C.; Izadmehr, Mahsa; Giesy, John P.; Li, An; Sturchio, Neil C.; Rockne, Karl J.
Despite being the largest freshwater lake system in the world, relatively little is known about the sestonic microbial community structure in the Laurentian Great Lakes. The goal of this research was to better understand this ecosystem using high-throughput sequencing of microbial communities as a function of water depth at six locations in the westernmost Great Lakes of Superior and Michigan. The water column was characterized by gradients in temperature, dissolved oxygen (DO), pH, and other physicochemical parameters with depth. Mean nitrate concentrations were 32 μmol/L, with only slight variation within and between the lakes, and with depth. Mean available phosphorus was 0.07 μmol/L, resulting in relatively large N:P ratios (97:1) indicative of P limitation. Abundances of the phyla Actinobacteria, Bacteroidetes, Cyanobacteria, Thaumarchaeota, and Verrucomicrobia differed significantly among the Lakes. Candidatus Nitrosopumilus was present in greater abundance in Lake Superior compared to Lake Michigan, suggesting the importance of ammonia-oxidating archaea in water column N cycling in Lake Superior. The Shannon diversity index was negatively correlated with pH, temperature, and salinity, and positively correlated with DO, latitude, and N2 saturation. Results of this study suggest that DO, pH, temperature, and salinity were major drivers shaping the community composition in the Great Lakes.
Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland
(FEMS Microbiology Ecology, 2023-02-14) Cooper, Rebecca E.; Finck, Jessica; Chan, Clara; Küsel, Kirsten
Sideroxydans sp. CL21 is a microaerobic, acid-tolerant Fe(II)-oxidizer, isolated from the Schlöppnerbrunnen fen. Since the genome size of Sideroxydans sp. CL21 is 21% larger than that of the neutrophilic Sideroxydans lithotrophicus ES-1, we hypothesized that strain CL21 contains additional metabolic traits to thrive in the fen. The common genomic content of both strains contains homologs of the putative Fe(II) oxidation genes, mtoAB and cyc2. A large part of the accessory genome in strain CL21 contains genes linked to utilization of alternative electron donors, including NiFe uptake hydrogenases, and genes encoding lactate uptake and utilization proteins, motility and biofilm formation, transposable elements, and pH homeostasis mechanisms. Next, we incubated the strain in different combinations of electron donors and characterized the fen microbial communities. Sideroxydans spp. comprised 3.33% and 3.94% of the total relative abundance in the peatland soil and peatland water, respectively. Incubation results indicate Sideroxydans sp. CL21 uses H2 and thiosulfate, while lactate only enhances growth when combined with Fe, H2, or thiosulfate. Rates of H2 utilization were highest in combination with other substrates. Thus, Sideroxydans sp. CL21 is a mixotroph, growing best by simultaneously using substrate combinations, which helps to thrive in dynamic and complex habitats.
Frequent Storm Surges Affect the Groundwater of Coastal Ecosystems
(Geophysical Research Letters, 2023-01-09) Nordio, Giovanna; Frederiks, Ryan; Hingst, Mary; Carr, Joel; Kirwan, Matt; Gedan, Keryn; Michael, Holly; Fagherazzi, Sergio
Recent studies have focused on the effect of large tropical cyclones (hurricanes) on the shore, neglecting the role of less intense but more frequent events. Here we analyze the effect of the offshore tropical storm Melissa on groundwater data collected along the North America Atlantic coast. Our meta-analysis indicates that both groundwater level and specific conductivity significantly increased during Melissa, respectively reaching maximum values of 1.09 m and 25.2 mS/cm above pre-storm levels. Time to recover to pre-storm levels was 10 times greater for groundwater specific conductivity, with a median value of 20 days, while groundwater level had a median recovery time of 2 days. A frequency-magnitude analysis indicates that the percent of time with salinization is higher for Melissa than for energetic hurricanes. Given the high frequency of these events (return period of 1–2 years), and the long time needed for groundwater conditions to return to normal levels, we conclude that increasingly frequent moderate storms will have a significant impact on the ecology of vegetated shorelines. Key Points: - Salinization - Coastal areas - Groundwater Plain Language Summary: Salinization and flooding events due to sea level rise and storm surges threaten coastal ecosystems, changing groundwater characteristics. Moderate and more frequent storm surges can have a significant impact on coastal ecology, similar to larger tropical cyclones. Salinity and water table elevation need time to recover to normal conditions. The recovery time is compared to the frequency of these moderate storm surge events to determine the effect on the coastal groundwater.
Coastal topography and hydrogeology control critical groundwater gradients and potential beach surface instability during storm surges
(Hydrology and Earth System Sciences, 2022-12-02) Paldor, Anner; Stark, Nina; Florence, Matthew; Raubenheimer, Britt; Elgar, Steve; Housego, Rachel; Frederiks, Ryan S.; Michael, Holly A.
Ocean surges pose a global threat for coastal stability. These hazardous events alter flow conditions and pore pressures in flooded beach areas during both inundation and subsequent retreat stages, which can mobilize beach material, potentially enhancing erosion significantly. In this study, the evolution of surge-induced pore-pressure gradients is studied through numerical hydrologic simulations of storm surges. The spatiotemporal variability of critically high gradients is analyzed in three dimensions. The analysis is based on a threshold value obtained for quicksand formation of beach materials under groundwater seepage. Simulations of surge events show that, during the run-up stage, head gradients can rise to the calculated critical level landward of the advancing inundation line. During the receding stage, critical gradients were simulated seaward of the retreating inundation line. These gradients reach maximum magnitudes just as sea level returns to pre-surge levels and are most accentuated beneath the still-water shoreline, where the model surface changes slope. The gradients vary along the shore owing to variable beach morphology, with the largest gradients seaward of intermediate-scale (1–3 m elevation) topographic elements (dunes) in the flood zone. These findings suggest that the common practices in monitoring and mitigating surge-induced failures and erosion, which typically focus on the flattest areas of beaches, might need to be revised to include other topographic features.
Hydrologic Control on Arsenic Cycling at the Groundwater–Surface Water Interface of a Tidal Channel
(Environmental Science and Technology, 2023-01-10) Yu, Xuan; LeMonte, Joshua J.; Li, Junxia; Stuckey, Jason W.; Sparks, Donald L.; Cargill, John G.; Russoniello, Christopher J.; Michael, Holly A.
Historical industrial activities have resulted in soil contamination at sites globally. Many of these sites are located along coastlines, making them vulnerable to hydrologic and biogeochemical alterations due to climate change and sea-level rise. However, the impact of hydrologic dynamics on contaminant mobility in tidal environments has not been well studied. Here, we collected data from pressure transducers in wells, multi-level redox sensors, and porewater samplers at an As-contaminated site adjacent to a freshwater tidal channel. Results indicate that sharp redox gradients exist and that redox conditions vary on tidal to seasonal timescales due to sub-daily water level fluctuations in the channel and seasonal groundwater–surface water interactions. The As and Fe2+ concentrations decreased during seasonal periods of net discharge to the channel. The seasonal changes were greater than tidal variations in both Eh and As concentrations, indicating that impacts of the seasonal mechanism are stronger than those of sub-daily water table fluctuations. A conceptual model describing tidal and seasonal hydro-biogeochemical coupling is presented. These findings have broad implications for understanding the impacts of sea-level rise on the mobility of natural and anthropogenic coastal solutes.

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