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  • 1
    Publication Date: 2022-01-07
    Description: Marine macroalgae, seaweeds, are exceptionally prolific producers of halogenated natural products. Biosynthesis of halogenated molecules in seaweeds is inextricably linked to reactive oxygen species (ROS) signaling as hydrogen peroxide serves as a substrate for haloperoxidase enzymes that participate in the construction these halogenated molecules. Here, using red macroalga Asparagopsis taxiformis, a prolific producer of the ozone depleting molecule bromoform, we provide the discovery and biochemical characterization of a ROS-producing NAD(P)H oxidase from seaweeds. This discovery was enabled by our sequencing of Asparagopsis genomes, in which we find the gene encoding the ROS-producing enzyme to be clustered with genes encoding bromoform-producing haloperoxidases. Biochemical reconstitution of haloperoxidase activities establishes that fatty acid biosynthesis can provide viable hydrocarbon substrates for bromoform production. The ROS production haloperoxidase enzymology that we describe here advances seaweed biology and biochemistry by providing the molecular basis for decades worth of physiological observations in ROS and halogenated natural product biosyntheses.
    Type: Article , PeerReviewed
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  • 2
    Publication Date: 2022-01-07
    Description: Fusarium oxysporum is a destructive root-infecting plant pathogen that causes significant yield losses in many economically important crop species. Hence, a deeper understanding of pathogen infection strategies is needed. With liquid chromatography-tandem mass spectrometry and gas chromatography-time of flight mass spectrometry platforms, we analyzed the metabolic changes in a time-course experiment with Arabidopsis accessions either resistant (Col-0) or susceptible (Ler-0) to isolates of Fusarium oxysporum forma specialis matthioli infection. We showed a concurrent effect of Fusarium-derived polyols and the mycotoxin beauvericin in the suppression of the immune response of susceptible hosts. A significant increase in oxidized glutathione in the resistant host was probably associated with effective reactive oxygen species-mediated resistance responses. Through a combination of targeted and untargeted metabolomics, we demonstrated the concurrent action of several Arabidopsis defense systems as well as the concurrent action of several virulence systems in the fungal attack of susceptible Arabidopsis.
    Type: Article , PeerReviewed
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  • 3
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ferrer-González, F. X., Widner, B., Holderman, N. R., Glushka, J., Edison, A. S., Kujawinski, E. B., & Moran, M. A. Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy. ISME Journal, (2020), doi:10.1038/s41396-020-00811-y.
    Description: The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-d-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.
    Description: This work was supported by grants from the Gordon and Betty Moore Foundation (5503) and the National Science Foundation (IOS-1656311) to MAM, ASE, and EBK, and by the Simons Foundation grant 542391 to MAM within the Principles of Microbial Ecosystems (PriME) Collaborative.
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zakem, E. J., Mahadevan, A., Lauderdale, J. M., & Follows, M. J. Stable aerobic and anaerobic coexistence in anoxic marine zones. ISME Journal, 14, (2019): 288–301, doi: 10.1038/s41396-019-0523-8.
    Description: Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.
    Description: We are grateful for the thorough and thoughtful comments of two anonymous reviewers. We also thank Andrew Babbin for helpful comments. EJZ was supported by the Simons Foundation (Postdoctoral Fellowship in Marine Microbial Ecology). AM was supported by the Office of Naval Research (ONR #N000-14-15-1-2555). JML was supported by U.S. National Science Foundation (NSF #OCE-1259388). MJF was supported by the Gordon and Betty Moore Foundation (GBMF #3778) and the Simons Foundation: the Simons Collaboration on Ocean Processes and Ecology (SCOPE #329108) and the Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES #549931).
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ponnudurai, R., Heiden, S. E., Sayavedra, L., Hinzke, T., Kleiner, M., Hentschker, C., Felbeck, H., Sievert, S. M., Schlüter, R., Becher, D., Schweder, T., & Markert, S. Comparative proteomics of related symbiotic mussel species reveals high variability of host-symbiont interactions. ISME Journal, 14, (2019): 649–656, doi: 10.1038/s41396-019-0517-6.
    Description: Deep-sea Bathymodiolus mussels and their chemoautotrophic symbionts are well-studied representatives of mutualistic host–microbe associations. However, how host–symbiont interactions vary on the molecular level between related host and symbiont species remains unclear. Therefore, we compared the host and symbiont metaproteomes of Pacific B. thermophilus, hosting a thiotrophic symbiont, and Atlantic B. azoricus, containing two symbionts, a thiotroph and a methanotroph. We identified common strategies of metabolic support between hosts and symbionts, such as the oxidation of sulfide by the host, which provides a thiosulfate reservoir for the thiotrophic symbionts, and a cycling mechanism that could supply the host with symbiont-derived amino acids. However, expression levels of these processes differed substantially between both symbioses. Backed up by genomic comparisons, our results furthermore revealed an exceptionally large repertoire of attachment-related proteins in the B. thermophilus symbiont. These findings imply that host–microbe interactions can be quite variable, even between closely related systems.
    Description: Thanks to captain, crew, and pilots of the research vessels Atlantis (ROV Jason cruise AT26–10 in 2014) and Meteor (cruise M82–3 in 2010). We thank Jana Matulla, Sebastian Grund, and Annette Meuche for excellent technical assistance during sample preparation, MS measurements in the Orbitrap Classic, and TEM imaging preparation, respectively. We appreciate Nikolaus Leisch’s help with TEM image interpretation, Inna Sokolova’s advice on bivalve physiology, and Marie Zühlke’s support during manuscript revision. RP was supported by the EU-funded Marie Curie Initial Training Network ‘Symbiomics’ (project no. 264774) and by a fellowship of the Institute of Marine Biotechnology e.V. TH was supported by the German Research Foundation DFG (grant MA 6346/2–1 to SM). The Atlantis cruise was funded by a grant of the US National Science Foundation’s Dimensions of Biodiversity program to SMS (OCE-1136727).
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Miller, C. A., Holm, H. C., Horstmann, L., George, J. C., Fredricks, H. F., Van Mooy, B. A. S., & Apprill, A. Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion. ISME Journal, 14, (2019): 688-701, doi: 10.1038/s41396-019-0549-y.
    Description: Whale digestion plays an integral role in many ocean ecosystems. By digesting enormous quantities of lipid-rich prey, whales support their energy intensive lifestyle, but also excrete nutrients important to ocean biogeochemical cycles. Nevertheless, whale digestion is poorly understood. Gastrointestinal microorganisms play a significant role in vertebrate digestion, but few studies have examined them in whales. To investigate digestion of lipids, and the potential contribution of microbes to lipid digestion in whales, we characterized lipid composition (lipidomes) and bacterial communities (microbiotas) in 126 digesta samples collected throughout the gastrointestinal tracts of 38 bowhead whales (Balaena mysticetus) harvested by Alaskan Eskimos. Lipidomes and microbiotas were strongly correlated throughout the gastrointestinal tract. Lipidomes and microbiotas were most variable in the small intestine and most similar in the large intestine, where microbiota richness was greatest. Our results suggest digestion of wax esters, the primary lipids in B. mysticetus prey representing more than 80% of total dietary lipids, occurred in the mid- to distal small intestine and was correlated with specific microorganisms. Because wax esters are difficult to digest by other marine vertebrates and constitute a large reservoir of carbon in the ocean, our results further elucidate the essential roles that whales and their gastrointestinal microbiotas play in the biogeochemical cycling of carbon and nutrients in high-latitude seas.
    Description: Devonshire Foundation (to CAM), Marine Mammal Center, Woods Hole Oceanographic Institution (WHOI; to CAM), WHOI Ocean Life Institute (to AA and CAM), Dalio Foundation’s Dalio Ocean Initiative (now ‘OceanX’) (to AA), National Science Foundation (OCE-1756254 and OPP-1543328 to BASVM). Samples were collected under Department of Commerce National Oceanic and Atmospheric Administration National Marine Fisheries Service permit numbers 17350-00, 17350-01, and 17350-02 to North Slope Borough Department of Wildlife Management.
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  • 7
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gazitua, M. C., Vik, D. R., Roux, S., Gregory, A. C., Bolduc, B., Widner, B., Mulholland, M. R., Hallam, S. J., Ulloa, O., & Sullivan, M. B. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. Isme Journal, (2020), doi:10.1038/s41396-020-00825-6.
    Description: Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.
    Description: We thank Sullivan Lab members and Heather Maughan for comments on the paper, Bess Ward for her contribution in the N-cycle context of our story, Kurt Hanselmann for his assistance in the calculations of the Gibbs-free energies, and the scientific party and crew of the R/V Atlantis (grant OCE-1356056 to MRM) for the sampling opportunity and support at sea. This work was funded in part by awards from the Agouron Institute to OU and MBS, a Gordon and Betty Moore Foundation Investigator Award (#3790) and NSF Biological Oceanography Awards (#1536989 and #1829831) to MBS, and the Millennium Science Initiative (grant ICN12_019-IMO) to OU. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
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  • 8
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Breusing, C., Mitchell, J., Delaney, J., Sylva, S. P., Seewald, J. S., Girguis, P. R., & Beinart, R. A. Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails. Isme Journal, (2020), doi:10.1038/s41396-020-0707-2.
    Description: Symbioses between invertebrate animals and chemosynthetic bacteria form the basis of hydrothermal vent ecosystems worldwide. In the Lau Basin, deep-sea vent snails of the genus Alviniconcha associate with either Gammaproteobacteria (A. kojimai, A. strummeri) or Campylobacteria (A. boucheti) that use sulfide and/or hydrogen as energy sources. While the A. boucheti host–symbiont combination (holobiont) dominates at vents with higher concentrations of sulfide and hydrogen, the A. kojimai and A. strummeri holobionts are more abundant at sites with lower concentrations of these reductants. We posit that adaptive differences in symbiont physiology and gene regulation might influence the observed niche partitioning between host taxa. To test this hypothesis, we used high-pressure respirometers to measure symbiont metabolic rates and examine changes in gene expression among holobionts exposed to in situ concentrations of hydrogen (H2: ~25 µM) or hydrogen sulfide (H2S: ~120 µM). The campylobacterial symbiont exhibited the lowest rate of H2S oxidation but the highest rate of H2 oxidation, with fewer transcriptional changes and less carbon fixation relative to the gammaproteobacterial symbionts under each experimental condition. These data reveal potential physiological adaptations among symbiont types, which may account for the observed net differences in metabolic activity and contribute to the observed niche segregation among holobionts.
    Description: We thank the Schmidt Ocean Institute, the crew of the R/V Falkor and the pilots of the ROV ROPOS for facilitating the sample collections and shipboard experiments, and the Broad Institute Microbial ‘Omics Core for preparing and sequencing the transcriptomic libraries. This material is based in part upon work supported by the National Science Foundation under Grant Numbers NSF OCE-1536653 (to PRG), OCE-1536331 (to RAB and JSS), OCE-1819530 and OCE-1736932 (to RAB).
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McLean, C., & Kujawinski, E. B. AutoTuner: high fidelity and robust parameter selection for metabolomics data processing. Analytical Chemistry, 92(8), (2020): 5724-5732, doi:10.1021/acs.analchem.9b04804.
    Description: Untargeted metabolomics experiments provide a snapshot of cellular metabolism but remain challenging to interpret due to the computational complexity involved in data processing and analysis. Prior to any interpretation, raw data must be processed to remove noise and to align mass-spectral peaks across samples. This step requires selection of dataset-specific parameters, as erroneous parameters can result in noise inflation. While several algorithms exist to automate parameter selection, each depends on gradient descent optimization functions. In contrast, our new parameter optimization algorithm, AutoTuner, obtains parameter estimates from raw data in a single step as opposed to many iterations. Here, we tested the accuracy and the run-time of AutoTuner in comparison to isotopologue parameter optimization (IPO), the most commonly used parameter selection tool, and compared the resulting parameters’ influence on the properties of feature tables after processing. We performed a Monte Carlo experiment to test the robustness of AutoTuner parameter selection and found that AutoTuner generated similar parameter estimates from random subsets of samples. We conclude that AutoTuner is a desirable alternative to existing tools, because it is scalable, highly robust, and very fast (∼100–1000× speed improvement from other algorithms going from days to minutes). AutoTuner is freely available as an R package through BioConductor.
    Description: We thank Titus Brown and Ben Temperton for advice on the algorithm validation, Arthur Eschenlauer for constructive feedback on the software design, Krista Longnecker for continuous support and discussions, Gabriel Leventhal for mathematics advice, the users of AutoTuner for debugging help through Github, and David Angeles-Albores and two anonymous reviewers for critical feedback on the manuscript. Funding support included the National GEM Consortium and NSF graduate research program fellowships (C.M.) and grants from the MIT Microbiome Center (Award 6936800, E.B.K.) and the Simons Foundation (Award ID #509034, E.B.K.).
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-05-26
    Description: Author Posting. © American Chemical Society, 2020. This is an open access article published under an ACS AuthorChoice License. The definitive version was published in Chemical Research in Toxicology, 33(4), (2020): 860-879, doi:10.1021/acs.chemrestox.9b00476.
    Description: The Ah receptor (AHR) has been studied for almost five decades. Yet, we still have many important questions about its role in normal physiology and development. Moreover, we still do not fully understand how this protein mediates the adverse effects of a variety of environmental pollutants, such as the polycyclic aromatic hydrocarbons (PAHs), the chlorinated dibenzo-p-dioxins (“dioxins”), and many polyhalogenated biphenyls. To provide a platform for future research, we provide the historical underpinnings of our current state of knowledge about AHR signal transduction, identify a few areas of needed research, and then develop concepts such as adaptive metabolism, ligand structural diversity, and the importance of proligands in receptor activation. We finish with a discussion of the cognate physiological role of the AHR, our perspective on why this receptor is so highly conserved, and how we might think about its cognate ligands in the future.
    Description: This review is dedicated in memory of the career of Alan Poland, one of the truly great minds in pharmacology and toxicology. This work was supported by the National Institutes of Health Grants R35-ES028377, T32-ES007015, P30-CA014520, P42-ES007381, and U01-ES1026127, The UW SciMed GRS Program, and The Morgridge Foundation. The authors would like to thank Catherine Stanley of UW Media Solutions for her artwork.
    Repository Name: Woods Hole Open Access Server
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  • 11
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mara, P., Vik, D., Pachiadaki, M. G., Suter, E. A., Poulos, B., Taylor, G. T., Sullivan, M. B., & Edgcomb, V. P. Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. ISME Journal, (2020), doi:10.1038/s41396-020-00739-3.
    Description: Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.
    Description: This work was supported by the National Science Foundation grant OCE-1336082 to VPE, OCE-1335436 to GTT, OCE-1536989, a Moore Foundation Award (#3790) to MBS, and WHOI subaward A101259 to MP. The sequencing conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
    Repository Name: Woods Hole Open Access Server
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  • 12
    Publication Date: 2022-05-26
    Description: Author Posting. © Springer Nature , 2020. This article is posted here by permission of Springer Nature for personal use, not for redistribution. The definitive version was published in Nowacki, D. J., & Ganju, N. K. Sediment dynamics of a divergent bay-marsh complex. Estuaries and Coasts, (2020), doi:10.1007/s12237-020-00855-5.
    Description: Bay–marsh systems, composed of an embayment surrounded by fringing marsh incised by tidal channels, are widely distributed coastal environments. External sediment availability, marsh-edge erosion, and sea-level rise acting on such bay–marsh complexes may drive diverse sediment-flux regimes. These factors reinforce the ephemeral and dynamic nature of fringing marshes: material released by marsh-edge erosion becomes part of a bay–marsh exchange that fuels the geomorphic evolution of the coupled system. The dynamics of this sediment exchange determine the balance among seaward export, deposition on the embayment seabed, flux into tidal channels, and import to the marsh platform. In this work, we investigate the sediment dynamics of a transgressive bay–marsh complex and link them to larger-scale considerations of its geomorphic trajectory. Grand Bay, Alabama/Mississippi, is a shallow microtidal embayment surrounded by salt marshes with lateral erosion rates of up to 5 m year−1. We collected 6 months of oceanographic data at four moorings within Grand Bay and its tidal channels to assess hydrographic conditions and net sediment-flux patterns and augmented the observations with numerical modeling. The observations imply a divergent sedimentary system in which a majority of the suspended sediment is exported seaward, while a smaller fraction is imported landward via tidal channels, assisting in vertical marsh-plain accumulation, maintenance of channel and intertidal-flat morphologies, and landward transgression. These results describe a dynamic system that is responsive to episodic atmospheric forcing in the absence of a strong tidal signal and the presence of severe lateral marsh loss.
    Description: We thank the staff of the Grand Bay NERR for their role in facilitating fieldwork within Grand Bay. Jonathan Pitchford, also of the Grand Bay NERR, provided the SET data. Giulio Mariotti and an anonymous reviewer are acknowledged for their helpful comments.
    Keywords: Salt marsh ; Geomorphic trajectory ; Sediment flux
    Repository Name: Woods Hole Open Access Server
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