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  • Salt marsh  (4)
  • Animal evolution
  • Bacteria
  • American Geophysical Union  (5)
  • Oxford University Press  (2)
  • 2020-2023  (7)
  • 1970-1974
  • 1950-1954
  • 1935-1939
  • 1
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    Sediment delivery to a tidal marsh platform is minimized by source decoupling and flux convergence (2020)
    American Geophysical Union
    Details
    Publication Date: 2022-10-27
    Description: Author Posting. © American Geophysical Union, 2020. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Earth Surface 125(8),(2020): e2020JF005558, doi:10.1029/2020JF005558.
    Description: Sediment supply is a primary factor in determining marsh response to sea level rise and is typically approximated through high‐resolution measurements of suspended sediment concentrations (SSCs) from adjacent tidal channels. However, understanding sediment transport across the marsh itself remains limited by discontinuous measurements of SSC over individual tidal cycles. Here, we use an array of optical turbidity sensors to build a long‐term, continuous record of SSC across a marsh platform and adjacent tidal channel. We find that channel and marsh concentrations are correlated (i.e., coupled) within tidal cycles but are largely decoupled over longer time scales. We also find that net sediment fluxes decline to near zero within 10 m of the marsh edge. Together, these results suggest that large sections of the marsh platform receive minimal sediment independent of flooding frequency or channel sediment supply. Marsh‐centric, as opposed to channel‐centric, measures of sediment supply may better characterize marsh platform vulnerability.
    Description: This work was funded by NSF Awards 1529245, 1654374, 1426981, 1637630, and 1832221, the NSF Graduate Research Fellowship Program, and the USGS Climate and Land Use Research and Development program. We thank D. Walters, J. Himmelstein, D. Nicks, R. Walker, T. Messerschmidt, and the Plum Island Ecosystems LTER, especially S. Kelsey for laboratory and field assistance. Additionally, we thank C. Friedrichs, G. Guntenspergen, and O. Duran Vinent for contributing ideas that helped develop the work, and the reviewers who helped improve the manuscript. This work is Contribution Number 3928 of the Virginia Institute of Marine Science. In memoriam of David Nicks.
    Description: 2021-01-27
    Keywords: Salt marsh ; Sediment transport ; Turbidity ; Flux convergence ; Decoupling
    Repository Name: Woods Hole Open Access Server
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  • 2
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    TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tassia, M. G., David, K. T., Townsend, J. P., & Halanych, K. M. TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution, 38(12), (2021): 5806–5818, https://doi.org/10.1093/molbev/msab258.
    Description: Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
    Description: This work was supported by The National Science Foundation (Grant No. IOS—1755377 to K.M.H., Rita Graze, and Elizabeth Hiltbold Schwartz), and K.T.D. was supported by The National Science Foundation’s Graduate Research Fellowship Program.
    Keywords: Protein evolution ; Domain annotation ; Animal evolution ; Innate immunity
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  • 3
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    Sources, mechanisms, and timescales of sediment delivery to a New England salt marsh (2022)
    American Geophysical Union
    Details
    Publication Date: 2022-10-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Baranes, H., Woodruff, J., Geyer, W., Yellen, B., Richardson, J. & Griswold, F. Sources, mechanisms, and timescales of sediment delivery to a New England salt marsh. Journal of Geophysical Research: Earth Surface, 127, (2022): e2021JF006478, https://doi.org/10.1029/2021jf006478.
    Description: he availability and delivery of an external clastic sediment source is a key factor in determining salt marsh resilience to future sea level rise. However, information on sources, mechanisms, and timescales of sediment delivery are lacking, particularly for wave-protected mesotidal estuaries. Here we show that marine sediment mobilized and delivered during coastal storms is a primary source to the North and South Rivers, a mesotidal bar-built estuary in a small river system impacted by frequent, moderate-intensity storms that is typical to New England (United States). On the marsh platform, deposition rates, clastic content, and dilution of fluvially-sourced contaminated sediment by marine material all increase down-estuary toward the inlet, consistent with a predominantly marine-derived sediment source. Marsh clastic deposition rates are also highest in the storm season. We observe that periods of elevated turbidity in channels and over the marsh are concurrent with storm surge and high wave activity offshore, rather than with high river discharge. Flood tide turbidity also exceeds ebb tide turbidity during storm events. Timescales of storm-driven marine sediment delivery range from 2.5 days to 2 weeks, depending on location within the estuary; therefore the phasing of storm surge and waves with the spring-neap cycle determines how effectively post-event suspended sediment is delivered to the marsh platform. This study reveals that sediment supply and the associated resilience of New England mesotidal salt marshes involves the interplay of coastal and estuarine processes, underscoring the importance of looking both up- and downstream to identify key drivers of environmental change.
    Description: The project described in this publication was in part supported by Grant or Cooperative Agreement No. G20AC00071 from the U.S. Geological Survey and a Department of Interior Northeast Climate Adaptation Science Center graduate fellowship awarded to H.E.B (G12AC00001).
    Keywords: Salt marsh ; Sediment ; Estuary ; Tides ; Massachusetts
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Soil organic carbon development and turnover in natural and disturbed salt marsh environments (2021)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © American Geophysical Union, 2021. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 48(2), (2021): e2020GL090287, https://doi.org/10.1029/2020GL090287.
    Description: Salt marsh survival with sea‐level rise (SLR) increasingly relies on soil organic carbon (SOC) accumulation and preservation. Using a novel combination of geochemical approaches, we characterized fine SOC (≤1 mm) supporting marsh elevation maintenance. Overlaying thermal reactivity, source (δ13C), and age (F14C) information demonstrates several processes contributing to soil development: marsh grass production, redeposition of eroded material, and microbial reworking. Redeposition of old carbon, likely from creekbanks, represented ∼9%–17% of shallow SOC (≤26 cm). Soils stored marsh grass‐derived compounds with a range of reactivities that were reworked over centuries‐to‐millennia. Decomposition decreases SOC thermal reactivity throughout the soil column while the decades‐long disturbance of ponding accelerated this shift in surface horizons. Empirically derived estimates of SOC turnover based on geochemical composition spanned a wide range (640–9,951 years) and have the potential to inform predictions of marsh ecosystem evolution.
    Description: This work was supported by NSF (OCE1233678) and NOAA (NA14OAR4170104 and NA14NOS4190145) grants to ACS, USGS Coastal & Marine Geology Program, and PIE‐LTER (NSF OCE1238212 and OCE1637630).
    Description: 2021-06-11
    Keywords: Carbon isotopes ; Decomposition ; Organic matter composition ; Salt marsh ; Soil organic carbon
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Exploring the boundaries of microbial habitability in soil (2021)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dragone, N. B., Diaz, M. A., Hogg, I., Lyons, W. B., Jackson, W. A., Wall, D. H., Adams, B. J., & Fierer, N. Exploring the boundaries of microbial habitability in soil. Journal of Geophysical Research: Biogeosciences, 126(6), (2021): e2020JG006052, https://doi.org/10.1029/2020JG006052.
    Description: Microbes are widely assumed to be capable of colonizing even the most challenging terrestrial surface environments on Earth given enough time. We would not expect to find surface soils uninhabited by microbes as soils typically harbor diverse microbial communities and viable microbes have been detected in soils exposed to even the most inhospitable conditions. However, if uninhabited soils do exist, we might expect to find them in Antarctica. We analyzed 204 ice-free soils collected from across a remote valley in the Transantarctic Mountains (84–85°S, 174–177°W) and were able to identify a potential limit of microbial habitability. While most of the soils we tested contained diverse microbial communities, with fungi being particularly ubiquitous, microbes could not be detected in many of the driest, higher elevation soils—results that were confirmed using cultivation-dependent, cultivation-independent, and metabolic assays. While we cannot confirm that this subset of soils is completely sterile and devoid of microbial life, our results suggest that microbial life is severely restricted in the coldest, driest, and saltiest Antarctic soils. Constant exposure to these conditions for thousands of years has limited microbial communities so that their presence and activity is below detectable limits using a variety of standard methods. Such soils are unlikely to be unique to the studied region with this work supporting previous hypotheses that microbial habitability is constrained by near-continuous exposure to cold, dry, and salty conditions, establishing the environmental conditions that limit microbial life in terrestrial surface soils.
    Description: This work was supported by grants from the U.S. National Science Foundation (ANT 1341629 to B. J. Adams, N. Fierer, W. Berry Lyons, and D. H. Wall and OPP 1637708 to B. J. Adams) with additional support provided to N. B. Dragone from University Colorado Department of Ecology and Evolutionary Biology.
    Keywords: Antarctica ; Soils ; Bacteria ; Fungi ; Extremophiles ; Astrobiology
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Characterizing the culturable surface microbiomes of diverse marine animals (2021)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keller, A. G., Apprill, A., Lebaron, P., Robbins, J., Romano, T. A., Overton, E., Rong, Y., Yuan, R., Pollara, S., & Whalen, K. E. Characterizing the culturable surface microbiomes of diverse marine animals. FEMS Microbiology Ecology, 97(4), (2021): fiab040, https://doi.org/10.1093/femsec/fiab040.
    Description: Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.
    Description: Funding was provided by the National Science Foundation (Biological Oceanography) award #1657808 and National Institutes of Health grants 1R21-AI119311–01 to K. E. Whalen, as well as funding from the Koshland Integrated Natural Science Center and Green Fund at Haverford College. This constitutes scientific manuscript #298 from the Sea Research Foundation.
    Keywords: Bacteria ; SSU rRNA ; Coral ; Whale ; Microbiome ; Skin
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Salt marsh pond biogeochemistry changes hourly-to-yearly but does not scale with dimensions or geospatial position (2020)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © American Geophysical Union, 2020. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Biogeosciences 125(10), (2020): e2020JG005664, doi:10.1029/2020JG005664.
    Description: Shallow ponds are expanding in many salt marshes with potential impacts on ecosystem functioning. Determining how pond characteristics change over time and scale with physical dimensions and other spatial predictors could facilitate incorporation of ponds into projections of ecosystem change. We evaluated scaling relationships across six differently sized ponds in three regions of the high marshes within the Plum Island Ecosystems‐Long Term Ecological Research site (MA, USA). We further characterized diel fluctuations in surface water chemistry in two ponds to understand short‐term processes that affect emergent properties (e.g., habitat suitability). Primary producers drove oxygen levels to supersaturation during the day, while nighttime respiration resulted in hypoxic to anoxic conditions. Diel swings in oxygen were mirrored by pH and resulted in successive shifts in redox‐sensitive metabolisms, as indicated by nitrate consumption at dusk followed by peaks in ammonium and then sulfide overnight. Abundances of macroalgae and Ruppia maritima correlated with whole‐pond oxygen metabolism rates, but not with surface area (SA), volume (V), or SA:V. Moreover, there were no clear patterns in primary producer abundances, surface water chemistry, or pond metabolism rates across marsh regions supplied by different tidal creeks or that differed in distance to upland borders or creekbanks. Comparisons with data from 2 years prior demonstrate that plant communities and biogeochemical processes are not in steady state. Factors contributing to variability between ponds and years are unclear but likely include infrequent tidal exchange. Temporal and spatial variability and the absence of scaling relationships complicate the integration of high marsh ponds into ecosystem biogeochemical models.
    Description: Thanks to S. McNichol, S. Jayne, E. Neel, and PIE‐LTER (NSF‐OCE1238212) for field assistance; I. Forbrich for meteorological data (Giblin & Forbrich, 2018); J. Jennings for dissolved nutrient analyses; J. Seewald for ion chromatograph access; and G. Mariotti for elevation data. C. Wilson and an anonymous reviewer provided comments that greatly improved our manuscript. A. C. S. was supported by NSF (OCE1233678), NOAA (NA14NOS4190145), and Sea Grant (NA14OAR4170104) awards, and A. D. by the MIT Undergraduate Research Opportunities Program.
    Description: 2021-03-15
    Keywords: Salt marsh ; Global change ; Biogeochemistry ; Metabolism ; Scaling ; Ecosystem function
    Repository Name: Woods Hole Open Access Server
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