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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses

ABSTRACT Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances. IMPORTANCE Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.

Lui, Lauren M.↗
DOE OSTI2024

Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient

ABSTRACT Estuarine wetlands harbor considerable carbon stocks, but rising sea levels could affect their ability to sequester soil carbon as well as their potential to emit methane (CH 4 ). While sulfate loading from seawater intrusion may reduce CH 4 production due to the higher energy yield of microbial sulfate reduction, existing studies suggest other factors are likely at play. Our study of 11 wetland complexes spanning a natural salinity and productivity gradient across the San Francisco Bay and Delta found that while CH 4 fluxes generally declined with salinity, they were highest in oligohaline wetlands (ca. 3-ppt salinity). Methanogens and methanogenesis genes were weakly correlated with CH 4 fluxes but alone did not explain the highest rates observed. Taxonomic and functional gene data suggested that other microbial guilds that influence carbon and nitrogen cycling need to be accounted for to better predict CH 4 fluxes at landscape scales. Higher methane production occurring near the freshwater boundary with slight salinization (and sulfate incursion) might result from increased sulfate-reducing fermenter and syntrophic populations, which can produce substrates used by methanogens. Moreover, higher salinities can solubilize ionically bound ammonium abundant in the lower salinity wetland soils examined here, which could inhibit methanotrophs and potentially contribute to greater CH 4 fluxes observed in oligohaline sediments. IMPORTANCE Low-level salinity intrusion could increase CH4 flux in tidal freshwater wetlands, while higher levels of salinization might instead decrease CH4 fluxes. High CH4 emissions in oligohaline sites are concerning because seawater intrusion will cause tidal freshwater wetlands to become oligohaline. Methanogenesis genes alone did not account for landscape patterns of CH4 fluxes, suggesting mechanisms altering methanogenesis, methanotrophy, nitrogen cycling, and ammonium release, and increasing decomposition and syntrophic bacterial populations could contribute to increases in net CH4 flux at oligohaline salinities. Improved understanding of these influences on net CH4 emissions could improve restoration efforts and accounting of carbon sequestration in estuarine wetlands. More pristine reference sites may have older and more abundant organic matter with higher carbon:nitrogen compared to wetlands impacted by agricultural activity and may present different interactions between salinity and CH4. This distinction might be critical for modeling efforts to scale up biogeochemical process interactions in estuarine wetlands.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Propagation of the 2014–2016 Northeast Pacific Marine Heatwave Through the Salish Sea

Effects and impacts of the Northeast Pacific marine heatwave of 2014–2016 on the inner coastal estuarine waters of the Salish Sea were examined using a combination of monitoring data and an established three-dimensional hydrodynamic and biogeochemical model of the region. The anomalous high temperatures reached the U.S. Pacific Northwest continental shelf toward the end of 2014 and primarily entered the Salish Sea waters through an existing strong estuarine exchange. Elevated temperatures up to + 2.3°C were observed at the monitoring stations throughout 2015 and 2016 relative to 2013 before dissipating in 2017. The hydrodynamic and biogeochemical responses to this circulating high-temperature event were examined using the Salish Sea Model over a 5-year window from 2013 to 2017. Responses of conventional water-quality indicator variables, such as temperature and salinity, nutrients and phytoplankton, zooplankton, dissolved oxygen, and pH, were evaluated relative to a baseline without the marine heatwave forcing. The simulation results relative to 2014 show an increase in biological activity (+14%, and 6% Δ phytoplankton biomass, respectively) during the peak heatwave year 2015 and 2016 propagating toward higher zooplankton biomass (+14%, +18% Δ mesozooplankton biomass). However, sensitivity tests show that this increase was a direct result of higher freshwater and associated nutrient loads accompanied by stronger estuarine exchange with the Pacific Ocean rather than warming due to the heatwave. Strong vertical circulation and mixing provided mitigation with only ≈+0.6°C domain-wide annual average temperature increase within Salish Sea, and served as a physical buffer to keep waters cooler relative to the continental shelf during the marine heatwave.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Manganese: The overlooked contaminant in the world largest mine tailings dam collapse

Manganese (Mn) is an abundant element in terrestrial and coastal ecosystems and an essential micronutrient in the metabolic processes of plants and animals. Mn is generally not considered a potentially toxic element due to its low content in both soil and water. However, in coastal ecosystems, the Mn dynamic (commonly associated with the Fe cycle) is mostly controlled by redox processes. Here, we assessed the potential contamination of the Rio Doce estuary (SE Brazil) by Mn after the world’s largest mine tailings dam collapse, potentially resulting in chronic exposure to local wildlife and humans. Estuarine soils, water, and fish were collected and analyzed seven days after the arrival of the tailings in 2015 and again two years after the dam collapse in 2017. Using a suite of solid-phase analyses including X-ray absorption spectroscopy and sequential extractions, our results indicated that a large quantity of Mn II arrived in the estuary in 2015 bound to Fe oxyhydroxides. Over time, dissolved Mn and Fe were released from soils when Fe III oxyhydroxides underwent reductive dissolution. Due to seasonal redox oscillations, both Fe and Mn were then re-oxidized to Fe III , Mn III , and Mn IV and re-precipitated as poorly crystalline Fe oxyhydroxides and poorly crystalline Mn oxides. In 2017, redox conditions (Eh: -47 ± 83 mV; pH: 6.7 ± 0.5) favorable to both Fe and Mn reduction led to an increase (~880%) of dissolved Mn (average for 2015: 66 ± 130 μg L -1 ; 2017: 582 ± 626 μg L -1 ) in water and a decrease (~75%, 2015: 547 ± 498 mg kg -1 ; 2017: 135 ± 80 mg kg -1 ) in the total Mn content in soils. The crystalline Fe oxyhydroxides content significantly decreased while the fraction of poorly ordered Fe oxides increased in the soils limiting the role of Fe in Mn retention. The high concentration of dissolved Mn found within the estuary two years after the arrival of mine tailings indicates a possible chronic contamination scenario, which is supported by the high levels of Mn in two species of fish living in the estuary. Our work suggests a high risk to estuarine biota and human health due to the rapid Fe and Mn biogeochemical dynamic within the impacted estuary.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Seasonal changes in the drivers of water physico-chemistry variability of a small freshwater tidal river

Where rivers meet the sea, tides can exert a physical and chemical influence on the lower reaches of a river. How tidal dynamics in these tidal river reaches interact with upstream hydrological drivers such as storm rainfall, which ultimately determines the quantity and composition of material transferred from watersheds to estuaries, is currently unknown. We monitored a small freshwater tidal river in the Pacific Northwest, USA in high resolution over one year to evaluate the relative importance of tides versus upstream hydrological flows (i.e., base flow and precipitation events) on basic physico-chemical parameters (pH, dissolved oxygen, turbidity, specific conductivity, and temperature), and how these interactions relate to the downstream estuary. Tidal variability and diurnal cycles (i.e. solar radiation) dominated water physico-chemical variability in the summer, but the influence of these drivers was overshadowed by storm-driven sharp pulses in river physico-chemistry during the remainder of the year. Within such events, we found incidences of counterclockwise hysteresis of pH, counterclockwise hysteresis of dissolved oxygen, and clockwise hysteresis of turbidity, although systematic trends were not observed across events. The dominance of storm rainfall in the river’s physico-chemistry dynamics, and similar pulses of decreased pH observed in adjacent estuarine waters, suggest that the linkage between tidal streams and the broader system is variable throughout the year. High-frequency monitoring of tidal river biogeochemistry is therefore crucial to enable the assessment of how the relative strength of these drivers may change with future sea level rise and altered precipitation patterns to modulate biogeochemical dynamics across the land-ocean-atmosphere continuum.

aquatic↗
DOE OSTI2026

Capturing soil moisture and salinity changes in flooded coastal forests using electrical resistivity and induced polarization

Geophysical methods provide high-resolution spatial measurements of physical quantities sensitive to changes in soil moisture and salinity and can be used to monitor soil hydrological responses to flooding. However, extracting quantitative hydrological information from geophysical data remains challenging. In this study, we extended existing petrophysical models to estimate soil moisture and salinity from electrical measurements to address this challenge. We manipulated two hydrologically isolated 2000 m 2 experimental plots by simultaneously inundating them with 265 m 3 of either freshwater or estuarine water. Repeated electrical resistivity and induced polarization measurements were used to image the water and solute infiltration along two transects that are 100 and 42 m in length. Petrophysical models derived from laboratory multi-salinity electrical measurements were used to estimate changes in soil moisture and fluid salinity from field measurements of real and imaginary conductivity during the ecosystem-scale flooding experiment. The real conductivity increased by ∼100% in the freshwater plot and ∼570% in the saltwater plot. The change in imaginary conductivity in the freshwater plot was <1 mS/m, whereas that of the estuarine water plot was ∼5 mS/m. Real conductivity shows dependence on soil moisture content with a coefficient of determination (R 2 ) > 0.7, while the imaginary conductivity shows a dependence on soil salinity with R 2 > 0.6. The results validate the use of electrical resistivity for estimating changes in soil moisture content in response to flooding. Combining electrical resistivity imaging with induced polarization measurements provides the possibility to account for changes in pore fluid conductivity.

Adebayo, Moses B. [Univ. of Toledo, OH (United Sta↗
DOE OSTI2025

Sediment transport and morphodynamic changes due to upstream variation and sea level rise on the Western Mekong Delta, Vietnam

The hydrological and morphological dynamics across the Vietnam Mekong Delta (VMD) coastline are increasingly shaped by human interventions and climate change, affecting the sustainability of socio-economic environments. This study employs the TELEMAC-MASCARET modeling system (TELEMAC-2D, TOMAWAC, and SISYPHE modules) to simulate hydrodynamics, sediment transport, and morphological changes for a 10-year period under baseline (SC1) and future climate (SC2) scenarios, considering wave climatology of Northeast (NEM) and Southwest monsoons (SWM). The results of sedimentation and erosion were analyzed across five key coastal zones from Ca Mau Cape (KV1) to Ha Tien (KV5). Model results highlight distinct seasonal patterns of sediment redistribution shaped by monsoonal flows, wave action, and seabed morphology. During the NEM, sediment deposition is concentrated near estuarine zones, while the SWM favors offshore sediment accumulation due to perpendicular wave actions, and shallow, gently sloping bathymetry that dissipates wave energy. Coastal erosion predominantly occurs at convex shoreline features subjected to stronger coastal currents, particularly in fine-grained sediment areas. Under future sea level rise and land subsidence scenarios, reduced flow velocities lead to lower bottom shear stress, promoting deposition and mitigating erosion problems despite increased wave energy. Besides that, sediment transport analyses across 14 cross-sections (C-S) reveal a southward trend during the NEM and a northward reversal during the SWM, with upstream sediment reductions primarily influencing near-estuarine zones and exerting minimal impact beyond the mid-coastal regions. Furthermore, these findings advance the understanding of sediment redistribution processes under climate change and seasonal change, and provide a scientific basis for adaptive coastal management and sustainable development.

Climate change↗
DOE OSTI2022

Water level changes in Lake Erie drive 21st century CO 2 and CH 4 fluxes from a coastal temperate wetland

Wetland water depth influences microbial and plant communities, which can alter the above- and below-ground carbon cycling of a wetland. Wetland water depths are likely to change due to shifting precipitation patterns, which will affect projections of greenhouse gas emissions; however, these effects are rarely incorporated into wetland greenhouse gas models. Seeking to address this gap, we used a mechanistic model, ecosys, to simulate a range of water depth scenarios in a temperate wetland, and analyzed simulated predictions of carbon dioxide (CO 2 ) andmethane (CH 4 ) fluxes over the 21st century. We tested our model using eddy covariance measurements of CO 2 and CH 4 fluxes collected at the Old Woman Creek National Estuarine Research Reserve (OWC) during 2015 and 2016. OWC is a lacustrine, estuarine, freshwater, mineral-soil marsh. An empirical model found that the wetland water depth is highly dependent on the water depth of the nearby Lake Erie. Future wetland surface water depths were modeled based on projection of Lake Erie's water depth using four separate NOAA projections, resulting in four wetland water-depth scenarios. Two of the four 21st century projections for Lake Erie water depths used in this study indicated that the water depth of the wetland would remain nearly steady; however, the other two indicated decreases in the wetland water depth. In our scenario where the wetland dries out, we project the wetland's climatological warming effect will decrease due to smaller CH 4 fluxes to the atmosphere and larger CO 2 uptake by the wetland. We also found that increased water level can lower emissions by shifting the site towards more open water areas, which have lower CH 4 emissions. We found that decreased water depths would cause more widespread colonization of the wetland by macrophyte vegetation. Using an empirical relationship, we also found that further drying could result in other, non-wetland vegetation to emerge, dramatically altering soil carbon cycling. In three of our four projections, we found that in general the magnitude of CO 2 and CH 4 fluxes steadily increase over the next 100 years in response to higher temperatures. However, in our driest simulations, we projected a different response due to increased oxidation of soil carbon, with CH 4 emissions decreasing substantially from an annual cumulative peak of 224.6 to a minimum of 104.7 gC m –2 year –1 . In that same simulation, net cumulative flux of CO 2 changed from being a sink of 56.5 gC m –2 year –1 to a source of 369.6 gCm –2 year –1 over the same period, despite a temperature increase from 13.7 °C to 14.2 °C. This temperature shift in our other three cases with greater water depths increased the source strength of CH 4 and the sink strength of CO 2 . Here, we conclude that the magnitude of wetland greenhouse-gas fluxes depended on the water depth primarily as it affected the areal percentage of the wetland available for plant colonization, but dramatic decreases in water depths could cause significant reductions in the wetland CH 4 fluxes, while simultaneously altering the wetland vegetation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Extreme flood return levels in a U.S. mid-Atlantic estuary using 40-year fluvial-coastal model simulations

Using an integrated watershed-coastal modeling framework, we conducted long-term historical simulations (1980-2019) of fluvial and coastal flooding in the Delaware Bay and River, a vulnerable estuarine system in the U.S., at high spatial resolutions. By applying process-based models, we generated physically consistent and spatially detailed estimates of estuarine, riverine, and surge-driven extreme water level compared to previous studies that used field data only. We then evaluated changes in the magnitude of flood events using the 40-year simulations and detrended Floodwater Depth values with stationary extreme value analysis. Our detailed assessment of spatial-varying extreme values revealed how different flood-generation mechanisms can dominate various zones in the estuary. The datasets produced through this work will be valuable for long-term flood hazard mitigation planning in coastal communities in the Delaware Bay and River region. Additionally, this work will serve as a benchmark for other coastal flood hazard modeling communities worldwide, aiding them in systematically modeling long-term and continuous extreme flood events.

Coastal and Riverine Flooding↗
DOE OSTI2024

Response of hypoxia to future climate change is sensitive to methodological assumptions

Climate-induced changes in hypoxia are among the most serious threats facing estuaries, which are among the most productive ecosystems on Earth. Future projections of estuarine hypoxia typically involve long-term multi-decadal continuous simulations or more computationally efficient time slice and delta methods that are restricted to short historical and future periods. We make a first comparison of these three methods by applying a linked terrestrial–estuarine model to the Chesapeake Bay, a large coastal-plain estuary in the eastern United States. Results show that the time slice approach accurately captures the behavior of the continuous approach, indicating a minimal impact of model memory. However, increases in mean annual hypoxic volume by the mid-twenty-first century simulated by the delta approach (+ 19%) are approximately twice as large as the time slice and continuous experiments (+ 9% and + 11%, respectively), indicating an important impact of changes in climate variability. Our findings suggest that system memory and projected changes in climate variability, as well as simulation length and natural variability of system hypoxia, should be considered when deciding to apply the more computationally efficient delta and time slice methods.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Enhanced flood synchrony and downstream severity in the Delaware River under rising temperatures

River floods threaten life and economic stability, with risks increasing globally, especially in densely populated coastal areas. In mountainous coastal watersheds like the Delaware River Basin, rising temperature is projected to reduce snowpack, reshaping upstream–downstream flood dynamics. However, the impact on flood synchronization between upland tributaries and estuarine mainstems remains poorly understood. Using multidecadal streamflow simulations from a high-resolution hydrological model, we find significant increases in the frequency and magnitude of synchronized floods under future warming scenarios, particularly severe floods (above the 75 th percentile). Under higher warming scenarios, snowpack and rain-on-snow floods in headwater subbasins nearly vanish. Surprisingly, this regime shift amplifies estuarine flooding by enhancing synchronization between historically snow-dominated subbasins and their downstream counterparts. Despite intensified synchronization and flood magnitude, cold-season flood risk declines due to fewer rain-on-snow events. Conversely, summer floods grow larger, more frequent, and synchronized, driving a seasonal reconfiguration of flood risk that should be considered in future mitigation strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Response of salt intrusion in a tidal estuary to regional climatic forcing

Abstract Salinity distribution in a large tidal estuary is subject to estuarine adjustment under the influences of multiple physical drivers such as freshwater pulses and sea level rise, and is crucial to upstream water quality, aquaculture, and ecosystem functions of the estuary. To better understand the estuarine salinity response to climate change, the unstructured-grid Finite Volume Community Ocean Model was implemented to simulate the salt intrusion in the Delaware Bay Estuary. The model was first validated by multiple observational data sets and subsequently applied in an idealized setting to examine the response of salt front to freshwater pulses in high flow conditions, followed by a long-term drought condition supported by a multi-decadal streamflow drought analysis in the estuary. The model results showed that after the freshwater pulses the salt front location moved further upstream with sea level rise. Under the simulated long-term drought condition, the adjustment timescale of salt intrusion varies nonlinearly with sea level rise. With a significant increase in sea level rise, the adjustment timescale starts to decrease. This shift suggests a transition into a different regime where the estuary becomes more stratified, as indicated by an increasing bulk Simpson number with rising sea levels.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Mixing and dilution controls on marine CO 2 removal using alkalinity enhancement

Marine CO 2 removal (CDR) using enhanced-alkalinity seawater discharge was simulated in the estuarine waters of the Salish Sea, Washington, US. The high-alkalinity seawater would be generated using bipolar membrane electrodialysis technology to remove acid and the alkaline stream returned to the sea. Response of the receiving waters was evaluated using a shoreline resolving hydrodynamic model with biogeochemistry, and carbonate chemistry. Two sites, and two deployment scales, each with enhanced TA of 2997 mmol m -3 and a pH of 9 were simulated. The effects on air-sea CO 2 flux and pH in the near-field as well as over the larger estuary wide domain were assessed. The large-scale deployment (addition of 164 Mmoles TA yr -1 ) in a small embayment (Sequim Bay, 12.5 km 2 ) resulted in removal of 2066 T of CO 2 (45% of total simulated) at rate of 3756 mmol m -2 yr -1 , higher than the 63 mmol m -2 yr -1 required globally to remove 1.0 GT CO 2 yr -1 . It also reduced acidity in the bay, ΔpH ≈ +0.1 pH units, an amount comparable to the historic impacts of anthropogenic acidification in the Salish Sea. The mixing and dilution of added TA with distance from the source results in reduced CDR rates such that comparable amount 2176 T CO 2 yr -1 was removed over >1000 fold larger area of the rest of the model domain. There is the potential for more removal occurring beyond the region modeled. The CDR from reduction of outgassing between October and May accounts for as much as 90% of total CDR simulated. Of the total, only 375 T CO 2 yr -1 (8%) was from the open shelf portion of the model domain. With shallow depths limiting vertical mixing, nearshore estuarine waters may provide a more rapid removal of CO 2 using alkalinity enhancement relative to deeper oceanic sites.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces

Coastal soils are dynamic systems where unique microbial niches are shaped by the intensity and duration of flooding between the terrestrial and aquatic boundaries of the terrestrial-aquatic interface (TAI). We aimed to understand the soil microbial community (16S rRNA gene) along the TAIs of a freshwater versus estuarine region and how it relates to organic matter (OM, via Fourier Transform Ion Cyclotron Resonance Mass Spectrometry). We studied the TAI gradients along a transect from upland (forested), transition (stressed forest), to wetland at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. Microbial communities differed significantly by region, transect position, and site. Contrary to expectations, given their dynamic hydrologies, transitions represented midpoints in microbial richness and diversity. We identified a core microbiome conserved across all transect positions within a region, highlighting potential microbial functions most resilient to environmental change. Indicator taxa unique to each transect position defined specific niches shaped by soil biogeochemistry. Co-expression networks of feature-level β-nearest-taxon indices revealed positive relationships in bacterial and OM feature contributions to community assembly. Our study provides critical insights into microbial communities at the forefront of hydrological changes in coastal areas that connect the land to lakes and oceans and remain vulnerable to changing weather patterns.

coastal ecosystems↗
DOE OSTI2020

Novel fisheries investigations by Harald Dannevig: some parallels with Johan Hjort on the other side of the world

Abstract Harald Dannevig was Australia’s first Director of fisheries research and Director of Australia’s first ocean-going research vessel. Dannevig’s initial contributions concerned hatchery technology, freshwater fisheries, and impacts of estuarine prawn trawling. Later, he revealed the growth and migration of sea mullet, the spawning of pelagic eggs in the coastal ocean, and he was the first to demonstrate the effect of onshore winds on recruitment to estuarine fisheries. Using plans of the first Norwegian research trawler Michael Sars, he advised on the construction and commissioning of Endeavour. He organized 99 research voyages over 6 years to determine suitable trawling grounds over ∼7000 km, discovering 263 new species, including 96 new fish species and ∼5000 catalogued specimens. Harald Dannevig’s significant achievements in Australia were soon forgotten after his death with the loss of Endeavour in the Southern Ocean at the beginning of World War I. Both Johan Hjort and Dannevig were numerate, loved natural history, and were keenly observant on the deck. As these two scientists did not correspond, their innovative and parallel thinking stems from the shared university environment with G.O. Sars, and the rapport between Sars and Harald’s father Gunder Dannevig, concerning the fish hatchery and stocking of larval cod.

Suthers, Iain M.↗
DOE OSTI2025

Rising Water Levels and Vegetation Shifts Drive Substantial Reductions in Methane Emissions and Carbon Dioxide Uptake in a Great Lakes Coastal Freshwater Wetland

ABSTRACT Coastal freshwater wetlands are critical ecosystems for both local and global carbon cycles, sequestering substantial carbon while also emitting methane (CH 4 ) due to anoxic conditions. Estuarine freshwater wetlands face unique challenges from fluctuating water levels, which influence water quality, vegetation, and carbon cycling. However, the response of CH 4 fluxes and their drivers to altered hydrology and vegetation remains unclear, hindering mechanistic modeling. To address these knowledge gaps, we studied an estuarine freshwater wetland in the Great Lakes region, where rising water levels led to a vegetation shift from emergent Typha dominance in 2015–2016 to floating‐leaved species in 2020–2022. Using eddy covariance flux measurements during the peak growing season (June–September) of both periods, we observed a 60% decrease in CH 4 emissions, from 81 ± 4 g C m −2 in 2015–2016 to 31 ± 3 g C m −2 in 2020–2022. This decline was driven by two main factors: (1) higher water levels, which suppressed ebullitive fluxes via increased hydrostatic pressure and extended CH 4 residence time, enhancing oxidation potential in the water column; and (2) reduced CH 4 conductance through plants. Net carbon dioxide (CO 2 ) uptake decreased by 90%, from −267 ± 26 g C m −2 in 2015–2016 to −27 ± 49 g C m −2 in 2020–2022. Additionally, diel CH 4 flux patterns shifted, with a distinct morning peak observed in 2015–2016 but absent in 2020–2022, suggesting changes in plant‐mediated transport and a potential decoupling from photosynthesis. The dominant factors influencing CH 4 fluxes shifted from water temperature and gross primary productivity in 2015–2016 to atmospheric pressure in 2020–2022, suggesting an increased role of ebullition as a primary transport pathway. Our results demonstrate that changes in water levels and vegetation can substantially alter CH 4 and CO 2 fluxes in coastal freshwater wetlands, underscoring the critical role of hydrological shifts in driving carbon dynamics in these ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Biogeochemical Changes in Estuaries

The biogeochemical composition of materials suspended and dissolved in estuarine waters is substantially transformed by biological and abiotic processes as water from rivers and subterranean aquifers travels through estuaries to the coastal ocean, influencing the rate of storage and/or exchange of carbon with the atmosphere. Biogeochemical signatures in the upper reaches of estuaries (e.g., low salinity) generally reflect characteristics of the rivers and groundwater draining into the estuary. The composition of organic matter (OM) where rivers meet estuaries is a mixture of terrigenous signatures dependent on watershed landscape features, aquatic signatures dependent on the prominence of freshwater primary productivity, and intermediate metabolites (i.e., byproducts of in situ transformation) of these terrigenous and aquatic OM sources. The prominence of aquatic primary production-derived OM and products of microbial decomposition generally increases towards the lower reaches of estuaries where they meet the coastal ocean (i.e.., continental shelf). The nature of biogeochemical transformations occurring along estuarine gradients is closely coupled with factors that are poised to change under multiple compounding disturbances and stress factors related to both climate change and other anthropogenic global changes. This chapter describes the fundamental mechanisms that drive the transport, transformation, and storage of OM in estuaries and how these dynamics have and may continue to change in response to key disturbances and stressors related to climate change and other anthropogenic global changes including warming, intensifying hydrological extremes (e.g., droughts and floods), sea level rise, and acidification.

Ward, Nicholas D.↗
DOE OSTI2023

Stable water isotopes and tritium data from porewater at Elkhorn Slough

Salt marshes are dynamic hydrologic systems where terrestrial groundwater, terrestrial surface water, and seawater mix due to bi-directional flows and pressure gradients. Due to the counteracting terrestrial and marine forcings that control these environments, we do not comprehensively understand water fluxes in these complex coastal systems. To understand the water sources, flow directions, and velocities in salt marsh porewater, we collected geochemical tracers across a hillslope-to-salt marsh continuum in a salt marsh experiencing daily inundation of estuarine surface water (SW) from tides and mixing of fresh seasonal groundwater. The experimental transect is located at the Elkhorn Slough National Estuarine Research Reserve.Here we present a data table (.csv) with the results of electrical conductivity, stable water isotopes, and tritium in porewater across several elevations in the hillslope-to-salt marsh continuum (information in the data set). We analyzed the stable water isotope samples by cavity ring-down spectroscopy in a Picarro L2130-i at the University of California Santa Cruz (accuracy of 0.025‰ and 0.1‰ for δ18O and δ2H, respectively). We measured the electric conductivity of the samples with an Orion Star™ A329 multiparameter meter (0.5% accuracy, Thermo Fisher Scientific, Massachusetts, USA). We analyzed 3H samples at Lawrence Livermore National Laboratory by helium-3 accumulation (Clarke et al., 1976; Surano et al., 1992).

54 ENVIRONMENTAL SCIENCES↗