Variable Nitrification Rates Across Environmental Gradients in Turbid,Nutrient-Rich Estuary Waters of San Francisco Bay

Understanding rates of nitrogen cycling in estuaries is crucial for understanding their productivity and resilience to eutrophication. Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, links reduced and oxidized forms of inorganic nitrogen and is therefore an important step of the nitrogen cycle. However, rates of nitrification in estuary waters are poorly characterized. In fall and winter of 2011–2012, we measured nitrification rates throughout the water column of all major regions of San Francisco Bay, a large, turbid, nutrient-rich estuary on the west coast of North America. Nitrification rates were highest in regions furthest from the ocean, including many samples with rates higher than those typically measured in the sea. In bottom waters, nitrification rates were commonly at least twice the magnitude of surface rates. Strong positive correlations were found between nitrification and both suspended particulate matter and ammonium concentration. Our results are consistent with previous studies documenting high nitrification rates in brackish, turbid regions of other estuaries, many of which also showed correlations with suspended sediment and ammonium concentrations. Overall, nitrification in estuary waters appears to play a significant role in the estuarine nitrogen cycle, though the maximum rate of nitrification can differ dramatically between estuaries.     

Wetland Loss,Juvenile Salmon Foraging Performance,and Density Dependence in Pacific Northwest Estuaries

During the transition of juveniles from fresh water to estuarine and coastal environments, the survival of Pacific salmon (Oncorhynchus spp.) can be strongly size selective and cohort abundance is partly determined at this stage. Because quantity and quality of food influence juvenile salmon growth, high rates of prey and energy acquisition during estuarine residence are important for survival. Human activities may have affected the foraging performance of juvenile salmon in estuaries by reducing the area of wetlands and by altering the abundance of salmon. To improve our understanding of the effects of wetland loss and salmon density on juvenile salmon foraging performance and diet composition in estuaries, we assembled Chinook salmon (Oncorhynchus tshawytscha) diet and density data from nine US Pacific Northwest estuaries across a gradient of wetland loss. We evaluated the influence of wetland loss and density on juvenile Chinook salmon instantaneous ration and energy ration, two measures of foraging performance, and whether the effect of density varied among estuaries with different levels of wetland loss. We also assessed the influence of wetland loss and other explanatory variables on salmon diet composition. There was no evidence of a direct effect of wetland loss on juvenile salmon foraging performance, but wetland loss appeared to mediate the effect of density on salmon foraging performance and alter salmon diet composition. Specifically, density had no effect on foraging performance in the estuaries with less than 50 % wetland loss but had a negative effect on foraging performance in the estuaries with greater than 50 % wetland loss. These results suggest that habitat loss may interact with density to constrain the foraging performance of juvenile Chinook salmon, and ultimately their growth, during a life history stage when survival can be positively correlated with growth and size.     

Influence of Environmental Factors on Spawning of the American Horseshoe Crab (<Emphasis Type="Italic">Limulus polyphemus</Emphasis>) in the Great Bay Estuary,New Hampshire,USA

The Great Bay Estuary, New Hampshire, USA is near the northern distribution limit of the American horseshoe crab (Limulus polyphemus). This estuary has few ideal beaches for spawning, yet it supports a modest population of horseshoe crabs. There is no organized monitoring program in the Great Bay Estuary, so it is unclear when and where spawning occurs. In this 2-year study (May through June, 2012 and 2013), >5,000 adult horseshoe crabs were counted at four sites in the estuary. The greatest densities of horseshoe crabs were observed at Great Bay sites in the upper, warmer reaches of the estuary. Peaks of spawning activity were not strongly correlated with the times of the new or full moons, and similar numbers of horseshoe crabs were observed mating during daytime and nighttime high tides. While many environmental factors are likely to influence the temporal and spatial patterns of spawning in this estuary, temperature appears to have the most profound impact.     

Contemporary Deposition and Long-Term Accumulation of Sediment and Nutrients by Tidal Freshwater Forested Wetlands Impacted by Sea Level Rise

Contemporary deposition (artificial marker horizon, 3.5 years) and long-term accumulation rates (²¹⁰Pb profiles, ~150 years) of sediment and associated carbon (C), nitrogen (N), and phosphorus (P) were measured in wetlands along the tidal Savannah and Waccamaw rivers in the southeastern USA. Four sites along each river spanned an upstream-to-downstream salinification gradient, from upriver tidal freshwater forested wetland (TFFW), through moderately and highly salt-impacted forested wetlands, to oligohaline marsh downriver. Contemporary deposition rates (sediment, C, N, and P) were greatest in oligohaline marsh and lowest in TFFW along both rivers. Greater rates of deposition in oligohaline and salt-stressed forested wetlands were associated with a shift to greater clay and metal content that is likely associated with a change from low availability of watershed-derived sediment to TFFW and to greater availability of a coastal sediment source to oligohaline wetlands. Long-term accumulation rates along the Waccamaw River had the opposite spatial pattern compared to contemporary deposition, with greater rates in TFFW that declined to oligohaline marsh. Long-term sediment and elemental mass accumulation rates also were 3–9× lower than contemporary deposition rates. In comparison to other studies, sediment and associated nutrient accumulation in TFFW are lower than downriver/estuarine freshwater, oligohaline, and salt marshes, suggesting a reduced capacity for surface sedimentation (short-term) as well as shallow soil processes (long-term sedimentation) to offset sea level rise in TFFW. Nonetheless, their potentially large spatial extent suggests that TFFW have a large impact on the transport and fate of sediment and nutrients in tidal rivers and estuaries.     

Continental margin syn‐rift salt tectonics at intermediate width margins

This paper examines interactions among syn‐rift continental margin extension, evaporites, particularly rocksalt (halite), deposited in the overlying sedimentary basins, and clastic sediment loading. We present dynamically evolving 2D numerical models that combine syn‐rift lithospheric extension, with salt (viscous halite, 10¹⁸–10¹⁹ Pa s) and clastic (frictional‐plastic) sediment deposition to investigate how salt is distributed and subsequently mobilized during syn‐rift extension. Example results are shown, contrasting salt deposition in the early, mid and late syn‐rift phases of a single lithospheric extension model. The lithospheric model is chosen to give depth‐dependent extension and intermediate width margins with proximal grabens and a hyperextended distal region. The models exhibit diachronous migration of extension towards the rift axis and this is reflected in the faulting of overlying sediments. The models illustrate the roles of timing of salt deposition, relative to rifting and subsequent sedimentation, in defining the location and deformation of syn‐rift salt, with post‐salt sediment progradation in some models. Late deposition of salt leads to increased lateral extent of the original salt body and decreased variation in salt thickness. Seaward flow of salt increases with later deposition; early syn‐rift salt is deposited and trapped in the grabens, whereas mid and late syn‐rift salt tends to flow towards the distal margin or even over the oceanic crust. Prograding clastic post‐salt sediments drive more substantial seaward movement of mid and late syn‐rift salt. A numerical model of the Red Sea with evaporite deposition during the mid to late syn‐rift period, preceded and followed by aggrading and prograding clastic sediment, shows reasonable agreement with observations from the central Red Sea.     

Long-range precipitation forecasts using paleoclimate reconstructions in the western United States

Long-range precipitation forecasts are useful when managing water supplies.Oceanicatmospheric oscillations have been shown to influence precipitation.Due to a longer cycle of some of the oscillations,a short instrumental record is a limitation in using them for long-range precipitation forecasts.The influence of oscillations over precipitation is observable within paleoclimate reconstructions;however,there have been no attempts to utilize these reconstructions in precipitation forecasting.A data-driven model,KStar,is used for obtaining long-range precipitation forecasts by extending the period of record through the use of reconstructions of oscillations.KStar is a nearest neighbor algorithm with an entropy-based distance function.Oceanic-atmospheric oscillation reconstructions include the El Nino-Southern Oscillation(ENSO),the Pacific Decadal Oscillation(PDO),the North Atlantic Oscillation(NAO),and the Atlantic Multi-decadal Oscillation(AMO).Precipitation is forecasted for 20 climate divisions in the western United States.A 10-year moving average is applied to aid in the identification of oscillation phases.A lead time approach is used to simulate a one-year forecast,with a 10-fold cross-validation technique to test the models.Reconstructions are used from 1658-1899,while the observed record is used from 1900-2007.The model is evaluated using mean absolute error(MAE),root mean squared error(RMSE),RMSE-observations standard deviation ratio(RSR),Pearson’s correlation coefficient(R),NashSutcliffe coefficient of efficiency(NSE),and linear error in probability space(LEPS) skill score(SK).The role of individual and coupled oscillations is evaluated by dropping oscillations in the model.The results indicate ’good’ precipitation estimates using the KStar model.This modeling technique is expected to be useful for long-term water resources planning and management.     

Characterization of fresh and weathered petroleum for potential impacts to soil fertility

In many petroleum-producing regions, there are not adequate controls to prevent pipeline breaks and spills, and thus soil is frequently contaminated with petroleum hydrocarbons. Different petroleum oil compounds may produce negative impacts on soil fertility. In this study, four fresh crudes, a weathered petroleum, and oils from bioremediated and burned sites were investigated (specific gravities 0.83–1.27). Fourier transform infrared spectroscopy revealed three predominant polar functional groups to be more plentiful in the heavier crudes. The relative abundance of these groups was used to calculate an index that was directly correlated with specific gravity (R ² = 0.9960) and the percent of asphaltene plus (polars + resins) fractions in the oil (R ² = 0.9643). This index correlated exponentially to the water repellency caused by petroleum in an alluvial soil (R ² = 0.9928). Furthermore, extra-heavy oil at a concentration of 10,000 ppm, the maximum allowable oil concentration in the soil that is within regulatory norms in many US states and other countries, and with a specific gravity >1.002, showed severe water repellency. This study presents an alternative for determining soil remediation criteria based on the API gravity of the oil rather than the C-range of the hydrocarbon mixtures, simplifying analytical methods and systematically studying the interaction between the kinds of petroleum mixtures and potential impacts to soil fertility.     

Tailings composition effects on shear strength behavior of co-mixed mine waste rock and tailings

The objective of this study was to evaluate the effect of mine tailings composition on shear behavior and shear strength of co-mixed mine waste rock and tailings (WR&T). Crushed gravel was used as a synthetic waste rock and mixed with four types of tailings: (1) fine-grained garnet, (2) coarse-grained garnet, (3) copper, and (4) soda ash. Co-mixed WR&T specimens were prepared to target mixture ratios of mass of waste rock to mass of tailings (R) such that tailings “just filled” interparticle void space of the waste rock (i.e., optimum mixture ratio, R _opt). Triaxial compression tests were conducted on waste rock, tailings, and mixed waste at effective confining stresses (\(\sigma_{\text{c}}^{{\prime }}\)) ranging from 5 to 40 kPa to represent stresses anticipated in final earthen covers for waste containment facilities. Waste rock and co-mixed WR&T specimens were 150 mm in diameter by 300 mm tall, whereas tailings specimens were 38 mm in diameter by 76 mm tall. Shear strength was quantified using effective stress friction angles (?′) from undrained tests: ?′ for waste rock was 37°, ?′ for tailings ranged from 34° to 41°, and ?′ for WR&T mixtures ranged from 38° to 40°. Thus, shear strength of co-mixed WR&T was comparable to waste rock regardless of tailings composition. Shear behavior of WR&T mixtures was a function of R and tailings composition. Tailings influenced shear behavior for R < R _opt and when tailings predominantly were silt. Shear behavior was influenced by waste rock for R ≥ R _opt and when tailings predominantly were sand or included clay particles.     

Impacts of hydrous manganese oxide on the retention and lability of dissolved organic matter

Minerals constitute a primary ecosystem control on organic C decomposition in soils, and therefore on greenhouse gas fluxes to the atmosphere. Secondary minerals, in particular, Fe and Al (oxyhydr)oxides—collectively referred to as “oxides” hereafter—are prominent protectors of organic C against microbial decomposition through sorption and complexation reactions. However, the impacts of Mn oxides on organic C retention and lability in soils are poorly understood. Here we show that hydrous Mn oxide (HMO), a poorly crystalline δ-MnO₂, has a greater maximum sorption capacity for dissolved organic matter (DOM) derived from a deciduous forest composite O_i, O_e, and O_a horizon leachate (“O horizon leachate” hereafter) than does goethite under acidic (pH 5) conditions. Nonetheless, goethite has a stronger sorption capacity for DOM at low initial C:(Mn or Fe) molar ratios compared to HMO, probably due to ligand exchange with carboxylate groups as revealed by attenuated total reflectance-Fourier transform infrared spectroscopy. X-ray photoelectron spectroscopy and scanning transmission X-ray microscopy–near-edge X-ray absorption fine structure spectroscopy coupled with Mn mass balance calculations reveal that DOM sorption onto HMO induces partial Mn reductive dissolution and Mn reduction of the residual HMO. X-ray photoelectron spectroscopy further shows increasing Mn(II) concentrations are correlated with increasing oxidized C (C=O) content (r = 0.78, P < 0.0006) on the DOM–HMO complexes. We posit that DOM is the more probable reductant of HMO, as Mn(II)-induced HMO dissolution does not alter the Mn speciation of the residual HMO at pH 5. At a lower C loading (2 × 10² μg C m^?2), DOM desorption—assessed by 0.1 M NaH₂PO₄ extraction—is lower for HMO than for goethite, whereas the extent of desorption is the same at a higher C loading (4 × 10² μg C m^?2). No significant differences are observed in the impacts of HMO and goethite on the biodegradability of the DOM remaining in solution after DOM sorption reaches steady state. Overall, HMO shows a relatively strong capacity to sorb DOM and resist phosphate-induced desorption, but DOM–HMO complexes may be more vulnerable to reductive dissolution than DOM–goethite complexes.     

Evaluating Tidal Wetland Restoration Performance Using National Estuarine Research Reserve System Reference Sites and the Restoration Performance Index (RPI)

Evaluations of tidal wetland restoration efforts suffer from a lack of appropriate reference sites and standardized methods among projects. To help address these issues, the National Estuarine Research Reserve System (NERRS) and the NOAA Restoration Center engaged in a partnership to monitor ecological responses and evaluate 17 tidal wetland restoration projects associated with five reserves. The goals of this study were to (1) determine the level of restoration achieved at each project using the restoration performance index (RPI), which compares change in parameters over time between reference and restoration sites, (2) compare hydrologic and excavation restoration projects using the RPI, (3) identify key indicator parameters for assessing restoration effectiveness, and (4) evaluate the value of the NERRS as reference sites for local restoration projects. We found that the RPI, modified for this study, was an effective tool for evaluating relative differences in restoration performance; most projects achieved an intermediate level of restoration from 2008 to 2010, and two sites became very similar to their paired reference sites, indicating that the restoration efforts were highly effective. There were no differences in RPI scores between hydrologic and excavation restoration project types. Two abiotic parameters (marsh platform elevation and groundwater level) were significantly correlated with vegetation community structure and thus can potentially influence restoration performance. Our results highlight the value of the NERRS as reference sites for assessing tidal wetland restoration projects and provide improved guidance for scientists and restoration practitioners by highlighting the RPI as a trajectory analysis tool and identifying key monitoring parameters.