Mudflat Morphodynamics and the Impact of Sea Level Rise in South San Francisco Bay

Estuarine tidal mudflats form unique habitats and maintain valuable ecosystems. Historic measurements of a mudflat in San Fancsico Bay over the past 150 years suggest the development of a rather stable mudflat profile. This raises questions on its origin and governing processes as well as on the mudflats’ fate under scenarios of sea level rise and decreasing sediment supply. We developed a 1D morphodynamic profile model (Delft3D) that is able to reproduce the 2011 measured mudflat profile. The main, schematised, forcings of the model are a constant tidal cycle and constant wave action. The model shows that wave action suspends sediment that is transported landward during flood. A depositional front moves landward until landward bed levels are high enough to carry an equal amount of sediment back during ebb. This implies that, similar to observations, the critical shear stress for erosion is regularly exceeded during the tidal cycle and that modelled equilibrium conditions include high suspended sediment concentrations at the mudflat. Shear stresses are highest during low water, while shear stresses are lower than critical (and highest at the landward end) along the mudflat during high water. Scenarios of sea level rise and decreasing sediment supply drown the mudflat. In addition, the mudflat becomes more prone to channel incision because landward accumulation is hampered. This research suggests that sea level rise is a serious threat to the presence of many estuarine intertidal mudflats, adjacent salt marshes and their associated ecological values.     

Late Holocene Marsh Expansion in Southern San Francisco Bay, California

Currently, the largest tidal wetlands restoration project on the US Pacific Coast is being planned and implemented in southern San Francisco Bay; however, knowledge of baseline conditions of salt marsh extent in the region prior to European settlement is limited. Here, analysis of 24 sediment cores collected from ten intact southern San Francisco Bay tidal marshes were used to reconstruct spatio-temporal patterns of marsh expansion to provide historic context for current restoration efforts. A process-based marsh elevation simulation model was used to identify interactions between sediment supply, sea-level rise, and marsh formation rates. A distinct age gradient was found: expansion of marshes in the central portion of southern San Francisco Bay dated to 500 to 1500 calendar years before present, while expansion of marshes in southernmost San Francisco Bay dated to 200 to 700 calendar years before present. Thus, much of the tidal marsh area mapped by US Coast Survey during the 1853–1857 period were in fact not primeval tidal marshes that had persisted for millennia but were recently formed landscapes. Marsh expansion increased during the Little Ice Age, when freshwater inflow and sediment influx were higher than during the previous millennium, and also during settlement, when land use changes, such as introduction of livestock, increased watershed erosion, and sediment delivery.     

The influence of phytoplankton community composition on primary productivity along the riverine to freshwater tidal continuum in the San Joaquin River,California

Differences in phytoplankton community composition along a riverine to, freshwater tidal continuum was an important factor affecting the primary productivity and quantity of phytoplankton biomass available to the San Francisco Estuary food web downstream. The relative contribution of riverine and freshwater tidal phytoplankton was determined using measurements of primary productivity, respiration, and phytoplankton species composition along a riverine to freshwater tidal gradient in the San Joaquin River, one of two major rivers that flow into, the San Francisco Estuary. Chla-specific net primary productivity was greater in the freshwater tidal habitat and was correlated with both a higher growth efficiency and maximum growth potential compared with the river upstream. Cluster analysis indicated these differences in growth parameters were associated with differences in species composition, with greater percent diatom and green algal species biomass upstream and flagellate biomass downstream. Correlation between the chla specific net productivity and phytoplankton species composition suggested the downstream shift from riverine diatom and green algal species to flagellate species contributed to the seaward increase in net primary productivity. Environmental conditions, such as specific conductance and water transparency, may have influenced primary productivity along the riverine to freshwater tidal continuum through their effect on both species composition and growth rate. Data suggest light was not the sole controlling factor for primary productivity in this highly turbid estuary; phytoplankton growth rate did not increase when riverine plankton communities from low light conditions upstream were exposed to higher light conditions downstream. This study suggests that the availability of phytoplankton biomass to the estuarine food web may be influenced by management of both phytoplankton growth and community composition along the riverine to freshwater tidal continuum.     

Phytoplankton blooms and nitrogen productivity in San Francisco Bay

San Francisco Bay has been considered an HNLC or HNLG (high nutrient low chlorophyll or low growth) region with nonlimiting concentrations of inorganic nutrients yet low standing stocks of phytoplankton. Most of the studies leading to this conclusion come from the South Bay and little is known about nutrient processes and phytoplankton productivity in the northern and central parts of the estuary. Data collected over 3 yr (1999–2003) in Suisun, San Pablo, and Central Bays describe the availability of dissolved inorganic nitrogen (DIN), silicate, and phosphate and the seasonal variability in phytoplankton abundance. Rate measurements of fractionated nitrogen productivity provide the relative contributions of different forms of DIN (ammonium and nitrate) and different sized phytoplankton to the development of seasonal phytoplankton blooms. Regional differences in bloom dynamics are observed with Suisun Bay, the least saline, highest nutrient, most turbid region having less phytoplankton biomass and productivity than San Pablo and Central Bays, except in the abnormally wet spring of 2000. Spring blooms in San Francisco Bay are driven primarily by high rates of nitrate uptake by larger phytoplankton cells following a period of increased ammonium uptake that depletes the ambient ammonium. The smaller occasional fall blooms are apparently flueled mostly by ammonium uptake by small sized phytoplankton. The data suggest that the HNLC condition in the northern and central parts of San Francisco Bay is due primarily to light availability modulated by the interaction between ammonium and nitrate, and the relative amounts of the two forms of the DIN pool available to the phytoplankton.     

基于植被和潮动力作用的潮滩剖面演变数值模拟

为研究多因子共同作用下的潮滩演变机制,开发了基于植被生长和潮动力作用的潮滩剖面演变数学模型。在不考虑植被作用下,模拟得到了潮滩中长期演变后的上凸形剖面特征;泥沙供给是决定潮滩宽度的因素,供给越充分,潮滩宽度越大。模型考虑植被过程时,结果表明不同的植被生物量分布形式对潮滩水动力的影响程度不同,在潮间带上部,生物量抛物线分布时的减流效果强于生物量线性分布形式;而在潮间带下部则相反。模拟结果显示盐沼和光滩之间出现陡坎,且随着滩面的逐步淤高,陡坎逐步向海移动。     

Exchange Between an Estuary and an Intertidal Marsh and Slough

The hydrodynamic characteristics of small, intertidal perimeter habitats make flushing and residence times in these environments difficult to quantify using conventional approaches. The flooding and draining of intertidal shallows surrounding small perimeter sloughs result in large volume changes relative to total system volume during each tidal cycle. In such environments, an Eulerian framework of flushing and residence time may not be the best approach for quantifying tidal exchange; thus, alternative approaches should be considered in analyzing hydrodynamic exchange in small perimeter habitats. In this study, the results of applying such an approach to a small intertidal perimeter slough in South San Francisco Bay are presented. Previous work has shown that hydrodynamic exchange in an estuarine system can be analyzed by making Eulerian measurements of hydrodynamic fluxes and binning them according to salinity and temperature classes, thus providing a quasi-Lagrangian method of analyzing exchange and transport in an estuarine system. We apply a method which uses this approach to estimate the volumetric exchange ratio M, which is used to estimate the tidal exchange within an estuary during each tidal cycle. We find that the estimation of volumetric exchange ratios and the calculation of hydrodynamic residence times in estuarine systems can be complicated by mixing conditions associated with very strong tidal forcing, particularly in small-volume systems such as small perimeter sloughs, where the tidal prism can be on the scale of or greater than the total system volume.     

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.     

The effects of the San Francisco Bay plume on trace metal and nutrient distributions in the Gulf of the Farallones

The distributions of particulate elements (Al, P, Mn, Fe, Co, Cu, Zn, Cd, and Pb), dissolved trace metals (Mn, Fe, Co, Cu, Zn, and Cd), and dissolved nutrients (nitrate, phosphate, and silicic acid) were investigated in the Gulf of the Farallones, a region of high productivity that is driven by the dynamic mixing of the San Francisco Bay plume, upwelled waters, and California coastal surface waters. Particulate metals were separated into >10 and 0.4-10 μm size-fractions and further fractionated into leachable (operationally defined with a 25% acetic acid leach) and refractory particulate concentrations. Dissolved metals (< 0.4 μm pore-size filtrate) were separated into colloidal (0.03-0.4 μm) and soluble (<0.03 μm) fractions. The percent leachable particulate fractions ranged from 2% to 99% of the total particulate concentration for these metals with Mn and Cd being predominantly leachable and Fe and Al being predominantly refractory. The leachable particulate Pb concentration was associated primarily with suspended sediments from San Francisco Bay and was a tracer of the plume in coastal waters. The particulate trace metal data suggest that the leachable fraction was an available source of trace metal micronutrients to the primary productivity in coastal waters. The dissolved trace metals in the San Francisco Bay plume and freshly upwelled surface waters were similar in concentration, with the exception of Cu and Co, which exhibited relatively high concentrations in plume waters and served as tracers of this water mass. The dissolved data and estimates of the plume dynamics suggest that the impact of anthropogenic inputs of nutrients and trace metals in the San Francisco Bay plume contributes substantially to the concentrations found in the Gulf of the Farallones (10-50% of estimated upwelled flux values), but does not greatly disrupt the natural stoichiometric balance of trace metal and nutrient elements within coastal waters given the similarity in concentrations to sources in upwelled water. In all, the data from this study demonstrate that the flux of dissolved nutrients and bioactive trace metals from the San Francisco Bay plume contribute to the high and relatively constant phytoplankton biomass observed in the Gulf of the Farallones.     

What have natural and human changes wrought on the foraminifera of San Francisco Bay late Quaternary estuaries?

In this study we compare the foraminifera of modern South San Francisco Bay with fossils from sediments of a previous estuary at 125 ka to provide a basis for interpreting the impact of natural and human change on the benthic ecosystem. All the species found in the Pleistocene sediments of this study are estuarine and/or shallow-water species occurring commonly in San Francisco Bay today, except for the introduced foraminifer Trochammina hadai, a native of Japan that was not found in samples taken in San Francisco Bay before 1983. The biodiversity and species composition of the fossil and modern assemblages before the introduction of T. hadai are nearly identical, suggesting that the environmental and physical changes in the 125,000-year-old and modern estuaries have not had a significant effect on the meiofauna of the Bay. In contrast, modern anthropogenic change in the form of species introductions has impacted the modern foraminiferal assemblage: T. hadai began to dominate the modern assemblage a decade after its introduction. Similar to the recorded impacts of introductions of marine metazoan invertebrate species, the dominance of T. hadai changed species proportions in the post-1980s foraminiferal assemblage, however no known extinctions in the native foraminiferal fauna occurred.     

Likely Population-Level Effects of Contaminants on a Resident Estuarine Fish Species: Comparing <Emphasis Type="Italic">Gillichthys mirabilis</Emphasis> Population Static Measurements and Vital Rates in San Francisco and Tomales Bays

Gillichthys mirabilis population static measurements (abundance, age, and size class structures) and vital rates (growth, mortality, recruitment) were monitored on an annual basis from 2002 to 2007. Population-level metrics were used to gauge habitat quality at two study sites (a contaminated site and a reference site) in two large northern California estuaries (San Francisco and Tomales Bays). San Francisco Bay populations exhibited slower growth and higher mortality rates and contained higher amounts of contaminants than Tomales Bay. Recruitment rates were highest at contaminated sites (Stege Marsh and Walker Creek) in 3 years out of 5 years, suggesting low adult survival. This study suggests that population-level effects on a residential fish may be attributed to estuarine contamination on the US Pacific coast.     

江苏淤泥质潮滩剖面演变现场观测

为探究江苏中部沿海双凸型剖面演变特性,在江苏盐城川东港南侧潮间带布设了10个水准观测站,2012年9月至2013年11月对该潮滩剖面演变过程开展了现场观测.结果表明:该潮滩剖面呈现出双凸型特征,平均高、低潮位线附近的滩涂形成淤积率较高的地形凸点;潮间上带受潮流影响小,滩面高程相对稳定;平均高、低潮位之间的区域滩面高程季节性变化明显,总体呈现冲刷状态;潮间下带冲刷显著,滩面坡度增大.全剖面自岸向海呈现"稳定—淤积—稳定—淤积—冲刷"的双凸型剖面特征.     

Probabilistic estimation of numbers and costs of future landslides in the San Francisco Bay region

We used historical records of damaging landslides triggered by rainstorms and a newly developed Probabilistic Landslide Assessment Cost Estimation System (PLACES) to estimate the numbers and direct costs of future landslides in the 10-county San Francisco Bay region. Historical records of damaging landslides in the region are incomplete. Therefore, our estimates of numbers and costs of future landslides are minimal estimates. The estimated mean annual number of future damaging landslides for the entire 10-county region is about 65. Santa Cruz County has the highest estimated mean annual number of damaging future landslides (about 18), whereas Napa, San Francisco, and Solano Counties have the lowest estimated mean numbers of damaging landslides (about 1 each). The estimated mean annual cost of future landslides in the entire region is about US $14.80 million (year 2000 $). The estimated mean annual cost is highest for San Mateo County ($3.24 million) and lowest for Solano County ($0.18 million). The annual per capita cost for the entire region will be about $2.10. Santa Cruz County will have the highest annual per capita cost at $8.45, whereas San Francisco County will have the lowest per capita cost at $0.31. Normalising costs by dividing by the percentage of land area with slopes equal to or greater than 17% indicates that San Francisco County will have the highest cost per square km ($7,101), whereas Santa Clara County will have the lowest cost per square km ($229). These results indicate that the San Francisco Bay region has one of the highest levels of landslide risk in the United States. Compared with landslide cost estimates from the rest of the world, the risk level in the Bay region seems high, but not exceptionally high.     

An assessment of the utility of regional diatom‐based tidal‐level transfer functions

In order to understand natural sea‐level variability, and to enhance future predictions, accurate and precise estimates of Holocene tidal levels are required. Although the application of diatom‐based transfer functions can yield such data, these work best when underpinned by local training sets. Urbanized estuaries offer little prospect of obtaining local training sets and, instead, the reliability of regional transfer functions has to be assessed. The performance of a published regional (UK) diatom‐based tidal‐level transfer function applied to fossil assemblages from two contrasting core sites in the Mersey Estuary, UK, is assessed using modern analogue techniques and sediment isotope data. We find that, although estimated tidal levels coincide with changes in organic matter source, the frequent lack of modern analogues mean that palaeotide estimates are without basis. This is likely a consequence of the site‐specific nature of diatom assemblages in higher intertidal and supratidal areas in particular, where local factors are expected to exert a greater control on their ecology. This situation may be partly resolved by constructing and applying much larger regional training sets from multiple higher intertidal and supratidal sites (where intact). Otherwise the application of alternative techniques, such as regional foraminiferal tidal‐level transfer functions, may be more appropriate. Copyright © 2011 John Wiley & Sons, Ltd.     

Tidal Stage Changes in Structure and Diversity of Intertidal Benthic Diatom Assemblages: a Case Study from Two Contrasting Charleston Harbor Flats

Benthic microalgae are key contributors to near-shore food webs and sediment stabilization. Temporal variability in microalgal biomass and production throughout the tidal cycle has been well documented; however, due to limitations of traditional methods of analysis patterns of community composition and diversity over such time scales have not been revealed. To explore the latter and better understand how short-term changes throughout the tidal cycle may affect community functioning, we compared benthic diatom composition and diversity over tidal stage shifts. We employed two disparate molecular techniques (denaturing gel gradient electrophoresis with Sanger DNA sequencing of excised bands and high-throughput community metagenome sequencing) to characterize diatom assemblages in representative muddy and sandy intertidal sites in Charleston Harbor, SC, USA. In support of prior studies, we found higher diatom diversity in sandbar as compared to mudflat sediments. Spatial differences were stronger relative to tidal temporal differences, although diversity metrics generally were highest after prolonged tidal immersion as compared to low-tide emersion or just after immersion at flood tide. Composition of the diatom assemblage differed markedly between sites, with species in genera Halamphora, Amphora, and Navicula dominating the sandbar, whereas Cyclotella, Skeletonema, and Thalassiosira were the most prevalent genera on the mudflat. Diatom composition differed by tidal stage, with assemblages during low-tide exposure distinct from samples taken after immersion. Both sandbar and mudflat sediments exhibited increases in relative proportion of epipelic diatoms and decreases in planktonic taxa during low-tide exposure. Our findings of short-term changes in species composition and dominance could inform primary productivity models to better estimate understudied diatom contributions in heterogeneous and highly variable tidal systems.     

Tidal flat macrofaunal communities and their associated environments in estuaries of southern California and northern Baja California, Mexico

Several tidal flats in both Estero de Punta Banda and Bahia de San Quintín, Baja California, and one in Mission Bay, southern California, were sampled for macrofaunal properties (taxonomic composition, density, species richness, and functional groups for animals ≥0.3 mm) and associated environmental variables (sediment properties, salinity, plant belowground biomass, and cover ofZostera marina) in order to establish a benchmark data set for these areas. The grouping of macrofauna into higher taxonomic or functional groups for these comparisons reduced variability and revealed stronger relationships. Each estuary had a fairly distinct macrofaunal assemblage, with that of Estero de Punta Banda being different from Bahia de San Quintín and Mission Bay primarily due to dominance by a capitellid polychaete, lower proportions of surface deposit feeders, and higher proportions of fauna with a planktonic stage. The flats in Mission Bay and Bahia de San Quintín were dominated by peracarid crustaceans, oligochaetes and polychaetes and had higher proportions of direct developers and macrofauna with mobile adult stages than did Estero de Punta Banda. There was an overlap of the environmental characteristics among estuaries, with more variability of sediment and vegetation properties within than among estuaries. Within Bahia de San Quintín, there was an oceanic to back-bay distribution gradient of macrofauna that was similar to that found in estuaries in wetter climates, despite the lack of a salinity gradient in San Quintín. A decoupling of the benthos and the assumed anthropogenic stresses was observed with the degraded site, Mission Bay, being most similar to the relatively pristine Bahia de San Quintín. Selection of reference sites and sampling variables should be made cautiously because effects of disturbance factors on the benthos may be site-dependent, scale-dependent, or negligible.     

Dissolved sulfides in the oxic water column of San Francisco Bay,California

Trace contaminants enter major estuaries such as San Francisco Bay from a variety of point and nonpoint sources and may then be repartitioned between solid and aqueous phases or altered in chemical speciation. Chemical speciation affects the bioavailability of metals as well as organic ligands to planktonic and benthic organisms, and the partitioning of these solutes between phases. Our previous, work in south San Francisco Bay indicated that sulfide complexation with metals may be of particular importance because of the thermodynamic stability of these complexes. Although the water column of the bay is consistently well-oxygenated and typically unstratified with respect to dissolved oxygen, the kinetics of sulfide oxidation could exert at least transient controls on metal speciation. Our initial data on dissolved sulfides in the main channel of both the northern and southern components of the bay consistently indicate submicromolar concenrations (from <1 nM to 162 nM), as one would expect in an oxidizing environment. However, chemical speciation calculations over the range of observed sulfide concentrations indicate that these trace concentrations in the bay water column can markedly affect chemical speciation of ecologically significant trace metals such as cadmium, copper, and zinc.     

Spatiotemporal Models of an Estuarine Fish Species to Identify Patterns and Factors Impacting Their Distribution and Abundance

Understanding the distribution and abundance of organisms can be exceedingly difficult for pelagic fish species that live in estuarine environments. This is particularly so for fish that cannot be readily marked and released or otherwise tracked, such as the diminutive delta smelt, Hypomesus transpacificus, endemic to the San Francisco Estuary. The environmental factors that influence their distribution operate at multiple scales, from daily tidal cycles and local perceptual fields to seasonal and annual changes in dominant environmental gradients spanning the entire San Francisco Estuary. To quantify scale-specific patterns and factors shaping the spatiotemporal abundance dynamics of adult delta smelt, we fit a suite of models to an extensive, spatially resolved, catch survey time series from 13 annual cohorts. The best model included cohort-specific abundance indicators and daily mortality rates, a regional spatial adjustment, and haul-specific environmental conditions. The regional adjustment identified several density hot spots that were persistent across cohorts. While this model did include local environmental conditions, the gain in explained variation was relatively slight compared to that explained by the regional adjustment. Total abundance estimates were derived by multiplying habitat volume by catch density (design-based) and modeled density (model-based), with both showing severe declines in the population over the time period studied. The design-based approaches had lower uncertainty but potentially higher bias. We discuss the implications of our results for advancing the science and improving management of delta smelt, and future data collection needs.     

Influence of an Observed Decadal Decline in Wind Speed on Turbidity in the San Francisco Estuary

Turbidity is an important habitat component in estuaries for many fishes and affects a range of other ecological functions. Decadal timescale declines in turbidity have been observed in the San Francisco Estuary (Estuary), with the declines generally attributed to a reduction in sediment supply to the Estuary and changes to the erodible sediment pool in the Estuary. However, we analyzed hourly wind data from 1995 through 2015 and found statistically significant declines of 13 to 48% in wind speed around the Estuary. This study applied a 3-D hydrodynamic, wave, and sediment transport model to evaluate the effects of the observed decrease in wind speed on turbidity in the Estuary. The reduction in wind speed over the past 20 years was predicted to result in a decrease in turbidity of 14 to 55% in Suisun Bay from October through January. These results highlight that the observed declines in both wind speed and sediment supply over the past 20 years have resulted in reduced turbidity in the San Francisco Estuary from October through January. This decline in turbidity in Suisun Bay potentially has negative effects on habitat for fish like the endangered Delta Smelt which are more commonly caught in relatively turbid water.     

Estuarine Dispersion from Tidal Trapping: A New Analytical Framework

Observations of tidal trapping in a channel connected to large volumes along its perimeter showed that the exchange between them is driven by advection due to tidal flows. Therefore, quantifying the longitudinal dispersion of scalars in the channel that results from tidal trapping was not possible using traditional frameworks, which assume that the exchange is a diffusive process. This study uses the concentration moment method to solve analytically for the dispersion coefficient of a solute in a tidal channel which exchanges advectively with volumes along its edges. This constitutes a new framework for analyzing the longitudinal dispersion that results from tidal trapping in systems such as a branching tidal channel or the breached salt ponds of San Francisco Bay. A comparison of dispersion coefficients from traditional, diffusion-driven frameworks for tidal trapping, the new advective framework derived in the present study, and observations show that the new formulation is best suited to this environment.