Geology topics

Research about San Francisco Bay

Source-linked reports with geographic coverage including San Francisco Bay.

At least 91 records · Page 5Linked to original sources

USGS2015

Science foundation Chapter 5 Appendix 5.1: Case study marsh macroinvertebrates

This case study includes representative macroinvertebrates that live in the marsh plain, its associated channels and pannes (ponds), and the marsh-upland transition zone. While less visible than animals such as birds, invertebrates play important roles in physical and biological processes (e.g., burrowing activity and channel bank erosion, and detritivores breaking down organic matter) and are important food resources for higher trophic animals. Common invertebrates in these habitats include plant-hopper ( Prokelisia marginata ), beach hopper ( Traskorchestia traskiana ), pygmy blue butterfly ( Brephidium exilis ), inchworm moth ( Perizoma custodiata ), western tanarthus beetle ( Tanarthus occidentalis ), salt marsh mosquitoes ( Aedes spp.; Maffei 2000a, Maffei 2000b, Maffei 2000c), crabs (native Hemigrapsus oregonensis and introduced Carcinus maenas ), copepods, snails (e.g. native California horn snail Cerithidea californica and introduced Ilyanassa obsoleta , Myosotella myosotis ), polychaetes (e.g. Capitella spp., Eteone californica , Neanthes brandti ), small clams ( Macoma petalum / M. balthica ), and corophiid amphipods (Cohen 2011, Race 1982, Robinson et al. 2011). Some common species were described in detail in the San Francisco Bay Goals Project Species and Community Profiles (Goals Project 2000).

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USGS2014

Earliest record of the invasive Foraminifera Trochammina hadai in San Francisco Bay, California, USA

In 1995, Trochammina hadai , a benthic Foraminifera prevalent in Japanese estuaries, was found in San Francisco Bay, California, USA. Subsequent field investigations determined that the species was also present in nearly all of the major ports and estuaries along the western United States. Because of its widespread colonization, it is of interest to determine when T. hadai first appeared as an invasive in the coastal regions of the North Pacific. In San Francisco Bay, the species was not found in 404 surface samples collected between 1930 and 1981. In 1983, however, a grab sediment sample from one of four sites in the southern portion of the bay contained T. hadai . This site was the most northern of the four and contained 12 specimens of the invasive, comprising 1.5% of the assemblage. This is the earliest appearance on record of T. hadai in San Francisco Bay.

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USGS2014

Comparative reproductive biology of sympatric species: Nest and chick survival of American avocets and black-necked stilts

Identifying differences in reproductive success rates of closely related and sympatrically breeding species can be useful for understanding limitations to population growth. We simultaneously examined the reproductive ecology of American avocets Recurvirostra americana and black-necked stilts Himantopus mexicanus using 1274 monitored nests and 240 radio-marked chicks in San Francisco Bay, California. Although there were 1.8 times more avocet nests than stilt nests, stilts nonetheless fledged 3.3 times more chicks. Greater production by stilts than avocets was the result of greater chick survival from hatching to fledging (avocet: 6%; stilt: 40%), and not because of differences in clutch size (avocet: 3.84; stilt: 3.77), nest survival (avocet: 44%; stilt: 35%), or egg hatching success (avocet: 90%; stilt: 92%). We reviewed the literature and confirmed that nest survival and hatching success are generally similar when avocets and stilts breed sympatrically. In addition to species, chick survival was strongly influenced by age, site, and year. In particular, daily survival rates increased rapidly with chick age, with 70% of mortalities occurring ≤ 1 week after hatch. California gulls Larus californicus caused 55% of avocet, but only 15% of stilt, chick deaths. Differential use of micro-habitats likely reduced stilt chick’s vulnerability to gull predation, particularly during the first week after hatch, because stilts nested in vegetation 2.7 times more often than avocets and vegetation height was 65% taller at stilt nests compared with avocet nests. Our results demonstrate that two co-occurring and closely related species with similar life history strategies can differ markedly in reproductive success, and simultaneous studies of such species can identify differences that limit productivity.

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USGS2014

Forster's tern chick survival in response to a managed relocation of predatory California gulls

Gull populations can severely limit the productivity of waterbirds. Relocating gull colonies may reduce their effects on nearby breeding waterbirds, but there are few examples of this management strategy. We examined gull predation and survival of Forster's tern (Sterna forsteri) chicks before (2010) and after (2011) the managed relocation of the largest California gull (Larus californicus) colony (24,000 adults) in San Francisco Bay, California. Overall, survival of radio-marked Forster's tern chicks from hatching to fledging was 0.22 ± 0.03 (mean ± SE), and daily survival rates increased with age. Gulls were the predominant predator of tern chicks, potentially causing 54% of chick deaths. Prior to the gull colony relocation, 56% of radio-marked and 20% of banded tern chicks from the nearest tern colony were recovered dead in the gull colony, compared to only 15% of radio-marked and 4% of banded chicks recovered dead from all other tern colonies. The managed relocation of the gull colony substantially increased tern chick survival (by 900%) in the nearby (<1 km) colony from 0.04 ± 0.02 in 2010 to 0.40 ± 0.12 in 2011 but not at the more distant (>3.8 km) reference tern colony (0.29 ± 0.10 in 2010 and 0.25 ± 0.09 in 2011). Among 19 tern nesting islands, fledging success was higher when gull abundance was lower at nearby colonies and when gull colonies were farther from the tern colony. Our results indicate that the managed relocation of gull colonies away from preferred nesting areas of sensitive waterbirds can improve local reproductive success, but this conservation strategy may shift gull predation pressure to other areas or species.

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USGS2014

Vocal activity as a low cost and scalable index of seabird colony size

Although wildlife conservation actions have increased globally in number and complexity, the lack of scalable, cost-effective monitoring methods limits adaptive management and the evaluation of conservation efficacy. Automated sensors and computer-aided analyses provide a scalable and increasingly cost-effective tool for conservation monitoring. A key assumption of automated acoustic monitoring of birds is that measures of acoustic activity at colony sites are correlated with the relative abundance of nesting birds. We tested this assumption for nesting Forster's terns (Sterna forsteri) in San Francisco Bay for 2 breeding seasons. Sensors recorded ambient sound at 7 colonies that had 15–111 nests in 2009 and 2010. Colonies were spaced at least 250 m apart and ranged from 36 to 2,571 m 2 . We used spectrogram cross-correlation to automate the detection of tern calls from recordings. We calculated mean seasonal call rate and compared it with mean active nest count at each colony. Acoustic activity explained 71% of the variation in nest abundance between breeding sites and 88% of the change in colony size between years. These results validate a primary assumption of acoustic indices; that is, for terns, acoustic activity is correlated to relative abundance, a fundamental step toward designing rigorous and scalable acoustic monitoring programs to measure the effectiveness of conservation actions for colonial birds and other acoustically active wildlife.

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USGS2014

Resource selection and space use by sea ducks during the non-breeding season: Implications for habitat conservation planning in urbanized estuaries

Wide-ranging marine birds rely on multiple habitats for wintering, breeding, and migrating, and their conservation may be dependent on protecting networks of key areas. Urbanized estuaries are critical wintering and stopover areas for many declining sea ducks in North America; however, conservation measures within estuaries are difficult to establish given lack of knowledge about habitat use by these species and the variety of competing human interests. We applied hierarchical modeling to evaluate resource selection of sea ducks (surf scoters, Melanitta perspicillata) wintering in San Francisco Bay, California, USA, a large and highly urbanized estuary. We also examined their distribution, home range, and movements with respect to key habitat features and regions within the estuary. Herring roe was the strongest predictor of bird locations; however, eelgrass, water depth and salinity were also highly-ranked, with sea ducks using deeper areas of higher salinity associated with herring roe and eelgrass presence during mid-winter. Sea ducks were also strongly associated with ferry routes, suggesting these areas may contain resources that are too important to avoid and emphasizing the need to better understand water traffic effects. Movements and home range size differed between males and females in early winter but became more similar in late winter. Birds traveled farther and used several sub-bays in early winter compared to mid-winter when herring roe availability peaked in the Central Bay. Our findings identified key environmental variables, highlighted core use areas, and documented critical periods for consideration when developing conservation plans for sea ducks in urbanized estuaries.

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USGS2014

Sedimentary organic biomarkers suggest detrimental effects of PAHs on estuarine microbial biomass during the 20th century in San Francisco Bay, CA, USA

Hydrocarbon contaminants are ubiquitous in urban aquatic ecosystems, and the ability of some microbial strains to degrade certain polycyclic aromatic hydrocarbons (PAHs) is well established. However, detrimental effects of petroleum hydrocarbon contamination on nondegrader microbial populations and photosynthetic organisms have not often been considered. In the current study, fatty acid methyl ester (FAME) biomarkers in the sediment record were used to assess historical impacts of petroleum contamination on microbial and/or algal biomass in South San Francisco Bay, CA, USA. Profiles of saturated, branched, and monounsaturated fatty acids had similar concentrations and patterns downcore. Total PAHs in a sediment core were on average greater than 20× higher above ∼200 cm than below, which corresponds roughly to the year 1900. Isomer ratios were consistent with a predominant petroleum combustion source for PAHs. Several individual PAHs exceeded sediment quality screening values. Negative correlations between petroleum contaminants and microbial and algal biomarkers – along with high trans/cis ratios of unsaturated FA, and principle component analysis of the PAH and fatty acid records – suggest a negative impacts of petroleum contamination, appearing early in the 20th century, on microbial and/or algal ecology at the site.

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USGS2014

Occurrence of contaminants of emerging concern along the California coast (2009-10) using passive sampling devices

Three passive sampling devices (PSDs), polar organic chemical integrative samplers (POCIS), polyethylene devices (PEDs), and solid-phase microextraction (SPME) samplers were used to sample a diverse set of chemicals in the coastal waters of San Francisco Bay and the Southern California Bight. Seventy one chemicals (including fragrances, phosphate flame retardants, pharmaceuticals, PAHs, PCBs, PBDEs, and pesticides) were measured in at least 50% of the sites. The chemical profile from the San Francisco Bay sites was distinct from profiles from the sites in the Southern California Bight. This distinction was not due to a single compound or class, but by the relative abundances/concentrations of the chemicals. Comparing the PSDs to mussel ( Mytilus spp.) tissues, a positive correlation exists for the 25 and 26 chemicals in common for the PEDs and SPME, respectively. Diphenhydramine was the only common chemical out of 40 analyzed in both POCIS and tissues detected at a common site.

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USGS2014

Effects of wetland management on carrying capacity of diving ducks and shorebirds in a coastal estuary

With global loss of natural wetlands, managed wetlands increasingly support energy requirements for wintering shorebirds and waterfowl. Despite numerous studies of avian bioenergetics in freshwater systems, less is known of the energetic capacity of estuarine systems. In San Francisco Bay, managed saline ponds converted from former commercial salt evaporation ponds form part of the largest wetland restoration project on the Pacific coast of North America. A daily-ration model was applied to assess carrying capacity for diving ducks and shorebirds during four winter seasons (2007–2010) in seasonal and circulation ponds, each in two salinity classes. Diving ducks comprised an estimated 35,450 ± 1,559 ( ± SE) in average years and 45,458 ± 1,653 in peak years with > 95% in circulation ponds. Shorebirds comprised 64,253 ± 14,838 ( ± SE) in average years and 108,171 ± 4,854 in peak years with > 64% in seasonal ponds. Macroinvertebrate energy density was highest in mesohaline (5–30 ppt) circulation ponds and lowest in seasonal ponds for both guilds. Energy requirements for diving ducks in mesohaline followed by low-hyperhaline (30–80 ppt) circulation ponds were mostly met by available prey energy. Available energy for shorebirds was substantially less than they required in seasonal ponds but exceeded their needs in mesohaline circulation ponds. Mesohaline circulation ponds supported 9,443 ± 1,649 ( ± SE) shorebird use-days·ha -1 of accessible habitat and 2,297 ± 402 diving duck use-days·ha -1 of accessible habitat, twice the capacity of low-hyperhaline circulation ponds and greater than five times that of seasonal ponds for both guilds. Our results indicated that reducing salinity to mesohaline levels and altering water depth to increase accessibility substantially increased energy available for these species in estuarine managed ponds.

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USGS2014

Continuous water-quality and suspended-sediment transport monitoring in the San Francisco Bay, California, water years 2011–13

The U.S. Geological Survey (USGS) monitors water quality and suspended-sediment transport in the San Francisco Bay. The San Francisco Bay area is home to millions of people, and the bay teems with both resident and migratory wildlife, plants, and fish. Fresh water mixes with salt water in the bay, which is subject both to riverine and marine (tides, waves, influx of salt water) influences. To understand this environment, the USGS, along with its partners, has been monitoring the bay’s waters continuously since 1988. Several water-quality variables are of particular importance to State and Federal resource managers and are monitored at key locations throughout the bay. Salinity, which indicates the relative mixing of fresh and ocean waters in the bay, is derived from specific conductance measurements. Water temperature, along with salinity, affects the density of water, which causes gravity driven circulation patterns and stratification in the water column. Turbidity is measured using light-scattering from suspended solids in water, and is used as a surrogate for suspended-sediment concentration (SSC). Suspended sediment often carries adsorbed contaminants; attenuates sunlight in the water column; deposits on tidal marsh and intertidal mudflats, which can help sustain these habitats as sea level rises; and deposits in ports and shipping channels, which can necessitate dredging. Dissolved oxygen, which is essential to a healthy ecosystem, is a fundamental indicator of water quality, and its concentration is affected by water temperature, salinity, ecosystem metabolism, tidal currents, and wind. Tidal currents in the bay reverse four times a day, and wind direction and intensity typically change on a daily cycle: consequently, salinity, water temperature, suspendedsediment concentration, and dissolvedoxygen concentration vary spatially and temporally throughout the bay, and continuous measurements are needed to observe these changes. The purpose of this fact sheet is to inform the public and resource managers of the availability of these water-quality data.

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USGS2014

Progress toward a safer future since the 1989 Loma Prieta earthquake

The 1989 Loma Prieta earthquake interrupted several decades of seismic tranquility in the San Francisco Bay Area. It caused damage throughout the region and was a wakeup call to prepare for potentially even more damaging future quakes. Since 1989, the work of the U.S. Geological Survey and many other organizations has improved the understanding of the seismic threat in the Bay Area, promoted awareness of earthquake hazards, and contributed to more effective strategies to reduce earthquake losses. These collective efforts will help reduce the impact of future large earthquakes in the Bay Area.

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USGS2014

Waterbird egg mercury concentrations in response to wetland restoration in south San Francisco Bay, California

The conversion of 50–90 percent of 15,100 acres of former salt evaporation ponds to tidal marsh habitat in the south San Francisco Bay, California, is planned as part of the South Bay Salt Pond Restoration Project. This large-scale habitat restoration may change the bioavailability of methylmercury. The South Bay already is known to have high methylmercury concentrations, with methylmercury concentrations in several waterbirds species more than known toxicity thresholds where avian reproduction is impaired. In this 2013 study, we continued monitoring bird egg mercury concentrations in response to the restoration of the Pond A8/A7/A5 Complex to a potential tidal marsh in the future. The restoration of the Pond A8/A7/A5 Complex began in autumn 2010, and the Pond A8 Notch was opened 5 feet (one of eight gates) to muted tidal action on June 1, 2011, and then closed in the winter. In autumn 2010, internal levees between Ponds A8, A7, and A5 were breached and water depths were substantially increased by flooding the Pond A8/A7/A5 Complex in February 2011. In June 2012, 15 feet (three of eight gates) of the Pond A8 Notch was opened, and then closed in December 2012. In June 2013, 15 feet of the Pond A8 Notch again was opened, and the Pond A8/A7/A5 Complex was a relatively deep and large pond with muted tidal action in the summer. This report synthesizes waterbird data from the 2013 breeding season, and combines it with our prior study’s data from 2010 and 2011.

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USGS2014

Late Holocene sedimentary environments of south San Francisco Bay, California, illustrated in gravity cores

Data are reported here from 51 gravity cores collected from the southern part of San Francisco Bay by the U.S. Geological Survey in 1990. The sedimentary record in the cores demonstrates a stable geographic distribution of facies and spans a few thousand years. Carbon-14 dating of the sediments suggests that sedimentation rates average about 1 mm/yr. The geometry of the bay floor and the character of the sediment deposited have remained about the same in the time spanned by the cores. However, the sedimentary record over periods of centuries or decades is likely to be much more variable. Sediments containing a few bivalve shells and bivalve or oyster coquinas are most often found west of the main channel and near the San Mateo Bridge. Elsewhere in the south bay, shells are rare except in the southernmost reaches where scattered gastropod shells are found.

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USGS2014

The critical role of islands for waterbird breeding and foraging habitat in managed ponds of the South Bay Salt Pond Restoration Project, South San Francisco Bay, California

The South Bay Salt Pond Restoration Project aims to restore 50–90 percent of former salt evaporation ponds into tidal marsh in South San Francisco Bay, California. However, large numbers of waterbirds use these ponds annually as nesting and foraging habitat. Islands within ponds are particularly important habitat for nesting, foraging, and roosting waterbirds. To maintain current waterbird populations, the South Bay Salt Pond Restoration Project plans to create new islands within former salt ponds in South San Francisco Bay. In a series of studies, we investigated pond and individual island attributes that are most beneficial to nesting, foraging, and roosting waterbirds.

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USGS2014

Late 20th Century benthic foraminiferal distribution in Central San Francisco Bay, California: Influence of the Trochammina hadai invasion

The distribution of foraminifera in most of San Francisco Bay is well documented, but this is not the case for the subembayment known as Central Bay. To resolve this, 55 grab samples obtained in 1998 were analyzed to characterize the foraminiferal fauna in the surface sediments of the area. Thirty-five species were identified, including the invasive Japanese species Trochammina hadai that was introduced into the bay in the early 1980s. A cluster analysis of the samples from Central Bay produced three groups (biofacies) and one outlier. The Shallow Subtidal Biofacies is characterized by a marsh to shallow-subtidal agglutinated fauna, dominated by T. hadai but also including T. inflata , T. macrescens , Haplophragmoides subinvolutum , and Miliammina fusca . The Intermediate Subtidal Biofacies, the Intermediate Subtidal Outlier, and the Deep Subtidal Biofacies are dominated by calcareous taxa, most notably Ammonia tepida , Elphidium excavatum , and Elphidiella hannai . Ammonia tepida is most abundant in the warmer, intermediate depths of eastern Central Bay, abundances of E. excavatum peak in the cooler estuarine water near Alcatraz Island, and E. hannai thrives in the cold water west of Angel Island in a transitional setting between the deep subtidal estuarine and the nearshore marine environments. The recovery of oceanic species as far east as Angel Island indicate that western Central Bay is the most marine-influenced region of San Francisco Bay. Samples collected from 1965 onward were also compared with those from 1998 to investigate how the distribution of benthic foraminifera in Central Bay has changed over the latter half of the 20th Century, particularly in response to the invasion by Trochammina hadai . In 1998, T. hadai was recovered at 46 of 55 sites in Central Bay, comprising from 0.3 to 97% (mean = 23%) of the foraminiferal fauna. With the species’ affiliation for shallow environments, it is not unexpected that it dominated the fauna of the Shallow Subtidal Biofacies (68-97%, mean = 77%) and was also a significant component of the Intermediate Subtidal Biofacies (7-51%, averaging 28%). In the deeper waters west of Alcatraz Island, the abundance of T. hadai was significantly less (mean = 8%), most likely reflecting allochthonous specimens that were the result of post-mortem transport. A cluster analysis clearly distinguishes pre- and post-invasion biofacies, illustrating how dominant T. hadai has become in Central Bay.

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USGS2013

The significance of ultra-refracted surface gravity waves on sheltered coasts, with application to San Francisco Bay

Ocean surface gravity waves propagating over shallow bathymetry undergo spatial modification of propagation direction and energy density, commonly due to refraction and shoaling. If the bathymetric variations are significant the waves can undergo changes in their direction of propagation (relative to deepwater) greater than 90° over relatively short spatial scales. We refer to this phenomenon as ultra-refraction. Ultra-refracted swell waves can have a powerful influence on coastal areas that otherwise appear to be sheltered from ocean waves. Through a numerical modeling investigation it is shown that San Francisco Bay, one of the earth's largest and most protected natural harbors, is vulnerable to ultra-refracted ocean waves, particularly southwest incident swell. The flux of wave energy into San Francisco Bay results from wave transformation due to the bathymetry and orientation of the large ebb tidal delta, and deep, narrow channel through the Golden Gate. For example, ultra-refracted swell waves play a critical role in the intermittent closure of the entrance to Crissy Field Marsh, a small restored tidal wetland located on the sheltered north-facing coast approximately 1.5 km east of the Golden Gate Bridge.

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USGS2013

Understanding processes controlling sediment transports at the mouth of a highly energetic inlet system (San Francisco Bay, CA)

San Francisco Bay is one of the largest estuaries along the U.S. West Coast and is linked to the Pacific Ocean through the Golden Gate, a 100 m deep bedrock inlet. A coupled wave, flow and sediment transport model is used to quantify the sediment linkages between San Francisco Bay, the Golden Gate, and the adjacent open coast. Flow and sediment transport processes are investigated using an ensemble average of 24 climatologically derived wave cases and a 24.8 h representative tidal cycle. The model simulations show that within the inlet, flow and sediment transport is tidally dominated and driven by asymmetry of the ebb and flood tides. Peak ebb velocities exceed the peak flood velocities in the narrow Golden Gate channel as a result of flow convergence and acceleration. Persistent flow and sediment gyres at the headland tips are formed that limit sediment transfer from the ebb-tidal delta to the inlet and into the bay. The residual transport pattern in the inlet is dominated by a lateral segregation with a large ebb-dominant sediment transport (and flow) prevailing along the deeper north side of the Golden Gate channel, and smaller flood dominant transports along the shallow southern margin. The seaward edge of the ebb-tidal delta largely corresponds to the seaward extent of strong tidal flows. On the ebb-tidal delta, both waves and tidal forcing govern flow and sediment transport. Wave focusing by the ebb-tidal delta leads to strong patterns of sediment convergence and divergence along the adjacent Ocean Beach.

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USGS2013

A Sr-Nd isotopic study of sand-sized sediment provenance and transport for the San Francisco Bay coastal system

A diverse suite of geochemical tracers, including 87 Sr/ 86 Sr and 143 Nd/ 144 Nd isotope ratios, the rare earth elements (REEs), and select trace elements were used to determine sand-sized sediment provenance and transport pathways within the San Francisco Bay coastal system. This study complements a large interdisciplinary effort (Barnard et al., 2012) that seeks to better understand recent geomorphic change in a highly urbanized and dynamic estuarine-coastal setting. Sand-sized sediment provenance in this geologically complex system is important to estuarine resource managers and was assessed by examining the geographic distribution of this suite of geochemical tracers from the primary sources (fluvial and rock) throughout the bay, adjacent coast, and beaches. Due to their intrinsic geochemical nature, 143 Nd/ 144 Nd isotopic ratios provide the most resolved picture of where sediment in this system is likely sourced and how it moves through this estuarine system into the Pacific Ocean. For example, Nd isotopes confirm that the predominant source of sand-sized sediment to Suisun Bay, San Pablo Bay, and Central Bay is the Sierra Nevada Batholith via the Sacramento River, with lesser contributions from the Napa and San Joaquin Rivers. Isotopic ratios also reveal hot-spots of local sediment accumulation, such as the basalt and chert deposits around the Golden Gate Bridge and the high magnetite deposits of Ocean Beach. Sand-sized sediment that exits San Francisco Bay accumulates on the ebb-tidal delta and is in part conveyed southward by long-shore currents. Broadly, the geochemical tracers reveal a complex story of multiple sediment sources, dynamic intra-bay sediment mixing and reworking, and eventual dilution and transport by energetic marine processes. Combined geochemical results provide information on sediment movement into and through San Francisco Bay and further our understanding of how sustained anthropogenic activities which limit sediment inputs to the system (e.g., dike and dam construction) as well as those which directly remove sediments from within the Bay, such as aggregate mining and dredging, can have long-lasting effects

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