Ecosystem Restoration Program Bibliography Documents

Monitoring of the threatened Delta Green Ground Beetle at the East Wilcox Ranch (Solano County, CA) in 2007

Thu, 12 Mar 2015 16:44:15 -0700

Upland Habitat and Wildlife Friendly Agriculture - This report describes the findings of the first year of monitoring for the Delta Green Ground Beetle, a federally-listed threatened species that is known to occur in the Jepson Prairie region. Prior surveys at East Wilcox Ranch have found the beetle at seven of 18 playa pools that occur there. The 2007 surveys for the DGGB at East Wilcox Ranch performed the following tasks: a) assessed habitat suitability for the beetle at the 18 playas at East Wilcox Ranch; b) identified which of the 18 playa pools East Wilcox Ranch supported the beetle; c) surveyed for the beetle at 6 playa pools at the Jepson Prairie Preserve; d) prepared a data dictionary for use with a Trimble GeoXH GPS unit to gather data on habitat features and beetle occurrences; and e) developed a survey design for subsequent monitoring the beetle. The remainder of this report provides background information on the beetle, describes the survey methods and findings. Based on the 2007 survey results, this report also offers recommendations for future monitoring surveys at the East Wilcox Ranch.

Potential Sensitive Plant Species at Selby Creek

Thu, 12 Mar 2015 16:43:46 -0700

Upland Habitat and Wildlife Friendly Agriculture - A botanical survey was conducted along a 1 .6 mi. (8,350 ft) corridor of Selby Creek on June 6, 2006. The project area is located between Dutch Henry Canyon and the Napa River in north Napa Valley. The purpose of the survey was to map special status plant species, assess vegetation conditions, inventory all vascular plant species, and identify noxious weed problems. Landscape architect, Ann Baker, provided orientation to the project area and project goals prior to the initiation of the survey. The project area was searched by walking both banks and intermittently transecting the creek bed. No special status plant species were observed within the project area.

Selby Creek - Silverado Trail Culvert Fish Passage Assessment

Thu, 12 Mar 2015 16:37:06 -0700

Upland Habitat and Wildlife Friendly Agriculture - Selby Creek is formed by the junction of Dutch Henry Creek and Biter Creek, which join at the Silverado Trail (Figure 1). The Dutch Henry and Biter Creek watersheds cover an area of 5.19 square miles of primarily steep terrain dominated by oak woodland and chaparral with extensive rock outcroppings. The upper watershed that drains to the Silverado Trail culvert is largely undeveloped, with approximately 2.8% of its land area covered with vineyards and the remainder as open space and rural residential land. This report addresses fish passage conditions for steelhead (Oncorhynchus mykiss) at two potential impediments in Selby Creek and Dutch Henry Creek (Figure 2). The Silverado Trail crossing consists of a four-barrel concrete box culvert with a two-lane highway on top. Immediately upstream of this site is another culvert on Dutch Henry Road, a single lane road that crosses Dutch Henry Creek. The Dutch Henry crossing consists of a primary single-bore round steel culvert in the low flow channel and a secondary corrugated steel pipe arch at a slightly higher elevation. Both sites have been identified as potential fish migration barriers warranting thorough analysis of their severity. Steelhead are known to spawn and rear in Dutch Henry and Biter Creeks (Ecotrust & FONR 2002, NCRCD 2002). Juvenile steelhead densities appear to be relatively high in upper reaches that maintain perennial pools and high-quality habitat. Selby Creek is intermittent and goes completely dry every year by June. Due to this seasonal drying, Selby Creek acts primarily as a migration corridor for adult steelhead moving upstream to spawn in winter and juvenile steelhead migrating to the ocean (smolts) during spring. Partial migration barriers in this corridor could delay spawning by days or weeks and have negative effects on spawning success.

Wilcox Ranch 2008-2011 Ecological Monitoring Report

Thu, 12 Mar 2015 16:33:03 -0700

Upland Habitat and Wildlife Friendly Agriculture - This report summarizes the methods and results of the 4-year vernal pool monitoring conducted between 2008 and 2011, as well as recommendations for future monitoring and assessments for Wilcox Ranch (‘site’) in Solano County, CA (Figure 1). Monitoring surveys were conducted on East Wilcox Ranch, a 1,497-acre Preserve Area comprised of high quality vernal pool and grassland habitat that is owned and managed by the Solano Land Trust (SLT). Vernal pools on site range from large playa pools to small vernal pools and swales (Figure 2). The site provides documented habitat for multiple special-status species including vernal pool fairy shrimp (Branchinecta lynchi), Conservancy fairy shrimp (B. conservatio), vernal pool tadpole shrimp (Lepidurus packardi), California tiger salamander (Ambystoma californiense) (CTS) and the delta green ground beetle (Elaphrus viridis), as documented by Larry Serpa (Serpa 2002). The site also provides habitat for midvalley fairy shrimp (B. mesovallensis), a non-listed large branchiopod.

Monitoring of the threatened Delta Green Ground Beetle at the East Wilcox Ranch (Solano County, CA) in 2008

Thu, 12 Mar 2015 16:29:31 -0700

Upland Habitat and Wildlife Friendly Agriculture - This report describes the findings of the second year of monitoring for the Delta Green Ground Beetle (DGGB), a federally-listed threatened species that is known to occur at the East Wilcox Ranch. Arnold (2007) presented background information on the DGGB, an assessment of the playa pool habitat suitability at East Wilcox Ranch, and other information about the site. The 2008 monitoring focused on presence-absence surveys of the DGGB at the ranch.

Monitoring of the threatened Delta Green Ground Beetle at the East Wilcox Ranch (Solano County, CA) in 2009

Thu, 12 Mar 2015 16:29:16 -0700

Monitoring of the threatened Delta Green Ground Beetle at the East Wilcox Ranch (Solano County, CA) in 2010

Thu, 12 Mar 2015 16:28:58 -0700

Upland Habitat and Wildlife Friendly Agriculture - This report describes the findings of the fourth and final year (2010) of monitoring for the Delta Green Ground Beetle (Elaphrus viridus, Coleoptera: Carabidae), a federally-listed threatened species that is known to occur at the East Wilcox Ranch. One of the goals of the beetle (hereafter referred to by the acronym DGGB) monitoring was to develop a methodology to estimate population numbers of the beetle. Because adults seem to normally occur at low levels, their cryptic coloration, and shy behavior, many standard population estimation techniques cannot be used due to inadequate sample sizes to accurately estimate population numbers. Also, monitoring funds are limited so it is difficult to increase the sampling efforts to obtain the samples sizes necessary for accurate population estimates . For these reasons during the past four years a few different survey methods have been tested in the field to determine the most cost-effective approach to accurately estimate DGGB population numbers. Refinement of a suitable survey methodology relied on information collected throughout this initial four-year monitoring period. This report presents a method that can be used in future DGGB monitoring efforts to estimate the beetle's density and population numbers.

Flooded Islands Pre-Feasibility Study Report

Thu, 12 Mar 2015 16:27:40 -0700

Shallow Water and Marsh Habitat -

Tidal wetland restoration in San Francisco Bay: History and current issues

Thu, 12 Mar 2015 16:25:14 -0700

Shallow Water and Marsh Habitat - Early restoration efforts in San Francisco Bay focused primarily on establishing appropriate elevations for plant recruitment, based on plant distributions in natural marshes. Sites were graded and planted, and tidal connections were re-established with the expectation that restored wetlands would quickly resemble natural ecosystems. Over time, restoration efforts have evolved, with the realization that natural development of restoration sites is preferable, including a dense channel network and the accumulation of soils of appropriate texture. Bay restoration efforts also have grown substantially in size and scope. Whereas projects of 50 hectares were considered large in the 1980s, now many projects are 100’s of hectares. Larger projects are on the scale of 1000’s of hectares, with the largest approximately 6000 hectares (the South Bay Salt Pond Restoration Project). This massive increase in scale has brought enormous restoration opportunities, but it also has increased the complexity of restoration projects and highlighted the necessity of large-scale public involvement. Awareness of non-native plants at restoration sites is just one example of factors that have increased restoration complexity. Potential impacts of climate change also have moved to the forefront of restoration design, as sea-level rise and potential shifts in salinity are critical factors for long-term restoration planning.

Restoration trajectories and food web linkages in San Francisco Bay's estuarine marshes: a manipulative translocation experiment

Thu, 12 Mar 2015 16:25:04 -0700

Shallow Water and Marsh Habitat - We measured d13C, d15N and d34S signatures of natural and translocated mussels Ischadium demissum to identify food web source differences among estuarine marshes displaying various stages of restorative development. We hypothesized that mussels inhabiting younger marshes would be more dependent on allochthonous organic matter sources, while those inhabiting mature marshes would depend on autochthonous sources. Mussels collected from an undisturbed (reference) marsh located within the Napa River estuarine complex in San Francisco Bay were translocated to a series of restoring marsh sites located within the same river system. The isotopic composition of naturally growing mussels was compared with translocated mussels, which were incubated in restoring sites for 5 and 7 mo. Measurements of d13C, d15N, and d34S indicated differences in food web sources supporting I. demissum among the 4 marsh sites. A strong cage effect was detected during the initial 5 mo collection interval, indicating that translocated mussels had yet to equilibrate with their new environments. Multiple source mixing model analysis indicated that C3 emergent vascular plants and brackish phytoplankton contributed most of the organic matter consumed by I. demissum over both time periods, but that mussels collected from the downstream sites exhibited higher dependence upon vascular plant detritus. Bay produced phytoplankton contributed very little to I. demissum diets, suggesting that the pelagic waters of San Francisco Bay have less influence on marsh food web dynamics than previously anticipated. The results of this experiment show that food web pathways are strongest at intermediate scales; they can be relatively short and unique to specific marshes along the estuarine gradient, but similarities in mussel diets among marshes in close proximity to one another suggests inter-marsh exchange of organic matter. It is, therefore, likely that food webs in young restoration sites depend upon organic matter subsidies from neighboring marshes, rather than from San Francisco Bay.

Isotopic determination of food web origins in restoring and ancient estuarine wetlands of the San Francisco Bay and Delta

Thu, 12 Mar 2015 16:24:52 -0700

Shallow Water and Marsh Habitat - We compared the extent to which ancient and restoring wetlands in three estuary regions of San Francisco Bay support estuarine ecosystems through food web contributions. In comparison to mature marshes, we hypothesized that food webs of increasingly younger restoration sites would display increased dependency upon allochthonous subsidies due to nominal internal production. Using multiple stable isotopes (d13C, d15N, d34S) in a mixing model, we traced links among primary producers and estuarine consumers. Results indicate that food webs of estuarine marshes are heavily dependent upon autochthonous marsh materials (76±17%), even within the youngest restoration marshes (11 years). Nearly all sampled organisms relied upon autochthonous marsh materials, with the exception of Neomysis kadiakensis, a mysid shrimp, which derived the majority of its support from freshwaterproduced phytoplankton. Marsh-derived organic matter (OM) support was consistent both temporally throughout the year and spatially along the three estuary regions, but evidence suggests that the specific type of OM supporting estuarine consumers depends on position along the estuarine gradient and on seasonal shifts in freshwater flow. These results indicate that wetland restoration rapidly provides important contributions to marsh consumers and potentially bolsters food web linkages in shallow-water ecosystems

Landscape influence on the quality of heron and egret colony sites

Thu, 12 Mar 2015 16:24:44 -0700

Shallow Water and Marsh Habitat - We evaluated landscape associations related to heron and egret colony site selection and the productivity of successful great blue heron (Ardea herodias) and great egret (Ardea alba) nests. The study was based on annual observations (1991–2005) at 45 colony sites known to be active within 10 km of historic tidal marshes of northern San Francisco Bay. The analyses focused on a priori models analyzed within 1, 3, 5, 7, and 10 km of colony sites, using the areal extents of several NOAA land cover types (Landsat images, 2000–2002), number of wetland patches, and total wetland edge as predictor variables. A comparison of landscape characteristics surrounding colony sites with those surrounding randomly selected, unoccupied sites revealed the primary importance of estuarine emergent wetland and open water within 1 km of colony sites. Increased productivity in successful great blue heron nests was associated with more estuarine emergent wetland, open water, and low-intensity development, and less grassland, but was not differentially related to the extent of habitat available within any particular distance from colony sites. The productivity in successful great egret nests was associated with variation in habitat extent at larger spatial scales, especially within 10 km of heronies, with nests producing more young at sites surrounded by more estuarine emergent wetland and low-intensity development, less open water and palustrine emergent wetland, and more patches of wetland habitat. To estimate landscape foraging patterns, we used aircraft to track the flights of great egrets departing from heronries and used the observed flight distances, colony sizes, and the regional distribution of wetland habitat to model regional foraging densities. Results suggested that increasing the extent of wetland feeding areas for herons and egrets might improve reproductive performance in colony sites up to 10 km away, increase foraging by herons and egrets in created or restored wetlands within 3–10 km of sites, and enhance nest abundance at colony sites within 1 km of restoration sites. Regional maps based on the distribution of colony-sites and predictions of landscape influences on colony site selection, nest productivity, and foraging dispersion, suggested areas potentially suitable for colonization.

Vegetation colonization in a restoring tidal marsh: a remote sensing approach

Thu, 12 Mar 2015 16:21:57 -0700

Shallow Water and Marsh Habitat - Although remote sensing offers the ability to monitor wetland restoration, few have tested automated methods for quantifying vegetation change. We implemented a semiautomated technique using color infrared aerial photography and a common vegetation index, Normalized Difference Vegetation Index (NDVI), to document vegetation colonization in a restoring salt marsh. Change in vegetation over a period of 10 years was analyzed using a postclassification comparison technique where each image year was classified individually into vegetated and nonvegetated areas using NDVI thresholds and then differenced between years to identify areas of vegetation change. Vegetated and nonvegetated areas were identified using this technique, as were areas and time periods of vegetation change. By comparing classified NDVI imagery, we calculated that 90% of our study site was vegetated 10 years after restoration. This study demostrated that high resolution remotely sensed data can be analyzed with common geospatial software to mointor change in a rapidly vegetating wetland and that long time frames with yearly image acquisition are needed to quantify plant colonization rates. This method was effective at detecting change in vegetaion over time in a variable tidal marsh environment using imagery that had inconsistent specifications and quality across years. Inconsistencies included interannual climate variation, phenology, and presence of algae, as well as differences in pixel size and image brightness. Our findings indicate that remote sensing is useful for postrestoration monitoring of tidal marsh ecosystems.

Primary productivity rates and nutrient availability in natural and restoring wetlands of the northern San Francisco Estuary

Thu, 12 Mar 2015 16:21:46 -0700

Shallow Water and Marsh Habitat - High rates of primary productivity within estuaries and wetlands largely result from the diversity 3 of autotrophs present. Not only are there are many sources of organic carbon in estuarine 4 wetlands, but the rates of production for each type of producer differs due to a number of 5 interacting factors, including water and sediment chemical characteristics. This study was 6 designed to obtain some of the first direct measures of water nutrient concentrations and rates of 7 productivity for multiple groups of autotrophs in both natural and restoring wetlands of the 8 northern San Francisco Estuary (SFE). Water nutrient concentrations and carbon fixation rates of 9 phytoplankton, benthic microalgae, submerged aquatic vegetation (SAV) and low marsh 10 emergent vegetation were measured in two natural reference and 4 restoring estuarine wetlands 11 over two growing seasons (2004 and 2005). Water nutrient concentrations were generally highest 12 in spring and decreased as the growing season progressed. Nutrient availability in the water was 13 an important predictor of rates of production of phytoplankton and benthic diatoms. Sediment 14 nitrogen and organic content, and interstitial nutrient concentrations influenced productivity of 15 the low marsh vegetation. Low marsh vegetation had the overall highest rates of production, 16 followed by SAV, benthic microalgae and phytoplankton. Productivity rates of low marsh 17 vegetation were also higher in natural compared to restoring marshes early in the growing 18 season, but in general rates of primary production appeared to be a function of the physical 19 conditions and location of each wetland rather than restoration stage

Mapping changes to vegetation pattern in a restoring wetland: finding pattern metrics that are consisten across spatial scale and time

Thu, 12 Mar 2015 16:21:35 -0700

Shallow Water and Marsh Habitat - Tidal salt marshes in the San Francisco Estuary region display heterogeneous vegetation patterns that influence wetland function and provide adequate habitat for native or endangered wildlife. In addition to analyzing the extent of vegetation, monitoring the dynamics of vegetation pattern within restoring wetlands can offer valuable information about the restoration process. Pattern metrics, derived from classified remotely sensed imagery, have been used to measure composition and configuration of patches and landscapes, but they can be unpredictable across scales, and inconsistent across time. We sought to identify pattern metrics that are consistent across spatial scale and time – and thus robust measures of vegetation and habitat configuration – for a restored tidal marsh in the San Francisco Bay, CA, USA. We used high-resolution (20 cm) remotely sensed color infrared imagery to map vegetation pattern over 2 years, and performed a multi-scale analysis of derived vegetation pattern metrics. We looked at the influence on metrics of changes in grain size through resampling and changes in minimum mapping unit (MMU) through smoothing. We examined composition, complexity, connectivity and heterogeneity metrics, focusing on perennial pickleweed (Sarcocornia pacifica), a dominant marsh plant. At our site, pickleweed patches grew larger, more irregularly shaped, and closely spaced over time, while the overall landscape became more diverse. Of the two scale factors examined, grain size was more consistent than MMU in terms of identifying relative change in composition and configuration of wetland marsh vegetation over time. Most metrics exhibited unstable behavior with larger MMUs. With small MMUs, most metrics were consistent across grain sizes, from fine (e.g. 0.16 m2) to relatively large (e.g. 16 m2) pixel sizes. Scale relationships were more variable at the landcover class level than at the landscape level (across all classes). This information may be useful to applied restoration practitioners, and adds to our general understanding of vegetation change in a restoring marsh

Genetic Assay Technical Paper

Thu, 12 Mar 2015 16:21:17 -0700

Non-Native Invasive Species - The project, “Linking habitat and spatial variability to native fish predation” aims to enumerate predation rates on species of concern in the delta. Genentic assays have been designed to detect DNA sequences specific to each target species. The assays utilize traditional PCR with the added specificity of a hydrolysis probe, a third component that virtually eliminates false positives associated with traditional PCR. The custom primer-probe sets are call TaqMan assays by the company that creates them, and are the industry standard of specificity and sensitivity for genetic detection. We have successfully developed TaqMan assays for the identification of Delta Smelt and Mississippi silverside DNA for a previous study with high accuracy and sensitivity (Baerwald et al. 2012). Assay design was accomplished in a similar manner to the assays previously deisgned in the Genomic Variation Lab with a couple exceptions, detailed below. The first publication under this grant will be a "primer note", which will include further technical details and assay specifications for these assays.

Captive Feeding Trial Report

Thu, 12 Mar 2015 16:20:51 -0700

Non-Native Invasive Species - The primary objective of ERP grant E1183009 is to quantify incidence of predation by Striped Bass (Morone saxatilis) on species of interest across the North Sacramento-San Joaquin Delta. To put thses data to use, it is necessary to know how long prey DNA is detectable in the gut of Striped Bass, specifically with respect to using the genetic assays we disgned for the grant. We fed Chinook Salmon (Oncorhynchus tshawytscha) smolt to striped bass in a controlled environment; at regular intervals we sampled the guts of ten fish to verify the presence or absence of prey DNA by the signal produced by the assay. We found the salmon were detectable in 100% of the bass for the first 36 hours, prey were detected in 90% of the bass after 48 hours, in 73% of the bass after 60 hours, in 20% after 72 hours, in 10% after 84 hours, 0% after 96 hours and 108 hours, 22% after 120 hours and 0% after 168 hours. (Two possible reasons for the positive detection at the 120 hour stage - metabolic rate was lower in this fish tank than that of the other tanks; and/or these fish were the only ones infected with a waterbourne fungus-Saprolegnia - this fungus can cause significantly reduced growth rates.)

Quantifying incidence of predation on salmonids and other species of interest using high-throughput qPCR found in gut contents

Thu, 12 Mar 2015 16:20:42 -0700

Non-Native Invasive Species - Quantify incidence of predation in the North Delta region. Find spatial or temporal trends in undesirable predation. Find correlations between predation and habitat condition (water temperature, salinity, turbidity, pH, density of submerged aquatic vegetation and others). Target species: predators sampled- striped bass, largemouth bass, smallmouth bass, pikeminnow. Prey detected - Chinook salmon, steelhead, green sturgeon, white sturgeon, Mississippi silverside, Wakasagi smelt, Delta smelt, Longfin smelt, Splittail, Threadfin Shad.

Persistence of delta smelt DNA in the gut of Mississippi silversides and other preliminary experiments for detecting prey in non-native fish stomachs using real-time PCR.

Thu, 12 Mar 2015 16:20:32 -0700

Non-Native Invasive Species - The Bay-Delta Conservation Plan has identified predation by no-native piscivores as a major stressor threatened native fish in the delta. Our primary objective is to investigate the frequency of predation by non-native bass and the native Sacramento pikeminnow on larval and sub-adult threatened and endagered species using quantitative PCR. The data on incidnece of predation will be used to identify locations non-native piscivores prey heavily on at-risk species. With this data habitat restoration efforts can focus on areas that minimize danger to at-risk species. Genetic gut content analysis offers two notable advantages over visual gut content studies. The sensitivity of the entod allows us to identify prey species for a longer time post-ingestion and species composed of soft tissue, namely larval fish, can be indentified. Our current objective is to characterize the genetic assay and optimize the methods to be used in the primary study. We conducted a series of preliminary experiments in which we fed delta smelt larvae to Mississippi silverside and striped bass in a controlled environment. Three questions were addressed during these experiments: How long is DNA of prey fish detectable in th stomach of a predator? Can we detect multiple prey of a given species in a stomach using microsatellite DNA? Lastly, what method of preservatio keeps the most usable DNA intact during field sampling? DNA barcoding and qPCR will be introduced and the results from our preliminary experiments will be discussed.

Surveys of selected marshlands in the San Francisco Estuary California Clapper Rail (Rallus longirostris obsoletus): Invasive Spartina Project, 2007.

Thu, 12 Mar 2015 16:20:13 -0700

Non-Native Invasive Species - Avocet Research Associates (ARA) conducted surveys of 24 marshes or marsh parcels in the San Francisco Bay estuary to determine the presence or absence of the federally endangered California Clapper Rail during the 2007 nesting season (January 15 - April 15) These field studies were conducted under contract with Olofson Environmental, Inc. as a part of the larger Invasive Spartina Project (ISP). Additionally, ARA in cooperation with Point Reyes Bird Observatory Conservation Science (PRBO), the U.S. Fish and Wildlife Service (USFWS), and the California Department of Fish and Game (CDFG) has been conducting protocol-level surveys of clapper rails annually since 2004 in an ongoing effort to monitor the size and distribution of this endangered population. Although the final results of those surveys are not currently available, the results of this study will augment and amplify the findings of that baywide effort.

Laboratory Protocols for Genotyping Spartina

Thu, 12 Mar 2015 16:18:07 -0700

Non-Native Invasive Species - The protocols described are those used by the U.C. Davis Spartina lab in the laboratory of Professor Donald R. Strong for the purpose of genotyping Spartina. The methods were developed by a number of researchers in the laboratory, primarily Drs. Debra Ayres, Christina Sloop and Curtis Daehler. Most of the work is targeted at differentiating native S. foliosa from exotic S. alterniflora and S. alterniflora x foliosa hybrids. There also are RAPD genetic markers that are useful for identifying two other species and hybrids that occur in San Francisco Bay. S. densiflora is originally from South America and produces sterile hybrids with S. foliosa. S. anglica is an allopolyploid hybrid of S. alterniflora x maritima that arose in England and was introduced to San Francisco Bay.

San Francisco Estuary Invasive Spartina Project 2008-2009 Monitoring Report

Thu, 12 Mar 2015 16:16:07 -0700

Non-Native Invasive Species - As part of its regional program, the ISP conducts annual baywide and outer coast monitoring to track and map the extent and rate of spread of nonnative Spartina, and to monitor the efficacy of the ISP's Spartina Control Program's treatment efforts. This report presents the results of regionwide monitoring conducted by the ISP in 2008 - 2009.

San Francisco Estuary Invasive Spartina Project Monitoring Program Quality Assurance Document

Thu, 12 Mar 2015 16:15:29 -0700

Non-Native Invasive Species - The primary goal of the Monitoring Program is to provide the Control Program timely, high quality data regarding the location and extent of non-native Spartina, so that they Control Program staff may plan and rapidly implement cost-effective weed control measures and determine when site-specific and regional control objectives have been met. In addition, the Monitoring Program provides accurate data on the status of endangered California clapper rails at the Spartina treatment sites, to allow Spartina control to be implemented while avoiding significant long-term adverse effects and minimizing short term effects on rails, in compliance with State and Federal regulatory requirements.

Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2001

Thu, 12 Mar 2015 16:12:51 -0700

Hydrodynamics, Sediment Transport, and Flow Regimes - Suspended-sediment concentration data were collected in San Francisco Bay during water year 2001 (October 1, 2000â€“September 30, 2001). Optical backscatterance sensors and water samples were used to monitor suspended sediment at two sites in Suisun Bay, three sites in San Pablo Bay, two sites in Central San Francisco Bay, and three sites in South San Francisco Bay. Sensors were positioned at two depths at most sites. Water samples were collected periodically and were analyzed for concentrations of suspended sediment. The results of the analyses were used to calibrate the electrical output of the optical backscatterance sensors so that a record of suspended-sediment concentrations could be derived. This report presents the data-collection methods used and summarizes the suspended-sediment concentration data collected from October 2000 through September 2001. Calibration curves and plots of edited data for each sensor also are presented.

Sacramento River Ecological Flows Study: Off-Channel Habitat Study Results

Thu, 12 Mar 2015 16:12:41 -0700

Hydrodynamics, Sediment Transport, and Flow Regimes -

Sacramento River Ecological Flows Study: Meander Migration Modeling Final Report

Thu, 12 Mar 2015 16:12:31 -0700

Hydrodynamics, Sediment Transport, and Flow Regimes -

Sacramento River Ecological Flows Study: Final Report

Thu, 12 Mar 2015 16:12:20 -0700

Hydrodynamics, Sediment Transport, and Flow Regimes -

Sacramento River Ecological Flows Study: State of the System Report (Public Review Draft)

Thu, 12 Mar 2015 16:12:08 -0700

Hydrodynamics, Sediment Transport, and Flow Regimes -

Linking Biological Responses to River Processes: Implications for Conservation and Management of the Sacramento River – A Focal Species Approach: Final Report

Thu, 12 Mar 2015 16:11:58 -0700

Hydrodynamics, Sediment Transport, and Flow Regimes -

Sacramento River Ecological Flows Study: Gravel Study Final Report

Thu, 12 Mar 2015 16:11:45 -0700

Hydrodynamics, Sediment Transport, and Flow Regimes -

Physical Modeling Experiments to Guide River Restoration Projects: Restoration Manuals

Thu, 12 Mar 2015 16:11:32 -0700

Hydrodynamics, Sediment Transport, and Flow Regimes -

Stockton Deep Water Ship Channel tidal hydraulics and downstream tidal exchange.

Thu, 12 Mar 2015 16:11:10 -0700

Ecosystem Water and Sediment Quality -

Zooplankton abundance and diversity in the lower San Joaquin River above the Stocton Deep Water Ship Channel.

Thu, 12 Mar 2015 16:10:10 -0700

Ecosystem Water and Sediment Quality - As part of a larger study investigating algal dynamics in the San Joaquin River, an analysis of zooplankton was coordinated with a dye monitoring study during the summers of 2005 and 2006. Zooplankton were collected from the dye plume along a tidal freshwater reach of the river spanning 30 miles above the Stockton Deep Water Ship Channel (DWSC). Rotifera comprised the most diverse group with 42 species. Rotifer diversity over the study reach varied greatly with several species exhibiting site preferences. Copepoda followed rotifers in diversity however their biomass was generally higher, especially downstream. Approximately four species of copepods occur; all three major orders are represented. The introduced Pseudodiaptomus forbesi was the dominant copepod. Nauplii occur throughout the reach, their numbers increasing downstream. Cladocera are represented by six species, but abundance is low and distribution inconsistent. Peaks in zooplankton biomass occurred sporadically over the study period: in 2005 peaks occurred about 15 miles above the DWSC; in 2006 they occur in the five mile reach above the DWSC. In 2006, peaks are strongly correlated with reversal in flow during flood tides. In August and September 2005 and July and August 2006 zooplankton biomass peaked during night hours. The DWSC maintained a considerably higher biomass than other sites in half of the sample periods. Multivariate analysis suggests a strong correlation between total zooplankton biomass and water age. These data suggest that algal dynamics are controlled, in part, by zooplankton grazing.

Evaluation of aeration technology for the Stockton Deep Water Ship Channel

Thu, 12 Mar 2015 16:08:30 -0700

Ecosystem Water and Sediment Quality -

Task 6: Modeling Study, Forecasting Procedure Report

Thu, 12 Mar 2015 16:08:10 -0700

Ecosystem Water and Sediment Quality -

Sources and Transport of Nutrients, Organic Carbon, and Chlorophyll-a in the San Joaquin River Upstream of Vernalis, California, during Summer and Fall, 2000 and 2001

Thu, 12 Mar 2015 16:05:43 -0700

Ecosystem Water and Sediment Quality - Oxidizable materials from the San Joaquin River upstream of Vernalis can contribute to low dissolved oxygen episodes in the Stockton Deep Water Ship Channel that can inhibit salmon migration in the fall. The U.S. Geological Survey collected and analyzed samples at four San Joaquin River sites in July through October 2000 and June through November 2001, and at eight tributary sites in 2001. The data from these sites were supplemented with data from samples collected and analyzed by the University of California at Davis at three San Joaquin River sites and eight tributary sites as part of a separate study. Streamflows in the San Joaquin River were slightly above the long-term average in 2000 and slightly below average in 2001. Nitrate loads at Vernalis in 2000 were above the long-term average, whereas loads in 2001 were close to average. Total nitrogen loads in 2000 were slightly above average, whereas loads in 2001 were slightly below average. Total phosphorus loads in 2000 and 2001 were well below average. These nutrient loads correspond with the flow-adjusted concentration trends-nitrate concentrations significantly increased since 1972 (p < 0.01), whereas total nitrogen and total phosphorus concentrations did not (p > 0.05). Loading rates of nutrients and dissolved organic carbon increased in the San Joaquin River in the fall with the release of wetland drainage into Mud Slough and with increased reservoir releases on the Merced River. During August 2000 and September 2001, the chlorophyll-a loading rates and concentrations in the San Joaquin River declined and remained low during the rest of the sampling period. The most significant tributary sources of nutrients were the Tuolumne River, Harding Drain, and Mud Slough. The most significant tributary sources of dissolved organic carbon were Salt Slough, Mud Slough, and the Tuolumne and Stanislaus Rivers. Compared with nutrients and dissolved organic carbon, the tributaries were minor sources of chlorophyll-a, suggesting that most of the chlorophyll-a was produced in the San Joaquin River rather than its tributaries. On the basis of the carbon-to-nitrogen ratios and the ?13C of particulate organic matter in the San Joaquin River and tributaries, the particulate organic matter in the river was mostly phytoplankton. On the basis of the ?15N values of the particulate organic matter, and of total dissolved nitrogen and nitrate, the nitrate in the San Joaquin River probably was a significant nutrient source for the phytoplankton. The range of ?15N and ?18O values of nitrate in the San Joaquin River and tributaries suggest that animal waste or sewage was a significant source of nitrate in the river at the time the samples were collected.

Linking the San Joaquin River to the Stockton Deep Water Ship Channel Draft Final Report

Thu, 12 Mar 2015 16:05:18 -0700

Ecosystem Water and Sediment Quality - A three-year effort to characterize the presence, transport and fate of algae in the San Joaquin River (SJR) was performed during the summers of 2005 to 2007 as part of a larger study investigating low dissolved oxygen in the Stockton Deep Water Ship Channel (DWSC). Previous investigations show that algae dominate the oxygen demands entering the DWSC during summer months (Lehman et al. 2004). In the present study, the mechanisms controlling algal fate in the San Joaquin River were investigated by characterizing changes in chlorophyll and other water quality parameters and by determining the diversity and abundance of the zooplankton grazing community. Lagrangian monitoring was used to track a parcel of water over a 31 mile non-tidal to tidal reach upstream of the DWSC. A plug-flow reactor model was developed to describe and estimate the relative contribution of potential mechanisms responsible for the decline of algal populations upon entry into the tidal regime of the SJR and the 2 to 3 day travel time to the DWSC. The two dominant mechanisms for the decay of chlorophyll a below Mossdale appear to be zooplankton grazing and the reduction of available light associated with increased river depth. Settling during slack tide periods and dispersion associated with tidal flows may also contribute, but are much less important.

Bathymetric and geophysical surveys of Englebright Lake, Yuba-Nevada Counties, California

Thu, 12 Mar 2015 16:05:03 -0700

Ecosystem Water and Sediment Quality -

Transport, transformation, and effects of selenium and carbon in the Delta of the Sacramento-San Joaquin Rivers: implications for ecosystem restoration

Thu, 12 Mar 2015 16:04:36 -0700

Ecosystem Water and Sediment Quality -

Discriminating between west-side sources of nutrients and organic carbon contributing to algal growth and oxygen demand in the San Joaquin River

Thu, 12 Mar 2015 16:04:07 -0700

Ecosystem Water and Sediment Quality -

Real-Time Water Quality Management in the Grassland Water District

Thu, 12 Mar 2015 16:03:50 -0700

Ecosystem Water and Sediment Quality - The purpose of the research project was to advance the concept of real-time water quality management in the San Joaquin Basin by developing an application to drainage of seasonal wetlands in the Grassland Water District. Real-time water quality management is defined as the coordination of reservoir releases, return flows and river diversions to improve water quality conditions in the San Joaquin River and ensure compliance with State water quality objectives. Real-time water quality management is achieved through information exchange and cooperation between shakeholders who contribute or withdraw flow and salt load to or from the San Joaquin River. This project complements a larger scale project that was undertaken by members of the Water Quality Subcommittee of the San Joaquin River Management Program (SJRMP) and which produced foreca sts of flow, salt load and San Joaquin River assimilative capacity between 1999 and 2003. These forecasts can help those entities exporting salt load to the River to develop salt load targets as a mechanism for improving compliance with salinity objectives. The mass balance model developed by this project is the decision support tool that helps to establish these salt load targets. A second important outcome of this project was the development and application of a methodology for assessing potential impacts of real-time wetland salinity management. Drawdown schedules are typically tied to weather conditions and are optimized in traditional practices to maximize food sources for over-wintering wildfowl as well as providing a biological control (through germination temperature) of undesirable weeds that compete with the more proteinaceous moist soil plants such as swamp timothy, watergrass and smartweed. This methodology combines high resolution remote sensing, ground-truthing vegetation surveys using established survey protocols and soil salinity mapping using rapid, automated electromagnetic sensor technology. This survey methodology could be complemented with biological surveys of bird use and invertebrates to produce a robust long-term monitoring strategy for habitat health and sustainability.

San Joaquin River Up-Stream DO TMDL Project -- Task 12: DO Project Final Report

Thu, 12 Mar 2015 16:03:28 -0700

Ecosystem Water and Sediment Quality -

Mercury and methylmercury processes in north San Francisco Bay tidal wetland ecosystems

Thu, 12 Mar 2015 16:03:03 -0700

Ecosystem Water and Sediment Quality -

Task 6: Effluent Discharge Point Water Collection and Exposure Report

Thu, 12 Mar 2015 16:02:28 -0700

Ecosystem Water and Sediment Quality - Endocrine disrupting compounds (EDCs) originate from a variety of sources and are widespread in the aquatic environment, but are particularly concentrated downstream of treated wastewater outfalls. We proposed to investigate EDC effects on individual gene and protein expresssion and link these to changes in reproductive performance in the silverside (Menidia beryllina), exposed to contaminants commonly present in treate wastewater and surface waters downstream of outfalls.

Menidia beryllina baseline spawning trials

Thu, 12 Mar 2015 16:00:39 -0700

Ecosystem Water and Sediment Quality - Results indicate that the spwning functional response for Menidia beryllina is sigmoidal in shape and that per capita female egg output increases as the proportion male increases. In effect, females are compensating for masculinization. However, although per capita reproductive output increases as proportion male increases, total reporductive output decreases as the proportion males exceed 60%.

Interplay of environmental forcing and growth-selective mortality in the poor year-class success of delta smelt in 2005

Thu, 12 Mar 2015 15:53:22 -0700

At-Risk Species Assessment - Our primary objective was to estimate the ralative contribution of fedding success and chemical pooutants in determining patterns of growth and mortality of delta smelt throughout most of its, primarily annual, life cycle. This involved analyzing fish otoliths to estimate hatch-dates, growth rates, and likely spawning or rearing habitats (i.e. examining otolith micro-structure and micro-chemistry respectively), as well as histopathology of key fish organs to assess factors influencing health (i.e. qualitative and quantitative evalutions of liver and gonads). Distributional shifts among sampling perids suggest that natural selction favored individuals with a specific set of characters, including relatively slow larval development, but then faster than average juvenile growth in July: a period with extremely high water temperatures and salinity encroachment. Many of the fish survivng into the pre-adult stage had also hatched earlier in the spawning season. Overall, most individuals examined in this study showed signs of reduced glycofen content (energy reserves) in their liver and nearly one-half exhibited signs of single-cell necrosis (cell death). Taken together, these results suggest that selective mortality and poor body conditions were intensified by extreme environmental conditions, elevating mortality during late-summer and contributing to poor year-class success.

Monitoring Responses of the Delta Smelt Population to Multiple Restoration Actions in the San Fransico Estuary

Thu, 12 Mar 2015 15:51:10 -0700

At-Risk Species Assessment -

Lindsey Slough Freshwater Tidal Marsh Enhancement Project - Cultural Resources Asessment

Thu, 12 Mar 2015 15:48:35 -0700

Shallow Water and Marsh Habitat - This report details the results of a cultural resources inventory of the Lindsey Slough Freashwater Tidal Marsh Enhancement Project (Project), located in Solano County, California. The Solano Land Trust (SLT) is cooperation with the California Department of Fish and Game (CDFG) are developing a restoration plan for the 965-acre reserve to enhance aquatic, wetland, and riparian habitat at the Calhoun Cut Ecological Reserve (Reserve). Owned by CDFG, the Rwserve lies in the northwest edge of the Sacramento-San Joaquin Delta region, just west of the confluence of Lindsey Slough and Barker Slough. The U.S. Army Corp of Engineers jurisdictional determination identified 459 acres of wetlands on the Reserve, which has been defined as the project's Area of Potential Effects (APE). The project's direct effects (construction actions) and indirect effects (Tidal inundation and channel evolution) will be limited to approximately 197 acres within the project APE.

Delta Working Lands Final Report

Thu, 12 Mar 2015 15:41:41 -0700

Upland Habitat and Wildlife Friendly Agriculture - The Delta Working Landscapes Program (Program) is a group of projects which demonstrate how farmers can integrate habitat restoration into farming practices. The objectives of the Program are to improve the environmental quality of existing landscapes in the Delta; coordinate programs with local farmers; understand the social, economic, environmental and governmental policy hurdles and/or incentives to perform conservation practices; and communicate to farmers the advantages of implementing wildlife friendly agricultural practices. These projects total 312 acres of seasonal and permanent wetlands and 6.5 miles enhanced levees and waterways. Project areas established native plant life, have been repopulated by wildlife, and filter agricultural drainage which improves water quality and enhances levee stability. Multiple species of waterfowl are using the restoration habitat for brooding and feeding as well as staying later into the season. No easements, MOUs, fee purchases, or eminent domain were used. Challenges to Working Landscapes projects include prior long term use of pesticides and herbicides which have created a hostile environment for native plants and wildlife. Additionally, some cultural practices are not conducive to habitat creation such as practices which rely on herbicides instead of tillage. Furthermore, economic costs are affiliated with physical land alterations, and in some cases permit requirements are cumbersome. Despite these challenges, successful public/private partnerships are possible. Working Landscapes projects can be expanded through better communication between policy and regulatory agencies and publicizing successful projects.

Delta Working Landscapes -- Feasibility Report

Thu, 12 Mar 2015 15:41:10 -0700

Upland Habitat and Wildlife Friendly Agriculture - This report addresses the feasibility of the Delta Working Landscapes program and the continuation of completing similar restoration activities. The intent is to provide baseline information regarding the different restoration practices and restoration planting techniques in order to guide future grant or land owner based restoration activities. Although no two restoration projects are the same, understanding the restoration practices and restoration planting techniques for working landscape projects can inform decisions about the feasibility of success for a particular circumstance.

Delta Working Landscapes Technical Paper

Thu, 12 Mar 2015 15:40:57 -0700

Upland Habitat and Wildlife Friendly Agriculture - Delta Working Landscapes is a pilot program that includes a partnership of government (Delta Protection Commission and California Department of Fish and Wildlife), a nonprofit organization (Ducks Unlimited, Inc.), private local enterprose (formerly Hart Restoration, Inc., now Delta EcoFarm), and landowners to implement demonstration projects of farm habitat improvement and environmentally friendly agriculture practices to benefit fish and wildlife, reduce erosion and sediment runoff, and improve water quality. These pilot projects were intended to provide a basis for understanding potential constraints and opportunities for resource enhancement, such as economic, social, cultural and environmental factors; and further to serve as a catalytst for adoption by other farmers. This report focuses on various hedgerow and buffer planting projects.

Delta Working Landscapes -- Vegetative Buffer and Wetland Management Guide

Thu, 12 Mar 2015 12:16:25 -0700

Upland Habitat and Wildlife Friendly Agriculture - This guide has been prepared to provide an overview of management techniques for vegetative buffers and wetlands habitats that were established as part of the Delta Working Landscape Program and identify additional resources for landowners who are considering implementing Working Landscapes projects.This document is divided into two sections, each describing projects that require different plant species, establishment methods, and management protocols. The first section, vegetative buffers, presents a more intensive, small-scale approach often involving hand labor for planting, irrigation, and specialized methods of establishment. Native plants are used in this approach. The second approach involves the construction of larger-scale wetlands, an approach that includes site recontouring with heavy equipment, introduction of plants through transplanting of tule clumps or methods of seed application, establishment/water management techniques for precisely timed flooding and drawdowns, and mowing and herbicide application with large-sized equipment. Most of the plants favored by this approach are non-native species.

Delta Working Landscapes: Public and Private Partnerships for Habitat

Thu, 12 Mar 2015 12:10:09 -0700

Upland Habitat and Wildlife Friendly Agriculture - The objectives of the Program are to improve the environmental quality of existing landscapes in the Delta; coordinate programs with local farmers; understand the social, economic, environmental and governmental policy hurdles and/or incentives to perform conservation practices; and communicate to farmers the advantages of implementing wildlife friendly agricultural practices. Working Landscapes is a program with projects designed to encourage public/private partnerships to implement practices that address some of these threats while sustaining and enhancing agriculture. The goals of Working Landscapes are to: 1. Improve the environmental quality of Delta farmlands through a variety of demonstration projects; 2. Understand the interplay of social, political and economic factors that hinder implementing these type of projects; and 3. Facilitate information exchange to encourage expansion of incorporating habitat projects in commercial agricultural practices.

Emerging issues for the restoratio of tidal marsh ecosystems in the contect of predicted climate change

Thu, 12 Mar 2015 12:07:58 -0700

Shallow Water and Marsh Habitat - There is currently a large regional effort to restore tidal marsh ecosystems in the San Francisco Bay-Delta Estuary involving the commitment of hundreds of millions of dollars and broad landscape-scale habitat manipulations. Although climate change has been on the horizon for many years, recent developments suggest that it must be taken seriously as a factor to be considered in future planning for marsh restoration efforts. Tidal marshes are vulnerable to changes in salinity and inundation rates, both of which will be affected by climate change. Restoration sites may be particularly vulnerable given unpredictable sediment inputs and newly established vegetation. Predicted shifts in snowmelt and altered runoff will change estuarine salinity patterns and could have large-scale impacts on marsh dominance, especially for freshwater marshes. Even relatively small salinity changes could lead to shifts in dominant species, with freshwater marshes being replaced by brackish marshes and brackish marshes converted to salt marsh communities. This will cause a reduction in overall estuarine plant diversity and productivity, with possible reverberations for the estuarine food web. Based on monitoring data from San Francisco Bay marshes, we predict that salinity will have a more immediate impact on tidal marsh vegetation than sea-level rise. However, sea-level rise poses a potentially greater long-term threat, depending on its rate, because the effects of inundation and a more persistent salinity regime could cause widespread marsh loss. If ice sheets in Antarctica and Greenland begin melting at rapid rates, inundation impacts could be catastrophic for coastal marshes. Given the magnitude of these potential changes, we urge the restoration and conservation management community to integrate these contingencies into adaptive management process and to join with the broader community in forging more flexible governance institutions that can respond effectively to large-scale uncertainties and trajectories as they unfold.

Effects of Endocrine Disrupting Chemicals on Menidia beryllina, a Resident Fish in the Sacramento - San Joaquin Delta

Thu, 12 Mar 2015 12:06:24 -0700

Ecosystem Water and Sediment Quality - A diverse and growing number of endocrine disrupting chemicals (EDCs) are known to be present in the waters of the Sacramento-San Joaquin (SSJ) Delta. These EDCs can come from natural sources or from a range of anthropogenic sources including agricultural and urban run-off, as well as in treated wastewater effluent. We have developed Menidia beryllina, the Inland Silverside, as a model resident species for studying effects of EDCs on fish, and ultimately on fish populations, in the SSJ Delta and other impacted waterways in the United States. Currently, there is only a limited understanding of the impacts of exposure to combinations of EDCs, particularly when estrogenic and androgenic EDCs are mixed. As such this study focused on the biological of Menidia to natural SSJ Delta waters throughout the seasons. We have quantified the xpression of a suite of endocrine-related response genes and of choriogenin protein levels, using a Menidia-specific antibody to choriogenin, in wild populations around the Delta. Similar assays have also been performed on naÏve juvenile fish exposed to SSJ Delta water in one-week long flow-through exposures at two sites spread throughout the seasons. These latter experiments will enable direct comparison of the endocrine response in exposed fish to that in controls which have only experience EDC-free water. This study will provide time-integrated mechanistic data on the effects of EDCs on fish throughout the SSJ Delta, and should ultimately be able to inform the extent to which EDCs are responsible for the pelagic organism decline in the SSJ Delta.

Yolo Bypass Project Telemetry Task (4.3) 2012 Annual Report

Thu, 12 Mar 2015 11:58:29 -0700

At-Risk Species Assessment - With this dataset, we have estimated values for juvenile Chinook survival (first release), adult white sturgeon residence time, and transit time and migration route selection for the 12 adult Chinook salmon. These data are reported in the sections below. Also reported are planned analyses and future explorations before the telemetry portion of the project ends in February 2014.

Appendix A: Yolo Bypass Project Draft Final Telemetry Report 2012-2014

Thu, 12 Mar 2015 11:56:32 -0700

At-Risk Species Assessment - With this dataset, we have estimated values for juvenile Chinook survival and movement rates, adult white sturgeon residence time, and transit time and migration route selection for 64 of the 99 adult Chinook salmon. These data are reported in the sections below. Also reported are planned analyses and future explorations after the final detections for adult Chinook salmon migrating in fall 2014 are downloaded in spring of 2015. The yolo Bypass may serve as a sink for a large proportion (~25%) of the adult Chinook salmon that enter the Bypass during their spawning migration. White sturgeon are present in the Yolo Bypass throughout much of the year, and demonstrate the capability to exit the Bypass successfully under dry conditions. Survival in the Toe Drain from the I-5 Bridge to the Mouth of the Saramento River is relatively high for outmigrating late-fall Chinook smolts under dry conditions. There does not seem to be any obvious areas of the Yolo Bypass that represents high mortality for juvenile Chinook, but in-depth survival modeling will examine this further.

Diet and growth of non-native Mississippi silversides and yellowfin gobies in restored and natural wetlands in the San Francisco Estuary

Thu, 12 Mar 2015 11:53:17 -0700

Shallow Water and Marsh Habitat - We examined how wetland restoration status influenced habitat quality for fishes by comparing otolith-calculated growth rates and diets of 2 abundant non-native fish species, the locally transient planktivorous Mississippi silverside, Menidia audens, and the resident demersal-feeding yellowfin goby, Acanthogobius flavimanus, in 2 wetlands undergoing restoration (‘restoring’ wetlands) and 1 natural wetland (Napa River, San Francisco Estuary, California, USA; 38° 10’ N; 122° 18’ W). Native species with similar trophic requirements were too few in abundance to serve as study organisms. Differences in fish diet and growth based on restoration status were expected for the more resident goby species, but not for the transient silversides. Fish were collected in June 2004 and 2005 from a 10 yr old restoring marsh, a 50 yr old restoring marsh and a natural marsh, using a modified fyke net. Diet of silversides was primarily composed of copepods, cumaceans, and flying insects, while yellowfin goby diets were composed of annelids, cumaceans, and amphipods. Prey species biomass in the stomachs of yellowfin gobies was significantly different between marshes, but these differences were not dependent on restoration status. No significant differences in Mississippi silverside growth rates were detected, and yellowfin goby growth rates varied somewhat between marshes and years, but were not significantly different between restored versus reference sites. Based on these findings, we suggest that adequate prey abundance and prey species composition is available for these fish species in both our restored and natural study sites. It also appears that some restoring breached wetlands can quickly (within 10 yr) provide equivalent habitat to natural areas, at least for generalist, non-native fishes; however, consideration of underlying mechanisms of restoration will be important in designing wetlands that specifically favor native fish populations.

Delta Working Landscapes -- Cost Analysis Report

Thu, 12 Mar 2015 11:52:29 -0700

Upland Habitat and Wildlife Friendly Agriculture - This report discusses the costs associated with conservation practices of habitat friendly farming and wetland farming practices on agricultural lands for the Working Landscape projects and the potential for cost savings and other benefits.

Analyses of historical Yolo Bypass food web data

Thu, 12 Mar 2015 11:48:06 -0700

At-Risk Species Assessment - This study makes use of sampling data collected by the California Department of Water Resources as part of their food web studies conducted in the Yolo Bypass since 1998. The major components of the program include chlorophyll a, zooplankton, and drift sampling at the Toe Drain screw trap (Appendix B, Figure 1). Discrete water quality measurements were collected concurrently with the biological sampling (see above); secchi depth was recorded and electrical conductivity was measured using a YSI 556 MPS (Yellow Springs Instruments, Yellow Springs, OH, USA). Continuous water temperature data were also collected at the Ttoe Ddrain screw trap using fixed temperature recorders at hourly intervals (Onset Corporation). Stage measurements were obtained at fifteen minute intervals from gauges operated by the California Department of Water Resources below Lisbon Weir (Appendix B, Figure 1) (Station: LIS http://cdec.water.ca.gov/).

A cultural resources investigation of the Selby/Dutch Henry Creek stream bank stabilization project

Thu, 12 Mar 2015 11:47:39 -0700

Upland Habitat and Wildlife Friendly Agriculture - The project area is located within the ethnographic territory of the Wappo. The Wappo language belongs to the Yukian family of four small linguistic groups including Yuki, Coast Yuki, and Huchnom. The background research for this project included an examination of the archaeological site records, maps and project files a the the Northwest Information Center (NWIC) on July 17, 2006. An intensive archeological field reconnaissance of the project area was conducted on July 18, 2006. The archeological field investigation involved an intensive pedestrian survey of the cut bank for buried subsurface soils or deposits, and survey of the adjacent vineyard road which generally offered the best ground visibility. Additionally, adjacent flats/landings that could potentially be used for equipment and material storage was surveyed. The results of this archeological inventory resulted in the identification of one previously recoreded resource, one newly recorded prehistoric archeological site and four isolated finds.

Findings, Conclusions and Recommendations for Bioengineered Installations in Hydrogeomorphic Settings similar to Selby Creek

Tue, 10 Mar 2015 08:57:28 -0700

Upland Habitat and Wildlife Friendly Agriculture - Climate, topography, hydrology, watershed drainage area, and geomorphology define a stream's hydrogeomorphic setting. Bioengineered installations in similar hydrogeomorphic settings may benefit from these findings from the Selby Creek project. Projects operating within a similar geomorphic feature (alluvial fan) should expect high bed mobility, channel avulsion, and unstable streambanks. Recommendations: Identify and address salmon migration issues first; use independent watershed specific geomorphic interpretation; use wood to compliment rock based bioengineered treatments.

Lindsey Slough Enhancement pre-construction Methlymercury characterization study

Mon, 09 Mar 2015 14:43:13 -0700

Riparian Habitat - Freshwater wetlands, particularly those created by inundatino of vegetated terrestrial areas, have been deomonstrated in the literature to often be sites of enhanced methylmercury concentrations in water and biota. Because of this risk, the Central Valley Regional Water Quality Control Board has requested monitoring in order to evaluate the potential impact of the restoration project on methylmercury levels, in particular to: determine potential effects of Lindsey Slough Enhancement Project (Project) on methlymercury levels and related constituents in and around the project area; and, evaluate the potential methlymercury effects of the Project in terms of the proposed methylmercury TMDL for the Delta.

Results of Surveys for Giant Garter snakes (Thamnophis gigas) in the Lindsey and Barker Slough area of Solano County

Mon, 09 Mar 2015 14:43:12 -0700

Riparian Habitat - Giant garter snakes (Thamnophis gigas) (GGS) are endemic to wetlands of the Central Valley and are federally and state listed as threatened (U.S. Fish and Wildlife Service 1993) because of loss of ovver 95% of original wetlands in the Central Balley (Frayer et al. 1989) and fragmentation of remaining habitat. Because of their association with wetlands and waterways and their listed status, GGS are as species of interst for CALFED and were included in the grant proposal funded by CALFED with the Yolo County Resource Conservation District. One requirement of this proposal was to survey for GGS in Lindsey-Barker Slough/Calhoun Cut area of Solano County, hereinafter referred to as LBC. Little information existed before 2004 on GGS in Solano County beyond historic observations conducted on a haphazard basis. THe USGS previously conducted systematic surveys for GGS in Solano County in 2004 and 2005, but did not include the LBC area in these surveys (Wylie and Martin 2004, 2005). This report summarizes the results of the USGS surveys for GGS in Solano County during 2008 and again in 2010. Sampling was interrupted by a funding freeze in 2009.

Rare Plant Survey and Mapping of Calhoun Cut Ecological Reserve

Mon, 09 Mar 2015 14:43:11 -0700

Riparian Habitat - Rare plant surveys of the Calhoun Cut Ecological Reserve and the historic Lindsey Slough were conducted during the period of Sept. 18-30, 2007. The focus of the surveys was summer blooming special-status plants associated with the slough and marsh habitats. Surveys were conducted on foot and by boat. Surveys were not conducted in extremely dense vegetation as it tends not to be suitable for most of the species surveyed with the exception of Delta Tule Pea.

Juvenile Chinook Salmon Radio-Telemetry Studies in the Northern and Central Sacramento-San Joaquin Delta 2002-2003

Mon, 22 Dec 2014 15:25:20 -0800

X2 Relationships -

Chlorsulfuron soil residues in a seasonal in a Seasonal Floodplain

Mon, 22 Dec 2014 15:22:44 -0800

Non-Native Invasive Species -

San Francisco Estuary Invasive Spartina Project Monitoring Report for 2004 & 2005

Mon, 22 Dec 2014 15:20:47 -0800

Non-Native Invasive Species -

Compendium report of Red Bluff Diversion Dam rotary screw trap juvenile anadromous fish production indices for years 2002-2012

Mon, 22 Dec 2014 15:19:30 -0800

At-Risk Species Assessment -

Brood-year 2005 winter Chinook juvenile production indices with comparisons to juvenile production estimates derived from adult escapement.

Mon, 22 Dec 2014 15:19:00 -0800

Non-Native Invasive Species -

Food resources for zooplankton in the Sacramento-San Joaquin River Delta Final Report

Mon, 22 Dec 2014 15:18:53 -0800

Estuary Foodweb Productivity -

Butte and Big Chico Creeks spring-run Chinook salmon, Oncorhynchus Tshawytscha life history investigation

Mon, 22 Dec 2014 15:18:32 -0800

At-Risk Species Assessment -

Phloroglucinol root staining: testing the ability to age the roots of perennial pepperweed (Lepidium latifolium)

Mon, 22 Dec 2014 15:16:48 -0800

Non-Native Invasive Species -

Final Report: Consumnes River Preserve Perennial Pepperweed Control Project

Mon, 22 Dec 2014 15:16:47 -0800

Non-Native Invasive Species -

Survey and Eradication of Arundo donax and Tamarix parviflora Tehama County

Mon, 22 Dec 2014 15:15:22 -0800

Non-Native Invasive Species - The primary objective of this project was to identify and eradicate areas infested by Arundo donax and Tamarix on Red Bank Creek, Reed's Creek, and Deer Creek. The project provided a forum for information exchange and coordination with other groups in the region and provided outreach to the landowners affected by these plants. There was a strong focus on landowner education, specifically, why these non-natives are detrimental to the health of their streams and the methods used to remove them.

Biological assessment of green sturgeon in the Sacramento-San Joaquin Watershed (Phase 2) Final Report

Mon, 22 Dec 2014 15:15:07 -0800

At-Risk Species Assessment -

San Joaquin Basin Ecological Flow Analysis

Mon, 22 Dec 2014 15:14:55 -0800

Environmental Water Management -

Monitoring adult Chinook salmon, rainbow trout, and steelhead in Battle Creek, Calfiornia, from March through October 2001

Mon, 22 Dec 2014 15:13:39 -0800

At-Risk Species Assessment -

Delta smelt culture and Research Program Final Report: 2003-2005

Mon, 22 Dec 2014 15:13:22 -0800

At-Risk Species Assessment -

Manual for the Culture of Delta Smelt (Hypomesus transpacificus).

Mon, 22 Dec 2014 15:13:20 -0800

At-Risk Species Assessment -