San Francisco Estuary and Watershed Science

CalJep is a spatially enabled database that reconciles or cross-walks the two prominent electronic plant distribution lists for California: CalFlora and Jepson. We intersected the distribution information from the two data sources to create a refined spatial distribution repository that can be used to examine patterns of plant diversity, distribution ranges of individual plant species or infrataxa, or vegetation associations. These data will allow scientists and resource managers to examine potential range maps for non-native plants, create range maps for plant species of restoration interest, and corroborate lines of evidence for determining appropriate management and conservation activities. We present here a detailed description of the methods used to create the CalJep geodatabase, data rendered from its creation, and a discussion of its applicability to a wide range of biogeographical and ecological questions, including restoration planning and adaptive management for the Bay-Delta ecosystem. CalJep records 7,887 plant species, subspecies, and varieties mapped onto 228 ecological subunits with corresponding distributional information for vascular plant species at varying levels of confidence. Information derived from this geodatabase is inherently as accurate as the digital floras used to create it; hence, its utility is best realized when implemented at the regional or statewide scale. CalJep provides a previously unavailable service to vegetation science in California and to resource managers operating within the Bay-Delta ecosystem.

The dynamics of IHNV infection and disease were followed in a juvenile Chinook salmon population both during hatchery rearing and for two weeks post-release. Cumulative weekly mortality increased from 0.03%–3.5% as the prevalence of viral infection increased from 2%–22% over the same four-week period. The majority of the infected salmon was asymptomatic. Salmon demonstrating clinical signs of infection shed 1000 pfu mL^-1 of virus into the water during a 1 min observation period and had a mean concentration of 10⁶ pfu mL^-1 in their mucus. The high virus concentration detected in mucus suggests that it could act as an avenue of transmission in high density situations where dominance behavior results in nipping. Infected smolts that had migrated 295 km down river were collected at least two weeks after their release. The majority of the virus positive smolts was asymptomatic. A series of transmission experiments was conducted using oral application of the virus to simulate nipping, brief low dose waterborne challenges, and cohabitation with different ratios of infected to naïve fish. These studies showed that asymptomatic infections will occur when a salmon is exposed for as little as 1 min to >10² pfu mL^-1, yet progression to clinical disease is infrequent unless the challenge dose is >10⁴ pfu mL^-1. Asymptomatic infections were detected up to 39 d post-challenge. No virus was detected by tissue culture in natural Chinook juveniles cohabitated with experimentally IHNV-infected hatchery Chinook at ratios of 1:1, 1:10, and 1:20 for either 5 min or 24 h. Horizontal transmission of the Sacramento River strain of IHNV from infected juvenile hatchery fish to wild cohorts would appear to be a low ecological risk. The study results demonstrate key differences between IHNV infections as present in a hatchery and the natural environment. These differences should be considered during risk assessments of the impact of IHNV infections on wild salmon and trout populations.

Effective conservation and recovery planning for Central Valley steelhead requires an understanding of historical population structure. We describe the historical structure of the Central Valley steelhead evolutionarily significant unit using a multi-phase modeling approach. In the first phase, we identify stream reaches possibly suitable for steelhead spawning and rearing using a habitat model based on environmental envelopes (stream discharge, gradient, and temperature) that takes a digital elevation model and climate data as inputs. We identified 151 patches of potentially suitable habitat with more than 10 km of stream habitat, with a total of 25,500 km of suitable habitat. We then measured the distances among habitat patches, and clustered together patches within 35 km of each other into 81 distinct habitat patches. Groups of fish using these 81 patches are hypothesized to be (or to have been) independent populations for recovery planning purposes. Consideration of climate and elevation differences among the 81 habitat areas suggests that there are at least four major subdivisions within the Central Valley steelhead ESU that correspond to geographic regions defined by the Sacramento River basin, Suisun Bay area tributaries, San Joaquin tributaries draining the Sierra Nevada, and lower-elevation streams draining to the Buena Vista and Tulare basins, upstream of the San Joaquin River. Of these, it appears that the Sacramento River basin was the main source of steelhead production. Presently, impassable dams block access to 80% of historically available habitat, and block access to all historical spawning habitat for about 38% of the historical populations of steelhead.

A two-dimensional, depth-averaged kinetic model of copper cycling was developed for the San Francisco Bay estuary. Adsorption and desorption reaction rate constants were determined from experimental sorption experiments. To calibrate the model, processes related to aqueous speciation were included. The model was used to predict spatial and seasonal trends in the adsorption and desorption of copper. Model predictions show that copper is continually being re-partitioned between sediment and water. Re-partitioning is prevalent near tributary and anthropogenic sources. It also occurs between segments of the bay, in response to differences in salinity and the availability of organic ligands dissolved in the water. In areas of restricted circulation such as the South Bay, copper adsorbed onto settling particles during wet season storm events acts as a source to the water column during the dry season. The relative contribution of resuspended benthic sediment to dissolved copper concentrations is highly variable in the bay. In the North Bay, dissolved copper is principally introduced from the San Joaquin-Sacramento Delta. In the South and lower South bays, desorption from sediment during the dry season may contribute as much as 20% of the total mass input of dissolved copper. Improvement of water quality can be achieved by reducing loads; however, changes are predicted to take years.