A molecular system was developed and tested to efficiently analyze algal communities in river water samples. Polymerase Chain Reaction (PCR) primers were designed to amplify the 18S rRNA gene of certain taxonomic groups of freshwater algae; there was limited success in specific amplification. Additionally, a primer pair utilizing both the 16S plastid gene and the 16S rRNA gene was tested with success, amplifying both prokaryotic and eukaryotic algae while excluding other taxonomically similar organisms. The terminal restriction fragment length polymorphism (TRFLP) fingerprinting method, which has been used in previous studies to examine prokaryotic community structure, was modified with the successful algae primers to selectively fingerprint all algal groups in two San Joaquin River water samples. Triplicates of two TRFLP profiles have been generated and terminal restriction fragments (TRFs) have been assigned to specific algal species.

Several species of the diatom genus Thalassiosira Cleve, were observed in freshwater phytoplankton samples collected from a fifty-two kilometer reach of the San Joaquin River in the vicinity of Stockton, California, USA. The study was conducted between the South Airport Way bridge near Vernalis and the Stockton Deep Water Ship Channel during fall and summer of both 2005 and 2006. The entire reach is freshwater habitat with the lower twenty-eight km strongly influenced by tidal flow reversals driven by the San Francisco Estuary. Ninety four whole water samples were collected from surface waters during the months of July, August, September and October in 2005 and the months of July and August in 2006. Six species of Thalassiosira were identified using scanning electron and light microscopy: T. weissjlogii (Grunow), T. gessneri Hustedt, T. lacustris (Grunow), T. visurgis (Grunow), T. decipiens (Grunow), and T. incerta (Makarova). Of the species observed, only T. weissjlogii has been previously reported in the freshwater portion of the San Joaquin River. The other five species have been previously reported from sites in the San Joaquin- San Francisco Estuary characterized as brackish, suggesting they are distributed in waters of various salinities ranging from freshwater to brackish within the river and estuary.

This thesis is a history of the navigation on the San Joaquin River from 1848 until 1925. The main purpose of the thesis will be to examine chronologically any and all events and factors concerned with the navigation of the river during that period of time. The first chapter will survey the geographical and historical background of the San Joaquin River. The emphasis will be placed on the river's use for navigation. Since the upper, southern third of the San Joaquin Valley does not drain into the San Joaquin River, only those areas between the Kings River on the south and the Cosumnes River on the north will be included in this study.

It has been the object of the writer to compile as complete a bibliography, as the time allowed, on the History of the Deep Water Project at Stockton, California. ... The thesis proper has been directed to cover the major attempts to deepen the water channel from Stockton to San Francisco. Much of this material is not in a form to be readily accessible to the layman so I have included a great deal of it in the form of an Appendix; thus bringing it together, but not making it necessary for the reader to review it unless he or she feels the need of so doing. I believe that the field of research regarding this problem has merely been "scratched along the surface," and it offers to the student and the community at large an opportunity to study "conflicting interests" and economic history in general.

The dynamics of zooplankton and phytoplankton growth and interactions play a significant role in water quality (e.g., pH and dissolved oxygen [DO]) and the available food supply for higher order organisms in the San Joaquin River Delta. Algae have been shown to significantly impact DO concentrations in the Deep Water Ship Channel (DWSC) of the San Joaquin River (SJR) estuary. Zooplankton grazing is one of the important mechanisms that influence the fate and spatial distribution of algae, and therefore, may contribute to DO deficits that adversely impact aquatic habitat and salmonid migration in the SJR estuary. Numerical water quality models developed to simulate and predict dissolved oxygen in the SJR rely on mathematical algorithms that link chemical and biological mechanisms. Due to the complexity of natural systems, calibrating these models is challenging and often requires independent investigations to estimate input parameters, such as zooplankton grazing and algal growth rates. This investigation explored the applicability of three methods to quantify the rates that zooplankton graze on algae populations in the SJR. Zooplankton grazing studies were performed in the DWSC of the SJR from June 2012 through July 2013. Light and dark bottle microcosm studies using the dilution method, the food-removal method, and the grazer concentration method were tested. A modified microcosm approach similar to the grazer concentration method was developed that yielded changes in chlorophyll a concentrations that were sufficient to separate zooplankton grazing from algal growth and respiration. Microcosms contained zooplankton concentrations that were up to 30 times higher than natural, background levels. Zooplankton grazing rates were consistent in both magnitude and variability with literature values reported for other waters, ranging from 0.295-3.404-m 3 gC -1 d -1 and 0.006-1.413-m 3 gC -1 d -1 for light and dark bottle microcosms, respectively.