DELTA SCIENCE FELLOW 2013 Optimizing salt marsh harvest mouse conservation through an investigation of demography, habitat use and multi-species management LEFT: The research crew tags and collars the mice, then tracks their move- ment with radio telemetry receivers. BELOW: A salt marsh harvest mouse. K. Smith/UC Davis Katherine Smith Doctoral Student University of California, Davis WHY THIS RESEARCH MATTERS The Delta’s salt marsh harvest mouse (SMHM)(Reithrodontomys raviventris) has been federally listed for over 40 years, yet detailed demographic data has never been collected. A basic understanding of demographics is necessary for a complete management plan. The historic range of the SMHM has been reduced by almost 95% to 12,555 hectares. A large proportion of remaining habitat exists as diked wetlands managed for waterfowl, and the value of this habitat type relative to their historical tidal wetlands is largely unknown. Tidal habitat restoration is one of the primary conservation strategies for SMHM, but the immediate effects of restoration activities, and habitat shifts on SMHM populations are uncertain. Image: NMSU PROJECT This project characterized the demographic and life history attributes of the salt marsh harvest mouse and the effects of tidal restoration. The Fellow used monthly live-trapping, mark and recapture techniques over a period of three years, and existing datasets to evaluate demographic characteristics and population sizes for the SMHM, as well as estimate the relative value of various habitat types for this endangered species. To develop recommendations for improved multispecies management, the Fellow also studied the relationship between SMHM and common waterfowl species. The Fellow used radiotelemetry to evaluate habitat use of SMHM, and made important observations of behaviors such as feeding and nesting. The fellow also used a cafeteria trial to examine the diet preferences of SMHM. The Fellow alone spent ~2,900 hours over 500+ days in the field collecting this data and managed a field crew consisting of 5+ state employees, a total of 10 undergraduate assistants from UC Davis, and more than 100 volunteers, mostly UC Davis undergraduates.
Natural products from the marine environment constitute one of the richest and most reliable sources of bioactive molecules for drug discovery and biotechnology. Filamentous marine cyanobacteria are among the most prolific natural product producers, and with significant advances in genetics and genomics over the past decade are gaining increasing recognition for unusual or unprecedented biochemistry involved in natural product biosynthesis. However, the further development of several of these cyanobacterial secondary metabolites has not been accomplished because of low yields from field collections, slow growth of these organisms in laboratory cultures, and an absence of any genetic techniques for DNA manipulation. The aim of the research presented in this dissertation is to study the biosynthesis of natural products from the marine filamentous cyanobacterium majuscula to investigate how access to these compounds can be improved and the full potential of cyanobacterial strains can be realized. A variety of experiments are described herein, including : 1) A transcriptional analysis of the neurotoxin jamaicamide gene cluster from Lyngbya majuscula, which employed RT-PCR and reporter gene assays to better understand how cyanobacterial biosynthetic pathways are transcribed; 2) Investigations into jamaicamide regulation, which included a) protein pulldown assays to isolate possible light related regulatory proteins for this pathway and b) the development of a novel mass spectrometry approach to monitor natural product biosynthetic turnover, the effect of environmental parameters on this turnover, and confirm the impact of light on jamaicamide production; 3) Evaluating different methods for transferring DNA into Lyngbya filaments and taking the first steps in heterologously expressing portions of a Lyngbya gene cluster in the actinomycete Streptomyces coelicolor, and 4) Sequencing the genome of Lyngbya majuscula 3L, thereby revealing its natural product potential, a complex gene regulatory network and a surprising inability to fix atmospheric nitrogen. Collectively, these experiments provide new perspective on natural product biosynthesis in Lyngbya strains and direction on how these organisms and their natural products can be harnessed for biomedical and biotechnological applications
The same waves that pound the shore off California also tear large amounts of seaweed from the region’s giant kelp forests and rocky reefs. Much of this drift seaweed, known as wrack, is eventually washed ashore. On many of Southern California’s beaches, tractors will remove this wrack (along with trash and litter) and rake the sand, in a process known as beach grooming.
In this project, scientists describe the processes by which a subsurface nearshore algal bloom is carried to the surface, swept closer to the shore and ultimately blocked from entering the surf zone at Huntington Beach in Orange County, California.
Gopher Rockfish diets will differ inside vs. outside of marine protected areas (MPAs) due to higher Gopher Rockfish densities inside MPAs.
Biomonitoring, in its most liberal definition, is as old as humanity. Early humans would have been keenly aware of changes in animal and plant communities, especially those that were part of their prey and food supply, and they may have been able to make some tenuous connections between these changes and their changing environment. However, these early humans (and indeed many modern ones) would have been completely unaware of the changing populations of microscopic organisms under their feet, and what can be learned by scientific study of these sentinels.
In most ecosystems, the distribution of species across a landscape is greatly influenced by the type, amount, and spatial configuration of habitats. Studies in terrestrial environments have shown that species diversity, density, and length frequency often positively correlate with the size of a habitat patch, patch shape, and proximity to a patch edge. These patterns, however, have not been conclusively shown in temperate sub-tidal marine studies. Data from visual strip-transects collected from the Delta submersible were used to characterize fish assemblages with respect to rocky bank habitat patches. Specifically, the density, diversity, and length frequency of nearshore fishes were examined with respect to 1) proximity to the patch edge, 2) patch shape, and 3) patch size near Point Lobos and Point Sur, California. Diversity and length distributions of fishes were significantly greater at the edge than the interior of rocky bank patches. Therefore, landscape-scale patterns with respect to the distribution of nearshore fishes exist. However, this study also demonstrated that terrestrial paradigms are not directly applicable to temperate sub-tidal marine habitats. The relationship between species richness and patch shape was opposite of patterns observed in terrestrial systems. Additionally, patch size explained more of the variability in the nearshore fish assemblages than patch shape; however, neither were good predictive indicators of the density of fishes.
Based on an analysis of a 37-year time series, zooplankton biomass and species composition appear to have changed profoundly in Suisun Bay and Sacramento-San Joaquin Delta, in response to invasive species introductions and hydrological conditions. Results are consistent with other studies linking a majority of species interactions in the upper San Francisco Estuary to non-native invasions. The Asian clam and several exotic zooplankton species appear to have capitalized, directly and indirectly, on the long drought from 1987 to 1994 and exacerbating water management practices. During this period of sustained high-salinity conditions, larger native copepods – the preferred prey of larval fishes – were replaced by smaller Asian zooplankton, notably Limnoithona tetrapsina, likely introduced via ballast water. In addition to the new species, total zooplankton biomass dropped significantly during the last four decades; however, the pace and timing of the decline does not explain the sudden collapse of pelagic fishes around 2002. While the shear abundance of smaller non-native zooplankton appears to have offset the loss of biomass from larger native zooplankton, it is plausible, even likely, that the new plankton community has degraded food quality for larval fishes. The Delta Science Fellow is currently exploring this idea and its link to larval fish survivorship.
With Sea Grant support, medical researchers helped fish growers develop a control method for a deadly bacterial infection that costs the global aquaculture industry about $100 million annually.
The extent to which marine populations are connected by dispersing larvae and the ramifications of this connectivity for population dynamics was investigated for the temperate damselfish, Hypsypops rubicundus, in San Diego County, USA. Surveys identified six source populations for this species: Carlsbad, Cardiff, Torrey Pines, La Jolla, Mission Point, and Zuniga Point. Three of these reefs are within or adjacent to existing marine protected areas. Trace elemental fingerprinting was used to quantify the connectivity of populations in 2008-2009. High-resolution sampling over a protracted spawning season revealed that elemental fingerprints of reefs earlier in the spawning season became indistinguishable from other reefs later in the spawning season, resulting in inaccurate assignment of natal origin of post-dispersal fish. When natal origins of fish were assessed using appropriately binned data, one reef, La Jolla, emerged as the predominant source population, supplying itself and three other reefs with recruits. The northernmost reef, Cardiff was a “pure” sink, in that it unilaterally imported fish. Dispersal trajectories predominantly were in a northerly direction, but sporadic southerly dispersal was documented, corresponding to empirically measured current reversals. On intra-annual time scales this network of reefs resembles a source-sink metapopulation, but over annual time scales it functions as an open metapopulation with a well-mixed larval pool. To assess the demographic significance of observed connectivity patterns, empirically parameterized, stage-based matrix models were coupled with connectivity matrices. Elasticity analyses suggest inter-reef connectivity acts primarily to regulate which vital rates are demographically most significant; at low levels of connectivity adult survivorship has the greatest influence on population growth rate; at high levels of connectivity, juvenile growth is most influential. Quantitative metrics of sources and sinks were developed and node deletion experiments conducted to better characterize reef connectivity within the metapopulation. La Jolla was identified as the most valuable reef within the metapopulation in terms of connectivity; it may regulate how populations of fish at other reefs persist over time, and as such should be a conservation priority. New knowledge of the magnitude, directionality and variability of connectivity, and its roles in regulating local and metapopulation dynamics will aid local marine conservation efforts.
Nematodes, also known as roundworms, are among the most abundant groups of animals on the planet. If you had pinworms as a child, you’ve experienced nematodes firsthand – and are not alone, as at any given time, about a third of the world’s population is believed to be infected by some kind of nematode para- site. Nematodes, many species of which are not parasitic, are also incredibly common denizens of coastal sediments, and an important source of nourishment for shellfish and bigger worms, which themselves are forage species for other animals. Because of this, roundworms are critical components of the coastal food web, and hence a meaningful “bottom-up” indicator of coastal ecosystem functioning.
How might climate change alter California’s risk of floods in the future? Findings from this project suggest that flooding will become more intense in the San Joaquin and (to a lesser extent) Sacramento watersheds by the end of the century, irrespective of whether the climate becomes wetter or drier. More intense flooding appears to be a consequence of several factors—principally bigger storms, more frequent big storms and more days of precipitation falling as rain instead of snow. Moister winter soils, which may be too saturated to absorb added water, also contribute to flooding in some areas.
Avian predators, Western Gulls in particular, are having significant impacts on juvenile salmonid populations along the central California coast. Exclusion efforts can reduce predator impact and increase juvenile salmonid survival.
Fewer white sharks (Carcharodon carcharias) inhabit the northeast Pacific Ocean than scientists previously thought. The first official count of the iconic marine predator is consistent with genetic studies that have shown a low degree of genetic variability among the animals.
The focus of this dissertation is submarine groundwater discharge (SGD), the direct flow of groundwater from the seabed to the sea, and onsite wastewater treatment systems in coastal California. The research focuses primarily on a single coastal community in central California, Stinson Beach, where conventional onsite treatment systems, or septic systems, are used exclusively for wastewater disposal. The overarching goal of the work has been to quantify the magnitude and timing of SGD at the site and to provide insight into how onsite wastewater treatment at Stinson Beach affects local groundwater quality and, via SGD, surface water quality, all with the broader goal of informing and guiding future development along the California coast.
Tidal wetlands can be important sources of methylmercury (MeHg) in aquatic ecosystems, such as the San Francisco Bay-Delta estuary. As a result of the tendency of bacteria in wetland sediments to methylate mercury, the restoration of wetland habitat may cause an increase of MeHg concentrations. To balance the need for tidal wetland habitat with concerns over increased MeHg exposure, landscape-scale techniques for minimizing the production and export of MeHg from wetland sediments are needed. One potential approach is to use an iron sediment amendment to reduce net MeHg production. The addition of Fe[II] decreases MeHg production by lowering the concentration of the inorganic Hg[II] species that are methylated by bacteria. In this research, the potential for reducing MeHg production and export via an iron amendment was evaluated in laboratory microcosm experiments and a field study in a tidal salt marsh in the San Francisco Bay estuary. Additionally, sediment incubation experiments were conducted in anaerobic containers and in in situ cores to evaluate the effect of iron and sulfur redox cycling on MeHg production. Two laboratory microcosm experiments (Chapter 2) were conducted to test the iron amendment hypothesis under simulated tidal wetland conditions: one with devegetated sediments and one with live wetland vegetation. The microcosms consisted of intact sediment cores collected from Gambinini Marsh, a tidal salt marsh in the San Francisco Bay estuary dominated by pickleweed (Sarcocornia pacifica). The microcosms were maintained under simulated tidal conditions and amended at four iron doses (0, 180, 360, and 720 g-Fe/m2). Following iron addition to the devegetated sediments, porewater S[-II] concentrations decreased for each dose relative to the control. The average weekly export of MeHg in the surface water decreased by 82% and 89% for the two highest iron doses, respectively. Despite substantial variability within treatment groups, similar trends were observed in the vegetated microcosms. The results suggest that iron addition has the potential to provide a landscape-scale control on MeHg export from restored tidal wetlands under certain conditions. The cycling of iron, sulfur, and mercury in tidal wetlands is a complex process, with the combination of daily tides, changes in the growth state of wetland plants, and a highly productive microbial community resulting in temporal and spatial variations in MeHg production and export. Sediment incubation experiments (Chapter 3) were used to evaluate the effect of these processes on MeHg concentrations in the sediments of Gambinini Marsh. Sediments were incubated for 7-days in sealed jars under the following conditions: untreated sediments, addition of sodium molybdate to suppress sulfate reduction, and the addition of formaldehyde as an abiotic control. Similar rates of Fe[II] production were observed in both the untreated and Mo-amended incubations, suggesting that both iron-reducing and sulfate-reducing bacteria co-existed in the same sediment layers. Additionally, MeHg production was not observed when sulfate reduction was suppressed, suggesting that mercury methylation was mediated by sulfate- reducing bacteria. The in situ incubations, which were conducted with open and closed cores, demonstrated that during the summer months when plants were active, separation of sediments from live plant roots and gas exchange with the atmosphere resulted in more reduced sediment conditions. Additionally, sediments at the surficial layers (0-1 cm and 3-4 cm depths) exhibited more reducing conditions during the winter than in the summer, suggesting that the oxidation of reduced iron species occurs more rapidly during the summer. To better understand the effect of iron amendments on in situ tidal marsh biogeochemistry, a 17-month field study was conducted in the Gambinini Marsh (Chapter 4). Before and after amending the sediments with 77 g-Fe/m2, porewater from pickleweed-dominated sediments in the high marsh plain were analyzed for iron, sulfur, organic carbon, and methylmercury. Sulfide was not detected in the sediment porewater, and the iron amendment had no observable effect on net MeHg production. However, porewater iron concentrations were elevated for at least 6 weeks following the amendment. Porewater concentrations of MeHg and dissolved organic carbon were lower throughout 2010 than during the summer of 2009 when the experiment was initiated. However, these concentrations increased during the period of pickleweed flowering in 2010, further demonstrating the strong effect that wetland vegetation can have on sediment biogeochemical processes. This research demonstrated that an iron sediment amendment has the potential to be an effective control of MeHg production and export in tidal wetland sediments under certain conditions. While the in situ amendment showed no effect in the high marsh plain of Gambinini Marsh, the microcosm experiments demonstrated that a strong effect may be possible in sulfide- rich sediments. Additional research is necessary to evaluate the efficacy of the iron amendment in sulfide-rich field sediments, such as those found in low marsh environments.
This dissertation provided novel insights on the dynamics and consequences of harmful algal blooms (HABs) in the California Current System (CCS). Parasitism is described as a biological control agent of harmful dinoflagellate blooms and referred to as a novel factor influencing HAB dynamics in coastal upwelling environments. Chapter 1 documented, for the first time, the presence of Amoebophrya, an endoparasitic dinoflagellate that infects and kills 7 bloom-forming dinoflagellate host species that occur throughout the CCS. Chapter 1 also discussed parasitism effects on (1) host population dynamics, (2) dinoflagellate species diversity, (3) net phytoplankton community composition and (4) trophic web structure within the planktonic community of an upwelling environment. Chapter 2 specifically verified the role of such a parasite in controlling harmful dinoflagellate blooms caused by one of its hosts in Monterey Bay. Findings of Chapter 2 suggested that blooms might develop when the host ‘escapes’ parasitism by Amoebophrya. In contrast, epidemic parasitic outbreaks may contribute to stoping or preventing the occurrence of dinoflagellate harmful blooms. Chapter 3 and 4 focused on the consequences of HABs caused by diatoms of the genus Pseudo-nitzschia, which cannot be parastitized by Amoebophrya and produces the neurotoxin domoic acid (DA). Chapter 3 verified that human consumers of recreationally-caught fishes can be exposed to asymptomatic doses of domoic acid. Lastly, Chapter 4 dealt with the hypothesis that the pelagic predator Humboldt squid (Dosidicus gigas), which recently invaded the domains of CCS, is exposed to domoic acid. However, beach strandings of this species in Southern California could not be linked to domoic acid exposure and was likely related to other unknown causes.
UNIVERSITY OF CALIFORNIA, SAN DIEGO On the evolution of the sghC1q gene family, with bioinformatic and transcriptional case studies in zebrafish A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Marine Biology by Tristan Matthew Carland Committee in charge: Lena G. Gerwick, Chair Eric E. Allen Phillip A. Hastings Victor Nizet Victor D. Vacquier
This project examines whether rocky intertidal nudibranchs (brightly colored shallow-water mollusks also known as sea slugs) can be used as fine-scale indicators of inter-annual and decadal-scale climate variability. As part of this research, biologists offer a partial explanation for an observed decline in sea slugs off Central California, and document the climate-induced range shift of one particularly aggressive predatory “killer” sea slug and its effect on intertidal ecology at Duxbury Reef in Marin County. Field studies have led to the discovery of two new species of sea slugs.
All natural fluids stratify. Stable stratifications, in which isobars and isopycnals are parallel, are capable of supporting internal wave motion. Unstable stratification, in which density and pressure gradients are not aligned, results in gravity-driven flow. Gravity currents are a subset of these flows in which horizontal density gradients sharpen and propagate horizontally, transporting mass, momentum, and energy. If the density of the gravity current is within the density extrema of the stably stratified ambient fluid, it propagates as an intrusion at an intermediate height. Through laboratory experiments and numerical simulations, this dissertation explores the influence of stratification on the dynamics of gravity- driven intrusions. Intrusions require stable stratification in the ambient fluid, which is capable of transporting momentum and energy away from the current in the form of internal waves. We investigate the constant velocity propagation of well-mixed intrusions propagating into a linearly stratified ambient fluid. Varying the level of neutral buoyancy, we quantify the corresponding variation in structure, momentum, and energy of the upstream wave field. Adjacent stable stratifications of differing vertical density structure necessarily entail horizontal density gradients. These gradients determine the hydrostatic pressure differences driving the ensuing gravity current. We examine the mid-depth, constant velocity propagation of one linearly stratified fluid into another more strongly linearly stratified fluid. Working from the available potential energy of the system and measurements of the intrusion thickness, we develop an energy model to describe the speed of the intrusion in terms of the ratio of the two buoyancy frequencies. Distinct from adjacent linear stratifications, adjacent discrete stratifications may create flow consisting of interleaving intrusions. Single intrusions into a two- layer ambient fluid are well understood. Limiting our study to an idealized system of multiple intrusions, we attempt to extend the two-layer model to describe the interleaving process. We show that this simple extension fails when the average densities of the two stratifications are unequal, and suggest that this failure is due to the coupling of interfacial waves across constant density layers
