Adaptive Mechanisms of an Estuarine Synechococcus based on Genomics, Transcriptomics, and Proteomics

Picocyanobacteria are important phytoplankton and primary producers in the ocean. Although extensive work has been conducted for picocyanobacteria (i.e. Synechococcus and Prochlorococcus) in coastal and oceanic waters, little is known about those found in estuaries like the Chesapeake Bay. Synechococcus CB0101, an estuarine isolate, is more tolerant to shifts in temperature, salinity, and metal toxicity than coastal and oceanic Synechococcus strains, WH7803 and WH7805. Further, CB0101 has a greater sensitivity to high light intensity, likely due to its adaptation to low light environments. A complete and annotated genome sequence of CB0101 was completed to explore its genetic capacity and to serve as a basis for further molecular analysis. Comparative genomics between CB0101, WH7803, and WH7805 show that CB0101 contains more genes involved in regulation, sensing, and stress response. At the transcript and protein level, CB0101 regulates its metabolic pathways, transport systems, and sensing mechanisms when nitrate and phosphate are limited. Zinc toxicity led to oxidative stress and a global down regulation of photosystems and the translation machinery. From the stress response studies seven chromosomal toxin-antitoxin (TA) genes, were identified in CB0101, which led to the discovery of TA genes in several marine Synechococcus strains. The activation of the relB2/relE1 TA system allows CB0101 to arrest its growth under stressful conditions, but the growth arrest is reversible, once the stressful environment dissipates. The genome of CB0101 contains a relatively large number of genomic island (GI) genes compared to known marine Synechococcus genomes. Interestingly, a massive shutdown (255 out of 343) of GI genes occurred after CB0101 was infected by a lytic phage. On the other hand, phage-encoded host-like proteins (hli, psbA, ThyX) were highly expressed upon phage infection. This research provides new evidence that estuarine Synechococcus like CB0101 have inherited unique genetic machinery, which allows them to be versatile in the estuarine environment.

A MEMETIC/PARTICIPATORY APPROACH FOR CHANGING SOCIAL BEHAVIORS AND PROMOTING ENVIRONMENTAL STEWARDSHIP IN JALISCO, MEXICO

This dissertation addressed the issue of sustainable development at the level of individual behaviors. Environmental perceptions were obtained from people living around the biosphere reserve Chamela-Cuixmala in Jalisco, Mexico. Several environmental issues were identified by the people, such as garbage and grey water on the streets, burning plastics, and the lack of usage of recreational areas. All these issues could be addressed with a change in behavior by the villagers. Familiarization activities were conducted to gain people's trust in order to conduct a community forum. These activities included giving talks to school children and organizing workshops. Four different methodologies were generated using memetics and participation to test which would ameliorate those environmental issues identified by the people through a change in behavior. The methodologies were 1) Memes; 2) Participation and Memes; 3) Participation; 4) Neither Participation nor Memes. A meme is an idea expressed within a linguistic structure or architecture that provides it with self-disseminating and self-protecting characteristics within and among the minds of individuals congruent with their values, beliefs and filters. Four villages were chosen as the treatments, and one as the control, for a total of five experimental villages. A different behavior was addressed in each treatment village (garbage, grey-water, burning plastics, recreation.) A nonequivalent control-group design was established. A pretest was conducted in all five villages; the methodologies were tested in the four treatment villages; a posttest was conducted on the five villages. The pretest and posttest consisted in measuring sensory specific indicators which are manifestations of behavior that can either be seen, smelled, touched, heard or tasted. Statistically significant differences in behavior from the control were found for two of the methodologies 1) Memes (p=0.0403) and 2) Participation and Memes (p=0.0064). For the methodologies of 3) Participation alone and 4) Neither, the differences were not significant (p=0.8827, p=0.5627 respectively). When using memes, people's behavior improved when compared to the control. Participation alone did not generate a significant difference. Participation aided in the generation of the memes. Memetics is a tool that can be used to establish a linkage between human behavior and ecological health.

Mycobacteriosis in Chesapeake Bay Striped Bass (Morone saxatilis): The Interaction of Nutrition and Disease

Field and laboratory studies were conducted from 1998 - 2005 to examine the relationship between nutritional status and mycobacteriosis in Chesapeake Bay striped bass (Morone saxatilis). A review of DNA from archived tissue blocks indicated that the disease has been present since at least 1984. Field surveys and feeding trials were conducted from 1998-1999 to determine the nutritional condition of striped bass and the association with disease state. Proximate composition revealed elevated moisture (~ 80%) and low storage lipids (< 0.5% ww), characteristic of a poorly nourished population. These findings were not consistent with data collected in 1990-1991, or with experimentally fed fish. Mycobacteriosis explained little of the variance in chemical composition (p > 0.2); however elevated moisture and low lipid concentration were associated with fish with ulcerative lesions (p < 0.05). This suggests that age 3 and 4 striped bass were in poor nutritional health in 1998-1999, which may be independent from the disease process. Challenge studies were performed to address the hypothesis that disease progression and severity may be altered by nutritional status of the host. Intraperitoneal inoculation of 104 CFU M. marinum resulted in high mortality, elevated bacterial density, and poor granuloma formation in low ration (0.15% bw/d) groups while adequately fed fish (1% bw/d) followed a normal course of granulomatous inflammation with low mortality to a steady, equilibrium state. Further, we demonstrated that an active inflammatory state could be reactivated in fish through reductions in total diet. The energetic demand of mycobacteriosis, was insignificant in comparison to sham inoculated controls in adequately fed fish (p > 0.05). Declines in total body energy were only apparent during active, inflammatory stages of disease. Overall, these findings suggest that: 1) mycobacteriosis is not a new disease of Chesapeake Bay striped bass, 2) the disease has little energetic demand in the normal, chronic progression, and 3) poor nutritional health can greatly enhance the progression and severity, and reactivation of disease. The implications of this research are that management strategies focused on enhancing the nutritional state of striped bass could potentially alter the disease dynamics in Chesapeake Bay.

Biodeposition and Biogeochemical Processes in Shallow, Mesohaline Sediments of Chesapeake Bay

Stocks of the eastern oyster, Crassostrea virginica, have been declining in Chesapeake Bay since the late 19th century, and current strategies involve restoring culture of Crassostrea virginica on-bottom and in devices suspended within the water column. Sub-tidal suspension culture of Crassostrea virginica in Chesapeake Bay occurs mostly in sheltered inlets and tidal creeks and, thereby, has the potential to influence shallow water biogeochemical processes. To assess the influence of Crassostrea virginica biodeposits and benthic microalgae on sediment nitrogen and phosphorus exchange, field studies with Crassostrea virginica held in aquaculture floats and laboratory experiments were conducted. Enhanced organic nitrogen deposition from Crassostrea virginica biodeposits led to gradual increases in surface sediment nitrogen and pore water ammonium concentrations; however, modifications to pore water concentrations were not always expressed at the sediment-water interface. Benthic microalgae often modulated the influence of biodeposits on sediment nitrogen exchange but, as observed in laboratory experiments, the supply of nitrogen from Crassostrea virginica biodeposits may exceed their biological demand. Organic carbon from biodeposits had varying influences on aerobic respiration but consistently stimulated anaerobic metabolism. Shifts in net phosphorus exchange were driven by this anaerobic remineralization and concentrations of iron and manganese oxy(hydr)oxides, with transitions in fluxes coinciding with changes in benthic photosynthesis and oxidation of surface sediments. Manganese and iron oxy(hydr)oxides from biodeposits supported incorporation of added phosphorus and prevented exchange at the sediment-water interface in the absence of iron-sulfide mineral formation. Differences in the response of shallow water sediments to Crassostrea virginica biodeposits were due to the quality and quantity of biodeposits supplied, as well as the spatial and temporal variability within these sediments. Initial conditions and corresponding reference sediments illustrated the potential for sediment biogeochemistry and nutrient exchange from tidal creek sediments to vary spatially and temporally on relatively small scales. Factors influencing variability within tidal creek sediments were related to shifts in riverine freshwater inputs, macroalgal blooms, nutrient concentrations in overlying waters, and bioirrigation from the clam, Macoma balthica.

Nutrient enrichment effects on mangrove sediments from differing tree height zones in Bocas del Toro, Panama

Red mangrove (Rhizophora mangle L.) forests have distinct tree-height zones, with tall trees fringing the ocean and shorter trees in interior stands. A long-term nitrogen (N) and phosphorus (P) fertilization experiment in Almirante Bay, Bocas del Toro Province, Panama has shown that tree-height zonation is primarily related to nutrient limitation. This experiment was used to test the effects of in-situ nutrient additions and tree zonation on mangrove sediments. The sediments underlying the experimental R. mangle trees were sampled and N₂ fixation, ¹⁵N, chlorophyll a, percent N and P, and percent organic biomass were quantified. Both N and P additions significantly affected almost every parameter measured in both zones within this experiment. These results are likely to have implications for management since N and P inputs are predicted to increase throughout the tropics and subtropics worldwide.

A von Bertalanffy Based Model for the Estimation of Oyster (Crassostrea virginica) Growth on Restored Oyster Reefs in Chesapeake Bay

A model to estimate the mean monthly growth of Crassostrea virginica oysters in Chesapeake Bay was developed. This model is based on the classic von Bertalanffy growth function, however the growth constant is changed every monthly timestep in response to short term changes in temperature and salinity. Using a dynamically varying growth constant allows the model to capture seasonal oscillations in growth, and growth responses to changing environmental conditions that previous applications of the von Bertalanffy model do not capture. This model is further expanded to include an estimation of Perkinsus marinus impacts on growth rates as well as estimations of ecosystem services provided by a restored oyster bar over time. The model was validated by comparing growth estimates from the model to oyster shell height observations from a variety of restoration sites in the upper Chesapeake Bay. Without using the P. marinus impact on growth, the model consistently overestimates mean oyster growth. However, when P. marinus effects are included in the model, the model estimates match the observed mean shell height closely for at least the first 3 years of growth. The estimates of ecosystem services suggested by this model imply that even with high levels of mortality on an oyster reef, the ecosystem services provided by that reef can still be maintained by growth for several years. Because larger oyster filter more water than smaller ones, larger oysters contribute more to the filtration and nutrient removal ecosystem services of the reef. Therefore a reef with an abundance of larger oysters will provide better filtration and nutrient removal. This implies that if an oyster restoration project is trying to improve water quality through oyster filtration, it is important to maintain the larger older oysters on the reef.

Bioenergetic and ecological consequences of diet variability in Atlantic croaker Micropogonias undulatus

Atlantic croaker Micropogonias undulatus is a commercially and ecologically important bottom-associated fish that occurs in marine and estuarine systems from Cape Cod, MA to Mexico. I documented the temporal and spatial variability in the diet of Atlantic croaker in Chesapeake Bay and found that in the summer fish, particularly bay anchovies Anchoa mitchilli, make up at least 20% of the diet of croaker by weight. The use of a pelagic food source seems unusual for a bottom-associated fish such as croaker, but appears to be a crepuscular feeding habit that has not been previously detected. Thus, I investigated the bioenergetic consequences of secondary piscivory to the distribution of croaker, to the condition of individuals within the population and to the ecosystem. Generalized additive models revealed that the biomass of anchovy explained some of the variability in croaker occurrence and abundance in Chesapeake Bay. However, physical factors, specifically temperature, salinity, and seasonal dynamics were stronger determinants of croaker distribution than potential prey availability. To better understand the bioenergetic consequences of diet variability at the individual level, I tested the hypothesis that croaker feeding on anchovies would be in better condition than those feeding on polychaetes using a variety of condition measures that operate on multiple time scales, including RNA:DNA, Fulton's condition factor (K), relative weight (Wr), energy density, hepatosomatic index (HSI), and gonadosomatic index (GSI). Of these condition measures, several morphometric measures were significantly positively correlated with each other and with the percentage (by weight) of anchovy in croaker diets, suggesting that the type of prey eaten is important in improving the overall condition of individual croaker. To estimate the bioenergetic consequences of diet variability on growth and consumption in croaker, I developed and validated a bioenergetic model for Atlantic croaker in the laboratory. The application of this model suggested that croaker could be an important competitor with weakfish and striped bass for food resources during the spring and summer when population abundances of these three fishes are high in Chesapeake Bay. Even though anchovies made up a relatively small portion of croaker diet and only at certain times of the year, croaker consumed more anchovy at the population level than striped bass in all simulated years and nearly as much anchovy as weakfish. This indicates that weak trophic interactions between species are important in understanding ecosystem processes and should be considered in ecosystem-based management.

Interactive Effects of Plant Species and Organic Carbon on Nitrate Removal in Chesapeake Bay Treatment Wetlands

Nitrate from agricultural runoff are a significant cause of algal blooms in estuarine ecosystems such as the Chesapeake Bay. These blooms block sunlight vital to submerged aquatic vegetation, leading to hypoxic areas. Natural and constructed wetlands have been shown to reduce the amount of nitrate flowing into adjacent bodies of water. We tested three wetland plant species native to Maryland, Typha latifolia (cattail), Panicum virgatum (switchgrass), and Schoenoplectus validus (soft-stem bulrush), in wetland microcosms to determine the effect of species combination and organic amendment on nitrate removal. In the first phase of our study, we found that microcosms containing sawdust exhibited significantly greater nitrate removal than microcosms amended with glucose or hay at a low nitrate loading rate. In the second phase of our study, we confirmed that combining these plants removed nitrate, although no one combination was significantly better. Furthermore, the above-ground biomass of microcosms containing switchgrass had a significantly greater percentage of carbon than microcosms without switchgrass, which can be studied for potential biofuel use. Based on our data, future environmental groups can make a more informed decision when choosing biofuel-capable plant species for artificial wetlands native to the Chesapeake Bay Watershed.