A one-year experimental fishery for P. delagoae was established in April 2004 to determine the frequency and magnitude at which pulse fishing may be sustainable (Government Gazette 2004). Determining the extent of recovery after fishing is one aim of the experimental fishery. Assessments of the growth rate, size at sex maturity and natural mortality of P. delagoae were performed in 2000 (Groeneveld et al) and can be supplemented by the results of this study, which assess the reproductive biology of the East Coast spiny lobster in order to address this aim. A recent study (Groeneveld in press) assessed fecundity, egg loss during gestation, relative reproductive potential and lifetime egg production per recruit for P. gilchristii from three areas along the South African south coast. A general east-west trend of increasing fecundity, size at sexual maturity, and lifetime egg production per recruit was found for P. gilchristii. Examining egg-loss through the first four ( of six) developmental stages of gestation showed significant loss of around 15 % by stage four, irrespective of lobster size (Groeneveld in press). The study of fecundity in P. gilchristii ( Groeneveld in press) was used as a framework for assessing the fecundity of P. delagoae in this study.

Nitrate (NO3-) and uranium (U) are priority co-contaminants at U.S. Department of Energy (DOE) managed nuclear legacy waste sites, where nitric acid was extensively used to process uranium waste. This combination of a low pH and mixed metal contamination in a subsurface environment is also representative of legacy nuclear waste sites worldwide. The subsurface at DOE's Oak Ridge Integrated Field Scale Research Challenge (OR-IFRC) site is heavily contaminated with NO3-, radionuclides, heavy metals, and halogenated organics. NO3- concentrations in the near source zone (adjacent to the former S-3 ponds) reaches extraordinarily high concentrations (in the range of 10-1000 mM). Extensive research and field scale experiments have focused on ways of removing nitrate and recognize microbially-mediated denitrification as the most significant process in bioremediation and natural attenuation strategies. However, high levels of contamination decreases diversity of cultivable and non-cultivable bacterial populations in OR-IFRC groundwater, and low pH can inhibit denitrification activity. Denitrification is a microbially mediated dissimilatory reduction of nitrate to produce gaseous end products (N2O, N2). Denitrification is mediated by a group of facultative anaerobes including bacteria, fungi and archaea which display a wide range in phylogenetic affiliation and metabolic capabilities. Though nitrate respiring microorganisms have been studied extensively in soils and aquatic environments, the mechanisms controlling in situ metabolism of NO3- reduction remain poorly understood in terrestrial aquifers. The relationships between environmental factors (e.g. geochemistry, contaminant, pH), denitrifying community composition, and denitrification rates are intertwined and complex. Hence, the main objective of this dissertation was characterization of the microbial community mediating denitrification and understand their mechanisms and controls in a radionuclide contaminated terrestrial subsurface. The objectives of Chapter 1 were to extensively characterize microbial diversity and composition in acidic to circumneutral subsurface groundwater samples (pH 3.1-7.1) using a polyphasic approach. Multivariate analyses with geochemical and contaminant variables, and microbial community indices, showed the groundwater pH had the strongest effect of any variable on these communities. Our pyrosequencing survey of microbial diversity across the watershed has provided an initial insight into the large-scale distribution patterns of microbes in this unique environment, with greater variability in physical and geochemical attributes. The community was strongly dominated (>80%) by Proteobacteria, most of which fell into the Gamma-, Beta- and Alpha-Proteobacteria, and community composition was driven primarily by differences in diversity of the proteobacteria. This study also confirms that Gammaproteobacteria as the most dominant taxa with correlation to low pH, with Rhodanobacter sp. as the predominant genus. Furthermore, the data indicates that: (1) the diversity of microbial communities, more specifically that of Gammaproteobacteria is affected by the measured geochemical variables more notably pH, NO3-, N2 and TOC; (2) the diversity of Alphaproteobacteria and Deltaproteobacteria were higher in low contaminant wells; (3) pH appeared to be a strong predictor of relative lineage abundance with samples with low pH levels (pH <4.5) clustering separately from those with moderate pH values and (4) bacterial assemblages identified included genera related to known nitrate, U(VI), sulfate and Fe(III) reducers and fermenters. Bacterial SSU rRNA gene copy numbers did not change significantly between circumneutral pH groundwater samples and low pH samples. In Chapter 2, we report for the first time fungal communities characterized in a uranium and nitrate contaminated subsurface environment and also the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution, and diversity of fungi in subsurface groundwater samples were determined using quantitative and semi quantitative molecular techniques, including quantitative PCR of eukaryotic small-subunit rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from the subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH<4.5) conditions. Fungal isolates recovered from subsurface sediments, including cultures of the genus Coniochaeta, which were detected in abundance in pyrosequence libraries of site groundwater samples, were shown to reduce nitrate to nitrous oxide. Denitrifying fungal isolates recovered from the site were classified and found to be distributed broadly within the phylum Ascomycota and within a single genus of the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions. A concerted field-scale effort was undertaken to test the hypothesis that the microbial denitrification is stimulated by pH adjustment due to the alleviation of low pH stress and/or metal toxicity at the OR-IFRC site (Chapter 3). Sediment and groundwater samples were collected over a year, and microbial enumeration by DAPI counts and MPNs, SSU rRNA gene amplicon pyrosequencing, potential metabolic rate measurements for denitrification and oxygen consumption and geochemical analysis were used to evaluate the shifts in community composition as a function of pH manipulation. The potential denitrification rates measured for contaminated sediments prior to pH manipulation ranged from 0.39 nmol gdry wt-1 day-1 to 8.70 nmol N2O-N gdry wt-1 day-1; and denitrification optima was observed at pH 5.5 with maximum potential rates of 156.9 nmol N2O-N gwet wt-1 day-1. Addition of base resulted in an increase of groundwater pH from 3.5 to 5.5 in the injection well (FW128). However, little or no change in pH was observed in down-gradient wells. Similar trends were observed in total bacterial and denitrifier counts such that total bacterial numbers decreased with change in pH and over time. Potential rates were variable but generally decreased with time in those wells where the pH substantially increased after base addition. Shifts in community composition were observed, and addition of base resulted in a strong selection of a limited number of microbial groups, predominantly of phylum Proteobacteria. The results from this study demonstrate that the denitrifying community is sensitive to perturbation and responds slowly to pH elevation. A relatively rapid pH increase may act as a stressor that inhibits microbial activity over the short term of this study. / A Dissertation submitted to the Department of Earth, Ocean, and Atmospheric Sciences in partial fulfillment of the Doctor of Philosophy. / Spring Semester 2016. / April 4, 2016. / Denitrification, low pH, Radionuclinde, Subsurface Bacteria, Subsurface Fungi, Terrestrial Subsurface / Includes bibliographical references. / Jeffrey P. Chanton, Professor Directing Dissertation; Christopher Coutts, University Representative; Marcus Huettel, Committee Member; Amy Baco-Taylor, Committee Member; Christopher W. Schadt, Committee Member; Stefan J. Green, Committee Member; Joel E. Kostka, Committee Member.

Large gelatinous zooplankton (GZ) blooms of lobate ctenophores, Mnemiopsis leidyi, and scyphomedusae, Chrysaora quinquecirrha , occur throughout Chesapeake Bay and its tributaries. The mechanisms of GZ bloom formation, and the roles GZ blooms play in dissolved organic matter (DOM) and carbon (C) cycling are not fully understood. During 2003--2006, I conducted laboratory experiments and field surveys in the lower York River to determine factors controlling timing and magnitude of GZ blooms, and to evaluate their effects on C cycling. Highest biomass of M. leidyi occurred in early summer (May-June) and in late winter. Peaks in ctenophore biomass in the mesohaline region occurred one-month earlier than in downriver, polyhaline regions, due to higher ctenophore reproduction and larval dispersal upriver. High predation by C. quinquecirrha scyphomedusae on M. leidyi appears to cause the rapid decline in summer ctenophore blooms, and we hypothesize that subsequently medusae become C-limited. High GZ biomass coincides with peaks in microbial biomass, and as DOM is released by zooplankton but consumed by bacteria, these disparate trophic levels may be linked. I measured DOM production by GZ and the response of free-living bacterioplankton to GZ DOM, quantified in terms of bacterial metabolism, and bacteria phylogenetic community composition. Release rate of DOC by both GZ species was high relative to simultaneous release of DON and DOP, and for M. leidyi DOM metabolites were C-rich due to high mucus production in ctenophores. Furthermore, bacterioplankton abundance and production rapidly increased (within 6 hours) in response to uptake of GZ metabolites; however, decreases in bacterial growth efficiencies indicated that increases in bacterial C respiration were greater relative to changes in bacterial biomass. Enumeration of microbial assemblages using the fluorescence in situ hybridization (FISH) technique showed specific bacterial groups, namely gamma-proteobacteria, are responsible for increased metabolism of GZ DOM metabolites. In the context of worldwide increases in GZ, my results have significant implications for C transfer in marine food webs, with the potential for more C to be shunted to the microbial loop away from higher trophic levels.

A comprehensive understanding of migration dynamics, within-estuary behaviors and physiological tolerances of fish is needed to assess and predict future responses of fish to environmental disturbance and to protect habitat necessary for growth and survival. This study adds to current knowledge of summer flounder (Paralichthys dentatus) responses to environmental conditions by (1) examining migration and within-estuarine behaviors of adult summer flounder and (2) establishing summer flounder metabolic requirements and cardiorespiratory responses to variations in hypoxia and temperature. To elucidate use of a southern mid-Atlantic Bight estuary by adult summer flounder, the movements of 45 fish were monitored using acoustic telemetry within a seaside lagoon along Virginia‟s Eastern Shore. Mean residence time in this region was 1.5 times greater than previously reported for this species. The majority of fish remained within the estuary until mid-October, although some fish dispersed from the system earlier, and some temporarily exited and re-entered the system before final dispersal. Migration into or out of the system most closely followed seasonal changes in mean water temperature, but photoperiod and other factors may also play a role. Fish resided primarily in the deeper regions of the lagoon system, where strong currents preclude the development of suboptimal conditions such as hypoxia. Summer flounder also generally exhibited low levels of large-scale activity (e.g., 100s of meters). Variations in the migratory and within-estuary behaviors indicate that individual fish use different strategies to maximize food and habitat resources. Additional research is necessary to identify preferences and behaviors of summer flounder within estuaries and along the inner continental shelf and to relate these to prey distribution. To provide a metabolic framework for understanding how summer flounder respond to hypoxia, stopflow respirometry was used to measure changes in resting metabolic rate, oxygen extraction, gill ventilation and heart rate during progressive hypoxia at an acclimation temperature (22°C) and after an acute increase to 30°C. Summer flounder experience a 6-fold increase in gill ventilation while maintaining oxygen extraction above 50%. However, the critical oxygen saturation increased significantly from 27% at 22°C to 39% at 30°C, suggesting a lower tolerance to hypoxia after exposure to an acute increase in temperature. In addition, fish subjected to 30°C were unable to increase gill ventilation to as great an extent as at 22°C. At both temperatures, significant bradycardia was only observed when oxygen levels decreased to levels below critical oxygen saturation. Due to their ability to maintain aerobic metabolism in low oxygen conditions, summer flounder are not likely to avoid hypoxic conditions to maintain aerobic metabolism in the wild. However, exposure to hypoxia can decrease aerobic scope and consequently affect somatic and gonadal growth rates. Additional studies specifically examining the effects of hypoxia and temperature on aerobic scope are necessary to fully understand the effects of variable environmental conditions on growth and reproduction in this species.

Surficial sediments and sediment cores were collected from two distinct depositional regimes of the York River subestuary of Chesapeake Bay to document seasonal inputs, spatial variability, and longer-term (>40 years) fate of total organic carbon (TOC), lipid biomarker compounds and polycyclic aromatic hydrocarbons (PAHs). These regimes included biological mixing in the lower York and episodic mixing at the mid river site. Compounds were selected to represent a range of chemical reactivities, biological and anthropogenic sources, and modes of entry to the environment. The depositional environments were characterized with a suite of analytical tools: x-radiographs, Eh, 210Pb and 137Cs, total organic carbon, total nitrogen, and their stable isotopes. Each compound class was quantified in extractable and "bound" phases. Episodic mixing at the mid-river site resulted in stronger oxidizing conditions that promoted enhanced degradation of labile organic matter (e.g. diatoms) vs. refractory material (e.g. higher plants) in extractable sedimentary phases from sediments <5 yrs old. However, while apparent rate constants for bulk organic matter and total lipid were higher in older sediments (<40 years) under physically mixed conditions, degradation rates of fatty acid and sterol biomarkers were similar at both study sites. PAHs and lipid biomarkers isolated from "bound" phases were better preserved over time than corresponding "extractable" compounds. However, stabilization in the bound phase was not the same among compound classes. Differences in compound class fate were a function of inherent compound class reactivity (fatty acids > sterols and PAHs) rather than source or depositional regime. While compounds in bound phases may be formed over time during organic matter diagenesis, organic compounds did not increase in bound residues over time regardless of depositional regime, suggesting that bound phase compounds are formed within the source organism or very rapidly upon cell death and/or deposition to the sediments. The fate of organic carbon in coastal sediments is dependent upon the source and reactivity of organic carbon, the depositional regime, and its association with the underlying sediment/macromolecular matrix. Models of coastal carbon dynamics that consider these parameters and how they change will yield more accurate forecasts of coastal biogeochemical cycling.

Since the square-foot bottom sampler was described by Surber it has been the principle instrument used for quantitative studies of the bottom fauna in riffle areas of streams. However, little has been written concerning the actual number of square-foot samples necessary to describe stream bottom fauna in terms of the number or volume of organisms.

Metabolites of DDT were detected in five out of six major organs of blue crabs, Callinectes sapidus, taken from estuarine populations. Residue concentrations were highest in the hepatopancreas and below the limit of detection in the heart. Concentrations in pooled gonad samples (ovaries + testes) depended on the stage of development of the ovaries. Residue levels were low in claw and backfin muscles. Adult blue crabs were exposed for 12 hours to 0.01, 0.1, and 1.0 ppm DDT in water. No significant mortality was recorded. DDT was absorbed through the gills and transported to the hepatopancreas via the hemolymph. Biotransformation and distribution of DDT and its metabolites was regulated by the hepatopancreas. Induction of metabolic transformation of DDT to DDD and DDE occurred immediately. Storage of residues was greatest in the hepatopancreas and developing ovaries . Rates of loss of DDT residues from organs was subject to considerable variation. This dissertation is from the Joint Program Degree from the College of William & Mary and University of Virginia and awarded by the University of Virginia.

Zooplankton composition, distribution, biomass and biochemical constituents were determined monthly in the lower Chesapeake Bay for two years beginning in August 1971. Settled volume, dry weight, and ash-free dry weight estimates of total biomass were generally consistent in showing summer and late winter peaks. A mean dry weight peak of 258 mg/m3 in August 1971 decreased precipitously to a December low of 9 mg/m3, then increased to a March 1972 peak of 199 mg/m3. The second year mirrored this pattern, except that the passage of Tropical Storm Agnes in June 1972 lowered the summer peak values for July and August considerably. In August 1971 and again in August 1972, a total of 53 species, from four dominant major groups, were used to characterize four distinct geographical cluster zones. The summer zooplankton was dominated by cladocerans, largely Penilia avirostris and Evadne tergestina, and the copepod Acartia tonsa. Decapod larvae proved to be the most diverse summer group studied, containing 30 species in August 1971 and 33 species in August of 1972. Dominant species included Upogebia affinis, Callinectes sapidus, and Uca sp. Chaetognath peaks in September of each year consisted almost entirely of Sagitta tenuis. Winter populations contained less than half the number of taxa as summer zooplankton and were dominated by Acartia clausi. This species almost completely replaced Acartia tonsa by April of each year. The most notable effects of the lowered salinities caused by Tropical Storm Agnes in the summer of 1972 were a drastic reduction in cladoceran abundance and a compression of chaetognath distribution to the higher salinity areas near the bay mouth. Protein, the largest organic fraction of the zooplankton, usually accounted for 40-60% of the total dry weight. Mean monthly lipid values ranged from 1.9 to 9.5% of the dry weight, and carbohydrate appeared only as a minor organic fraction. This dissertation is from the Joint Program Degree from the College of William & Mary and University of Virginia and awarded by the University of Virginia.

Laboratory and environmental studies of striped bass (Morone saxatilis) X white perch (M. americana) and striped bass X white bass (M. chrysops) were used to-determine the feasibility of introducing these hybrids into an estuary as a supplement to natural populations of the parental species. Growth patterns, survival, and general hardiness of the hybrids were used as criteria. Growth of striped bass X white perch hybrids in the laboratory was apparently somewhat less than growth of natural populations of striped bass, but was much greater than growth of natural populations of white perch. Hybrid growth was slower than striped bass growth under the same conditions, but hybrid survival was much better than striped bass survival. The hybrids were able to survive and grow in estuarine salinities. Most hybrids matured at two years of age. Striped bass X white bass hybrids were able to adapt to an estuarine environment (the Rappahannock River, Virginia) and could successfully compete with striped bass and other resident ichthyofauna. Hybrid growth was faster than striped bass growth in the Rappahannock and was considerably faster than growth of various freshwater populations of white bass. Hybrids were caught in salinities as high as 17%. They were mature at two years of age. Both hybrids were described using meristic and morphometric characteristics. They were both found to be generally intermediate to the parental species, but in certain traits they tended to resemble one parent more closely than the other. Striped bass, white perch, and their hybrid all had a diploid chromosome number of 48. Possible karyological differences are discussed. One or both hybrids may be suitable for introduction into an estuary to supplement natural populations of striped bass and white perch, but more comprehensive environmental experiments are needed. This dissertation is from the Joint Program Degree from the College of William & Mary and University of Virginia and awarded by the University of Virginia.

I used 1.75 m&\sp2& drop rings and throw rings to sample communities of nekton at high and low tides in contiguous salt marshes, unvegetated flats, and seagrass beds (Ruppia maritima) of lower Chesapeake Bay. Thirty-two species of nekton were captured between June and October 1995, with a mean overall abundance of 28.6 inds m&\sp{lcub}-2{rcub}& and a mean biomass of 3.8 g m&\sp{lcub}-2{rcub}& (dry weight, dw). Blue crabs, Callinectes sapidus, were the biomass dominants and used seagrass and marsh edge habitats extensively from recruitment to maturity. Palaemonetes shrimp were the most abundant nekton; patterns of allopatry and apparent sympatry were found among the three species present. Menidia menidia used the marsh surface at night. Behavioral patterns for marsh residents Fundulus heteroclitus, F. majalis, Lucania parva, Gobiosoma bosc, and P. intermedius differed from patterns reported elsewhere. This suggests behavioral flexibility in habitat use between regions. Seagrass and marsh edges supported a large biomass of nekton. Secondary production on the marsh surface was estimated at 7.4-8.0 gdw m&\rm\sp{lcub}-2{rcub}150\ d\sp{lcub}-1{rcub}& (28.4-30.7 gww m&\rm\sp{lcub}-2{rcub}150\ d\sp{lcub}-1{rcub}&) between June and October 1995 (150 days). Gut contents of predators were examined, and a mathematical model was constructed to estimate consumption and export by nekton. Predation on invertebrates was highest in marsh edge areas, at 44.2 gdw m&\rm\sp{lcub}-2{rcub}150\ d\sp{lcub}-1{rcub}& removed; predation at the edge by transients (export) was 28.0 gdw m&\rm\sp{lcub}-2{rcub} 150\ d\sp{lcub}-1{rcub}.& The value of marsh edge was clearly linked to both vegetated and unvegetated components as refuge and feeding. Predation in the entire marsh was approximately 13 gdw m&\rm\sp{lcub}-2{rcub} 150\ d\sp{lcub}-1{rcub},& and transient export was 5.6 gdw m&\rm\sp{lcub}-2{rcub} 150\ d\sp{lcub}-1{rcub}.& Most export from marsh interior habitats was via blue crab predation on Uca and Sesarma. Predation in unvegetated areas was 13.3-17.0 gdw m&\rm\sp{lcub}-2{rcub} 150\ d\sp{lcub}-1{rcub};& export was 8.0-11.7 gdw m&\rm\sp{lcub}-2{rcub}150\ d\sp{lcub}-1{rcub}.& The unvegetated intertidal was an important resource for nekton due to lengthy inundation and abundant polychaete prey. The trophic contribution of each habitat was significant. Marsh, unvegetated, and seagrass habitats function together in this area to provide feeding and refuge for intertidal nekton.