A shortage of shell resources for restoring reefs of the Eastern oyster, Crassostrea virginica, has led to widespread use of substitute materials. The effectiveness of such alternative substrates as habitat for reef-associated fauna other than oysters is largely unresolved. I investigated the habitat value of oyster shell, surf clam (Spisula solidissima) shell, and pelletized coal ash reefs for benthic and nektonic communities. Oyster recruitment, survival, and growth were monitored on reefs of oyster and surf clam shell near the mouth of Chesapeake Bay and York River, USA. Oyster shell supported greater oyster growth and survival and offered the highest degree of structural complexity. On the York River subtidal clam shell reef, the quality of substrate varied with reef elevation. Oysters were more abundant and larger at the reef base and less abundant and smaller on the crest. The availability of interstitial space and appropriate settlement surfaces likely accounts for observed differences in oyster abundance across reef systems. These patterns give further context to the importance of substrate selection in restoration activities. Invertebrate fauna associated with oyster shell, clam shell, and pelletized coal ash reefs were investigated. Diversity and production were greatest on oyster shell reef. Species richness was lowest on coal ash; however, total community abundance was significantly greater than on the other reef types. Clam shell reefs showed intermediate abundance and diversity patterns but had the lowest values for production. Nekton abundance, diversity, and community structure between reef types were measured. Data show differences in community structure across habitat types. Species richness was greatest on oyster shell and coal ash. Significant differences in nekton presence and abundance between oyster and clam shell reefs were detected. Clam shell reefs were similar in species composition and abundance to a beach habitat. These reef habitats are refuges, as demonstrated by the transient nekton species that dominated all habitats. Oyster shell and coal ash reefs served as habitat to many ecologically, commercially, and recreationally important species, providing food and shelter during juvenile life stages, and suggest reef habitats are of great importance as habitat to finfish communities.

Vitellogenin (VTG) is widely used as a biomarker for environmental estrogens and reproductive disruption in fish. Vitellogenesis is the process by which yolk is formed. The endpoint is most sensitive in male fish where vitellogenesis is an abnormal process. Research examining effects of environmental mixtures of chemicals (e.g. creosote) on vitellogenesis is limited. This study examines plasma VTG expression in both male and female mummichog, Fundulus heteroclitus, collected from a creosote-contaminated site and two reference sites in lower Chesapeake Bay, USA, and in wild-caught male reference fish exposed in the laboratory to creosote-contaminated sediment. Further, this study uses tissue somatic indices (gonadosomatic index, hepatosomatic index, and condition factor) as organ-level indicators of reproductive status and creosote exposure. Western blotting with an anti-vitellogenin monoclonal antibody (FY 10- 9) was used to identify an abundant (approx. 218 kDa) protein in F. heteroclitus plasma samples. Vitellogenin was not observed in any male fish collected from any of the field sites. No sitespecific differences were observed in plasma VTG of females from these sites. Overall, fish from the creosote-contaminated site appear resilient and reproductively fit. After seven days of exposure, reference fish exposed to sediment from the creosote-contaminated site suffered extensive mortality (approx. 25% ), but displayed no expression of VTG and had no alterations in other measured indices except for increased hepatosomatic index and induction of the biotransformation enzyme, cytochrome P4501A (CYPlA). Lack of response in Atlantic Wood fish could be due to: (1) physiological adaptation of the population from the creosotecontaminated site to creosote exposure (2) species-specific sensitivity (3) creosote not exerting estrogenic effects and regulating vitellogenesis. Thus, while VTG has been used successfully as a practical and reliable screening method for wildlife toxicity, results herein do not support use of this biomarker for F. heteroclitus from creosote-contaminated sites. This study does reaffirm constituents of creosote binding to the aryl hydrocarbon receptor resulting in induction of CYP IA. More attention needs to be given to developing alternative biomarkers not sensitive to aryl hydrocarbon-mediated antiestrogens if detection of weak estrogens and reproductive disruption in creosote and other complex mixtures is to be achieved.

High latitude mountain environments are experiencing disproportionately adverse effects in a currently changing climate. The Gulf of Alaska (GoA) region is an exemplar of this. Dramatic shifts are occurring in the region’s freshwater reservoirs as glaciers retreat more with each passing year. Research in the region places much focus on observing and predicting climate driven shifts in glacier mass balance, surface discharge, and associated nutrient fluxes to the ocean. On the other hand, coastal groundwater discharge (CGD) is given very little attention. Global and near-global estimates of CGD indicate variable results spanning an order of magnitude. Focusing on regionally specific processes may provide more reliable estimates of CGD and allow isolation of CGD hotspots. This is of particular importance in the GoA region where complex topography, geology, and climate are coupled with recharge derived from rain, snow, and ice. I estimate CGD to the GoA with a water balance that integrates high temporal and spatial resolution recharge inputs and distinguishes between high conductivity surficial deposit and bedrock catchments. I find that CGD contributes nearly 3% of the total freshwater flux to the GoA, equivalent to a mean annual flux of 20.8 km3, and that CGD has been increasing by 0.5%/year over the past 4 decades. Although freshwater discharge to the GOA is well-constrained, the importance of fresh CGD to the GoA has, thus far, been overlooked.

River herring, collectively alewives (Alosa pseudoharengus) and blueback herring (A. aestivalis), have experienced substantial population declines over the past five decades due in large part to overfishing, combined with other sources of mortality, and disrupted access to critical freshwater spawning habitats. Anadromous river herring populations are currently assessed by counting adults in rivers during upstream spawning migrations, but no field-based assessment methods exist for estimating juvenile densities in freshwater nursery habitats. Counts of 4-year-old migrating adults are variable and prevent understanding about how mortality acts on different life stages prior to returning to spawn (e.g., juveniles and immature adults in lakes, rivers, estuaries, and oceans). This in turn makes it challenging to infer a link between adult counts and juvenile recruitment and to develop effective management policy. I used a pelagic purse seine to investigate juvenile river herring densities, growth, and mortality across 16 New England lakes. First, I evaluated the effectiveness and sampling precision of a pelagic purse seine for capturing juvenile river herring in lakes, since this sampling gear has not been systematically tested. Sampling at night in June or July resulted in highest catches. Precision, as measured by the coefficient of variation, was lowest in July (0.23) compared to June (0.32), August (0.38), and September (0.61). Simulation results indicated that the effort required to produce precise density estimates is largely dependent on lake size with small lakes (<50 >ha) requiring up to 10 purse seine hauls and large lakes (>50 ha) requiring 15–20 hauls. These results suggested that juvenile recruitment densities can be effectively measured using a purse seine at night in June or July with 10–20 hauls. Using juvenile fishes captured during purse seining in June–September 2015, I calculated growth and mortality rates from sagittal otoliths. Density, growth, and mortality were highly variable among lakes, and mixed-effects regression models explained 11%–76% of the variance in these estimates. Juvenile densities ranged over an order of magnitude and were inversely related to dissolved organic carbon. Juvenile growth rates were higher in productive systems (i.e., low secchi depth, high nutrients) and were strongly density-dependent, leading to much larger fish at age in productive lakes with low densities of river herring compared to high density lakes. Water temperature explained 56%–85% of the variation in juvenile growth rates during the first 30 days of life. Mortality was positively related to total phosphorous levels and inversely related to hatch date, with earlier hatching cohorts experiencing higher mortality. These results indicate the importance of water quality and juvenile densities in nursery habitats for determining juvenile growth and survival. This study encourages future assessments of juvenile river herring in freshwater and contributes to an understanding of factors explaining juvenile recruitment that can guide more effective and comprehensive management of river herring.

Cyanobacteria blooms have increased in Lake Champlain due to excessive nutrient loading, resulting in negative impacts on the local economy and environmental health. While climate warming is expected to promote increasingly severe cyanobacteria blooms globally, predicting the impacts of complex climate changes on individual lakes is complicated by the many physical, chemical, and biological processes which mediate nutrient dynamics and cyanobacteria growth across time and space. Furthermore, processes influencing bloom development operate on a variety of temporal scales (hourly, daily, seasonal, decadal, episodic), making it difficult to identify important factors controlling bloom development using traditional methods or coarse temporal resolution datasets. To resolve these inherent problems of scale, I use 4 years of high-frequency biological, hydrodynamic, and biogeochemical data from Missisquoi Bay, Lake Champlain; 23 years of lake-wide monitoring data; and integrated process-based climate-watershed-lake models driven by regional climate projections to answer the following research questions: 1) To what extent do external nutrient inputs or internal nutrient processing control nutrient concentrations and cyanobacteria blooms in Lake Champlain; 2) how do internal and external nutrient inputs interact with meteorological drivers to promote or suppress bloom development; and 3) how is climate change likely to impact these drivers and the risk of cyanobacteria blooms in the future? I find that cyanobacteria blooms are driven by specific combinations of meteorological and biogeochemical conditions in different areas of the lake, and that in the absence of strong management actions cyanobacteria blooms are likely to become more severe in the future due to climate change.

The future of Lake Baikal’s biodiversity is uncertain in response to climate change. Unlike its diverse benthos, Lake Baikal’s zooplankton is species poor, with up to 96% of its biomass being composed of a single Calanoid copepod species, Epischura baikalensis. This study characterizes the genetic differentiation and differential gene expression of E. baikalensis. Using partial-transcriptome sequences obtained by 454 Rosche and Illumina sequencing technologies, the genetic differentiation at inferred single nucleotide polymorphism (SNP) sites and differential gene expression in populations sampled from various parts of the lake were analyzed. The functional genomics of genes showed significant differential expression among the lake’s regions with some genes being highly up-or down-regulated. High genetic differentiation among regions suggests isolated subpopulations. Moreover, significantly differentially expressed transcripts were significantly more genetically differentiated than transcripts exhibiting no differential expression. These results suggest high potential phenotypic plasticity and adaptability in response to climate change, e.g., temperature.

A major economic constraint in the Bahamas, and other small carbonates islands world-wide, is the lack of fresh water resources. To combat these socio-economic problems on San Salvador Island I sought to gain a more detailed understanding of the extent, behavior, and controls on the island’s fresh-water lens. DC electrical resistivity tomography and time-series geochemical data are used to study the fresh water lens at the Line Hole well field. Electrical Resistivity profiles are used to image the extent of fresh water resources. Time-series geochemical data provide information on the behavior of the fresh water resources as a function of time. The inversion models of the electrical resistivity profiles illustrate a fresh water lens less than 3 meters thick on average. The mixing zone is diffuse in nature, and substantially thicker than the fresh water lens. The geochemical results corroborate the fresh water lens dimensions predicted by the electrical resistivity model. In addition, mixed semi-diurnal and spring/neap tidal cycles are the primary control on the water level. Statistical analysis of specific conductance and temperature illustrate a positive and negative correlation with water level, respectively. Analysis of precipitation with respect to water level and geochemistry indicate low effective recharge rates during the period of study. The current state of the water resources at the Line Hole well field is strained. Despite moderate levels of freshening since the termination of pumping in December 2006; the system continues to be in a state of disequilibrium. The problem is compounded by abnormal thickening of the mixing zone due to communication of the well field with the ocean, and a limited volume of fresh water. In conclusion, the two techniques used in conjunction provide a non-invasive method of estimating fresh water resources in this type of setting. Conversely, the high RMS and L2 values for the electrical resistivity models and limited time-series data create a high level of uncertainty in the interpretation of results.

The City of Auburn is faced with a number of problems relating to its dependency on two karst springs, Auburn and Summers Springs, to meet its water requirements. Besides being extremely vulnerable to contamination, the springs often discharge and insufficient volume of water needed for public consumption and dilution of the City’s treated wastewater. Thus the City wishes to find an additional source of water and views nearby Shakertown Spring as a possibility. The study has three main objectives: 1) delineation of the Auburn, Summers, and Shakertown Springs ground water basins, 2) determination of the volume of available water at each spring, and 3) investigation of additional potential water supplies as alternatives to the use of Shakertown Spring. A well survey and karst hydrogeological inventory, supplemented by dye tracing, were conducted to reveal water table information necessary for ground water basin delineation and construction of a potentiometric map. Water monitoring stations were constructed at the three springs, discharge measurements performed and stage monitored over a fifteen month period. The Auburn, Summers, and SHakertown Springs Karst Ground Water Basins are estimated to possess areas of 9.74, 3.49 and 19.02 square miles (25.23, 9.04, and 49.26 square kilometers) respectively. Summers Spring was found to have an estimated base flow discharge of 1 – 2 cubic feet per second (cfs) (0.03 – 0.06 cubic meters per second (cms)) and Shakertown Spring an estimated base flow discharge of 8 – 9 cfs (0.2-0.3 cms). Estimation of base flow discharge at Auburn Spring was not possible due to the location of the City’s water intake pipe at the spring head. However, a minimum discharge of .22 cfs (0.01 cms) was recorded on thirteen separate occasions during the period monitored. Five alternatives for the City of Auburn, including Shakertown Spring and two additional, though smaller, water sources are presented. The best source of water for the City must be decided with consideration of cost and need. A potentiometric map depicting ground water basins, water table contours and subsurface flow routes is presented as a tool for the City of Auburn to aid in decisions regarding its water resources.

Vernal pools are small, ephemeral wetlands lacking an inlet or outlet. These wetlands, also known as seasonal pools, are found in a wide range of biomes, and their characteristics vary based on location. While the vegetation of western U.S. pools, and amphibians of eastern U.S. pools have been extensively studied, many aspects of vernal pools have not been fully characterized. In particular, although the general seasonal wetting and drying cycle is understood qualitatively, few studies have attempted to quantify the hydrological regime of vernal pools in New England. As water level variation drives many, if not all, of the characteristics unique to these systems, more research on this aspect of vernal pool functioning is needed. The primary objective of this study was to gain a better understanding of vernal pool hydrology through the study of a complex of three pools in South Deerfield, MA. The water level in the South Deerfield pools has been monitored since 2009. For this study, the most recently recorded water year (1 October 2017 to 30 September 2018) was used to characterize the water level fluctuations in the Middle Pool. Water level was monitored manually (weekly intervals) and with pressure transducers (4-hour intervals) in permanently installed wells. The effects of precipitation and evapotranspiration on water level were quantified with a water balance analysis. This analysis also estimated changes in storage by estimated inflow from the uplands and outflow via deep seepage. Water level changes in the Middle Pool were consistent with qualitative descriptions and trends described in earlier studies in the region. We found that the countervailing effects of precipitation and evapotranspiration were the primary drivers of water level fluctuations throughout the year. However, the estimate of storage derived as a water balance residual was not representative of water level in the vernal pools. The storage estimate derived for the Middle Pool was more successful at estimating the water level during spring transition, the high water period most important to amphibian breeding.

The Saltville valley in southwestern Virginia is home to Quaternary localities containing paleontological and archaeological remains. Historically the valley has been mined for salt and the small lakes, ponds and springs along the valley floor have a brackish signature. A preliminary report on the site’s ostracode fauna suggested that the site’s water was not always saline. This study analyzed modern and Quaternary ostracodes to understand the valley’s hydrologic and chemical evolution. Sediments contained primarily freshwater species, including the environmentally sensitive Candona crogmaniana. The presence of Pelocypris tuberculatum and a new Fabaeformiscandona species throughout a vertical section spanning the latest Pleistocene and Holocene suggests that ephemeral pools were being fed by freshwater springs throughout the latest Quaternary. Climate ranges, estimated through species autecology and MOTR, reveal that the site’s mean annual temperature was between 0 - 19.1℃. Ostracode salinity tolerances suggest that the site was fresh during the sampled record.