Blue marlin Makaira nigricans and white marlin Kajikia albida (formerly Tetrapturus albidus) are overfished in the Atlantic Ocean, with the vast majority of fishing mortality resulting from the pelagic longline fishery that targets tunas (Thunnus spp.) and swordfish Xiphias gladius. Time series of catch-per-unit-effort (CPUE) data have been fundamental to assessments of blue marlin and white marlin stocks, but these time series have been affected by a shift over time in pelagic longline fishing practices from shallow to deeper sets. One method for adjusting CPUE data for changes in fishing practices is a habitat-based standardization that modifies fishing effort in proportion to the vertical distribution of the species of interest and the fishing gear. For these models to be successfully applied to population assessments, the vertical habitat utilized by blue marlin and white marlin must be known. Pop-up satellite archival tags (PSATs) provide a means of collecting high resolution vertical movement and distribution data for billfishes. In my study, 62 blue marlin and 40 white marlin were caught in recreational fisheries off the U.S. mid-Atlantic, Yucatan Peninsula, northern Caribbean, Venezuela, and Brazil, tagged with Microwave Telemetry, Inc. PTT-100 HR PSATs, and released. Data were recovered from PSATs attached to 57 surviving blue marlin and 36 surviving white marlin. PSATs successfully transmitted 18-100% of the data they recorded (mean 72%). The minimum 10-day displacements of both species averaged 242 km (range 9 to 942 km) and varied significantly between tagging locations, but not between species. Blue marlin spent a significantly higher (62%) amount of time in the upper 10 m of water than white marlin (56%). Both species spent greater than 95% of the time in water that was within 8o C of the sea surface temperature. Only 3.1% of white marlin demonstrated diel differences in the maximum depth of dives, while 29% of blue marlin dove into deeper waters during the day. Variables identified as explaining the most variation in dives were total dive duration, bottom time, ascent time, number of wiggles, wiggle depth, interdive interval, skew of ascent and descent, % time ascending, and % time descending. Using these variables, two dive types were identified through cluster analysis: simple dives representing traditional "U" and "V" shapes, and complex dives with multiple descents, plateaus, and wiggles. There were significant differences in dive variables among locations, individuals, diel periods, and dive types. There was significant overlap in range, habitat use, and vertical movement patterns, and therefore no strong evidence of niche partitioning between blue marlin and white marlin. My analyses can be used to further define the physical and physiological factors limiting marlins' vertical movements and therefore improve stock assessments based on longline CPUE data by correcting for changes in fishing practices.

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Microzooplankton (zooplankton 20 – 200 μm) are an integral part of aquatic food webs as they can be significant grazers of phytoplankton and bacteria, remineralizers of nutrients, and prey for higher trophic levels. The importance of microzooplankton in many pelagic ecosystems has been established, yet compared to larger zooplankton, microzooplankton are understudied in the Southern Ocean. I quantified microzooplankton community composition and grazing rates along the Western Antarctic Peninsula (WAP) as part of the Palmer Antarctica Long-Term Ecological Research project (PAL LTER). This region is experiencing rapid warming, causing declines in sea ice and changes in the marine food web. I determined distributions of major microzooplankton taxa in January 2010 and 2011 within the top 100 m of the water column, along both north-south and coastal-offshore gradients of the WAP, using microscopy. I found that microzooplankton are potentially adjusting to climate changes along with other trophic levels, as there was generally higher microzooplankton biomass in the south compared to the north. Biomass was higher in surface waters compared to 100 m, and variability in microzooplankton biomass between years and with distance from shore appeared to be influenced by sea ice dynamics. Microzooplankton biomass was also positively correlated with chlorophyll-a and particulate organic carbon (POC), and biomass of several microzooplankton taxonomic groups peaked near Marguerite Bay, historically a productivity hot spot. I also calculated phytoplankton and bacterial growth and grazing mortality rates using the dilution method at select stations along the WAP in January 2009 – 2011 and in the near shore waters near Palmer Station in February – March 2011. Microzooplankton exerted higher grazing pressure on bacteria, relative to grazing on phytoplankton. Microzooplankton also exhibited selective grazing on smaller phytoplankton (picoautotrophs and nanophytoplankton), and on the more actively growing bacterial cells, thus shaping phytoplankton and bacterial assemblages and effectively cropping production. There was a significant (albeit weak) positive correlation between temperature and phytoplankton grazing mortality. My research is the first to describe both the microzooplankton structure and grazing impact in the PAL LTER study region. This study contributes valuable information to studies modeling the flow of carbon through the WAP food web and provides a reference point for studying how future changes will affect microzooplankton community structure and food web dynamics in this region.

In terrestrial systems, seed burial is widely recognized as a vital process that influences small- and large-scale plant population patterns. Despite its demonstrated importance in terrestrial literature, very little is known about seed burial in seagrasses. Zostera marina is a perennial seagrass found in northern temperate oceans worldwide, and is the dominant seagrass found in the Chesapeake Bay. In terrestrial systems, seed burial is frequently mediated by soil-dwelling invertebrates. The goal of this work was to determine the role that benthic infauna play in the burial of Z. marina seeds by addressing the following questions: 1. Are seeds on sediments containing infauna buried more quickly than sediments without infauna, and 2. Does the infaunal feeding mode (e.g. head-up vs. head-down feeder, sessile vs. errant, or deposit feeder vs. omnivore) affect seed burial? Three mesocosm studies were conducted in sediment cores (80cm2 x 11cm) collected from the Chesapeake Bay, defaunated, and populated with single specimens of infauna of different feeding modes: Amphitrite ornata (sessile head-up deposit feeder), Neanthes succinea (errant omnivore), or Clymene/la torquata (sessile head down deposit feeder), or Pectinaria gou/di (errant head down deposit feeder). Control cores had no specimen added. Ten particles (either Z. marina seeds or colored beads) were added to the surface of each core, and the depth of the particles was detennined at different time scales up to 14 days. Seeds in all animal cores were significantly more likely to be buried than seeds in control cores (p~1.03x 1 0"6 ), although burial rates varied by species. N. succinea and P. gou/di showed the most dramatic burial: ~55% of seeds buried after 3 days and seeds buried below 2.5cm and 4.0cm, respectively, after 2 weeks. N. succinea also showed evidence for actively burying seeds. A. ornata and C. torquata had 12% and 24% of seeds buried, respectively, after 3 days and both had seeds buried below l.Ocm after 2 weeks. The results of this study indicate that Z. marina seed burial is facilitated by infaunal activity, and that burial patterns are species specific. In addition, burial is rapid and occurs on a time scale of days. While abiotic processes may be initially important in seed burial, the direct (active movement of sediment), and indirect (formation of mounds and holes) consequences of biotic processes by infauna may prove to be dominant and relevant to seed escape from predation, retention in suitable settlement sites, and movement to a sediment depth suitable for germination.

The Ross Sea is a highly productive region of the Southern Ocean characterized by spatially variable distribution of phytoplankton, primarily Phaeocystis antarctica, but phytoplankton growth rates in the region have not been thoroughly investigated. Variability in growth rates was investigated from January to February 2012 on a cruise to the Ross Sea using two methods: 14C-isotopic tracer incubations and dilution experiments. Because all methods of measuring growth rates may not be appropriate in all systems due to errors inherent to each method, I assessed and compared the two methods for possible sources of error by examining the effect of extended incubations on measured growth rates in 14C-incubations, quantifying phytoplankton growth and grazing mortality rates through dilution experiments, and analyzing the effect of irradiance in incubations on carbon:chlorophyll ratios in dilution experiments. I found that dilution experiments yielded variable growth rates based on chlorophyll and cell abundance; the mean growth rate based on chlorophyll was 0.11 d-1 while mean growth rate based on abundance was 0.12 d-1. Chlorophyll-based growth rates may be inaccurate due to carbon:chlorophyll ratios of phytoplankton changing during incubations. This unbalanced growth is likely due to variable mixed layer depth and subsequent variability in light history of phytoplankton. Grazing mortality rates were non-significant in 7 of the 11 dilution experiments conducted and significant mortality rates were low with a mean mortality rate of 0.09 d-1, most likely because of low temperatures rather than the presence of P. antarctica. Growth rates measured in 14C-incubations did not change in extended incubations, indicating that loss of fixed 14C through grazing and respiration was not a major source of error. Growth rates were below those predicted based on temperature alone (p<0.001), and mean growth rate in 14C-incubations was 0.14 d-1. Structural equation modeling indicated that growth rates in 14C-incubations did not strongly vary with mixed layer depth, but were significantly affected by low iron concentrations, most likely due to the seasonal depletion of iron. As grazing is low and physical conditions vary spatially, dilution experiments may not be an appropriate measure of growth rate in the Ross Sea, but 14C-incubations yield relatively low growth rates that are significantly affected by low iron concentrations in the region.#

Sexual reproduction and the production of seeds are important for the resilience of all angiosperm species. For clonal species, such as the seagrass Zostera marina, resource allocation is complicated because these species reproduce both asexually and sexually, and the factors contributing to allocation to these two processes remains unknown. The goal of this study was, therefore, to investigate the importance of critical light, nutrient, and rhizome resources on Z. marina sexual reproduction and flowering intensity. To evaluate the importance of sediment nutrients on Z. marina flowering intensity two distinct field manipulative experiments and one field survey were initiated: 1. Sediments within established Z. marina were fertilized during two periods of active growth (spring and fall) at two contrasting (estuarine and coastal lagoon) locations and the subsequent development of flowering was recorded, 2. Rhizome segments were transplanted to adjacent unvegetated environments to investigate the effects of sediment nutrients on individual shoots, 3. Surveys within and between three locations with apparent differences in sediment structure were designed to investigate the relationship between sediment conditions and flowering intensity. Rhizome segments were also transplanted to adjacent unvegetated environments to test the effect of shoot availability (with each segment having one, two, or three shoots) on sexual reproduction. To evaluate the importance of light and rhizome resources to flowering, two experiments and one field survey were also initiated: 1.In situ light availability was reduced using neutral density shading to test if light availability affected flowering intensity, 2. A field survey using fixed piers as shade structures was also used to determine if long-term shading influenced Z. marina flowering, 3. Cutting of rhizome connections of in situ plants was used to test if acute stress to below ground tissue prior to the development of flowering shoots would influence investment in sexual reproduction. The addition of supplemental nutrients to the sediment during the fall growth period increased the number of spathes per flowering shoot the following spring relative to control plots at both estuarine and coastal lagoon locations. Similarly, field surveys across three locations demonstrated a direct relationship between ammonium availability and the percentage of flowering shoots. Although short term in situ shading did not significantly affect flowering intensity, measurements of flowering intensity around piers revealed lower percentages of flowering shoots directly beneath piers than areas one or three meters perpendicular to the pier. Eleven percent of transplants also produced more flowering shoots than the initial shoots planted indicating the development of flowering shoots can occur on shoots less than three months old. Combined, these results indicate resource availability can influence sexual reproduction. Increasing belowground plant and nutrient resources increased investment in both vegetative and sexual reproduction, whereas, long term reductions in light resources were found to only decrease sexual reproduction. This suggests that the duration and magnitude of resource availability are both important in determining the allocation of resources towards sexual reproduction, and through this investment the degree of resiliency in seagrass populations in an increasingly stressed coastal environment.

Temporal changes in mesozooplankton community structure are influenced by a combination of environmental factors. Epipelagic mesozooplankton biomass in the Sargasso Sea has increased over the last two decades, with a related increase in zooplankton-mediated carbon export. Unknown, however, are the patterns and variability at different temporal scales (diel, seasonal, and interannual) in abundance of each major zooplankton taxon, and how these patterns relate to physical and other environmental changes. I enumerated major taxa of mesozooplankton collected from monthly day and night net tows in the epipelagic zone at the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea from 1999 to 2010. Abundances of each taxon were determined using a ZooScan optical imaging system and microscopy. Generalized Linear Models (GLMs) were used to determine what environmental parameters best explain abundance of major taxa. I used annual averages to determine broader patterns. Zooplankton taxa with the most pronounced diel vertical migration (i.e., night:day ratio, N:D, » 1 ) included euphausiids (N:D=1.9), Limacina spp. pteropods (1.5), and other thecosome (shelled) pteropods (1.6). Taxa with a pronounced spring abundance peak included euphausiids, larvaceans, and Limacina spp., while harpacticoid copepods peaked in late summer, and calanoid copepods in both spring and summer. There is some evidence of changes in phenology occurring in calanoid copepods and chaetognaths that exhibited spring abundance peaks on average 1-month earlier than reported for the same taxa in the early 1960’s. Many taxa, including all copepod taxa, exhibited a period of highest abundance increase in 2003, coinciding with a 2003 April diatom bloom and the largest primary production peak (April 2003) in the time series. There was also indication of a long-term increase in calanoid and oncaeid copepod abundance. Sub-decadal-scale climate oscillations, long term warming, and ocean acidification may be driving decreases in larvaceans, Limacina spp., and other shelled pteropod densities. Environmental variables affecting abundance differed among taxa. For example, calanoid copepod density was highly influenced by the abundance of a major predatorchaetognaths. Multi-year densities of calanoid copepods and ostracods both increased with increasing Water Column Stratification Index and the Atlantic Multidecadal Oscillation (AMO) index, indicating warmer sea surface temperatures are favorable for these taxa. These patterns in zooplankton community structure have important implications for energy transfer in pelagic food webs and for biogeochemical cycling.

Estuaries are biogeochemical hotspots connecting terrestrial and coastal ecosystems. Anthropogenic disturbances, including increased nitrogen loading and plastic pollution, may have significant impacts on estuarine carbon and nitrogen cycling by altering microbiome structure and functions. The overarching goal of this dissertation was to examine how microbiomes and their associated biogeochemical processes are influenced by natural variation and anthropogenic disturbances in the York River Estuary (YRE). In chapter 2, spatial and temporal variation in benthic microbiomes and the rates of denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) were examined to determine biotic and abiotic drivers of nitrogen removal and retention. In the YRE, nitrogen removal, largely in the form of denitrification, dominated at the head of the estuary while nitrogen retention through DNRA dominated at the mouth. Denitrification was linked to a large community of denitrifying organisms, sediment organic matter, nitrate/nitrite concentrations, salinity, and chlorophyll a, while DNRA was best predicted by the abundance of specific taxa, Desulfobacterales and Sphingobacteriales, as well as temperature and the concentration of ammonium. The impacts of the harmful algal blooms of Margalefidinium polykrikoides and Alexandrium monilatum that occur in the lower portion of the estuary were examined in Chapter 3. Blooms of both species altered the water column microbiome of the YRE. The M. polykrikoides bloom, with its higher concentration of dissolved organic carbon and close associations with heterotrophic bacteria, likely has a greater impact on the estuarine carbon cycle than the A. monilatum bloom. The A. monilatum bloom did not impact the overall prokaryotic community, but appeared to selectively enhance a small group of prokaryotes in the particle-associated fraction. Chapters 4 and 5 investigated plastic pollution in the YRE. A method was developed to isolate, quantify, and identify the polymer type of plastic particles in wastewater treatment plant effluents using Raman microspectroscopy (chapter 4); microplastic particles composed of polyethylene were found to be the most common. Microplastics composed of polyethylene, polyvinyl chloride, and polylactic acid were deployed to the YRE and the microbial biofilm communities growing on each type of plastic were examined over time to determine their taxonomic and functional profiles (chapter 5). All three microplastic types were found to contain potential hydrocarbon degrading bacteria, as well as nitrogen cycling bacteria capable of performing nitrification, denitrification, and DNRA. Overall, this dissertation investigated how microbially mediated nitrogen cycling processes can remove or retain fixed nitrogen, how algal blooms can change an estuary’s microbiome, and how the addition of microplastic pollution can provide new habitat for microbes that can perform nitrogen cycling and hydrocarbon degradation in the water column.

Chone mollis occurs in large numbers in Tomales Bay and is an ecologically important infaunal member of the bay community. As with most marine communities, very little work has been done with individual species of the community. The present study of C. mollis is a contribution towards an understanding of the community as an ecological unit. This study investigates the structure and function of the tube; tube-building habits; burrowing and locomotion; external anatomy; feeding; and internal anatomy of the muscular, skeletal, vascular, excretory, reproductive, and alimentary systems of C. mollis.