Dissertations / Theses on the topic 'Biological oceanography'

The work in this dissertation represents an attempt to investigate multiple temporal and spatial scales of inquiry relating to the variability of marine resources throughout the Gulf of Mexico large marine ecosystem (Gulf LME). This effort was undertaken over two spatial extents within the greater Gulf LME using two different time-series of fisheries monitoring data. Case studies demonstrating simple frameworks and best practices are presented with the aim of aiding researchers seeking to reduce errors and biases in scientific decision making. Two of the studies focused on three years of groundfish survey data collected across the West Florida Shelf (WFS), an ecosystem that occupies the eastern portion of the Gulf LME and which spans the entire latitudinal extent of the state of Florida. A third study was related to the entire area covered by the Gulf LME, and explored a 30-year dataset containing over 100 long-term monitoring time-series of indicators representing (1) fisheries resource status and structure, (2) human use patterns and resource extractions, and (3) large- and small-scale environmental and climatological characteristics. Finally, a fourth project involved testing the reliability of a popular new clustering algorithm in ecology using data simulation techniques.

The work in Chapter Two, focused on the WFS, describes a quantitatively defensible technique to define daytime and nighttime groundfish assemblages, based on the nautical twilight starting and ending times at a sampling station. It also describes the differences between these two unique diel communities, the indicator species that comprise them, and environmental drivers that organize them at daily and inter-annual time scales. Finally, the differential responses in the diel, and inter-annual communities were used to provide evidence for a large-scale event that began to show an environmental signal in 2010 and subsided in 2011 and beyond. The event was manifested in the organization of the benthic fishes beginning weakly in 2010, peaking in 2011, and fully dissipating by 2012. The biotic effects of the event appeared to disproportionately affect the nighttime assemblage of fishes sampled on the WFS.

Chapter Three explores the same WFS ecosystem, using the same fisheries-independent dataset, but also includes explicit modeling of the spatial variability captured by the sampling program undertaking the annual monitoring effort. The results also provided evidence of a disturbance that largely affected the nighttime fish community, and which was operating at spatial scales of variability that were larger than the extent of the shelf system itself. Like the previous study, the timing of this event is coincident with the 2010 Deepwater Horizon oil spill, the subsequent sub-marine dispersal of pollutants, and the cessation of spillage. Furthermore, the spatial models uncovered the influence of known spatial-abiotic gradients within the Gulf LME related to (1) depth, (2) temperature, and (3) salinity on the organization of daytime groundfish communities. Finally, the models developed also described which non-spatially structured abiotic variables were important to the observed beta-diversity. The ultimate results were the decomposition of the biotic response, within years and divided by diel classification, into the (1) pure-spatial, (2) pure-abiotic, (3) spatial-abiotic, and (4) unexplained fractions of variation.

Chapter Five employs a clustering technique to identify regime states that relies on hypothesis testing and the use of resemblance profiles as decision criteria. This clustering method avoids some of the arbitrary nature of common clustering solutions seen in ecology, however, it had never been rigorously subjected to numerical data simulation studies. Therefore, a formal investigation of the functional limits of the clustering method was undertaken prior to its use on real fisheries monitoring data, and is presented in Chapter Four. The results of this study are a set of recommendations for researchers seeking to utilize the new method, and the advice is applied in a case study in Chapter Five.

Chapter Five presents the ecosystem-level fisheries indicator selection heuristic (EL-FISH) framework for examining long-term time-series data based on ecological monitoring for resources management. The focus of this study is the Gulf LME, encompassing the period of 1980-2011, and it specifically sought to determine to what extent the natural and anthropogenic induced environmental variability, including fishing extractions, affected the structure, function, and status of marine fisheries resources. The methods encompassed by EL-FISH, and the resulting ecosystem model that accounted for ~73% of the variability in biotic resources, allowed for (1) the identification and description of three fisheries resource regime state phase shifts in time, (2) the determination of the effects of fishing and environmental pressures on resources, and (3) providing context and evidence for trade-offs to be considered by managers and stakeholders when addressing fisheries management concerns. The EL-FISH method is fully transferrable and readily adapts to any set of continuous monitoring data. (Abstract shortened by ProQuest.)

Recruitment of marine fishes is largely determined by biological and oceanographic factors acting on early life stages. Coastal upwelling has long been recognized as a critical factor influencing the survival of larvae and recruitment to adult populations. Dynamics in regional upwelling influence the magnitude and timing of primary productivity, affecting the availability of critical food sources for larval fish. In addition, upwelling-relaxation cycles affect the dispersal of marine larvae and their onshore delivery prior to settlement. Challenges with tracking larvae, however, have limited our understanding of how oceanography influences the early life stages of fishes. The objective of this dissertation is to evaluate the biological and oceanographic drivers of larval growth, settlement, and recruitment, using rockfishes ( Sebastes spp.) as model organisms.

Overlap of larval production and favorable feeding conditions may drive recruitment for many temperate marine fishes, as small changes in larval growth can result in order-of-magnitude differences in year-class-strength. In Chapter 1, I assess the influence of regional productivity, temperature, and larval condition in explaining growth in rockfishes. I employ a combination of otolith microstructure and satellite imagery to measure initial larval growth and estimate the productivity and temperature experienced by individuals to determine their relative importance in subsequent growth at metamorphosis. I compare model performance using indexed environmental conditions scaled over three different regions. In both years of study, net primary productivity explained the most variation in pre-metamorphic growth relative to temperature and initial growth. This relationship was consistent across spatial regions. Recent settlement, juvenile recruitment, and individual growth were significantly higher in a year when productivity bloomed earlier and individual larvae experienced higher levels of productivity. These results support the hypothesis that large-scale oceanographic processes that stimulate upwelling and secondary production are primary drivers of larval growth and subsequent year-class strength in rockfishes.

Characterizing the behavior of larvae prior to settlement is integral to understanding population dynamics because coastal oceanography may facilitate or limit settlement. Otolith microchemistry can be used to determine patterns of fish movement, although there is a limited understanding of how this tool can be applied in coastal marine systems. My goal in Chapter 2 is to evaluate the application of otolith microchemistry to characterize water mass associations of settlement-stage marine fish in a coastal upwelling region using a three-step approach. First, I characterize seawater chemistry of coastal water masses across multiple years, finding significant differences in the chemical signatures of strong upwelling, weak upwelling, and relaxation. Second, I experimentally determine the effect of temperature on the partitioning of trace elements in otoliths for two rockfishes to find that the effect of temperature on otolith partition coefficients was element- and species-specific. Finally, I compare the synchrony in seawater and otolith chemistry of settlement-stage rockfishes that were exposed to naturally variable conditions over an upwelling-relaxation cycle. I subsequently evaluate whether laser ablation inductively coupled plasma mass spectrometry effectively measures otolith chemistry over ecologically relevant time scales. I discovered that elemental concentrations in otoliths respond rapidly to changes in seawater chemistry and reflect equivalent proportional changes. This study provides evidence that elemental signatures are valuable tools for reconstructing larval histories of marine fish.

In Chapter 3, I use otolith chemistry to examine water mass associations of two juvenile rockfishes during onshore transport and settlement in an upwelling region. I develop a chemical proxy for upwelling and relaxation by characterizing Sr/Ca and Ba/Ca signatures of otoliths collected during these oceanographic conditions. Otolith chemistry differed between rockfishes collected during upwelling and relaxation, with signatures unique to each year. I subsequently compare otolith signatures of rockfishes collected during high and low settlement periods to determine whether specific water masses affect settlement. I provide evidence that copper rockfish associate with upwelling currents during periods of high settlement, suggesting that upwelling may facilitate settlement for these species. Conversely, I found evidence that the closely related gopher rockfish associate with relaxation events during peak settlement periods. This research takes an important first step at in evaluating the utility of trace element signatures to characterize larval fish movement during onshore delivery and settlement in marine systems. Together, these studies improve our understanding of how coastal upwelling impacts larval growth, settlement, and recruitment, which provides important information for understanding population dynamics in marine ecosystems.

Burial is an important life history strategy employed by benthic fishes that has not been fully explored in its diversity by the biomechanical literature. This thesis explores the mechanism by which the Pacific sandfish buries as well as the physical limitations of the behavior. We first investigate the role of the ventilatory pump in the burial behavior of sandfish by using high-speed videography, dye, and digital particle image velocimetry (DPIV). We determined that sandfish employ a modification of the ventilatory pump, which is used repeatedly to fluidize the substrate ventral to the head. This modification of the ventilatory pump should reduce the energetic costs associated with burial as it decreases the cost of transport typically associated with ‘shoveling’ substrate. Second, we investigate the physical limitations that are caused by the reliance on the ventilatory pump to fluidize substrate. We used sand beds of varying grain sizes, and therefore varied the minimum velocities of fluidization, to determine how sandfish respond variation in substrata. We determined that sandfish can bury in grains smaller than 1.00mm in diameter but were unable to bury in any substrate larger than 1.00mm. We also determined that there was an increase in the time it took sandfish to bury in those substrates smaller than 1.00mm as grain size increased. There was no change in the frequency of the behavior, however, suggesting that sandfish have very little ability to bury in larger substrates. We also determined that it is probably not the absolute velocity produced by the opercular jet that determines burial success, but the ability burying behavior to maintain the sand’s momentum during the expansive phase that occurs between bouts of opercular jetting.

Shallow subtidal epibenthic communities worldwide are under threat from exploitation, pollution, eutrophication, acidification, climate change, and invasive species, with implications for ecosystem diversity, productivity, function, and services. Subtidal ecosystems in the Gulf of Maine are particularly impacted, making it crucial to understand these habitats so that our impacts can be predicted and mitigated. I investigated the basic ecological forces that structure shallow subtidal epibenthic communities in this region, and how invasive species integrate themselves into these communities. I used community phylogenetic and functional trait analyses to investigate if invertebrate communities in the rocky subtidal are assembled via deterministic or random forces, experimental manipulations to quantify how macroalgae might influence sessile invertebrates on subtidal surfaces, and measurements of life history traits of Botrylloides violaceus, an invasive colonial ascidian, to estimate whether growth of this species differs among man-made versus natural habitats. Based on community phylogenetic analyses, rocky subtidal invertebrate communities appear to be structured by deterministic forces, with evidence for both competitive exclusion and environmental filtering operating at different spatial scales. These findings support existing studies that show that competition structures communities at local scales, and also expand our knowledge of the processes that act regionally, i.e. environmental filtering. On shallow sunlit experimental surfaces suspended from floating docks, macroalgae had little effect on invertebrate abundance or diversity, contrary to findings from experiments in the rocky subtidal. Macroalgae did influence composition as well as enhance invertebrate colonization in the early stages of community assembly. Different factors appear to influence the balance between heterotrophs and autotrophs in floating dock and rocky subtidal systems with implications for community structure, function and productivity. In different habitats, colonies of the invasive ascidian B. violaceus exhibited differences in life history traits. It grew faster and attained larger sizes in man-made floating dock versus natural rocky subtidal and eelgrass bed habitats. Again, differences among habitats appear to influence invasion success. In conclusion, competitive exclusion, facilitation, and environmental filtering play key roles in controlling the structure, composition, and function of shallow subtidal communities. Invasive species have the potential to disrupt these forces as they integrate themselves into man-made and subsequently natural habitats.

Most of the seafloor is soft sediment, so hard substrata are isolated and island-like. In this dissertation, I explore how species distribution patterns on isolated marine hard substrata resemble terrestrial island communities, drawing on classical island biogeography theory and assembly rules, and describe how benthic invertebrate communities assemble in these island-like habitats. Higher species richness occurred on larger substrata (dropstones and shipwrecks), paralleling terrestrial island communities. However, while larger islands have greater habitat diversity and primary productivity, marine hard substrata are simpler habitats. Greater elevation in the benthic boundary layer may expose fauna to faster current, higher food supply and larval flux. Substrata located closer together had more similar communities, another pattern that resembles terrestrial islands. Dropstone fauna had a clumped distribution, indicating that larvae may disperse among substrata located close together, resulting in similar communities. In Svalbard fjords, benthic megafaunal communities were significantly different between Arctic- and Atlantic-influenced fjords. Depth and temperature had the greatest influence, with the highest diversity occurring in cold Rijpfjorden and on the north Svalbard shelf. Recruitment in Svalbard fjords was spatially and temporally variable, with lower recruitment in Rijpfjorden than in Atlantic-influenced fjords and lower recruitment at greater depth. Most of the recruits in Svalbard fjords were fast-growing, poor-competitive opportunists. On shipwrecks, communities showed two mechanisms of colonization: mobile fauna with long-dispersing planktotrophic larvae, and encrusting fauna with lecithotrophic larvae. Encrusting species reproduce asexually to cover the wreck surface, and philopatry may build up dense populations, leading to uneven communities. On terrestrial islands, non-random co-occurrence is attributed to interspecific competition, but for marine substrata, there may not be a relationship. Fauna were distributed randomly on settlement plates in Svalbard fjords, even when interspecific competition was observed. On dropstones, some morphotypes co-occurred non-randomly in the absence of overgrowth competition. Non-random co-occurrence on isolated marine hard substrata may be a result of restricted larval dispersal (for pairs co-occurring less than by chance) or epibiontism (for pairs co-occurring more often than by chance). While species distribution patterns on island-like marine hard substrata resemble terrestrial islands, the mechanisms are not necessarily the same.

Ocean acidification can reduce survival and growth of marine larvae. However, if populations have the genetic capacity to adapt and increase their tolerance to low pH levels, then such genetic changes may offset the harmful effects of ocean acidification. I used methods in quantitative genetics to measure the genetic variance and project the potential rate of evolution for low pH tolerance in a nearshore forage-fish: the California grunion ( Leuresthes tenuis). I raised grunion larvae across an experimental pH gradient and measured their mortality and growth rates over a 14-day interval during the early larval stage. My results indicated that low pH levels significantly decreased the survival rates of grunion larvae overall. Surprisingly, low pH levels did not significantly affect larval growth rates. However, families varied widely with respect to pH tolerance, and many families had similar mortality and growth rates in high and low pH treatments. Quantitative genetic analyses indicated that low pH tolerance had a substantial genetic basis and is highly heritable within grunion populations. These results suggest that populations of California grunion, and possibly other nearshore fishes, may adapt relatively quickly to long-term changes in ocean pH.

SEM observations have revealed unknown and previously undetected stages of the bloom-forming dinoflagellate Prorocentrum growing inside calcium carbonate-encrusted perithallial cells of the rhodolith-forming Lithothamnion sp. (Hapalidiaceae, Hapalidiales, Rhodophyta) in the NW Gulf of Mexico. Roundish structures inside the coralline cells were clustered together, surrounded by a thin membrane. Organized blebs, projections of the cytoplasm into the plasma membrane, as well as a suite of varying extracellular ornamentation patterns, were observed. Openings on the surface of some of the structures looked like characteristic thecal pores found in thecal plates of some dinoflagellates. DNA was extracted from inside the rhodolith and sequenced using dinoflagellate-specific cob1-primers. When blasting the resulting DNA sequences, it proved to be an exact match for Prorocentrum lima. Cells were isolated from inside the rhodoliths and cultured, revealing the presence of another set of endolithic life stages identified as Haptophyta (Prymnesiophyta), confirmed by single cell 18S rDNA sequencing. This research illustrates and illuminates newly found benthic life history stages of two ecologically important taxa of primary producers that also cause harmful algal blooms, such as the formation of red tides, fish kills, or shellfish poisoning events in the Gulf of Mexico.

The Coastal and Marine Ecological Classification Standard (CMECS) provides a comprehensive framework of common terminology for organizing physical, chemical, biological, and geological information about marine ecosystems. Federally endorsed as a dynamic content standard, all federally funded data must be compliant by 2018; however, applying CMECS to deep sea datasets and underwater video have not been extensively examined. The presented research demonstrates the extent to which CMECS can be applied to deep sea benthic habitats, assesses the feasibility of applying CMECS to remotely operated vehicle (ROV) video data in near-real-time, and establishes best practices for mapping environmental aspects and observed deep sea habitats as viewed by the ROV’s forward-facing camera. All data were collected during 2014 in the Northern Gulf of Mexico by the National Oceanic and Atmospheric Administration’s (NOAA) ROV Deep Discoverer and ship Okeanos Explorer.

Oysters are important to estuarine ecosystems because of the functions they provide. Thus, oyster restoration projects are undertaken in areas where natural populations have declined. However, restoration techniques can impact sediment organic matter and benthic invertebrates that provide trophic support for important species. This study assesses the impacts of a constructed shell bed on associated sediment and invertebrate communities in a southern California bay. Within the bed site, organic matter, invertebrate abundance, and invertebrate species richness are lower only under the oyster bed. The alteration in the community under the shell is driven by a reduction in species. Tubificidae were the only remaining species under the shell. These results may be explained by the shells’ action as a barrier to the mud-water interface. While significant, impacts of oyster bed construction are spatially restricted to just under the bed. Longer-term studies should be conducted to address effects of the oysters themselves.

The purpose of this dissertation was to examine the influence of environmental variability on the distribution of prey, and the influence of prey spatial structure and habitat variability may have on the distributions of bottlenose dolphins (Tursiops truncatus). Additionally I examined how sociological differences (behavior type and the changes in a foraging behavior specific to Cedar Key Florida) influences the relative roles of bottlenose dolphins within the population.

The Gowans et al. scheme assumes that small groups form small communities and that foraging groups are small and rare as there are few foraging benefits to promote grouping. Using network analysis, I found that foraging occurs in small groups or alone, but there were preferential associations between individuals in Overall, Socialize, and Travel networks.

I examined driver-barrier foraging behavior over several field seasons to assess the prediction that there are few foraging benefits to promote grouping. The driver dolphin does have greater catch success than the barrier dolphins regardless of group size. There is also evidence that barrier dolphins may have a role in increasing foraging efficiency by decreasing the number of incomplete bouts. Both the driver and barrier dolphins do better in larger groups when incomplete bouts are factored in. Therefore there are some foraging benefits that can promote grouping.

In bottlenose dolphin foraging research, it is often assumed that habitat use is related to prey availability, though this is rarely directly tested. From my collaborative work using a database collected by the Florida Fish and Wildlife Commission’s Fisheries-Independent Monitoring (FIM) program, I evaluated the abundance of potential prey and their relationship to habitat and other biological and physical variables. I used MULTISPATI, which uses principal components analysis to partition and display patterns of spatial variation. The results show that there are correlations between fish-site scores and environmental variables. Spatial analysis of fish produced clear results, however neither PCA nor MULTISPATI could explain dolphin distribution. This is likely because the spatial scales are not the same grain for the comparisons; dolphins are highly mobile large marine predators (the scale is fine grained), and their prey are significantly smaller and habitat-specific (the scale is coarser).

Oceans are acidifying as atmospheric CO₂ is drawn down. This process, known as ocean acidification (OA), is well known and documented. Over the next 100 years, pH of the surface ocean is projected to decrease by up to 0.35 units. This CO₂ draw down has a direct effect on dissolved inorganic carbon (DIC) balance in the ocean. OA is expected to impact calcifying organisms that rely on constituencies of the DIC system, specifically carbonate ion [CO₃^2-]. It is clear that externally calcified structures, such as coral skeletons, bivalve shells, etc., will be significantly affected as pH, and consequently [CO₃²⁻ ], of the oceans decline. What is unclear, however, is how these changes will impact internally calcified structures, such as earstones (otoliths) of teleost fish. This dissertation examines the impacts of OA on otolith mineralization in larval reef fish (Amphiprion clarkiiand A. frenatus ). This research included the development of a laboratory controller system for control of experimental aquaria pH through pCO₂ dosing, exposure of larvae from hatch to settlement under various pCO2 treatments and evaluation of otolith structure and morphology across treatments within a single genus.

No standard method for pH-stat CO₂ dosing controllers existed prior to this study. Incorporating low-cost, flexible hardware allowed high precision and accuracy pH controllers to be designed and implemented. Following system stability studies, we found that our system performed at or beyond the level of control exhibited in the literature.

Two species of clownfish, Amphiprion clarkii and A. frenatus, were exposed to different pCO₂ conditions, reared to settlement and otoliths extracted and studied. I found that the sagittae (largest of the 3 otolith types) of both species exhibited circularity changes towards more oblong otoliths under increased pCO₂. For A. clarkii, I found a significant negative relation between pCO ₂ and lapilli otolith circularity, indicating a shift toward more circular lapilli under increased pCO₂. Since lapilli are critical to gravisensing in teleosts these results explain my anecdotal observations that, at high pCO₂, larvae exhibited lethargic, uncoordinated swim patterns. The core development of otoliths (sagittae, lapilli, and asterisci) from both species was analyzed using SEM imagery. Otolith images were scored by 6 independent readers for core development (poorly developed to well-developed). Otolith scores were regressed against aragonite saturation state (Ω_Ar). Results showed significant and strong relations between ΩAr and development score, indicating a shift toward protruding, unorganized crystal clusters within the core under high pH/low Ω_Ar.

This research is the first to comprehensively examine the impact of OA on the otolith system in larval fish. The research revealed direct impacts on otolith structure and morphology as well as mineralogy. These changes will directly impact survival of the larvae. It remains unknown whether the otolith system recovers post-settlement or whether the anecdotal observations on swimming behavior are directly related to otolith deformation. Future research will include exploration of these relations across genera as well as more deeply examine the recovery of the system and behavioral impacts of otolith deformation across life stages.