Ph.D. - Oceanography
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Item Drivers and Variability of Ocean Carbonate Chemistry near Hawai‘i(2024) Knor, Lucie Anna Christa Maria; Sabine, Christopher L.; OceanographyItem UNDERSTANDING LONG DISTANCE MIGRATION PATTERNS, TROPHIC DYNAMICS, AND HABITAT USES OF MOLIDS IN THE WESTERN PACIFIC OCEAN(2024) Chang, Ching-Tsun; Popp, Brian N.; OceanographyItem VIRAL GENOMIC DIVERSITY AND THE EVOLUTION OF HOST RESISTANCE IN MICROMONAS-VIRUS SYSTEMS FROM THE TROPICAL NORTH PACIFIC OCEAN(2024) Bedi de Silva, Anamica; Edwards, Kyle F.; OceanographyItem Drivers of Staphylococcus aureus dynamics and survival in recreational waters(2024) Steadmon, Maria; Frank, Kiana L.; OceanographyItem Biodiversity, ecosystem engineering, and trophic ecology of whale-bone and wood-fall habitats in the deep NE Pacific: A controlled experimental approach(University of Hawaii at Manoa, 2023) Young, Emily Louise; Smith, Craig R.; OceanographyOrganic-fall habitat islands are established when large organic-rich parcels, such as whale bones or wood, sink to the generally food-poor deep-sea floor. Organic-fall communities may pass through a succession of ecological stages, modulated by key ecosystem engineers that influence the availability of habitat and food resources in these ecosystems. Because biodiversity and ecosystem functions at organic falls are likely to vary with substrate type, size, and deployment times, comparisons between ocean regions and depths are problematic. In this study, a replicated experimental approach has been used to control the effects of substrate type, size, and deployment times. Three major aspects of organic-fall ecology were explored: patterns and drivers of biodiversity, the importance of a wood-boring ecosystem engineer to ecosystem structure and function, and variations in trophic structure between whale-bone and wood-fall assemblages. Four benthic landers containing replicate whale-bone, wood, and inorganic control substrates were concurrently deployed for 15 months on the Washington-Oregon margin; two each at depths of ~1600 and ~2800 m, separated by distances of > 200 km. Whale-bone, wood, and inorganic substrates supported assemblages with different community structures, even within landers. Community composition was significantly different between depths and between landers within a depth, indicating variability on bathymetric and regional scales. Wood blocks at ~1600 m were heavily degraded by wood-boring xylophagaid bivalves, which consumed up to ~90% of wood-block mass. Xylophagaid boring and defecation increased habitat availability and complexity as well as the range of nutritional niches; this led to a high abundance of macrofauna inhabiting the borings inside the wood. Xylophagaid colonization was absent to mild in deeper wood blocks at sites further offshore, which we hypothesize results partly from lower propagule supply at increased distances from terrestrial forests. Bulk stable isotope analyses revealed that co-located whale-bone and wood assemblages had different trophic structures. Whale-bone and wood were dominant basal food sources; however, the relative importance of background particulate organic matter (POM) to faunal diets varied among taxa, functional groups, and between whale-bone and wood substrates, with background POM less important on wood. We hypothesize that labile particulate organic material in xylophagaid feces provides an especially important food resource at wood falls. This dissertation provides deeper insight into drivers of variability and quantifies some important aspects of organic-fall ecology.Item Oceanographic Influences On Pelagic Community Ecology Across The Eastern Pacific Ocean: Insights From Acoustics And Combined Sampling Approaches(University of Hawaii at Manoa, 2022) Perelman, Jessica; Drazen, Jeffrey C.; OceanographyRemote open-ocean habitats are globally understudied due to their inaccessibility and the costs associated with sampling so far from land. The eastern Pacific Ocean is one such habitat whose pelagic biology is largely unsampled, despite a rapidly emerging deep-sea mining industry across much of this region and the presence of an expanding oxygen minimum zone (OMZ). In this dissertation, I use active acoustics to investigate the dynamics of pelagic prey populations, namely micronekton and large zooplankton, in relation to regional and mesoscale oceanography across the eastern Pacific. At the broadest scale, I find that depth structure and vertical migration patterns of pelagic fauna (observed as scattering layers) vary greatly across the region, with the eastern tropical Pacific OMZ acting as the strongest predictor of these dynamics. Using these relationships to predict behaviors across the eastern Pacific Ocean, I find that an existing network of no-mining reserves lies outside of the core OMZ and may not represent or protect the pelagic OMZ fauna at highest risk from future mining impacts. At smaller spatial and temporal scales within the region, I find that the passage of cyclonic and anticyclonic mid-ocean eddies, as well as a strong near-surface current boundary, greatly influence the vertical structure and strength of acoustic scattering layers. In addition to broader regional patterns, this work highlights the considerable daily and weekly variability of pelagic populations in the eastern Pacific Ocean that is inherent to open ocean conditions and plays a large role in aggregation and predator-prey interactions. As acoustic techniques are limited in what they sample, I further explore pelagic community dynamics through the various perspectives and biases of several different sampling approaches in the first integrated evaluation of micronekton in the remote eastern Pacific. Using active acoustics, MOCNESS trawls, and ROV video footage, I find that trawl and video data greatly expand perceived micronekton distributions suggested by surface-based acoustic profiles. I find that while acoustic and trawl data show similar seasonal trends with greater total backscatter, abundance, and biomass, during the spring, the vertical distributions of these metrics are quite variable between survey sites and seasons. At large, this dissertation highlights the strong variability of pelagic faunal communities in remote ocean habitats and the complexities of observing these populations through different lenses. The research discussed is the first to use Saildrones to examine micronekton in the open ocean and provides some of the only remote sampling of pelagic prey communities in the eastern Pacific Ocean.Item Resonant oscillations in the Hawai`ian archipelago and tropical instability vortices and their fronts, frontal instabilities, and cross-frontal differences(University of Hawaii at Manoa, 2022) Benjamin, Lindsey; Flament, Pierre; OceanographyThis dissertation consists of two unrelated parts: an analysis of resonance modes from tsunamis and potential meteotsunamis, and an analysis of tropical instability vortices (TIVs) and fronts. In the first part, the resonant response of tsunamis and possible meteotsunamis is examined. The 2011 Tohoku tsunami described from surface currents in high-frequency Doppler radio (HFDR) data and model simulations has two modes over Penguin Bank: a stronger mode with one larger and stronger antinode on the southern part of the bank and a weaker, smaller antinode of opposite polarity on the northern part with 43-min oscillations, and a weaker mode with two relatively equal antinodes of opposite polarity situated in a north-south fashion on the bank with oscillations with periods between 15 and 30 min. Resonance modes depend on local features of bathymetry and coastlines, not the excitation force; other seismic tsunamis as well as meteotsunamis, or long-period waves caused by atmospheric pressure anomalies interacting resonantly with the ocean surface, would be expected to excite the same modes. A search in 29-mo of data using the 2011 Tohoku tsunami modes as a spatial filter not only did not detect any likely meteotsunami events, but it failed to detect two other, weaker, seismic tsunamis that occurred. The HFDR used was not optimally positioned to detect currents on Penguin Bank, and the inverse relationship between time step width and velocity resolution in all HFDRs means this instrument could only detect stronger currents in the resonance modes. In response, it is recommended that Penguin Bank be instrumented with five moorings, each with an upward-looking ADCP and a bottom pressure sensor, at locations chosen based on modeled resonance modes that would allow in-situ detection of resonance mode oscillations; also, another HFDR could be placed in a more optimal position to detect currents on Penguin Bank. Additionally, changes to the currently-installed HFDR and modeling of meteotsunamis in the Hawai`ian Islands is recommended. In the second part, the fronts, frontal instabilities, and cross-frontal differences in TIVs are examined. TIVs are 500-km diameter anticyclones with Rossby number ∼ − 1 on the North Equatorial Front that swirl colder, upwelled equatorial waters northward on their western flanks and advect warmer surface water of ITCZ-origin to the south on their eastern flanks. This swirling creates a cusp of colder water that extends northward of the mean meridional position of the North Equatorial Front with two roughly north-south fronts separating water of different temperatures, salinities, and densities: the leading front on the western side of the cusp separates warm, fresh, less-dense water to the west from the cold, salty, more-dense water in the cusp to the east, while the trailing front on the eastern side of the cusp separates cold cusp water to the west from warmer water to the east. The fronts are rotated and deformed by the swirling currents and simultaneously develop waves, cusps, and breaks due to shear current instabilities. The orientation of TIV fronts, which changes by advection of swirling large-scale currents, means that winds generally support frontogenesis on the trailing front, but either oppose frontogenesis or have littleimpact on leading fronts. Temperature effects on the wind, including changes in wind speed and drag coefficient, typically explain surface roughness differences across leading fronts, but some of the trailing fronts have large enough differences in currents that can overpower that effect. Currents around sub-mesoscale fronts within TIVs evolve as the fronts are advected. TIV fronts and frontal instabilities should be modeled to determine specifically which shear current instability is present and the amount of energy and heat involved. Wind estimates derived from SAR can be significantly altered by a difference in the currents across the front. SAR can be used to observe sub-mesoscale fronts and frontal instabilities.Item Too Much Of A Good Thing? The Influence Of Benthic Community & Chronic Nutrient Enrichment On Reef Microbial Assemblages(University of Hawaii at Manoa, 2021) Remple, Kristina L.; Nelson, Craig E.; OceanographyCoral reefs are among the most productive ecosystems on the planet and their survival is integral to maintaining the ocean’s biodiversity. However, shifts in benthic communities, away from reef building corals toward reefs dominated by fleshy algae are documented worldwide and linked with anthropogenic activities including nutrient pollution and overfishing. It is established that algae produce higher quantities of labile organic matter compared with that of corals resulting in a restructuring of bacterioplankton communities toward less diverse, potentially pathogenic assemblages. Although marine biofilms are lauded for their role in settling invertebrate larvae, including that of corals; the effect of these phase shifts on surface attached microbial communities (e.g. biofilms) has been previously unknown. Submarine groundwater discharge (SGD) is one way that anthropogenic nutrient pollution can enter coastal ecosystems and may potentially deliver microbial populations to these environments. However, until now it was unclear how SGD associated nutrients or the possible delivery of microorganisms might influence reef microbial communities. In this dissertation, I characterize microbial communities associated with SGD and describe the effect of the associated nutrient flux on microbial communities across a coral reef in Maunalua Bay and use tidal influence to inform our findings. At low tide, accompanying the strongest effect of SGD associated nutrients; distinct microbial communities from each sampling location were identified. Samples collected from the SGD spring displayed the highest microbial diversity and contained taxa not found at other sampling locations. Mid-reef samples were enriched with populations of copiotrophic taxa and coincided with a peak in ammonium concentrations, suggesting that SGD associated nutrients stimulate nitrogen metabolism and may shift microbial assemblages on coral reefs. Additionally, to investigate the effect of benthic organism and inorganic nutrients on surface attached microbial communities, I cultured biofilms with constituent reef primary producers (algae, coral, and sand), factorially crossed with three levels of continuous nutrient enrichment (ambient, low, and high). Samples were collected at 2-week intervals over the course of 6 weeks. Taxonomic comparison of biofilm communities revealed successional trajectories that were divergent from the temporal dynamics of the planktonic community. Both taxonomic and functional profiles were structured by benthic organism and nutrient treatments within biofilm communities. Overall this work demonstrates that both benthic community and nutrient availability influence microbial community structure in both surface attached and planktonic microbial communities.Item Ocean Biogeochemical Responses To Forcings On Weekly To Centennial Timescales(University of Hawaii at Manoa, 2021) Gallego, M. Angeles; Timmermann, Axel; OceanographyAnthropogenic carbon emissions are altering the Earth’s climate and oceans. Sea-water is a major sink for carbon dioxide (CO2), and the strength of this sink - about one third of human emissions - depends largely on the oceanic carbon cycle. This cycle is controlled by complex interactions between oceanic currents, mixing, temperature, primary productivity and carbonate chemistry. The intricacy of the carbon cycle poses a challenge for determining the present and future partitioning of carbon between the atmospheric, oceanic and terrestrial reservoirs. Observational, theoretical and numerical modeling efforts have been undergoing to elucidate the present-day processes that increase/decrease the carbon dioxide content in the ocean. These efforts have made it possible to estimate the Earth’s carbon budget and have informed policy makers about the urgency of reducing carbon emissions and protecting marine ecosystems. Yet, the future impacts of climate change on the carbon cycle need to be further refined to improve the accuracy of climate and marine ecosystem projections. In this context, this thesis contributes to the understanding of two components of the carbon cycle at different spatiotemporal scales. In Part I, the mechanisms of the future changes in seasonal and interannual variability of the global ocean’s partial pressure of CO2 (pCO2) are examined. In Part II, an offline high-resolution advection-diffusion model is developed and coupled to a marine ecosystem model based on the Marine Biogeochemistry Library (MARBL). This model is used to study the local effects of tropical cyclones on the biological activity of the Kuroshio region.In Part I, several fully coupled atmosphere-ocean-biogeochemistry models from the Coupled Model Intercomparison Project 5 (CMIP5), under the high emission scenario pathway 8.5 (RCP8.5), are used to answer the following questions: (1) what changes will the future temporal variability of the oceanic partial pressure of CO2 (pCO2) experience?, and (2) what are the mechanisms driving those changes? These questions are answered for two different time-scales: the annual seasonal cycle (Chapter 2) and interannual scales (Chapter 3). The global simulations reveal that the seasonal amplitude (climatological maximum-minus- minimum) of upper ocean pCO2 will increase by a factor of 1.5 to 3 times by 2080-2100 compared to 2006-2026 for the RCP8.5 emission scenario. The global interannual variability of the sea-surface pCO2 (calculated as 1σ) will increase by ∼ 64 ± 20% by 2045-2095 relative to the beginning of the industrial revolution. To unravel the mechanisms behind the amplification we use a complete analytical Taylor expansion of pCO2 variability in terms of its four drivers: dissolved inorganic carbon (DIC), total alkalinity (TA), temperature (T) and salinity (S). The linear approximation allows a separation of the effect of the buffering capacity of the ocean, from the drivers induced by physical and biological phenomena. This study shows that a decrease in buffering capacity is the main cause of pCO2 variability amplification, but not the only one. In regions dominated by T, the amplification is a consequence of mean CO2 build up. Further, a decrease in DIsC variability counteracts the seasonal and interannual amplifications. The intra-model differences in pCO2 variability are also characterized. For example, in the equatorial Pacific, at interannual scales, some models feature an amplification of the pCO2 variability dominated by T, while others show a decrease in pCO2 variability dominated by DIC. In Part II of this thesis, an offline marine ecosystem model is described (Chapter 3). The model is forced with ocean currents from the high-resolution Community Earth System Model 1.2.2., which features several nutrients, phytoplankton groups, zooplankton, dissolved organic matter and particulate matter. In Chapter 4, the following questions are studied: (1) How do tropical cyclones (TCs) affect nutrients and primary productivity on the Kuroshio region? and (2) what are some factors that control the magnitude of the TC-induced anomalies? Surface chlorophyll blooms due to TCs have been widely detected with satellite observations. But the phytoplankton’s response at depth is still not well understood. The results of this chapter show that a TC encountering a cyclonic-eddy largely promotes upwelling of nutrients and subsequent increase in subsurface primary productivity. However, the impact at the surface is negligible. Initially, the TC induces a negative chlorophyll anomaly, due to vertical advection of water from below the euphotic zone. About a week after the TC, an increase in new primary productivity is observed. This suggests that satellites may be missing these TC-induced subsurface anomalies, which could be a mechanism to sustain life in regions with deep nutriclines.Item Characterization of exocellular DNA in the oligotrophic ocean(University of Hawaii at Manoa, 2021) Linney, Morgan Donerly; Karl, David M.; OceanographyApproximately half of the DNA in the open ocean is present outside of living cells. Together, this exocellular DNA (or dissolved DNA; D-DNA) is comprised of truly dissolved “free” DNA (F-DNA), virion encapsidated DNA, and DNA inside of membrane vesicles. It is ubiquitous in nature yet its sources, sinks, and ecological characteristics are largely unknown. One reason for the uncertainty is the methodological limitation that precludes a distinction among the three pools that comprise D-DNA. Using a novel method that provides complete separation of vesicles, viruses, and F-DNA, the first fully sequenced open ocean water-column profile of exocellular DNA was obtained. Euphotic zone F-DNA (75-125 m) contained mostly bacterial and viral sequences, with bacteria dominating in the mesopelagic zone (500-1000 m). A high proportion of mesopelagic zone (500 and 1000 m) F-DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. These results indicate the composition of F-DNA in different regions of the water-column (euphotic and mesopelagic) and suggest potential mechanisms for dissolved organic matter cycling and export. Experiments designed to examine the dynamics of F-DNA suggest that it is produced by viral lysis of microbial cells, and may be consumed by heterotrophic bacteria and protists. Collectively, this research provides novel insights into the microbial origins and dynamics of F-DNA in the open ocean.