Ph.D. - Oceanography

Permanent URI for this collectionhttps://hdl.handle.net/10125/2126

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Ecotypic differentiation within abundant Magnimaribacterales marine bacteria
(University of Hawai'i at Manoa, 2025) Ramfelt, Oscar H.; Rappé, Michael S.; Oceanography
The bacterial clade SAR86, recently reclassified as the order Magnimaribacterales, is one of the most abundant and globally distributed groups of heterotrophic bacteria in surface ocean waters. Despite being discovered thirty years ago, our understanding of its ecology and evolution still has significant gaps. This dissertation addresses these gaps through a combination of comparative genomics and metagenomic analyses drawn from a range of marine environments. In Chapter 2, a phylogenomic survey of over 700 genomes— including those from major global ocean surveys and the first fully sequenced cultured representative— reveals that Magnimaribacterales comprises four distinct families, each containing multiple clades with different biogeographical distributions. Although the capacity for fatty acid degradation via β-oxidation is broadly conserved, certain clades exhibit additional metabolic specializations such as α-oxidation and pathways for degrading complex, steroid-like polycyclic compounds. These findings indicate that a few dominant clades account for much of the group’s global abundance, while many others are more spatially restricted. Chapter 3 focuses on the ecological differentiation of Magnimaribacterales within Kāneʻohe Bay, Hawaiʻi, a coastal environment characterized by strong spatial gradients. Here, habitat-specific genotypes were identified, with niche specialization linked to differences in sugar metabolism and membrane biosynthesis, suggesting fine-scale adaptation to distinct inshore and offshore conditions. In Chapter 4, the vertical distribution of Magnimaribacterales is examined across the stratified water column of the North Pacific Ocean. Certain lineages are confined to surface waters, while others are enriched at depth and possess genes associated with the breakdown of more chemically recalcitrant organic compounds, highlighting functional adaptation to carbon-limited environments. Taken together, these findings demonstrate that Magnimaribacterales is a phylogenetically diverse and functionally versatile lineage that has undergone extensive ecological diversification, enabling it to thrive across a various marine environments and help sto start to explain its ubiquitous presence in the global oceans.
Microbial influences on deep-sea deposit feeders and detrital food sources
(University of Hawai'i at Manoa, 2025) Miller, Lee; Drazen, Jeffrey C.; Popp, Brian N.; Oceanography
Deep-sea communities are food limited, relying on detritus exported from surface waters for energy. Microbes produce, consume, and transform detrital particles, affecting their availability to deep-sea metazoans. I examined the microbial communities associated with particulate organic matter as it sinks from the euphotic zone to the abyssal plain more than four kilometers below. Compound-specific stable isotope analysis allowed me to trace both metazoan and microbial trophic processes. I found that most microbial alteration occurs in the top 500 m of the water column, the products of which support nitrifying archaeal communities. I also characterized microbial communities in sediments and in the digestive tracts of deposit-feeding echinoderms (sea cucumbers and sea urchins) to understand how microbial and metazoan food webs interact. Abyssal deposit feeders showed niche partitioning at two sites in the North Pacific, with interspecific differences in their consumption and utilization of fresh phytodetritus versus more heavily reworked small particles. More mobile species, especially holothurians capable of swimming, were able to consume fresher material, while the slower-moving species appear to rely more on microbially reworked detritus. Both small, heavily reworked particles and large, fresh particles are important to abyssal fauna, but the smaller particles are not well represented in sediment traps. The use of sediment traps to measure flux has therefore led to an underestimation of the importance of small particles to the deep benthos. Finally, I looked at changes in deposit feeder trophic ecology and gut microbiota throughout a depth gradient from shallow reefs to the abyssal plain and found that depth was the major driver of both. Deposit feeder trophic position increased from two to three (primary to secondary consumers) within the first 500 m of depth, which corresponded to the decline in particulate flux across the same depth range. Deeper-living deposit feeders are more reliant on microbial trophic intermediates than their shallow counterparts, and as depth increases the dominant gut taxa change. Detritus-based food webs in the deep ocean are influenced at multiple levels by microbial reworking, including in the often-overlooked gut microbiome.
Community ecology and spatio-temporal patterning of abyssal invertebrates in the Clarion Clipperton Zone
(University of Hawai'i at Manoa, 2025) Ellis, Gabrielle N.; Goetze, Erica; Oceanography
The abyssal zone (> 3500 m) represents an important biodiversity reservoir due to its vast size, species richness, and high rates of community turnover. Most abyssal invertebrate communities are poorly described, including the environmental drivers of diversity and biogeography. These communities are susceptible to species extinction and reduced ecosystem services with forthcoming anthropogenic impacts, including climate change and deep-sea mining. The Clarion-Clipperton Zone (CCZ), a 6 million km2 region of the Eastern Pacific, is characterized by abundant and mineral-rich polymetallic nodules that are of increasing economic and technological interest to support renewable energy development. Baseline descriptions of ecology and biogeography in the CCZ can be used to test hypotheses about the maintenance of diversity in the deep sea, in addition to meaningful applications toward management objectives. This dissertation addresses the community ecology and spatiotemporal patterning of abyssal marine invertebrates of the CCZ. Chapter 1 provides the environmental and management background of the CCZ as well as a brief literature review of faunal communities occupying sediments, nodules, and benthic boundary layer (BBL) seawater and their associated ecological patterns. In Chapter 2, patterns of diversity at the scale of a mining license area (10-100 km) were evaluated across habitats using a multigene, environmental DNA approach from seafloor sediments (24 cores; 0 – 2 cm, 2 – 5 cm in triplicate), and the targeted mineral deposits, polymetallic nodules (365 nodules) from the NORI-D license area. Nodule-obligate taxa contributed substantially to gamma diversity in the NORI-D license area, with many fauna found only in the target mining zone and not in the respective preservation region. These results suggest that the designated preservation region of this license may not adequately represent a control site for monitoring impacts or safeguarding local biodiversity. We demonstrate the use of eDNA as a baseline surveying method at the scale of an exploration license area in this work. Chapter 3 quantifies temporal variability in the abyssal benthopelagic plankton and larval communities of NORI-D collected via in-situ plankton pumps from paired cruises (22 deployments, avg. 14 m3 seawater/pump). High community turnover and changes in abundance between sampling periods was observed, suggesting a distinct community exists in the BBL under high and low organic matter flux events, with select taxa displaying seasonal reproductive cycles. These results suggest that biodiversity loss associated with polymetallic nodule mining is unlikely to be reduced if mining occurs only during select seasonal time periods, as high species richness and distinct community structure were observed in both sampling periods. Chapter 4 explores the influence of adult mobility and habitat requirement on abyssal biogeography among the benthic-boundary layer (BBL) zooplankton assemblage. Benthic, benthopelagic, and holoplanktonic assemblages were evaluated from collections across the eastern and western margins of the CCZ (four cruises, >3,700 km, 39 deployments). Community dissimilarity increased with increasing geographic distance across the abyssal seafloor, with increasing steepness in the relationship with increased affinity for the seafloor. Results suggest that increasing community dissimilarity with distance was not due to range limitation but rather a result of underlying habitat availability and habitat requirements. In Chapter 5, I describe the composition of the BBL plankton, with a focus on demersal larvae. Taxonomic data is presented for 48 morphotypes from 715 records using a combination of morphological and genetic approaches. This work represents the first morphotaxonomic and molecular faunal guide for the BBL zooplankton of the Pacific Ocean, and is an important step in facilitating adult-larval relationships in deep-sea ecology. This dissertation explores patterns of ecology across habitat, time, and space among abyssal invertebrates. A holistic methodological framework using molecular and morphotaxonomic techniques integrates information across size class, habitat, and life history. I demonstrate that abyssal communities of CCZ are highly diverse and dynamic, with biogeographic patterns influenced by dependency to the seafloor. A summary of the dissertation is found in Chapter 6, including a discussion of anthropogenic impacts and outstanding questions stimulated by this work.
Investigations on phytoplankton - giant virus interactions and dynamics
(University of Hawai'i at Manoa, 2025) Gajigan, Andrian Paladar; Steward, Grieg F.; Oceanography
Marine viruses have a profound impact on phytoplankton ecology and diversity. They are ubiquitous source of mortality, driving carbon and nutrient remineralization, and carbon sequestration to the deep ocean. They are also agents of evolutionary changes and genetic diversification through horizontal gene transfer. Despite recent appreciation of the ecological role of marine viruses, there is still limited knowledge of host-virus microscale interactions and environmental dynamics for most marine viruses. Progress on these fronts is hampered by the limited number and diversity of virus isolates and challenges in ecological monitoring. We leveraged existing cultures of host-virus systems, including a green alga and a dinoflagellate, to investigate various aspects of the virus particles (virions) as well as the phytoplankton-virus interactions during infection. Here, we focused on giant viruses belonging to the Nucleocytoplasmic Large DNA Viruses (NCLDVs), formally classified as Phylum Nucleocytoviricota. We focused on giant viruses because of their diversity, which exceeds that of marine prokaryotes, and their immense coding capacity compared to other viral taxa. Because they code for unusually large number and diverse types of metabolic genes, giant viruses could have a significant influence on plankton metabolism and, consequently, on global biogeochemical cycles. We documented the ultrastructural changes in the green alga Tetraselmis when infected by the virus, TetV-1. We analyzed the temporal gene program of TetV-1 as well as the host transcriptional response leading to an improved mechanistic understanding of the infection process. We also conducted a genomic and structural analysis of a novel giant virus with a micron-length tail, PelV-1, that infects the dinoflagellate Pelagodinium. PelV-1 is a pleiomorphic virus that enters the cell through a phagocytosis-like mechanism and a tail that potentially develops independently of the host. Interestingly, PelV-1 encodes for numerous auxiliary metabolic genes, including light-harvesting complex, rhodopsin, tail-fiber proteins, and carbohydrate and lipid metabolism genes. We further expanded our investigations from lab-based model systems to a natural ecological setting, examining the associations of giant viruses to harmful algal bloom event, a fish kill, and monsoon seasons. We uncovered 82 giant virus metagenome-assembled genomes belonging to thirteen NCLDV families in a tropical coastal environment. We found evidence of associations between several phytoplankton-giant virus pairs and found a strong seasonal influence on phytoplankton-giant virus community structure. Overall, this dissertation highlights the diverse mechanisms and microscale interactions that ultimately influence ocean-scale processes, specifically advancing our understanding of phytoplankton-giant virus interactions and dynamics.
Drivers and Variability of Ocean Carbonate Chemistry near Hawai‘i
(University of Hawai'i at Manoa, 2024) Knor, Lucie Anna Christa Maria; Sabine, Christopher L.; Oceanography
Ocean carbon uptake, cycling and sequestration are variable on all time scales, and modulated by an interplay of complex physical and biogeochemical drivers, including anthropogenic CO2 increase and associated ocean acidification. This dissertation disentangles the contributions of and feedbacks between these drivers to assess past changes and potential future shifts in biological production, carbon sequestration and the interplay between ocean physics and carbon speciation. The variability of the CO2-carbonate system is investigated from seasonal to interannual time scales at two different locations in the North Pacific that represent crucial environments to study in the face of global change. The first two studies investigate dynamics in the oligotrophic North Pacific Subtropical Gyre near Hawai‘i, which is the largest ecosystem on earth, and a significant sink for anthropogenic carbon from the atmosphere. A seasonal mixed layer carbon budget stresses the importance of the (relatively steady) carbon supply from horizontal transport balanced by the (spring to summer) biological drawdown over a year. Long-term changes over 35 years are then explored in the mixed layer, as well as subsurface water masses, at the same location. A substantial enhancement of ocean acidification is detected in several subsurface layers, driven by multiple combinations of source water changes from atmospheric forcing (with a focus on freshwater forcing), and/or biological productivity, as well as increasing ingrowth of respired carbon and alkalinity during subduction. The influence of salinity changes in addition to biological and temperature changes on modulation of ocean acidification is then further examined in a coastal coral reef environment on the shores of O‘ahu, Hawai‘i, where an increase in seawater carbon dioxide has not led to a measurable decline in calcium carbonate saturation state. Here, global temperature and regional salinity changes exert opposing influences on coastal acidification. This is additionally exacerbated by local high respiration, but also buffered by dissolution of calcium carbonate in sediments and/or the water column. Insights from all three chapters shed a light on the complex interplay of physical, geochemical, and biological drivers of marine CO2-carbonate chemistry in these locations, and on the implications for global carbon cycling and the fate of anthropogenic CO2.
UNDERSTANDING LONG DISTANCE MIGRATION PATTERNS, TROPHIC DYNAMICS, AND HABITAT USES OF MOLIDS IN THE WESTERN PACIFIC OCEAN
(University of Hawai'i at Manoa, 2024) Chang, Ching-Tsun; Popp, Brian N.; Oceanography
Members of the family of Molidae have a circumglobal distribution from tropical to temperate regions and they can undergo long-distance migration in the western Pacific Ocean. Molids plays a unique ecological role as predators of gelatinous zooplankton in the food web. Due to their slow growth rate and high bycatch, it is important to know Molidae trophic ecology across regions, which allows development of effective management strategies and policies. The overarching goal of this research is to explore the migration patterns, habitat use and feeding ecology of molids using electronic tagging, stomach content analysis (SCA) and stable carbon and nitrogen isotopic data (SIA) in the western Pacific Ocean. First, the tagging data revealed that molids made norward movements from Taiwan to Japan, and southward movements from Taiwan to the southern hemisphere. The N–S migrants demonstrate different habitat utilization patterns. Instead of using prevailing currents, the northward movements of molid cohorts exhibit extensive use of mesoscale eddies. Southward movement patterns are associated with major currents and thermal stratification of the water column. Second, isotope data suggested that some large molids found in Japan and Taiwan might have migrated from the warm pool region and one molid from New Caledonia might have migrated from Taiwan, consistent with satellite tagging data. Coupled with the captured timing of these large migrants and the spawning period of molids in Taiwan and Japan, it is suggested that the migration of the molids from the warm pool is likely related to spawning behavior. Third, a comprehensive diet description, breadth and overlap of each species in the Family Molidae were examined by literature review, SIA, and SCA. The literature review revealed that molids are predators of gelatinous plankton but exhibit broader diets than previously characterized as predators of gelatinous plankton almost exclusively. Ocean sunfish, bumphead sunfish, and hoodwinker sunfish reportedly consume prey from epi/mesopelagic environments, while sharptail sunfish and slender sunfish consume prey from both epi/mesopelagic environments and benthic habitats. Off Taiwan, ocean sunfish and bumphead sunfish had similar and relatively narrow diet breadths, differing from sharptail sunfish, which exhibited a broader diet. Unlike other moildes that typically feed on scyphozoans, sharptail sunfish primarily consumed tunicates. The diet of sharptail sunfish changed significantly with size and seasons. This study provides new insights into the movement and feeding ecology of molids in the western Pacific Ocean.
VIRAL GENOMIC DIVERSITY AND THE EVOLUTION OF HOST RESISTANCE IN MICROMONAS-VIRUS SYSTEMS FROM THE TROPICAL NORTH PACIFIC OCEAN
(University of Hawai'i at Manoa, 2024) Bedi de Silva, Anamica; Edwards, Kyle F.; Oceanography
Viruses in the ocean outnumber microbes by approximately an order of magnitude. These pathogens shape microbial communities via manipulation of host metabolism, through the mortality of host cells, and by causing evolutionary change in the host population. While the dynamics of cyanobacteria and their phages have provided a foundation of knowledge on coevolutionary dynamics through the lens of genetics and phenotypic selection, there is a smaller foundation for marine eukaryotic phytoplankton and their associated viruses. The important role of eukaryotic phytoplankton in marine primary production and biogeochemical cycling merits further investigations into how these phytoplankton interact with their pathogens. The question of how viruses evolve to successfully infect their hosts may be answered in part by examination of viral gene content and the evolutionary origins of such genes. Furthermore, virus-induced mortality selects for host phenotypes that are resistant to lysis. It has been hypothesized that the evolution of resistance results in a fitness cost that could alter phytoplankton productivity, but the magnitude of this cost, and how it varies under different resource regimes, is not clear. Such selection is presumably tied to genomic change in resistant cells, but resistance mutations and their mechanistic effects are poorly understood. We sought to examine questions on the dynamics of marine viruses infecting eukaryotic hosts using isolates of the common and ecologically relevant alga Micromonas commoda and strains of its double-stranded DNA viruses in the genus Prasinovirus. These isolates represent the first prasinophyte-prasinovirus systems isolated from the North Pacific Subtropical Gyre. Through four new genomic assemblies of Micromonas commoda virus strains, we found 61 putative genes not seen in other prasinoviruses. Additionally, 192 putative genes varied in occurrence among the four virus strains, despite the fact that they have overlapping host ranges. Across prasinoviruses, 25% of gene content is strongly correlated with host genus, and the functions of these genes suggests that successful lytic infection is achieved through a diversity of genetic strategies. We subsequently used experimental evolution to create 88 resistant M. commoda cell lines and found a large decrease in fitness, particularly when cells were grown at a higher light level. This fitness cost attenuated after 15 months even while cell populations maintained resistance, suggesting compensatory mutations can ameliorate the cost of resisting infection. The genomes of resistant cell lines had a larger number of non-synonymous variants than susceptible control lines. The genes affected by such variants were dependent on the identity of the ancestral cell line, and indicated a diverse suite of mechanisms of resistance among closely related isolates. Both resistance mutations and viral gene content imply that host stress responses, such as programmed cell death, are an important site of coevolutionary antagonism, as are genes potentially related to viral attachment and entry. This work demonstrates a complex network of coevolutionary strategies among marine eukaryotes and their viruses.
Drivers of Staphylococcus aureus dynamics and survival in recreational waters
(University of Hawai'i at Manoa, 2024) Steadmon, Maria; Frank, Kiana L.; Oceanography
Staphylococcus aureus is the leading cause of bacterial fatalities worldwide. Previously only an issue in health-care settings, the rise of community-acquired (CA) S. aureus infections has become a global health concern. Investigating S. aureus in the environment, such as recreational waters, has become a crucial area of research to prevent CA-S. aureus infections since heightened recreational water activity is correlated to higher rates of S. aureus infections. Despite this known elevated risk of S. aureus infection after swimming, many impacts of physicochemical and environmental factors on the distribution, abundance, and persistence of S. aureus in fresh, estuarine, and marine waters are still unknown. The purpose of this dissertation is to model the abundance, virulence, and survival of S. aureus in diverse aquatic environments by integrating high resolution spatial and temporal environmental data with experimental mesocosms and advanced statistical approaches to create predictive mixed effects models. My overarching hypothesis is that physicochemical factors associated with increased anthropogenic influences will be significantly predictive of increased S. aureus concentrations and survival. High spatial and temporal sampling of a marine system, detected S. aureus, methicillin-resistant S. aureus (MRSA), and fecal indicator bacteria (FIB) in seawater and sand using standard microbial culturing techniques, with the highest concentrations observed at beaches with freshwater input and during conditions of elevated water turbidity. The results from predictive generalized linear models (GLM) and generalized linear mixed models (GLMM) also revealed elevated bacterial concentrations at beaches with higher densities of on-site sewage disposal systems (OSDS). Notably, the predictive models developed herein are for practical application, representing the first of their kind in predicting S. aureus and MRSA presence in recreational waters. These data underscore the importance of freshwater, especially surface waters, as potential sources of S. aureus and MRSA. Expanding on these findings, we utilized culture-based and molecular methods to detect and model S. aureus, including the identification of antibiotic-resistant and virulent S. aureus genes across multiple seasons to determine environmental predictors across a watershed level gradient. GLM and GLMM show seasonal and spatial variations in S. aureus concentrations, highlighting method-dependent differences and uncovering potential sources of antibiotic-resistant and virulent S. aureus strains, including human and zoonotic origins. Furthermore, we investigated the potential link between turbidity and enhanced S. aureus survival. This was tested through a microcosm incubation using unfiltered fresh and brackish water samples. GLMM analysis and decay calculations revealed that salinity and turbidity were significant predictors of environmental S. aureus concentrations, showing the lowest decay rates in brackish, highly turbid microcosms. This suggests that saline and turbid environments, particularly in the absence of sunlight, create favorable conditions for the prolonged persistence of S. aureus communities. Overall, many physicochemical factors, especially those linked to increased anthropogenic influences (e.g., turbidity, OSDS, human shedding) were found as significant predictors of heightened S. aureus concentrations and survival. Collectively, these chapters provide a comprehensive examination of S. aureus dynamics in different aquatic settings, offering valuable insights for water quality management and public health interventions to mitigate the impact of S. aureus in recreational waters.
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.; Oceanography
Organic-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.
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.; Oceanography
Remote 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.
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; Oceanography
This 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.
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.; Oceanography
Coral 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.
Ocean Biogeochemical Responses To Forcings On Weekly To Centennial Timescales
(University of Hawaii at Manoa, 2021) Gallego, M. Angeles; Timmermann, Axel; Oceanography
Anthropogenic 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.
Characterization of exocellular DNA in the oligotrophic ocean
(University of Hawaii at Manoa, 2021) Linney, Morgan Donerly; Karl, David M.; Oceanography
Approximately 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.
Tertiary and quaternary sediments of the Ontong Java Plateau area
(University of Hawaii at Manoa, 1972) Valencia, Mark John.; Oceanography
Forty-seven free-fall, trigger-weight and piston-core tops from an area in the western equatorial Pacific (155° E -175°E , 10°N-10°S) were separated into three size-fractions (<44, 44-246 , >246 p,) and the calcium carbonate content of the total sample an
Annual variation in the depth of 14° C in the tropical Pacific Ocean
(University of Hawaii at Manoa, 1978) Meyers, Gary; Oceanography
Annual variation in the depth of 14°C throughout the tropical Pacific Ocean between 30°N and 30°S is studied on the basis of 156,000 bathythermographs. Large amplitude variations are found in the region between 4°N and 15°N. Near 6°N the variations in dep
Interactions of biogenic opal, sediment, and seawater in the central equatorial Pacific
(University of Hawaii at Manoa, 1972) Hurd, David C.; Oceanography
The solution rate of biogenic opal in near-surface sediments in the Central Equatorial Pacific is three to eight orders of magnitude lower than similar acid-cleaned samples. Iron, magnesium, and calcium alumino-silicates may be the minerals which are form
Chemistry and morphology of deep-sea manganese nodules and the significance of associated encrusting protozoans on nodule growth
(University of Hawaii at Manoa, 1976) Dugolinsky, B. K.; Oceanography
Scanning electron and light microscopic examination and x-ray spectroscopic analysis of deep-sea manganese nodules from the Northeast Equatorial Pacific have revealed that portions of nodules above the sediment layer display hard, smooth surfaces that are
Effect of irregular, abrupt topography on near-inertial currents and waves
(University of Hawaii at Manoa, 2021) Siegelman, Mika Natalie; Merrifield, Mark A.; Oceanography
An impulsive or rotary wind stress excites inertial oscillations (IOs) in the ocean mixed layer. In the open ocean, IOs behave as uniform slabs rotating anti-cyclonically. However, IOs can become divergent by features, such as the spatial variability of the winds, latitudinal variations in the Coriolis frequency, f, and coastal topography, pumping the base of the mixed layer and exciting near-inertial waves (NIWs). Studies have found IOs in the mixed layer weaken near coastal topography due to the reflection of NIWs excited by the IOs impinging on a boundary; however, few studies have considered island topography. Here, the encounter between wind-generated near-inertial oscillations (NIOs) and islands, with particular focus on the island chain of Palau, is examined using observational and analytical techniques, and numerical modelling In the first chapter, mean surface current (0-50 meters) observations from a 10-month field deployment of moored Acoustic Doppler Current Profilers (ADCPs) are used to examine how near-inertial oscillations (NIOs) are modified by coastal boundaries around the island chain of Palau. At moorings farthest from Palau, near-inertial surface currents are intermittent and clockwise rotational, suggestive of wind-generated NIOs. Closer to topography, near-inertial currents become rectilinear, with enhanced energy at the northern and southern tips of the meridionally elongated island. EOF analysis reveals that most of the NIO variance is explained by coherent flow across the breadth of the island (approximately 150 km), suggestive of a slab-like NIO response to local wind stress, which is strongly modulated as the island topography blocks the flow. Vorticity estimates from a cluster of moorings at the northern tip of Palau further reveal that near-inertial vorticity generation increases during bouts of strong near-inertial currents. The second chapter dives deeper into the dynamics of these observations using analytical techniques in conjunction with a linear, inviscid, 1.5-layer reduced gravity model of idealized, circular island topography. Longuet-Higgins (1970) first presented the analytical solutions of IOs around a circular and elliptical island. Here, I revisit this work to understand the limitations and relevance of the solution to the ocean. The reduced gravity model is used to assess the solution under more realistic ocean conditions, most notably when a wind forcing is used to excite IOs and when free waves are allowed to propagate. The numerical model shows the response of IOs around circular islands is composed of three primary components: the radiation of Poincaré waves, a blocking IO response, and an island trapped wave (ITW). Finally, the third chapter presents results from the 1.5-layer reduced gravity model to explain the observed spatial variability of inertial currents around Palau (Chapter 1) and understand their contribution to the generation of vorticity. First, results from Chapter 2 are extended to an elliptical island, which more similarly reflects the geometry of Palau than a circular island. Second, non-linear and viscous terms are considered to examine the generation of vorticity around an ellipse. Third, a Palau shaped land mask is used to understand how features specific to Palau, such as a deep channel separating the main island, Babeldaob, from the northern region, Velasco Reef, impact the behavior of IOs. Finally, because Palau is situated near the equator, the effect of latitudinal variations of f on the behavior of IOs, Poincaré waves, and ITWs around circular islands is explored.
Scattering and nonlinear transformations of internal tide beams
(University of Hawaii at Manoa, 2020) Chou, Sherry Hsiao-Hua; Carter, Glenn S.; Oceanography
The fate of internal tides as they propagate in non-uniform stratification is studied using two different numerical models, a linear and inviscid modes model (LIMM) and the nonlinear Massachusetts Institute of Technology general circulation model (MITgcm). As an internal tide beam propagates through varying density stratification, wave energy can be scattered through linear processes such as internal reflection and refraction. Scattering can lead to the splitting of beams so that the energy density of individual beams is decreased. Beam scattering can also cause horizontal ducting, or partial vertical confinement, of internal tide energy in the pycnocline and mixed layer. Two different beam scattering regimes are identified through LIMM experiments, and a non-dimensional parameter predicting the amount of internal reflection that occurs due to changing stratification is proposed. Kinetic energy from internal tide beams can also be transferred to non-tidal frequencies and vertical scales through the nonlinear generation of internal solitary waves, higher harmonics, and, depending on latitude, triadic resonant interactions. We find that interfacial waves in the pycnocline can be generated for a range of latitudes with stratification representative of the Bay of Biscay, but not with a profile representative of Hawaii. The Bay of Biscay experiments also show more horizontal ducting of energy in the pycnocline, for all frequencies. Both sets of experiments show transfers of energy to subharmonic frequencies and small vertical scales that suggest the presence of triadic resonant interactions. At latitudes where triadic resonant interactions are most active, energy transferred to subharmonic secondary waves can grow with time until it becomes greater than the energy remaining at the forcing frequency. For the Bay of Biscay experiments, degradation of the tidal beam due to triadic resonant interactions can interfere with the generation of interfacial waves in the pycnocline.

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