Marine microorganisms are a key vector in global carbon cycling, supporting an annual flux of 5 – 12 gigatons of carbon to the ocean interior via the biological carbon pump. While methodological advances over the last half century have greatly advanced our understanding of the factors influencing variability in this flux, the contributions of individual components in the microbial food web remain poorly resolved. Utilizing a combination of laboratory, field and remote sensing studies, this dissertation addresses several different aspects of this challenge. In the second chapter, unsupervised learning methods are applied to a global bio-optical data set from biogeochemical Argo floats to identify six oceanic biomes characterized by distinct seasonal trends in vertical phytoplankton distributions. This study demonstrated the great potential for using data from autonomous profiling floats to generalize seasonal trends in vertical phytoplankton distributions across vast regions of the global ocean, while also providing new insight on the hydrological and biogeochemical drivers of this variability. The third chapter reports the development of a novel method for the direct measurement of chlorophyll a attributable to individual phytoplankton groups in natural samples via cell sorting by flow cytometry. Critically, this approach makes it possible to evaluate phytoplankton community structure in terms of a parameter measured by autonomous platforms, while simultaneously quantifying sources of variability not captured by existing methods. The fourth chapter investigates the environmental drivers of phytoplankton distributions within the Western Tropical South Pacific, providing a case study for the biogeographical provinces identified in chapter 2 while also investigating how biogeochemical gradients influence linkages between heterotrophic groups central to carbon cycling within the microbial food web. Chapter five reports series of experiments investigating cell physiology as a driver of predator-prey interactions between heterotrophic bacteria and algal phagomixotrophs—eukaryotic algae that supplement requirements for carbon and/or nutrients by ingesting smaller cells. By validating the predictions of a gene-based model of algal trophic modes, the results from these experiments point toward the potential widespread occurrence of phagomixotrophy amongst green algae, while highlighting potential sources of bias in field and laboratory studies of bacterivory. With global climate change expected to produce rapid changes in ocean circulation and biogeochemistry, the urgency of understanding the role of marine microbes in global biogeochemical cycling has never been greater. This dissertation represents an advance in this larger goal, providing an expanded framework for the broad distribution of microbial communities in addition to novel insight into the environmental and physiological drivers of microbial community structure from the global to cellular scale.

Periodically-harvested fisheries closures (PHCs) are a widespread form of community-based marine spatial management used throughout the Indo-Pacific that also is currently being intensively advocated by conservation organizations for supporting productive fisheries and healthy marine ecosystems. However, local implementation of PHCs has historically been designed to support occasional and efficient exploitation of fish stocks, and not necessarily sustainable fisheries yields and stock conservation. The efficacy of PHCs for achieving their historical cultural objectives of periodicity and efficiency of harvest, simultaneously with achieving contemporary fisheries objectives of fisheries productivity and conservation is undetermined. As a result, the utility of PHCs for supporting contemporary ecosystem-based fisheries management is uncertain given environmental, social and climate change. We developed a biological-economic fisheries model of PHCs to test the value of this form of marine resource management for achieving cultural, fisheries and conservation objectives under sustainable and overfishing scenarios. Our results reveal PHCs to be more effective at achieving the multiple objectives than either non-spatial or fully-protected area management when fisher impact on fish behavior is considered. These results describe the performance of PHCs in general when fish behavior is considered, but does not provide detailed guidance for a particular PHC. Thus, we modified and calibrated our biological-economic fisheries model with empirical data from Nakodu Village on Koro Island in Fiji. The calibrated model allowed us to estimate the effectiveness of Nakodu Village’s current PHC management and predict consequences of future management actions. Results suggest that 5-year PHC closures are optimal for simultaneously achieving fisheries productivity and conservation goals in Nakodu Village. These findings challenge the dogma that PHCs are simply a cultural legacy and warrant further investigation of the utility of PHCs for supporting ecosystem-based management beyond the Indo-Pacific.

The objectives of the present study are to: (1) Describe the macro-invertebrate species composition and seasonal changes in abundance of the benthic infauna within an eelgrass bed; (2) Observe what immediate effects occur to the benthic community as a result of experimental removal of eelgrass plants from plants within the Zostera bed; (3) Measure the seasonal variation of eelgrass turion length over an annual cycle and determine its correlation to biomass (dry weight); (4) Examine, by means of field experiments, the importance of incident solar irradiation in affecting the seasonal growth of Zostera; and (5) Determine the relationship, if any, between the abundance of major invertebrate species and the abundance of eelgrass as determined by mean turion length.

Large-scale circulation in the northern North Atlantic plays a crucial role in the global climate by influencing ocean storage of atmospheric heat and carbon. Temperature and salinity changes in this region can have important consequences on ocean circulation due to density stratification at sites of deep water formation. Such influences can involve feedback mechanisms related to the Atlantic Meridional Overturning Circulation, which has been shown to influence the hydrography of the northern North Atlantic on decadal timescales. Current expectations are that through increasing sea-ice melting, river discharge, an intensifying hydrological cycle and glacial melt anomalies, future climate change could disrupt North Atlantic circulation patterns with cascading effects on carbon cycling and global climate. These interactions were investigated through circulation changes associated with salinity and freshwater variability, as well as variability in temperature and heat content. Recent changes in phytoplankton concentration and biological productivity in the Labrador Sea were also examined as part of this study. Spatial and temporal patterns of salinity in the North Atlantic were examined with the help of objective analysis and reanalysis salinity products using Argo observations of the recent decade (2005 to 2015). An overall freshening trend was evident, but with clear regional differences, particularly between the western subpolar gyre and the central North Atlantic. In general, the western subpolar region exhibited high interannual variability in surface salinity compared to the central North Atlantic. The western subpolar region also revealed a seasonal pattern of salinity fluctuation related to sea ice retreat and accretion, but with some years (i.e., 2008, 2012 and 2015) showing unusually large and negative salinity anomalies which were not present in the central or eastern North Atlantic. To understand the dominant factors influencing salinity and freshwater in the northern North Atlantic, budgets for liquid freshwater content over the northern North Atlantic were derived using a state-of-the-art ocean state estimate (ECCOv4). Here the subpolar North Atlantic (between $\sim$45\oN and the Greenland Scotland ridge) is distinguished from the Nordic Seas (north of the Greenland Scotland ridge). In a separate investigation ECCOv4 was used to describe global ocean heat budgets at varying spatial and temporal resolutions. This analysis showed that anomalies in temperature tendency are driven by atmospheric forcing at short time scales, while advection is the principle term at long time scales. ECCOv4 budget analysis was then used to investigate mechanisms behind interannual freshwater content variability in the northern North Atlantic over the time period 1992-2015. From the mid-1990s to the mid-2000s warming and salinification occurred in the subpolar North Atlantic. Consistent with the upper layer analysis with Argo-observations, ECCOv4 confirmed an overall freshening since about 2005. This freshening occurs simultaneously with an overall cooling in the subpolar North Atlantic. Advective convergence has been identified as the dominant driver of liquid freshwater content and ocean heat content variability in the subpolar North Atlantic, with liquid freshwater and heat content being anti-correlated. Consistent with the global heat analysis in ECCOv4, our results revealed that forcing is only important for establishing anomalies over shorter time scales (i.e., seasonal to interannual), but advective convergence becomes more important at longer (i.e., decadal) scales. Advection is the dominant term due to changes across the southern boundary on the decadal time scale, while exchanges with the Arctic Ocean have minor impact. Changes in freshwater and heat content in the subpolar North Atlantic due to advection occur through anomalies in the circulation itself, and not by the advection of anomalies in either liquid freshwater or heat content. In contrast to the subpolar North Atlantic, in the Nordic Seas interannual changes in liquid freshwater content are predominantly driven by forcing due to sea ice melting, which is in turn strongly correlated with Arctic sea ice export through Fram Strait. The overall concurrent warming and salinification followed by cooling and freshening in the subpolar North Atlantic suggests a relationship with changes in northward heat and salt transport through the Atlantic Meridional Overturning Circulation. This is consistent with decadal variability in deep convection in the Labrador Sea. It is evident that another consequence of changes in the Labrador Sea deep convection is the potential effects on nutrient availability and thus biological productivity. The Labrador Sea has become more productive in recent years, with mean chlorophyll-a concentrations closely correlated with silicate concentrations in the upper waters, which in turn are strongly correlated with wintertime convection depth. Thus annual production in the Labrador Sea appears to be influenced by the extent of deep winter mixing, thereby linking the Atlantic Meridional Overturning Circulation and deep convection to nutrient availability and ocean productivity in the subpolar North Atlantic.

Benthic animals have been widely used as health indicators of the marine benthic ecosystems in temperate regions. My PhD thesis mainly aimed to understand the responses of benthic ecosystem in tropical Hong Kong waters to the two management measures - pollution control and trawling ban. My study was based on sediment grab samples collected from 28 stations in three territory-wide surveys conducted in 2001, 2012 and 2015 in Hong Kong waters. I compared the spatial and temporal changes in macrobenthic community structure as well as physical and chemical characteristics of benthic habitats between surveys conducted before and after the pollution control measures in 2001 and 2012, as well as surveys before and after the fishery management measure in 2012 and 2015. The impacts of sewage pollution to benthic ecosystems had been noted in many studies, which included deteriorated water quality and bottom sediment, and disturbed, less diverse macrobenthic community dominated by opportunistic small-sized species. Therefore, sewage treatment and cessation of sewage effluent discharge were expected to lead to notable improvement in benthic habitats, biodiversity and macrobenthic communities; besides, responses of benthic ecosystems to pollution control may be hydrologically varied. In Hong Kong, a series of sewage treatment schemes, e.g. Stage 1 of Harbour Area Treatment Scheme (HATS), Tolo Harbour Action Plan (THAP), Tolo Harbour Effluent Export Scheme (THEES) and a number of sewage treatment works had been conducted in different areas of Hong Kong. Changes in the community structure were noted in the three focal areas with pollution control measures, i.e. Victoria Harbour, Deep Bay and Tolo Harbour; while apparent recoveries were noted inside the Victoria Harbour, the changes in benthic communities inside the Tolo Harbour and Deep Bay could not be attributed to the pollution control measures. Specifically, a decline in nutrient input to the eastern part of Victoria Harbour due to the implementation of HATS might have led to declined sedimentary total organic matter and the disappearance of the opportunistic species, and hence a recovery of benthic ecosystem therein. But in the sheltered Tolo Harbour and Deep Bay, neither improvement in sediment quality nor biodiversity were noted, thus indicating a longer duration is needed for the recovery of benthic ecosystems to take place in these land-locked bays. Degraded marine fishery resources and destruction in marine ecosystems had been noted since the introduction of modern trawling vessels had into Hong Kong since the 1950s and 1960s. Currently, most reports of benthic ecosystem responses to cessation of trawling originate from temperate regions, while it is not well understood for the situation in tropical areas. The territory-wide trawling ban in tropical Hong Kong waters was implemented by the Hong Kong government since December 31, 2012. Although improvement in benthic ecosystems was anticipated after the ban, it was unknown when this would happen and how different parts of the Hong Kong waters would respond to the trawling ban. My study showed that, around 3 years after the trawling ban, sedimentary organic matter content had increased significantly, and bottom water suspended solid loads had decreased in most of the survey stations, indicating territory-wide improvement in the benthic environment. Moreover, significant increases in richness, abundance and functional diversity of macrobenthos, as well as a more aggregated, fewer but larger station groups of macrobenthic communities were also detected after the trawling ban, indicating rapid recovery of the benthic communities. In conclusion, my study indicates that benthic communities in tropical Hong Kong can be used as bioindicators of environmental changes. Due to their restricted mobility, benthic organisms should be an integral part of the ecosystem monitoring aiming to detect the consequences of management measures to the marine environment. Environmental data including habitat complexity and hydrology are also required to fully understand the spatial and temporal dynamics of benthic ecosystems. Besides, my study has provided two territory-wide baseline data on the biodiversity and macrobenthic community structure in the tropical Hong Kong waters, which will be valuable for detecting future changes in the benthic ecosystems. My benthic ecology studies have resulted in a published paper and a manuscript ready for submission for publication. Besides focusing on benthic ecology, I have conducted taxonomic studies on benthic polychaetes, resulting in two published papers. As good taxonomy is the basis of high-quality data in benthic ecology, the training I received from studying these benthic polychaetes has enhanced my understanding of the biology of benthos, which is also important for my career development. However, since these papers do not fall into the main theme of my thesis, they are included in the thesis as appendixes only.

This study deals with the reproductive ecology and larval development of Mytilus californianus. Mytilus californianus is the common mussel found along the more exposed west coast of North America from the Aleutian Islands south Isla Socorro, Mexico (Soot-Ryen, 1955) and was chosen because it is an important species in rocky intertidal communities (being the most abundant if not the most conspicuous) and forms the basis for diverse associations of numerous other species. The reproductive cycle, larval development to settlement, comparisons of reproduction in high and low populations and field observations on larval settlement are described.

Confronted with a diverse sandflat community of interacting organisms and a spectrum of physical forces, a meaningful community analysis should begin with a description of physical characteristics and faunal distributions over time. The functional importance of certain species in the community should then be investigated by using both field and laboratory experiments. Consequently, the purpose of this research was twofold: (1) to apply the methods of similarity and gradient analysis to describe the faunal gradation on an intertidal sandflat and; (2) use these data to design a predator exclusion field experiment aimed at assessing the effects of shorebird, crab and fish predation on certain infaunal and epifaunal invertebrates.

Life history patterns of individual organisms are the result of natural selection and should be correlated with particular physical and biological characteristics of habitats in which they live. The littoral fringe is known to be the most severe physical habitat in the intertidal zone, and it is expected that organisms in it should have population characteristics associated with selective response to physical adversity rather than biological interaction. Ecological studies of populations of Littorina planaxis were made in the Dillon Beach and Bodega Head areas. The study localities differed principally in extent of wave exposure rather than geographical location.

An elasmobranch survey conducted from 2013-2018 in the waters adjacent to Pinellas County, Florida, was used for a baseline assessment of the local shark population. ArcGIS and Boosted Regression Trees were used to identify hot spots of abundance and links between environmental predictors and distribution, as well as create species distribution models. A diverse assemblage of sharks, dominated by five species: nurse shark, bonnethead, Atlantic sharpnose shark, blacktip shark, and blacknose shark, was identified. A large proportion of captures (~42%) were immature sharks. Results indicate areas characterized by seagrass and “No Internal Combustion Engine” zones correlate with greater diversity and abundance, particularly for immature sharks. BRT results underscored the importance of seagrass bottoms, as well as warm (>31℃) and shallow (< 6m) waters as essential habitat. By identifying spatially explicit areas and environmental conditions suited for shark abundance, this study provides practical resources for managing and protecting Florida’s sharks.

The composition of a community and the environmental conditions in which they exist fundamentally influence productivity and responses of systems to change. In the Northern Gulf of Mexico (NGoM), the relationships between nutrients, salinity, and phytoplankton populations are complex and have been changing over time. This work focuses on describing and analyzing: 1) a case study of diversity and recommendations for change within an academic institution; 2) spatial and temporal trends in surface dissolved inorganic nitrogen (DIN) and phosphorus (DIP) in the NGoM over 35 years; 3) nutrient addition experiments (NAEs) to determine prevailing NGoM surface slope region nutrient limitation; and 4) NGoM surface continental slope phytoplankton community composition and dynamics. Over time, academic institutions have not made progress toward increasing diversity, equity, and inclusion (DEI) in the geosciences. The first chapter of this work serves as a roadmap for other institutions to make progress toward ingraining DEI frameworks into the foundations of our institutional systems. Toward explaining trends in nutrients from 1985 to 2019, I compiled the largest data set of NGoM surface dissolved nutrient concentrations to date and analyzed it to delineate spatiotemporal trends and identify potential drivers of nutrient change. DIP concentrations in both the Mississippi-Atchafalaya River system (MAR) and in the NGoM increased over time, but the increase of NGoM DIP exceeded the DIP loads coming from only the MAR, suggesting additional sources of P to the NGoM. To determine nutrient controls on surface slope NGoM phytoplankton growth and populations, we calculated growth rates and pigment composition using redundancy analyses and a variety of nutrient limitation criteria for each nutrient amendment over 48 hours. Nutrient limitation criteria concluded predominant NP limitation in the NGoM, though single N and P limitation and nutrient replete conditions were also present. In individual NAEs with N and NP amendments, phytoplankton pigment changes were driven by the growth of diatoms and Synechococcus (Syn). Though release from nutrient limitation stimulated responses in some phytoplankton groups, nutrient limitation of phytoplankton growth could not fully be predicted by the criteria and response thresholds evaluated in this study. Additionally, an analysis of environmental variables and phytoplankton pigments was conducted for the surface slope region of the NGoM to determine how phytoplankton community composition varies spatially with the influence of the MAR plume using group-specific chlorophyll a (Chl-a) calculations, bivariate linear regression, multivariate redundancy analysis, and cluster analysis. The largest proportion of Chl-a occurred in the nano/microphytoplankton group, followed by Syn, with both peaking at the high and low ends of the salinity gradient. Redundancy and cluster analyses showed that nutrients and salinity alone cannot predict or subdivide phytoplankton community composition; however, with the addition of pigments, we can characterize specific regions based on shared environmental variables (i.e., low salinity, high biomass) and pigment abundance. In sum, this work produced a straightforward and reproducible guide to leading a DEI task force, the largest NGoM surface nutrient data set to date, and characterizations of NGoM continental slope nutrient limitation and pigment composition and their relation to environmental variables.