Thesis (Ph. D.)--Oregon State University, 2005. / Includes bibliographical references.

Thesis (Ph. D.)--Oregon State University, 2006. / Printout. Includes bibliographical references. Also available online.

The colonial, N2 fixing cyanobacterium Trichodesmium is a keystone species in oligotrophic ocean ecosystems. Trichodesmium is responsible for approximately 50% of the total biologically fixed N2 in the ocean, and this “new” nitrogen fuels primary productivity and the amount of carbon sequestered by the ocean. Trichodesmium does not exist in isolation. Colonies occur ubiquitously with an assemblage of epibiotic microorganisms that are distinct from planktonic microbes and modulated across environments, yet the implications of this relationship have not been explored. In this thesis, the ecology, physiology, and potential geochemical impact of interactions within the Trichodesmium host-microbiome system were examined across three different oligotrophic ocean environments. First, to establish the metabolic diversity contributed by the microbiome to Trichodesmium consortia, a whole community metagenomic sequencing approach was used across a transect the western North Atlantic. This study demonstrated that the microbiome contributes a large amount of unique functional potential and is modulated across a geochemical gradient. In the following study, metatranscriptomics was used to show that such metabolic potential in Trichodesmium and the microbiome was expressed and modulated across the environment. Colonies were sampled in the western tropical South Pacific and gene expression dynamics indicated co-limitation by iron and phosphorus, and revealed a mechanism for phosphate reduction by Trichodesmium and subsequent utilization by the microbiome. These activities were verified with phosphate reduction rate measurements and indicated cryptic phosphorus cycling within colonies. Next, the suite of potential physiological interactions between host and microbiome was assessed with metatranscriptome sequencing on high frequency samples of Trichodesmium colonies from the North Pacific subtropical gyre. Synchronized day-night gene expression periodicity between consortia members indicated tightly linked metabolisms. The functional annotations of these synchronous genes indicated intra-consortia cycling of nitrogen, phosphorus and iron, as well as a microbiome dependence on Trichodesmium-derived cobalamin—interactions that could alter the transfer of these resources to the surrounding water column. In the final study, the effect of the microbiome on Trichodesmium N2 fixation was assessed. Using colonies obtained from the North Atlantic, activity in the microbiome was selectively modified using quorum sensing acyl homoserine lactone cell-cell signaling, a mechanism that Trichodesmium itself does not possess. These experiments indicated that the microbiome has the potential to increase or decrease Trichodesmium N2 fixation to a degree that rivals the effects of alterations in nutrient concentration, but at a more rapid rate. In all, the research presented in this thesis demonstrates the integral importance of the microbiome to Trichodesmium physiology and ecology, highlighting the importance of an unexplored facet of marine microbial systems that likely influences the biogeochemistry of the planet.

Thesis (Ph.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / Whether a species will flourish or face extinction under a new climate regime is largely determined by its dispersal ability, its adaptive capacity or some combination of these processes. These processes have also played important roles in the evolutionary histories of species, ultimately shaping their contemporary distributions. In terrestrial studies, a landscape genetics approach is often used to explain how geographic, ecological and evolutionary processes interact to structure spatial genetic variation across populations, but these approaches have only begun to be used in marine ecosystems. This dissertation fills an emerging niche in marine ecology by taking an interdisciplinary seascape genetics approach to investigating the interplay of climate, dispersal and adaptation as shallow-water marine fishes respond to environmental heterogeneity over space and climatological shifts over time. [TRUNCATED] / 2031-01-02

Abstract not available

Macroalgae are abundant on shallow temperate reef environments, often forming complex communities that comprise several strata. In southern Australia, these assemblages are dominated by large canopy forming taxa from the Orders Laminariales and Fucales. The presence of subtidal fucoid macroalgae differentiates these communities from that elsewhere, and emphasises the need for local studies rather than relying on generalisations made elsewhere. Like most natural systems, temperate reefs are often threatened by human activity with degradation reported from many locations in close proximity to urban settlements. The work presented in this thesis involves an examination of the temporal and spatial variability in the structure of macroalgal communities from reefs along the Adelaide (South Australia) metropolitan coast. The work looked specifically at the effects of a dispersed sediment plume, resulting from the 1997 beach sand-replenishment dredging program, on shallow sub-tidal reef systems. An examination of the structure of canopy forming phaeophycean macroalgae in Gulf St Vincent (South Australia), noted large amounts of both spatial and temporal heterogeneity. Notwithstanding, this variation was not random, but demonstrated considerable structure that could be linked to a number of important underlying processes. In particular, macroalgal assemblages appeared as a mosaic of patches, each of which comprised a high-density state clearly dominated by a single genus (Cystophora, Sargassum, or Ecklonia), or alternatively a lower density mixed assemblage (Variable Low Abundance, VLA). Macroalgal community structure appeared to be driven by biotic interactions at small scales (metres), such that patches comprised of different species of algae in high density states rarely abutted one another. Instead, VLA assemblages frequently formed a buffer being situated between these mono generic patches. In terms of successional processes, the high-density states appeared to be relatively stable whereas the VLA state, at least in some systems, was transitory. This finding was supported by the absence of intermediary high- density states (e.g. a mix of Cystophora and Ecklonia) implying that state changes must occur via the VLA state following some form of disturbance. Larger scale patterns appeared to be driven by environmental variation, with factors such as wave exposure influencing habitat suitability for individual species and thereby affecting community composition. These phenomena were examined in terms of life history strategies that tend to promote stability, and which are common in late successional taxa. The importance of properties enhancing stability and the role of disturbance was investigated experimentally using a dispersed sediment plume, which entirely engulfed two reefs, as a pulse impact. This disturbance was of particular relevance given that degradation of macroalgal communities in close proximity to the City of Adelaide has been, at least in part, attributed to the effects of elevated levels of sediment. Follow up surveys revealed that the sedimentation from the plume had primarily affected newly recruiting individuals, with few juveniles surviving to one year of age. Over the following few years, the effect of this recruitment failure cascaded into the adult stand. In broader terms, unfavourable climatic conditions prior to the start of the study, including a particularly severe El Nino event, had a widespread effect on local assemblages, causing high levels of both adult and juvenile mortality. As such, at the commencement of the study, macroalgal communities across the study area were in the process of recovery. This was observed at control sites over the duration of the study. In contrast, recruitment failure at the sediment-affected sites retarded the recovery process, exacerbating the problems associated with prior unfavourable climatic events and leaving them in a degraded state. This study demonstrated that macroalgal assemblages are equipped (under natural conditions) to handle 'normal' environmental fluctuations (such as inter-annual variability). However, the additional stress associated with certain anthropogenic impacts has the potential to push them over the limit, causing degradation. The loss of canopy macroalgae reduces the structural complexity of the system, leading to a concomitant reduction in their ability to recover. As such, these findings are of particular relevance to those charged with the responsibility for managing near-shore marine environments. The plume was created accidentally during a dredging operation for beach sand replenishment of Adelaide's eroding shoreline. / Thesis (Ph.D.)--School of Earth and Environmental Sciences, 2004.

Seagrasses provide an important habitat for gillfish, crustacea and migratory birds. Extensive losses of seagrass in the Northern Hemisphere have occurred since the 1930's in what has been described as a 'wasting disease'. More recently, point-source contamination by nutrient inflows, herbicides (anti-fouling agents used on commercial shipping), heavy metals and fresh water inflows have helped explain localised losses of seagrass amounting to 20% in the case of Adelaide's metropolitan coastline, South Australia. However, losses of seagrass acreage have also occurred in regions that are far removed from anthropogenic activity and these are less easily explained by pointsource contamination. Intertidal seagrasses, such as Zostera muelleri, are subjected to environmental pressures imposed on them by the marine and terrestrial environments. For the purpose of this thesis, the intertidal environment is regarded as a complex of several components or micro-environments, each imposing a selective pressure or stress upon seagrass. The many stress factors create a tolerance zone in which Z. muelleri can survive. Zostera muelleri has adapted its physiology and biochemistry to the selective pressures that operate within the intertidal region. Zostera muelleri's internal leaf morphology has many gas storage compartments (lacunae) that extend from the leaves to the roots of the plants and its photosynthetic biochemistry has also adapted to the intertidal region enabling the sequestering of carbon under conditions of high irradiance and temperatures. It is evident from the literature that the survival of intertidal seagrasses requires effective photosynthesis. It is also evident that events that interfere with the synthesis, translocation and release of photosynthesised oxygen from the roots of Z. muelleri will compromise seagrass survival. The present study has revealed that herbicides, used in broad- acre farming, can be transported to the intertidal environment and negatively impact upon Z. muelleri. Extensive studies by others have shown that transport mechanisms, such as 'spray drift' and 'run-off', can move herbicides from their point of usage. However, 'dust' (wind-eroded soil ) as a transport mechanism for herbicides to the intertidal environment is less well studied. This is surprising, inasmuch as there is a known rate of pedogenesis in Adelaide of five to ten tonnes per km2 per annum from the accretion of dust. Results of the present study suggest that farmed soils of the Yorke Peninsula have a range of potentials to form fine particulate matter ('dust') and this potential is likely determined by the soil type and farming practices. Soil surface applied herbicides, such as 2,4-D, are 'lost' from land at 5% of the applied rate while soil-incorporated herbicides, such as treflan (trifluralin), are lost at 1.5% of the applied rate. Indeed, such herbicides can be transported as dust for tens to thousands of kilometres. Instrumental analytical techniques used in the present study have detected 2,4-D, trifluralin and sulfonylurea herbicides on whole soil. Additionally, 2,4-D- like chemicals have also been detected in whole soil and in dust obtained from whole soil. Bioassay techniques using Z. muelleri have shown that its photosynthetic pathways are negatively impacted upon by micromolar concentrations of 2,4-D that are similar to the known losses of this herbicide from land. It is concluded that, at these concentrations, 2,4-D acts as an auxin, up-regulating growth in affected plants. Such up-regulation is unlikely to be problematic in terrestrial plants since gas flows to the external environment are largely controlled by stomata. However, seagrasses lack stomata and the auxin-like activity of 2,4-D appears to have a negative impact on Z. muelleri. This is probably caused by an up - regulation in oxygen production and a subsequent oxygen-inhibition of a key enzyme ( ribulose 1,5- bisphosphate carboxylase, RUBISCO ) used in the carbon-sequestering photosynthetic process. The proposed inhibition of RUBISCO is then likely to cause a carbon deficit and a subsequent energy deficit within affected plants. One interpretation of the results presented is that Z. muelleri simply outgrows its intertidal environment after a transient exposure to an auxin-like concentration of 2,4-D. With increasing use of auxin-like herbicides, and the associated increasing stress imposed on photosynthetic processes, it is likely that further negative impacts will occur on intertidal seagrass species. Continued depletion of seagrass acreage will further adversely affect fishing yields unless appropriate measures are not taken. Closer collaboration between regulators, farm managers and herbicide manufacturers is now necessary in order to minimise the negative impact of herbicides on intertidal species. / Thesis (M.App.Sc.)--School of Earth and Environmental Sciences, 2005.

Samples of benthic organisms off the coast of Oregon, taken from depths varying from 50 to 2900 meters, have been analyzed in terms of diversity at a given station, and similarity and ecological distance to other stations. Estimates of epifauna abundance were also made. In the analysis an important distinction is made between diversity, abundance, and variety indices; the three measures are considered independent pieces of information relevant to the ecological structure of the population of interest. Two types of sampling gear were used. Large epifauna were sampled with a beam trawl. Polychaetous infauna were sampled with an anchor-box dredge. The diversity index chosen is Simpson's index; the measures of similarity and ecological distance are related. These measures are preferred because of their ease in calculation and basic simplicity. In addition these measures may be interpreted as estimates of well-defined population parameters (as Simpson has pointed out) which have straightforward probabilistic interpretation. A valid measure of diversity is one piece of relevant information necessary for elucidating the sufficient parameters of ecological systems. Therefore the methodology presented has broad application to studies of population structure. / Graduation date: 1970

The purpose of this thesis is to provide a first look at the spatial and temporal distributions of dissolved organic material (DOM) off the Oregon coast of North America. While this paper is not a comprehensive examination of these distributions, several patterns are identified as promising candidates for continued research. Most of the data presented was acquired during a strong El Nino event. The DOM data is presented as dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) and is accompanied by temperature, salinity, nitrate plus nitrite (N+N), ammonium, silicate, chlorophyll, total organic carbon (TOC), particulate organic carbon (POC), total nitrogen (TN), total organic nitrogen (TON), and zooplankton biomass measurements. During July 1997, we examined the distribution of DOM in the surface waters off the Oregon and Southern Washington coasts. Eleven east-west transects were sampled from nearshore waters to 190km offshore. DOC concentrations as high as 180 iM were observed in the Columbia River plume. Patterns in the DOC distribution were also associated with upwelling regions, an offshore coastal jet, and an oligotrophic water mass in the northern portion of our study area. Beginning with the July 1997 study and continuing until July 1998, samples were collected on weekly and seasonal time scales at station NH-05, located 9km offshore from Newport, Oregon. Various problems have limited our seasonal comparisons, but we were able to collect high quality data depicting the changes in organic matter partitioning during a phytoplankton bloom and its decline during a two month period from mid-July through mid-September in 1997. During the bloom, POC increased dramatically, but DOC decreased. Possible explanations for this decrease and for changes in the C/N ratio of the DOM during the bloom are explored. Suggestions for future research are presented in the final chapter. / Graduation date: 2000

Abstract Taiwan is surrounded by seas. The extensive seas cover tropical and sub-tropical zones. In this environment of diverse marine ecology, seas surrounding Taiwan are rich fisheries. In recent years, in addition to fishing boats of Taiwan fishing in these zones, there are also China fishing boats always trying to trespass. They fish by such operating methods as poisoning, dynamiting, and sea bed roller nets. Long-term excessive catching abuses have severely damaged the fishing resources and marine ecology in the seas surrounding Taiwan, leading to declining fishing yields and jeopardizing the livelihood of fishermen of Taiwan and operating safety in the seas. Sea patrol authorities have long caught and expelled these trespassing ships, but they have been at the same time unable to prevent China fishing boats from trespassing and fishing illegally, especially in winter months when the weather is bad. In this season, due to the unfavorable weather, the patrol ships cannot endure the maximum wave endurance and cannot go out to expel China ships. This has caused that China fishing boats continue trespassing, making the problem of excessive catching in our seas persist. China fishing boats trespass our seas to make inappropriate excessive catch. At the same time, some Taiwan fishermen make transactions with China fishing boats in the high sea. All these have influenced the fishing resources and economy of Taiwan and obscured the reality that the two sides on the Taiwan Strait are under separate administrative jurisdiction. China fishing boats trespassing the territorial sea of Taiwan and Taiwan¡¦s sea patrol units towing back the caught fishing boats for ensuing handling have made it possible for China fishermen to understand the harbor environment and shipping routes. This has been a worry for our sea defense. It is very important to devise and formulate counter strategies to respond to the problems derived from China fishing boats trespassing Taiwan¡¦s territorial seas so that Taiwan¡¦s limited patrol and law enforcement capacities can yield the maximum enforcement efficiency. In view of this, this research conducted in-depth investigations into the current conditions of Taiwan¡¦s sea patrol authorities in expelling and forfeiting China fishing boats and the difficult parts with relation to laws and practical execution aspect, and brought up concrete solution ideas that will be referred to by decision-makers and executors. It is hoped to construct an excellent marine environment and facilitate the perennial development and exploitation of marine resources. Keywords: China fishing boat, trespassed fishing, marine ecology