A luminescence based marker system was developed for detection of genetically modified Pseudomonas fluorescens and E. coli. During batch growth in liquid culture, luminescence measured by luminometry was directly proportional to biomass concentration and enabled detection of 104 - 106 cells ml-1 of P. fluorescens and 101 cells ml-1 of E. coli, in actively growing cultures. Following inoculation into soil, detection levels were reduced ten-fold. After the subsequent utilisation of available nutrients, activity and luminescence decreased and luminometry then provided a direct, non-extractive means of measuring population activity of lux-marked inocula. Potential luminescence, measured as luminescence following amendment with nutrients, enabled assessment of the rate of reactivation of the lux-marked inocula and quantification of the size of the activatable population. Both these techniques, and traditional techniques, were used to investigate the survival of P. fluorescens and E. coli in soil microcosms. The effect of matric potential and indigenous organisms on luminescence and on survival of P. fluorescens was assessed. Matric potential significantly decreased the activity of both introduced and indigenous populations, but the indigenous population also significantly decreased the activity and biomass concentration of the introduced P. fluorescens population. Use of luminometry as a non-extractive measure of biomass concentration provided qualitative correlation with viable cell concentration, suggesting its potential for rapid enumeration of marked inocula. Reactivation of cells at increased matric stress was decreased, but use of high substrate:cell ratios at -30 kPa produced higher levels of luminescence and may, therefore, improve the use of luminometry as an estimate of biomass.

Methods currently available for the detection and enumeration of genetically modified micro-organisms in the environment include culturing methods, direct microscopic detection and nucleic hybridization techniques. The aim of this project was to develop luminescence as a molecular based-marker system in Pseudomonas fluorescens. The lux genes, originally isolated from Vibrio fischeri, were introduced into Ps. fluorescens on plasmid vectors and on the chromosome. The efficiency of these two strategies for the detection of Ps. fluorescens in soil was assessed. Luminometry was used to estimate biomass concentration during growth. The sensitivity of luminescence detection was greater for the plasmid marked Ps. fluorescens in both liquid culture and soil, however, cellular light output was less closely linked to biomass concentration. Enumeration of cells by luminometry was only possible for growing cells as light output is correlated with microbial activity. The lux chromosomal marker was stable in liquid culture for at least 200 generations and in soil for up to 135 days. The plasmid borne lux genes had a half-life of 20 generations in liquid culture. After inoculation in sterile soil, plasmid loss was only observed during cellular growth. The frequency of transfer of the lux genes from Ps. fluorescens, by conjugation and transformation, was assessed in liquid culture. Mobilisation of these genes by three self transmissible plasmids was negligible due to the instability of these vectors in this host. Transformation of Ps. stutzeri with lux genes, by cell contact, was at frequencies below levels of detection. Luminescence provided a valuable marker for tracking pseudomonads in soil. Detection of marked strains by luminometry provided a sensitive, rapid and non-extractive technique for enumeration of growing cells and measurement of microbial activity. As the chromosomally encoded lux genes were stable, regardless of growth conditions, and emitted sufficient levels of light to enable visual enumeration of colonies by eye, this was considered the best system for long term risk assessment studies.

Calanus helgolandicus is a key copepod species occurring in the North East Atlantic that is responding to oceanic warming through an expansion of its geographic range. This range extension has led to concerns about how this may affect ecosystem trophodynamics. Here I investigate the interannual variability and seasonality of C. helgolandicus, using a ~28 year time-series from the western English Channel (station L4). I focus specifically on the role of mortality, as a key life history process that is challenging to quantify and historically has received little attention. C. helgolandicus abundance remained within a narrow ~four-fold interannual envelope, which was a consequence of multiple losses that removed ~99% of the potential population. Loss of early life stages occurred through the incidence of non-viable eggs and abnormal nauplii (both higher in spring), and via predation; egg mortality rates were positively correlated with C. helgolandicus copepodite abundance and total copepod biomass, indicative of intraguild predation and cannibalism. By contrast, late-stage copepodite mortality rates were highest in autumn, and were positively related to gelatinous predator abundance and biomass (medusae, ctenophores and chaetognaths). Molecular gut-content analyses revealed that two abundant jellyfish species present during 2015 (Pleurobrachia pileus and Leuckartiara octona) both preyed on C. helgolandicus. Adult male consumptive mortality rates were ~6 times higher than that of adult females; whereas male non-consumptive rates were only ~1.5 times that of females, providing evidence that predation was the primary mortality source in males. Non-consumptive mortality rates contributed 0-54% (median of 4.5%) to total mortality and were positively related to the 72-hour maximum wind speed, implying that turbulence created during extreme weather events may increase zooplankton mortality. I conclude that C. helgolandicus population control is modulated via a series of mortality-related losses occurring through the different development stages; from reduced egg viability to predation of copepodites by gelatinous carnivores. Although I find little evidence for changing ecosystem trophodynamics at L4, my results contribute to the knowledge of C. helgolandicus population dynamics at a site near the centre of its distribution, and suggest that a future expanding population may be a valuable food source for a variety of predators.

Harmful phytoplankton occur naturally in British waters. However, little is known about the environmental drivers that lead to the formation and advection of harmful algae blooms (HABs). To minimise adverse effects of HABs it is necessary to improve our understanding of links between advection, environmental changes and HAB development. The aims of this PhD project were therefore to: 1) Provide a better understanding of the relationship between harmful phytoplankton, environmental drivers and key hydrodynamic features such as the shelf edge; 2) Determine the role of advection in bloom transport and development; 3) Utilise computational modelling to study environmental drivers and advection of HABs. To achieve these aims, field data was collected from two cruises and a glider mission. During the cruises, data on phytoplankton community was collected alongside physical data with a focus on key features such as the shelf edge and seasonal coastal fronts. This data provided an updated, detailed assessment of phytoplankton across the Hebridean and Malin Shelves. Field data showed that the European Slope Current (ESC) and Islay front can separate phytoplankton communities on the shelf. Lack of community differences along the ESC suggested stronger transport and exchange of phytoplankton within the ESC than adjacent shelf waters. Nutrients, nutrient ratios and light conditions were also found to play major structuring roles in determining phytoplankton assemblage. Data collected during field work can also be useful for regulatory assessment of shelf seas by providing baseline information about phytoplankton communities in the area. The glider mission provided an additional high resolution dataset of biological and physical water column properties across the Malin shelf. Vertical resolution showed that phytoplankton distribution was strongly linked to thermal stratification and temperature changes. Horizontal resolution was highly patchy, suggesting that scientific cruises could easily miss high density blooms with small spacial extent. The glider successfully monitored a high density HAB, suggesting that gliders could potentially be used for phytoplankton surveillance and detection of high biomass blooms. In addition to field data, a bio-physical individual based model (IBM) was used to simulate HAB progression. The IBM was coupled with a hydrodynamic ocean model to show the role of advection and importance of offshore seed populations in coastal HAB development. Model output was compared to coastal count data and satellite images whenever possible. Running the model under different conditions for phytoplankton growth and behaviour, suggest that it was crucial to include Abstract 5 biological processes to simulate HABs. The IBM could be initialised with data from satellite images, field data or discrete seed populations. Model simulations with different initial cell concentrations and locations could help to explain observed bloom pathways and suggest possible offshore origins for observed exceptional HABs. The results from field work and model simulations showed the role of the ESC in structuring phytoplankton community and transporting seed populations of HABs along the Scottish west coast. This suggests that future cruises and offshore monitoring should focus on the ESC and shelf break region. The bio-physical model could hindcast HAB pathways along the ESC, suggesting that modelling of HAB pathways of known seed populations could be integrated into an early warning system for aquaculture sites along the Scottish west coast in the future. Such an early warning system would allow the protection, relocation or early harvesting of affected aquaculture sites.

Reed canarygrass (Phalaris arundinacea) has long been recognized as adapted to wetlands and those subject to periodic flooding. In Utah, Wilson (1955) estimate that 40 percent of the valley bottom land is flooded at least part of the year. Much of this land is very dry late in the summer. Forages such as Alsike clover tolerate flooding and some salt but do not perform well under drouth. Work by Bolton (1946) indicated that flooding for 49 day did not cause serious permanent damage to Reed canarygrass. The author baa observed Reed canarygrass growing in a shallow reservoir which is flooded 90 days or more. Reed canarygrass is also one of the most drouth tolerant of the cool season grasses when grown on upland soils.

Abstract The Balance Balanus albicostatus is the dominant species of fouling organism in Kaohsiung Port. In different harbor district environments In Kaohsiung Port, one can discriminate the population of B. albicostatus into three different groups¡Gthe estuary area of Love River, the outer harbor area, and the harbor area. The variation of estuary area¡¦s (Jhongjheng Bridge Station on Love River) population is the highest with the averaged survival rate of 53.8¡Ó21.7%. The population in the harbor area (The First Harbor Mouth station) is more stable with the averaged survival rate of 62.5¡Ó8.1%. The composition of population in the eliminated area in all stations after one year is similar to the previous one. It is suggested that barnacle population in Kaohsiung port can recover from environmental disturbance throughout larval recruitment within a year. Based on the results from the growth experiment of the settled barnacle¡¦s larvae, it was indicated that the growth and survival rate of the settled larvae was least affected by the recruitment of any kinds of settled larvae including barnacle itself. To understand the influence of environmental factors on the hatching of egg and development of larvae, we cultivated the larvae of B. albicostatus under the control of temperatures and salinities in the laboratory. The hatching rate of egg and times required for larvae to metamorphosis at each stage is the shortest under the condition of high temperature and high salinity. The larvae can metamorphose into cyprid in five days after hatching at the high temperature (35¢J), while it is prolonged to 19 days after hatching under the low temperature (15¢J) and low salinity (22 psu). The settlement rate of cyprids is better under high salinity (33 psu). To understand the effects of biofilm on settlement of cyprids, the biofilms are cultured under the conditions of the non-filtered, 80£gm, 20£gm, and 1£gm filtered seawater. When the biofilms have grown for 5 days, the settlement rate of cyprids on the biofilm cultured by the filtered seawater is higher than those on the non-filtered biofilms and alcohol-sterilized ones. At the day 12, the 1£gm filtered treatments had a greatest quantity of settled larvae while the number of settled cyprids in the other treatments decreased. The number of settled cyprids on panels with biofilms cultured for 15 days in non-filtered seawater and the one with biofilms fallen off for more than 75% of the total area did not significantly differ from the one with biofilms cultured in the seawater filtered with the 1£gm mesh. This showed that biofilms cultured under different filtered conditions affect the settlement of cyprids over time. It is concluded that the population of barnacle Balanus albicostatus, based on survival rate and growth, can be grouped into three different groups in the Kaohsiung Port. From the laboratory experiments, it is showed that the type of biofilm and the aging processes over time can affect the settlements of cyprids. It therefore suggested that the larval recruitments of the barnacle B. albicostatus can be affected by the types of biofilm on the different substrates, and consequently the larval recruitments in the different environmental conditions in Kaohsiung Port.

Thesis (M.S.)--Texas State University--San Marcos, 2009. / Vita. Reproduction permission applies to print copy: Blanket permission granted per author to reproduce. Includes bibliographical references (leaves 68-70).

Thesis (Ph. D.)--University of Hong Kong, 2009. / Includes bibliographical references (p. 176-203). Also available online.

Thesis (M.S.)--California Polytechnic State University, 2010. / Title from PDF title page; viewed on March 18, 2010. Major professor: Dean E. Wendt, Ph.D. "Presented to the faculty of California Polytechnic State University, San Luis Obispo." "In partial fulfillment of the requirements for the degree [of] Master of Science in Biological Sciences." "March, 2010." Includes bibliographical references (p. 53-61).

Thesis (Ph. D.)--University of Hong Kong, 2009. / Includes bibliographical references (p. 176-203). Also available in print.