Analyses of foraminiferal assemblages involve time consuming microscopic assessment of sediment samples. Image recognition software, which systematically matches features within sample images against an image library, is widely used in contexts ranging from law enforcement to medical research. At present, scientific applications such as identification of specimens in plankton samples utilize flow through systems in which samples are suspended in liquid and pass through a beam of light where the images are captured using transmitted light. Identification of foraminifers generally utilizes reflected light, because most shells are relatively opaque. My goal was to design and test a protocol to directly image foraminiferal specimens using reflected light and then apply recognition software to those images. A library of high quality digital images was established by photographing foraminifers identified conventionally from sediment samples from the west Florida shelf. Recognition software, VisualSpreadsheet™ by Fluid Imaging Technologies, Inc., was then trained to improve automated assemblage counts and those results were compared to results from direct visual assessment. The auto classification feature produced composite accuracies of foraminiferal groups in the range of 60–70% compared to traditional visual identification by a researcher using a stereo microscope. Site SC34, the source of images for the original image library, had an initial accuracy of 75% that was improved slightly through an alteration to one of the software classes, but composite accuracy plateaued at 60% with the updated filters. Thus, image acquisition advancements and further development of image recognition software will be required to improve automated or semi automated foraminiferal classifications. However, other potential applications were noted. For example, an advantage of acquiring digital images of entire samples or subsamples is the ability to collect quantitative data such as diameter and length, allowing size-frequency assessments of foraminiferal populations while possibly automating grain size analyses without requiring separate processing. In addition, data files of library and sample specimens can be readily shared with other researchers.

Suspension-feeding bivalves produce biodeposits (faeces and pseudofaeces) that have much higher sinking velocities than their constituent particles. Consequently they cause sedimentation of material that might otherwise not be deposited. The benthic remineralisation of biodeposits increases sediment oxygen demand and nutrient regeneration, thus enhancing the benthic-pelagic coupling of nearshore ecosystems. In New Zealand the mussel Perna canaliculus has a high natural abundance and is also intensively cultured. This thesis examines the dispersal and remineralisation characteristics of mussel P. canaliculus biodeposits and the impacts of sedimentation from a mussel farm in the Firth of Thames on sediment biogeochemistry by combining laboratory, field and modelling studies. Dispersal characteristics were examined in the laboratory by measuring sinking velocities and erosion thresholds of biodeposits produced by mussels of a wide size range fed three experimental diets. The results show that biodeposit dispersal is a function of mussel diet and size and thus could differ significantly between locations and seasons. Estimates of dispersal distances based on these results demonstrated that the initial dispersal of biodeposits produced by cultured mussels is not far. Depending on the hydrodynamic conditions, secondary dispersal via resuspension potentially plays a more important role in the dispersal of biodeposits from mussel farms than initial dispersal and almost certainly serves as the major means of transport of biodeposits from natural mussel beds. Biodeposit mineralisation was studied by incubating coastal sediments with added biodeposits and measuring oxygen and nutrient fluxes as well as sediment characteristics over an 11 d period. Sediment oxygen consumption and ammonium release increased immediately after biodeposit addition and remained elevated compared to control cores without additions for the incubation period. A biodeposit decay rate (0.16 d-1) was calculated by fitting a first-order G model to the observed increase in oxygen consumption. This rate is 1 - 2 orders of magnitude higher than published decay rates of coastal sediments without organic enrichment or plant material. Nutrient fluxes during the incubation period illustrated that biodeposit remineralisation alters the stoichiometry of the nutrients released from the sediments which may potentially be more significant than the changes of the individual fluxes. To determine the impact of a mussel farm in the Firth of Thames I measured sediment oxygen and nutrient fluxes by deploying benthic chambers, sediment characteristics by collecting sediment cores and sedimentation rates by deploying sediment traps in four seasons. Oxygen consumption and sediment nutrient release rates were generally higher under the farm compared to a reference site, demonstrating the typical response to increased organic input. Unusually low nitrogen release rates measured in summer may indicate enhanced denitrification under the farm. A simple budget demonstrated the importance of benthic nutrient regeneration in maintaining primary production in this region and that mussel culture can lead to a redistribution of nutrients. This study showed that site-specific hydrodynamic and biogeochemical conditions have to be taken into account when planning new mussel farms to prevent excessive modifications of nutrient dynamics. Results of the laboratory and field studies conducted in this thesis were used to parameterise, calibrate and validate models of mussel biodeposit dispersal and remineralisation. A particle tracking model showed that the maximum initial dispersal of faecal pellets from the mussel farm is approximately 300 m and that pellets can be transported several times this distance via resuspension. The remineralisation model was able to simulate the increased nitrogen fluxes from the sediments well and highlighted the need for thorough calibration and parameterisation of the model. This thesis contributed to the current understanding of the ecosystem impacts of mussel culture and provided numerical models and model parameters that will assist in the assessment of mussel culture sustainability and the contribution of mussels to the nutrient cycling in nearshore ecosystems.

South Australian mangroves consist of only one single species Avicennia marina (Fosk.) Vierh.var australasica (Walp) Moldenke, 1960. They are distributed discontinuously within St. Vincent Gulf and Spencer Gulf and provide significant valuable habitat both in economical and ecological terms. The Fisheries Act 1971-1982 protected the existence of mangroves and the Harbour Act 1936-1981 controlled removal of mangrove areas in coastal development. To date very few ecological studies have been conducted in the South Australian mangroves, particularly on the infaunal organisms that have an important role in maintaining the ecological dynamic within the estuaries systems. As this is the first study on infaunal mangrove communities in the inverse estuaries of South Australia, there was no prior data for ecological comparison. The study was conducted at three mangroves location (Garden Island, Middle Beach and Saint Kilda) close to Adelaide in May 2000 and 2001. Overall the study has reported that the infaunal mangrove assemblages of South Australian mangroves were comparable to other temperate mangroves. The infaunal communities were characterised by lower diversity and abundance compared to the tropical or subtropical mangroves. The infaunal zonation related to the tidal gradient and habitat variation was detected. Most infauna organisms occupied the surface layers and substantially decreased towards the deeper layers. The study also suggested that sediment structure of mangrove systems were complex and infaunal communities responded differently to the change of environmental conditions both in small scale and larger scale. Thus, assessing the infaunal communities structure in mangrove systems should be based on ecological characteristics rather than geographical positions. The examination of dominant polychaetes families showed that different species have different responses to the environmental cues within mangrove systems. The study did not find that any polychaete species was restricted to mangroves only as they all were also found in the habitat adjacent mangrove forest. / Thesis (Ph.D.)--School of Earth and Environmental Sciences, 2003.

Benthic microalgae (BMA) living within the surface sediment of salt marshes are highly productive organisms that provide a significant proportion of organic carbon inputs into estuarine systems. BMA secrete extracellular carbohydrates in the form of low molecular weight carbohydrates and extracellular polymeric substances (EPS) as they migrate within the sediment. EPS plays an important role in the structure and function of BMA biofilms in shallow-water systems as EPS affects habitat structure, stabilizes the sediment, reduces sediment erosion, and is a carbon source for organisms. This study looked at the effect of nutrients and carbohydrate additions on BMA biomass, bacterial biomass, carbohydrate production, and glycosidase activity in the surface 5 mm of intertidal sediment in a subtropical salt marsh (Galveston Bay, Texas). Nitrogen and phosphorus were added to cores collected from the salt marsh and incubated in the lab over four days. Very little change was seen in the biomass of the benthic microalgae or in the different carbohydrate fractions with the added nutrients. The mean chlorophyll a concentration was 13 +/- 5 ug g-1 sediment, the mean saline extractable carbohydrate concentration was 237 +/- 113 ug g-1 sediment, and the mean EPS concentration was 48 +/- 25 ug g-1 sediment. The chlorophyll a and saline extractable carbohydrate concentrations initially decreased over the first 24 hours, but then increased over the rest of the experiment, indicating a possible species compositional shift in the BMA. With no major response with nutrient additions, it is likely that a different environmental factor is limiting for the growth of the benthic microalgae, and therefore the production of sEPS, in this salt marsh. A series of experiments was conducted in situ by adding glucose, alginic acid, and phosphorus to sediment within experimental plots. Samples were taken periodically over three to seven days to determine the biomass of the microbial community, enzyme activities and kinetics, and changes in the concentrations of several sediment carbohydrate pools. u-glucosidase activities (15 +/- 3 nmol g-1 h-1) were significantly higher than u-xylosidase (6 +/- 2 nmol g-1 h-1) and u-galactosidase (8 +/- 2 nmol g-1 h-1) activities within the sediment, and there was no suppression of u-glucosidase activity measured with the glucose addition. These data represent the first measurement of u- xylosidase and u-galactosidase activity in intertidal sediment dominated by BMA. Although preliminary experiments suggested a possible phosphorus limitation within the sediment, there was little change in the bacteria abundance or the benthic microalgae biomass when phosphorus was added in situ. This study begins to illustrate the dynamics of carbohydrate production and loss in this salt marsh, and the ability for the microbial community in the salt marshes of Galveston Bay to adjust to the nutrient and carbohydrate treatments.

The subject of this study was to provide the link between benthic foraminiferal assemblages and the surrounding environments. Stained sediment samples were collected from northeast and southwest South China Sea. In addition to the faunal census, cluster analysis and the stable isotope of benthic foraminiferal shells were measured. The results were compared with other parameters, such as %TOC, %CaCO3, and coarse fraction in the sediment. The spatial distribution of stained and total benthic foraminifera seems not to be related with either TOC contents in sediment or the sampling water depth. This is probably because of the TOC contents may not reflect the food supply directly. Cluster analysis of the faunal assemblages in Kaoping submarine canyon shows that all species in this study could be divided into three main groups. The first group is the shallow-intermediate infauna. It distributes in the inner shelf and the proportion decreases as the water depth increased. The second group is those species live in the shallow water. The third group is infauna along the outer shelf and slope. The cluster analysis of the faunal assemblages in the Sunda Shelf can be also divided into three groups. The first group is infaunal taxa. The second is epifauna- shallow infauna and disseminates in the shallow water. The third group is epifaunal taxa. The result of stable isotope of benthic foraminiferal shells in Kaoping submarine canyon does not show any clear relationship between oxygen and carbon isotopes. It is possibly because the selected species is not suitable for isotope analysis or the specimens are not sufficient. But the isotope measurements obtained from the Sunda Shelf reveal the great consistence with the variation of temperature and salinity in bottom water. Some species found in the Sunda Shelf even have great potential in paleoceanography study.

Coral community at Tiaoshi in Nanwan Bay, southern Taiwan was originally dominated by branching Acropora corals which formed some monopolized patches. The community had been changed apparently on a local scale (<2 km) since 1994. Several Acropora patches were almost completely replaced by the solitary sea anemone Condylactis sp. after man-made and typhoon disturbances. However, sea anemones were apparently decreased in 2002. To understand the change of the benthic communities, three areas, including Anemone-dominated, Coral-recovery and Acropora-dominated, at depths of 6 to 10 m were selected and monitored by permanent transects from 2003 to 2005. Each site included three replicate patches. At Anemone-dominated area, the mean cover of sea anemone ranged from 24.6 to 15.3% and that of the hard corals was low with 1.4 to 3.9%. At Coral-recovery area, the mean cover of the hard corals was significantly increased from 21.3 to 38.9%, while macroalgae was significantly decreased from 20.7 to 6.1% and sea anemone was low with 1.4 to 3.0%. At Acropora-dominated area, the cover of the hard corals was ranged from 70.0 to 56.6% while macroalgae and anemone was 1.1 - 3.4% and 3.5 - 4.7%, respectively. In general, the results showed that anemone and macroalgae were decreased and corals were recovery. In addition, the diversity index of coral genera at Anemone-dominated area was higher due to coral recruitment in 2004 and 2005. The new recruits were dominated by Montipora stellata.

Benthic community structure was studied by sample quadrates on transects at depths of 5 to 10 m in four sites, including Wanlitong, Leidashih, Siangjiao Bay, and Longkun, in coral reefs of southern Taiwan from 2003 to 2005. Totally 154 species in 45 genera of hard coral and 45 species in 10 genera of soft coral, representing 67% of known coral species were recorded. Covers of benthic organisms and hard coral growth forms were similar among years, but were significantly different among sites. Mean cover of all corals was high in Siangjiao Bay (56.88%) and Leidashih (65.69%), but hard coral (65.43%) was dominanted in Siangjiao Bay while soft coral (39.00%) was dominanted in Leidashih. Mean cover of all coral and benthic algae was similar in Wanlitong and Longkun. For hard coral growth forms, massive and encrusting corals were dominanted in three of four sites. This may be resulted from the strong wave. Cover of bare substrate was high (21.39%) in Longkun which was the most exposed to wind and wave stress. Foliaceous coral was abundant with the dominated species, Montipora aequituberculata (20.59%) in Siangjiao Bay which was a more protected site. However, foliaceous coral was more susceptibe to typhoon. Coral diversity was higher in Leidashih. This was related to both hard and soft corals were common and no dominant species. Comparing to previous studies, the long term change of coral abundance shows stable and/or increasing trends. It may be related to the dominance of massive and encrusting coral communities in southern Taiwan.

Plankton communities are important members of the food web in coastal systems and are regulated by top-down and bottom-up controls. This study examined the influence of bottom-up controls, such as physicochemical factors, and top-down controls, such as predation, on the plankton communities in South Bay, Texas. Microalgal photopigments were ascertained by high-performance liquid chromatography (HPLC) to determine the relative abundances of major algal classes. Zooplankters were identified to the lowest possible taxon and enumerated. No spatial trends were observed for the physicochemical factors. The northern bay sections exhibited significantly higher phytoplankton and microphytobenthic diatom biomass, probably due to their proximity to the bay inlet. Copepod, gastropod veliger and brachyuran zoea abundances were also higher in this area, albeit insignificantly. The southern bay sections experienced significantly higher cyanobacterial, euglenophyte and chlorophyte biomass, and polychaete larval abundances. Total zooplankton and nauplii abundances were also higher in the southern areas, albeit insignificantly. Sampling the inaccessible areas of the bay in the future may reveal spatial variability among the physicochemical factors which could be influencing the distribution of plankton. Temporal variation for the physicochemical factors followed a typical trend for subtropical climates and influenced the seasonality of the plankton communities. Phytoplankton biomass peaked in February, August and October but these maximums were not significantly different from the other months sampled. Microphytobenthic biomass peaked during the summer months, while diatom biomass also peaked in February. Zooplankton abundances peaked in October, while nauplii and polychaete larvae also peaked in February. Relationships between wind speed, turbidity and the microalgal pigments were assessed to determine if wind-induced resuspension influenced the location of the major algal classes within the water column compared to the sediments. Wind speed and turbidity were directly related to each other, albeit insignificantly. Some phytoplankton and microphytobenthos were considered tychopelagic because wind-induced resuspension increased their biomass in the water column compared to the sediments. The physicochemical factors exerted bottom-up control of plankton community dynamics in this study, while top-down controls, such as predation, require further investigation. Future studies should focus on which of these controls have more influence on plankton community dynamics in South Bay.

Thesis (Ph. D.)--University of Hong Kong, 2001. / Includes bibliographical references (leaves 131-143).

Thesis (M.S.)--West Virginia University, 2002. / Title from document title page. Document formatted into pages; contains viii, 96 p. : ill., maps (some col.). Includes abstract. Includes bibliographical references (p. 41-51).