The Great Australian Bight (GAB) was for many years thought to be an area of limited biological productivity due to a perceived lack of nutrient enrichment processes. These conclusions, however, were based on data from few studies in the western GAB which were assumed to reflect conditions throughout the entire GAB. More recent studies have reported the occurrence of coastal upwelling in the eastern GAB (EGAB) during summer/autumn (November-April), characterized by low sea surface temperatures and elevated concentrations of chlorophyll α, which suggests that certain areas of the GAB may be highly productive during certain times of the year. The eastern Great Australian Bight (EGAB) forms part of the Southern and Indian Oceans and is an area of high ecological and economic importance. Although it supports the largest fishery in Australia (the South Australian Sardine fishery, annual catches since 2004 ~ 25,000 to 42,500 t), quantitative estimates of the primary productivity underlying this industry are open to debate. Estimates range from < 100 mg C m⁻² day⁻¹ to > 500 mg C m⁻² day⁻¹. Part of this variation may be due to the unique upwelling circulation of shelf waters in summer/autumn (November-April), which shares some similarities with highly productive eastern boundary current upwelling systems, but differs due to the influence of a northern boundary current, the Flinders current, and a wide continental shelf. Shelf waters encompass an area of ~115,000 km², and the diverse coastal topography forms part of one of the longest stretches of southward facing coastline in the world. In summer-autumn, winds are upwelling favourable, and the Flinders current running along the continental slope causes the upwelling of the deep permanent thermocline from around 600 m depth (dynamic uplift), allowing nutrient rich cold water to entrain onto the shelf. In winterspring, the EGAB is dominated by westerly downwelling-favourable winds, and upwelling via the Flinders current is suppressed. Thus, the area is highly dynamic, with significant spatial and temporal variations in meteorology and oceanography which may drive variations in nutrient enrichment and productivity. This study represents the first intensive investigation of the primary and secondary productivity of the EGAB, and was designed to evaluate the general hypothesis that spatial and temporal variations in meteorology and oceanography in the EGAB will drive spatial and temporal variations in phytoplankton size structure, and primary and secondary productivity. It examines variations in primary and secondary productivity in the EGAB during the upwelling and downwelling seasons of 2004, and the upwelling seasons of 2005 and 2006. Daily integral productivity calculated using the vertically generalised production model (VGPM) showed a high degree of spatial variation. Productivity was low (<800 mg C m⁻² day⁻¹) in offshore central and western regions of the EGAB. High productivities (1600-3900 mg C m⁻² day⁻¹) were restricted to hotspots in the east that were influenced by the upwelled water mass. There was a strong correlation between the depth of the euphotic zone and the depth of the mixed layer that suggested that ~50% of the euphotic zone lay below the mixed layer depth. As a result, high rates of primary productivity did not require upwelled water to reach the surface. A significant proportion of total productivity in the euphotic zone (57% in 2005 and 65% in 2006) occurred in the upwelled water mass below the surface mixed layer. This result has implications for daily integral productivities modelled with the VGPM, which uses surface measures of phytoplankton biomass to calculate productivity. Macro nutrient concentrations could not be used to explain the difference in the low and high productivities (silica >1 μmol L⁻¹, nitrate/nitrite >0.4 μmol L⁻¹, phosphate >0.1 μmol L⁻¹). Mixing patterns or micro-nutrient concentrations are possible explanations for spatial variations in primary productivity in the EGAB. On a global scale, daily rates of primary productivity of the EGAB lie between the highly productive eastern boundary current upwelling systems, and less productive coastal regions of western and south eastern Australia, and the oligotrophic ocean. However, daily productivity rates in the upwelling hotspots of the EGAB rival productivities in Benguela and Humbolt currents. Temporal variation in mixing and primary productivity was examined in upwelling influenced nearshore waters off south western Eyre Peninsula (SWEP) in the EGAB. Mixing/stratification in the region was highly temporally variable due to the unique upwelling circulation in summer/autumn, and downwelling through winter/spring. Highest productivity was associated with pwelled/stratified water (up to 2958 mg C m⁻² d⁻¹), with low productivity during periods of downwelling and mixing (~300-550 mg C m⁻² d⁻¹), yet no major variations in macro-nutrient concentrations were detected between upwelling and downwelling events (silica >1 μmol L⁻¹, nitrate/nitrite >0.4 μmol L⁻¹, phosphate >0.1 μmol L⁻¹). We hypothesise that upwelling enriches the region with micro-nutrients. High productivity off SWEP appears to be driven by a shallowing of mixed layer depth due to the injection of upwelled waters above Z[subscript]cr. Low productivity follows the suppression of enrichment during downwelling/mixing events, and is exacerbated in winter/spring by low irradiances and short daylengths. Phytoplankton abundance and community composition was also examined in the shelf waters of the EGAB. Phytoplankton abundances were generally higher in near shore waters compared with offshore waters, and during the summer/autumn upwelling season compared with the winter/spring downwelling season. Three distinctly different phytoplankton communities were present in the region during the upwelling and downwelling seasons of 2004, and the upwelling season of 2005, with distinctions manifest in variations in the abundance of dominant types of phytoplankton, and differences in average cell sizes. In summer/autumn, waters influenced by upwelling were characterised by high phytoplankton abundances (particularly diatoms) and larger average cell sizes, while the warmer high-nutrientlow- chlorophyll (HNLC) waters in the region had lower phytoplankton abundances and smaller average cell sizes. The winter/spring community was made up of low abundances of relatively large cells. Diatoms always dominated, but evidence of Si limitation of further diatom growth suggests there may be an upper limit to diatom productivity in the region. The maximum observed diatom concentration of ~164,000 cells L⁻¹ occurred in February/March 2004, in an area influenced by the upwelled water mass. Variations in phytoplankton biodiversity in the shelf waters of southern Australia appear to be related to variations in the influence of upwelling in the region. Meso-zooplankton abundance and community composition was examined in the coastal upwelling system of the EGAB. Spatial and temporal variations were influenced by variations in primary productivity and phytoplankton abundance and community composition, which were driven by variations in the influence of upwelling in the region. Peak meso-zooplankton abundances and biomass occurred in the highly productive upwelling influenced nearshore waters of the EGAB. However, abundances were highly variable between regions and years, reflecting the high spatial and temporal variations in primary productivity and phytoplankton abundance that characterise the shelf waters of the region. Spatial and temporal variations in community composition were driven by changes in the abundance of classes of meso zooplankton common to all regions in both years of this study. Meroplanktonic larvae and opportunistic colonizers dominated the community through the upwelling season, in response to increased primary productivity and phytoplankton blooms. Differences in community composition between upwelling influenced waters and the more HNLC regions appear to be reflected in the relative abundances of cladocera and appendicularia, with cladocera more abundant in productive upwelling influenced areas, and appendicularia thriving in the more HNLC regions of the EGAB. Highest potential grazing rates in the EGAB occurred in nearshore regions with highest mesozooplankton biomass, most likely in response to the high phytoplankton biomass that occurs in the same regions. Peak meso-zooplankton grazing rates in the EGAB were ~80% less than those measured in south west Spencer Gulf in March 2007, and ~35% greater than grazing rates in the Huon Estuary in February 2005. Productivity in the EGAB shows significant spatial and temporal variation, with changes reflecting regional and seasonal variation in meteorology and oceanography, and the water masses present in the region. The overall productivity of a summer/autumn upwelling season was highly dependent on within-season variations in wind strength and direction, which dictate the number, intensity, and duration of upwelling events. Rates of primary productivity measured in the EGAB at a given time depended on the meteorological and oceanographic conditions in the region in the lead up to, and during, the sampling event. We hypothesise that during upwelling events, high productivity in the EGAB is driven by the enrichment of waters above Z[subscript]cr, but below the surface mixed layer, with micro-nutrients. Low productivity within summer/autumn upwelling seasons follows the suppression of this enrichment during downwelling/mixing events, and the overall productivity of the upwelling season will depend on the number, duration and intensity of these downwelling/mixing events. Low productivity during winter/spring is driven by the absence of upwelling, low irradiances and short daylengths. / Thesis (Ph.D.) - University of Adelaide, School of Earth and Environmental Sciences, 2009

The Great Australian Bight (GAB) was for many years thought to be an area of limited biological productivity due to a perceived lack of nutrient enrichment processes. These conclusions, however, were based on data from few studies in the western GAB which were assumed to reflect conditions throughout the entire GAB. More recent studies have reported the occurrence of coastal upwelling in the eastern GAB (EGAB) during summer/autumn (November-April), characterized by low sea surface temperatures and elevated concentrations of chlorophyll α, which suggests that certain areas of the GAB may be highly productive during certain times of the year. The eastern Great Australian Bight (EGAB) forms part of the Southern and Indian Oceans and is an area of high ecological and economic importance. Although it supports the largest fishery in Australia (the South Australian Sardine fishery, annual catches since 2004 ~ 25,000 to 42,500 t), quantitative estimates of the primary productivity underlying this industry are open to debate. Estimates range from < 100 mg C m⁻² day⁻¹ to > 500 mg C m⁻² day⁻¹. Part of this variation may be due to the unique upwelling circulation of shelf waters in summer/autumn (November-April), which shares some similarities with highly productive eastern boundary current upwelling systems, but differs due to the influence of a northern boundary current, the Flinders current, and a wide continental shelf. Shelf waters encompass an area of ~115,000 km², and the diverse coastal topography forms part of one of the longest stretches of southward facing coastline in the world. In summer-autumn, winds are upwelling favourable, and the Flinders current running along the continental slope causes the upwelling of the deep permanent thermocline from around 600 m depth (dynamic uplift), allowing nutrient rich cold water to entrain onto the shelf. In winterspring, the EGAB is dominated by westerly downwelling-favourable winds, and upwelling via the Flinders current is suppressed. Thus, the area is highly dynamic, with significant spatial and temporal variations in meteorology and oceanography which may drive variations in nutrient enrichment and productivity. This study represents the first intensive investigation of the primary and secondary productivity of the EGAB, and was designed to evaluate the general hypothesis that spatial and temporal variations in meteorology and oceanography in the EGAB will drive spatial and temporal variations in phytoplankton size structure, and primary and secondary productivity. It examines variations in primary and secondary productivity in the EGAB during the upwelling and downwelling seasons of 2004, and the upwelling seasons of 2005 and 2006. Daily integral productivity calculated using the vertically generalised production model (VGPM) showed a high degree of spatial variation. Productivity was low (<800 mg C m⁻² day⁻¹) in offshore central and western regions of the EGAB. High productivities (1600-3900 mg C m⁻² day⁻¹) were restricted to hotspots in the east that were influenced by the upwelled water mass. There was a strong correlation between the depth of the euphotic zone and the depth of the mixed layer that suggested that ~50% of the euphotic zone lay below the mixed layer depth. As a result, high rates of primary productivity did not require upwelled water to reach the surface. A significant proportion of total productivity in the euphotic zone (57% in 2005 and 65% in 2006) occurred in the upwelled water mass below the surface mixed layer. This result has implications for daily integral productivities modelled with the VGPM, which uses surface measures of phytoplankton biomass to calculate productivity. Macro nutrient concentrations could not be used to explain the difference in the low and high productivities (silica >1 μmol L⁻¹, nitrate/nitrite >0.4 μmol L⁻¹, phosphate >0.1 μmol L⁻¹). Mixing patterns or micro-nutrient concentrations are possible explanations for spatial variations in primary productivity in the EGAB. On a global scale, daily rates of primary productivity of the EGAB lie between the highly productive eastern boundary current upwelling systems, and less productive coastal regions of western and south eastern Australia, and the oligotrophic ocean. However, daily productivity rates in the upwelling hotspots of the EGAB rival productivities in Benguela and Humbolt currents. Temporal variation in mixing and primary productivity was examined in upwelling influenced nearshore waters off south western Eyre Peninsula (SWEP) in the EGAB. Mixing/stratification in the region was highly temporally variable due to the unique upwelling circulation in summer/autumn, and downwelling through winter/spring. Highest productivity was associated with pwelled/stratified water (up to 2958 mg C m⁻² d⁻¹), with low productivity during periods of downwelling and mixing (~300-550 mg C m⁻² d⁻¹), yet no major variations in macro-nutrient concentrations were detected between upwelling and downwelling events (silica >1 μmol L⁻¹, nitrate/nitrite >0.4 μmol L⁻¹, phosphate >0.1 μmol L⁻¹). We hypothesise that upwelling enriches the region with micro-nutrients. High productivity off SWEP appears to be driven by a shallowing of mixed layer depth due to the injection of upwelled waters above Z[subscript]cr. Low productivity follows the suppression of enrichment during downwelling/mixing events, and is exacerbated in winter/spring by low irradiances and short daylengths. Phytoplankton abundance and community composition was also examined in the shelf waters of the EGAB. Phytoplankton abundances were generally higher in near shore waters compared with offshore waters, and during the summer/autumn upwelling season compared with the winter/spring downwelling season. Three distinctly different phytoplankton communities were present in the region during the upwelling and downwelling seasons of 2004, and the upwelling season of 2005, with distinctions manifest in variations in the abundance of dominant types of phytoplankton, and differences in average cell sizes. In summer/autumn, waters influenced by upwelling were characterised by high phytoplankton abundances (particularly diatoms) and larger average cell sizes, while the warmer high-nutrientlow- chlorophyll (HNLC) waters in the region had lower phytoplankton abundances and smaller average cell sizes. The winter/spring community was made up of low abundances of relatively large cells. Diatoms always dominated, but evidence of Si limitation of further diatom growth suggests there may be an upper limit to diatom productivity in the region. The maximum observed diatom concentration of ~164,000 cells L⁻¹ occurred in February/March 2004, in an area influenced by the upwelled water mass. Variations in phytoplankton biodiversity in the shelf waters of southern Australia appear to be related to variations in the influence of upwelling in the region. Meso-zooplankton abundance and community composition was examined in the coastal upwelling system of the EGAB. Spatial and temporal variations were influenced by variations in primary productivity and phytoplankton abundance and community composition, which were driven by variations in the influence of upwelling in the region. Peak meso-zooplankton abundances and biomass occurred in the highly productive upwelling influenced nearshore waters of the EGAB. However, abundances were highly variable between regions and years, reflecting the high spatial and temporal variations in primary productivity and phytoplankton abundance that characterise the shelf waters of the region. Spatial and temporal variations in community composition were driven by changes in the abundance of classes of meso zooplankton common to all regions in both years of this study. Meroplanktonic larvae and opportunistic colonizers dominated the community through the upwelling season, in response to increased primary productivity and phytoplankton blooms. Differences in community composition between upwelling influenced waters and the more HNLC regions appear to be reflected in the relative abundances of cladocera and appendicularia, with cladocera more abundant in productive upwelling influenced areas, and appendicularia thriving in the more HNLC regions of the EGAB. Highest potential grazing rates in the EGAB occurred in nearshore regions with highest mesozooplankton biomass, most likely in response to the high phytoplankton biomass that occurs in the same regions. Peak meso-zooplankton grazing rates in the EGAB were ~80% less than those measured in south west Spencer Gulf in March 2007, and ~35% greater than grazing rates in the Huon Estuary in February 2005. Productivity in the EGAB shows significant spatial and temporal variation, with changes reflecting regional and seasonal variation in meteorology and oceanography, and the water masses present in the region. The overall productivity of a summer/autumn upwelling season was highly dependent on within-season variations in wind strength and direction, which dictate the number, intensity, and duration of upwelling events. Rates of primary productivity measured in the EGAB at a given time depended on the meteorological and oceanographic conditions in the region in the lead up to, and during, the sampling event. We hypothesise that during upwelling events, high productivity in the EGAB is driven by the enrichment of waters above Z[subscript]cr, but below the surface mixed layer, with micro-nutrients. Low productivity within summer/autumn upwelling seasons follows the suppression of this enrichment during downwelling/mixing events, and the overall productivity of the upwelling season will depend on the number, duration and intensity of these downwelling/mixing events. Low productivity during winter/spring is driven by the absence of upwelling, low irradiances and short daylengths. / Thesis (Ph.D.) - University of Adelaide, School of Earth and Environmental Sciences, 2009

The Great Australian Bight (GAB) was for many years thought to be an area of limited biological productivity due to a perceived lack of nutrient enrichment processes. These conclusions, however, were based on data from few studies in the western GAB which were assumed to reflect conditions throughout the entire GAB. More recent studies have reported the occurrence of coastal upwelling in the eastern GAB (EGAB) during summer/autumn (November-April), characterized by low sea surface temperatures and elevated concentrations of chlorophyll α, which suggests that certain areas of the GAB may be highly productive during certain times of the year. The eastern Great Australian Bight (EGAB) forms part of the Southern and Indian Oceans and is an area of high ecological and economic importance. Although it supports the largest fishery in Australia (the South Australian Sardine fishery, annual catches since 2004 ~ 25,000 to 42,500 t), quantitative estimates of the primary productivity underlying this industry are open to debate. Estimates range from < 100 mg C m⁻² day⁻¹ to > 500 mg C m⁻² day⁻¹. Part of this variation may be due to the unique upwelling circulation of shelf waters in summer/autumn (November-April), which shares some similarities with highly productive eastern boundary current upwelling systems, but differs due to the influence of a northern boundary current, the Flinders current, and a wide continental shelf. Shelf waters encompass an area of ~115,000 km², and the diverse coastal topography forms part of one of the longest stretches of southward facing coastline in the world. In summer-autumn, winds are upwelling favourable, and the Flinders current running along the continental slope causes the upwelling of the deep permanent thermocline from around 600 m depth (dynamic uplift), allowing nutrient rich cold water to entrain onto the shelf. In winterspring, the EGAB is dominated by westerly downwelling-favourable winds, and upwelling via the Flinders current is suppressed. Thus, the area is highly dynamic, with significant spatial and temporal variations in meteorology and oceanography which may drive variations in nutrient enrichment and productivity. This study represents the first intensive investigation of the primary and secondary productivity of the EGAB, and was designed to evaluate the general hypothesis that spatial and temporal variations in meteorology and oceanography in the EGAB will drive spatial and temporal variations in phytoplankton size structure, and primary and secondary productivity. It examines variations in primary and secondary productivity in the EGAB during the upwelling and downwelling seasons of 2004, and the upwelling seasons of 2005 and 2006. Daily integral productivity calculated using the vertically generalised production model (VGPM) showed a high degree of spatial variation. Productivity was low (<800 mg C m⁻² day⁻¹) in offshore central and western regions of the EGAB. High productivities (1600-3900 mg C m⁻² day⁻¹) were restricted to hotspots in the east that were influenced by the upwelled water mass. There was a strong correlation between the depth of the euphotic zone and the depth of the mixed layer that suggested that ~50% of the euphotic zone lay below the mixed layer depth. As a result, high rates of primary productivity did not require upwelled water to reach the surface. A significant proportion of total productivity in the euphotic zone (57% in 2005 and 65% in 2006) occurred in the upwelled water mass below the surface mixed layer. This result has implications for daily integral productivities modelled with the VGPM, which uses surface measures of phytoplankton biomass to calculate productivity. Macro nutrient concentrations could not be used to explain the difference in the low and high productivities (silica >1 μmol L⁻¹, nitrate/nitrite >0.4 μmol L⁻¹, phosphate >0.1 μmol L⁻¹). Mixing patterns or micro-nutrient concentrations are possible explanations for spatial variations in primary productivity in the EGAB. On a global scale, daily rates of primary productivity of the EGAB lie between the highly productive eastern boundary current upwelling systems, and less productive coastal regions of western and south eastern Australia, and the oligotrophic ocean. However, daily productivity rates in the upwelling hotspots of the EGAB rival productivities in Benguela and Humbolt currents. Temporal variation in mixing and primary productivity was examined in upwelling influenced nearshore waters off south western Eyre Peninsula (SWEP) in the EGAB. Mixing/stratification in the region was highly temporally variable due to the unique upwelling circulation in summer/autumn, and downwelling through winter/spring. Highest productivity was associated with pwelled/stratified water (up to 2958 mg C m⁻² d⁻¹), with low productivity during periods of downwelling and mixing (~300-550 mg C m⁻² d⁻¹), yet no major variations in macro-nutrient concentrations were detected between upwelling and downwelling events (silica >1 μmol L⁻¹, nitrate/nitrite >0.4 μmol L⁻¹, phosphate >0.1 μmol L⁻¹). We hypothesise that upwelling enriches the region with micro-nutrients. High productivity off SWEP appears to be driven by a shallowing of mixed layer depth due to the injection of upwelled waters above Z[subscript]cr. Low productivity follows the suppression of enrichment during downwelling/mixing events, and is exacerbated in winter/spring by low irradiances and short daylengths. Phytoplankton abundance and community composition was also examined in the shelf waters of the EGAB. Phytoplankton abundances were generally higher in near shore waters compared with offshore waters, and during the summer/autumn upwelling season compared with the winter/spring downwelling season. Three distinctly different phytoplankton communities were present in the region during the upwelling and downwelling seasons of 2004, and the upwelling season of 2005, with distinctions manifest in variations in the abundance of dominant types of phytoplankton, and differences in average cell sizes. In summer/autumn, waters influenced by upwelling were characterised by high phytoplankton abundances (particularly diatoms) and larger average cell sizes, while the warmer high-nutrientlow- chlorophyll (HNLC) waters in the region had lower phytoplankton abundances and smaller average cell sizes. The winter/spring community was made up of low abundances of relatively large cells. Diatoms always dominated, but evidence of Si limitation of further diatom growth suggests there may be an upper limit to diatom productivity in the region. The maximum observed diatom concentration of ~164,000 cells L⁻¹ occurred in February/March 2004, in an area influenced by the upwelled water mass. Variations in phytoplankton biodiversity in the shelf waters of southern Australia appear to be related to variations in the influence of upwelling in the region. Meso-zooplankton abundance and community composition was examined in the coastal upwelling system of the EGAB. Spatial and temporal variations were influenced by variations in primary productivity and phytoplankton abundance and community composition, which were driven by variations in the influence of upwelling in the region. Peak meso-zooplankton abundances and biomass occurred in the highly productive upwelling influenced nearshore waters of the EGAB. However, abundances were highly variable between regions and years, reflecting the high spatial and temporal variations in primary productivity and phytoplankton abundance that characterise the shelf waters of the region. Spatial and temporal variations in community composition were driven by changes in the abundance of classes of meso zooplankton common to all regions in both years of this study. Meroplanktonic larvae and opportunistic colonizers dominated the community through the upwelling season, in response to increased primary productivity and phytoplankton blooms. Differences in community composition between upwelling influenced waters and the more HNLC regions appear to be reflected in the relative abundances of cladocera and appendicularia, with cladocera more abundant in productive upwelling influenced areas, and appendicularia thriving in the more HNLC regions of the EGAB. Highest potential grazing rates in the EGAB occurred in nearshore regions with highest mesozooplankton biomass, most likely in response to the high phytoplankton biomass that occurs in the same regions. Peak meso-zooplankton grazing rates in the EGAB were ~80% less than those measured in south west Spencer Gulf in March 2007, and ~35% greater than grazing rates in the Huon Estuary in February 2005. Productivity in the EGAB shows significant spatial and temporal variation, with changes reflecting regional and seasonal variation in meteorology and oceanography, and the water masses present in the region. The overall productivity of a summer/autumn upwelling season was highly dependent on within-season variations in wind strength and direction, which dictate the number, intensity, and duration of upwelling events. Rates of primary productivity measured in the EGAB at a given time depended on the meteorological and oceanographic conditions in the region in the lead up to, and during, the sampling event. We hypothesise that during upwelling events, high productivity in the EGAB is driven by the enrichment of waters above Z[subscript]cr, but below the surface mixed layer, with micro-nutrients. Low productivity within summer/autumn upwelling seasons follows the suppression of this enrichment during downwelling/mixing events, and the overall productivity of the upwelling season will depend on the number, duration and intensity of these downwelling/mixing events. Low productivity during winter/spring is driven by the absence of upwelling, low irradiances and short daylengths. / Thesis (Ph.D.) - University of Adelaide, School of Earth and Environmental Sciences, 2009

Made available in DSpace on 2016-06-02T19:28:57Z (GMT). No. of bitstreams: 1 TeseMVR.pdf: 1800586 bytes, checksum: c44cb463d61ffeb5394f543684f66e59 (MD5) Previous issue date: 2003-06-24 / Concern with the effect of oil spills in coastal regions resulting from the production, refining and transport of this product has been one of the priorities of the institutions working with this sector. Consequently, there is a large demand for research on the impacts of by accidents on the environment and, particularly, on natural communities. In the present study, a mesocosm experiment was used to evaluate the effects of a mixture of light Arabian and Russian oil with the chemical dispersant Corexit® 9500, over a coastal plankton community. The experiment was carried out in Rio de Janeiro and lasted 25 consecutive days. Three replicates were used as control, with only seawater, three were treated with 800 mL of petroleum and the other three were treated with the mixture 800 mL of petroleum and 80 mL of dispersant. The chemical alterations in the water were striking, especially the rise in the concentration of organic compounds. The results demonstrated a severe reduction of phytoplankton density, as a result of the addition of oil. There was also a change in the composition of the organism groups, with alteration of dominance of diatoms to phytoflagelates. Similar effect was found for the zooplankton. Both the oil and its mixture with dispersant resulted in a reduction of population densities and changes, or disappearance, of some components. Meroplanktonic organisms had a higher sensitivity to the acute effects of the oil and oil-dispersant mixture than holoplanktonic organisms. Copepods were resistant to the effects of oil and oil-dispersant mixture. Among the herbivores, Acartia lilljeborgi had greater resistance to the acute toxic effect of oil, whereas Pseudodiaptomus acutus was more resistant to the chronic effects of both oil and the mixture. Among carnivores, Oithona hebes appeared as a resistant species to both acute and chronical effects. Mesocosms were shown to be useful for investigating the effects of oil spills on marine environments since standardized laboratory tests with algae and invertebrate test-organisms corroborated the field findings. / A avaliação dos efeitos de derrames de petróleo nas regiões costeiras decorrentes das atividades de produção, refinamento ou transporte deste produto tem sido uma das prioridades das instituições ligadas a este setor e há uma demanda muito grande de pesquisas sobre os impactos ocasionados por estes sobre o ambiente e as comunidades naturais, em particular. No presente estudo a experimentação em mesocosmos foi utilizada para avaliar os efeitos do derrame do petróleo ARLE/URAL e deste tratado com o dispersante químico Corexit® 9500, sobre uma comunidade planctônica costeira. O experimento foi realizado no Rio de Janeiro, Brasil e teve a duração de 25 dias consecutivos (19/06 a 13/07/2002). Os tratamentos foram feitos em triplicata com um volume aproximado de 1,7m3 de água do mar em cada unidade. Foram utilizadas três réplicas como controle, contendo apenas água do mar, três réplicas foram tratadas com 800 mL de petróleo e três outras réplicas foram tratadas com a mistura de 800 mL de petróleo e 80 mL de dispersante. As alterações químicas na água foram marcantes, principalmente em relação ao aumento na concentração dos compostos orgânicos. Os resultados evidenciaram uma redução severa na densidade do fitoplâncton, em decorrência da adição do óleo ou da mistura de óleo e dispersante. Houve também uma mudança na composição dos grupos, com alteração da dominância de diatomáceas para fitoflagelados. Em relação aos grupos zooplanctônicos também foi observado um efeito mais acentuado no tratamento com petróleo e dispersante. Os organismos meroplanctônicos foram mais sensíveis ao petróleo do que os holoplanctônicos. Os copépodes foram dominantes, em todos os tratamentos. A espécie herbívora Acartia lilljeborgi foi mais resistente ao efeito agudo do petróleo, enquanto Pseudodiaptomus acutus foi mais resistente ao efeito crônico Entre os Copepoda carnívoros Oithona hebes foi a espécie mais resistente, tanto ao impacto agudo quanto ao impacto crônico. Os mesocosmos são adequados para a avaliação dos efeitos do derrame de petróleo ou da mistura de petróleo e dispersante, como corroborado pelos estudos de toxicidade com algas e organismos-teste invertebrados, que corroboraram os efeitos observados em campo. A utilização de dispersante químico na etapa de remediação após os derrames necessita ser reavaliada tendo em vista os resultados deste trabalho que indicam que a mistura petróleodispersante é ainda mais tóxica do que o petróleo sozinho.

Os colifagos somáticos (CS) são os melhores indicadores de poluição fecal. Neste trabalho, foi determinada a abundância de CS em amostras de água do mar, plâncton, e bivalves coletadas em Santos, São Sebastião e Ubatuba. Houve correlação positiva entre CS e as bactérias marinhas viáveis, coliformes termotolerantes, E.coli e enterococos intestinais, e a correlação foi negativa com a temperatura. As maiores contagens de CS foram obtidas em Santos. As freqüências das famílias encontradas nas amostras de água do mar e plâncton foram: Siphoviridae (50% e 65,8%), Podoviridae (36% e 15,8%), Microviridae (9% e 15,8%) e Myoviridae (5%, 2,6%), respectivamente. Em bivalves, só foi observada Siphoviridae. Os morfotipos observados foram A1 (3%), B1 (63%), C1 (21%) e D1 (13%). As técnicas de RFLP e rep-PCR não foram discriminatórias. 9,6% dos colifagos apresentaram os genes que codificam para as toxinas ST e/ou LT. O presente estudo está identificando os colifagos como perigos microbiológicos e gerando subsídios para avaliação de riscos microbiológicos no ecossistema marinho. / The somatic coliphages (SC) are the better indicator for fecal pollution. In this research, it was obtained the SC abundance in seawater, plankton and bivalves samples collected from Santos, São Sebastiâo and Ubatuba. SC counts were correlated with marine viable bacteria, thermotolerant coliforms, E. coli and intestinal enterococci, and the correlation was negative with the temperature. Highest SC counts were obtained from samples collected at Santos. The frequency of SC families found in seawater and plankton samples were: Siphoviridae (50% and 65.8%), Podoviridae (36% and 15.8%), Microviridae (9% and 15.8%), and Myoviridae (5%, 2.6%), respectively. In bivalves, only Siphoviridae was found. Morphotypes A1 (3%), B1 (63%), C1 (21%) and D1 (13%) were observed. The RFLP and rep-PCR techniques were not discriminatory. 9.6% of coliphages contained genes codifying for thermostable toxin (ST) and/or thermolabil toxin (LT). This study is identifying the coliphages as microbial hazard and giving support to later studies for microbial risk assessment of marine ecosystem.

Les diatomées sont une composante majeure des écosystèmes marins et sont caractérisées par une grande diversité. L’objectif général de cette thèse est d’étudier les facteurs de contrôle des diatomées dans la Zone Côtière Belge (ZCB). Pour ce faire, la modélisation par groupes fonctionnels et l’approche basée sur les traits sont combinées :la première fournit un cadre écosystémique utile pour étudier les interactions des diatomées avec les compartiments biotiques et abiotiques de l’écosystème, et la seconde permet de représenter de façon efficace leur diversité fonctionnelle.<p><p>Dans un premier temps, puisque la taille est reconnue comme un trait majeur affectant de nombreux aspects de la valeur sélective du phytoplancton, la dépendance au biovolume de différents traits des diatomées a été établie sur base d’observations disponibles dans la littérature. Cette revue a montré qu’un compromis sépare les diatomées sur base de leur biovolume :les petites espèces sont meilleures compétitrices pour l’acquisition des ressources mais plus sensibles au broutage, et inversement. <p>Sur cette base, un ré-analyse d’un jeu de données incluant des comptages et mesures de biométrie avec l’identification de 68 taxons dans la ZCB entre 1992 et 2000 a été réalisée, avec une attention particulière pour la structure en termes de taille de la communauté de diatomées. Un regroupement des diatomées en fonction de leur biovolume a été réalisé sur base de leur évolution saisonnière typique. L’analyse de leur évolution temporelle suggère que la communauté des diatomées est composée d’assemblages avec une évolution saisonnière et interannuelle distinctes qui répondent vraisemblablement différemment aux conditions environnementales.<p>Afin d’étudier plus en profondeur les facteurs environnementaux contrôlant la structure en termes de taille de la communauté des diatomées dans la ZCB, le module diatomées du modèle MIRO, qui représente l’écosystème planctonique de la ZCP, a été modifié afin d’inclure les dépendances à la taille de quatre traits des diatomées. Cet outil reproduit correctement l’évolution saisonnière du biovolume moyen de la communauté, qui est caractérisé par de plus petites diatomées au printemps qui maximisent l’acquisition de ressources tandis que la prévalence du broutage en été induit une transition vers des espèces plus grandes. Le modèle a également été exploité pour étudier la gamme de tailles viables dans la ZCB en fonction des conditions environnementales. <p>Les résultats du modèle basés sur les traits ont ensuite été analysés sur la période 1992-2000. Les simulations ont mis en évidence les interactions complexes entre les processus physiques, de contrôles par les ressources et par le broutage, qui sont susceptibles de déterminer la variabilité interannuelle de la structure en termes de taille des diatomées dans la ZCB. La comparaison de ce modèle adaptatif avec un modèle plus conventionnel qui ne représente pas de diversité interne aux diatomées suggère que le premier produit une réponse légèrement plus flexible que le dernier, mais que la rigidité de la réponse simulée demeure un problème avec le modèle adaptatif qui reste incapable de représenter des évènements extrêmes de biomasse ou de structure de la communauté. Cela suggère que des développements supplémentaires du modèle sont nécessaires, en particulier du module zooplancton.<p>Finalement, une fonction écologique particulière est abordée dans une dernière section de cette thèse :la production d’une neurotoxine par certaines diatomées du genre Pseudo-nitzschia. Cette fonction a été incluse comme un métabolisme secondaire dans un modèle idéalisé de la croissance de Pseudo-nitzschia afin d’étudier les facteurs contrôlant la production de la toxine. Il est notamment montré que l’environnement lumineux est déterminant lorsque les conditions menant à la production de toxine sont rencontrées. <p><p>/<p><p>Diatoms are a key component of marine ecosystems and are characterized by an important diversity. The general objective of this thesis is to investigate the bottom-up and top-down controls of diatoms in the Belgian Coastal Zone (BCZ). This is done through the integration of their functional diversity into a coherent framework. In order to achieve this, Plankton Functional Type modelling and trait-based approaches are combined: the former provides an ecosystem context convenient to study the interactions of diatoms with biotic and abiotic compartments, and the latter allows an efficient representation of their functional diversity. <p><p>As a first step, since size is recognized as a master trait shaping many aspects of phytoplankton fitness, the cell volume dependences of diatom functional traits were compiled from observations available in the literature. This review showed that a trade-off distinguishes diatoms on the basis of their cell volume: smaller species are better competitor for resource acquisition but sensitive to grazing, and inversely. <p>On this basis, a re-analysis of a dataset including diatom cell counts and biometry with the identification of 68 taxa in the BCZ over the 1992-2000 period was carried out, with a focus on the size structure of the diatom community. A clustering of diatoms according to their cell volume was realized on the basis of their average seasonality. Investigation of their time evolution suggested that the diatom community in the area is composed of assemblages with distinct seasonal and interannual evolution that likely respond differently to environmental conditions.<p>In order to further investigate the bottom-up and top-down constrains on the size structure of the diatom community in the BCZ, the diatom module of the MIRO model, which represents the planktonic ecosystem of the BCZ, was modified in order to accommodate size-dependences of four diatom functional traits. This tool adequately reproduced the seasonal evolution of the mean cell volume of the diatom community, which is characterized by smaller diatoms in spring that maximize resource acquisition while the prevalence of grazing pressures in summer induces a shift towards larger species. The model was also used to investigate the range of viable diatom sizes in response to the bottom-up and top-down pressures in the BCZ.<p>Results of the trait-based adaptive model were then analysed over the 1992-2000 period. Simulations evidenced the complex interactions between physical, bottom-up and top-down processes that are likely to govern the interannual variability in the size structure of diatom in the area. Comparison of the adaptive model with a more conventional model resolving no diversity within diatoms suggested that the former produces a slightly more flexible response than the latter, but showed that the rigidity of the simulated response persists with the adaptive model which remains unable to catch extreme biomass and community structure events. This calls for further developments of other compartments of the model, more particularly zooplankton.<p>Finally, a peculiar ecological function is addressed on its own in the last section of this thesis: the toxigenicity of some species of the genus Pseudo-nitzschia. This function was added as a secondary metabolism in an idealized model of Pseudo-nitzschia growth in order to investigate the factors affecting toxin production. It notably showed that light was determinant under conditions leading to its production.<p> / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Bactérias quitinolíticas são autóctones do ecossistema marinho e tem um importante papel no processo de degradação de quitina. Relativamente pouco é conhecido sobre a diversidade e potencial enzimático de bactérias quitinolíticas isoladas de ambientes tropicais costeiros. Amostras de água do mar e de plâncton foram coletadas no Canal de São Sebastião, Baixada Santista e Ubatuba. As bactérias quitinolíticas foram enumeradas e isoladas em meio mínimo contendo quitina coloidal e caracterizadas através de métodos fenotípicos e genotípicos. As maiores contagens de bactérias quitinolíticas foram observadas em amostras de água do mar e plâncton coletadas na Baixada Santista. A diversidade de bactérias quitinolíticas e o potencial de produção de quitinases foram influenciados pelo nível de contaminação fecal presente no ecossistema marinho. Uma maior diversidade foi encontrada em ambiente com médio e baixo impacto antropogênico, mas bactérias quitinolíticas isoladas de ambiente com alta atividade antropogênica mostraram os maiores valores de produção de quitinases. / Chitinolytic bacteria are autochthonous in marine ecosystems and have an important role in chitin degradation process. A very little is know about the diversity and enzymatic potential of chitinolytic bacteria isolated from coastal tropical environments. Seawater and plankton samples were collected at Canal de São Sebastião, Baixada Santista and Ubatuba. Chitinolytic bacteria were counted and isolated in minimal media containing colloidal chitin and characterized using phenotypic and genotypic methods. Highest counts of chitinolytic bacteria were observed in seawater and plankton samples collected at Baixada Santista. The diversity of chitinolytic bacteria and the potential of chitinases production were influenced by the level of fecal contamination present in the marine ecosystem. Highest diversity was found in environment with medium and low anthropogenic impact, but chitinolytic bacteria isolated from environment with high anthropogenic influences showed highest chitinases production.

Plankton microorganisms constitute the base of the marine food web and play a great role in global atmospheric carbon dioxide drawdown. Moreover, being very sensitive to any environmental changes they allow noticing (and potentially counteracting) them faster than with any other means. As such they not only influence the fishery industry but are also frequently used to analyze changes in exploited coastal areas and the influence of these interferences on local environment and climate. As a consequence, there is a strong need for highly efficient systems allowing long time and large volume observation of plankton communities. This would provide us with better understanding of plankton role on global climate as well as help maintain the fragile environmental equilibrium. The adopted sensors typically provide huge amounts of data that must be processed efficiently without the need for intensive manual work of specialists. A new system for general purpose particle analysis in large volumes is presented. It has been designed and optimized for the continuous plankton monitoring problem; however, it can be easily applied as a versatile moving fluids analysis tool or in any other application in which targets to be detected and identified move in a unidirectional flux. The proposed system is composed of three stages: data acquisition, targets detection and their identification. Dedicated optical hardware is used to record images of small particles immersed in the water flux. Targets detection is performed using a Visual Rhythm-based method which greatly accelerates the processing time and allows higher volume throughput. The proposed method detects, counts and measures organisms present in water flux passing in front of the camera. Moreover, the developed software allows saving cropped plankton images which not only greatly reduces required storage space but also constitutes the input for their automatic identification. In order to assure maximal performance (up to 720 MB/s) the algorithm was implemented using CUDA for GPGPU. The method was tested on a large dataset and compared with alternative frame-by-frame approach. The obtained plankton images were used to build a classifier that is applied to automatically identify organisms in plankton analysis experiments. For this purpose a dedicated feature extracting software was developed. Various subsets of the 55 shape characteristics were tested with different off-the-shelf learning models. The best accuracy of approximately 92% was obtained with Support Vector Machines. This result is comparable to the average expert manual identification performance. This work was developed under joint supervision with Professor Rubens Lopes (IO-USP). / Microorganismos planctônicos constituem a base da cadeia alimentar marinha e desempenham um grande papel na redução do dióxido de carbono na atmosfera. Além disso, são muito sensíveis a alterações ambientais e permitem perceber (e potencialmente neutralizar) as mesmas mais rapidamente do que em qualquer outro meio. Como tal, não só influenciam a indústria da pesca, mas também são frequentemente utilizados para analisar as mudanças nas zonas costeiras exploradas e a influência destas interferências no ambiente e clima locais. Como consequência, existe uma forte necessidade de desenvolver sistemas altamente eficientes, que permitam observar comunidades planctônicas em grandes escalas de tempo e volume. Isso nos fornece uma melhor compreensão do papel do plâncton no clima global, bem como ajuda a manter o equilíbrio do frágil meio ambiente. Os sensores utilizados normalmente fornecem grandes quantidades de dados que devem ser processados de forma eficiente sem a necessidade do trabalho manual intensivo de especialistas. Um novo sistema de monitoramento de plâncton em grandes volumes é apresentado. Foi desenvolvido e otimizado para o monitoramento contínuo de plâncton; no entanto, pode ser aplicado como uma ferramenta versátil para a análise de fluídos em movimento ou em qualquer aplicação que visa detectar e identificar movimento em fluxo unidirecional. O sistema proposto é composto de três estágios: aquisição de dados, detecção de alvos e suas identificações. O equipamento óptico é utilizado para gravar imagens de pequenas particulas imersas no fluxo de água. A detecção de alvos é realizada pelo método baseado no Ritmo Visual, que acelera significativamente o tempo de processamento e permite um maior fluxo de volume. O método proposto detecta, conta e mede organismos presentes na passagem do fluxo de água em frente ao sensor da câmera. Além disso, o software desenvolvido permite salvar imagens segmentadas de plâncton, que não só reduz consideravelmente o espaço de armazenamento necessário, mas também constitui a entrada para a sua identificação automática. Para garantir o desempenho máximo de até 720 MB/s, o algoritmo foi implementado utilizando CUDA para GPGPU. O método foi testado em um grande conjunto de dados e comparado com a abordagem alternativa de quadro-a-quadro. As imagens obtidas foram utilizadas para construir um classificador que é aplicado na identificação automática de organismos em experimentos de análise de plâncton. Por este motivo desenvolveu-se um software para extração de características. Diversos subconjuntos das 55 características foram testados através de modelos de aprendizagem disponíveis. A melhor exatidão de aproximadamente 92% foi obtida através da máquina de vetores de suporte. Este resultado é comparável à identificação manual média realizada por especialistas. Este trabalho foi desenvolvido sob a co-orientacao do Professor Rubens Lopes (IO-USP).

There is growing concern that the worldwide loss in biodiversity will harm the stability of the ecosystems, and thereby, the carrying capacity and critical ecosystem services the biosphere provides. Phytoplankton (microalgae) in lakes and oceans are arguably the most important primary producers. They are responsible for approximately half of the earth's primary production. However, there is little research into what influences the biodiversity of phytoplankton communities and of those studies the mechanisms for coexistence of phytoplankton have so far almost exclusively been studied on ecological time scales. We, therefore, explored how biodiversity and biomass (a proxy to primary production) of phytoplankton communities respond to co-varied environmental drivers over evolutionary time scales. We model adaptive evolution of phytoplankton' resource use, with a non-dimensionalized model of negatively buoyant phytoplankton inhabiting a partially mixed one-dimensional water column using reaction-advection-diffusion equations. We show that a number of environmental drivers have novel effects on biodiversity and biomass on evolutionary timescales. In contrast with previous non-evolutionary work, we found that decreasing light attenuation or increasing resource use efficiency can result in decreased biomass of plankton communities and nutrient-poor environments. One novel driver of species diversity was the combination of low rates of diffusion with relatively intermediate rates of sinking promote species diversity. Furthermore, we show that the phytoplankton turnover rate affects environmental heterogeneity and is, therefore, a contributing driver to species diversity.The evolution of half saturation constants can produce a variety of biodiversity-ecosystem function patterns as two positive, one unimodal, and one negative association were found when comparing biodiversity-ecosystem function. Collectively, our analyses suggest that environmental drivers can have substantially different effects over evolutionary timescales than those effects ecological modeling has previously shown.

Tato práce pojednává o technikách automatické analýzy obrazu založené na konvolučních neuronových sítích (CNN), zaměřených na klasifikaci planktonu. V oblasti studování planktonu panuje velká diverzita v jeho tvarech a velikostech. Kvůli tomuto bývá klasifikace pomocí CNN náročná, jelikož CNN typicky požadují definovanou velikost vstupu. Běžné metody využívají škálování obrazu do jednotné velikosti. Avšak kvůli tomuto jsou ztraceny drobné detaily potřebné ke správné klasifikaci. Cílem práce bylo navrhnout a implementovat CNN klasifikátor obrazových dat planktonu a prozkoumat metody, které jsou zaměřené na problematiku různorodých velikostí obrázků. Metody, jako jsou patch cropping, využití spatial pyramid pooling vrstvy, zahrnutí metadat a sestavení multi-stream modelu jsou vyhodnoceny na náročném datasetu obrázků fytoplanktonu. Takto bylo dosaženo zlepšení o 1.0 bodů pro InceptionV3 architekturu s výslednou úspěšností 96.2 %. Hlavním přínosem této práce je vylepšení CNN klasifikátorů planktonu díky úspěšné aplikaci těchto metod.