An Investigation of the Impacts of Ponded Pastures on Barramundi and Other Finfish Populations in Tropical Coastal Wetlands

Objectives: 1) To document the extent of ponded pastures and other pondage systems in and adjacent to coastal wetlands on the central coast of Queensland. 2) To assess the movement, growth and survival of barramundi in ponded pastures. 3) To assess the utilisation by barramundi of ponded pastures and wetlands dominated by exotic grass species. 4) To identify appropriate wetland management strategies for facilitating barramundi movement and survival in ponded pastures and other pondage systems. 5) To document the species composition of finfish populations and their relative abundance in ponded pastures.

The Kinome of Pacific Oyster Crassostrea gigas, Its Expression during Development and in Response to Environmental Factors

Oysters play an important role in estuarine and coastal marine habitats, where the majority of humans live. In these ecosystems, environmental degradation is substantial, and oysters must cope with highly dynamic and stressful environmental constraints during their lives in the intertidal zone. The availability of the genome sequence of the Pacific oyster Crassostrea gigas represents a unique opportunity for a comprehensive assessment of the signal transduction pathways that the species has developed to deal with this unique habitat. We performed an in silico analysis to identify, annotate and classify protein kinases in C. gigas, according to their kinase domain taxonomy classification, and compared with kinome already described in other animal species. The C. gigas kinome consists of 371 protein kinases, making it closely related to the sea urchin kinome, which has 353 protein kinases. The absence of gene redundancy in some groups of the C. gigas kinome may simplify functional studies of protein kinases. Through data mining of transcriptomes in C. gigas, we identified part of the kinome which may be central during development and may play a role in response to various environmental factors. Overall, this work contributes to a better understanding of key sensing pathways that may be central for adaptation to a highly dynamic marine environment.

Adaptive Mechanisms of an Estuarine Synechococcus based on Genomics, Transcriptomics, and Proteomics

Picocyanobacteria are important phytoplankton and primary producers in the ocean. Although extensive work has been conducted for picocyanobacteria (i.e. Synechococcus and Prochlorococcus) in coastal and oceanic waters, little is known about those found in estuaries like the Chesapeake Bay. Synechococcus CB0101, an estuarine isolate, is more tolerant to shifts in temperature, salinity, and metal toxicity than coastal and oceanic Synechococcus strains, WH7803 and WH7805. Further, CB0101 has a greater sensitivity to high light intensity, likely due to its adaptation to low light environments. A complete and annotated genome sequence of CB0101 was completed to explore its genetic capacity and to serve as a basis for further molecular analysis. Comparative genomics between CB0101, WH7803, and WH7805 show that CB0101 contains more genes involved in regulation, sensing, and stress response. At the transcript and protein level, CB0101 regulates its metabolic pathways, transport systems, and sensing mechanisms when nitrate and phosphate are limited. Zinc toxicity led to oxidative stress and a global down regulation of photosystems and the translation machinery. From the stress response studies seven chromosomal toxin-antitoxin (TA) genes, were identified in CB0101, which led to the discovery of TA genes in several marine Synechococcus strains. The activation of the relB2/relE1 TA system allows CB0101 to arrest its growth under stressful conditions, but the growth arrest is reversible, once the stressful environment dissipates. The genome of CB0101 contains a relatively large number of genomic island (GI) genes compared to known marine Synechococcus genomes. Interestingly, a massive shutdown (255 out of 343) of GI genes occurred after CB0101 was infected by a lytic phage. On the other hand, phage-encoded host-like proteins (hli, psbA, ThyX) were highly expressed upon phage infection. This research provides new evidence that estuarine Synechococcus like CB0101 have inherited unique genetic machinery, which allows them to be versatile in the estuarine environment.

Neustonic distribution of decapod planktonic stages and competence of brachyuran megalopae in coastal waters

Settlement rate may not reflect larval supply to coastal waters in different marine invertebrates and demersal fishes. The importance of near-shore oceanography and behaviour of late larval stages may be underestimated. The present study conducted neustonic sampling over station grids and along full-length transects at two embayments in south-eastern Brazil to (1) compare diurnal and nocturnal occurrence of most frequent decapod stages to assess their vertical movements, (2) describe the formation of larval patches and (3) measure competence of crab megalopae according to their distance to recruitment grounds. Several shrimp species apparently undergo a diel vertical migration, swimming crab megalopae showed no vertical movements and megalopae of the intertidal crab Pachygrapsus transversus revealed a reversed vertical migration. During the day, crab megalopae aggregated in convergence zones just below surface slicks. These larvae consisted of advanced, pre-moult stages, at both mid-bay and near-shore patches. Competence, measured as the time to metamorphosis in captivity, was similar between larval patches within each taxon. Yet, subtidal portunids moulted faster to juveniles than intertidal grapsids, possibly because they were closer to settlement grounds. Megalopae of Pachygrapsus from benthic collectors moulted faster than those from bay areas. These results suggest that alternative vertical migration patterns of late megalopae favour onshore transport, and actual competence takes place very close to suitable substrates, where larvae may remain for days before settlement. Lack of correlation between larval supply and settlement for Pachygrapsus suggests that biological processes, besides onshore transport, may play an important role in determining settlement success of coastal crabs.

Developing European operational oceanography for Blue Growth, climate change adaptation and mitigation, and ecosystem-based management

Operational approaches have been more and more widely developed and used for providing marine data and information services for different socio-economic sectors of the Blue Growth and to advance knowledge about the marine environment. The objective of operational oceanographic research is to develop and improve the efficiency, timeliness, robustness and product quality of this approach. This white paper aims to address key scientific challenges and research priorities for the development of operational oceanography in Europe for the next 5-10 years. Knowledge gaps and deficiencies are identified in relation to common scientific challenges in four EuroGOOS knowledge areas: European Ocean Observations, Modelling and Forecasting Technology, Coastal Operational Oceanography and Operational Ecology. The areas "European Ocean Observations" and "Modelling and Forecasting Technology" focus on the further advancement of the basic instruments and capacities for European operational oceanography, while "Coastal Operational Oceanography" and "Operational Ecology" aim at developing new operational approaches for the corresponding knowledge areas.

Genetic diversity across geographical scales in marine coastal ecosystems: Holothuria arguinensis a model species

Coastal lagoons are considered one of the most productive areas of our planet harboring a large variety of habitats. Their transitional character, between terrestrial and marine environments, creates a very particular ecosystem with important variations of its environmental conditions. The organisms that are able to survive on these ecosystems frequently experience strong selective pressures and constrictions to gene flowwith marine populations, which could contribute to genetic divergence among populations inhabiting coastal lagoon and marine environments. Therefore, the main aims of this study are to asses the genetic diversity and population structure of Holothuria arguinensis across geographical ranges, to test the hypothesis of coastal lagoons as hotspots of genetic diversity in the Ria Formosa lagoon, and to determine the role of exporting standing genetic variation from the lagoon to open sea and their implications to recent geographical expansion events. To reach these objectives, we investigate the genetic structure of H. arguinensis using two mitochondrial DNA markers (COI and 16S) at different spatial scales: i) small, inside Ria Formosa coastal lagoon, South Portugal; 2) large, including most of the geographical distribution of this species (South and Western Portuguese coast and Canary islands); these results will allow us to compare the genetic diversity of lagoonal and marine populations of H. arguinensis. On this framework, its recent geographical expansion events, recorded by Rodrigues (2012) and González-Wangüemert and Borrero-Pérez (2012), will be analyzed considering the potential contribution from lagoonal genetic pool. Non-significant genetic structure and high haplotypic diversity were found inside the Ria Formosa coastal lagoon. Both genes were unable to detect significant genetic differentiation among lagoonal and marine localities, suggesting a high rate of gene flow. The results supported our hypotheses that coastal lagoons are not only acting as hotspots of genetic diversity, but also contributing for the genetic variability of the species, working as a source of new haplotypes and enhancing adaptation to the high variable conditions. Different genetic patterns of colonization were found on H. arguinensis, but they must be studied more deeply.

Comprehensive characterization of snowfall in terms of microphysical features, quantitative precipitation estimation and scavenging properties by in situ and remote sensing observations at an Antarctic coastal site

Snow plays a crucial role in the Earth's hydrological cycle and energy budget, making its monitoring necessary. In this context, ground-based radars and in situ instruments are essential thanks to their spatial coverage, resolution, and temporal sampling. Deep understanding and reliable measurements of snow properties are crucial over Antarctica to assess potential future changes of the surface mass balance (SMB) and define the contribution of the Antarctic ice sheet on sea-level rise. However, despite its key role, Antarctic precipitation is poorly investigated due to the continent's inaccessibility and extreme environment. In this framework, this Thesis aims to contribute to filling this gap by in-depth characterization of Antarctic precipitation at the Mario Zucchelli station from different points of view: microphysical features, quantitative precipitation estimation (QPE), vertical structure of precipitation, and scavenging properties. For this purpose, a K-band vertically pointing radar collocated with a laser disdrometer and an optical particle counter (OPC) were used. The radar probed the lowest atmospheric layers with high vertical resolution, allowing the first trusted measurement at only 105 m height. Disdrometer and OPC provided information on the particle size distribution and aerosol concentrations. An innovative snow classification methodology was designed by comparing the radar reflectivity (Ze) and disdrometer-derived reflectivity by means of DDA simulations. Results of classification were exploited in QPE through appropriate Ze-snow rate relationships. The accuracy of the resulting QPE was benchmarked against a collocated weighing gauge. Vertical radar profiles were also investigated to highlight hydrometeors' sublimation and growth processes. Finally, OPC and disdrometer data allowed providing the first-ever estimates of scavenging properties of Antarctic snowfall. Results presented in this Thesis give rise to advances in knowledge of the characteristics of snowfall in Antarctica, contributing to a better assessment of the SMB of the Antarctic ice sheet, the major player in the global sea-level rise.

Absorption of metals and characterization of chemical elements present in three species of Gracilaria (Gracilariaceae) Greville: a genus of economical importance

Gracilaria Greville is a genus of seaweed that is economically explored by the cosmetic, pharmaceutical and food industries. One of the biggest problems associated with growing Gracilaria is the discharge of heavy metals into the marine environment. The absorption of heavy metals was investigated with the macroalga Gracilaria tenuistipitata Zhang et Xia, cultivated in a medium containing copper (Cu) and cadmium (Cd). In biological samples, EC50 concentrations of 1 ppm for cadmium and 0.95 ppm for copper were used. These concentrations were based on seaweed growth curves obtained over a period of six days in previous studies. ICP-AES was used to determine the amount of metal that seaweeds absorbed during this period. G. tenuistipitata was able to bioaccumulate both metals, about 17% of copper and 9% of cadmium. Basal natural levels of Cu were found in control seaweeds and in G. tenuistipitata exposed to Cd. In addition, the repertoire of other important chemical elements, as well as their concentrations, was determined for G. tenuistipitata and two other important seaweeds, G. birdiae Plastino & Oliveira and G. domingensis (Kützing) Sonder ex Dickie, collected in natural environments on the Brazilian shore.

Meiobenthic communities of seagrass beds (Zostera capricorni) and unvegetated sediments along the coast of New South Wales, Australia

Seagrass beds have higher biomass, abundance, diversity and productivity of benthic organisms than unvegetated sediments. However, to date most studies have analysed only the macrofaunal component and ignored the abundant meiofauna present in seagrass meadows. This study was designed to test if meiobenthic communities, especially the free-living nematodes, differed between seagrass beds and unvegetated sediments. Sediment samples from beds of the eelgrass Zostera capricorni and nearby unvegetated sediments were collected in three estuaries along the coast of New South Wales, Australia. Results showed that sediments below the seagrass were finer, with a higher content of organic material and were less oxygenated than sediments without seagrass. Univariate measures of the fauna (i.e. abundance, diversity and taxa richness of total meiofauna and nematode assemblages) did not differ between vegetated and unvegetated sediments. However multivariate analysis of meiofaunal higher taxa showed significant differences between the two habitats, largely due to the presence and absence of certain taxa. Amphipods, tanaidacea, ostracods, hydrozoans and isopods occurred mainly in unvegetated sediments, while kinorhyncs, polychaetes, gastrotrichs and turbellarians were more abundant in vegetated sediments. Regarding the nematode assemblages, 32.4% of the species were restricted to Z. capricorni and 25% only occurred in unvegetated sediments, this suggests that each habitat is characterized by a particular suite of species. Epistrate feeding nematodes were more abundant in seagrass beds, and it is suggested that they graze on the microphytobenthos which accumulates underneath the seagrass. Most of the genera that characterized these estuarine unvegetated sediments are also commonly found on exposed sandy beaches. This may be explained by the fact that Australian estuaries have very little input of freshwater and experience marine conditions for most of the year. This study demonstrates that the seagrass and unvegetated sediments have discrete meiofaunal communities, with little overlap in species composition. (C) 2010 Elsevier Ltd. All rights reserved.

Effect of crab size and habitat type on the locomotory activity of juvenile shore crabs, Carcinus maenas

Post-settlement processes are a major focus in the study of the dynamics of marine populations and communities. Post-settlement movement of juveniles is an important, but often ignored, process which affects local predator-prey and competitive interactions. We used benthic suction sampling and pitfall traps to examine density and locomotory activity of Carcinus maenas juveniles in different intertidal habitat types in the Rio Mira Estuary, Portugal, to better understand intra-specific interactions in a system where density-dependent processes are known to regulate population dynamics. As expected, significantly higher densities of juvenile shore crabs were found from bare mud compared to densely vegetated habitats. At the time of sampling, small and intermediate stages together outnumbered by far the larger juveniles. Conversely, larger crabs were much more frequent than smaller ones in traps. A locomotory index (LI), i.e. the ratio between crab catch in pitfall traps and their density within their moving range, is proposed as a measure of movement. LI analyses indicated that: (1) movement is an order of magnitude higher in large than small juveniles and much higher in sparse than dense vegetation cover; (2) activity of small juveniles is mostly crepuscular, regardless of vegetation cover; and (3) movement of large juveniles is very limited in dense Zostera patches, but very high in sparsely vegetated areas, during the day and night. These results suggest that small juveniles are relatively protected under dense vegetation cover due to lower mobility of larger crabs, and provide evidence of temporal segregation of activity windows between juvenile crabs of different sizes, which may be a key mechanism to reduce cannibalism and therefore increase the carrying capacity of nursery habitats. (C) 2008 Elsevier Ltd. All rights reserved.

Shelf and estuarine transport mechanisms affecting the supply of competent larvae in a suite of brachyuran crabs with different life histories

Supply of competent larvae to the benthic habitat is a major determinant of population dynamics in coastal and estuarine invertebrates with an indirect life cycle. Larval delivery may depend not only on physical transport mechanisms, but also on larval behavior and physiological progress to the competent stage. Yet, the combined analysis of such factors has seldom been attempted. We used time-series analyses to examine tide- and wind-driven mechanisms responsible for the supply of crab megalopae to an estuarine river under a major marine influence in SW Spain, and monitored the vertical distribution of upstream moving megalopae, their net flux and competent state. The species Panopeus africanus (estuarine), Brachynotus sexdentatus (euryhaline) and Nepinnotheres pinnotheres (coastal) comprised 80% of the whole sample, and responded in a similar way to tide and wind forcing. Tidal range was positively correlated to supply, with maxima 0 to 1 d after spring tides, suggesting selective tidal stream transport. Despite being extensively subjected to upwelling, downwind drift under the effect of westerlies, not Ekman transport, explained residual supply variation at our sampling area. Once in the estuary, net flux and competence state matched the expected trends. Net upstream flux increased from B. sexdentatus to P. africanus, favoring transport to a sheltered coastal habitat (N. pinnotheres), or to the upper estuary (P. africanus). Competence state was highest in N. pinnotheres, intermediate in B. sexdentatus and lowest in P. africanus, as expected if larvae respond to cues from adequate benthic habitat. P. africanus megalopae were found close to the bottom, not above, rendering slower upstream transport than anticipated.

Influence of the bacterioplankton community of a tropical eutrophic lagoon on the bacterial community of its neighbouring ocean

The Rodrigo de Freitas lagoon (RFL) is a tropical eutrophic coastal ecosystem located in the urban area of Rio de Janeiro, Brazil. This environment consists of freshwater but has communication with the ocean through a channel (Jardim de Alah`s Channel). The aim of this study was to evaluate the influence of lagoon water on the nearby ocean using molecular and traditional microbiological methods. We hypothesised that due to the eutrophic low-salinity environment, the bacterioplankton community from the RFL would have a native ""brackish"" composition influenced by both freshwater and marine phylotypes, and that bacterial phylotypes of this community would be detected in oceanic samples closer to the channel between the lagoon and the ocean. The cultivation and microscopy experiments clearly showed this influence. Bacterial cell counts revealed that the greater amounts of bacterial cells present in the lagoon increased the observed values seen at oceanic stations near the channel. The Denaturing gradient gel eletrophoresis community profiles also showed a clear influence of Rodrigo de Freitas lagoon waters on the adjacent beaches. The band patterns found for the stations near the channel showed that these communities were mixtures of the communities of the lagoon and sea, and as the distance from the channel increased, the samples became more similar to ocean bacterial communities. A 16S rRNA gene clone library was constructed using a sample acquired from the connection point between the lagoon and the ocean. Around 52% of the sequences in the library showed similarity to the genus Proteobacteria (1% Alpha, 21% Beta, 19% Gamma and 29% unclassified Proteobacteria), and the second most abundant genus was Bacteroidetes, with 15% of the total clones. The results showed that the structure of the bacterial community had both freshwater and marine characteristics.

Influence of the slice position on chloride migration tests for concrete in marine conditions

Chloride migration tests are used to measure the concrete capacity to inhibit chloride attack. Many researchers carry out this test in a slice of concrete extracted from the central part of cylindrical specimens, discarding about 75% of the concrete used to mold the specimens. This fact generated the question: would it be possible to extract more slices from a same specimen without losing the confidence in the results? The main purpose of this work is to answer this question. Moreover, another aim of this study was to show the difference of chloride penetration between finished faces and the formwork surfaces of concrete beams and slabs. The results indicated that it is possible to use more slices of a single specimen for a chloride migration test. Moreover, it was demonstrated that there is a significant difference of chloride penetration between the finished surface and the formwork surface of the specimens. (C) 2008 Elsevier Ltd. All rights reserved.

Efficacy of surface hydrophobic agents in reducing water and chloride ion penetration in concrete

Hydrophobic agents are surface protection materials capable of increasing the angle of contact between the water and the concrete surface. For this reason, hydrophobic agents reduce water (in liquid form) penetration in concrete. Therefore, many European construction regulating agencies recommend this treatment in their maintenance policy. Nonetheless, there continues to be a gap in the understanding about which transport mechanisms of the concrete are modified by the hidrophobic agents. The aim of this study was to fill this gap in regards to reinforced concrete structures inserted in a marine environment. To this end, certain tests were used: Two involving permeability mechanism, one determining capillary absorption, and the last, a migration test used to estimate the chloride diffusion coefficient in saturated condition. Results indicated the efficacy of the hydrophobic agents in cases where capillary suction is the mechanism of water penetration (reduced by 2.12 and 7.0 times, depending of the product). However, when the transport mechanism is permeability this product is not advisable. Moreover, it was demonstrated that the chloride diffusion coefficient (in saturated condition) is reduced by the hydrophobic agents, however, the magnitude of this reduction is minor (reduced by 11% and 17%, depending on the product).

Morphological and biological notes on Polymorphus (Profilicollis) sphaerocephalus and Corynosoma stanleyi (Polymorphidae : Acanthocephala)

Polymorphus (Profilicollis) sphaerocephalus (Bremser in Rudolphi, 1819) Van Cleave, 1947 (Polymorphidae) cystacanths were recovered from 5 species of grapsid crabs (Paragrapsus gaimardii (Milne Edwards, 1837), Paragrapsus laevis (Dana, 1852), Paragrapsus quadridentatus (Milne Edwards, 1837), Brachynotus spinosus (Milne Edwards, 1853), and Cyclograpsus granulosus (Milne Edwards, 1853)) and 1 species of portunid crab (Nectocarcinus integrifrons (Linnaeus, 1766)) from intertidal zones in southern temperate waters of Australia. Cystacanths of Corynosoma stanleyi Smales, 1986 (Polymorphidae) were also recovered from P. gaimardii, P. quadridentatus, and C. granulosus. Polymorphus (P.) sphaerocephalus was the most prevalent (100%) in C. granulosus at Flinders I. and C. stanleyi was most prevalent (59.1%) in C. granulosus at Dunally Channel, Tasmania.