Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Characterication of metals in hemolymph and tissues of the Antarctic bivalve Laternula elliptica

A high input of lithogenic sediment from glaciers was assumed to be responsible for high Fe and Mn contents in the Antarctic soft shell clam Laternula elliptica at King George Island. Indeed, withdrawal experiments indicated a strong influence of environmental Fe concentrations on Fe contents in bivalve hemolymph, but no significant differences in hemolymph and tissue concentrations were found among two sites of high and lower input of lithogenic debris. Comparing Fe and Mn concentrations of porewater, bottom water, and hemolymph from sampling sites, Mn appears to be assimilated as dissolved species, whereas Fe apparently precipitates as ferrihydrite within the oxic sediment or bottom water layer prior to assimilation by the bivalve. Hence, we attribute the high variability of Fe and Mn accumulation in tissues of L. elliptica around Antarctica to differences in the geochemical environment of the sediment and the resulting Fe and Mn flux across the benthic boundary.

Results of wave modelling for Moreton Bay, Southeast Queensland, and a reef lagoon off Lizard Island, Great Barrier Reef, Australia

The distribution, abundance, behaviour, and morphology of marine species is affected by spatial variability in the wave environment. Maps of wave metrics (e.g. significant wave height Hs, peak energy wave period Tp, and benthic wave orbital velocity URMS) are therefore useful for predictive ecological models of marine species and ecosystems. A number of techniques are available to generate maps of wave metrics, with varying levels of complexity in terms of input data requirements, operator knowledge, and computation time. Relatively simple "fetch-based" models are generated using geographic information system (GIS) layers of bathymetry and dominant wind speed and direction. More complex, but computationally expensive, "process-based" models are generated using numerical models such as the Simulating Waves Nearshore (SWAN) model. We generated maps of wave metrics based on both fetch-based and process-based models and asked whether predictive performance in models of benthic marine habitats differed. Predictive models of seagrass distribution for Moreton Bay, Southeast Queensland, and Lizard Island, Great Barrier Reef, Australia, were generated using maps based on each type of wave model. For Lizard Island, performance of the process-based wave maps was significantly better for describing the presence of seagrass, based on Hs, Tp, and URMS. Conversely, for the predictive model of seagrass in Moreton Bay, based on benthic light availability and Hs, there was no difference in performance using the maps of the different wave metrics. For predictive models where wave metrics are the dominant factor determining ecological processes it is recommended that process-based models be used. Our results suggest that for models where wave metrics provide secondarily useful information, either fetch- or process-based models may be equally useful.

Projecting Changes in the Distribution and Productivity of Living Marine Resources: A Critical Review of the Suite of Modeling Approaches used in the Large European Project VECTORS

We review and compare four broad categories of spatially-explicit modelling approaches currently used to understand and project changes in the distribution and productivity of living marine resources including: 1) statistical species distribution models, 2) physiology-based, biophysical models of single life stages or the whole life cycle of species, 3) food web models, and 4) end-to-end models. Single pressures are rare and, in the future, models must be able to examine multiple factors affecting living marine resources such as interactions between: i) climate-driven changes in temperature regimes and acidification, ii) reductions in water quality due to eutrophication, iii) the introduction of alien invasive species, and/or iv) (over-)exploitation by fisheries. Statistical (correlative) approaches can be used to detect historical patterns which may not be relevant in the future. Advancing predictive capacity of changes in distribution and productivity of living marine resources requires explicit modelling of biological and physical mechanisms. New formulations are needed which (depending on the question) will need to strive for more realism in ecophysiology and behaviour of individuals, life history strategies of species, as well as trophodynamic interactions occurring at different spatial scales. Coupling existing models (e.g. physical, biological, economic) is one avenue that has proven successful. However, fundamental advancements are needed to address key issues such as the adaptive capacity of species/groups and ecosystems. The continued development of end-to-end models (e.g., physics to fish to human sectors) will be critical if we hope to assess how multiple pressures may interact to cause changes in living marine resources including the ecological and economic costs and trade-offs of different spatial management strategies. Given the strengths and weaknesses of the various types of models reviewed here, confidence in projections of changes in the distribution and productivity of living marine resources will be increased by assessing model structural uncertainty through biological ensemble modelling.

Projecting Changes in the Distribution and Productivity of Living Marine Resources: A Critical Review of the Suite of Modeling Approaches used in the Large European Project VECTORS

We review and compare four broad categories of spatially-explicit modelling approaches currently used to understand and project changes in the distribution and productivity of living marine resources including: 1) statistical species distribution models, 2) physiology-based, biophysical models of single life stages or the whole life cycle of species, 3) food web models, and 4) end-to-end models. Single pressures are rare and, in the future, models must be able to examine multiple factors affecting living marine resources such as interactions between: i) climate-driven changes in temperature regimes and acidification, ii) reductions in water quality due to eutrophication, iii) the introduction of alien invasive species, and/or iv) (over-)exploitation by fisheries. Statistical (correlative) approaches can be used to detect historical patterns which may not be relevant in the future. Advancing predictive capacity of changes in distribution and productivity of living marine resources requires explicit modelling of biological and physical mechanisms. New formulations are needed which (depending on the question) will need to strive for more realism in ecophysiology and behaviour of individuals, life history strategies of species, as well as trophodynamic interactions occurring at different spatial scales. Coupling existing models (e.g. physical, biological, economic) is one avenue that has proven successful. However, fundamental advancements are needed to address key issues such as the adaptive capacity of species/groups and ecosystems. The continued development of end-to-end models (e.g., physics to fish to human sectors) will be critical if we hope to assess how multiple pressures may interact to cause changes in living marine resources including the ecological and economic costs and trade-offs of different spatial management strategies. Given the strengths and weaknesses of the various types of models reviewed here, confidence in projections of changes in the distribution and productivity of living marine resources will be increased by assessing model structural uncertainty through biological ensemble modelling.

Studies on Bio-Geochemistry, Bio-Optical Properties and Satellite Validation of Coastal Waters of South Eastern Arabian Sea

In situ methods used for water quality assessment have both physical and time constraints. Just a limited number of sampling points can be performed due to this, making it difficult to capture the range and variability of coastal processes and constituents. In addition, the mixing between fresh and oceanic water creates complex physical, chemical and biological environment that are difficult to understand, causing the existing measurement methodologies to have significant logistical, technical, and economic challenges and constraints. Remote sensing of ocean colour makes it possible to acquire information on the distribution of chlorophyll and other constituents over large areas of the oceans in short periods. There are many potential applications of ocean colour data. Satellite-derived products are a key data source to study the distribution pattern of organisms and nutrients (Guillaud et al. 2008) and fishery research (Pillai and Nair 2010; Solanki et al. 2001. Also, the study of spatial and temporal variability of phytoplankton blooms, red tide identification or harmful algal blooms monitoring (Sarangi et al. 2001; Sarangi et al. 2004; Sarangi et al. 2005; Bhagirathan et al., 2014), river plume or upwelling assessments (Doxaran et al. 2002; Sravanthi et al. 2013), global productivity analyses (Platt et al. 1988; Sathyendranath et al. 1995; IOCCG2006) and oil spill detection (Maianti et al. 2014). For remote sensing to be accurate in the complex coastal waters, it has to be validated with the in situ measured values. In this thesis an attempt to study, measure and validate the complex waters with the help of satellite data has been done. Monitoring of coastal ecosystem health of Arabian Sea in a synoptic way requires an intense, extensive and continuous monitoring of the water quality indicators. Phytoplankton determined from chl-a concentration, is considered as an indicator of the state of the coastal ecosystems. Currently, satellite sensors provide the most effective means for frequent, synoptic, water-quality observations over large areas and represent a potential tool to effectively assess chl-a concentration over coastal and oceanic waters; however, algorithms designed to estimate chl-a at global scales have been shown to be less accurate in Case 2 waters, due to the presence of water constituents other than phytoplankton which do not co-vary with the phytoplankton. The constituents of Arabian Sea coastal waters are region-specific because of the inherent variability of these optically-active substances affected by factors such as riverine input (e.g. suspended matter type and grain size, CDOM) and phytoplankton composition associated with seasonal changes.

The “social” aspect of social-ecological systems: a critique of analytical frameworks and findings from a multisite study of coastal sustainability

We evaluate whether society can adequately be conceptualized as a component of social-ecological systems, given social theory and the current outputs of systems-based research. A mounting critique from the social sciences posits that resilience theory has undertheorized social entities with the concept of social-ecological systems. We trace the way that use of the term has evolved, relating to social science theory. Scientometic and network analysis provide a wide range of empirical data about the origin, growth, and use of this term in academic literature. A content analysis of papers in Ecology and Society demonstrates a marked emphasis in research on institutions, economic incentives, land use, population, social networks, and social learning. These findings are supported by a review of systems science in 18 coastal assessments. This reveals that a systems-based conceptualization tends to limit the kinds of social science research favoring quantitative couplings of social and ecological components and downplaying interpretive traditions of social research. However, the concept of social-ecological systems remains relevant because of the central insights concerning the dynamic coupling between humans and the environment, and its salient critique about the need for multidisciplinary approaches to solve real world problems, drawing on heuristic devices. The findings of this study should lead to more circumspection about whether a systems approach warrants such claims to comprehensiveness. Further methodological advances are required for interdisciplinarity. Yet there is evidence that systems approaches remain highly productive and useful for considering certain social components such as land use and hybrid ecological networks. We clarify advantages and restrictions of utilizing such a concept, and propose a reformulation that supports engagement with wider traditions of research in the social sciences.

Phytoplankton versus macrophyte contribution to primary production and biogeochemical cycles of a coastal mesotidal system. A modelling approach

This study presents an assessment of the contributions of various primary producers to the global annual production and N/P cycles of a coastal system, namely the Arcachon Bay, by means of a numerical model. This 3D model fully couples hydrodynamic with ecological processes and simulates nitrogen, silicon and phosphorus cycles as well as phytoplankton, macroalgae and seagrasses. Total annual production rates for the different components were calculated for different years (2005, 2007 and 2009) during a time period of drastic reduction in seagrass beds since 2005. The total demand of nitrogen and phosphorus was also calculated and discussed with regards to the riverine inputs. Moreover, this study presents the first estimation of particulate organic carbon export to the adjacent open ocean. The calculated annual net production for the Arcachon Bay (except microphytobenthos, not included in the model) ranges between 22,850 and 35,300 tons of carbon. The main producers are seagrasses in all the years considered with a contribution ranging from 56% to 81% of global production. According to our model, the -30% reduction in seagrass bed surface between 2005 and 2007, led to an approximate 55% reduction in seagrass production, while during the same period of time, macroalgae and phytoplankton enhanced their productions by about +83% and +46% respectively. Nonetheless, the phytoplankton production remains about eightfold higher than the macroalgae production. Our results also highlight the importance of remineralisation inside the Bay, since riverine inputs only fulfill at maximum 73% nitrogen and 13% phosphorus demands during the years 2005, 2007 and 2009. Calculated advection allowed a rough estimate of the organic matter export: about 10% of the total production in the bay was exported, originating mainly from the seagrass compartment, since most of the labile organic matter was remineralised inside the bay.

Determination of ecological sensitive areas of the coastal areas of Caspian Sea (Boujagh Wetland National Park) based on ecological carrying capacity and economical valuation region

The coastal districts, as an intersection of two perfectly different ecosystems of dry land and sea, is one of the most complicated and the richest natural system on earth. Considering these areas are constantly exposed to aggregation of water pollutants and also consequence resulting from construction and development activities, they are very vulnerable. Therefore, "sensitive Coastal areas" has become a common word in the related subjects to marine environment recently. The said title relates to the areas of the coastal lines which are vulnerable to the natural condition or human actions because of ecological, social, economic, educational and research importance, also they need particular supports. The southern coasts of Caspian Sea, In Iran prominent samples are of these sensitive areas which their environment are exposed to demolition and destruction intensely, due to increasing and uncontrolled development. The first stage of protecting and managing the coastal areas is identifying sensitive Coastal areas and broadening the Coasts. In this survey, we attempted to examine a definite area in the southern coasts of Caspian Sea. In Iran, by profiting from the world experiences and concluded researches in Iran especially the concluded studies by marine environment office and the Environment protection organization on the subject of determination criteria of the sensitive ecological districts. For this purpose (In Gilan Province) Boujagh national park district which is located in the mouth of sefidroud river and also is possessed of the special ecological and environmental features and distinctions. In this survey, first they said district is divided proportionally on the basis of using a grid system in order to identify the sensitive ecological districts and broaden the coast, and then the desired indices have been determined and scored by numeral valuation method in each unit and then analysis has been done by using of the geography information system (GIS) and final has estimated economic valuation of sensitive ecological areas that is presented in this essay.

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.

Development of molecular approaches to assess the diversity and abundance of marine nematodes assemblages for assessment of Good Environmental Status of the estuarine and marine ecosystems

In Europe, the concerns with the status of marine ecosystems have increased, and the Marine Directive has as main goal the achievement of Good Environmental Status (GES) of EU marine waters by 2020. Molecular tools are seen as promising and emerging approaches to improve ecosystem monitoring, and have led ecology into a new era, representing perhaps the most source of innovation in marine monitoring techniques. Benthic nematodes are considered ideal organisms to be used as biological indicator of natural and anthropogenic disturbances in aquatic ecosystems underpinning monitoring programmes on the ecological quality of marine ecosystems, very useful to assess the GES of the marine environment. dT-RFLP (directed Terminal-Restriction Fragment Length Polymorphism) allows to assess the diversity of nematode communities, but also allows studying the functioning of the ecosystem, and combined with relative real-time PCR (qPCR), provides a high-throughput semi-quantitative characterization of nematode communities. These characteristics make the two molecular tools good descriptors for the good environmental status assessment. The main aim of this study is to develop and optimize the dT-RFLP and qPCR in Mira estuary (SW coast, Portugal). A molecular phylogenetic analysis of marine and estuarine nematodes is being performed combining morphological and molecular analysis to evaluate the diversity of free-living marine nematodes in Mira estuary. After morphological identification, barcoding of 18S rDNA and COI genes are being determined for each nematode species morphologically identified. So far we generated 40 new sequences belonging to 32 different genus and 17 families, and the study has shown a good degree of concordance between traditional morphology-based identification and DNA sequences. These results will improve the assessment of marine nematode diversity and contribute to a more robust nematode taxonomy. The DNA sequences are being used to develop the dT-RFLP with the ability to easily process large sample numbers (hundreds and thousands), rather than typical of classical taxonomic or low throughput molecular analyses. A preliminary study showed that the digest enzymes used in dT-RFLP for terrestrial assemblages separated poorly the marine nematodes at taxonomic level for functional group analysis. A new digest combination was designed using the software tool DRAT (Directed Terminal Restriction Analysis Tool) to distinguished marine nematode taxa. Several solutions were provided by DRAT and tested empirically to select the solution that cuts most efficiently. A combination of three enzymes and a single digest showed to be the best solution to separate the different clusters. Parallel to this, another tool is being developed to estimate the population size (qPCR). An improvement in qPCR estimation of gene copy number using an artificial reference is being performed for marine nematodes communities to quantify the abundance. Once developed, it is proposed to validate both methodologies by determining the spatial and temporal variability of benthic nematodes assemblages across different environments. The application of these high-throughput molecular approaches for benthic nematodes will improve sample throughput and their implementation more efficient and faster as indicator of ecological status of marine ecosystems.

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.

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.

Mean sea-level rise impacts on Santos Bay, Southeastern Brazil - physical modelling study

The greenhouse effect and resulting increase in the Earth`s temperature may accelerate the mean sea-level rise. The natural response of bays and estuaries to this rise, such as this case study of Santos Bay (Brazil), will include change in shoreline position, land flooding and wetlands impacts. The main impacts of this scenario were studied in a physical model built in the Coastal and Harbour Division of Hydraulic Laboratory, University of Sao Paulo, and the main conclusions are presented in this paper. The model reproduces near 1,000 km(2) of the study area, including Santos, Sao Vicente, Praia Grande, Cubatao, Guaruja and Bertioga cities.