A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes

The main scope of my PhD is the reconstruction of the large-scale bivalve phylogeny on the basis of four mitochondrial genes, with samples taken from all major groups of the class. To my knowledge, it is the first attempt of such a breadth in Bivalvia. I decided to focus on both ribosomal and protein coding DNA sequences (two ribosomal encoding genes -12s and 16s -, and two protein coding ones - cytochrome c oxidase I and cytochrome b), since either bibliography and my preliminary results confirmed the importance of combined gene signals in improving evolutionary pathways of the group. Moreover, I wanted to propose a methodological pipeline that proved to be useful to obtain robust results in bivalves phylogeny. Actually, best-performing taxon sampling and alignment strategies were tested, and several data partitioning and molecular evolution models were analyzed, thus demonstrating the importance of molding and implementing non-trivial evolutionary models. In the line of a more rigorous approach to data analysis, I also proposed a new method to assess taxon sampling, by developing Clarke and Warwick statistics: taxon sampling is a major concern in phylogenetic studies, and incomplete, biased, or improper taxon assemblies can lead to misleading results in reconstructing evolutionary trees. Theoretical methods are already available to optimize taxon choice in phylogenetic analyses, but most involve some knowledge about genetic relationships of the group of interest, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. The method I proposed measures the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, it also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses.

Evaluation of Microbial Contamination in Bivalve Mollusks: Epidemiology and Diagnosis

Shellfish are filter-feeding organisms that can accumulate many bacteria and viruses. Considering that depuration procedures are not effective in removal of certain microorganisms, shellfish-borne diseases are frequent in many parts of the world, and their control must rely primarily on investigation of prevalence of human pathogens in shellfish and water environment. However, the diffusion of enteric viruses and Vibrio bacteria is not known in many geographical areas, for example in Sardinia, Italy. A survey aimed at investigating the prevalence of Norovirus (NoV), hepatitis A virus (HAV), V. parahaemolyticus, V. cholerae and V. vulnificus was carried out, analyzing both local and imported purified, non-purified and retail shellfish from North Italy and Sardinia. Shellfish from both areas were found contaminated by NoVs, HAV and Vibrio, including retail and purified animals. Molecular analysis evidenced different NoV genogroups and genotypes, including bovine NoVs, as well as pathogenic Vibrio strains, underlining the risk for shellfish consumers. However, also other approaches are needed to control the diffusion of shellfish-borne diseases. It was originally thought that enteric viruses are passively accumulated by shellfish. Recently, it was proven that NoVs bind to specific carbohydrate ligands in oysters, and various NoV strains are characterized by a different bioaccumulation pattern. To deepen the knowledge on this argument, a study was carried out, analyzing bioaccumulation of up to 8 different NoV strains in four different species of shellfish. Different bioaccumulation patterns were observed for each shellfish species and NoV strain used, potentially important in setting up effective shellfish purification protocols. Finally, a novel study of evaluation of viral contamination in shellfish from the French Atlantic coast was carried out following the passage of Xynthia tempest over Western Europe which caused massive destruction. Different enteric viruses were found over a one month period, evidencing the potential of these events of contaminating shellfish.

Use of bioassays and biomarkers in Daphnia magna to assess the effect of pharmaceutical residuals in freshwater ecosystems

Widespread occurrence of pharmaceuticals residues has been reported in aquatic ecosystems. However, their toxic effects on aquatic biota remain unclear. Generally, the acute toxicity has been assessed in laboratory experiments, while chronic toxicity studies have rarely been performed. Of importance appears also the assessment of mixture effects, since pharmaceuticals never occur in waters alone. The aim of the present work is to evaluate acute and chronic toxic response in the crustacean Daphnia magna exposed to single pharmaceuticals and mixtures. We tested fluoxetine, a SSRI widely prescribed as antidepressant, and propranolol, a non selective β-adrenergic receptor-blocking agent used to treat hypertension. Acute immobilization and chronic reproduction tests were performed according to OECD guidelines 202 and 211, respectively. Single chemicals were first tested separately. Toxicity of binary mixtures was then assessed using a fixed ratio experimental design with concentrations based on Toxic Units. The conceptual model of Concentration Addition was adopted in this study, as we assumed that the mixture effect mirrors the sum of the single substances for compounds having similar mode of action. The MixTox statistical method was applied to analyze the experimental results. Results showed a significant deviation from CA model that indicated antagonism between chemicals in both the acute and the chronic mixture tests. The study was integrated assessing the effects of fluoxetine on a battery of biomarkers. We wanted to evaluate the organism biological vulnerability caused by low concentrations of pharmaceutical occurring in the aquatic environment. We assessed the acetylcholinesterase and glutathione s-transferase enzymatic activities and the malondialdehyde production. No treatment induced significant alteration of biomarkers with respect to the control. Biological assays and the MixTox model application proved to be useful tools for pharmaceutical risk assessment. Although promising, the application of biomarkers in Daphnia magna needs further elucidation.

Water, sediment and soil physicochemical interactions in freshwater, brackish and saline systems

The physicochemical interactions between water, sediment and soil deeply influence the formation and development of the ecosystem. In this research, different freshwater, brackish and saline subaqueous environments of Northern Italy were chosen as study area to investigate the physicochemical processes which occur at the interface between water and sediments, as well as the effects of soil submergence on ecosystem development. In the freshwater system of the Reno river basin, the main purpose was to define the heavy metals hazard in water and sediments of natural and artificial water courses. Heavy metals partitioning and speciation allowed to assess the environmental risk linked to the critical action of dredging canal sediments, for the maintenance of the hydraulic safety of plain lands. In addition, some bioremediation techniques were experimented for protecting sediments from heavy metals contamination, and for giving an answer to the problem of sediments management. In the brackish system of S. Vitale park, the development of hydromorphic and subaqueous soils was investigated. The study of soil profiles highlighted the presence of a soil continuum among pedons subjected to different saturation degrees. This investigation allowed to the identification of both morphological and physicochemical indicators, which characterize the formation of subaqueous soils and describe the soil hydromorphism in transitional soil systems. In the saline system of Grado lagoon, an ecosystem approach was used to define the role of water oscillation in soil characterization and plants colonization. This study highlighted the close relationship and the mutual influence of soil submergence and aeration, tide oscillation and vegetation cover, on the soil development. In view of climate change, this study contribute to understand and suppose how soil and landscape could evolve. However, a complete evaluation of hydromorphic soil functionality will be achieved only involving physiological and biochemical expertise in these kind of studies.

Relationship between phenotype and environment in marine calcifying organisms: exploring growth and shell properties of different mollusks species in past and modern scenario

Coastal ecosystems represent an inestimable source of biodiversity, being among the most productive areas on the planet. Despite the great ecological and economic value of those environments, many threats endanger the species living in this ecosystem, like the rapid warming and the sea acidification, among many other. Benthic calcifying organisms (e.g. mollusks, corals and echinoderms) in particular, are among the most exposed to those hazards. These organisms use calcium carbonate as a structural and protective material through the biomineralization process, biologically controlled by the organism, but nevertheless, strongly influenced by the environmental surroundings. Evaluating how a changing environment can influence the process of biomineralization is critical to understand how those species of great ecological and economic importance will face the ongoing climate change. This thesis investigates the mechanism of biomineralization in different mollusks’ species of the Adriatic Sea, providing detailed descriptions of shells skeletal, biometric and growth parameters. Applying a multidisciplinary and multi-scale research approach, the influence of external environmental factors on the process of shell formation has been investigated. To achieve this purpose analysis were conducted both on current populations and on fossil remain, which allows to investigate ecological responses to past climate transitions. Mollusks’ shells in fact are one of the best tools to understand climate change in the past, present and future, since they record the environmental conditions prevailed during their life, reflected on the geochemical properties, microstructure and growth of the shell. This approach allowed to overcome the time scale limit imposed by field and laboratory survey, and better understand species long term adaptive response to changing environment, a crucial issue to define proper conservation and management strategies. Furthermore, the investigation of fossil record of mollusks assemblages offered the opportunity to evaluate the long-term biotic response to anthropogenic stressors in the north Adriatic Sea.