Functional Genomics and Cell Biology of the Dolphin (Tursiops runcatus): Establishment of Novel Molecular Tools to Study Marine Mammals in Changing Environments

The dolphin (Tursiops truncatus) is a mammal that is adapted to life in a totally aquatic environment. Despite the popularity and even iconic status of the dolphin, our knowledge of its physiology, its unique adaptations and the effects on it of environmental stressors are limited. One approach to improve this limited understanding is the implementation of established cellular and molecular methods to provide sensitive and insightful information for dolphin biology. We initiated our studies with the analysis of wild dolphin peripheral blood leukocytes, which have the potential to be informative of the animal’s global immune status. Transcriptomic profiles from almost 200 individual samples were analyzed using a newly developed species-specific microarray to assess its value as a prognostic and diagnostic tool. Functional genomics analyses were informative of stress-induced gene expression profiles and also of geographical location specific transcriptomic signatures, determined by the interaction of genetic, disease and environmental factors. We have developed quantitative metrics to unambiguously characterize the phenotypic properties of dolphin cells in culture. These quantitative metrics can provide identifiable characteristics and baseline data which will enable identification of changes in the cells due to time in culture. We have also developed a novel protocol to isolate primary cultures from cryopreserved tissue of stranded marine mammals, establishing a tissue (and cell) biorepository, a new approach that can provide a solution to the limited availability of samples. The work presented represents the development and application of tools for the study of the biology, health and physiology of the dolphin, and establishes their relevance for future studies of the impact on the dolphin of environmental infection and stress.

Evidenze micropaleontologiche e sedimentologiche di cicli deposizionali e climatici circa millenari nei Depositi Tardoquaternari della Piana dell'Arno e del Delta del Po

A multidisciplinary study was carried out on the Late Quaternary-Holocene subsurface deposits of two Mediterranean coastal areas: Arno coastal plain (Northern Tyrrhenian Sea) and Modern Po Delta (Northern Adriatic Sea). Detailed facies analyses, including sedimentological and micropalaeontological (benthic foraminifers and ostracods) investigations, were performed on nine continuously-cored boreholes of variable depth (ca. from 30 meters to100 meters). Six cores were located in the Arno coastal plain and three cores in the Modern Po Delta. To provide an accurate chronological framework, twenty-four organic-rich samples were collected along the fossil successions for radiocarbon dating (AMS 14C). In order to reconstruct the depositional and palaeoenvironmental evolution of the study areas, core data were combined with selected well logs, provided by local companies, along several stratigraphic sections. These sections revealed the presence of a transgressive-regressive (T-R) sequence, composing of continental, coastal and shallow-marine deposits dated to the Late Pleistocene-Holocene period, beneath the Arno coastal plain and the Modern Po Delta. Above the alluvial deposits attributed to the last glacial period, the post-glacial transgressive succession (TST) consists of back-barrier, transgressive barrier and inner shelf deposits. Peak of transgression (MFS) took place around the Late-Middle Holocene transition and was identified by subtle micropalaeontological indicators within undifferentiated fine-grained deposits. Upward a thick prograding succession (HST) records the turnaround to regressive conditions that led to a rapid delta progradation in both study areas. Particularly, the outbuilding of modern-age Po Delta coincides with mud-belt formation during the late HST (ca. 600 cal yr BP), as evidenced by a fossil microfauna similar to the foraminiferal assemblage observed in the present Northern Adriatic mud-belt. A complex interaction between allocyclic and autocyclic factors controlled facies evolution during the highstand period. The presence of local parameters and the absence of a predominant factor prevent from discerning or quantifying consequences of the complex relationships between climate and deltaic evolution. On the contrary transgressive sedimentation seems to be mainly controlled by two allocyclic key factors, sea-level rise and climate variability, that minimized the effects of local parameters on coastal palaeoenvironments. TST depositional architecture recorded in both study areas reflects a well-known millennial-scale variability of sea-level rising trend and climate during the Late glacial-Holocene period. Repeated phases of backswamp development and infilling by crevasse processes (parasequences) were recorded in the subsurface of Modern Po Delta during the early stages of transgression (ca. 11,000-9,500 cal yr BP). In the Arno coastal plain the presence of a deep-incised valley system, probably formed at OSI 3/2 transition, led to the development of a thick (ca. 35-40 m) transgressive succession composed of coastal plain, bay-head delta and estuarine deposits dated to the Last glacial-Early Holocene period. Within the transgressive valley fill sequence, high-resolution facies analyses allowed the identification and lateral tracing of three parasequences of millennial duration. The parasequences, ca. 8-12 meters thick, are bounded by flooding surfaces and show a typical internal shallowing-upward trend evidenced by subtle micropalaeontological investigations. The vertical stacking pattern of parasequences shows a close affinity with the step-like sea-level rising trend occurred between 14,000-8,000 cal years BP. Episodes of rapid sea-level rise and subsequent stillstand phases were paralleled by changes in climatic conditions, as suggested by pollen analyses performed on a core drilled in the proximal section of the Arno palaeovalley (pollen analyses performed by Dr. Marianna Ricci Lucchi). Rapid shifts to warmer climate conditions accompanied episodes of rapid sea-level rise, in contrast stillstand phases occurred during temporary colder climate conditions. For the first time the palaeoclimatic signature of high frequency depositional cycles is clearly documented. Moreover, two of the three "regressive" pulsations, recorded at the top of parasequences by episodes of partial estuary infilling in the proximal and central portions of Arno palaeovalley, may be correlated with the most important cold events of the post-glacial period: Younger Dryas and 8,200 cal yr BP event. The stratigraphic and palaeoclimatic data of Arno coastal plain and Po Delta were compared with those reported for the most important deltaic and coastal systems in the worldwide literature. The depositional architecture of transgressive successions reflects the strong influence of millennial-scale eustatic and climatic variability on worldwide coastal sedimentation during the Late glacial-Holocene period (ca. 14,000-7,000 cal yr BP). The most complete and accurate record of high-frequency eustatic and climatic events are usually found within the transgressive succession of very high accommodation settings, such as incised-valley systems where exceptionally thick packages of Late glacial-Early Holocene deposits are preserved.

Effects of artificial defences and flooding on coastal habitats and assemblages

Since large stretches of European coasts are already retreating and projected scenarios are worsening, many artificial structures, such as breakwaters and seawalls, are built as tool against coastal erosion. However artificial structures produce widespread changes that alter the coastal zones and affect the biological communities. My doctoral thesis analyses the consequences of different options for coastal protection, namely hard engineering ‘artificial defences’ (i.e. impact of human-made structures) and ‘no-defence’ (i.e. impact of seawater inundation). I investigated two new aspects of the potential impact of coastal defences. The first was the effect of artificial hard substrates on the fish communities structure. In particular I was interested to test if the differences among breakwaters and natural rocky reef would change depending on the nature of the surrounding habitat of the artificial structure (prevalent sandy rather than rocky). The second was the effect on the native natural sandy habitats of the organic detritus derived from hard-bottom species (green algae and mussels) detached from breakwaters. Furthermore, I investigated the ecological implication of the “no-defend” option, which allow the inundation of coastal habitats. The focus of this study was the potential effect of seawater intrusion on the degradation process of marine, salt-marsh and terrestrial detritus, including changes on the breakdown rates and the associated macrofauna. The PhD research was conducted in three areas along European coasts: North Adriatic sea, Sicilian coast and South-West England where different habitats (coastal, estuarine), biological communities (soft-bottom macro-benthos; rocky-coastal fishes; estuarine macro-invertebrates) and processes (organic enrichment; assemblage structure; leaf-litter breakdown) were analyzed. The research was carried out through manipulative and descriptive field-experiments in which specific hypothesis were tested by univariate and multivariate analyses.