Department of Integrative Marine Ecology

Director of Studies: Marina Montresor

Project Summary/Abstract

The formation of resting stages – i.e. stages capable to enter a reversible stage of reduced metabolic activity, or "dormancy" - is widespread amongst all organisms spanning from bacteria, to protists, animals and plants. This life cycle trait allows organisms to cope with environmental conditions sub-optimal for growth, seasonality of food availability and plays a fundamental role in shaping population dynamics. Resting stages form "seed banks" in marine sediments, where they can survive for long time, and subsequently germinate bringing back to the water column actively growing cells/organisms. The formation and germination of dormant stages is linked to the perception of external cues, whose mechanisms have been elucidated for higher plants and animals and partly for bacteria. However, information on these processes in marine microalgae is still limited.

The main objective of the project is to investigate the factors that trigger the formation and germination of spores in diatoms. Diatom spores are formed by subsequent mitotic divisions in which the highly silicified thecae are synthesized. Target species will be one species of the genus Chaetoceros and Leptocylindrus danicus, in which spore formation is linked to the sexual phase. Laboratory experiments suggest that spore formation is induced by nutrient starvation but field observations do not entirely support this observation. A detailed experimental set up in which e.g. both the external and internal nitrogen pools have been measured are however lacking. The main cue for spore germination is exposure to light. However, also on this aspect the information available is limited.

The backbone of the project will focus on the role of nutrient (nitrogen) concentration in inducing the formation of spores and on the role of light (both as quality and quantity) in inducing the germination of resting stages. The project will also include transcriptomic approaches on key time points/phases of the life cycle transitions to gain insights on the molecular mechanisms involved in the perception of the cues and in the physiological response.

The results of the project have ecological (insights on the cues triggering two key life phase transitions that have implications for e.g. bloom termination, inoculum of the water column upon germination, species succession), applicative (induction of spore formation may represent as a way to preserve strains over time) and evolutionary implications. Moreover, the molecular results will be important for the interpretation of meta-transcriptomic data gained in situ.

Department of Integrative Marine Ecology

Director of Studies: Gabriele Procaccini

Project Summary/Abstract

Despite their key ecological value, coastal ecosystems such as seagrass meadows are experiencing a progressive decline, due to a number of threats associated to human activities along the coastline, as well as climate changes. In the Mediterranean, the marine angiosperm Posidonia oceanica forms dense meadows, which provide important ecological functions and services, being crucial for maintaining the quality of coastal waters, for the cycling of nutrients, for stabilizing sediments and reducing shoreline erosion. The conservation of P. oceanica meadows has become a key objective on actual European environmental and water policies. They are protected at the European level, as a priority habitat (Habitats Directive, Dir 92/43/CEE and Directive 97/62/CE) and as a species (Bern Convention, Annex 1), and are under specific legal protection actions in several European countries. Policies aiming at improving quality of coastal waters and marine environments across Europe are also being developed in European countries (Water Framework Directive and Marine Strategy Framework Directive), recognizing the large potential of P. oceanica meadows as bioindicators of ecological quality. In this context, investigation of the effects of climate and non-climate stressors in P. oceanica became crucial, in order to determine both the physiological response, and the potential adaptive response of the species. Effects of single environmental drivers (i.e. light, temperature and CO₂) have been studied in different seagrass species, both in natural and controlled conditions. Nonetheless, in natural environments, those drivers often do not act in isolation, but additive, synergistic or antagonistic effects can occur. This PhD project aims to investigate the effects of "multiple stressors" in Posidonia oceanica. The combined effects of pairs of factors (e.g. Temperature vs. Light; Temperature vs. CO₂ and Light vs. CO₂) will be investigated looking at the expression of target genes selected in previous single-stressor studies, via RT-qPCR. The photophysiological response will also be assessed looking at changes in the pigmentary pool, as well as characterizing the functionality and structure of the photosynthetic apparatus through chlorophyll a fluorescence measures. Changes in the morphology of the plants will also be considered in the project, as well as changes in some plant fitness traits. Finally, changes in the epiphytic community on rhizomes and leaves will be assessed in order to get an insight into potential indirect effects of stressors on P. oceanica. Experiments will be carried out in the new benthic mesocosm facility available at the SZN.

Project results will be useful for designing new management strategies of coastal resources in two different ways. First, allowing to move away from the impact-by-impact framework, to which management processes are strongly focused. Second, providing new generation of early warning indicators for environmental assessment.

Department of Integrative Marine Ecology

Director of Studies: Valerio Zupo

Project Summary/Abstract

Model species are commonly adopted for investigations in various fields of biology and ecology, to test hypotheses and perform bioassays. However, only a few organisms are universally considered and the narrow list limits science to the answers that those organisms can provide. In addition, models are scarcely representative samples of biological diversity, being often chosen according to evolutionary constraints. It is time to think more critically about how we choose and use animal models. We propose to define a list of candidate model species chosen among a broad set of marine organisms and test their performances –in terms of efficiency to answer scientific questions- by means of a set of characters and bioassays. According to the results obtained, the value of each species, as a model organism, will be defined and ranked, to avoid the influence of personal confidence with peculiar taxonomical groups, that determined the choice of most model species up to date. In the selection of animal models, both classical systems (Ciona, Zebrafish, sea urchins) and new candidates will be considered and their performances will be compared. We will consider a broad assortment of animals, from polychaetes to vertebrates, in order to avoid limitations due to taxonomical constraints. The research will initially evaluate the possibility to rear, culture, reproduce each species by simple and cheap methods. Then, developmental biology, physiology, toxicology, chemical ecology and molecular ecology techniques will be applied to measure the answers of each species to a common set of scientific questions. Finally, the value of each model species will be determined by ranking them according to the previous measurements. The project has clear intellectual merits, since it aims, for the first time, at providing a comprehensive survey of candidate model species, compare them and re-define, through quantitative evaluations, the features best suited to express the usefulness of a species for answering a wide set of scientific questions. In addition, it will allow for testing natural products on a range of organisms and describing their mechanisms of action, with the possibility to develop novel biotechnologies. The research could have broad impacts on future investigations involving model species, by indicating canonical choices for given purposes, avoiding the adoption of model species based on scientist’s personal confidence or due to the simple availability in given geographical locations, as widely applied at present. The completion of these researches, in addition, will provide the student with a wide experience in key disciplines and techniques, as culture of marine micro- and macro-algae, devising of experimental automatized culture systems for animal models, extracting, analyzing and testing algal secondary metabolites, testing the effect of natural substances on various marine organisms, analyzing the histological effects of natural products as candidate drugs, disclosing the molecular effects of algal metabolites by means of micro-arrays. On the whole, the candidate will acquire a vast knowledge on the manipulation and culture of model species and this will obviously increase his/her possibilities to be quickly hired as a post-doc.

Department of Integrative Marine Ecology

Director of Studies: Maria I. Ferrante

Project Summary/Abstract

Signal transduction mechanisms are extremely well defined in multicellular organisms and unicellular model systems such as yeast and Chlamydomonas but very little is known for phytoplankton. Yet, understanding how cells sense and integrate environmental signals is fundamental to explain population dynamics, community interactions and ultimately ecosystem functioning.

Diatoms, among phytoplanktonic organisms, are one of the most important and abundant groups and, because of the availability of genomic data and genetic resources for a selection of species, represent currently the most suitable system to approach molecular and functional studies.

Among the possible signals that a cell can send and receive, we have chosen to investigate the chemical communication during sexual reproduction in the pennate marine diatom Pseudo-nitzschia multistriata, a species for which we produced a reference genome and transcriptomes.

We undertook gene expression studies to investigate the pathways and gene networks used by diatoms to process the signals. The data revealed complex changes in gene expression of cells engaged in the initial phases of sexual reproduction. Importantly, we observed changes in the expression of genes well-characterized in animals or plants but so far scarcely or not at all described for diatoms.

This project aims at developing on these findings, providing further support to the hypothesis that specific signaling pathways well described in other systems are active in diatoms and are being used to process the reception of chemical cues (pheromones). This will be done by expanding the studies on gene expression, and by perturbation experiments, exploiting functional genomics techniques recently developed in the laboratory.

The data generated will allow to define gene networks in diatoms and to carry out comparative studies to identify specific and general characteristics of diatom responses to external stimuli.

Eventually, we will integrate the information obtained in the laboratory with metagenomics and metatranscriptomics data collected across the world’s oceans, such as data collected during the TARA Oceans expedition, strengthening the integration of environmental and experimental data.