Department of Biology and Evolution of Marine Organisms

Director of Studies: Remo Sanges

Project Summary/Abstract

There is a battle going on in our genomes. This battle is present in an overwhelming portion of the tree of life. A transposable element (TE) is a genomic sequence that can duplicate itself in a different position within the genome. During a wave of transposition insertions, a specific TE invades a specific genome having a limited range of time to amplify itself until the assaulted genome evolve the epigenetic competence to silence it. This control is not always complete, some TE copies might retain limited activity to perpetuate their amplification. In this way they bypass their extinction as a consequence of the accumulation of mutations, but do not retain the potential to completely destroy the invaded genome. At this stage, TEs are defined "domesticated" and they should not be considered anymore mere barbarian parasites. A growing body of evidences suggests they should be better regarded as "symbionts". Indeed, although mutagenic, they provide fresh genomic matter that can be shaped by the host genome to evolve genetic novelties. The genomes of living organisms contain a high percentage of TEs. This can vary substantially among different species, but researchers are beginning to demonstrate that the more an organism is complex (it presents many different kind of cells), the higher is the percentage of such elements into the genome. Therefore, understanding the evolution of these elements would allow us to better understand how complexity evolved. We propose to develop specific bioinformatics pipelines to evaluate how these features of the genome are evolutionary related and how they shaped the eukaryotic genomes and complexity. This project departs from interesting outcomes recently gained in our research projects focusing around the sequencing of transcriptomes from diverse marine organisms and the development of related bioinformatics pipelines. Analyzing the genome and the transcriptome from many  sequenced species, at different level of complexity, we aim at understand whether the expansion of TEs, in relation to the evolution of complexity, is a basic principle of biology. Finally, the better understanding of the evolution and the functional impact of these element is also important from a biotechnological perspective, indeed the unique characteristic of these elements, to specifically bind, edit and modify any genome, make them an attractive system for a vast repertoire of molecular applications.

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: Daniele Iudicone

Project Summary/Abstract

This project will address the overarching question of how geophysical variability in time and space affects ecosystem diversity, focusing on oceanic plankton as a model system. A long-standing, as yet unresolved challenge---the "plankton paradox"---is to understand how phytoplankton maintain their observed rich biodiversity while inhabiting a relatively unstructured environment and competing for only a few resources. In fact, the local structure and function of their communities is organized by ocean circulation and resource delivery, together with organismal acclimation and adaptation. How these factors interplay to maintain ocean biomes is a key question of phytoplankton ecology, with important implications for the structure of marine food webs and climate. Specifically, we will bring together expertise in theoretical ecology, genomics and oceanography to explore how spatial-temporal variability in the environment may allow for the stable coexistence of many species in competition while favoring the establishment of new species. We will pay particular attention to the novel hypothesis that plankton do not always respond to high frequency environmental signals in order to competitively exploit environmental variability.

Marine biology is under-going a rapid and significant transition due to the availability of new, cost-effective molecular and bioinformatics tools. The recent Tara Oceans global survey provides one of the first, and certainly the most comprehensive survey of detailed molecular information and oceanographic context. Using an holistic approach, the work will focus on examining the environmental seasonality vs ocean circulation as factors shaping the diversity in real data (Tara Oceans) and in a hierarchy of models describing climate-plankton interaction at increasing levels of detail and realism. The combined expertise will allow to make informed, innovative modelling choices at each level of complexity and test the results against the observed distribution of species and associated traits. The simulations will inform future models of global scale organization of phytoplankton populations and their response to climate change. Specifically, by combining curated transcriptome datasets from key selected, evolutionarily distant organism groups with diversity analyses and tracking their dispersal across the oceans, we will develop models to test hypotheses on plasticity, adaptation, microevolution, speciation and collective processes in globally relevant unicellular communities.

As main intellectual merit, the interdisciplinary team of oceanographers, modelers and biologists will allow an innovative end-to-end (molecular mechanisms - organisms - communities) analysis of phytoplankton dynamics and the validation of hypotheses in well contextualized water masses. In turn this will inform conceptual models directly from data in addition to building up upon previous modelling exercises. Finally, the study of the impact of seasonality upon plankton will allow to bridge terrestrial and marine ecology to a point rarely reached before, with broad impact on the marine community. In addition, the evolutionary significance of overlooked traits and the dynamical balance with oceanic dispersal will inform new directions of theoretical and applied research.

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.