MODELLI DATA-DRIVEN PER STUDIARE LA DINAMICA E FISIOLOGIA DEL FITOPLANCTON

Phytoplankton are the foundation of marine ecosystems and a major driver of global biogeochemical cycles. Their composition and productivity are shaped by environmental gradients, physical mixing, and nutrient availability, while at the cellular level, their life-cycle transitions are controlled by complex gene regulatory programs. Understanding these processes across ecological and molecular scales is crucial for predicting how marine primary producers respond to environmental change. This thesis addresses these two complementary dimensions: the large-scale spatial and seasonal organization of phytoplankton communities along the Italian coastline, and the regulation of gene expression underlying sexual competence in the pennate diatom Pseudo-nitzschia multistriata. In the first part, We analyzed an extensive dataset comprising over 2,200 phytoplankton samples collected between 2015 and 2017 across 15 Italian coastal subregions. By integrating taxonomic counts with concurrent environmental variables, We characterized patterns of richness, abundance, and community composition. Species accumulation and indicator-taxon analyses revealed marked biogeographical structuring, primarily driven by nutrient availability and hydrographic connectivity. The northern Adriatic emerged as a high-abudance, diatom-dominated system with clear diatom–dinoflagellate succession, whereas the Ligurian and Tyrrhenian coasts displayed more oligotrophic, low-diversity assemblages. Constrained ordination analyses identified temperature, salinity, and nutrient gradients as the main drivers of community turnover, though together they explained only a modest portion of variance, which suggest additional unresolved influences such as episodic mixing, trace-metal inputs, or local hydrodynamics. These results provide one of the most comprehensive, process-oriented portraits of Italian coastal phytoplankton communities and highlight the strengths and limitations of monitoring data for ecological inference. The second part explores transcriptional regulation in Pseudo-nitzschia multistriata, a model species for studying diatom sexual reproduction. By integrating published and newly processed RNA-seq libraries from both mating types and from cells above and below the sexualization size threshold, We constructed gene co-expression networks using the Weighted Gene Co-expression Network Analysis framework. We identified robust modules of co-regulated genes and linked them to traits of interest. Several modules were consistently associated with mating type and enriched in genes related to metabolism, redox homeostasis, and calcium signaling. While modules related to size were fewer and less stable. The known mating-type determinants exhibited expected expression biases but limited co-clustering, suggesting independent regulatory pathways or condition-specific activation. Together, the two parts of this thesis connect ecosystem-scale phytoplankton dynamics with the molecular mechanisms governing life-cycle regulation in diatoms. At the community level, they reveal how nutrient gradients and hydrography shape coastal biodiversity; at the cellular level, they potentially delineate mating-type–specific transcriptional programs coordinating sexualization. By combining large-scale ecological analyses with systems-level transcriptomics, this work provides a multiscale view of phytoplankton, from population assemblages to gene regulatory networks, and establishes a foundation for future integrative studies linking environmental variability, life-cycle transitions, and evolutionary innovation in marine microalgae.

Il fitoplancton è alla base degli ecosistemi marini e guida i cicli biogeochimici globali. La sua composizione e produttività dipendono da gradienti ambientali, mescolamento fisico e disponibilità di nutrienti, mentre a livello cellulare il ciclo vitale è controllato da complessi programmi di regolazione genica. Comprendere questi processi è essenziale per prevedere la risposta dei produttori primari marini ai cambiamenti ambientali. Questa tesi affronta due dimensioni complementari: (1) la struttura spaziale e stagionale delle comunità fitoplanctoniche lungo le coste italiane e (2) la regolazione genica della competenza sessuale nella diatomea Pseudo-nitzschia multistriata. Nella prima parte, sono stati analizzati oltre 2.200 campioni raccolti tra il 2015 e il 2017 in 15 sottoregioni costiere. L’integrazione di dati tassonomici e ambientali ha rivelato una marcata struttura biogeografica, guidata da nutrienti e connettività idrografica. L’Adriatico settentrionale si distingue per un’elevata abbondanza di diatomee e una chiara successione diatomee–dinoflagellati, mentre le coste liguri e tirreniche mostrano assemblaggi più oligotrofici e poveri di specie. Temperatura, salinità e nutrienti sono risultati i principali fattori di variazione, pur spiegando solo parzialmente la diversità osservata. La seconda parte indaga la regolazione trascrizionale in P. multistriata attraverso reti di co-espressione genica (WGCNA) basate su dati RNA-seq. Sono stati identificati moduli di geni associati al tipo di accoppiamento, arricchiti in funzioni metaboliche, redox e di segnalazione del calcio. I determinanti noti del tipo di accoppiamento mostrano espressione differenziata ma scarsa co-clusterizzazione, suggerendo percorsi regolatori indipendenti. Complessivamente, la tesi collega i processi ecologici su larga scala ai meccanismi molecolari del ciclo vitale nelle diatomee, offrendo una visione integrata del fitoplancton — dalle comunità costiere alle reti di regolazione genica — e ponendo le basi per studi futuri sull’interazione tra ambiente, riproduzione e innovazione evolutiva nelle microalghe marine.