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Background: The increasing availability of multi-omics data is leading to regularly revised estimates of existing biodiversity data. In particular, the molecular data enable novel species to be characterized and the information linked to those already observed to be increased with new genomics data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy-to-use IT tools have become a key point to design future research. The more users are able to access biodiversity-related information, the greater the ability of the scientific community to expand its knowledge in this area. Results: In this article we focus on the development of ExTaxsI (Exploring Taxonomy Information), an IT tool that can retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. We use 3 case studies to show how an efficient organization of the available data can lead to obtaining new information that is fundamental as a starting point for new research. Using this approach highlights the limits in the distribution of data availability, a key factor to consider in the experimental design phase of broad-spectrum studies such as metagenomics. Conclusions: ExTaxsI can easily retrieve molecular data and its metadata with an explorable visualization, with the aim of helping researchers to improve experimental designs and highlight the main gaps in the coverage of available data.

Pollination is mainly mediated by animals and is fundamental for plants reproduction and for maintaining ecosystem resilience and human wellbeing. However, pollinator decline is occurring at the global scale due to multiple threats, related to human activities, with the intensification of land use ranking first. This phenomenon, driven by the growing urbanization and agricultural pressures, directly or indirectly affect pollinator communities, causing biodiversity loss, altering plant-pollinator interactions, and thus impairing the overall pollination service. In this PhD thesis the effects of land use composition and configuration have been investigated at different levels (e.g., species, community, and interactions). A multidisciplinary approach has been adopted, through the integration of field sampling activities and GIS-based analyses, with laboratory ones, such as morphometric evaluations, analysis of pollen deposited on flower’s stigmas and taxonomic identification of pollen and insects through DNA-based tools (e.g., DNA metabarcoding). The general aim of this PhD project was to provide advice for land use management policies has been addressed through intermediate goals, treated in different case studies. In the first study case, the effects of urbanization and agricultural land uses have been addressed by focusing on pollinator insects and plants inhabiting smallholder farms of Tanzania. The obtained plant-pollinator networks indicated a general decrease of pollinator richness with increasing proportion of urban and agricultural land, and an increased competition for resources among individuals. At local scale, the availability of floral resources reversed this trend, thus supporting the adoption of nature-based solutions to create suitable conditions for pollinators. In the second study case, the effects green habitat fragmentation have been investigated in Maldivian islands. Results indicated that low degrees of green areas fragmentation in anthropic habi, Pollination is mainly mediated by animals and is fundamental for plants reproduction and for maintaining ecosystem resilience and human wellbeing. However, pollinator decline is occurring at the global scale due to multiple threats, related to human activities, with the intensification of land use ranking first. This phenomenon, driven by the growing urbanization and agricultural pressures, directly or indirectly affect pollinator communities, causing biodiversity loss, altering plant-pollinator interactions, and thus impairing the overall pollination service. In this PhD thesis the effects of land use composition and configuration have been investigated at different levels (e.g., species, community, and interactions). A multidisciplinary approach has been adopted, through the integration of field sampling activities and GIS-based analyses, with laboratory ones, such as morphometric evaluations, analysis of pollen deposited on flower’s stigmas and taxonomic identification of pollen and insects through DNA-based tools (e.g., DNA metabarcoding). The general aim of this PhD project was to provide advice for land use management policies has been addressed through intermediate goals, treated in different case studies. In the first study case, the effects of urbanization and agricultural land uses have been addressed by focusing on pollinator insects and plants inhabiting smallholder farms of Tanzania. The obtained plant-pollinator networks indicated a general decrease of pollinator richness with increasing proportion of urban and agricultural land, and an increased competition for resources among individuals. At local scale, the availability of floral resources reversed this trend, thus supporting the adoption of nature-based solutions to create suitable conditions for pollinators. In the second study case, the effects green habitat fragmentation have been investigated in Maldivian islands. Results indicated that low degrees of green areas fragmentation in anthropic habi

Gli approcci metagenomici hanno cambiato il modo di studiare la biologia e la biodiversità in diversi campi. In particolare, il progresso tecnologico ci consente di determinare la composizione tassonomica dei campioni e di studiare la biodiversità in ambienti molto diversi. Al giorno d'oggi, il DNA metabarcoding è una procedura standard, applicata in un'ampia gamma di settori, dalla salute umana all'ecologia, alle applicazioni industriali. Negli ultimi anni, il DNA metabarcoding applicato al 16S rRNA è stato ampiamente utilizzato per studiare la comunità batterica, portando ad analisi di routine che hanno creato enormi quantità di dati, consentendo ai ricercatori di sviluppare strategie data-driven per rispondere a domande biologiche complesse. Inoltre, il DNA metabarcoding può essere utilizzato anche per studiare Piante, Animali o Funghi, grazie allo sviluppo di diversi marcatori molecolari. In entrambi i casi, considerando l'enorme quantità di dati prodotti dai ricercatori e disponibili nelle banche dati, una prospettiva di ‘data mining’ nella gestione e nell'esplorazione dei dati di DNA metabarcoding potrebbe essere utile per identificare nuovi pattern ed estrarre maggiori informazioni dai dati. Nella mia tesi di dottorato, mi sono focalizzata su una prospettiva incentrata sui dati di DNA metabarcoding, toccando quattro punti principali che possono potenziare e migliorare le strategie attuali: i) considerare le informazioni molecolari ottenute dal sequenziamento high-throughput del DNA (HTS) e disponibili in archivi pubblici, ii ) migliorare la fase di assegnazione della tassonomia, iii) studiare nuovi metodi per la ricostruzione di pattern di biodiversità e iv) utilizzare dati già prodotti come risorsa preziosa per la ricerca. Questi quattro punti possono migliorare a diversi livelli le potenzialità delle applicazioni di tecniche fondate sul DNA metabarcoding, aprendo la strada a procedure di standardizzazione per marcatori meno diffusi e all'integraz, Metagenomic approaches have changed the way to study biology and biodiversity in several fields. In particular, technology advancement enables us to determine taxa composition and to study complex biodiversity patterns in very different environments. Nowadays, DNA metabarcoding is a standard procedure, applied on a wide range of fields, from human health to ecology, to industry applications. In the last few years, 16S rRNA metabarcoding was widely used to study the bacterial community, leading to routine analysis which created huge amounts of data, bringing researchers to develop data mining strategies in order to answer complex biological questions. On the other hand, DNA metabarcoding can be applied also to study Plants, Animals or Fungi, as very different molecular markers have been identified. In both cases, considering the huge amount of data produced by researchers and available in repositories, a data-driven perspective in managing and exploring DNA metabarcoding data could be useful to collect hidden information and potentially determine undiscovered aspects. In this PhD dissertation, I focused the attention on a data-centered perspective of DNA metabarcoding data, touching four main points that can enhance and ameliorate the current strategies: i) consider the molecular information obtained from high-throughput DNA sequencing (HTS) and available in public repositories, ii) enhance taxonomy assignment step, iii) investigate new methods for pattern reconstruction and iv) use data as a valuable resource for research. These four steps can enhance at different levels the potentials of DNA metabarcoding applications, paving the way for standardization procedures for uncommon markers and the integration of new data mining and data reuse strategies of metabarcoding data.