Biology subjects

Corso, D.

Publications and source records attributed to Corso, D..

4 recordsLinked to original sources

bioRxiv2026

Geomosaic: a flexible bioinformatics platform integrating complementary metagenomic analyses from sequencing reads to genomes

Metagenomic analyses can be performed at multiple analytical levels, including read-based, assembly-based, and genome-resolved approaches, each capturing complementary biological information while introducing distinct analytical biases and trade-offs. However, existing workflows are commonly optimized for a single analytical strategy, making it difficult to integrate these complementary representations within a unified, reproducible framework. Here we present Geomosaic, a modular framework that integrates complementary analytical representations of metagenomic data, from reads to genomes, within a single scalable, customizable, and reproducible workflow. Built on a graph-based architecture implemented in Snakemake, Geomosaic enables users to construct complete end-to-end workflows or execute individual analytical modules while selecting among interchangeable software packages. The framework supports read preprocessing, quality control, taxonomic and functional profiling, assembly, genome reconstruction, genome-resolved annotation, custom HMM-based analyses, and automated downstream result aggregation. Automatic generation of execution scripts, modular workflows, and multiple analysis entry points make Geomosaic accessible to researchers approaching metagenomic analyses for the first time, while providing the flexibility and control required by expert users. Native support for HPC environments enables efficient analysis of datasets ranging from individual projects to large-scale metagenomic surveys. Rather than treating read-, assembly-, and genome-resolved metagenomics as alternative analytical strategies, Geomosaic integrates them as complementary representations of the same biological system, allowing users to move seamlessly between community-wide patterns and organism-resolved functional interpretation. By combining workflow flexibility, computational reproducibility, standardized analysis-ready outputs, and extensive documentation, Geomosaic provides a unified platform for environmental metagenomic analyses and facilitates reproducible downstream ecological and evolutionary investigations.

bioinformatics↗

bioRxiv2025

Ancient Roman saltworks drive the present-day microbial community profiles in a coastal aquifer

Historical salinization from ancient saltworks can leave a long-lasting imprint on coastal aquifers, but its impacts on subsurface microbial communities and ecosystem functioning remain poorly understood. This study examined how legacy salt inputs from Roman saltworks in the Tiber River delta (Fiumicino, Italy) continue to shape present-day groundwater chemistry, microbial community structure, and metabolic potential of the coastal aquifer. We analyzed groundwater samples from non-salinized and salinized units of the same aquifer using integrated hydrogeochemical characterization, flow cytometry, 16S rRNA gene amplicon sequencing, and functional metabolic assays. Salinized samples exhibited elevated chloride, bromide, sodium, and sulfate concentrations, with distinctive ionic ratios (Br/Sr, Cl/K, SO/Ca) indicating dissolution of salt deposits rather than contemporary seawater intrusion. Salinization reduced the microbial diversity and shifted communities from diverse freshwater-adapted families toward an abundant halotolerant assemblage dominated by Campylobacterota (families Sulfurimonadaceae and Sulfurovaceae). Functional annotation suggested broadly conserved potentials for carbon, nitrogen, and sulfur cycling. However, the Biolog assays revealed higher heterotrophic respiration and carbon substrate use but lower functional diversity in salinized samples, with particularly enhanced polymer degradation. Ordination analyses showed a clear separation of aquifer units along the salinization gradient, with coordinated chemical and microbial vectors indicating alternative ecosystem states sustained by millennia-old anthropogenic salt inputs. Our findings showed that ancient saltworks can drive persistent hydrogeochemical alteration, select specialized halotolerant microbiomes, and reconfigure carbon and nutrient processing while maintaining core biogeochemical functions, with critical implications for coastal groundwater management strategies.

microbiology↗

bioRxiv2025

Constructed wetlands for aquaculture wastewater treatment: insights on the structural and functional shifts of the aquatic microbial community

Aquaculture practices generate nutrient-rich effluents with associated microbiological hazards, such as pathogens and antimicrobial resistance genes (ARGs). Despite their growing popularity as nature-based solutions, little is known about how constructed wetlands (CWs) affect the dynamics of microbial communities at the field scale. By combining flow cytometry, 16S rRNA gene sequencing, shotgun metagenomics, and metabolic potential assays, we investigated the structural and functional responses of the aquatic microbial community following the recurrent exposure to CW-treated effluents from an intensive marine fish farm (Orbetello lagoon, Italy). While the CW promoted abundant, metabolically active, and functionally redundant microbial communities, the phylogenetic composition diverged primarily between water and sediments. Microbial profiles in CW outlet waters converged towards those of the lagoon baselines, suggesting gradual ecological recovery. The CW attenuated the occurrence of potential pathogens (e.g., Francisella spp., Campylobacter spp.) and limited ARG dissemination, though sediments remained reservoirs of microbial and genetic signatures. Functional profiles, dominated by chemoheterotrophy, denitrification, and sulfur respiration, remained stable across environments, reflecting microbial resilience. Our results highlight CWs as effective, field-proven solutions to mitigate aquaculture wastewater impacts while preserving core ecosystem services.

ecology↗

bioRxiv2021

The most comprehensive annotation of the Krill transcriptome provides new insights for the study of physiological processes and environmental adaptation

The krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem, as the abundance of its biomass affects trophic levels both below it and above. Major changes in climate conditions observed in the Antarctic Peninsula region in the last decades have already altered the distribution of the krill population and its reproductive dynamics. A deeper understanding of the adaptation capabilities of this species, and of the molecular mechanisms behind it are urgently needed. The availability of a large body of RNA-seq assays gave us the opportunity to extend the current knowledge of the krill transcriptome, considerably reducing errors and redundancies. Our study covered the entire developmental process, from larval stages to adult individuals, providing information of central relevance for ecological studies. Here we describe the KrillDB2 database, a resource combining the latest annotation of the krill transcriptome with a series of analyses specifically targeting genes and molecular processes relevant to krill physiology. KrillDB2 provides in a single resource the most complete collection of experimental data and bioinformatic annotations: it includes an extended catalog of krill genes; an atlas of their expression profiles over all RNA-seq datasets publicly available; a study of differential expression across multiple conditions such as developmental stages, geographical regions, seasons, and sexes. Finally, it provides initial indications about non-coding RNAs, a class of molecules whose contribute to krill physiology has never been reported before.

ecology↗