Biology subjects

Sommaruga, R.

Publications and source records attributed to Sommaruga, R..

5 recordsLinked to original sources

bioRxiv2026

Single-cell-resolved natural giant virus infections reveal conserved protist immunity

Single-cell eukaryotes (protists) are key players in microbial ecosystems. Yet, our understanding of how they interact with viruses in nature and how antiviral defenses shape these relationships remains limited. Using a single-cell multi-omics approach, we mapped associations between giant viruses and their hosts and identified active giant-virus infections in an alpine lake protist community. In naturally infected dinoflagellates, infection was accompanied by the selective induction of viperin, an ancient antiviral enzyme conserved from bacteria to humans. We also observed virus-encoded homologs of immunity-related genes whose expression correlated with viperin expression, raising the possibility of a role in viral counter-defense. These findings reveal an ecological dimension of protist immunity and provide a framework for tracing the host-virus arms race across divergent cellular lineages.

microbiology↗

bioRxiv2026

A framework for Polinton-like virus diversity across aquatic microbiomes reveals links to multiple viral classes and Nucleocytoviricota

Polinton-like viruses (PLVs) are among the most abundant eukaryotic DNA viruses in aquatic environments. Despite their extensive diversity, broad host range and variable gene content, they are commonly treated as a single group, which obscures their evolutionary relationships and complicates their classification. Through analysing thousands of viral genomes from aquatic ecosystems and public metagenomic datasets, we clarify the evolutionary structure encompassed by the term PLV. Using sensitive profile Hidden Markov Model (HMM) comparisons, phylogenies of conserved capsid morphogenetic genes and gene content analysis, we show that viruses referred to as PLVs are distributed across multiple deep lineages spanning at least three currently recognised viral classes. These include the Gosseviruses, aquatic viruses related to Maverick-Polintons in animal genomes. They also include a continuum of related viruses from 15 kb PLVs to the 45 kb Mriyaviruses and more broadly, to the Nucleocytoviricota, potentially representing extant relatives of giant viruses. Our findings suggest that PLVs do not fit neatly within existing taxonomic boundaries, reflecting a complex history of horizontal gene transfer and diversification of life strategies. To support future discovery, we provide a curated set of HMMs representing the known capsid diversity of PLVs, Maverick-Polintons, and virophages. This toolkit enables sensitive detection and identification of PLVs across metagenomic and eukaryotic genome datasets. Our study provides an evolutionary framework for interpreting PLV diversity and a foundation for future refinement of their classification.

microbiology↗

bioRxiv2023

A novel method for characterising the inter- and intra-lake variability of CH4 emissions: validation and application across a latitudinal transect in the Alpine region

Lakes in the Alpine region are recognised as critical CH4 emitters, but a robust characterisation of the magnitude and variability of CH4 fluxes is still needed. We developed a mobile platform for CH4 eddy covariance (EC) flux measurements to tackle this gap. Our approach was shown to be well suited to catch all CH4 emission pathways and overcome the limitations of other methods (e.g., gradient-based). This is by surpassing their local nature and thus being suited for characterising the variability of the within-lake emissions, primarily because of CH4 emissions by ebullition stochasticity. The mobile system was deployed at nine lakes across a latitudinal transect in the Alps and validated by comparing the measured fluxes with a fixed EC station and to chambers and boundary layer estimates. Methane fluxes were explained by water turbidity, dissolved organic carbon, dissolved nitrogen, elevation, particulate organic carbon, and total phosphorus. The highest fluxes and most substantial seasonal variability were found in a shallow low-altitude lake in the Southern Alps. Additionally, the mobile EC permitted to resolve the spatial structure of fluxes at the selected lakes. Finally, we demonstrated the usability of our novel mobile system to characterise intra- and inter-lake variability of fluxes. We suggest that characterising the intra-lake emission heterogeneity and a deeper understanding of inter-lake emission magnitude differences is fundamental for a solid estimate of freshwater CH4 budgets. Key PointsO_LICH4 emissions from alpine lakes are recognised to be an important component to the global methane budget but they are poorly characterized C_LIO_LIWe developed and validated a mobile eddy covariance platform for capturing CH4 fluxes across lakes in the alpine region for two years C_LIO_LIA robust statistical model based on a few in-situ physicochemical and biological parameters can be generally used to predict CH4 fluxes C_LI

ecology↗

bioRxiv2019

Polinton-like viruses and virophages are widespread in aquatic ecosystems

Polintons are virus-like transposable elements found in the genomes of eukaryotes that are considered the ancient ancestors of most eukaryotic dsDNA viruses1,2. Recently, a number of Polinton-Like Viruses (PLVs) have been discovered in algal genomes and environmental metagenomes3, which share characteristics and core genes with both Polintons and virophages (Lavidaviridae)4. These viruses could be the first members of a major class of ancient eukaryotic viruses, however, only a few complete genomes are known and it is unclear whether most are free viruses or are integrated algal elements3. Here we show that PLVs form an expansive network of globally distributed viruses, associated with a range of eukaryotic hosts. We identified PLVs as amongst the most abundant individual viruses present in a freshwater lake virus metagenome (virome), showing they are hundreds of times more abundant in the virus size fraction than in the microbial one. Using the major capsid protein genes as bait, we retrieved hundreds of related viruses from publicly available datasets. A network-based analysis of 976 new PLV and virophage genomes combined with 64 previously known genomes revealed that they represent at least 61 distinct viral clusters, with some PLV members associated with fungi, oomycetes and algae. Our data reveals that PLVs are widespread in predominantly freshwater environments and together with virophages, represent a broad group of eukaryotic viruses which share a number of genes.

microbiology↗

bioRxiv2019

Stable species boundaries despite ten million years of hybridization in tropical eels

Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla), and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past gene flow across a time-calibrated phylogeny. We show that the seven species have remained distinct entities for up to 10 million years, despite a dynamic scenario of incomplete isolation whereby the current frequencies of hybridization across species pairs (over 5% of all individuals were either F1 hybrids or backcrosses) contrast remarkably with patterns of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we identify cytonuclear incompatibilities and hybrid breakdown as two powerful mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of entire clades.

evolutionary biology↗