Biology subjects

Gabrielli, M.

Publications and source records attributed to Gabrielli, M..

15 recordsLinked to original sources

bioRxiv2026

Amino acid auxotrophy is a feature of a distinct bacterial lifestyle across environments

Amino acid auxotrophy, the loss of biosynthetic potential for an amino acid, is a highly prevalent feature of microbial life, yet the evolutionary processes driving its distribution in nature remain unclear. Here, we sought to determine whether auxotrophy emerges as an independent response to nutrient availability or as part of a broader transition in genomic lifestyle. By first predicting auxotrophies through genome-scale metabolic models and flux-balance analysis, and subsequently applying phylogenetically informed statistical frameworks, we tested the predictions of the Black Queen Hypothesis, which posits that auxotrophy evolves as a dynamic response to metabolite availability, and disentangled the signal of convergent environmental selection from the background of shared evolutionary history. This approach reveals that phylogeny is the dominant predictor of auxotrophy, vastly outweighing environmental context. Beyond correcting for ancestry, our analysis uncovered a previously obscured signal of consistent, co-occurring genomic changes: auxotrophies do not occur as independent losses, but rather as part of a broader reorganization of the genome. We show that auxotrophies co-occur significantly more often than predicted by chance and that the probability of loss scales with the number of other auxotrophies. These findings reveal auxotrophy as a feature of a conserved, phylogenetically entrenched lifestyle rather than a transient response to nutrient availability -- inconsistent with the Black Queen Hypothesis and instead aligning with genome streamlining as the overarching driver of metabolic dependency in natural microbial systems.

evolutionary biology↗

bioRxiv2026

The relationship between genomic variation and genetic load: insights from small island populations

Small populations face high extinction risks. This can be explained by several non-genetic and genetic factors, the latter including the loss of genetic diversity and evolutionary potential, as well as the accumulation of harmful mutations (genetic load). Using whole-genome data from island populations with different effective sizes, we estimated genetic variation and load and explored the relationship between these quantities. An extremely small population of the Aeolian wall lizard, Podarcis raffonei, likely isolated for tens of thousands of years, shows the lowest genome-wide heterozygosity observed in wild eukaryotes (one polymorphic site every 300 kb on average). Despite this, its realized genetic load is comparable to that observed in another larger and more genetically variable population. Both populations have lower variation and higher load than the much more abundant sister species, the Sicilian wall lizard. These observations are consistent with the hypothesis that populations experiencing severe bottlenecks may persist for extended periods with extremely low genomic variation, provided that their burden of deleterious mutations remains within tolerable bounds.

genomics↗

bioRxiv2026

Genomics of speciation in a great speciator (Aves: Zosterops) reveals the roles of both natural and sexual selection

Examining patterns of differentiation among lineage pairs at different stages of the speciation continuum can help disentangle the effects of linked and divergent selection, and identify lineage-specific targets of selection that may act as barrier loci during speciation. Here, we developed this approach using genomic data from a set of African and Indian Ocean belonging to the Zosteropidae family, commonly referred to as a "Great Speciator". We sampled a divergence continuum aiming to identify candidate barrier loci in phenotypically, genetically distinct, and parapatrically distributed, forms from a species complex, through comparisons with closely related species. Using three independent approaches, we showed that divergence at selected loci between geographic forms is mainly concentrated on the Z chromosome, unless forms differ in their ecologies. Functional annotation revealed that genes linked to song formation and immunity could be involved in reproductive isolation between forms only separated by physical barriers, while it is mostly genes related to adaptation to local conditions, morphology, and song behaviour that may explain reproductive isolation between forms with different ecologies, highlighting a role for combined effects of natural and sexual selection in driving the evolution of reproductive barriers in this rapidly speciating lineage

genomics↗

bioRxiv2026

Siderophore-mediated inhibition of Legionella pneumophila by environmental Pseudomonas isolates

The genus Legionella comprises opportunistic pathogenic bacteria commonly found in natural and engineered water systems, where they interact with environmental microbes and protozoa, primarily in biofilms. Legionella pneumophila is the main causative agent of Legionnaires disease and is transmitted through inhalation of contaminated aerosols. Iron availability is a critical factor for L. pneumophila growth, persistence, and virulence, yet iron is often limited in aquatic environments. To overcome iron scarcity, many bacteria produce siderophores, secondary metabolites that scavenge ferric iron. Because siderophores are chemically diverse and species specific, they play a key role in inter-species competition and can withhold iron from competitors. Here, we investigated the effects of iron depletion and siderophore-mediated competition on L. pneumophila using commercial pyoverdines and extracellular metabolites from environmental Pseudomonas strains. Growth assays showed that L. pneumophila can grow under iron-limited conditions but with lag phases extended by more than 20 hours. Pyoverdines inhibited growth in a concentration-dependent manner, primarily increasing the time to mid-log phase (t_mid). Supernatants and crude pyoverdine extracts from siderophore-producing Pseudomonas strains caused the strongest inhibition, including lag-phase extensions of up to 55 hours or complete growth arrest. These results demonstrate that siderophore-producing bacteria can suppress L. pneumophila by limiting iron availability.

microbiology↗

bioRxiv2025

Small-scale biogeography of biofilms and its implications for sequencing-based studies

Biofilm microbial communities are characterized by spatial heterogeneity arising in response to environmental characteristics and the metabolic requirements of their inhabitants, which create biogeographical patterns at both large and small scales. While the impact of small-scale biogeography on several emergent biofilm properties has been characterized by a variety of laboratory studies using simple synthetic communities, the extent of small-scale biogeography in environmental biofilms, as well as its impact on sequencing-based studies, remain poorly characterized. Here, we investigate centimeter-scale biogeography in potable water biofilms developed in environments with distinct levels of heterogeneity. We then estimate microbial diversity at scales relevant for microbial interactions and characterize the impact of sampling strategies on both alpha and beta diversity metrics, as well as on inferred co-occurrences and scaling laws. Our results show that biofilm sections in seemingly homogeneous environments are characterized by similar biogeographic patterns as the ones in a more heterogeneous one, albeit with lower cm-scale variability. We estimated that, despite the overall richness over the entire biofilms, single cells are surrounded by local neighborhoods of limited diversity, strongly limiting their possibility for diverse interactions. Larger sampling areas average such local heterogeneities and distort community structure estimates, leading to an inflated and erroneous estimation of co-occurrences and potential metabolic interactions. Finally, we report how both environmental heterogeneity, as well as sample area size, influence scaling law performances. Our results highlight the ubiquitous nature of biofilm biogeography and call for the adaptation of biofilm sampling strategies to consider this phenomenon relative to specific research questions.

microbiology↗

bioRxiv2025

Coexisting with humans: genomic and behavioural consequences in a small and isolated bear population

Climate and land use change have increased human-wildlife interactions, potentially reducing wild species density and prompting behavioural adaptations to urbanised environments. It is still debated if behavioural responses are mainly the result of phenotypic plasticity or if they were driven by anthropic selective pressures, especially in small populations. Our study focused on the Apennine brown bear population (Ursus arctos marsicanus), which has coexisted with humans in Central Italy for millennia. We characterised genomic diversity and identified adaptation signals distinctive to this population by comparing whole genome resequencing data across the Holarctic species range. We show that Apennine brown bears possess a unique genomic diversity pattern including selective signatures at genes associated with reduced aggressiveness, possibly involving alternative splicing mechanism. Our findings suggest that even in small and long-isolated populations, selection may shape behavioural traits. We hypothesise that human-induced selection has influenced these changes, reducing conflicts and contributing to the long-term persistence of the Apennine bear and its coexistence with humans.

genomics↗

bioRxiv2025

MICROGLIAL EXTRACELLULAR VESICLES MEDIATE C1Q DEPOSITION AT THE PRE-SYNAPSE AND PROMOTE SYNAPTIC PRUNING

C1q is released by microglia, localizes on weak synapses and acts as a tag for microglial synaptic pruning. However, how C1q tags synapses during the pruning period remains to be fully elucidated. Here, we report that C1q is delivered by microglia to pre-synaptic sites that externalize phosphatidylserine through extracellular vesicles. Using approaches to increase or reduce vesicles production in microglia, by C9orf72 knock out or pharmacological inhibition respectively, we provided mechanistic evidence linking extracellular vesicle release to pre-synaptic remodelling in neuron-microglia cultures. In C9orf72 knockout mice, we confirmed larger production of microglial extracellular vesicles, and showed augmented C1q presynaptic deposition associated with enhanced engulfment by microglia in the early postnatal hippocampus. Finally, we provide evidence that microglia physiologically release more vesicles during the period of postnatal circuit refinement. These findings implicate abnormal release of microglial extracellular vesicles in both neurodevelopmental and age-related disorders characterized by dysregulated microglia-mediated synaptic pruning.

neuroscience↗

bioRxiv2024

Variable inhibition of different Legionella species by antagonistic bacteria

The genus Legionella includes opportunistic pathogens inhabiting engineered aquatic ecosystems, where managing their presence and abundance is crucial for public health. In these environments, Legionella interact positively or negatively with multiple members of the microbial communities. Here, we identified bacteria and compounds with Legionella-antagonistic properties. We isolated 212 bacterial colonies from various water sources in Switzerland and screened them for their ability to inhibit one reference strain of L. pneumophila. Ten selected antagonistic isolates were subsequently tested with spot-on-lawn-assays for inhibition towards seven environmental and two clinical isolates of Legionella, representing different species and strains. The antagonists produced highly variable inhibition patterns, highlighting distinct differences in susceptibility among Legionella species, and even strains. Only three isolates, all identified as Pseudomonas lurida, inhibited all Legionella species. Furthermore, we analysed the genomes of the antagonistic bacteria, and identified genes for several probable inhibitory compounds. We specifically found the gene cluster for the biosurfactant viscosin to be uniquely encoded by three Pseudomonas lurida isolates. This compound was subsequently detected in the supernatant of co-cultures inoculated with the antagonists and Legionella. This study provides new insights on the ability of aquatic microorganisms to compete with Legionella in controlled laboratory settings. It also highlights the diversity across and within Legionella species in their resistance to external antagonistic stress, and confirms the anti-Legionella activity of selected biosurfactants. These results can contribute to the understanding of how different species inhabit separate niches in the environment, and expand the discussion around alternative Legionella mitigation strategies.

microbiology↗

bioRxiv2024

Expansion, restructuring and characterization of the Legionellaceae family

Legionellaceae is a large and widespread family of facultative intracellular bacteria with high clinical relevance. While Legionella pneumophila, the most clinically relevant species, is relatively well studied, very limited information is available regarding the other species belonging to this family, despite its only recognized genus (i.e., Legionella) being included in water regulations worldwide. Here, we analyzed publicly-available Legionellaceae isolates and metagenome-assembled genomes, nearly doubling the number of recognized species and highlighting the need to consider restructuring the familys taxonomy to include multiple genera that present distinct clinical relevance. We further found that, except for Type II and IVB secretion systems, traits linked to host invasion vary significantly across species, likely influencing their host range and survival in the environment. Presumptive genus clusters exhibited variations in metabolic capabilities, but L. pneumophila and closely related species generally displayed more complete pathways and fewer auxotrophies, suggesting a less strict intracellular lifestyle. On the contrary, specific deep-branching clades show reduced genome size and the lack of poly-3-hydroxybutyrate biosynthetic potential suggesting a stronger host association. Finally, we showed that most species are present across various environments and that, while they have apparently distinct environmental distributions, niche overlap increases at higher metabolic similarity. Together, our results shed light on the ecology of these microorganisms, highlight the diversity of traits that can occur in closely related facultative intracellular bacteria, and call for the restructuring of this family to align with genomic information and clinical relevance to aid the management of Legionellaceae bacteria. ImportanceSpecies belonging to the Legionellaceae family are responsible for Legionnaires disease, the leading waterborne disease in many industrialized countries. Historically, the focus was (and still is) on Legionella pneumophila, and the ecology of other species remained largely unknown and unexplored. However, several water safety regulations cover the entire Legionella genus,currently the only recognized within this large family, thus including species with unknown health relevance and ecology. This work provides an in-depth characterization of the genomic diversity across the family Legionellaceae, highlighting the concentration of clinically-relevant species in specific clades presenting distinct putative phenotypes linked to host invasion, metabolism and environmental niches. These findings highlight the need to consider restructuring the taxonomy of the family Legionellaceae in multiple genera to prioritize interventions to control the presence of the most clinically-relevant ones and advance public health protection.

microbiology↗

bioRxiv2024

New drinking water genome catalog identifies a globally distributed bacterial genus adapted to disinfected drinking water systems.

Genome-resolved insights into the structure and function of the drinking water microbiome can advance the effective management of drinking water quality. To enable this, we constructed and curated thousands of metagenome-assembled and isolate genomes from drinking water distribution systems globally to develop a Drinking Water Genome Catalog (DWGC). The current DWGC disproportionately represents disinfected drinking water systems due to a paucity of metagenomes from non-disinfected systems. Using the DWGC, we identify core genera of the drinking water microbiome including a genus (UBA4765) within the order Rhizobiales that is frequently detected and highly abundant in disinfected drinking water systems. We demonstrate that this genus has been widely detected but incorrectly classified in previous amplicon sequencing-based investigations of the drinking water microbiome. Further, we show that a single genome variant (genomevar) within this genus is detected in >82% of drinking water systems included in this study. We propose a provisional name for this uncultured bacterium as "Raskinella chlorumaquaticus" and describe the genus as "Raskinella" (pending SeqCode approval). Metabolic annotation and modeling-based predictions indicate that this bacterium is capable of necrotrophic growth, able to metabolize halogenated compounds, proliferates in a biofilm-based environment and shows clear indications of disinfection-mediated selection. SynopsisCreation and analysis of a new curated drinking water genome catalog identifies uncharacterized bacterial species that is widely distributed in disinfected drinking water systems.

microbiology↗

bioRxiv2024

The impact of DNA extraction on the quantification of Legionella, with implications for ecological studies

Monitoring the levels of opportunistic pathogens in drinking water is important to plan interventions and understand the ecological niches that allow them to proliferate. Quantitative PCR is an established alternative to culture methods that can provide a faster, higher throughput, and more precise enumeration of the bacteria in water samples. However, PCR-based methods are still not routinely applied for Legionella monitoring, and techniques such as DNA extraction differ notably between laboratories. Here, we quantify the impact that DNA extraction methods had on downstream PCR quantification and community sequencing. Through a community science campaign, we collected 50 water samples and corresponding shower hoses, and compared two commonly used DNA extraction methodologies to the same biofilm and water phase samples. The two methods showed clearly different extraction efficacies, which was reflected in both the quantity of DNA extracted and the concentrations of Legionella enumerated in both the matrices. Notably, one method resulted in higher enumeration in nearly all samples by about one order of magnitude and detected Legionella in 21 samples that remained undetected by the other method. 16S rRNA amplicon sequencing revealed that the relative abundance of individual taxa, including sequence variants of Legionella, significantly varied depending on the extraction method employed. Given the implications of these findings, we advocate for improvement in documentation of the performance of DNA extraction methods used in drinking water to detect and quantify Legionella, and characterise the associated microbial community.

microbiology↗

bioRxiv2023

Unravelling species demographic responses to local and global past ecological disruptions using whole-genome sequencing in volcanic oceanic island organisms

Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species demography is particularly important in the current context of rapid environmental changes driven by both local and regional factors. We argue that volcanic oceanic islands provide useful settings to study the influence of past ecological disruptions operating at local and regional scales on population demographic histories. We investigate potential drivers of past population dynamics for three closely related species of passerine birds from two volcanic oceanic islands, Reunion and Mauritius (Mascarene archipelago), with distinct volcanic history. Using ABC and PSMC inferences from complete genomes, we reconstructed the demographic history of the Reunion Grey White-eye (Zosterops borbonicus (Pennant, 1781)), the Reunion Olive White-eye (Z. olivaceus (Linnaeus, 1766)), and the Mauritius Grey White-eye (Z. mauritianus (Gmelin, 1789)), and searched for possible causes underlying similarities or differences between species living on the same or different islands. Both demographic inferences strongly support ancient and long-term expansions in all species. They also reveal different trajectories between species inhabiting different islands, but consistent demographic trajectories in species or populations from the same island. Species from Reunion appear to have experienced synchronous reductions in population size during the Last Glacial Maximum, a trend not seen in the Mauritian species. Overall, this study suggests that local events may have played a role in shaping population trajectories of these island species. It also highlights the potential of our conceptual framework to disentangle the effects of local and regional drivers on past species demography and long-term population processes.

evolutionary biology↗

bioRxiv2022

Identifying eukaryotes in drinking water metagenomes and factors influencing their biogeography.

The biogeography of eukaryotes in drinking water systems is poorly understood relative to prokaryotes or viruses. A common challenge with studying complex eukaryotic communities from natural and engineered systems is that the metagenomic analysis workflows are currently not as mature as those that focus on prokaryotes or even viruses. In this study, we benchmarked different strategies to recover eukaryotic sequences and genomes from metagenomic data and applied the best-performing workflow to explore eukaryotic communities present in drinking water distribution systems (DWDSs). We developed an ensemble approach that exploits k-mer and reference-based strategies to improve eukaryotic sequence identification from metagenomes and identified MetaBAT2 as the best performing binning approach for clustering of eukaryotic sequences. Applying this workflow on the DWDSs metagenomes showed that eukaryotic sequences typically constituted a small proportion (i.e., <1%) of the overall metagenomic data. Eukaryotic sequences showed higher relative abundances in surface water-fed and chlorine disinfected systems. Further, the alpha and beta-diversity of eukaryotes were correlated with prokaryotic and viral communities. Finally, a co-occurrence analysis highlighted clusters of eukaryotes whose presence and abundance in DWDSs is affected by disinfection strategies, climate conditions, and source water types. SynopsisAfter benchmarking tools and developing a dedicated consensus workflow for eukaryotic sequence detection in metagenomes, the experimental, environmental, and engineering factors affecting their biogeography in drinking water distribution systems were investigated Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/518372v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1ae8423org.highwire.dtl.DTLVardef@653471org.highwire.dtl.DTLVardef@5606b7org.highwire.dtl.DTLVardef@1d30cde_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Astrocytic extracellular vesicles modulate neuronal calcium homeostasis via transglutaminase-2

We have uncovered a novel role for astrocytes-derived extracellular vesicles (EVs) in controlling intraneuronal Ca2+ concentration ([Ca2+]i) and identified transglutaminase-2 (TG2) as a surface-cargo of astrocytes-derived EVs. Incubation of hippocampal neurons with primed astrocyte-derived EVs have led to an increase in [Ca2+]i, unlike EVs from TG2-knockout astrocytes. Exposure of neurons or brain slices to extracellular TG2 promoted a [Ca2+]i rise, which was reversible upon TG2 removal and was dependent on Ca2+ influx through the plasma membrane. Patch-clamp and calcium imaging recordings revealed TG2-dependent neuronal membrane depolarisation and activation of inward currents, due to the opening of L-type-VOCCs and to Na+/Ca2+ -exchanger (NCX) operation in the reverse mode, as indicated by VOCCs/NCX pharmacological inhibitors. A subunit of Na+/K+-ATPase was selected by comparative proteomics and identified as being functionally inhibited by extracellular TG2, implicating Na+/K+-ATPase inhibition in NCX reverse mode-switching leading to Ca2+ influx and higher basal [Ca2+]i. These data suggest that reactive astrocytes control intraneuronal [Ca2+]i through release of EVs with TG2 as responsible cargo, which could have a significant impact on synaptic activity in brain inflammation.

neuroscience↗

bioRxiv2018

A bird’s white-eye shot: looking down on a new avian sex chromosome evolution

AO_SCPCAPBSTRACTC_SCPCAPChromosomal organization is relatively stable among avian species, especially with regards to sex chromosomes. Members of the large Sylvioidea clade however have a pair of neo-sex chromosomes which is unique to this clade and originate from a parallel translocation of a region of the ancestral 4A chromosome on both W and Z chromosomes. Here, we took advantage of this unusual event to study the early stages of sex chromosome evolution. To do so, we sequenced a female (ZW) of two Sylvioidea species, a Zosterops borbonicus and a Z. pallidus. Then, we organized the Z. borbonicus scaffolds along chromosomes and annotated genes. Molecular phylogenetic dating under various methods and calibration sets confidently confirmed the recent diversification of the genus Zosterops (1-3.5 million years ago), thus representing one of the most exceptional rates of diversification among vertebrates. We then combined genomic coverage comparisons of five males and seven females, and homology with the zebra finch genome (Taeniopygia guttata) to identify sex chromosome scaffolds, as well as the candidate chromosome breakpoints for the two translocation events. We observed reduced levels of within-species diversity in both translocated regions and, as expected, even more so on the neoW chromosome. In order to compare the rates of molecular evolution in genomic regions of the autosomal-to-sex transitions, we then estimated the ratios of non-synonymous to synonymous polymorphisms ({pi}N/{pi}S) and substitutions (dN/dS). Based on both ratios, no or little contrast between autosomal and Z genes was observed, thus representing a very different outcome than the higher ratios observed at the neoW genes. In addition, we report significant changes in base composition content for translocated regions on the W and Z chromosomes and a large accumulation of transposable elements (TE) on the newly W region. Our results revealed contrasted signals of molecular evolution changes associated to these autosome-to-sex transitions, with congruent signals of a W chromosome degeneration yet a surprisingly weak support for a fast-Z effect.

evolutionary biology↗