Biology subjects

Giovannelli, D.

Publications and source records attributed to Giovannelli, D..

12 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↗

bioRxiv2026

Global carbon fixation in Earth's subsurface biosphere

The subsurface of our planet hosts 15% of Earths biomass and plays a key role in mediating the exchange of volatiles and elements between deep, long-residence-time geological reservoirs and rapidly cycling surface environments, influencing planetary climate and habitability. While a significant fraction of subsurface microorganisms rely on surface-derived organic carbon, an unknown portion is sustained through chemolithotrophic carbon fixation. Despite its importance, the global diversity and distribution of microbial carbon fixation pathways in the subsurface, and the environmental drivers shaping them, remain poorly constrained. Here we systematically characterise carbon fixation pathways for 412 subsurface metagenomes, including 242 new metagenomes, and compare them to surface-derived datasets. We find that subsurface environments span a broader physicochemical space than surface systems and support a higher abundance and diversity of carbon fixation strategies. Using colocated geochemical data spanning >50 variables, we show that the reductive tricarboxylic acid cycle and the reductive acetyl-CoA pathway are enriched in reducing, geochemically evolved fluids. We use the metagenomic results together with previously published carbon fixation rates in the subsurface to derive a global continental subsurface carbon fixation rate of [~]2.65 Pg C yr-1 (range: 0.31-2.99). This represents [~]2% of terrestrial photosynthetic primary production, and is an order of magnitude higher than geological fluxes between the surface and the subsurface. These results identify the subsurface as a reservoir of autotrophic strategies organized along geochemical gradients, contributing substantially to the global carbon cycle. One Sentence SummaryThe subsurface is a widespread, environmentally and functionally diverse reservoir of autotrophic carbon fixation pathways that can contribute substantially to the global carbon cycle, fixing [~]2.65 Pg C yr-1 in continental settings alone.

microbiology↗

bioRxiv2025

The microbiology and geochemistry of the shallow-water hydrothermal vents of the Gulf of Naples, Italy

Shallow-water hydrothermal vents are dynamic ecosystems that occur below 200 m in tectonically active regions of the planet. While their geochemical composition has been investigated in several locations, knowledge about the microbial diversity they harbour remains scarce. Moreover, the relationships between hydrothermal fluid chemistry, geological settings and microbial community structure in shallow vents have not been explored in detail. Here, we investigate the interplay between fluid geochemistry and microbial diversity in two underwater volcanic regions in the Gulf of Naples, Italy, one under the influence of the Somma-Vesuvio volcano and the other located within the underwater portion of the Campi Flegrei caldera. By combining 16S rRNA amplicon sequencing with geochemical measurements, and by contextualizing it with previous geochemical measurements done in the region, we found that hydrothermal fluid chemistry, influenced by the geological setting where the vents are hosted, plays a key role in shaping microbial ecological niches, and imposes strong selective pressures on the resident microbial communities. We additionally describe two new shallow vent sites, contributing to the characterization of the hydrothermalism in the area and unveiling the biodiversity associated with shallow-water hydrothermalism in the region.

microbiology↗

bioRxiv2025

Tectonic setting shapes microbial biosynthetic potential across global geothermal environments

Microbial communities in geothermal environments constitute an underexplored reservoir of biosynthetic gene clusters with significant biotechnological potential. Here, we investigate the secondary metabolite potential of 219 microbial communities across marine and continental geothermal field sites, encompassing broad environmental gradients in temperature (4.7{degrees}C to 93.5{degrees}C), pH (0.85 to 10.3), and tectonic setting, including volcanic arcs, backarcs, divergent margins at on-axis mid-ocean ridges, post-subduction extensional arcs, and paleo-convergent intraplate plume systems. We identified 9,019 putative new biosynthetic gene cluster families, mostly lacking similarity to known biosynthetic gene clusters. Volcanic arc systems consistently exhibit the highest diversity of biosynthetic repertoires, whereas intraplate plume systems showed a greater representation of terpene-associated gene cluster families. In contrast, divergent margin systems were primarily characterized by nonribosomal peptide synthetases and ribosomally synthesized and post-translationally modified peptides pathways, together accounting for a large fraction of their predicted biosynthetic diversity. These findings suggest that tectonic context could be associated with large-scale patterns in microbial biosynthetic potential and provide a geobiological framework for guiding natural product discovery in geothermal ecosystems.

microbiology↗

bioRxiv2025

Nitrification in a seagrass-sponge association

AO_SCPLOWBSTRACTC_SCPLOWIn the Mediterranean Sea, the demosponge Chondrilla nucula can occur in close association with the native seagrass Posidonia oceanica. C. nucula harbors a diverse and abundant microbial community, including potential nitrifiers. Thus, the sponge may contribute to the nitrogen (N) demand of the seagrass holobiont. In this study, we investigated potential nitrification rates (PNR) and inorganic N fluxes within this association at a site where C. nucula covered 18 {+/-} 3 % of the seagrass meadow area, during plant growth (spring) and senescence (autumn). Using incubation experiments with 15N-labeled ammonium, we measured PNR and inorganic N of the seagrass-sponge association, and of sponge and seagrass independently, under light and dark conditions. We supplemented these experiments with 16s rRNA gene amplicon sequencing to characterize the microbial community of the sponge. PNR was exclusively measured when the sponge was present (alone or in association with the seagrass). PNR was highest in the dark and when C. nucula was associated with the seagrass, ranging from 21 {+/-} 7 to 267 {+/-} 33 nmol N g DW-1 h-1 in spring and autumn, respectively. Sponge-mediated PNR can support 8% of the N demand of the P. oceanica holobiont during growth and 47 % during senescence. We identified key nitrifying bacterial and archaeal groups as members of the sponges microbial community. While C. nucula released inorganic N, potentially sustaining the seagrass, it benefitted from dissolved organic carbon released by P. oceanica. These results suggest that the interaction between C. nucula and P. oceanica is mutually beneficial, ultimately supporting and stabilizing the seagrass ecosystem.

ecology↗

bioRxiv2025

Trace metals availability controls terminal electron acceptor utilization in Escherichia coli

Trace metals play an essential role in the metabolism of all living organisms and many metal-containing enzymes contribute to key physiological and ecological processes such as aerobic and anaerobic respiration, photosynthesis, carbon and nitrogen fixation. Despite this, trace metals potential to control microbial functional diversity and metabolic shifts is unknown. Here we demonstrate that the availability of trace metals controls electron acceptors utilization in Escherichia coli. Physiological and proteomic data show that trace metals depleted cultures have significantly reduced growth, start fermentation and increase energy expenditure for metal homeostasis even when more energetically favourable electron acceptors are present. Overall these results suggest how evolutionary and competitive pressures arising from changes in biological trace metals availability in deep time have contributed to shaping evolution and competition.

microbiology↗

bioRxiv2023

Complex organic matter degradation by secondary consumers in chemolithoautotrophy-based subsurface geothermal ecosystems

Microbial communities in terrestrial geothermal systems often contain chemolithoautotrophs with well-characterized distributions and metabolic capabilities. However, the extent to which organic matter produced by these chemolithoautotrophs supports heterotrophs remains largely unknown. Here we compared the abundance and activity of peptidases and carbohydrate active enzymes (CAZymes) that are predicted to be extracellular identified in metagenomic assemblies from 63 springs in the Central American and the Andean convergent margin (Argentinian backarc of the Central Volcanic Zone), as well as the plume-influenced spreading center in Iceland. All assemblies contain two orders of magnitude more peptidases than CAZymes, suggesting that the microorganisms more often use proteins for their carbon and/or nitrogen acquisition instead of complex sugars. The CAZy families in highest abundance are GH23 and CBM50, and the most abundant peptidase families are M23 and C26, all four of which degrade peptidoglycan found in bacterial cells. This implies that the heterotrophic community relies on autochthonous dead cell biomass, rather than allochthonous plant matter, for organic material. Enzymes involved in the degradation of cyanobacterial- and algal-derived compounds are in lower abundance at every site, with volcanic sites having more enzymes degrading cyanobacterial compounds and non-volcanic sites having more enzymes degrading algal compounds. Activity assays showed that many of these enzyme classes are active in these samples. High temperature sites (> 80{degrees}C) had similar extracellular carbon-degrading enzymes regardless of their province, suggesting a less well-developed population of secondary consumers at these sites, possibly connected with the limited extent of the subsurface biosphere in these high temperature sites. We conclude that in < 80{degrees}C springs, chemolithoautotrophic production supports heterotrophs capable of degrading a wide range of organic compounds that do not vary by geological province, even though the taxonomic and respiratory repertoire of chemolithoautotrophs and heterotrophs differ greatly across these regions.

biochemistry↗

bioRxiv2022

Quantifying the bioavailable energy in an ancient hydrothermal vent on Mars and a modern Earth-based analogue.

Putative alkaline hydrothermal systems on Noachian Mars were potentially habitable environments for microorganisms. However, the types of reactions that could have fueled microbial life in such systems and the amount of energy available from them have not been quantitatively constrained. In this study, we use thermodynamic modeling to calculate which catabolic reactions could have supported ancient life in a saponite-precipitating hydrothermal vent system in the Eridania basin on Mars. To further evaluate what this could mean for microbial life, we evaluated the energy potential of an analogue site in Iceland, the Strytan Hydrothermal Field (SHF). Results show that out of the 85 relevant redox reactions that were considered, the highest energy-yielding reactions in the Eridania hydrothermal system were dominated by methane formation. By contrast, Gibbs energy calculations carried out for Strytan indicate that the most energetically favorable reactions are CO2 and O2 reduction coupled to H2 oxidation. In particular, our calculations indicate that an ancient hydrothermal system within the Eridania basin could have been a habitable environment for methanogens using NH4+ as an electron acceptor. Differences in Gibbs energies between the two systems were largely determined by oxygen - its presence on Earth and absence on Mars. However, Strytan can serve as a useful analogue for Eridania when studying methane producing reactions that do not involve O2.

microbiology↗

bioRxiv2021

mebipred: identifying metal-binding potential in protein sequences.

Metal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability. We developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is nearly 90% accurate in recognizing proteins that bind metal ions and ion containing ligands. Moreover, the identity of ten ubiquitously present metal ions and ion-containing ligands can be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and outperforms other prediction methods, both in speed and accuracy. mebipred can also identify protein metal-binding capabilities from short sequence stretches and, thus, may be useful for the annotation of metagenomic samples metal requirements inferred from translated sequencing reads. We performed an analysis of microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human-hosted microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results are highlight mebipreds utility in analyzing microbiome metal requirements. mebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/

bioinformatics↗

bioRxiv2021

Bacterioplankton Diversity and Distribution in Relation to Phytoplankton Community Structure in the Ross Sea surface waters

Primary productivity in the Ross Sea region is characterized by intense phytoplankton blooms whose temporal and spatial distribution are driven by changes in environmental conditions as well as interactions with the bacterioplankton community. Exchange of exudates, metabolism by-products and cofactors between the phytoplankton and the bacterioplankton communities drive a series of complex interactions affecting the micronutrient availability and co-limitation, as well as nutrient uptakes in Antarctic waters. Yet, the number of studies reporting the simultaneous diversity of the phytoplankton and bacterioplankton in Antarctic waters are limited. Here we report data on the bacterial diversity in relation to phytoplankton community in the surface waters of the Ross Sea during the austral summer 2017. Our results show partially overlapping bacterioplankton communities between the stations located in the Terra Nova Bay coastal waters and the Ross Sea open waters, suggesting that the two communities are subjected to different drivers. We show that the rate of diversity change between the two locations is influenced by both abiotic (salinity and the nitrogen to phosphorus ratio) and biotic (phytoplankton community structure) factors. Our data provides new insight into the coexistence of the bacterioplankton and phytoplankton in Antarctic waters.

microbiology↗

bioRxiv2021

Genomic Mining and Physiological Characterization of new Halophilic Plant Growth Promoting Bacilli

Massive application of chemical fertilizers and pesticides has been the main strategy used to cope with the rising crop demands in the last decades. The indiscriminate use of chemicals while providing a temporary solution to food demand has led to a decrease in crop productivity and an increase in the environmental impact of modern agriculture. A sustainable alternative to the use of chemicals for crop production is the use of microorganisms naturally capable of enhancing plant growth and protecting crops from pests, known as Plant-Growth-Promoting Bacteria (PGPB). Aim of the present study was to isolate and characterize PGPB from salt-pans sand samples able to ameliorate plant fitness. To survive high salinity, salt-tolerant microbes produce a broad range of compounds with heterogeneous biological activities that are potentially beneficial for plant growth. We have isolated and screened in vitro a total of 20 halophilic spore-forming bacteria for phyto-beneficial traits and compared the results with two Bacilli recently isolated from the rhizosphere of the same collection site and recently characterized as potential biocontrol agents. Whole-genome analysis on five selected halophilic strains confirmed the presence of numerous gene clusters with PGP and biocontrol functions and of novel secondary-metabolite biosynthetic genes potentially involved in plant growth promotion and protection. The predicted biocontrol potential was confirmed in dual culture assays against several phytopathogenic fungi and bacteria. Interestingly, the absence of predicted gene clusters with known biocontrol functions in some of the isolates was not predictive of the in vitro results, supporting the need of combining laboratory assays and genome mining in PGPB identification for future applications.

microbiology↗

bioRxiv2020

Metaproteogenomic profiling of chemosynthetic microbial biofilms reveals metabolic flexibility during colonization of a shallow-water gas vent

Tor Caldara is a shallow-water gas vent located in the Mediterranean Sea, with active venting of CO2, H2S. At Tor Caldara, filamentous microbial biofilms, mainly composed of Epsilon- and Gammaproteobacteria, grow on substrates exposed to the gas venting. In this study, we took a metaproteogenomic approach to identify the metabolic potential and in situ expression of central metabolic pathways at two stages of biofilm maturation. Our findings indicate that inorganic reduced sulfur species are the main electron donors and CO2 the main carbon source for the filamentous biofilms, which conserve energy by oxygen and nitrate respiration, fix dinitrogen gas and detoxify heavy metals. Three metagenome-assembled genomes (MAGs), representative of key members in the biofilm community, were also recovered. Metaproteomic data show that metabolically active chemoautotrophic sulfide-oxidizing members of the Epsilonproteobacteria dominated the young microbial biofilms, while Gammaproteobacteria become prevalent in the established community. The co-expression of different pathways for sulfide oxidation by these two classes of bacteria suggests exposure to different sulfide concentrations within the biofilms, as well as fine-tuned adaptations of the enzymatic complexes. Taken together, our findings demonstrate a shift in the taxonomic composition and associated metabolic activity of these biofilms in the course of the colonization process.

microbiology↗