Leonardo Cerasino

Whether microbial community assembly is primarily deterministic (selection‐driven) or stochastic (dispersal‐driven) remains a central debate in microbial ecology. We investigated community assembly of bacteria and protists and their driving ecological processes in mountain Lake Tovel using a 5‐year 16S and 18S rRNA metabarcoding dataset. The frequencies of assembly mechanisms and their processes depend on the considered temporal scale. We assessed the influence of temporal scale (years, seasons, temporal distances from 1 to 48 months across all years) and year‐pooling (a common strategy in the assessment of assembly patterns) on the inference of community assembly in the upper euphotic (0–3 m), lower euphotic (3–25 m) and deep hypolimnetic (30–35 m) layers. Focusing on single years, bacteria showed more often different assembly mechanisms (both deterministic and stochastic) across layers and years than protists. Year‐pooling hid the inter‐year differences and preserved the signal of the most frequent single‐year process. A lagged effect of water temperature on bacterial community assembly was found, while an immediate effect on protist assembly. Bacterial and protists' niche width was generally independent of year‐pooling and increased with depth. Our study showed that different temporal scales and depth layers should be considered to gain a comprehensive overview on community assembly.

This study aimed to unravel the taxonomic structure and functional potential of the cyanobacterial community in a large, shallow meso-eutrophic lake in Central Italy (Lake Trasimeno) through shotgun metagenomic analysis. The metagenomic profiling of samples allowed to characterize the structure of the bacterial community, also including the identification of rare species, not detected with the determination of metagenome-assembled genomes (MAGs), in the successive assembling and binning steps. The taxonomic identification of MAGs was based on the computation of genome similarity metrics (average nucleotide and amino acid identity values; ANI, AAI) and phylogenomic analyses, which confirmed the presence of several cyanobacteria previously identified during the monitoring campaigns, and the identification of taxa new for the Mediterranean region, such as Prochlorothrix hollandica and an uncharacterized Prochlorothrix . The genome annotation of the Prochlorothrix MAGs was consistent with that of oxygenic, non-diazotrophic, chlorophyll- b -producing, photosynthetic cyanobacteria. The annotation of cyanobacterial MAGs did not reveal the presence of operons encoding cyanotoxins. Based on a conservative analysis, the presence of antimicrobial resistance genes (ARGs) was exclusively identified in Vibrio cholerae (Enterobacterales) and in a few unbinned contigs, confirming the global relevance of the ARGs spread in freshwater environments.

Fungi are an important component of aquatic ecosystems because of their multifaceted roles such as organic matter decomposition, nutrient cycling and energy transfer to higher trophic levels. Despite their importance, little is known about the diversity and ecological functions of fungi in mountain lakes in general and specifically for different layers. We investigated the spatiotemporal distribution of fungi in mountain Lake Tovel (Northern Italy) over more than 3 years (September 2021 to February 2025) using metabarcoding (amplicon sequence variants—ASVs—of the ITS gene). We sampled the upper and lower euphotic layers and the hypolimnion of the deep basin and the surface and bottom of the shallow basin. The sampling period covered the year 2022, one of the hottest in Europe, and the year 2024, a very rainy year in Northern Italy. Fungi showed year differences in % read abundance at different taxonomic levels. Observed richness and Chao1 diversity of the upper and lower euphotic layer were lower in warm 2022 than rainy 2024. Basidiomycota showed lower mean % read abundance in 2022 than 2024 in the intermediate layer. In the lower euphotic layer and the hypolimnion, most fungal classes (one and six fungal classes, respectively) had a lower % read abundance in 2022 than 2024. In NMDS with ASVs (stress = 0.16), samples of the years 2022 and 2024 were generally separated. In a partial redundancy analysis conditioned on layers, 17.2% of ASV variability was explained by year ( p < 0.001) and season ( p < 0.001) as factors and pH ( p < 0.01) and P _tot ( p < 0.05) as continuous variables. In path analysis, precipitation and % DO directly increased and pH directly decreased fungal diversity. The % abundance of dominant fungal genera also varied by layer: Filobasidium and Rhodotorula had higher % read abundance in the hypolimnion than lower euphotic layer while Zygophlyctis showed the opposite pattern. In network analysis, the lower euphotic layer showed the highest topological complexity, indicative of robustness against perturbations. The interaction between Zygophlyctis (primary algal parasite) and Cystobasidium (mycoparasite) pointed to hyperparasitism in the lower euphotic layer. Year differences in fungal communities indicated that the higher diversity of fungal communities in rainy 2024 can be attributed to different aspects such as wash‐in of fungi and of allochthonous material by rain. Season and layer differences were weak and related to specific analyses and genera and phyla. Our study provided new information on the diversity of fungal communities occurring in mountain lakes. Fungal communities responded to altered weather patterns, an important aspect considering that ongoing climate change alters precipitation in mountain regions.

Microalgae offer a sustainable and versatile source of bioactive compounds. Their rapid growth, efficient CO₂ utilization, and adaptability make them a promising alternative to traditional production methods. Key compounds, such as proteins, polyunsaturated fatty acids (PUFAs), polyphenols, phytosterols, pigments, and mycosporine-like amino acids (MAAs), hold significant commercial value and are widely utilized in food, nutraceuticals, cosmetics, and pharmaceuticals, driving innovation across multiple industries. Their antiviral and enzyme-producing capabilities further enhance industrial and medical applications. Additionally, microalgae-based biostimulants and plant elicitor peptides (PEPs) contribute to sustainable agriculture by enhancing plant growth and resilience to environmental stressors. The GRAS status of several species facilitates market integration, but challenges in scaling and cost reduction remain. Advances in biotechnology and metabolic engineering will optimize production, driving growth in the global microalgae industry. With increasing consumer demand for natural, eco-friendly products, microalgae will play a vital role in health, food security, and environmental sustainability.

This paper introduces and summarises a selection of contributions that were presented during a workshop on cyanobacterial blooms held at S. Michele all’Adige (Trento) in December 2023. The meeting originated with an increasing interest in a reciprocal exchange of knowledge and experiences between government bodies and research institutions following the widespread cyanobacterial blooms detected in the southern Alpine area and other Italian regions. The papers have been collected in the special issue “Potentially toxic cyanobacteria blooms in the southern Alps and the Italian peninsula”.

In this work, we characterised the cyanobacterial communities in the plankton and littoral biofilm of 38 lakes and in the biofilm of 21 rivers in the Alps and surrounding subalpine regions by 16S rRNA gene metabarcoding. We found little overlap in the distribution of amplicon sequence variants (ASVs) between the three habitats and between water bodies. The differences were caused by environmental filtering acting on the selection of the most abundant ASVs and a high contribution of rare oligotypes. The differentiation of community and genotype composition from specific water bodies was explained to a significant extent by environmental variables and morphometry. The taxonomic consistency of ASVs classified under the same genus name was assessed by phylogenetic analyses performed on three representative dominant genera, namely Cyanobium, Tychonema and Planktothrix. The analyses revealed eco-evolutionary adaptations in lakes and rivers, including some evidence for a polyphyletic nature. Monitoring individual genotypes in relation to environmental conditions will be useful to define the ecological amplitude of these taxa. However, the persistence or ephemeral nature of some of the rarest and most unusual ASVs has remained unknown.

We report the draft genome sequence of strain B0820 of the cyanobacterium Tychonema bourrellyi isolated from the epilimnion of Lake Garda and assembled from a metagenome of a non-axenic culture. The strain analyzed was shown to produce anatoxin-a, a potent neurotoxin that can cause fatal intoxication in exposed organisms.

Rock glaciers are increasingly influencing the hydrology and water chemistry of Alpine catchments. During three consecutive summers (2017–2019), we monitored by recording probes and fortnightly/monthly field campaigns the physical and chemical conditions of two rock glacier springs (ZRG, SRG) in the Zay and Solda/Sulden catchments (Eastern Italian Alps). The springs have contrasting hydrological conditions with ZRG emerging with evident ponding (pond‐like), and SRG being a typical high‐elevation seep (stream‐like). Water temperature was constantly low (mean 1.2°C, standard deviation 0.1°C) at both springs. Concentrations of major ions (dominated by SO₄²⁻, HCO₃⁻, Ca²⁺ and Mg²⁺) and trace elements (As, Sr, Ba, U, Rb) increased, and water became more enriched in heavy stable isotopes (δ¹⁸O, δ²H) towards autumn. This solute and isotopic enrichment had an asymptotic trend at SRG, and a unimodal pattern at ZRG, where peaks occurred 60–80 days after the snowmelt end. Wavelet analysis of electrical conductivity (EC) and water temperature records revealed daily cycles only at SRG, and significant weekly/biweekly fluctuations at both springs attributable to oscillations of meteorological conditions. Several rainfall events triggered a transient (0.5–2 h) EC drop (of 5–240 μS cm⁻¹) and water temperature rise (of 0.2–1.4°C) at SRG (dilution and warming), whereas only intense rainfall events occasionally increased EC (by 15–85 μS cm⁻¹) at ZRG (solute enrichment and thermal buffering), with a long‐lasting effect (6–48 h). Building on previous research, we suggest that rock glacier springs with differing flow conditions, that is, stream‐like and pond‐like, have contrasting fluctuations of water parameters at different timescales. Thus, for pond‐like springs, peaks of EC/solute concentrations might indicate a seasonal window of major permafrost thaw. Our quantitative description of the hydrochemical seasonality in rock glacier outflows and the physical and chemical response to precipitation events provides relevant information for water management in mountain areas under climate change.

Due to increased frequency of cyanobacterial blooms and emerging evidence of cyanotoxicity in biofilm, reliable methods for early cyanotoxin threat detection are of major importance for protection of human, animal and environmental health. To complement the current methods of risk assessment, this study aimed to evaluate selected qPCR assays for detection of potentially toxic cyanobacteria in environmental samples. In the course of one year, 25 plankton and 23 biofilm samples were collected from 15 water bodies in Slovenia. Three different analyses were performed and compared to each other; qPCR targeting mcyE, cyrJ and sxtA genes involved in cyanotoxin production, LC-MS/MS quantifying microcystin, cylindrospermopsin and saxitoxin concentration, and microscopic analyses identifying potentially toxic cyanobacterial taxa. qPCR analyses detected potentially toxic Microcystis in 10 lake plankton samples, and potentially toxic Planktothrix cells in 12 lake plankton and one lake biofilm sample. A positive correlation was observed between numbers of mcyE gene copies and microcystin concentrations. Potential cylindrospermopsin- and saxitoxin-producers were detected in three and seven lake biofilm samples, respectively. The study demonstrated a potential for cyanotoxin production that was left undetected by traditional methods in both plankton and biofilm samples. Thus, the qPCR method could be useful in regular monitoring of water bodies to improve risk assessment and enable timely measures.