Biology subjects

Savaglia, V.

Publications and source records attributed to Savaglia, V..

4 recordsLinked to original sources

bioRxiv2025

Out of Antarctica: new insights into Antarctic Subcluster 5.2 picocyanobacteria based on high-quality genomes

2.Synechococcus-like cyanobacteria are cosmopolitan unicellular picocyanobacteria that have colonized diverse aquatic and terrestrial habitats. The so-called subcluster 5.2 represents a particularly diversified subgroup, including marine and freshwater organisms adapted to extreme conditions, notably polar environments. We increased the genomic representation of polar taxa in this subcluster by reconstructing new high-quality genomes from five Antarctic lacustrine strains and one Arctic freshwater isolate using a combination of small Illumina and long Nanopore reads. A maximum likelihood (ML) phylogenomic analysis of these new assemblies combined with all publicly available good quality assemblies of the subcluster 5.2 suggests evidence of a dispersal process from Antarctica. Indeed, the topology of the phylogenomic tree indicates one basal Antarctic lineage followed by the emergence of two lineages, one Antarctic and one non-Antarctic (Spain). This finding is further supported by a 16S rRNA ML phylogenetic and a pangenomic analysis. Although secondary colonization of Antarctica by cyanobacteria following the cooling of the continent 34 million years ago has been reported, this study is the first to support an Out-of-Antarctica scenario inside subcluster 5.2. 3. Impact statementThis study provides novel insights into the evolutionary history and biogeography of Synechococcus-like picocyanobacteria. By expanding the genomic sampling of polar subcluster 5.2, we reveal that Antarctic taxa are not monophyletic and are intermixed with non-Antarctic lineages, suggesting an unprecedented Out-of-Antarctica dispersal scenario. Our results, supported by 16S rRNA, phylogenomic and pangenomic analyses, highlight the role of polar regions as both a refuge and a source of microbial diversity. This work advances our understanding of cyanobacterial adaptation, radiation and genome evolution in extreme environments. 4. Data summaryRaw sequencing reads and genome assemblies from this study have been deposited in the European Nucleotide Archive (ENA) under Project accession number PRJEB103944. Raw sequencing reads are available under accession numbers ERR15933635 to ERR15933638, ERR15933641 to ERR15933644, ERR15903357, ERR15903358, ERR15905256 and ERR15905257. The assemblies can be accessed under accession numbers GCA_977927515, GCA_977927525, GCA_977927535, GCA_977927545, GCA_977927555 and GCA_977929215. The scripts and code as well as large supplementary files generated during this study are available on Figshare and can be downloaded from https://doi.org/10.6084/m9.figshare.30772781 [1]. Supplementary data files are also provided and contains supplementary figures (Fig. S1-S4) and tables (Table S1-S6).

ecology↗

bioRxiv2025

A FAIR Amplicon Sequencing Workflow for Long-term Environmental Monitoring

Antarctica represents one of the last pristine environments on Earth, providing a unique opportunity to to study the effects of climate change and anthropogenic activities. Ice-free areas, such as the inland nunataks of the Sor Rondane Mountains (SRM), host unique terrestrial and lacustrine ecosystems, of which the simplified food webs rely almost exclusively on microbial primary production. Because of their small size, low productivity and hence low biomass, these microbial communities are fragile. Seven SRM sites were selected to be part of the Antarctic Specially Protected Area (ASPA) 179. The MonASPA project has established an environmental monitoring program to evaluate the effectiveness of the management plan approved by the Antarctic Treaty System for these areas. A key component of MonASPA is the long-term monitoring of microbial biodiversity using 16S rRNA amplicon sequencing. To ensure consistent operation over decades, we developed the Reproducible Amplicon Sequencing Pipeline for Antarctic Monitoring (RASPAM), which is built on Apptainer containers and Nextflow workflows. RASPAM implements Amplicon Sequence Variants (ASVs) and Zero-radius Operational Taxonomic Units (ZOTUs) to provide high-resolution taxonomic affiliation. It incorporates, in addition to the SILVA database, a taxonomically curated 16S rRNA database for cyanobacteria and enables comparisons against NCBI databases to facilitate the identification of rare prokaryotic strains in environmental samples. RASPAM is Findable, Accessible, Interoperable, and Reproducible (FAIR) and represents a robust tool for long-term monitoring of microbial communities in Antarctic and other extreme environments.

bioinformatics↗

bioRxiv2023

Ecophysiological and genomic approaches to cyanobacterial hardening for soil restoration

Cyanobacteria inhabit extreme environments, including drylands, providing multiple benefits to the ecosystem. Soil degradation in warm drylands is increasing due to land-use intensification. Restoration methods adapted to the strong stress in drylands are being developed, i.e. cyanobacterial inoculation to recover biocrusts. For success, it is crucial to optimize the survival of inoculated cyanobacterial in field. One strategy is to harden them to be re-adapted to stressful conditions after laboratory culturing. Here, we analyzed the genome and ecophysiological response to osmotic, desiccation and UVR stresses of an Antarctic cyanobacterium, Stenomitos frigidus ULC029, closely related to other cyanobacteria from warm and cold dryland soils. Chlorophyll a concentrations show that preculturing ULC029 under moderate osmotic stress improved its survival during an assay of desiccation plus rehydration under UVR. Besides, its sequential exposition to these stress factors increased the production of exopolysaccharides, carotenoids and scytonemin. Desiccation, but not osmotic stress, increased the concentrations of the osmoprotectants, trehalose and sucrose. However, osmotic stress might induce the production of other osmoprotectants, for which the complete pathways were found in the ULC029 genome. In total, 140 genes known to be involved in stress resistance were annotated and could potentially help ULC029 under stress. Here, we confirm that the sequential application of moderate osmotic stress and dehydration, could improve cyanobacterial hardening for soil restoration, by inducing several resistance mechanisms. We provide a high-quality genome of ULC029 and a description of the main resistance mechanisms found (i.e. production of exopolysaccharides, osmoprotectants, chlorophyll and carotenoids; DNA repair; oxidative stress protection).

microbiology↗

bioRxiv2023

Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics

Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into their diversity, only a handful of genomes of polar Cyanobacteria have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic, and Antarctic microbial mats. We recovered 22 unique metagenome-assembled genomes (MAGs) of Cyanobacteria, most of which are only distantly related to genomes that have been sequenced so far. These include i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena, Leptolyngbya, Microcoleus/Tychonema, and Phormidium; ii) the less common taxa Crinalium and Chamaesiphon; iii) an enigmatic Chroococcales lineage only distantly related to Microcystis; and iv) an early branching lineage in the order Gloeobacterales that is almost exclusively restricted to the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments. Data summaryThe sequencing data generated in this study have been submitted to the European Nucleotide Archive (ENA) under the BioProject PRJEB59431. Individual accession numbers for raw reads and genomic bins are listed in Table S1 and Table S3, respectively. Genomic bins can also be downloaded from doi.org/10.6084/m9.figshare.22003967. The commands used throughout this study are available in github.com/igorspp/polar-cyanobacteria-MAGs. Impact statementCyanobacteria are photosynthetic microorganisms that play important roles in polar lacustrine ecosystems. Many Cyanobacteria are difficult to grow in the laboratory, particularly in isolation from other organisms, which makes it challenging to sequence their genomes. As such, considerably fewer genomes of Cyanobacteria have been sequenced so far compared to other bacteria. In this study, we used a metagenomics approach to recover novel genomes of Cyanobacteria from Arctic and Antarctic microbial mats without the need to isolate the organisms. The community DNA was extracted and sequenced, and the genomes of individual populations were separated using bioinformatics tools. We recovered 22 different genomes of Cyanobacteria, many of which have not been sequenced before. We describe in more detail an interesting lineage of ancestral Cyanobacteria in the order Gloeobacterales, for which we propose the name Candidatus Sivonenia alaskensis. Our study shows that genome-resolved metagenomics is a valuable approach for obtaining novel genomes of Cyanobacteria, which are needed to improve our understanding of life in the polar regions and the planet at large.

microbiology↗