Biology subjects

Sudianto, E.

Publications and source records attributed to Sudianto, E..

6 recordsLinked to original sources

bioRxiv2026

An endolithic Gloeobacter and other novel cyanobacterial diversity in alpine dolomites of Piora Valley

Background: Cyanobacteria are the major phototrophs in many endolithic ecosystems, yet their genomic diversity and metabolic adaptations remain poorly characterized. Here, we investigated cyanobacterial diversity in endolithic dolomite rocks from the Piora Valley in the southern Swiss Alps using genome-resolved metagenomics. Results: We reconstructed 138 medium-quality metagenome-assembled genomes (MAGs) from four neighboring endolithic rock communities, including 15 cyanobacterial MAGs distributed across six order-level lineages. The cyanobacterial communities showed limited taxonomic overlap among rocks, and most recovered MAGs represented potentially novel species. Only one Gloeobacter lineage occurred in all sampled rocks, which we propose as Gloeobacter dolomitensis sp. nov., representing the first Gloeobacter genome recovered from an endolithic environment. Comparative genomic analyses identified a cynS gene encoding cyanase unique to G. dolomitensis among the Gloeobacter. Phylogenetic analyses support its horizontal acquisition from Pseudomonadota. Interestingly, the genome of G. dolomitensis lacks a canonical CynABD cyanate transporter and instead contains a distinct ATP-synthase binding cassette (ABC) transporter adjacent to cynS. Although the available genomic and structural evidence does not establish cyanate transport, its genomic association with cynS suggests a potentially non-canonical mechanism. We further show that horizontal gene transfer was unevenly distributed among cyanobacterial lineages, with Acaryochloridales acting predominantly as donors, Chroococcidiopsidales as recipients, and Gloeobacterales showing a comparatively high frequency of interphylum gene exchange. Conclusions: The Piora Valley dolomite environment represents an underexplored reservoir of cyanobacterial diversity, including basal and previously undescribed lineages. The discovery of G. dolomitensis and its unusual cyanate-associated genomic architecture expands our understanding of Gloeobacterales diversity and highlights the potential importance of horizontal gene acquisition and metabolic innovation in endolithic microbial communities.

evolutionary biology↗

bioRxiv2026

Taxonomic Description of Uncultured Cyanobacteria from Extreme Habitats through Genome-Based Classification

Cyanobacteria form a morphologically and phylogenetically diverse group of oxygenic phototrophic bacteria inhabiting a wide range of environments, including extreme habitats such as hot springs and volcanic steam vents. Many lineages, particularly those from these extreme environments, remain uncultured and are known only from metagenome-assembled genomes (MAGs), limiting their integration into formal taxonomy. Analysis of 46 steam vent associated samples from Hawai i using 16S rRNA amplicon sequencing revealed that cyanobacteria dominate these communities. Gloeobacter kilaueensis dominated pit-like environments with low-light conditions, while Leptolyngbyaceae and other families are more dominant in structured soil and wall communities. We further reconstructed 38 high-quality cyanobacterial MAGs and incorporated them into a phylogenomic analysis comprising 343 cyanobacterial genomes, followed by genome-based comparisons against 9,026 reference genomes. This revealed eight novel species and one novel genus spanning five orders: Chroococcidiopsidales, Leptolyngbyales, Nostocales, Oculatellales, and Oscillatoriales. Following SeqCode guidelines, we provide the first formal taxonomic descriptions of cyanobacterial MAGs and propose guidelines for integrating genome-based and cultivated material. These findings highlight Hawaiian steam vents as hotspots of previously uncharacterized cyanobacterial diversity and underscore the importance of genome-based nomenclature.

genomics↗

bioRxiv2025

Horizontal Gene Transfers Underpin Ribose Heterotrophy and Central Carbon Metabolism Remodeling in Gloeobacteraceae

Gloeobacterales has long been considered a "living fossil" cyanobacterial order, owing to its lack of thylakoid membranes and basal phylogenetic position. However, our study reveals that Gloeobacterales actively integrate horizontally transferred genes into their core metabolism. In Gloeobacteraceae--one of the two families within the order--these genes encode a complete ribose ATP synthase binding cassette (ABC) importer and downstream enzymes, enabling the heterotrophic uptake of external ribose and its assimilation into central carbon metabolism, along with photosynthesis, indicative of photomixotrophy. Beyond ribose utilization, their central carbon metabolism exhibits a mosaic architecture shaped by the integration of foreign genes into the Calvin-Benson-Bassham cycle, the pentose phosphate pathway, and the Embden-Meyerhof-Parnas pathway. Uniquely, these genes appear to have been acquired through multiple independent transfer events, as reflected by their dispersed genomic locations and diverse bacterial donors, including other cyanobacteria and Pseudomonadota. These findings contradict the long-standing view of Gloeobacterales as metabolically primitive relics. Instead, Gloeobacterales is likely a dynamic lineage that continues to adapt and evolve through metabolic innovation and the assimilation of foreign genes into its genomes.

evolutionary biology↗

bioRxiv2025

Early-Diverging SQR Enzyme in Antarctic Gloeobacterales Indicates Sulfide Tolerance in Thylakoid-Lacking Cyanobacteria

Oxygenic photosynthesis, which converts solar energy into carbohydrates via a linear electron transport chain and two photosystems (PSII and PSI), first appeared in cyanobacteria approximately 3.3 Ga and drove the Great Oxidation Event around 2.4 Ga. During this period, euxinic conditions--characterized by sulfidic, anoxic oceans--posed a metabolic challenge to cyanobacteria, as sulfide inhibits PSII, the reaction center responsible for water splitting. Here, we report the presence of an early-diverging form of the sulfide quinone reductase (SQR) enzyme in Antarctic representatives of Gloeobacterales, the earliest-branching cyanobacterial lineage lacking thylakoids. Phylogenetic analyses reveal that these SQR sequences are the earliest-diverging cyanobacterial SQR known to date, predating the multiple lateral gene transfer events previously observed in the phylum. Additional searches in metagenomic datasets indicate that such sequences are restricted to cold environments. Our findings unveil possible adaptive strategies of early cyanobacteria to cope with sulfidic stress and point to Antarctic lakes as preserved natural laboratories for investigating cyanobacterial diversification and the evolution of oxygenic photosynthesis under euxinic conditions. Impact StatementThe diversification of cyanobacteria during and after the Great Oxidation Event occurred in early Proterozoic oceans that were partially euxinic (anoxic and sulfidic) a condition generally considered incompatible with oxygenic photosynthesis due to photosystem II inhibition. The presence of a sulfide quinone reductase in an Antarctic early diverging cyanobacterium lacking thylakoids gives credit on an ancestral evolutionary stage where oxygenic and anoxygenic traits coexisted within cyanobacteria. The occurrence of these organisms in Antarctic lakes under euxinic conditions offers a natural laboratory for studying the physiology and adaptation of the first oxygenic photosynthetic organisms.

evolutionary biology↗

bioRxiv2018

Enlarged and highly repetitive plastome of Lagarostrobos and plastid phylogenomics of Podocarpaceae

Podocarpaceae is the largest family in cupressophytes (conifers II), but their plastid genomes (plastomes) are poorly studied, with plastome data currently existing for only four of the 19 Podocarpaceous genera. In this study, we assembled the plastomes from representatives of eight additional genera, including Afrocarpus, Dacrydium, Lagarostrobos, Lepidothamnus, Microstrobos, Phyllocladus, Prumnopitys, and Saxegothaea. We found that Lagarostrobos, a monotypic genus native to Tasmania, has the largest plastome among any cupressophytes studied to date (151,496 bp). Plastome enlargement in Lagarostrobos coincides with increased intergenic spacers, repeats, and duplicated genes. Among Podocarpaceae, Lagarostrobos has the most rearranged plastome, but its substitution rates are modest. Plastid phylogenomic analyses clarify the positions of previously conflicting Podocarpaceous genera. Tree topologies firmly support the division of Podocarpaceae into two sister clades: (1) the Prumnopityoid clade and (2) the clade containing Podocarpoid, Dacrydioid, Microstrobos, and Saxegothaea. The Phyllocladus is nested within the Podocarpaceae, thus familial status of the monotypic Phyllocladaceae is not supported.

evolutionary biology↗

bioRxiv2018

Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution

We present reference-quality genome assembly and annotation for the stout camphor tree (SCT; Cinnamomum kanehirae [Laurales, Lauraceae]), the first sequenced member of the Magnoliidae comprising four orders (Laurales, Magnoliales, Canellales, and Piperales) and over 9,000 species. Phylogenomic analysis of 13 representative seed plant genomes indicates that magnoliid and eudicot lineages share more recent common ancestry relative to monocots. Two whole genome duplication events were inferred within the magnoliid lineage, one before divergence of Laurales and Magnoliales and the other within the Lauraceae. Small scale segmental duplications and tandem duplications also contributed to innovation in the evolutionary history of Cinnamomum. For example, expansion of terpenoid synthase subfamilies within the Laurales spawned the diversity of Cinnamomum monoterpenes and sesquiterpenes.

genomics↗