Cyanobacteria on Luc Cornet

On the non-oxygenic origins of thylakoids

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet
Thylakoid membranes are the site of oxygenic photosynthesis, one of the most important biochemical processes on earth. The ancestral state of these membranes is represented today in Gloeobacterales, where they are lacking and photosynthesis instead takes place in the cytoplasmic membrane. The evolutionary transition from this ancestral state to the modern thylakoid membranes provided a major advantage, as it increased photosynthetic efficiency. However, how this significant transition occurred remains an understudied question. The biogenesis of modern thylakoid membranes relies on a highly synchronized process involving numerous assembly factors and showing important differences between the two photosystems. Together, these features suggest the existence of intermediate evolutionary states during the emergence of this compartment. Here, I propose a non-oxygenic origin of thylakoid membranes, where these intermediate states were initially dedicated to alternative electron flows. This hypothesis further addresses the paradox of cyanobacterial diversification in an euxinic environment, toxic to photosystem II.
https://www.nature.com/articles/s42003-025-09100-w

From Cytoplasmic Membrane to Thylakoids: Evolution of Membrane Biogenesis and Photosystem II assembly in early-diverging Cyanobacteria

Mon, 01 Jan 0001 00:00:00 +0000

Louise Hambücken, Denis Baurain, Luc Cornet
Thylakoid membranes (TM) in cyanobacteria and chloroplasts host the light-dependent reactions of oxygenic photosynthesis which involve a linear electron transfer (LET) chain composed of multi- subunit complexes, including notably Photosystem II (PSII). Gloeobacterales, the earliest-diverging cyanobacterial lineage, lack TM and perform photosynthesis within specialized regions of the cytoplasmic membrane (CM), thereby representing an ancestral state with respect to other cyanobacteria, all equipped with TM and known as Phycobacteria. The emergence of TM, which increased the membrane surface available for oxygenic photosynthesis, was a key innovation that likely contributed to the Great Oxidation Event. This evolutionary transition involved the formation of a distinct membrane compartment, followed by the relocation of LET components from the CM to TM. Here, we present a phylogenomic analysis identifying three candidate proteins associated with membrane trafficking that may contribute to TM biogenesis, including the SPFH family member Slr1106, which we show was acquired via lateral gene transfer. Moreover, evolutionary analysis of 36 PSII assembly factors indicates key modifications in late-stage PSII assembly, notably in manganese homeostasis, and highlights structural changes in the early-acting YidC translocase that may have facilitated the relocation of LET components from the CM to TM. Altogether, our phylogenetic and functional prediction analyses of proteins involved in membrane dynamics and PSII assembly factors bring new insights into the molecular innovations that led to the emergence of TM.
https://doi.org/10.1101/2025.11.06.686923

A FAIR Amplicon Sequencing Workflow for Long-term Environmental Monitoring

Mon, 01 Jan 0001 00:00:00 +0000

Marie Harmel, Benoit Durieu, Valentina Savaglia, Bjorn Tytgat, Denis Baurain, Annick Wilmotte, Elie Verleyen, Luc Cornet
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 Sør 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.
https://doi.org/10.64898/2025.12.04.692289

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

Mon, 01 Jan 0001 00:00:00 +0000

Louise Hambücken, Edi Sudianto, Jimmy H. Saw, Denis Baurain, Luc Cornet
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.
https://doi.org/10.1101/2025.10.24.684318

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

Mon, 01 Jan 0001 00:00:00 +0000

Edi Sudianto, Denis Baurain, Luc Cornet
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.
https://doi.org/10.1101/2025.11.10.686926

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

Mon, 01 Jan 0001 00:00:00 +0000

Edi Sudianto, Maximillian D. Shlafstein, Benoit Durieu, Marie Harmel, Luc Cornet, Jimmy H. Saw 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.
https://doi.org/10.64898/2026.01.02.697360

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

Mon, 01 Jan 0001 00:00:00 +0000

Benoit Durieu, Valentina Savaglia, Mick Van Vlierberghe, Valérian Lupo, Denis Baurain, Annick Wilmotte, Luc Cornet
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.
https://doi.org/10.64898/2025.12.17.694815

ORPER: A Workflow for Constrained SSU rRNA Phylogenies

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Anne-Catherine Ahn, Annick Wilmotte, and Denis Baurain
he continuous increase in sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects ever more complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow “ORPER”, for “ORganism PlacER”, containerized in Singularity, which allows the determination the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.

Cyanobacteria evolution: Insight from the fossil record

Mon, 01 Jan 0001 00:00:00 +0000

Catherine F. Demoulin, Yannick J. Lara, Luc Cornet, Camille François, Denis Baurain, Annick Wilmotte, Emmanuelle J. Javaux
Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis.
https://doi.org/10.1016/j.freeradbiomed.2019.05.007

A constrained SSU-rRNA phylogeny reveals the unsequenced diversity of photosynthetic Cyanobacteria (Oxyphotobacteria)

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Annick Wilmotte, Emmanuelle J. Javaux and Denis Baurain
Cyanobacteria are an ancient phylum of prokaryotes that contain the class Oxyphotobacteria. This group has been extensively studied by phylogenomics notably because it is widely accepted that Cyanobacteria were responsible for the spread of photosynthesis to the eukaryotic domain. The aim of this study was to evaluate the fraction of the oxyphotobacterial diversity for which sequenced genomes are available for genomic studies. For this, we built a phylogenomic-constrained SSU rRNA (16S) tree to pinpoint unexploited clusters of Oxyphotobacteria that should be targeted for future genome sequencing, so as to improve our understanding of Oxyphotobacteria evolution.
https://link.springer.com/article/10.1186/s13104-018-3543-y

Consensus assessment of the contamination level of publicly available cyanobacterial genomes

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Loïc Meunier, Mick Van Vlierberghe, Raphaël R. Léonard, Benoit Durieu, Yannick Lara, Agnieszka Misztak, Damien Sirjacobs, Emmanuelle J. Javaux, Hervé Philippe, Annick Wilmotte, Denis Baurain
Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.
https://doi.org/10.1371/journal.pone.0200323

Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica)

Mon, 01 Jan 0001 00:00:00 +0000

Yannick Lara, Benoit Durieu, Luc Cornet, Olivier Verlaine, Rosmarie Rippka, Igor S. Pessi, Agnieszka Misztak, Bernard Joris, Emmanuelle J. Javaux, Denis Baurain, Annick Wilmotte
Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacterium. Its draft genome is 5,684,389 bp long. It contains a total of 5,604 protein-encoding genes, of which 22.2% have no clear homologues in known genomes. To date, this draft genome is the first one ever determined for an axenic cyanobacterium from Antarctica.
https://doi.org/10.1128/genomea.01546-16

Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures

Mon, 01 Jan 0001 00:00:00 +0000

Luc Cornet, Amandine R. Bertrand, Marc Hanikenne, Emmanuelle J. Javaux, Annick Wilmotte and Denis Baurain
Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.
https://doi.org/10.1099/mgen.0.000212