Biology subjects

Bowler, C.

Publications and source records attributed to Bowler, C..

At least 19 recordsLinked to original sources

bioRxiv2026

A quick and efficient method enabling lncRNA functional studies in the marine diatom Phaeodactylum tricornutum using a multiplexed CRISPR-Cas9 editing approach

Background: Long non protein coding (lnc)RNAs are ubiquitous transcripts known to be major regulators of cellular processes in eukaryotes. In diatoms, specific lncRNA expression is tightly correlated to nutrient fluctuations, which suggests function, but their biological relevance remains to be established. In order to fill this knowledge gap, we sought to design a protocol to generate diatom lncRNA knockout mutants by CRISPR-Cas9 enabling subsequent functional studies to shed light into their mechanistic roles. Since lncRNAs do not contain open reading frames that can be targeted by point mutations for the generation of functional knockouts, we designed a multiplexed CRISPR-Cas9 plasmid harboring two independent gRNA for the specific ablation of lncRNA loci in P. tricornutum. As proof of concept, we used our plasmid-based system to target three phosphate depletion responsive lncRNAs. Results: Using the golden gate based uLoop system, we assembled a single plasmid containing all the necessary components to generate CRISPR-Cas9 large genomic ablations of lncRNAs in P. tricornutum using bacterial conjugation. Three intergenic lncRNAs (Linc91, Linc77 and Linc24) responsive to phosphate fluctuations were selected and independently targeted. Around 32% of the exconjugants presented a monoallelic ablation of the targeted loci and 11% presented a biallelic ablation on the first PCR-screening round. Mutated lines, harboring biallelic lncRNAs ablations for each lncRNA targeted, were successfully generated for each of the targeted lncRNAs. Additionally, a first line of phenotypic analysis revealed significant growth rate differences for one of the mutants ({Delta}Lnc24) under both full and phosphate depleted conditions, suggesting its involvement in cell division regulation under nutrient fluctuations. Conclusions: This work provides a simple and efficient method for the generation of lncRNA knock-out mutants in P. tricornutum. Furthermore, this approach can be easily adapted to other microalgae amenable to transformation, enabling the enhancement of our understanding of these important cellular regulatory transcripts in the marine environment.

molecular biology↗

bioRxiv2026

PLMView: collaborative protein language model representations for fast and scalable specialized protein function inference

The functional classification of protein sequences remains a major bottleneck in biology. Although protein language model (PLM)-based approaches have substantially improved broad protein function prediction, most protein sequences still lack precise annotation at the level of specialized functions--the fine-grained molecular roles that define specificity within protein families. We present PLMView, an unsupervised framework for fine-grained protein function classification directly from sequence. PLMView reframes protein function inference as a relational problem: instead of embedding sequences in isolation, it positions them within a collaborative functional space defined by comparisons with PLM embeddings of anchor sequences, thereby capturing subtle sequence-function relationships. Without requiring labeled data, family-specific training, or PLM fine-tuning, PLMView accurately distinguishes specialized functions among homologous proteins and highlights residues likely to determine functional specificity. The method achieves high precision while remaining computationally efficient, classifying approximately 10,000 sequences with 1,000 anchors in under 40 minutes; compared with pooled-embedding approaches and, in challenging cases, Sequence Similarity Networks, PLMView provides finer and more biologically coherent functional resolution, while achieving more than 10-fold speed-up over SSN reconstruction on datasets of this scale. Applications to thioredoxins, visual opsins, and Tara Oceans environmental diatom cold-shock proteins show that PLMView can move from interpretable residue-level determinants in well-studied protein families to large-scale environmental functional discovery, linking molecular specialization to ecological distribution and transcriptional deployment across the global ocean.

bioinformatics↗

bioRxiv2026

Characterisation of the new microalgal protein xATPA related to the F-type ATP synthase α subunit, from the ecosystem to the molecule

Microalgal metabolism relies on their chloroplasts, and involves both nucleus and plastidial-encoded proteins of various evolutionary origins. The plastidial ATP synthase complex is a key player in photosynthesis, and has been extensively studied in plants. However, our knowledge in other photosynthetic eukaryotes remains limited, despite their importance in marine environments. Here, we report the characterisation of a novel homologue of the F-type ATP synthase alpha subunit, hereby named xATPA, widespread in microalgae but absent from other photosynthetic organisms. Comparisons of xATPA sequences and predicted structures revealed a specific feature, the bump domain, and highlighted the absence of an ATP-binding site. We assessed xATPA prevalence in microalgae in the global ocean using environmental data from Tara Oceans, with a particular focus on diatoms, and demonstrate that its expression is associated with polar summer conditions. Using a reverse genetic approach in the model diatom Phaeodactylum tricornutum, we show that xATPAPt has a plastidial localisation, and that xATPA KO mutants exhibit growth deficiencies in a combination of low temperature, low salinity and constant light, consistent with environmental analysis. Surprisingly, both RNAseq and physiological assays suggest that xATPA is not involved in ATP synthase functions. On the other hand, xATPA interacts with other F1 ATP synthase subunits in vitro, which we suggest forms transient unassembled complexes. This study hence represents a comprehensive analysis of a novel protein from the environment to the lab, and reveals a new player in the plastidial physiology of eukaryotic microalgae.

plant biology↗

bioRxiv2026

The ultrasmall ocean microbiome: a reservoir of microbial diversity and nitrogen fixation.

Marine microbiology has long considered ultrasmall (<0.2 {micro}m) size fractions as virus-dominated, yet emerging evidence suggests potential prokaryotic activity with implications for global biogeochemical cycles. Here, we present the first comprehensive genome-resolved survey of this fraction, built on 4,058 metagenome-assembled genomes (MAGs) representing 1,152 species across Bacteria (90.7%) and Archaea (9.3%), dominated by Pseudomonadota, Bacteroidota, and Nanoarchaeota. Over 490 non-redundant MAGs occurred exclusively in the ultrasmall fraction, with 66.8% representing novel taxa, particularly abundant in Arctic surface waters. Beyond known ultrasmall organisms (e.g., DPANN archaea and Patescibacteria), which show expected genomic and metabolic reduction, functional annotation revealed diverse metabolic potential across nitrogen, sulfur, and carbon cycling. Focusing on nitrogen fixation, we identified 13 non-cyanobacterial diazotroph species with complete nitrogenase operons spanning four bacterial classes. These resolved into two ecotypes: cosmopolitan low-abundance taxa, and Arctic ultrasmall-restricted strains reaching up to 16.7% relative abundance. Two lineages (50-400-T64 and Novosphingobium) showed ultrasmall exclusive bipolar distributions across Arctic and Southern Oceans. Beyond nitrogen fixation, these diazotrophs encoded pathways for denitrification, DNRA, sulfur oxidation, and carbon fixation. Our findings reveal an overlooked reservoir of microbial diversity including diazotrophs in the ultrasmall ocean microbiome, with significant implications for polar nitrogen budgets and global biogeochemical models.

microbiology↗

bioRxiv2026

Diversity, host-specificity, and environmental drivers of the coral reef eukaryome

Coral reefs are among the most diverse ecosystems on Earth, yet the diversity and structure of their associated microeukaryotic communities remain poorly resolved. We characterized reef-associated eukaryomes across 113 reefs spanning the Pacific Ocean using more than 6,300 samples from corals, seawater, and sediments during the Tara Pacific expedition. We identified [~]121,000 eukaryotic ASVs, revealing one of Earths largest undocumented reservoirs of eukaryotic diversity; over 80% of the recovered diversity was previously undetected in global ocean surveys and fewer than 2% of sequences matched reference databases. Reef habitats supported highly distinct communities, with sediments and seawater harboring 20-40-fold higher richness than corals. Unexpectedly, coral-associated communities across 29 host lineages were consistently dominated by small metazoans, particularly demosponges and maxillopods, identifying these taxa as pervasive and previously unrecognized components of coral eukaryomes alongside Apicomplexa. Across the Pacific, eukaryome composition was strongly structured by environmental gradients, with thermal stress emerging as the primary driver of community turnover. Together, these results identify coral reefs as a globally important reservoir of hidden eukaryotic diversity and reveal the reef eukaryome as a sensitive indicator of ecosystem reorganization under climate change.

systems biology↗

bioRxiv2026

Paradoxical energetics in the polar diatom Fragilariopsis cylindrus exposed to extreme low light

In the Arctic Ocean, diatoms initiate blooms under sea ice at extreme low-light levels, yet the limits and mechanisms behind this capability remain unknown. We investigated the steady-state physiological and molecular responses of the polar diatom Fragilariopsis cylindrus across a light gradient (0.1 to 30 {micro}mol photons m-2 s-1), representative of under-ice winter to early spring conditions, and reveals distinct strategies to cope with low light at both ends of this range. While cells optimize photon capture efficiency between 3 and 15 {micro}mol photons m-2 s-1 relative to 30 {micro}mol photons m-2 s-1, this strategy collapses below 1 {micro}mol photons m-2 s-1. In this dim-light regime, cells activate non-photochemical quenching and a sustained xanthophyll cycle, which indicates a paradoxical requirement for energy dissipation despite extreme photon scarcity. While cell division arrests at 0.18 {micro}mol photons m-2 s-1, photosynthetic electron transport seems to remain possible down to 0.1 {micro}mol photons m-2 s-1, which suggests an uncoupling between photosynthesis and biomass accumulation. Crucially, this low-light regime occurs without the consumption of reserves and represents a physiological state distinct from metabolic hypometabolism in prolonged darkness. We propose that this dim-light physiological state arises when residual light absorption exceeds the energetic requirements for cellular maintenance in the absence of division. The result is a regulated imbalance dissipated through heat and carbon excretion. This mechanism allows polar diatoms to maintain a primed photosynthetic metabolism to facilitate rapid growth recovery upon the return of light after the winter solstice.

plant biology↗

bioRxiv2025

Genomics-based quantitative biogeography of marine plankton

Marine plankton are key drivers of ocean productivity and global carbon cycling, yet their quantitative biogeography remains poorly characterized. Environmental genomic datasets are inherently compositional, restricting analyses to relative abundances and limiting their integration into ecological and biogeochemical models. Here we combine DNA mass measurements, filtered seawater volumes, and metagenomic relative abundances to generate absolute estimates of cell concentrations and carbon biomass of plankton across the global ocean. Leveraging thousands of samples, this approach provides quantitative estimates for hundreds of eukaryotic and thousands of prokaryotic environmental genomes, unveiling ecological associations not captured by compositional data. Using the psbO marker gene, we reconstruct quantitative biogeographies of photosynthetic lineages and, through global-scale modeling, project their distributions to generate quantitative maps of phytoplankton communities across the worlds ocean. By bridging genomic data with biogeochemical metrics, this study provides novel resources for integrating plankton at genomic resolution into next-generation biogeochemical models.

genomics↗

bioRxiv2025

The roles of Transposable Elements and Gene Family Dynamics in Shaping Diversity and Evolution in Diatoms

Diatoms are key players in aquatic ecosystems, having evolved through secondary endosymbiosis. Using long-read sequencing, we investigated how transposable elements (TEs) and gene family dynamics have shaped diatom diversification from inter-lineage to intra-species scales. Across diatom lineages, we identified ecological adaptation-linked expansions, including polyamine synthesis genes for silicification and glutathione S-transferases for oxidative stress resistance. Centric diatoms showed lineage-specific expansion of flotation-associated microtubule genes, while pennate diatoms expanded motility-related actin and myosin genes. At the intra-species level, distinct Phaeodactylum tricornutum strains revealed genomic adaptations correlated with their unique features, including strain-specific expansion and contraction in the cruciform strains morphological genes and the Baltic Sea isolates amine metabolism genes. Our estimates of major lineage divergence times in diatoms ([~]202 Ma and [~]173 Ma) were highly consistent with the two deep WGD events ([~]200 Ma and [~]170 Ma). At these evolutionary nodes, gene families showed extensive lineage-specific expansions and contractions, likely linking ancient polyploidy to subsequent gene content evolution. Substantial TE expansions occurred more recently (0.5-5 Ma), with most diatoms showing recent bursts of Long Terminal Repeat Retrotransposons (LTR-RTs) and araphid pennate diatoms displaying more ancient TE insertion peaks. This likely reflects the progressive loss of ancient TE copies, leaving only recent TE insertions detectable. Our findings provide genomic evidence for the adaptive evolution of diatoms, highlighting the crucial roles of TEs and gene family dynamics in shaping their morphological diversity and environmental adaptations, and suggesting a potential connection between WGDs, gene family dynamics, and TE insertions in genome evolution.

genomics↗

bioRxiv2025

Tryptophanol, a novel auxin analog found in marine diatoms, enhances nitrogen assimilation

Diatoms exhibit superior competitive capacity in nitrogen assimilation, largely contributing to their growth, although the mechanisms underpinning their success have not been completely understood. Here, a non-ribosomal peptide synthase-like (PtNRPS1, with an unusual domain structure A-T-R1-R2) gene was found to play a vital role in short-term nitrogen assimilation in the marine diatom Phaeodactylum tricornutum. In vitro biochemical assays and in vivo overexpression confirmed that PtNRPS1 catalyzed two sequential two-electron reductions of L-tryptophan to tryptophanol. Tryptophanol exhibits high structural and functional similarities to indole-3-acetic acid (IAA), the most typical phytohormone auxin. Surprisingly, the effective concentration of tryptophanol was lower than that of IAA by as much as 2-5 orders of magnitude for P. tricornutum. Compared with the action of IAA, a distinct molecular mode for tryptophanol was revealed by transcriptomic analysis, resulting mainly in enhanced short-term nitrogen assimilation, which was also confirmed by the elevated nitrogen uptake rates determined by stable-isotope tracking. Finally, global distribution of PtNRPS1 homologues from stramenopiles was found to be positively correlated with the abundance of genes involved in nitrogen assimilation pathways. Overall, our study provides evidence of an auxin-like derivative synthesized by an NRPS in a diatom. We speculate that tryptophanol may accelerate nitrogen assimilation, conferring advantages in the competition for nitrogen in the ocean.

plant biology↗

bioRxiv2025

Entry and exit of Fragilariopsis cylindrus diatoms from the polar night: evidence for chromatin-mediated genome control

Regulation of the epigenome landscape plays a crucial role in adaptation to environmental changes. However, the molecular mechanisms by which epigenome landscapes are established and tuned to adjust the cellular status to environmental cues remain poorly understood, especially in unicellular photosynthetic eukaryotes. Polar microalgae must adapt to extreme variations in light and temperature for survival and therefore represent excellent models to understand the diversity of gene regulatory mechanisms, yet chromatin-based mechanisms have never been explored in these organisms. In this study, we combined genome-wide profiling of histone and DNA modifications with transcriptomic analyses of the marine polar diatom Fragilariopsis cylindrus upon entry and exit of a 3-month-long polar night. We show that, in agreement with its established role in transcription facilitation, histone H2B monobiquitination (H2Bub) is modulated at active genes upon prolonged darkness to light re-exposure. In contrast, histone H3 lysine 27 trimethylation (H3K27me3) and DNA cytosine methylation (CG methylation), two modifications typically associated with the silencing of genes or transposable elements (TEs), remained stable throughout the transitions, reinforcing their role in transcriptional repression, particularly at TEs but also at a few genes. We further demonstrate that H3K27me3 and DNA methylation are physically associated at TEs, probably reflecting a dual locking system enabling F.cylindrus cells to cope with the invasive nature of these genetic elements under extreme environmental conditions. These findings enhance our understanding of genome and epigenome regulation in diatoms in response to environmental variability and open new avenues for exploring the role played by chromatin-level regulation in the unique evolutionary history of polar unicellular eukaryotes.

genomics↗

bioRxiv2024

Dynamic relocalization and divergent expression of a major facilitator carrier subfamily in diatoms

Eukaryotic organisms, including microbial members such as protists and green algae, utilise suites of transporter proteins to move essential metabolites across cell organelle membranes. Amongst these different transporter families, the MCF (Mitochondrial Carrier Family) is one of the most diverse, encompassing essential NAD+ and ADP/ ATP translocators, as well as amino acid, sugar and cofactor transporters. They are typically associated with the mitochondrial inner membrane but some display more dynamic localization. Here, we perform a brief census of MCF domains in the genome of the model diatom alga Phaeodactylum tricornutum, identifying a new family of three proteins (termed here and elsewhere "MCFc") with strong internal sequence conservation but limited similarity to other MCF proteins. Considering both phylogenetic data and experimental localization, we posit that MCFc is widespread across algae with complex red chloroplasts alongside some primary green algae, and contains multiple sub-families targeted to diatom mitochondria, plastids, and endomembranes. Finally, using data from Tara Oceans, we identify putative roles for MCFc in diatom cells, including a probable association of the plastid-targeted Phatr3_J46742 sub-family in cellular nitrate assimilation. Our data provide insights into the evolutionary diversification of the membrane transport mechanisms associated with diatoms and other eukaryotic algae.

cell biology↗

bioRxiv2024

DiatOmicBase, a gene-centered platform to mine functional omics data across diatom genomes

Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology and biotechnology. Since the first genome sequencing in 2008, numerous genome-enabled datasets have been generated, based on RNA-Seq and proteomics, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and two other diatoms to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior-art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non-coding RNAs, and read densities from RNA-Seq experiments. We developed a semi-automatically updated transcriptomic module to explore both publicly available RNA-Seq experiments and users private datasets. Using gene-level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co-expression network analysis. Users can create heatmaps to visualize precomputed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community. Significance statementIn recent years, diatoms have become the subject of increasing interest because of their ecological importance and their biotechnological potential for natural products such as pigments and polyunsaturated fatty acids. Here, we present an interactive web-based server that integrates public diatom omics data (genomics, transcriptomics, epigenomics, proteomics, sequence variants) to connect individual diatom genes to broader-scale functional processes.

genomics↗

bioRxiv2024

Genome-resolved diversity and biosynthetic potential of the coral reef microbiome

Coral reefs are marine biodiversity hotspots that provide a wide range of ecosystem services. They are also reservoirs of bioactive compounds, many of which are produced by microbial symbionts associated with reef invertebrate hosts. However, for the keystone species of coral reefs--the reef-building corals themselves--we still lack a systematic assessment of their microbially encoded biosynthetic potential, and thus the molecular resources that may be at stake due to the alarming decline in reef biodiversity and cover. Here, we analysed microbial genomes reconstructed from 820 reef-building coral samples of three representative coral genera collected at 99 reefs across 32 islands during a two-year expedition throughout the Pacific Ocean (Tara Pacific). By contextualising our analyses with the microbiomes of other reef species, we found that genomic information was previously available for only 10% of the 4,224 microbial species overall and for less than 1% of the 645 species exclusively identified in Tara Pacific samples. We found reef-building coral microbiomes to be host-specific and their biosynthetic potential to rival or even surpass that found in traditional targets for natural product discovery, such as sponges and soft corals. Fire corals were not only particularly diverse in microbially encoded biosynthetic gene clusters (BGCs), but also in BGC-rich bacteria, including Acidobacteriota spp., which have been recently highlighted for their promising natural product repertoire. Together, this study unveils new candidate sources for bioactive compound discovery, prioritises targets for microbial isolation, and underscores the importance of conservation efforts by linking macro-organismal biodiversity loss to host-specific microbiomes and their biotechnological potential.

microbiology↗

bioRxiv2024

Patterns and drivers of diatom diversity and abundance in the global ocean

Diatoms constitute one of the most diverse and ecologically important phytoplankton groups, yet their large-scale diversity patterns and drivers of abundance are unclear due to limited observations. Here, we utilize Tara Oceans molecular and morphological data, spanning pole to pole, to describe marine diatom diversity, abundance, and environmental adaptation and acclimation strategies. The dominance of diatoms among phytoplankton in terms of relative abundance and diversity was confirmed, and the most prevalent genera were Chaetoceros, Thalassiosira, Actinocyclus and Pseudo-nitzschia. We defined 25 distinct diatom communities with varying environmental preferences illustrative of different life strategies. The Arctic Ocean stands out as a diatom hotspot with 6 of the diatom communities being exclusive to it. Light harvesting and photoprotection were among the cellular functions in which natural diatom populations invested the bulk of their transcriptional efforts. This comprehensive study sheds light on marine diatom distributions, offering insights to assess impacts of global change and oceanic anthropogenic impacts.

ecology↗

bioRxiv2024

QuartPlotR: A quarternary phase diagram tool

MotivationLarge scale studies involving exploratory data analysis and important key discoveries require platform that provides comprehensive visualization. Density distribution analysis across multiple datasets is intuitive and summarization, visualization could reveal several biological information. Integration and visualization of sequence and annotation features in the context of composition of genomic mutation, microbiota, population are significantly challenging. ResultsWe propose a simple, novel strategy of visualization of multidimensional datasets involving multiple layers of data distribution which are interconnected. Also, we have implemented this phase diagram in an easy-to-use tool QuartPlotR, a resource for plotting charts from different genomic datasets. A generic data access and plotting framework has been designed and this is implemented as an R package. Availabilityhttps://github.com/AlagurajVeluchamy/QuartPlotR. Contactalaguraj.veluchamy@stjude.org Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2024

Ubiquity of inverted 'gelatinous' ecosystem pyramids in the global ocean

Summary paragraphPlankton are essential in marine ecosystems. However, our knowledge of overall community structure is sparse due to inconsistent sampling across their very large organismal size range. Here we use diverse imaging methods to establish complete plankton inventories of organisms spanning five orders of magnitude in size. Plankton community size and trophic structure variation validate a long-held theoretical link between organism size-spectra and ecosystem trophic structures. We found that predator/grazer biomass and biovolume unexpectedly exceed that of primary producers at most (55%) locations, likely due to our better quantification of gelatinous organisms. Bottom- heavy ecosystems (the norm on land) appear to be rare in the ocean. Collectively, gelatinous organisms represent 30% of the total biovolume (8-9% of carbon) of marine plankton communities from tropical to polar ecosystems. Communities can be split into three extreme typologies: diatom/copepod-dominated in eutrophic blooms, rhizarian/chaetognath-dominated in oligotrophic tropical oceans, and gelatinous-dominated elsewhere. While plankton taxonomic composition changes with latitude, functional and trophic structures mostly depend on the amount of prey available for each trophic level. Given future projections of oligotrophication of marine ecosystems, our findings suggest that rhizarian and gelatinous organisms will increasingly dominate the apex position of planktonic ecosystems, leading to significant changes in the oceans carbon cycle.

ecology↗

bioRxiv2024

Environmentally-informed functional characterization of a plastid diatom metabolic bridge of mitochondrial origin

Withdrawal statementThe authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2022/507166. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: 10.1101/2022.09.08.507166

evolutionary biology↗

bioRxiv2023

Towards modeling genome-scale knowledge in the global ocean

Earth System Models (ESMs) highly simplify their representation of biological processes, leading to major uncertainty in climate change impacts. Despite a growing understanding of molecular networks from genomic data, describing how changing phytoplankton physiology affects the production of key metabolites remains elusive. Here we embed a genome-scale model within a state-of-the-art ESM to deliver an integrated understanding of how gradients of nutritional constraints modulate metabolic reactions and molecular physiology. Applied to the prevalent marine cyanobacteria Prochlorococcus, we find that glycogen and lipid storage can be understood as a consequence of acclimation to environmental gradients. Given the pressing need to assess how biological diversity influences biogeochemical functions, genome-enabled ESMs allow the quantification of the contribution of modeled organisms to the production of dissolved organic carbon and its molecular composition.

bioinformatics↗