Biology subjects

D'hondt, S.

Publications and source records attributed to D'hondt, S..

8 recordsLinked to original sources

bioRxiv2026

Seasonal restructuring of heterotrophic microbial communities is differentially affected by glacier type in Greenland fjords

Accelerated retreat of the Greenland Ice Sheets is increasing freshwater discharge to coastal fjords and promoting transitions from marine-terminating glacier (MTG) regimes to land-terminating (LTG) ones. These changes strongly affect the physical and chemical features of the water column, which in turn impact the structure and functioning of fjord ecosystems. We used high-throughput imaging and DNA metabarcoding approaches to investigate seasonal (spring vs summer) differences in the structure of pelagic microbial communities in two contrasting fjord systems (MTG vs LTG) in southwest Greenland, with focus on the bacterial and heterotrophic protist components, which to date remain understudied in Greenland fjords. Our analyses revealed a marked seasonal restructuring in the microbial communities, especially in the surface layers. In spring, heterotrophic community composition in both fjords manifested a strong link with the diatom spring bloom, being dominated by typical phytoplankton-associated and copiotroph bacterial groups that can utilize algal-derived organic matter, and protists grazing on phytoplankton. In summer, heterotroph communities strongly diverged between the two fjords, most likely caused by the differential impact of MTG vs LTG glaciers on water column structure and chemistry. There was a marked increase in pico- and nano-sized heterotrophs, parasitic protists (dinoflagellate Syndiniales), and bacterial groups indicative of low-nutrient environments. In addition, bacterial, phytoplankton and heterotrophic protist communities become more strongly coupled, either through stronger interactions and/or stronger environmental filtering acting on all groups simultaneously. These observations are indicative of a shift from resource-replete systems in spring to more resourced-depleted systems in summer. However, this shift was less pronounced in the MTG fjord, where subglacial upwelling enabled the persistence of diatom bloom related communities into summer. Finally, we uncovered the presence of a unique, ice melange associated inner fjord microbial community, which shows similarities with both supraglacial and sea-ice associated communities, in the inner part of the MTG impacted fjord.

microbiology↗

bioRxiv2025

Rare sex but a long life sustain seaweed populations at the warm edge of their range

AimThe life cycle of many organisms is all but stable across their distribution range. Most commonly, populations respond to environmental variation by shifting the timing of reproductive events (phenology). Or more profoundly, populations may (partly) shift their mode of reproduction from sexual to asexual. Life cycle variation can impact reproductive success, gene flow, genetic diversity, and, ultimately, the evolutionary trajectory of populations. Understanding the factors that influence life cycle variation is essential for grasping the biology and ecological roles of species. This study investigates the variation in life cycles and its effects on the genetic diversity of a brown seaweed, Dictyota, across its European range. LocationNorth-East Atlantic Ocean and the Mediterranean Sea. TaxonDictyota dichotoma (Hudson) J.V. Lamouroux (Phaeophyceae, Dictyotales) MethodsWe monitored phenology, fertility and lifespan in Atlantic and Mediterranean populations at its northern and southern boundaries, and used microsatellite markers to assess how these factors influence genetic and genotypic diversity. ResultsWe observed significant differences in phenology, reproductive strategies, and genetic diversity among northern and southern European populations. In Mediterranean populations, D. dichotoma exhibited sporophytic dominance with gametophytes being extremely rare, suggesting a shift towards asexual reproduction. In contrast, North-East Atlantic populations displayed more pronounced seasonal reproductive patterns with higher frequencies of gametophytes, indicating predominant sexual reproduction. However, genetic analysis showed lower allelic richness and unique alleles in northern populations, whereas southern populations were genetically more diverse, reflecting historical biogeographic processes. Clonal reproduction was more pronounced in the Mediterranean populations, influencing the spatial genetic substructure and contributing to lower genotypic diversity compared to Atlantic populations. Main conclusionsOur findings demonstrate that life cycle variation and phenology in D. dichotoma are closely tied to regional environmental conditions and have significant implications for population structure and genetic diversity. Results highlight how shifts in reproductive strategies contribute to the evolutionary and ecological dynamics of marine macroalgae across biogeographical gradients.

ecology↗

bioRxiv2024

Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Genome merging is a common phenomenon in many organisms, causing a wide range of consequences on phenotype, adaptation, and gene expression, among other effects, yet its broader implications are not well understood. Two consequences of genome merging on gene expression remain poorly understood: dosage effects and evolution of expression. In this study, we employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection (LNS) experiment. Utilizing fitness assays, qPCR, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution over time. Our findings reveal substantial alterations in gene expression, protein homeostasis (proteostasis) and cytonuclear stoichiometry. Notably, gene expression exhibited expression level dominance and transgressivity (i.e., expression level higher or lower than either parent). Ongoing expression level dominance and a pattern of "functional dominance" from the haploid parent was observed, alongside remarkable stability in expression patterns across generations. Despite major nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.

evolutionary biology↗

bioRxiv2024

Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

Third-generation sequencing platforms, such as Oxford Nanopore Technology (ONT), have made it possible to characterise communities through the sequencing of long amplicons. Whilst this theoretically allows for an increased taxonomic resolution compared to short-read sequencing platforms such as Illumina, the high error rate remains problematic to accurately identify the community members present within a sample. Here we present and validate CONCOMPRA, a tool that allows the detection of closely related strains within a community by drafting and mapping to consensus sequences. We show that CONCOMPRA outperforms several other tools for profiling bacterial communities using full-length 16S rRNA gene sequencing. Since CONCOMPRA does not rely on a sequence database for profiling communities, it is applicable to systems and amplicons for which a reference framework is poorly developed. Our validation test shows that the amplification of long PCR products is likely to produce chimeric byproducts that inflate alpha diversity and skew community structure, stressing the importance of chimera detection. CONCOMPRA is available on GitHub (https://github.com/willem-stock/CONCOMPRA). Key points- We introduce a reference free tool for (long) amplicon Oxford Nanopore sequencing data - We show that it is capable of outperforming achieving a higher accuracy than preexisting tools - Chimera detection and removal is an essential step in the processing of long amplicon Oxford Nanopore sequencing data

bioinformatics↗

bioRxiv2024

Functional stability despite high taxonomic turnover characterizes the Ulva microbiome across a 2,000 km salinity gradient

The green seaweed Ulva depends on its associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. Yet little is known about the variation in the functional profile of Ulva-associated bacteria in relation to environmental changes. To test which microbial functions shift alongside a strong environmental gradient, we analysed microbial communities of 91 Ulva samples across a 2,000 km Atlantic-Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, sulphur, nitrogen, and vitamin metabolism, including amino acid and vitamin B biosynthesis. While salinity explained 70% of taxonomic variation, it only accounted for 17% of functional variation, indicating extensive functional stability. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis. These metabolic modules likely contribute to oxidative stress mitigation, cellular osmotic homeostasis, and membrane stabilization in response to salinity variations. Our results emphasise the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change.

microbiology↗

bioRxiv2024

Molecular fingerprints of cell size sensing and mating type differentiation in pennate diatoms

O_LIA unique cell size sensing mechanism is at the heart of the life cycle of diatoms. During population growth, cell size decreases until a Sexual Size Threshold (SST) is reached, below which cells become sexually competent. In most pennate diatoms, the two mating types undergo biochemical and behavioral differentiation below the SST, although the molecular pathways underlying their size-dependent maturation remain unknown. C_LIO_LIHere, we developed a method to shorten the generation time of Cylindrotheca closterium through single-cell microsurgery, enabling the transcriptomic comparison of genetically identical large and undifferentiated cells with small, sexually competent cells for six different genotypes. C_LIO_LIWe identified 21 genes upregulated in small cells regardless of their mating type, revealing how cells undergo specific transcriptional reprogramming when passing the SST. Furthermore, we revealed a size-regulated gene cluster with three mating type-specific genes susceptible to sex-inducing pheromones. In addition, comparative transcriptomics confirmed the shared mating type specificity of Mating-type Related Minus 2 homologs in three pennate diatoms, suggesting them to be part of a conserved partner-recognition mechanism. C_LIO_LIThis study sheds light on how diatoms acquire sexual competence in a strictly size-dependent manner, revealing a complex machinery underlying size-dependent maturation, mating behavior, and heterothally in pennate diatoms. C_LI

plant biology↗

bioRxiv2020

Diurnal transcript profiling of the diatom Seminavisrobusta reveals adaptations to a benthic lifestyle

1Coastal regions contribute an estimated 20% of annual gross primary production in the oceans, despite occupying only 0.03% of their surface area. Diatoms frequently dominate coastal sediments, where they experience large variations in light regime resulting from the interplay of diurnal and tidal cycles. Here, we report on an extensive diurnal transcript profiling experiment of the motile benthic diatom Seminavis robusta. Nearly 90% (23,328) of expressed protein-coding genes and 66.9% (1124) of expressed long intergenic non-coding RNAs (lincRNAs) showed significant expression oscillations and are predominantly phasing at night with a periodicity of 24h. Phylostratigraphic analysis found that rhythmic genes are enriched in deeply conserved genes, while diatom-specific genes are predominantly associated with midnight expression. Integration of genetic and physiological cell cycle markers with silica depletion data revealed potential new silica cell wall associated gene families specific to diatoms. Additionally, we observed 1752 genes with a remarkable semidiurnal (12-h) periodicity, while the expansion of putative circadian transcription factors may reflect adaptations to cope with highly unpredictable external conditions. Taken together, our results provide new insights into the adaptations of diatoms to the benthic environment and serve as a valuable resource for diurnal regulation in photosynthetic eukaryotes. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

systems biology↗

bioRxiv2019

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focusses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations, with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that the unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified following recolonization of benthic environments that became increasingly available as sea ice retreated. An increased supply of nutrients and biotic interactions such as grazing pressure has likely triggered the independent evolution of macroscopic growth via different strategies, including both true multicellularity, and multiple types of giant celled forms.\n\nSignificance StatementGreen seaweeds are important primary producers along coastlines worldwide, and likely played a key role in the evolution of animals. To understand their origin and diversification, we resolve key relationships among extant green algae using a phylotranscriptomic approach. We calibrate our tree using available fossil data, to reconstruct important evolutionary events such as transitions to benthic environments, and evolution of macroscopic growth. We estimate green seaweeds to have originated in the late Tonian/Cryogenian Period, followed by a marked Ordovician diversification of macroscopic forms. This ancient proliferation of green seaweeds likely modified shallow marine ecosystems, which set off an evolutionary arms race between ever larger seaweeds and grazers.

evolutionary biology↗