Biology subjects

Sabbe, K.

Publications and source records attributed to Sabbe, K..

6 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↗

bioRxiv2026

Unveiling protist composition and diversity patterns with eDNA metabarcoding: comparing short- and long-read approaches

Environmental DNA (eDNA) metabarcoding is a key tool in biodiversity monitoring due to its high-throughput, non-destructive nature. While short-read (SR) sequencing platforms such as Illumina Miseq have been routinely used in environmental monitoring, their limited read lengths (less than 600 bp) constrain the depth of taxonomic assignment, particularly for complex microbial eukaryotes like protists. Conversely, long-read (LR) sequencing technologies like Oxford Nanopore Technologies (ONT) offer promising alternatives but remain underutilized for studying protist communities. We conducted a comparative study of SR versus LR metabarcoding of protist communities along a coastal-offshore gradient in the Belgian part of the North Sea. Using amplicons targeting the V4 region (SR; 577 bp) and the V4-V5 region (LR; 745 bp) of the 18S rRNA gene, we compared diversity patterns, taxonomic assignment, and community composition between approaches. We observed general congruence in community composition at higher taxonomic levels, but under the applied workflows, LR metabarcoding yielded a greater depth of taxonomic annotation at lower taxonomic ranks. Notably, dinoflagellates were less overrepresented in LR data, and a unique detection of potential nuisance taxa (e.g., Bellerochea), and ecologically important genera such as haptophytes (e.g., Gephyrocapsa) was achieved. These results highlight the potential of LR metabarcoding to complement SR approaches by providing increased taxonomic annotation depth and ecological insights. Although both methods targeted only partial regions of the 18S rRNA gene, LR metabarcoding yielded a greater depth of taxonomic assignment under the applied workflows. As next-generation sequencing technologies continue to evolve, our research provides valuable insights for selecting optimal strategies in routine plankton monitoring and biodiversity assessment programs.

ecology↗

bioRxiv2022

Identification of microbial exopolymer producers in sandy and muddy intertidal sediments by compound-specific isotope analysis

Extracellular polymeric substances (EPS) refer to a wide variety of high molecular weight molecules secreted outside the cell membrane by biofilm microorganisms. In the present study, EPS from marine microphytobenthic biofilms were extracted and their isotope ratios were analysed. A comparison of these ratios with the carbon isotope ratios of fatty acid biomarkers allowed the identification of the main EPS producers of two contrasting types of intertidal marine sediments. Our study reveals that EPS sources are more diverse in sandy sediments than in muddy sediments. We also found distinct patterns in the production and breakdown of EPS in sandy and muddy environments. The main difference observed was in how epipelic and epipsammic diatoms affected the chemistry of EPS, which had significant implications for the growth of bacteria specialized in utilizing EPS. These differences were likely linked to variations in the functioning of epipelic and epipsammic communities, specifically in how EPS was used either for motility or for cell attachment.

ecology↗

bioRxiv2020

Mitotic interhomolog recombination drives genomic diversity in diatoms

Diatoms, an evolutionarily successful group of microalgae, display high levels of intraspecific variability in natural populations. However, the process generating such diversity is unknown. Here we estimated the variability within a natural diatom population and subsequently mapped the genomic changes arising within cultures clonally propagated from single diatom cells. We demonstrate that genome rearrangements and mitotic recombination between homologous chromosomes underlie clonal variability, resulting in haplotype diversity accompanied by the appearance of novel protein variants and loss of heterozygosity resulting in the fixation of alleles. The frequency of interhomolog mitotic recombination exceeds 4 out of 100 cell divisions and increases under environmental stress. We propose that this plastic response in the interhomolog mitotic recombination rate increases the evolutionary potential of diatoms, contributing to their ecological success. One Sentence SummaryRecombination between homologous chromosomes in diatom vegetative cells leads to extensive genomic diversity in clonal populations.

genomics↗

bioRxiv2020

Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta

Sexual reproduction is a fundamental phase in the life cycle of most diatoms. Despite its role as a source of genetic variation, it is rarely reported in nature and its molecular foundations remain largely unknown. Here, we integrate independent transcriptomic datasets, in order to prioritize genes responding to sex inducing pheromones (SIPs) in the pennate diatom Seminavis robusta. We observe marked gene expression changes associated with SIP treatment in both mating types, including an inhibition of S-phase progression, chloroplast division, mitosis and cell wall formation. Meanwhile, meiotic genes are upregulated in response to SIP, including a sexually induced diatom specific cyclin (dsCyc). Our data further suggest an important role for reactive oxygen species, energy metabolism and cGMP signaling during the early stages of sexual reproduction. In addition, we identify several genes with a mating type specific response to SIP, and link their expression pattern with physiological responses such as the production of the attraction pheromone diproline and mate-searching behaviour in MT+. Combined, our results provide a model for early sexual reproduction in pennate diatoms and significantly expand the suite of target genes to detect sexual reproduction events in natural diatom populations.

molecular biology↗

bioRxiv2020

The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms

Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer new insights on the genetic diversity and gene functions in benthic diatoms.

bioinformatics↗