Biology subjects

Gansemans, Y.

Publications and source records attributed to Gansemans, Y..

4 recordsLinked to original sources

bioRxiv2026

Salt-induced osmotic stress remodels osmoadaptive gene expression and physiology in the polyhydroxyalkanoate-accumulating thermophilic bacterium Caldimonas thermodepolymerans

Caldimonas thermodepolymerans is a thermophilic polyhydroxyalkanoate (PHA)-producing bacterium with strong potential for sustainable bioplastic production. Besides serving as intracellular carbon and energy storage compounds, PHAs are increasingly associated with bacterial stress resistance and cellular robustness. This study aimed to investigate the physiological and transcriptomic response of C. thermodepolymerans to osmotic stress induced by elevated NaCl concentrations. Growth analysis demonstrated tolerance up to a supplementation of 2% NaCl, while moderate salt concentrations enhanced PHA accumulation, reaching 65% cell dry weight at 1.5% NaCl supplementation. To better understand the bacterial response to osmotic stress, RNA sequencing was performed under sublethal salt stress conditions. Differential expression analysis revealed major changes in genes related to osmoprotection, trehalose metabolism and type VI secretion systems, whereas motility and chemotaxis genes were strongly repressed. Phenotypic assays confirmed increased biofilm formation and reduced swarming motility under salt-induced osmotic stress. Although canonical PHA biosynthesis genes were not significantly differentially expressed, increased polymer accumulation suggests other underlying mechanisms linked to osmoadaptation. Together, these findings demonstrate that osmotic stress induces metabolic, physiological and regulatory responses in C. thermodepolymerans, highlighting the importance of PHA in stress adaptation besides its industrial applicability.

microbiology↗

bioRxiv2025

On the edge of extinction: Delayed plant genetic response to forest edge dynamics

Understanding genetic responses to forest dynamics is essential for predicting the long-term viability of understory plant populations and for developing effective conservation strategies. This study investigates genetic extinction debt and colonization credit in Circaea lutetiana, a clonal forest understory species, across its European range. Using pooled genotype-by-sequencing data from 40 forest edge and core populations, we examined to what extent population size, latitude and historical changes in forest configuration predict genetic diversity. Our findings reveal that the historical forest configuration profoundly shapes present-day genetic diversity. Long-established forest edge populations exhibit significantly reduced allelic richness (-9%) compared to core populations, indicating the partial pay-off of a genetic extinction debt. In contrast, populations from recently established forest edges maintain comparable allelic richness to core populations, suggesting delayed population genetic responses to land use changes. Finally, populations established in areas that were afforested during the past 250 years exhibit lower genetic diversity than historical forest core populations, indicating a delay in genetic recovery and thus a potential genetic colonization credit. Our results highlight that C. lutetiana populations are not at equilibrium with the current forest configuration, underscoring the role of lagged genetic responses across very long time scales. Connectivity and population size further moderate genetic diversity, with smaller, isolated populations particularly vulnerable to genetic erosion. Given the limited research on delayed evolution in forest understory species, our results improve the understanding of extinction risk dynamics and underscore the need for history-informed restoration efforts.

ecology↗

bioRxiv2023

Non-random polymorphisms near transposable elements facilitate evolution across the genome of Arabidopsis thaliana

Evolution is a key characteristic of all life on earth, and is achieved mainly through mutation and recombination. To facilitate evolutionary rates in the absence of recombination, increased mutagenesis could provide essential opportunities for evolution. Here, we harness the genomes of 973 wild accessions of Arabidopsis thaliana, a self-fertilizing species characterized by reduced recombination rates, to study the role of transposable elements (TEs) as mutagenic drivers of non-random genetic variation. We found that multiple TE superfamilies accumulate large numbers of genetic variants in gene-rich regions of the genome. Moreover, TEs were enriched in genes underpinning key molecular processes, including fertilization and mRNA cis-splicing, suggesting that TEs generate genetic variation that is fundamental to organismal functioning and reproduction. An excess of common genetic variants (maf>0.4) flanking TEs, despite the extreme degree of self-fertilization, further corroborates the notion that TEs can generate substantial evolutionary potential in the absence of outcrossing. Nevertheless, while other studies point to TE mobilization as a strategy to facilitate adaptive evolution, we find that only a fraction (4.8%) of TE families was linked to genetic variants involved in climate adaptation to a significantly larger extent than background genomic variation, possibly because the high mutation rates near TEs dilute adaptive signals. Overall, all TE superfamilies but one (Gypsy) were significantly associated with evolutionary processes through their association with genes, functional molecular processes, flanking common variants and/or climate adaptation. We conclude that non-random mutations flanking TEs provide substantial evolutionary potential in a self-fertilizing species.

evolutionary biology↗

bioRxiv2020

Genome Report: De novo genome assembly and annotation for the Taita white-eye (Zosterops silvanus)

The Taita White-eye (Zosterops silvanus) is an endangered songbird endemic to the Taita Hills of Southern Kenya, where it is confined to small areas of fragmented forest. With diversification rates exceeding those reported in most other vertebrates, White-eyes are a prime example of a great speciator. Nevertheless, we still know surprisingly little about the genomic underpinnings leading to this extraordinary fast radiation. Here, we present a draft genome assembly (ZSil_MB_1.0) for the Taita White-eye generated from a blood sample of a wild, female bird captured in the Taita Hills, Kenya. By performing a de novo assembly with linked-reads and annotation of the assembly with the MAKER pipeline, we generated a 1.069 Gb assembly with a scaffold N50 of 1.105 Mb and an L50 of 244. After quality evaluation of the assembly, we identified 92.1% of BUSCOs complete or fragmented, indicating that our de novo assembly is of high quality. This new assembly provides a genomic resource for future studies into the evolutionary and comparative genomics of this rapidly diversifying group of birds.

genomics↗