Biology subjects

van Sluijs, L.

Publications and source records attributed to van Sluijs, L..

7 recordsLinked to original sources

bioRxiv2026

Exploring nematode diversity in soils: comparison of extraction methods and sequencing protocols

Soil nematodes play key roles in regulating organic matter decomposition, nutrient cycling and trophic interactions in the soil ecosystem, and are very useful bioindicators of soil condition and soil health. But to characterise them, we need reliable measurements of nematode biodiversity in soils. DNA-based techniques such as metabarcoding have recently explored their biodiversity, with successful results. However, there are many methodological steps that can modify the outcome considerably and require informed decisions. In this study, we tested the effect on nematode alpha and beta diversity metrics of three methodological steps, namely i) type of extraction of genetic material from the matrix, either from soil directly with different starting amount of material or extracting nematodes first via the Baermann or Oostenbrink methods, ii) the choice of taxonomically-relevant DNA segment for amplification, with a nematode specific primer (NemF/18Sr2b) and a universal eukaryotic primer (3NDf/1132rmod), both within 18S rDNA, and iii) the selection of appropriate reference library for taxonomic assignment (comparing three nematode specialised databases and three broad taxonomic databases). Observed differences in alpha diversity were more pronounced when comparing the nematode extraction vs soil extractions. In particular, direct soil extractions co-extracted many non-nematode taxa, especially if amplified with a universal primer, which can significantly reduce the number of nematode reads obtained and therefore the accuracy of nematode community indexes and other nematode-based metrics. The choice of the reference database strongly affected the taxonomic identification, which calls for extreme caution when making this selection. Notably, specialised databases tended to over assign reads to nematodes that were detected as non-nematodes by broad taxonomic databases. However, beta diversity metrics were consistent across methods, highlighting these metrics as robust against methodological choices. Our study clearly demonstrates that the choices of methods for nematode biodiversity studies using molecular tools can have a big impact on the results, and decisions should be made consciously and carefully.

ecology↗

bioRxiv2025

Natural variation suggests candidate genes underlying Caenorhabditis elegans susceptibility to diverse toxicants

Genetic differences among individuals shape how they respond to environmental toxicants, but the identification and validation of the genes responsible for this variation is difficult, particularly in humans. Consequently, our limited knowledge of the genes that influence susceptibility constrains our ability to accurately predict the risks posed by environmental toxicants. To identify genes underlying natural differences in toxicant susceptibilities, we measured the effects of 23 environmental toxicants on larval development across 195 genetically diverse Caenorhabditis elegans strains using a high-throughput imaging platform. We then combined these response data with whole-genome sequences to perform genome-wide association mappings, identifying 40 genomic regions where genetic variants are correlated with susceptibility differences. Many of these regions are enriched for genes involved in biological processes previously linked with toxicant responses, supporting the potential contributions of these genes to natural variation in susceptibility. Using a set of heuristics, we identified 94 candidate susceptibility genes, offering targets for experimental validation that could ultimately inform toxicant risk prediction and regulatory assessment by linking genetic variation to differences in susceptibility. Impact StatementAnalysis of natural genetic variation among 195 wild C. elegans strains identified 94 candidate genes putatively linked to differences in susceptibility to 23 environmental toxicants. These findings can inform the discovery of conserved susceptibility genes and the development of biomarkers that improve chemical risk assessment by accounting for genetic differences among humans.

pharmacology and toxicology↗

bioRxiv2024

Nematodes Vector Bacteriophages in Compost and Soil

Bacteriophages (phages) infect bacteria to reproduce and are often lethal to their host. To maintain the infection cycle, soil phages must travel from one suitable host to the next. However, traversing the soil matrix presents a dangerous journey for phages, which need to encounter the right hosts in this spatially complex habitat, but are not capable of active motion and can adsorb to soil particles. Here, we tested the hypothesis that bacterial-feeding nematodes (roundworms) present a reliable vehicle of soil transport for phages. First, we demonstrated that the bacterivorous nematode Caenorhabditis elegans vectored the laboratory model phage T7 as well as the soil phage {Phi} Ppu-W11 on agar. Sorption assays carried out with paralyzed and non-paralyzed nematodes showed that phage transport can occur via both external cuticular attachment and ingestion, and that the presence of host bacteria is not required for phage vectoring. Finally, we designed a microcosm to test phage transfer in compost and sandy soil using C. elegans and its sister species, C. remanei, respectively. This experiment confirmed that nematodes also enable phage movement through complex spatial habitats. This novel mechanism of phage vectoring extends our understanding of virus transmission in soil, revealing new multitrophic interactions that may influence soil functioning.

ecology↗

bioRxiv2023

Disease-decreasing diversity: evidence for lowered parasite prevalence in microscopic nematode communities with higher species numbers

Biodiversity can affect parasite prevalence, a phenomenon widely studied in macroscopic organisms. However, data from microscopic communities is lacking, despite their essential role in ecosystem functioning and the unique experimental opportunities microscopic organisms offer. Here, we study diversity-disease effects in wild nematode communities by profiting from the molecular tools available in the well-studied model nematode Caenorhabditis elegans. Nanopore sequencing was used to characterize nematode community diversity and composition, whereas parasites were identified using nine distinct experimental assays based on fluorescent staining or fluorescent reporter strains. Our results indicate biotic stress is abundant in wild nematode communities. Moreover, in two assays, diversity-disease relations were observed: microsporidia and immune system activation were more often detected in relatively species-poor communities. Other assays, targeting different parasites, were without diversity-disease relations. Together, this study provides the first demonstration of diversity-disease effects in microbial communities and establishes the use of nematode communities as model systems for disease dilution.

ecology↗

bioRxiv2023

eQTL mapping in transgenic alpha-synuclein carrying Caenorhabditis elegans recombinant inbred line

Protein aggregation of -synuclein (S) is a genetic and neuropathological hallmark of Parkinsons disease (PD). Studies in the model nematode Caenorhabditis elegans suggested that variation of S aggregation depends on the genetic background. However, which genes and genetic modifiers underlie individual differences in S pathology remains unknown. To study the genotypic-phenotypic relationship of S aggregation, we constructed a Recombinant Inbred Line (RIL) panel derived from a cross between genetically divergent strains C. elegans NL5901 and SCH4856, both harboring the human S gene. As a first step to discover genetic modifiers 70 S-RILs were measured for whole-genome gene expression and expression quantitative locus analysis (eQTL) were mapped. We detected multiple eQTL hot-spots, many of which were located on Chromosome V. To confirm a causal locus, we developed Introgression Lines (ILs) that contain SCH4856 introgressions on Chromosome V in an NL5901 background. We detected 74 genes with an interactive effect between S and the genetic background, including the human p38 MAPK homologue pmk-1 that has previously been associated with PD. Together, we present a unique S-RIL panel for defining effects of natural genetic variation on S pathology, which contributes to finding genetic modifiers of PD.

genomics↗

bioRxiv2020

Punctuated loci on chromosome IV determine natural variation in Orsay virus susceptibility of Caenorhabditis elegans strains Bristol N2 and Hawaiian CB4856

Host-pathogen interactions play a major role in evolutionary selection and shape natural genetic variation. The genetically distinct Caenorhabditis elegans strains, Bristol N2 and Hawaiian CB4856, are differentially susceptible to the Orsay virus (OrV). Here we report the dissection of the genetic architecture of susceptibility to OrV infection. We compare OrV infection in the relatively resistant wild-type CB4856 strain to the more susceptible canonical N2 strain. To gain insight into the genetic architecture of viral susceptibility, 52 fully sequenced recombinant inbred lines (CB4856 x N2 RILs) were exposed to OrV. This led to the identification of two loci on chromosome IV associated with OrV resistance. To verify the two loci and gain additional insight into the genetic architecture controlling virus infection, introgression lines (ILs) that together cover chromosome IV, were exposed to OrV. Of the 27 ILs used, 17 had an CB4856 introgression in an N2 background and 10 had an N2 introgression in a CB4856 background. Infection of the ILs confirmed and fine-mapped the locus underlying variation in OrV susceptibility and we found that a single nucleotide polymorphism in cul-6 contributes to the difference in OrV susceptibility between N2 and CB4856. An allele swap experiment showed the strain CB4856 became more susceptible by having an N2 cul-6 allele, although having the CB4856 cul-6 allele did not increase resistance in N2. Additionally, we found that multiple strains with non-overlapping introgressions showed a distinct infection phenotype from the parental strain, indicating that there are punctuated locations on chromosome IV determining OrV susceptibility. Thus, our findings reveal the genetic complexity of OrV susceptibility in C. elegans and suggest that viral susceptibility is governed by multiple genes.

genetics↗

bioRxiv2019

Balancing selection shapes the Intracellular Pathogen Response in natural Caenorhabditis elegans populations

Genetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation in the Intracellular Pathogen Response (IPR), an important antiviral pathway in the model organism Caenorhabditis elegans against Orsay virus (OrV). The IPR involves transcriptional activity of 80 genes including the pals-genes. We examine the genetic variation in the pals-family for traces of selection and explore the molecular and phenotypic effects of having distinct pals-gene alleles. Genetic analysis of 330 global C. elegans strains reveals that genetic diversity within the IPR-related pals-genes can be categorized in a few haplotypes worldwide. Importantly, two key IPR regulators, pals-22 and pals-25, are in a genomic region carrying signatures of balancing selection, suggesting that different evolutionary strategies exist in IPR regulation. We infected eleven C. elegans strains that represent three distinct pals-22 pals-25 haplotypes with Orsay virus to determine their susceptibility. For two of these strains, N2 and CB4856, the transcriptional response to infection was also measured. The results indicate that pals-22 pals-25 haplotype shapes the defense against OrV and host genetic variation can result in constitutive activation of IPR genes. Our work presents evidence for balancing genetic selection of immunity genes in C. elegans and provides a novel perspective on the functional diversity that can develop within a main antiviral response in natural host populations.

genetics↗