Arthropod pests cause significant problems in agricultural crops all around the world. As chemical pesticide use becomes less desired, there is a need for alternative methods of pest control.... Show moreArthropod pests cause significant problems in agricultural crops all around the world. As chemical pesticide use becomes less desired, there is a need for alternative methods of pest control. Inspired by the natural adhesiveness of arthropod trapping plants, we examined the effectiveness of adhesive droplets made from oxidised and cross-linked plant-derived oils for control of western flower thrips. Two filter paper droplet adhesiveness assays and three detached chrysanthemum leaf assays were carried out to test efficacy against thrips. Suspensions containing adhesive droplets and other constituents were applied to filter papers and leaves via spraying or dipping. On filter papers, droplets made from oxidised rice germ oil (RGO) of different sizes caught 40–93% of thrips. Droplets made of a mixture of sunflower, olive, and linseed oil (MIX) caught up to 94% of thrips. Likewise, adhesive droplet-treated filter papers showed higher thrips mortality than untreated or control solution-treated filter papers. On chrysanthemum leaves, thrips were caught by both RGO (up to 40%) and MIX droplets (up to 20%) and thrips damage and reproduction were reduced. On MIX-treated leaves, thrips mortality was also increased. Within treatments, droplets of different size classes occurred and larger droplets were more effective at catching thrips in general. Droplets were also robust to rinsing with water, which is of importance for their application in horticulture. In conclusion, adhesive droplets made from edible plant oils show potential for use in control of western flower thrips. Show less
Background Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a... Show moreBackground Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. Results In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. Conclusions The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity. Show less
Bertola, L.D.; Vermaat, M.; Lesilau, F.; Chege, M.; Tumenta, P.N.; Sogbohossou, E.A.; ... ; Vrieling, K. 2022
Background Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a... Show moreBackground Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. Results In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. Conclusions The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity. Show less
AimsSoil biotic communities can strongly impact plant performance. So far, most studies on plant-soil-interactions have estimated the effect of the soil microbial community on plant mass after a... Show moreAimsSoil biotic communities can strongly impact plant performance. So far, most studies on plant-soil-interactions have estimated the effect of the soil microbial community on plant mass after a fixed duration of plant growth. However, these interactions may change over time and several studies have argued that plant-soil interactions are more important for young seedlings than for older plants. In this paper we ask the question: how long-lasting the effect of the soil microbial community on plant growth is. This is important as the growth rate of a plant is not only determined by the growing conditions but also by the size of the plant itself. Therefore, plant with a reduced growth rate early in life, due to negative effects of the soil microbial community, may increase less in biomass for a much longer period even though the relative growth rates do not differ any longer.MethodsWe examined the plant growth rates at three stages: early growth (0-21 days), mid growth (22 to 42 days) and late growth (43 to 63 days). We performed two growth experiments with Jacobaea vulgaris lasting 49 and 63 days. Plants were grown in sterilized soil or in sterilized soil inoculated with natural dune soil. In a third experiment, we examined the effect of the timing of soil inoculation prior to planting on the (relative-) growth rate of J. vulgaris plants with four different timing treatments.Important findingsIn all experiments, differences in biomass of plants grown in sterilized soil and inoculated soil (live soil) increased throughout the experiment. Interestingly, linear regression models with ln transformed dry weight against time for younger plants and for older plants in sterilized soil and live soil, respectively, showed that the relative growth rate of plants in the sterilized soil was only significantly higher than that of plants in the live soil in the first two to three weeks. After that period there was no longer a negative effect of the live soil on the relative growth rate of plants. In the third experiment, plant biomass decreased with increasing time between inoculation and planting. Overall, our results show that plants of J. vulgaris grew less well in live soil than in sterilized soil. The negative effects of soil inoculation on plant mass appeared to extend over the whole growth period but arise from the negative effects on relative growth rates that occurred in the first weeks after planting when plants have only less than 5% of the mass they obtained after 42 days. Our study highlights the importance of examining relative growth rates rather than final biomass to estimate the effects of soil microbial communities on plants. Show less
AimsPlants can influence the level of herbivory experienced by neighboring plants. The importance of such belowground associational effects are poorly understood. In this study we examine whether... Show moreAimsPlants can influence the level of herbivory experienced by neighboring plants. The importance of such belowground associational effects are poorly understood. In this study we examine whether Jacobaea vulgaris provides associational resistance against nematodes to neighboring plants.MethodsThirteen species (6 forbs, 3 grasses and 4 legumes) were each grown in mixtures with J. vulgaris and in monocultures. A nematode community was introduced to half of the pots. After 12 weeks, plant dry mass was assessed for each individual plant in each pot, and the number of nematodes in the soil and roots were identified. We then examined for each plant species its performance in mixtures and in monocultures, in presence and absence of nematodes and analyzed the abundance and composition of nematodes.ResultsForbs produced more, grasses similar, and legumes less biomass in mixtures with J. vulgaris than in monocultures. Nematode addition did not influence biomass. There were fewer root-feeding nematodes in the soil in mixtures than in monocultures, but this was only true for plants that were good hosts for nematodes. The community composition of soil nematodes was different in monocultures and mixtures. Densities of migratory endoparasitic nematodes in the roots of neighboring plants were lower in mixtures than in monocultures. Moreover, the presence of nematodes changed the outcome of plant-plant interactions, often in favor of J. vulgaris.ConclusionsJacobaea vulgaris provides belowground associational resistance to other plants against migratory endoparasitic nematodes, and the presence of nematodes can change the outcome of plant-plant interactions. Show less
Background: Bulk segregant analysis (BSA) can help identify quantitative trait loci (QTLs), but this may result in sub‐ stantial bycatch of functionally irrelevant genes.Results: Here we develop a... Show moreBackground: Bulk segregant analysis (BSA) can help identify quantitative trait loci (QTLs), but this may result in sub‐ stantial bycatch of functionally irrelevant genes.Results: Here we develop a Gene Ontology‐mediated approach to zoom in on specific genes located inside QTLs identified by BSA as implicated in a continuous trait. We apply this to a novel experimental system: flowering time in the giant woody Jersey kale, which we phenotyped in four bulks of flowering onset. Our inferred QTLs yielded tens of thousands of candidate genes. We reduced this by two orders of magnitude by focusing on genes annotated with terms contained within relevant subgraphs of the Gene Ontology. A pathway enrichment test then led to the circadian rhythm pathway. The genes that enriched this pathway are attested from previous research as regulating flowering time. Within that pathway, the genes CCA1, FT, and TSF were identified as having functionally significant variation compared to Arabidopsis. We validated and confirmed our ontology‐mediated results through genome sequencing and homology‐based SNP analysis. However, our ontology‐mediated approach produced additional genes of puta‐ tive importance, showing that the approach aids in exploration and discovery.Conclusions: Our method is potentially applicable to the study of other complex traits and we therefore make our workflows available as open‐source code and a reusable Docker container. Show less
Background and aims Jacobaea vulgaris plants grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on plant growth. To examine what... Show moreBackground and aims Jacobaea vulgaris plants grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on plant growth. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the soil. Methods We studied the composition of the microbial community over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris. We initiated the experiment with an inoculum of live soil collected from the field, and at the start of each subsequent plant cycle, we inoculated a small part of the soil from the previous plant cycle into sterile bulk soil. Results Application of SA did not significantly increase or decrease the Shannon diversity at genus level within each generation, but several specific genera were enriched or depleted after foliar SA application. The composition of bacterial communities in the rhizosphere significantly differed between plant cycles (generations), but application of SA did not alter this pattern. In the first generation no genera were significantly affected by the SA treatment, but in the second, third and fourth generations, specific genera were significantly affected. 89 species out of the total 270 (32.4%) were present as the "core" microbiome in all treatments over four plant cycles. Conclusions Overall, our study shows that the composition of bacterial genera in the rhizosphere significantly differed between plant cycles, but that it was not strongly affected by foliar application of SA on J. vulgaris leaves. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere bacterial community. Show less
Wei, X.; Klinkhamer, P.G.L.; Mulder, P.P.J.; Veen, C.A.M. van der; Vrieling, K. 2021
Abiotic and biotic properties of soil can influence growth and chemical composition of plants. Although it is well-known that soil microbial composition can vary greatly spatially, how this... Show moreAbiotic and biotic properties of soil can influence growth and chemical composition of plants. Although it is well-known that soil microbial composition can vary greatly spatially, how this variation affects plant chemical composition is poorly understood. We grew genetically identical Jacobaea vulgaris in sterilized soil inoculated with live soil collected from four natural grasslands and in 100% sterilized soil. Within each grassland we sampled eight plots, totalling 32 different inocula. Two samples per plot were collected, leading to three levels of spatial variation: within plot, between and within grasslands. The leaf metabolome was analysed with 1H Nuclear magnetic resonance spectroscopy (NMR) to investigate if inoculation altered the metabolome of plants and how this varied between and within grasslands. Inoculation led to changes in metabolomics profiles of J. vulgaris in two out of four sites. Plants grown in sterilized and inoculated soils differed in concentrations of malic acid, tyrosine, trehalose and two pyrrolizidine alkaloids (PA). Metabolomes of plants grown in inoculated soils from different sites varied in glucose, malic acid, trehalose, tyrosine and in one PA. The metabolome of plants grown in soils with inocula from the same site was more similar than with inocula from distant sites. We show that soil influences leaf metabolomes. Performance of aboveground insects often depends on chemical composition of plants. Hence our results imply that soil microbial communities, via affecting aboveground plant metabolomes, can impact aboveground plant-insect food chains but that it is difficult to make general predictions due to spatial variation in soil microbiomes. Show less
Chen, Y.; Klinkhamer, P.G.L.; Memelink, J.; Vrieling, K. 2020
