Nanoplastics can cause severe malformations in chicken embryos. To improve our understanding of the toxicity of nanoplastics to embryos, we have studied their biodistribution in living chicken... Show moreNanoplastics can cause severe malformations in chicken embryos. To improve our understanding of the toxicity of nanoplastics to embryos, we have studied their biodistribution in living chicken embryos. We injected the embryos in the vitelline vein at stages 18–19. We injected polystyrene nanoparticles (PS-NPs) tagged with europium- or fluorescence. Their biodistribution was tracked using inductively-coupled plasma mass spectrometry on tissue lysates, paraffin histology, and vibratome sections analysed by machine learning algorithms. PS-NPs were found at high levels in the heart, liver and kidneys. Furthermore, PS-NPs crossed the endocardium of the heart at sites of epithelial-mesenchymal transformation; they also crossed the liver endothelium. Finally, we detected PS-NPs in the allantoic fluid, consistent with their being excreted by the kidneys. Our study shows the power of the chicken embryo model for analysing the biodistribution of nanoplastics in embryos. Such experiments are difficult or impossible in mammalian embryos. These findings are a major advance in our understanding of the biodistribution and tissue-specific accumulation of PS-NPs in developing animals. Show less
In this thesis, I focused on studying the above- and belowground interactions of J. vulgaris from a plant-soil feedback (hereafter, PSF) perspective. I investigated the temporal variation of... Show moreIn this thesis, I focused on studying the above- and belowground interactions of J. vulgaris from a plant-soil feedback (hereafter, PSF) perspective. I investigated the temporal variation of negative PSF and examined the effects of root-associated bacteria on plant performance and aboveground herbivores. Additionally, I tested the role of PSF in relation to plant population structure and the significance of soil legacy effects in natural conditions. The findings reveal that temporal dynamics in PSF are driven by changes in plant sensitivity and in the soil microbiome. Although bacteria isolated from J. vulgaris roots can negatively affect plant performance, they can also affect aboveground herbivores and other plant species. Consequently, these bacteria may not be suitable for biological control of J. vulgaris. Moreover, I discovered that soil nematodes can mediate plant-plant interactions, but often favoring J. vulgaris. In my field work, I detected soil legacy effects, but seedling recruitment spatial patterns of J. vulgaris were not soil-mediated. The insights gained from studying PSF and above- and belowground interactions have the potential to reshape traditional approaches employed in controlling invasive plants. This thesis emphasizes the importance of transitioning PSF experiments from indoor to outdoor settings considering various influencing factors simultaneously. Show less
Across the world, the number of citizen science projects focusing on plastic pollution is increasing. These projects often last for multiple years, which makes retaining volunteers challenging.... Show moreAcross the world, the number of citizen science projects focusing on plastic pollution is increasing. These projects often last for multiple years, which makes retaining volunteers challenging. However, our knowledge is limited regarding the effect of long-term involvement on citizen scientists’ motivation, attitude, and knowledge, especially for plastic pollution projects. Therefore, this study measured citizen scientists’ motivation, attitude, and knowledge in the Dutch Clean Rivers project before and during monitoring plastic pollution on riverbanks between 2017 and 2021.In total, 403 Clean Rivers participants completed a pre-survey, and a portion of them participated in one or multiple post-surveys throughout the years of monitoring. They were especially driven by Project Action motivations and Environmental motivations like tackling the source of pollution and doing something about the plastic soup, rather than being motivated by an Interest in Scientific Research like the desire to learn about scientific research. Project Action motivations increased significantly, especially within the first year of participation. Participants’ attitudes towards nature and science were initially high and did not increase significantly. Furthermore, while participants’ knowledge of plastic pollution was already high at the start, their knowledge of scientific research was not, and both increased significantly, especially in the first year of participation. The findings of this longitudinal study can contribute to improving the recruitment and retention of volunteers in current and future citizen science projects. Show less
Jensen, C.N.G.; Pang, J.K.Y.; Gottardi, M.; Kračun, S.K.; Svendsen, B.A.; Nielsen, K.F.; ... ; Schulz, A. 2024
Human vocal communication and music perception represent advanced cognitive skills, seemingly innate and universal. These faculties encompass a range of perceptual and cognitive abilities. Cross... Show moreHuman vocal communication and music perception represent advanced cognitive skills, seemingly innate and universal. These faculties encompass a range of perceptual and cognitive abilities. Cross-species research sheds light on the origins of musicality by investigating whether these traits are shared by nonhuman species. Songbirds, notably zebra finches, serve as valuable models due to their complex vocalizations and similarities to humans in auditory perception. My thesis explored zebra finches' sensitivity to spectral and temporal sound features. Chapter 2 examines the influence of song duration and spectral characteristics on song discrimination, while Chapter 3 tests song preferences. Chapter 4 investigates sequential and spectral feature recognition. Chapter 5 focuses on melody recognition. Zebra finches demonstrate perceptual flexibility, adapting focus based on stimulus characteristics. These findings underscore the importance of training conditions and stimulus nature in shaping auditory perception. Overall, my thesis enhances understanding of auditory cognition and cognitive flexibility among songbirds. Show less
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So... Show moreAngiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes. This 15-fold increase in genus-level sampling relative to comparable nuclear studies provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade. Show less
This thesis aims to investigate the effect of tripartite interaction between microbial inoculants, the plant, and herbivore insects on the rhizosphere microbiome and volatilome. We investigated the... Show moreThis thesis aims to investigate the effect of tripartite interaction between microbial inoculants, the plant, and herbivore insects on the rhizosphere microbiome and volatilome. We investigated the rhizosphere microbiome and volatilome of tomato plants exposed to insect herbivory and/or inoculated with beneficial microbes known to trigger ISR. First, we reviewed the abiotic and biotic factors that impact the success of ISR microbial inoculants (Chapter 2). Then, we tested microbial inoculants against different stresses and experimental conditions to compare interactions in variable contexts (Chapter 3). Next, we explored the impact of insect herbivory aboveground, on the volatile and microbial belowground compartment. In Chapter 4 we explored root volatiles under stress in two tomato species to evaluate the genotype impact on the stress-induced root volatilome. In Chapter 5, we studied the impact of endosymbiotic fungi arbuscular mycorrhizal fungi (AMF) on root volatiles in an in vitro bioassay and in a greenhouse setup with herbivory-stressed plants. In Chapter 6, we compared the effect of four phylogenetically diverse bacteria and fungi, inoculated as single-species and as a synthetic community, on the rhizosphere microbiome assembly and volatilome in herbivory-stressed plants. Overall, this thesis delves into overlooked interactions providing novel data on belowground plant-microbe interactions. Show less
Polymyxins are clinically used antibiotics, discovered in mid-20th century. Once abandoned due to excessive nephrotoxicity, they are now used increasingly to address infections caused by multi-drug... Show morePolymyxins are clinically used antibiotics, discovered in mid-20th century. Once abandoned due to excessive nephrotoxicity, they are now used increasingly to address infections caused by multi-drug resistant Gram-negative bacteria.In this thesis, we describe the development and synthesis of analogues of polymyxin, aimed at reducing its associated nephrotoxicity. Analogues were made by semisynthesis, with modifications introduced mostly in the exocyclic portion of the molecule. Especially the introduction of a disulfide bond within the linked lipid helped in reducing the toxicity of the molecules, as evidenced by testing on proximal tubule epithelial cells. For most potent analogues, the antimicrobial activity was completely retained.In addition, this thesis describes studies on the mechanism of action of polymyxin, mostly based on the full stereoisomer of polymyxin B4. This analogue lacks antimicrobial activity, indicating its original stereochemistry to be of utmost importance for its use as an antibiotic.Hybrids based on polymyxin B derivatives are described, addressing non-conventional targets. A hybrid with vancomycin (typically active on Gram-positive bacteria only) shows activity on Gram-negative bacteria. A polymyxin-based hybrid coupled to a peptide with a beta-hairpin motif addresses Gram-negative bacteria, presumably by binding to outer membrane protein BamA. Show less
Bierman, T.V.; Vrieling, K.; Zwieten, R. van; Kodger, T.E.; Marcel, M.; Bezemer, T.M. 2024
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
Members of the Bacillus genus are widely distributed throughout natural environments and have been studied for decades among others for their physiology, genetics, ecological functions, and... Show moreMembers of the Bacillus genus are widely distributed throughout natural environments and have been studied for decades among others for their physiology, genetics, ecological functions, and applications. However, despite its prevalence in nature, the characterization and classification of Bacillus remain challenging due to its complex and ever-evolving taxonomic framework. This review addresses the current state of the Bacillus taxo- nomic landscape and summarizes the critical points in the development of Bacillus phylogeny. With a clear view of Bacillus phylogeny as a foundation, we subsequently review the methodologies applied in identifying and quantifying Bacillus, while also discussing their respective advantages and disadvantages. Show less
Alvarez van Tussenbroek, I.; Knörnschild, M.; Nagy, M.; Cate, C.J. ten; Vernes, S.C. 2024
Comparative neurobiology allows us to investigate relationships between phylogeny and the brain and understand the evolution of traits. Bats constitute an attractive group of mammalian species for... Show moreComparative neurobiology allows us to investigate relationships between phylogeny and the brain and understand the evolution of traits. Bats constitute an attractive group of mammalian species for comparative studies, given their large diversity in behavioural phenotypes, brain morphology, and array of specialised traits. Currently, the order Chiroptera contains over 1,450 species within 21 families and spans ca. 65 million years of evolution. To date, 194 Neotropical bat species (ca. 13% of the total number of species around the world) have been recorded in Central America. This study includes qualitative and quantitative macromorphological descriptions of the brains of 12 species from six families of Neotropical bats. These analyses, which include histological neuronal staining of two species from different families (Phyllostomus hastatus and Saccopteryx bilineata), show substantial diversity in brain macromorphology including brain shape and size, exposure of mesencephalic regions, and cortical and cerebellar fissure depth. Brain macromorphology can in part be explained by phylogeny as species within the same family are more similar to each other. However, macromorphology cannot be explained by evolutionary time alone as brain differences between some phyllostomid bats are larger than between species from the family Emballonuridae despite being of comparable diverging distances in the phylogenetic tree. This suggests that faster evolutionary changes in brain morphology occurred in phyllostomids — although a larger number of species needs to be studied to confirm this. Our results show the rich diversity in brain morphology that bats provide for comparative and evolutionary studies. Show less
Oratie uitgesproken door Prof.dr. A.F.J. Ram bij de aanvaarding van het ambt van hoogleraar Schimmelgenetica en Biotechnologie aan de Universiteit Leiden op vrijdag 9 februari 2024
The haplolepideous mosses (Dicranidae) comprise about 4000 species distributed over a wide range of habitats, with great gametophytic and sporophytic morphological variation. Their monophyly is... Show moreThe haplolepideous mosses (Dicranidae) comprise about 4000 species distributed over a wide range of habitats, with great gametophytic and sporophytic morphological variation. Their monophyly is well supported by the results of several molecular phylogenetic studies, which shed light on their relationships and circumscriptions, and thus also contributed to identify many remaining problems. Dicranidae ordinal classification is not congruent with current relationship hypotheses and is not supported by morphology. Morphological circumscriptions of some families do not correspond to monophyletic groups. Furthermore, the monophyly of many families and genera with weak morphological circumscriptions remains to be tested. In this thesis, systematics and relationships of the leucobryoid mosses and some families and genera segregated from the former Dicranaceae s.l. were studied using molecular phylogenetic methods. 37 out of the 38 haplolepideous moss families were represented by markers from the three genomes (nrITS, nad5, trnS-trnF, atpB-rbcL). Phylogenetic reconstructions were based on maximum parsimony, maximum likelihood, and Bayesian inference. Ancestral state reconstructions, phylogenetic network analysis (NeighborNet), and relationship hypothesis testing (Shimodaira-Hasegawa test) were performed to contribute to the interpretation of the results of the phylogenetic reconstructions. Morphological circumscriptions were evaluated and improved whenever possible, in line with the results of all analyses performed. Show less
Phenological responses to climate change frequently vary among trophic levels, which can result in increasing asynchrony between the peak energy requirements of consumers and the availability of... Show morePhenological responses to climate change frequently vary among trophic levels, which can result in increasing asynchrony between the peak energy requirements of consumers and the availability of resources. Migratory birds use multiple habitats with seasonal food resources along migration flyways. Spatially heterogeneous climate change could cause the phenology of food availability along the migration flyway to become desynchronized. Such heterogeneous shifts in food phenology could pose a challenge to migratory birds by reducing their opportunity for food availability along the migration path and consequently influencing their survival and reproduction. We develop a novel graph-based approach to quantify this problem and deploy it to evaluate the condition of the heterogeneous shifts in vegetation phenology for 16 migratory herbivorous waterfowl species in Asia. We show that climate change-induced heterogeneous shifts in vegetation phenology could cause a 12% loss of migration network integrity on average across all study species. Species that winter at relatively lower latitudes are subjected to a higher loss of integrity in their migration network. These findings highlight the susceptibility of migratory species to climate change. Our proposed methodological framework could be applied to migratory species in general to yield an accurate assessment of the exposure under climate change and help to identify actions for biodiversity conservation in the face of climate-related risks. Show less
