32 Works

Data from: Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli

Sarah Duxbury, Jesse Alderliesten, Mark Zwart, Arjan Stegeman, Egil Fischer & Arjan De Visser
Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified in vitro, the influence of interactions with other microbiome members is largely unknown. Here, we investigated the influence of three genera of lactic acid bacteria (LAB) derived from the chicken gastrointestinal microbiome on...

Mutual mate choice and assortative mating in relation to a carotenoid-based color trait in blue tits

Samuel Caro, Léo Pierre, Matthieu Berges, Raldi Bakker, Claire Doutrelant & Francesco Bonadonna
Choosing an appropriate partner is a critical decision for many animal species. However, many mechanisms involved in mate choice are still poorly understood. Do both males and females choose their sexual partners, do both sexes use the same criteria for choosing, and do their own phenotype influence the choices they make, are questions that need further investigation. Over two successive experiments conducted in captivity with hand-reared blue tits (Cyanistes caeruleus), we manipulated the color of...

Data and code for Heterogeneous selection on exploration behavior within and among West European populations of a passerine bird

Alexia Mouchet, Ella Cole, Erik Matthysen, Marion Nicolaus, John Quinn, Allison Roth, Joost Tinbergen, Kees Van Oers, Thijs Van Overveld & Niels Dingemanse
Heterogeneous selection is often proposed as a key mechanism maintaining repeatable behavioral variation (“animal personality”) in wild populations. Previous studies largely focused on temporal variation in selection within single populations. The relative importance of spatial versus temporal variation remains unexplored, despite these processes having distinct effects on local adaptation. Using data from >3500 great tits (Parus major) and 35 nest box plots situated within five West-European populations monitored over 4-18 years, we show that selection...

Searching for the causes of decline in the Dutch population of turtle doves Streptopelia turtur

E.H.J. De Vries, Ruud.P.B. Foppen, Henk Van Der Jeugd & Eelke Jongejans
European Turtle Doves Streptopelia turtur have experienced a sharp decline in population numbers over past decades. Much uncertainty exists about the main cause or causes. Several pressures have been suggested, but because they affect different stages of the life cycle of the Turtle Dove, it is difficult to compare their contributions to population decline. Here we applied a full life cycle approach to study how different pressures may have resulted in the decline. This was...

Steering the soil microbiome by repeated litter addition

Ciska Veen, Freddy Ten Hooven, Carolin Weser & Emilia Hannula
1. Microbial communities drive plant litter breakdown. Litters originating from different plant species are often associated with specialized microbiomes that accelerate the breakdown of that litter, known as home-field advantage. Yet, how and how fast microbial communities specialize towards litter inputs is not known. 2. Here we study effects of repeated litter additions on soil microbial community structure and functioning. We set up a nine-month, full-factorial, reciprocal litter transplant experiment with soils and litters from...

Stimulated saprotrophic fungi in arable soil extend their activities to the rhizosphere and root microbiomes of crop seedlings

Anna Clocchiatti, Emilia Hannula, Maria Hundscheid, Paulien Klen Gunnewiek & Wietse De Boer
Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust-amended arable soil, we determined fungal...

Impact of cellulose-rich organic soil amendments on growth dynamics and pathogenicity of Rhizoctonia solani

Anna Clocchiatti, Emilia Hannula, Muhammad Syamsu Rizaludin, Maria Hundscheid, Paulien Klein Gunnewiek, Mirjam Schilder, Joeke Postma & Wietse De Boer
Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable...

Data from: A critical assessment of the stoichiometric knife-edge: no evidence for artefacts caused by the experimental P-supplementation of algae

Steven Declerck & Libin Zhou
The stoichiometric knife-edge refers to the reduced performance of consumers encountering food with excess phosphorus (P) relative to carbon (C) or nitrogen (N). Studies that provide evidence for such knife-edge in aquatic systems often apply phosphate supplementation to create P-rich food treatments. However, this method may suffer from artefacts, because after uptake algae may store P in a form different from the P-rich biomolecules typically consumed by zooplankton. Our aim was to test if P...

Data from: Why time-limited individuals can make populations more vulnerable to disturbance

Henk-Jan Van Der Kolk, Bruno Ens, Magali Frauendorf, Eelke Jongejans, Kees Oosterbeek, Willem Bouten & Martijn Van De Pol
Individual variation in disturbance vulnerability (i.e. the likelihood that disturbance negatively affects an individual’s fitness) can affect how disturbance impacts animal populations, as even at low disturbance levels some individuals could be severely affected and die. Individual variation in vulnerability can arise due to different responses to disturbance. We propose a new hypothesis that even when individuals respond similarly to disturbance, time-limited individuals are more at risk that their condition deteriorates since they have limited...

Data from: Severance of arbuscular mycorrhizal networks in restoration grasslands enhances seedling biomass

Dassen Sigrid, Wim Van Der Putten & Gerlinde De Deyn
1. Establishment and growth of grassland plant species is generally promoted by arbuscular mycorrhizal fungi (AMF) when grown in isolation. However, in grassland communities AMF form networks that may connect individual plants of different ages within and between species. Here, we use an in-growth core approach to examine how mycorrhizal networks influences performance of seedlings in grasslands. 2. We selected 4 grass and 4 forb species with known negative or neutral-positive plant-soil feedback and grew...

Color of artificial light at night affects incubation behavior in the great tit, Parus major

Natalie Van Dis, Kamiel Spoelstra, Marcel Visser & Davide Dominoni
Artificial light at night (ALAN) has been recognized as a biodiversity threat due to the drastic effects it can have on many organisms. In wild birds, artificial illumination alters many natural behaviors that are important for fitness, including chick provisioning. Although incubation is a key determinant of the early developmental environment, studies into the effects of ALAN on bird incubation behavior are lacking. We measured nest temperature in nest boxes of great tits during the...

Persistence of plant-mediated microbial soil legacy effects in soil and inside roots

Emilia Hannula, Robin Heinen, Martine Huberty, Katja Steinauer, Jonathan De Long, Renske Jongen & Martijn Bezemer
Plant-soil feedbacks are shaped by microbial legacies that plants leave in the soil. We tested the persistence of these legacies after subsequent colonization by the same or other plant species. Soil fungal legacies were detectable for months, but the current plant effect on fungi amplified in time. Contrary, in bacterial communities, legacies faded away rapidly and bacteria communities were influenced strongly by the current plant. However, both fungal and bacterial legacies were conserved inside the...

Warming and CO2 effects under oligotrophication on temperate phytoplankton communities

Marco J. Cabrerizo, M. Inmaculada Álvarez-Manzaneda, Elizabeth León-Palmero, Gerardo Guerrero-Jiménez, Lisette N. De Senerpont Domis, Sven Teurlincx & Juan M. González-Olalla
Eutrophication, global warming, and rising carbon dioxide (CO2) levels are the three most prevalent pressures impacting the biosphere. Despite their individual effects are well-known, it remains untested how oligotrophication (i.e. nutrients reduction) can alter the planktonic community responses to warming and elevated CO2 levels. Here, we performed an indoor mesocosm experiment to investigate the warming × CO2 interaction under a nutrient reduction scenario (40%) mediated by an in-lake management strategy (i.e. addition of a commercial...

Fungal, bacterial & plant biomass data: Evaluation of phenolic root exudates as stimulants of saprotrophic fungi in the rhizosphere

Anna Clocchiatti, Emilia Hannula, Marlies Van Den Berg, Maria Hundscheid & Wietse De Boer
The rhizosphere microbial community of crop plants in intensively managed arable soils is strongly dominated by bacteria, especially in the initial stages of plant development. In order to establish more diverse and balanced rhizosphere microbiomes, as seen for wild plants, crop variety selection could be based on their ability to promote growth of saprotrophic fungi in the rhizosphere. We hypothesized that this can be achieved by increasing the exudation of phenolic acids, as generally higher...

Enhancing ecological integrity while preserving ecosystem services: constructing soft-sediment islands in a shallow lake

Casper Van Leeuwen, Ralph Temmink, Hui Jin, Yvonne Kahlert, Bjorn Robroek, Matty Berg, Leon Lamers, Marloes Van Den Akker, Roel Posthoorn, Annemiek Boosten, Han Olff &
1. Ecosystems are increasingly managed to provide multiple benefits to humans, which often degrades their ecological integrity. This strongly applies to aquatic ecosystems, in which engineering can enhance flood protection, drinking water supply, fisheries and recreation. Although these activities typically increase ecosystem functionality to humans, they often impair key aspects of biodiversity and natural functioning. 2. Classical restoration of such degrading freshwater ecosystems can lead to societal opposition, if returning to a former ecosystem state...

The hidden potential of saprotrophic fungi in arable soil: Patterns of short-term stimulation by organic amendments

Anna Clocchiatti, Emilia Hannula, Marlies Van Den Berg, Gerard Korthals & Wietse De Boer
Saprotrophic fungi are abundant in soils of (semi-)natural ecosystems, where they play a major role in ecosystem functioning. On the contrary, saprotrophic fungal biomass is remarkably low in intensively managed soils and this can have a negative impact on soil functioning. Nevertheless, arable soils harbour a diverse pool of fungi, which can be stimulated by organic amendments. Management targeted towards increasing soil organic matter often coincides with an increase of fungal biomass, but it can...

Memory extinction and spontaneous recovery shaping parasitoid foraging behavior

Jessica De Bruijn
Animals can alter their foraging behavior through associative learning, where an encounter with an essential resource (e.g. food or a reproductive opportunity) is associated with nearby environmental cues (e.g. volatiles). This can subsequently improve the animal’s foraging efficiency. However, when these associated cues are encountered again, the anticipated resource is not always present. Such an unrewarding experience, also called a memory-extinction experience, can change an animal’s response to the associated cues. Although some studies are...

Multi-camera field monitoring reveals costs of learning for parasitoid foraging behaviour

Jessica De Bruijn
1. Dynamic conditions in nature have led to the evolution of behavioural traits that allow animals to use information on local circumstances and adjust their behaviour accordingly, for example through learning. Although learning can improve foraging efficiency, the learned information can become unreliable as the environment continues to change. This could lead to potential fitness costs when memories holding such unreliable information persist. Indeed, persistent unreliable memory was found to reduce the foraging efficiency of...

Data from: Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation

Kimberley Lemmen, Koen Verhoeven & Steven Declerck
The success of genetically depauperate populations in the face of environmental change is contrary to the expectation that high genetic diversity is required for rapid adaptation. Alternative pathways such as environmentally induced genetic modifications and non-genetic heritable phenotypes have been proposed mechanisms for heritable adaptation within an ecologically relevant timeframe. However, experimental evidence is currently lacking to establish if, and to what extent, these sources of phenotypic variation can produce a response. To test if...

Recent natural variability in global warming weakened phenological mismatch and selection on seasonal timing in great tits (Parus major)

Marcel E. Visser, Melanie Lindner, Phillip Gienapp, Matthew Long & Stephanie Jenouvrier
Climate change has led to phenological shifts in many species, but with large variation in magnitude among species and trophic levels. The poster child example of the resulting phenological mismatches between the phenology of predators and their prey is the great tit (Parus major), where this mismatch led to directional selection for earlier seasonal breeding. Natural climate variability can obscure the impacts of climate change over certain periods, weakening phenological mismatching and selection. Here, we...

Liquid chromatography measurement obtained from the chitin extracts of insect exuviae

Azkia Nurfikari & Wietse De Boer
Chitin, a biopolymer present in fungi and arthropods, is a compound of interest for various applications, such as in the agricultural and medical fields. With the recently growing interest in the development of insect farming, the availability of chitin-containing residual streams, particularly the molting skins (exuviae), is expected to increase in the near future. For application purposes, accurate quantification of chitin in these insect sources is essential. Previous studies on chitin extraction and quantification often...

Effects of soil phosphorus, light, AMF and jasmonic acid on growth and defense of Plantago lanceolata

Arjen Biere, Minggang Wang & Laiye Qu
This dataset contains data from a two-part greenhouse experiments described in the paper: “Qu, L., Wang, M., and Biere, A. (2021) Interactive effects of Mycorrhizae, Soil Phosphorus and Light on Growth and Induction and Priming of Defense in Plantago lanceolata. Frontiers in Plant Science 12: 647372”. The experiment investigates the effects of a factorial combination of three factors: inoculation with AMF (the arbuscular mycorrhizal fungus Funneliformis mosseae; yes/no), soil phosphorus level (Soil P, 10.5 vs....

Data from: Stay or fly away? Impact of human disturbance on shorebird individuals and populations

Henk-Jan Van Der Kolk
These data comprise the data of four chapters from the PhD thesis from van der Kolk (2021) entitled ‘Stay or fly away? Impact of human disturbance on shorebird individuals and populations.’ The thesis focusses on quantifying the impacts of human disturbance on oystercatchers. This dataset contains data from chapters 4, 5, 7 and 10. For Chapter 4 field observations were done to observe how shorebirds responded to aircraft overflights at different sites. The data provides...

Inconsistent effects of agricultural practices on soil fungal communities across twelve European long‐term experiments

S. Emilia Hannula, D. P. Di Lonardo, B. T. Christensen, F.V. Crotty, A. Elsen, P.J. Erp, E.M. Hansen, G. H. Rubæk, M. Tits, Z. Toth & A. J. Termorshuizen
Cropping practices have a great potential to improve soil quality through changes in soil biota. Yet the effects of these soil improving cropping systems on soil fungal communities are not well known. Here, we analysed soil fungal communities using standardized measurements in 12 long‐term experiments and 20 agricultural treatments across Europe. We were interested in whether the same practices (i.e. tillage, fertilization, organic amendments and cover crops) applied across different sites have predictable and repeatable...

Source code for R tutorials and dataset for empirical case study on Malurus elegans (red-winged fairy wren)

Martijn Van De Pol & Lyanne Brouwer
Biological processes exhibit complex temporal dependencies due to the sequential nature of allocation decisions in organisms’ life-cycles, feedback loops, and two-way causality. Consequently, longitudinal data often contain cross-lags: the predictor variable depends on the response variable of the previous time-step. Although statisticians have warned that regression models that ignore such covariate endogeneity in time series are likely to be inappropriate, this has received relatively little attention in biology. Furthermore, the resulting degree of estimation bias...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Netherlands Institute of Ecology
  • Nederlands Instituut voor Ecologie
  • University of Groningen
  • Radboud University Nijmegen
  • Wageningen University & Research
  • Dutch Centre for Field Ornithology
  • Leiden University
  • Estación Biológica de Doñana
  • Centre d'Ecologie Fonctionnelle et Evolutive
  • University of Antwerp