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Prof. dr. Luc De Meester

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Luc De MeesterI am fascinated by how communities and populations respond to environmental gradients, and to what extent ecological and evolutionary processes interact in shaping these responses. My research interests are broad, ranging from the ecology of lakes and ponds to ecological genomics.

Our aquatic ecological research focuses on analyzing the structure and functioning of lakes and pond ecosystems, and we study biodiversity and species composition in relation to environmental gradients and human impact. We study micro-evolutionary dynamics in response to environmental gradients, mainly using the waterflea Daphnia as a model species. We focus on trait evolution as well as on linking trait responses to population structure and signatures of evolution at the genome level.

By combining metacommunity research with analyses of micro-evolution, we explore eco-evolutionary dynamics, mainly focusing on how evolution may impact community dynamics at a local and regional scale. In this research, we focus on strong environmental gradients, including human impact (climate change, pollution). Exploring the importance of evolution-mediated priority effects is a key focus of our research.

While most of our research focuses on Daphnia and zooplankton as model organisms, some of our studies cover the whole range of organisms inhabiting ponds and lakes, from bacteria to fish. Our microbial ecological research mainly focuses on how metacommunity ecology and eco-evolutionary dynamics may increase our insight into the structure and dynamics of natural microbial communities.

Our research combines field observations and field experiments with large-scale outdoor container experiments, laboratory experiments, resurrection ecology and ecological genomics.

Postdocs: Till Czypionka, Mieke Jansen, Pieter Lemmens, Shinjini Mukherjee and Caroline Souffreau


Phd students:  Kristien Brans, Anurag Chaturvedi, Tom De Bie, Jessie Engelen, Andros Tarouco Gianuca, Eyerusalem Goitom, Lynn Govaert, Fabio Taquicava Hanashiro, Laurens Kilsdonk, Veerle Lemaire, Katina Spanier, Fassil E. Teffera, Hadush Haileselasie Tsegazeabe, Matthias Vanhamel and Evelyne Vanvlasselaer

Lab technicians: Carla Denis and Edwin van den Berg


Associated researchers and former team members: Ellen Decaestecker, Steven Declerck, Aurora Geerts, Joachim Mergeay, Luisa Orsini, Jelena Pantel, Adinda Putman, Sarah Rousseaux, Koen Rummens, Ine Swillen, Mekonen Teferi, Joost Vanoverbeke and Dino Verreydt

Research topics

 

Projects:

Eve-net

STRESSFLEA

Eco-evolutionary dynamics

Other research projects


 

METACOMMUNITY ECOLOGY

Starting with the pioneering work of Karl Cottenie on local and regional factors structuring zooplankton communities in the interconnected shallow lakes of the “De Maten” system, we developed a strong interest in metacommunity ecology. We focus on the relative importance of local and regional dynamics in structuring communities in nature, identifying the importance of habitat connectivity, habitat age, and environmental gradients including urbanization. Ponds are excellent model systems to study metacommunity structure. Our field studies involve analyses on different spatial scales and comparing different aquatic organism groups. Using outdoor container experiments, we study the impact of dispersal and its interaction with environmental gradients. In several of our studies, we explicitly link metacommunity structure to population genetic structure and to genetic differentiation in traits of focal species (cf. research line on eco-evolutionary dynamics). We also incorporate trait- and phylogenetic-based approaches to further increase our understanding of metacommunity dynamics.

Example studies:

  • Comparative metacommunity structure of aquatic organisms (De Bie et al. 2012 Ecology Letters)
  • Metacommunity structure of aquatic organisms along gradients of urbanization (PhD research Jessie Engelen, Andros T. Gianuca and Fabio Taquicava Hanashiro)
  • Metacommunity structure of zooplankton (Cottenie et al. 2003 Ecology; PhD research Tom De Bie, Jessie Engelen and Andros T. Gianuca)
  • Lineage sorting and metacommunity structure at various spatial scales in microbial communities (Van der Gucht et al. 2007 PNAS; Souffreau et al. 2015 Environmental Microbiology; PhD research Fabio Taquicava Hanashiro)
  • Trait-based and phylogenetic-based metacommunity approaches in zooplankton (PhD research Jessie Engelen and Andros T. Gianuca)
  • Field and mesocosm experiments on species sorting along environmental gradients, priority effects and community assembly in zooplankton (species sorting: Cottenie & De Meester 2004 Ecology; local interactions: Louette et al. 2006 Limnology & Oceanography; priority effects: Louette & De Meester 2007 Oikos; Phd research Tom De Bie and Andros T. Gianuca)
  • Dispersal and colonization in zooplankton (Louette & De Meester 2005 Ecology; Louette et al. 2007 Oikos; Van de Meutter et al. 2008 Biology Letters)
  • Historical reconstruction of zooplankton assemblages and priority effects (Mergeay et al. 2006 Freshwater Biology; Mergeay et al. 2011 Ecology)
  • Dispersal, biotic interactions and species sorting along environmental gradients (Verreydt et al. 2012 Ecology Letters; PhD research Andros T. Gianuca)
  • Metacommunity structure of macro-invertebrates in interconnected pond systems (Van de Meutter et al. 2006 Ecography; Van de Meutter et al. 2007 Ecology)
  • Metacommunity structure and dispersal in phytoplankton (Vanormelingen et al. 2008 Freshwater Biology; van Gremberghe et al. 2011 PLoS One)
  • Priority effects in protists and microbial communities (e.g. van Gremberghe et al. 2010 Environmental Microbiology)
  • Parasite community assembly (Jansen et al. 2010 Journal of Animal Ecology)
  • Ponds and pools as model systems for metacommunity ecology (De Meester et al. 2005 Aquatic Conservation)
  • Linking metacommunity ecology to biogeography (e.g. Jocque et al. 2010 Global Ecology and Biogeography)

People:

  • PhD students: Tom De Bie, Jessie Engelen, Andros T. Gianuca and Fabio Taquicava Hanashiro
  • Postdoctoral Researcher: Pieter Lemmens and Caroline Souffreau
  • Associated staff: Steven Declerck (NIOO, NL)

Partners within KU Leuven:

  • There is close collaboration on metacommunity ecology research with the research group of Luc Brendonck. This team focuses on metacommunity ecology of temporary pools, similarly using both field studies and mesocosm or field experiments, and both teams share the interest in pond systems as models for metacommunity studies at different spatial scales.

National and international partners:

  • Our interactions with Mathew Leibold (Univ. Texas at Austin) have been important in the development of our expertise in the field of metacommunity ecology. A large part of the metacommunity analyses on protists and microbial communities have been carried out as a joint effort with the research team of Wim Vyverman (UGent). Paleolimnological reconstructions of community dynamics were carried out in collaboration with Dirk Verschuren (UGent).

Broader picture and integration:

  • This research line is strongly linked to our studies on lake and pond ecology, evolutionary ecology and eco-evolutionary dynamics. The integration of metacommunity ecology and evolutionary ecology is a key focus of our research team.

 

EVOLUTIONARY ECOLOGY

We are interested in understanding micro-evolutionary responses of natural populations to environmental change, both in space (environmental gradients in natural landscapes) as well as in time. We study both responses to natural (e.g. predation, competition, parasite exposure) as well as anthropogenic stressors (climate change, pollution) stressors. We invest much energy in trying to obtain an encompassing view by taking a multi-stressor and multi-trait approach, so that trade-offs among responses to different stressors or among responses in different traits structuring evolutionary dynamics can be unveiled. Most of our work on evolutionary ecology focuses on the water flea Daphnia, where we capitalize on specific assets such as the short generation time, the possibility to work with clonal lineages and the formation of layered egg banks to study genotype x environment interactions as well as genotype x genotype interactions, and to use both experimental evolution and resurrection ecology to obtain better insight into evolutionary potential and constraints and into the dynamics of evolutionary change through time. There is a strong link between our evolutionary ecological work and our metacommunity (cf. eco-evo dynamics) and population genetics and genomics work. More recently, we increasingly use modelling approaches in close association with lab and field experiments.

Example studies:

  • Evolutionary ecology of anti-predator traits
    • Resurrection ecology analysis (Cousyn et al. 2001 PNAS)
    • Evolutionary ecology of diel vertical migration (e.g. De Meester 1993 Ecology; De Meester et al. 1995 Nature)
    • Multiple-trait analyses and biochemical traits (Boersma et al. 1998 American Naturalist; Pauwels et al. 2007 American Naturalist)
    • Interactions between anti-predator defences and food stress (Pauwels et al. 2010 Functional Ecology)
  • Host-parasite co-evolution
    • Resurrection ecology analysis of Red Queen dynamics in nature (Decaestecker et al. 2007 Nature)
    • Genotype-genotype interactions and trade-offs with predation risk (Decaestecker et al. 2002 PNAS; Decaestecker et al. 2003 Evolution)
    • Evolution of immune responses (Pauwels et al. 2010 Limnology and Oceanography; Pauwels et al. 2011 Biology Letters)
  • Adaptation to climate change
    • Quantifying thermal genetic adaptation in Daphnia populations (Geerts et al. 2015 Nature Climate Change)
    • Quantifying thermal genetic adaptation using experimental evolution (Van Doorslaer et al. 2007 Global Change Biology; Van Doorslaer et al. 2009 Evolution; Van Doorslaer et al. 2010 Climate Research; Van Doorslaer et al. 2011 Integrative and Comparative Biology)
  • Adaptation over gradients of urbanization (PhD research Kristien Brans)
  • Evolutionary ecotoxicology
    • Synergistic effects of pollution resistance and natural stressors (Coors et al. 2008 Oikos; Coors & De Meester 2008 Journal of Applied Ecology)
    • Local genetic adaptation to land use intensity (Coors et al. 2009 Aquatic Toxicology)
    • Genetic adaptation to pollution and its costs (experimental evolution and follow-up experiments: Jansen et al. 2011 Evolution; Jansen et al. 2011 Functional Ecology; Jansen et al. 2011 Ecotoxicology)
  • Evolutionary ecological consequences of inbreeding (Swillen et al. 2015 Ecology and Evolution)
  • Evolutionary ecology of DaphniaMicrocystis interactions (van Gremberghe et al. 2008 Oikos; van Gremberghe et al. 2008 Environmental Microbiology; Lemaire et al. 2012 Evolutionary Applications)
  • Evolutionary ecology of phytoplankton (Vanormelingen et al. 2009 Limnology and Oceanography; van Gremberghe et al. 2009 Oikos)

People:

  • PhD students: Kristien Brans and Veerle Lemaire
  • Postdoctoral Researcher: Mieke Jansen
  • Associated staff: Ellen Decaestecker (KU Leuven Campus KULAK), Jelena Pantel (CNRS Montpellier)

Partners within KU Leuven:

  • Several of the evolutionary ecological research lines, especially those focusing on physiological traits and multiple-trait analyses, are developed in close collaboration with the research group of Robby Stoks (Sarah Oexle: UV and Zink responses in Daphnia; Chao Zhang: C:N:P stoichiometry in Daphnia). The research on host-parasite co-evolution is developed in close collaboration with Ellen Decaestecker, who as an independent PI at KU Leuven Campus KULAK currently develops several additional research lines on host-parasite dynamics in Daphnia.

National and international partners:

  • Collaboration with Dieter Ebert (Univ. Basle) has been crucial in the development of our expertise in studying host-parasite interactions in Daphnia. The experimental evolution trials on climate change were only possible thanks to collaboration with the research teams of Erik Jeppesen (NERI) and Brian Moss (Univ. Liverpool). The development of our expertise in evolutionary ecotoxicology strongly benefited from the input of Dr Anja Coors (ECT Oekotoxicologie, D).

Broader picture and integration:

  • This research line together with our ecological and metacommunity research is a corner-stone for our integrated analysis of eco-evolutionary dynamics. It also links closely to our research on population genetics and genomics.

 

ECO-EVOLUTIONARY DYNAMICS AND EVOLVING METACOMMUNITIES

There is growing evidence that populations may show rapid evolutionary change in response to environmental challenges, which may potentially impact ecological dynamics, including community and ecosystem characteristics. We aim at gaining better insight into the importance of eco-evolutionary dynamics in nature. Building on our metacommunity and evolutionary ecological research, showing dynamics of species and genotype sorting along environmental gradients in space and time, we take an evolving metacommunity approach to study parallel patterns and interactions between genetic and ecological responses, and between metapopulation and metacommunity structure. More specifically, we aim at quantifying feedbacks of micro-evolutionary responses to ecological processes such as immigration, and to community structure and ecosystem functioning. We want to develop our insight into evolution-mediated priority effects (“monopolization”) and its consequences , and aim at quantifying the consequences of eco-evolutionary feedbacks in response to strong environmental gradients in space and time. In this latter research, we both focus on natural and anthropogenic selection pressures, and in the end aim for an integrated approach across levels of biological organization, traits, stressors and spatial scales. In addition to using experimental approaches (e.g. experimental evolution and follow-up experiments on feedbacks; transplant experiments), we also aim at findings ways to unveil the signature of eco-evolutionary dynamics in field surveys.

Example studies:

  • Evolution-mediated priority effects and the dispersal – gene flow paradox: the monopolization hypothesis (De Meester et al. 2002 Acta Oecologica)
  • Community monopolization: simulations (Urban & De Meester 2009 Proc. Roy. Soc. B; Vanoverbeke et al. 2015 Ecography; PhD research Laurens Kilsdonk) and concept (De Meester et al. 2015 Trends in Ecology and Evolution)
  • Genotype identity impacts establishment success of immigrant species (De Meester et al. 2007 Oecologia)
  • Evolving metacommunity concept (Urban et al. 2008 Trends in Ecology and Evolution)
  • Genetic adaptation to climate change reduces establishment success of immigrant genotypes (Van Doorslaer al. 2009 Global Change Biology)
  • Ecological feedback of genetic adaptation to predator exposure (Pantel et al. 2015 Ecology Letters)
  • The signature of evolving metacommunity dynamics in nature (PhD research Sarah Rousseaux)
  • Bottom-up impact of priority effects along the food chain (PhD research Veerle Lemaire)
  • Eco-evolutionary dynamics of colonization (PhD research Ine Swillen)
  • Eco-evolutionary dynamics over environmental gradients (urbanization: PhD research Kristien Brans; eutrophication: PhD research Matthias Vanhamel)
  • Mathematical metrics to calculate the relative contribution of ecology and evolution to trait change (PhD research Lynn Govaert)

People:

  • PhD students: Kristien Brans, Lynn Govaert, Laurens Kilsdonk, Veerle Lemaire and Matthias Vanhamel
  • Associated staff: Steven Declerck (NIOO, NL), Jelena Pantel (CNRS Montpellier) and Joost Vanoverbeke (INBO)

Partners within KU Leuven:

  • Our eco-evolutionary research is embedded in an Excellence Center financing of the K.ULeuven Research Fund. This project involves the research groups of Luc Brendonck, Ellen Decaestecker, Olivier Honnay, Herman Ramon, Robby Stoks, Filip Volckaert and Tom Wenseleers. This excellence financing integrates eco-evolutionary research across organism groups and across interaction types (competition, predation, parasitism, mutualism), both in terrestrial as well as in aquatic model systems.

National and international partners:

  • Our research on evolving metacommunities benefits strongly from collaboration with Mark Urban (Univ. Connecticut), Mathew Leibold (Univ. Texas at Austin) and Pedro Peres-Neto (UQUAM, Montreal, Ca). Within the framework of the Belspo project SPEEDY on eco-evolutionary dynamics over gradients in urbanization, we collaborate with the research groups of Hans Van Dyck (UCL), Erik Matthysen (UA), Frederik Hendrickx (RBINS) and Luc Lens (UGent).

Broader picture and integration:

  • This research line heavily builds on our expertise in aquatic ecology, metacommunity ecology, evolutionary ecology and population genetics/genomics. It also capitalizes strongly on the broad ecological and evolutionary knowledge on Daphnia, and on the assets of this model system for ecological and evolutionary research. In the longer term, we hope to be able to come to unified insights into eco-evolutionary dynamics and its consequences in natural systems across a broad range of organism types and systems.

 

ENVIRONMENTAL GENOMICS

We use genetic markers to understand the genetic structure of zooplankton populations in natural landscapes, combining phylogeographic analyses with more detailed analyses of genetic variation and differentiation. Questions include identification of colonization patterns and the impact of cyclic parthenogenetic reproduction on metapopulation structure. We also reconstruct genetic changes within natural populations through time using a paleogenetic approach on layered dormant egg banks. We contribute to the development of genomic resources for Daphnia magna as part of the Daphnia Genomics Consortium, and use these genomics tools to identify genomic regions under selection. We use a genome scan approach to link genomic regions to key environmental gradients, and verify the obtained signals using populations from layered dormant egg banks (reconstruction in time) and from experimental evolution trials. In addition to genomics, we also apply transcriptomics and proteomics in an effort to obtain better insight into the mechanistic underpinning of ecological responses.

Example studies:

  • Genetic structure of cyclical parthenogenetic populations and genetic differentiation in natural landscapes (De Meester et al. 2006 Archiv Hydrobiologie; Vanoverbeke et al. 2007 Heredity; Thielsch et al. 2009 Molecular Ecology; Vanoverbeke & De Meester, Journal of Evolutionary Biology)
  • Metapopulation structure in interconnected ponds (Michels et al. 2001 Molecular Ecology)
  • Phylogeography of Daphnia (De Gelas & De Meester 2005 Molecular Ecology; Mergeay et al. 2008 Molecular Ecology)
  • Concept papers on local genetic adaptation, dispersal and gene flow (De Meester 1996 Ecoscience; De Meester et al. 2002 Acta Oecologica), Orsini et al. 2013 Trends in Ecology and Evolution, Orsini et al. 2013a Molecular Ecology
  • Development of markers and genomics resources (Ortells et al. 2009 Molecular Ecology Resources; Routtu et al. 2010 BMC Genomics; Jansen et al. 2011 Molecular Ecology Resources; Orsini et al. 2011 BMC Genomics), Routtu et al. 2014 BMC Genomics)
  • Genome scan analyses identifying genome markers associated with environmental gradients Orsini et al. 2012 Molecular Ecology`, Orsini et al. 2013b Molecular Ecology, Orsini et al. 2013c Molecular Ecology
  • Transcriptome studies (Jansen et al. 2013 Ecotoxicology)

People:

  • PhD students: Anurag Chaturverdi and Katina Spanier
  • Postdoctoral researchers: Till Czypionka and Mieke Jansen
  • Associated staff: Joachim Mergeay (INBO), Luisa Orsini (Univ. Birmingham, UK) and Joost Vanoverbeke (INBO)

Partners within KU Leuven:

  • We collaborate intensively with Stein Aerts on the development of bioinformatics tools for the analysis of the Daphnia genome. Proteomics work is developed in collaboration with the teams of Liliane Schoofs and Rony Swennen / Bart Panis.

National and international partners:

  • Our expertise in population genetic analyses benefited strongly from long-standing collaborations with Piet Spaak (EAWAG, CH) and Klaus Schwenk (Univ. Koblenz-Landau, D). Our genomics work was developed within the framework of the Daphnia Genomics Consortium and benefited strongly from collaboration with John Colbourne (Univ. Indiana at Bloomington). Our current genomics work is carried out within the international ESF consortium STRESSFLEA (co-ordinated by KU Leuven) in which 9 teams are involved in addition to ourselves: Dieter Ebert (Univ. Basel), Christoph Haag (Univ. Fribourg), Adam Petrusek (Charles Univ. Prague), Chistian Laforsch (Univ. München), Mikko Frilander (Univ. Helsinki), Karel Deschamphelaere (UGent), Andrew Beckerman (Univ. Sheffield) and John Colbourne (Univ. Indiana at Bloomington). For transcriptomics work we collaborate with Dries Knapen (UAntwerpen).

Broader picture and integration:

  • Our population genetic and genomics analyses provide important insights for a broad range of questions, but also provide essential information on population history, colonization dynamics and dispersal that are crucial for our research on metacommunity ecology, evolutionary ecology and eco-evolutionary dynamics. In addition, we often use genetic markers in our manipulative mesocosm experiments.

 

ECOSYSTEM STABILITY

Within a recently developed research line on ecosystem stability, we aim to identify key determinants underpinning ecosystem stability, resilience and resistance. Using ponds and lakes as model systems, we examine early warning signals and tipping points of regime shifts. We are especially interested in the relation between biodiversity and ecosystem stability since diversity and the associated functional redundancy may play a key role in the resilience of ecosystems to environmental change. This research builds on a rich set of background data on which we can capitalize, but also involves additional field surveys (farmland ponds across Belgium and fish ponds in Midden-Limburg) and large scale outdoor container experiments to test specific hypotheses. We specifically focus on plankton communities as they play a pivotal role on the functioning and dynamics of lakes and ponds. This research is highly relevant for biodiversity conservation and is key to sustainable management of our ecosystems.

 

Example studies:

 

  • Year-to-year stability of ecosystem characteristics in ponds (PhD research of Eyerusalem Goitom)
  • Tipping points and early warning signals in plankton community dynamics (PhD research of Eyerusalem Goitom)
  • The contribution of evolutionary tracking to the resilience of ecosystems (PhD research of Matthias Vanhamel)
  • The relation between zooplankton diversity and ecosystem stability under eutrophication and climate change (PhD research of Matthias Vanhamel)

People:

  • PhD students: Matthias Vanhamel, Eyerusalem Goitom
  • Postdoctoral Researcher: Pieter Lemmens

National and international partners:

  • This research is part of the collaborative project TIPPINGPOND (Biodiversa, nationally funded by Belspo). Project partners are the research groups of Helmut Hillebrand (Carl-von-Ossietzky Universität Oldenburg, UOL, DE, UOL), Alex Wezel (engineering school in Agriculture, Food and Environment Lyon, ISARA-Lyon, FR) and Eva Lindström (Uppsala University, UU, SE).

Broader picture and integration:

  • This research builds on our expertise in lake and pond ecology and is highly complementary to the research on Eco- evolutionary dynamics. 

 


 

MICROBIAL ECOLOGY AND EVOLUTION

We aim at understanding how bacterial communities are structured in nature, and test how concepts such as metacommunities and evolving metacommunities apply to the microbial world. In this way, we want to use microbial communities to build more general insight in the processes determining the dynamics of (meta)communities in time and space, including mass effects, priority effects, biotic interactions and evolution. We have expertise in microbial culturing procedures, molecular fingerprinting and high throughput analyses, and work with both bacterioplankton and biofilms using field data, outdoor mesocosm and laboratory experiments. In addition to phylogenetic approaches, we also apply metagenomics in a molecular trait-based approach to get an integrated view of microbial community structure and function. Through this approach, we are mainly interested in understanding the impact of anthropogenic changes (urbanization, eutrophication, habitat-fragmentation e.t.c.) on the fundamental ecological processes related to microbial communities such as biogeochemical cycling, detoxification, and food web interactions in aquatic systems. Additionally, we explore eco-evolutionary dynamics in bacterioplankton using lab experiments with natural or artificial communities.

Example studies:

  • Lineage sorting and metacommunity structure of bacterial communities in shallow lakes (Van der Gucht et al. 2001 Environmental Microbiology; Muylaert et al. 2001 Applied and Environmental Microbiology; Van der Gucht et al. 2005 FEMS – Microbial Ecology; Van der Gucht et al. 2007 PNAS; Souffreau et al. 2015 Environmental Microbiology)
  • Mass effects and priority effects on metacommunity structure using lab experiments (mass effects: Souffreau et al. 2015 Freshwater Biology)
  • Metacommunity structure and traits over gradients of urbanization (PhD research Fabio Taquicava Hanashiro)
  • Metagenomic trait-based analysis of microbial metacommunity structure along urbanization gradients (MSCA IF project – “MicroCity”, postdoc research Shinjini Mukherjee)
  • Effects of ecologocial release on evolution and community build-up in bacterioplankton (postdoc research Caroline Souffreau)
  • Zooplankton grazing structuring bacterioplankton communities (Degans et al. 2001 FEMS - Microbial Ecology; van Gremberghe et al. 2009 Oikos)
  • Dormant stage banks of zooplankton microparasites (Decaestecker et al. 2004 Limnology and Oceanography; Jansen et al. 2010 Journal of Animal Ecology)
  • Microbial ecology in tropical lakes (Rejas et al. 2005 Aquatic Microbial Ecology)
  • Priority effects in microbial communities and its consequences (van Gremberghe et al. 2009 Environmental Microbiology; PhD research Veerle Lemaire).
  • Bacterial communities of activated sludge (Vanysacker et al. 2010 Applied Microbiology and Biotechnology)
  • Biofilm development on membrane surfaces (Piasecka et al. 2012 Biofouling)
  • Gut microbiota of fish in relation to pre- and probiotics (Geraylou et al. 2012, 2013 Fish and Shellfish Immunology; Geraylou et al. 2013 FEMS Microbiology Ecology)

People involved in the local team:

  • PhD student: Fabio Taquicava Hanashiro
  • Postdoctoral researchers: Shinjini Mukherjee and Caroline Souffreau

Partners within KU Leuven:

  • The research on membrane biofouling is developed in close collaboration with the research team of Ivo Vankelecom and em. Prof. Frans Ollevier. We collaborate on socio-microbiology and risk spreading strategies with Jan Michiels, Kevin Verstrepen and Tom Wenseleers.

National and international partners:

  • Much of our research on bacterioplankton communities in shallow lakes and on the ecology of Microcystis was developed in a joint effort with the research team of Wim Vyverman (UGent). We collaborate with the team of Jeroen Raes (VIB) for metagenomic studies.

Broader picture and integration:

  • The integration of metacommunity ecology and evolutionary ecology is a key focus of our research team. We work towards applying a metacommunity and evolving metacommunity approach on microbial communities to better understand how bacterial communities are structured.

 

LAKES AND PONDS

We have a long tradition in studying biodiversity and food web structure in shallow lakes and ponds, both in the context of European projects (BIOMAN, co-ordinated by KU Leuven; ALARM, EUROLIMPACS) and national consortia (Belspo projects on farmland ponds MANSCAPE and PONDSCAPE) as well as through targeted projects in Belgium (shallow lakes in nature reserve De Maten and Vijvergebied Midden-Limburg) and in other regions of the world (e.g. ecology of reservoirs and Rift Valley lakes in Ethiopia). We are interested in how food web structure impacts the functioning and biodiversity in shallow lakes, how environmental stress impacts biodiversity in lakes and ponds, and how biodiversity relates to ecosystem functioning. We explore the relation between management practices and biodiversity, and investigate how this translates to ecosystem services. Our studies involve lake restoration projects (biomanipulation), large-scale standardized field surveys, analyses of ecosystem services of lakes and ponds, field experiments, and population genetic analyses. We use genetic tools to document colonization dynamics and cryptic invasions.

Example studies:

  • Large-scale whole-lake experiment involving +20 shallow lakes to quantify the impact of fish community structure on biodiversity and ecosystem functioning in lakes in “Vijvergebied Midden-Limburg”; this study will contribute to an optimization of the management of this biodiversity hot-spot in Flanders (Lemmens et al. 2014 Aquatic Conservation; Lemmens et al. 2015 Fisheries Management and Ecology)
  • Linking land use to water quality and biodiversity in farmland ponds (e.g. Declerck et al. 2006 Biological Conservation)
  • Linking urbanization to pond characteristics (PhD research Jessie Engelen)
  • Across-group biodiversity patterns in shallow lakes along a North-South gradient in Europe; this study covered organism groups ranging from bacteria to fish (e.g. Declerck et al. 2005 Ecology)
  • Colonization of newly created ponds in natural settings, monitoring the success of nature restoration projects (e.g. Louette & De Meester 2005 Ecology; using genetic markers: Louette et al. 2007 Oikos)
  • Management, biodiversity and composition of aquatic communities (e.g. Lemmens et al. 2013 PLos One, Lemmens et al. 2015 PLos One)
  • Quantifying responses to lake restoration (e.g. Van de Meutter et al. 2006 Journal of Applied Ecology; Louette et al. 2009 Restoration Ecology)
  • Biodiversity in farmland ponds (PhD research Tom De Bie)
  • Plankton diversity and submerged aquatic vegetation (mesocosm experiment: Declerck et al. 2007 Ecology; conceptual paper discussing field patterns: Scheffer et al. 2006 Oikos)
  • Tracking invasion of an exotic species in Africa using a genetic marker and paleogenetics (Mergeay et al. 2005 Limnology and Oceanography; Mergeay et al. 2006 Proc. Roy. Soc. B)
  • Tracking extinction and recolonization using paleolimnology and paleogenetics (Mergeay et al. 2007 Ecology)
  • Quantifying cryptic invasion in the European water frog complex and its consequences using genetic tools (e.g. Holsbeek et al. 2008 Molecular Ecology; Holsbeek et al. 2009 Molecular Ecology; Holsbeek et al. 2010 Biological Invasions)
  • Quantifying biodiversity using dormant egg banks (e.g. Vandekerckhove et al. 2005a Oecologia; Vandekerckhove et al. 2005b Limnology and Oceanography Methods)
  • The ecology of artificial reservoirs in the semi-arid highlands of Tigray, Northern Ethiopia (PhD research Mekonen Teferi; e.g. Dejenie et al. 2008 Hydrobiologia; Dejenie et al. 2009 Freshwater Biology; Teferi et al. 2013 Inland Waters; Teferi et al. 2014 Freshwater Biology)
  • The ecology of the Ethiopian Rift Valley Lakes, Chamo and Abaya (PhD research Fassil E. Teffera)
  • Tropical lake ecology (e.g. Rejas et al. 2005 Freshwater Biology)
  • Ecological responses to climate warming (Jeppesen et al. 2010 Hydrobiologia; Moss et al. 2011 Inland Waters; Kosten et al. 2011 Global Change Biology)
  • Quantifying ecosystem services of shallow lakes and ponds (projects ECOFRESH and BEES; Landuyt et al. 2014 Journal of Environmental Management; case study of the ponds in Vijvergebied Midden-Limburg)

People:

  • PhD students: Tom De Bie, Jessie Engelen, Eyerusalem Goitom, Fassil E. Teffera, and Matthias Vanhamel
  • Postdoctoral Researcher: Pieter Lemmens
  • Associated staff: Steven Declerck (NIOO, NL) and Mekonen Teferi (Mekelle University, Ethiopia)

Partners within KU Leuven:

  • Our research on pond systems is closely linked to the research carried out in the research group of Luc Brendonck, who focuses mainly on temporary pools. Several of the research activities have and are being carried out in a joined effort with this team. There is also a strong link to this team with respect to egg bank ecology. The work on European water frogs has been done as a joined effort with the group of Filip Volckaert; the work on macro-invertebrates was developed together with the team of Robby Stoks. We also collaborate with the team of Koenraad Muylaert at KU Leuven Campus Kortrijk.

National and international partners:

  • This research is often done in larger national (Manscape/Pondscape projects, SPEEDY project) and international consortia (EU projects ALARM, EUROLIMPACS), involving many partners. Our collaboration with Erik Jeppesen (NERI, Denmark) has been crucial to the development of our expertise in standardized field surveys. Key partners in our national survey analyses are Wim Vyverman (UGent) and Koen Martens (RBINS). The work on ecosystem services is strongly rooted in our collaboration with the research team of Patrick Meire (UAntwerpen), as well as with the team of Peter Goethals (UGent) and VITO.

Broader picture and integration:

  • This research line is strongly linked to our studies on metacommunity structure, evolutionary ecology and eco-evolutionary dynamics. In these analyses, we often focus on strong environmental gradients in nature, and use the large data sets generated by our research on pond and shallow lake ecology to characterize abiotic and biotic characteristics of habitats. This integration of ecological and evolutionary biological research is very important to us.

 

DAPHNIA BIOLOGY

While we do not see the study of biology of Daphnia as a key focus of our research, our studies do capitalize very strongly on knowledge of the biology of this model, and have contributed to insights into its ecology and evolution. We here list the topics on which our analyses have shed some light, and refer to key publications.

  • Anti-predator defences
    • Genetic variation in diel vertical migration and phototactic behaviour (e.g. De Meester 1991 Hydrobiologia; De Meester 1993 Ecology)
    • Phototactic behaviour: changes in behaviour in response to environmental gradients (food availability: De Meester & Dumont 1989 Limnology and Oceanography; temperature and pH: Van Uytvanck & De Meester 1990 Journal of Plankton Research; food quality: Michels & De Meester 1998 Hydrobiologia)
    • Phototactic behaviour of males (De Meester 1992 Animal Behaviour)
    • Fish-induced plasticity in phototactic behaviour (De Meester 1993 Ecology; De Meester & Cousyn 1997 Hydrobiologia)
    • Habitat selection and genetic polymorphism (De Meester et al. 1995 Nature)
    • Local genetic adaptation for anti-predator defences (De Meester 1996 Evolution; Cousyn et al. 2001 PNAS)
    • Diel horizontal migration (Michels et al. 2007 Hydrobiologia)
    • Life history traits (De Meester 1994 Oecologia; Boersma et al. 1999 Limnology and Oceanography; De Meester & Weider 1999 Limnology and Oceanography)
    • Physiological and biochemical traits (Pauwels et al. 2005 Journal of Evolutionary Biology)
    • Integrated analysis of multiple traits (Boersma et al. 1998 American Naturalist)
    • Anti-predator defences under food stress (Pauwels et al. 2010 Functional Ecology)
    • Responses to invertebrate predators (Van de Meutter et al. 2004 Oikos; Van de Meutter et al. 2005a,b Oecologia)
  • Host-parasite interactions (see also Ellen Decaestecker)
    • Red Queen dynamics (Decaestecker et al. 2007 Nature)
    • Genotype-genotype interactions (Decaestecker et al. 2003 Evolution)
    • Trade-off with anti-predator behaviour (Decaestecker et al. 2002 PNAS)
    • Ecological impact of parasites (Decaestecker et al. 2005 Oecologia)
    • Evolution of heat shock protein expression and phenoloxidase (Pauwels et al. 2007 American Naturalist; Pauwels et al. 2010 Limnology and Oceanography; Pauwels et al. 2011 Biology Letters)
    • Dormant egg banks of Daphnia parasites (Decaestecker et al. 2004 Limnology and Oceanography; Jansen et al. 2010 Journal of Animal Ecology)
  • Thermal adaptation and climate change
    • Thermal genetic adaptation in Daphnia: Geerts et al. 2015 Nature Climate Change
    • Genetic adaptation: experimental evolution (laboratory: Van Doorslaer et al. 2009 Evolution; outdoor mesocosms: Van Doorslaer et al. 2010 Climate Research)
    • Feedback of evolution on establishment of immigrant genotypes (Van Doorslaer et al. 2009 Global Change Biology)
    • Thermal adaptation in Daphnia in an eco-evolutionary perspective (De Meester et al. 2011 Integrative and Comparative Biology)
  • Adaptation to habitat quality, land use and pollution
    • Genetic adaptation to land use in nature (Coors et al. 2009 Aquatic Toxicology)
    • Synergistic effect of exposure to pollution and parasites (Coors et al. 2008 Oikos; Coors & De Meester 2008 Journal of Applied Ecology; Jansen et al. 2011 Evolution)
    • Experimental evolution of pollution resistance (Jansen et al. 2011 Ecotoxicology)
    • Costs of evolution of pesticide resistance (Jansen et al. 2011 Functional Ecology; Jansen et al. 2011 Evolution)
    • Phototactic behaviour impacted by pollutants: Michels et al. 1998 Water Research; Michels et al. 2000 Ecotoxicology and Environmental Safety; Kieu et al. 2001 Environmental Toxicology and Chemistry)
  • Feeding
    • Top-down control of phyto- and bacterioplankton by Daphnia (Degans & De Meester 2002 Hydrobiologia)
    • Impact on Microcystis (van Gremberghe et al. 2009 Oikos; Dejenie et al. 2009 Freshwater Biology)
    • Impact on bacterial communities (Degans et al. 2002 FEMS – Microbial Ecology)
  • Physiology and biochemical characteristics
    • Carotenoid content (De Meester & Beenaerts 1993 Limnology and Oceanography)
    • Heat shock proteins (Pauwels et al. 2005 Journal of Evolutionary Biology; Pauwels et al. 2007 American Naturalist)
    • Phenoloxidase expression (Pauwels et al. 2010 Limnology and Oceanography; Pauwels et al. 2011 Biology Letters)
  • Dormant egg banks and hatching
    • Dormant egg banks: reviews (Jeppesen et al. 2001 Trends Ecology and Evolution; Brendonck & De Meester 2003 Hydrobiologia)
    • Hatching (De Meester & De Jager 1993ab Freshwater Biology; De Meester et al. 1998 Archiv Hydrobiologie; Vandekerckhove et al. 2004 Hydrobiologia)
    • The use of dormant egg banks to assess biodiversity (Vandekerckhove et al. 2005 Limnology and Oceanography Methods; Vandekerckhove et al. 2005 Freshwater Biology; Vandekerckhove et al. 2005 Oecologia)
    • Build-up of dormant egg banks in new habitats (Vandekerckhove et al. 2005 Archiv Hydrobiologie)
    • Viability of dormant eggs in layered egg banks (Cousyn & De Meester 1998 Archiv Hydrobiologie)
    • Recolonizaton of Daphnia populations from dormant egg banks (Mergeay et al. 2007 Ecology)
    • Risk spreading strategies and dormant egg banks (Vanoverbeke & De Meester 200 Ecoscience)
    • Ephippia morphology and species identification (Mergeay et al. 2005 Hydrobiologia)
    • Biochemical characteristics of dormant eggs (Pauwels et al. 2007 Hydrobiologia)
  • Population genetic structure and clonal erosion
    • Local genetic adaptation and gene flow: reviews (De Meester 1996 Ecoscience; De Meester et al. 2002 Acta Oecologica)
    • Local genetic adaptation within a regional metacommunity (to fish predation pressure: De Meester 1996 Evolution; to water quality and land use: Declerck et al. 2001 Freshwater Biology; Coors et al. 2009 Aquatic Toxicology)
    • Cyclical parthenogenesis and population genetic structure: review (De Meester et al. 2006 Archiv Hydrobiologie)
    • Population genetic differentiation in cyclical parthenogens (Vanoverbeke & De Meester 1997 Hydrobiologia; Vanoverbeke et al. 2007 Heredity; Michels et al. 2003 Freshwater Biology; Thielsch et al. 2009 Molecular Ecology; Vanoverbeke & De Meester 2010 Journal of Evolutionary Biology)
    • Genetic structure of recently founded populations (Louette et al. 2007 Oikos)
    • Population genetic structure of asexual Daphnia (Aguilera et al. 2007 Limnology and Oceanography)
    • Metapopulation structure (Michels et al. 2001 Molecular Ecology)
    • Phylogeography of Daphnia (De Gelas & De Meester 2005 Molecular Ecology; Mergeay et al. 2008 Molecular Ecology)
  • Genomics
    • Development of microsatellite markers (for D. atkinsoni: Ortells et al. 2009 Mol. Ecol. Resources; for D. magna: Jansen et al. 2011 Mol. Ecol. Resources)
    • SNP marker development (Orsini et al. 2011 BMC Genomics)
    • Genetic linkage map (Routtu et al. 2010 BMC Genomics)
  • Inbreeding and inbreeding avoidance
    • Inbreeding and outbreeding depression (De Meester 1993 Oecologia)
    • Inbreeding avoidance (De Meester & Vanoverbeke 1999 Proc Roy Soc B)
  • Invasion biology
    • Cryptic invasion documented by paleogenetics (Mergeay et al. 2005 Limnology and Oceanography; Mergeay et al. 2006 Proc. Roy. Soc. B)
  • Dispersal and (meta)community assembly
    • Zooplankton metacommunities (Cottenie & De Meester 2003 Freshwater Biology; Cottenie et al. 2003 Ecology; Cottenie & De Meester 2004 Ecology)
    • Dispersal (Michels et al 2001 Hydrobiologia; Van de Meutter et al. 2008 Biology Letters)
    • Habitat colonization (Louette & De Meester 2004 Hydrobiologia; Louette & De Meester 2005 Ecology)
    • Establishment success and community assembly (Louette et al. 2006 Limnology and Oceanography; Louette et al. 2008 Freshwater Biology)
    • Priority effects among Daphnia species (Louette & De Meester 1997 Oikos)
    • Paleolimnological reconstruction of Daphnia communities through time (Mergeay et al. 2004 Freshwater Biology; Mergeay et al. 2011 Ecology)
  • Eco-evolutionary dynamics
    • Daphnia genotype impacts community build-up (De Meester et al. 2007 Oecologia)
    • Feedback of thermal adaptation to establishment success of immigrant genotypes (Van Doorslaer et al. 2009 Global Change Biology)
    • Responses to climate change in an eco-evolutionary perspective (De Meester et al. 2011 Integrative and Comparative Biology)