1
|
Decaestecker E, Van de Moortel B, Mukherjee S, Gurung A, Stoks R, De Meester L. Hierarchical eco-evo dynamics mediated by the gut microbiome. Trends Ecol Evol 2024; 39:165-174. [PMID: 37863775 DOI: 10.1016/j.tree.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023]
Abstract
The concept of eco-evolutionary (eco-evo) dynamics, stating that ecological and evolutionary processes occur at similar time scales and influence each other, has contributed to our understanding of responses of populations, communities, and ecosystems to environmental change. Phenotypes, central to these eco-evo processes, can be strongly impacted by the gut microbiome. The gut microbiome shapes eco-evo dynamics in the host community through its effects on the host phenotype. Complex eco-evo feedback loops between the gut microbiome and the host communities might thus be common. Bottom-up dynamics occur when eco-evo interactions shaping the gut microbiome affect host phenotypes with consequences at population, community, and ecosystem levels. Top-down dynamics occur when eco-evo dynamics shaping the host community structure the gut microbiome.
Collapse
Affiliation(s)
- Ellen Decaestecker
- Laboratory of Aquatic Biology, Interdisciplinary Research Facility Life Sciences, KU Leuven, KULAK, Campus Kortrijk, B-8500 Kortrijk, Belgium.
| | - Broos Van de Moortel
- Laboratory of Aquatic Biology, Interdisciplinary Research Facility Life Sciences, KU Leuven, KULAK, Campus Kortrijk, B-8500 Kortrijk, Belgium
| | - Shinjini Mukherjee
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium; Laboratory of Reproductive Genomics, KU Leuven, B-3000 Leuven, Belgium
| | - Aditi Gurung
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium
| | - Robby Stoks
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, KU Leuven, B-3000 Leuven, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium; Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), D-12587 Berlin, Germany; Institute of Biology, Freie Universität Berlin, D-14195 Berlin, Germany
| |
Collapse
|
2
|
Coone M, Bisschop K, Vanoverberghe I, Verslype C, Decaestecker E. Genotype specific and microbiome effects of hypoxia in the model organism Daphnia magna. J Evol Biol 2023; 36:1669-1683. [PMID: 37822108 DOI: 10.1111/jeb.14233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/29/2023] [Accepted: 08/11/2023] [Indexed: 10/13/2023]
Abstract
The fitness of the host is highly influenced by the interplay between the host and its associated microbiota. The flexible nature of these microbiota enables them to respond swiftly to shifts in the environment, which plays a key role in the host's capacity to withstand environmental stresses. To understand the role of the microbiome in host tolerance to hypoxia, one of the most significant chemical changes occurring in water ecosystems due to climate change, we performed a reciprocal gut transplant experiment with the freshwater crustacean Daphnia magna. In a microbiome transplant experiment, two genotypes of germ-free recipients were inoculated with gut microbiota from Daphnia donors of their own genotype or from the other genotype, that had been either pre-exposed to normoxic or hypoxic conditions. We found that D. magna individuals had a higher survival probability in hypoxia if their microbiome had been pre-exposed to hypoxia. The bacterial communities of the recipients changed over time with a reduction in alpha diversity, which was stronger when donors were pre-exposed to a hypoxic environment. While donor genotype had no influence on the long-term survival probability in hypoxia, donor genotypes was the most influential factor of the microbial community 3 days after the transplantation. Our results indicate that microbiome influencing factors mediate host fitness in a hypoxic environment in a time depending way.
Collapse
Affiliation(s)
- Manon Coone
- Aquatic Biology, Department of Biology, KU Leuven, Kortrijk, Belgium
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Karen Bisschop
- Aquatic Biology, Department of Biology, KU Leuven, Kortrijk, Belgium
- Terrestrial Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | | | - Chris Verslype
- Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | | |
Collapse
|
3
|
Houwenhuyse S, Callens M, Bulteel L, Decaestecker E. Comparison between the gut bacterial community of laboratory cultured and wild Daphnia. FEMS Microbiol Ecol 2023; 99:fiad116. [PMID: 37740575 DOI: 10.1093/femsec/fiad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023] Open
Abstract
The fitness of an organism is often impacted by the composition and biological activity of its associated bacterial community. Many factors, including host genetics, diet, and temperature can influence the bacterial community composition. Furthermore, these factors can differ strongly between natural and laboratory environments. Consequently, several studies have highlighted results from laboratory experiments investigating host-associated bacterial communities to be conflicting with those obtained under field conditions. Here, we compared the Daphnia magna gut bacterial communities in natural host populations with those of laboratory cultured hosts. We further analyzed changes in the gut bacterial communities after transferring hosts from natural populations to the laboratory on the short- and long-term. Results show that, in general, the gut bacterial communities from natural populations differ from those of laboratory cultures and that their composition and diversity changed one hour after being transferred to the laboratory. Over the following 14 days, the composition and diversity changed gradually. On the longer term (after two years of rearing hosts in the laboratory) the composition and diversity of the gut bacterial communities was strongly altered compared to the initial state. Our findings indicate that the gut bacterial communities of Daphnia magna in laboratory experiments is not representative for natural field conditions, and that caution should be taken when interpreting results from laboratory experiments for natural settings.
Collapse
Affiliation(s)
- Shira Houwenhuyse
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven- KU Leuven, Campus KULAK, E. Sabbelaan 53, 8500 Kortrijk, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Gent University, Karel Lodewijk Ledeganckstraat 35, 9000, Gent, Belgium
| | - Martijn Callens
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven- KU Leuven, Campus KULAK, E. Sabbelaan 53, 8500 Kortrijk, Belgium
- Animal Sciences Unit - Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food, Oostende 8400, Belgium
| | - Lore Bulteel
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven- KU Leuven, Campus KULAK, E. Sabbelaan 53, 8500 Kortrijk, Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven- KU Leuven, Campus KULAK, E. Sabbelaan 53, 8500 Kortrijk, Belgium
| |
Collapse
|
4
|
Schols R, Vanoverberghe I, Huyse T, Decaestecker E. Host-bacteriome transplants of the schistosome snail host Biomphalaria glabrata reflect species-specific associations. FEMS Microbiol Ecol 2023; 99:fiad101. [PMID: 37632232 PMCID: PMC10481996 DOI: 10.1093/femsec/fiad101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/09/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023] Open
Abstract
Microbial symbionts can affect host phenotypes and, thereby, ecosystem functioning. The microbiome is increasingly being recognized as an important player in the tripartite interaction between parasitic flatworms, snail intermediate hosts, and the snail microbiome. In order to better understand these interactions, transplant experiments are needed, which rely on the development of a reliable and reproducible protocol to obtain microbiome-disturbed snails. Here, we report on the first successful snail bacteriome transplants, which indicate that Biomphalaria glabrata can accrue novel bacterial assemblies depending on the available environmental bacteria obtained from donor snails. Moreover, the phylogenetic relatedness of the donor host significantly affected recipients' survival probability, corroborating the phylosymbiosis pattern in freshwater snails. The transplant technique described here, complemented by field-based studies, could facilitate future research endeavors to investigate the role of specific bacteria or bacterial communities in parasitic flatworm resistance of B. glabrata and might ultimately pave the way for microbiome-mediated control of snail-borne diseases.
Collapse
Affiliation(s)
- Ruben Schols
- Department of Biology, Royal Museum for Central Africa, 3080 Tervuren, Belgium
- Laboratory of Aquatic Biology, KU Leuven, Campus Kortrijk, 8500 Kortrijk, Belgium
| | - Isabel Vanoverberghe
- Laboratory of Aquatic Biology, KU Leuven, Campus Kortrijk, 8500 Kortrijk, Belgium
| | - Tine Huyse
- Department of Biology, Royal Museum for Central Africa, 3080 Tervuren, Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, KU Leuven, Campus Kortrijk, 8500 Kortrijk, Belgium
| |
Collapse
|
5
|
Callens M, De Meester L, Muylaert K, Mukherjee S, Decaestecker E. The bacterioplankton community composition and a host genotype dependent occurrence of taxa shape the Daphnia magna gut bacterial community. FEMS Microbiol Ecol 2021; 96:5861314. [PMID: 32573725 PMCID: PMC7360484 DOI: 10.1093/femsec/fiaa128] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022] Open
Abstract
The assembly of host-associated bacterial communities is influenced by a multitude of biotic and abiotic factors. It is essential to gain insight in the impact and relative strength of these factors if we want to be able to predict the effects of environmental change on the assembly of host-associated bacterial communities, or deliberately modify them. The environmental pool of bacteria, from which the host is colonized, and the genetic background of the host are both considered to be important in determining the composition of host-associated bacterial communities. We experimentally assessed the relative importance of these two factors and their interaction on the composition of Daphnia magna gut bacterial communities. Bacterioplankton originating from natural ponds or a laboratory culture were used to inoculate germ-free Daphnia of different genotypes. We found that the composition of the environmental bacterial community has a major influence on the Daphnia gut bacterial community, both reflected by the presence or absence of specific taxa as well as by a correlation between abundances in the environment and on the host. Our data also indicate a consistent effect of host genotype on the occurrence of specific bacterial taxa in the gut of Daphnia over different environments.
Collapse
Affiliation(s)
- Martijn Callens
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven - Campus KULAK, E. Sabbelaan 53, B-8500 Kortrijk, Belgium.,CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Charles Deberiotstraat 32, 3000 Leuven, Belgium.,Institute of Biology, Freie Universität Berlin, Köning-Luise-Strasse 1-3, 14195 Berlin, Germany.,Leibniz Institut für Gewasserökologie und Binnenfischerei (IGB), Müggelseedamm 310, 12587 Berlin, Germany
| | - Koenraad Muylaert
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven - Campus KULAK, E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Shinjini Mukherjee
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Charles Deberiotstraat 32, 3000 Leuven, Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven - Campus KULAK, E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| |
Collapse
|
6
|
Bulteel L, Houwenhuyse S, Declerck SAJ, Decaestecker E. The Role of Microbiome and Genotype in Daphnia magna upon Parasite Re-Exposure. Genes (Basel) 2021; 12:70. [PMID: 33430247 PMCID: PMC7825712 DOI: 10.3390/genes12010070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Recently, it has been shown that the community of gut microorganisms plays a crucial role in host performance with respect to parasite tolerance. Knowledge, however, is lacking on the role of the gut microbiome in mediating host tolerance after parasite re-exposure, especially considering multiple parasite infections. We here aimed to fill this knowledge gap by studying the role of the gut microbiome on tolerance in Daphnia magna upon multiple parasite species re-exposure. Additionally, we investigated the role of the host genotype in the interaction between the gut microbiome and the host phenotypic performance. A microbiome transplant experiment was performed in which three germ-free D. magna genotypes were exposed to a gut microbial inoculum and a parasite community treatment. The gut microbiome inocula were pre-exposed to the same parasite communities or a control treatment. Daphnia performance was monitored, and amplicon sequencing was performed to characterize the gut microbial community. Our experimental results showed that the gut microbiome plays no role in Daphnia tolerance upon parasite re-exposure. We did, however, find a main effect of the gut microbiome on Daphnia body size reflecting parasite specific responses. Our results also showed that it is rather the Daphnia genotype, and not the gut microbiome, that affected parasite-induced host mortality. Additionally, we found a role of the genotype in structuring the gut microbial community, both in alpha diversity as in the microbial composition.
Collapse
Affiliation(s)
- Lore Bulteel
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, 8500 Kortrijk, Belgium; (S.H.); (E.D.)
| | - Shira Houwenhuyse
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, 8500 Kortrijk, Belgium; (S.H.); (E.D.)
| | - Steven A. J. Declerck
- Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6700 AB Wageningen, The Netherlands;
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, KULeuven, 3000 Leuven, Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, 8500 Kortrijk, Belgium; (S.H.); (E.D.)
| |
Collapse
|
7
|
Massol F, Macke E, Callens M, Decaestecker E. A methodological framework to analyse determinants of host-microbiota networks, with an application to the relationships between Daphnia magna's gut microbiota and bacterioplankton. J Anim Ecol 2020; 90:102-119. [PMID: 32654135 DOI: 10.1111/1365-2656.13297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 06/25/2020] [Indexed: 01/04/2023]
Abstract
The past 30 years have seen both a surge of interest in assessing ecological interactions using tools borrowed from network theory and an explosion of data on the occurrence of microbial symbionts thanks to next-generation sequencing. Given that classic network methods cannot currently measure the respective effects of different environmental and biological drivers on network structure, we here present two methods to elucidate the determinants of bipartite interaction networks. The first method is based on classifications and compares communities within networks to the grouping of nodes by treatment or similar controlling groups. The second method assesses the link between multivariate explanatory variables and network structure using redundancy analyses after singular value decomposition. In both methods, the significance of effects can be gauged through two randomizations. Our methods were applied to experimental data on Daphnia magna and its interactions with gut microbiota and bacterioplankton. The whole network was affected by Daphnia's diet (algae and/or cyanobacteria) and sample type, but not by Daphnia genotype. At coarse grains, bacterioplankton and gut microbiota communities were different. At this scale, the structure of the gut microbiota-based network was not linked to any explanatory factors, while the bacterioplankton-based network was related to both Daphnia's diet and genotype. At finer grains, Daphnia's diet and genotype affected both microbial networks, but the effect of diet on gut microbiota network structure was mediated solely by differences in microbial richness. While no reciprocal effect between the microbial communities could be found, fine-grained analyses presented a more nuanced picture, with bacterioplankton likely affecting the composition of the gut microbiota. Our methods are widely applicable to bipartite networks, can elucidate both controlled and environmental effects in experimental setting using a large amount of sequencing data and can tease apart reciprocal effects of networks on one another. The twofold approach we propose has the advantage of being able to tease apart effects at different scales of network structure, thus allowing for detailed assessment of reciprocal effects of linked networks on one another. As such, our network methods can help ecologists understand huge datasets reporting microbial co-occurrences within different hosts.
Collapse
Affiliation(s)
- François Massol
- UMR 8198 Evo-Eco-Paleo, SPICI Group, University of Lille, Lille, France.,CNRS, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, University of Lille, Lille, France
| | - Emilie Macke
- Laboratory of Aquatic Biology, Department of Biology, KU Leuven (Kulak), Kortrijk, Belgium
| | - Martijn Callens
- Laboratory of Aquatic Biology, Department of Biology, KU Leuven (Kulak), Kortrijk, Belgium.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Department of Biology, KU Leuven (Kulak), Kortrijk, Belgium
| |
Collapse
|
8
|
Boudry A, Devliegere S, Houwenhuyse S, Clarysse L, Macke E, Vanoverberghe I, Decaestecker E. Daphnia magna tolerance to toxic cyanobacteria in the presence of an opportunistic infection within an evolutionary perspective. BELG J ZOOL 2020. [DOI: 10.26496/bjz.2020.75] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In aquatic environments, interactions between cyanobacteria and their grazers are crucial for ecosystem functioning. Cyanobacteria are photosynthetic prokaryotes, which are able to produce large blooms and associated toxins, some of which are able to suppress grazer fitness. Cyanobacterial blooms are intensified by global warming and eutrophication. In our experiments, the tolerance of Daphnia magna (Straus, 1820), an efficient grazer of toxic cyanobacteria, was studied. We used different D. magna clones sampled from different sediment depths, which corresponded to different time periods of eutrophication. Our results showed that different clones had a different tolerance towards the toxic cyanobacterial species, Microcystis aeruginosa, confirming the presence of genetic variation in D. magna tolerance to cyanobacteria. However, there was not a significant adaptive effect of sediment depth. As expected, in general under controlled, infection-free conditions M. aeruginosa reduced D. magna survival. However, a coincidental, non-intended opportunistic fungal infection in a first experiment allowed us to compare the response of D. magna to M. aeruginosa in infected individuals and non-infected individuals (from a second experiment). In the presence of this opportunistic infection, there was no negative effect of M. aeruginosa in the D. magna clones, suggesting that exposure to the infection provided protection for Daphnia individuals towards Microcystis. Biotic interactions can thus be important in the interpretation of cyanobacterial effects in zooplankton grazers and in finding appropriate solutions to reduce the occurrence of cyanobacterial blooms.
Collapse
|
9
|
Macke E, Callens M, Massol F, Vanoverberghe I, De Meester L, Decaestecker E. Diet and Genotype of an Aquatic Invertebrate Affect the Composition of Free-Living Microbial Communities. Front Microbiol 2020; 11:380. [PMID: 32256467 PMCID: PMC7090131 DOI: 10.3389/fmicb.2020.00380] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/20/2020] [Indexed: 12/04/2022] Open
Abstract
In spite of the growing interest in the role of the gut microbiome (GM) in host physiology and health, the mechanisms governing its assembly and its effects on the environment are poorly understood. In this article, we show that the host genotype and the GM of Daphnia influence the community structure of the surrounding bacterioplankton (BPK). When Daphnia genotypes were placed in an identical environment, both the GM and BPK showed a genotype and diet-dependent taxonomic composition. Overall, the GM strongly differed from the BPK in taxonomic composition and was characterized by a lower α-diversity, suggesting a selective rejecting of bacteria from the regional species pool. In a microbiome transplant experiment, the assembly of both the GM and BPK was strongly affected by the host genotype and the inoculum to which germ-free Daphnia were exposed. The combination of these results suggests a strong interaction between the host genotype, its GM and free-living microbial communities. Currently, it is generally assumed that an animal’s diet has a strong effect on the animal’s GM, but only a negligible (if any) effect on the surrounding environment. However, our results indicate that the diet/microbiome inocula have a small effect on the gut community and a large effect on the community in the surrounding environment. This structuring genotype × microbiome × environment effect is an essential prerequisite that could indicate that microbiomes play an important role in eco-evolutionary processes.
Collapse
Affiliation(s)
- Emilie Macke
- Aquatic Biology, IRF Life Sciences, KU Leuven, Kortrijk, Belgium
| | - Martijn Callens
- Aquatic Biology, IRF Life Sciences, KU Leuven, Kortrijk, Belgium.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - Francois Massol
- CNRS, Lille-Sciences et Technologies, UMR 8198 Evo-Eco-Paleo, SPICI Group, Villeneuve-d'Ascq, France.,University of Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | | | - Luc De Meester
- Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | | |
Collapse
|
10
|
Piano E, Souffreau C, Merckx T, Baardsen LF, Backeljau T, Bonte D, Brans KI, Cours M, Dahirel M, Debortoli N, Decaestecker E, De Wolf K, Engelen JMT, Fontaneto D, Gianuca AT, Govaert L, Hanashiro FTT, Higuti J, Lens L, Martens K, Matheve H, Matthysen E, Pinseel E, Sablon R, Schön I, Stoks R, Van Doninck K, Van Dyck H, Vanormelingen P, Van Wichelen J, Vyverman W, De Meester L, Hendrickx F. Urbanization drives cross-taxon declines in abundance and diversity at multiple spatial scales. Glob Chang Biol 2020; 26:1196-1211. [PMID: 31755626 DOI: 10.1111/gcb.14934] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 11/01/2019] [Indexed: 05/12/2023]
Abstract
The increasing urbanization process is hypothesized to drastically alter (semi-)natural environments with a concomitant major decline in species abundance and diversity. Yet, studies on this effect of urbanization, and the spatial scale at which it acts, are at present inconclusive due to the large heterogeneity in taxonomic groups and spatial scales at which this relationship has been investigated among studies. Comprehensive studies analysing this relationship across multiple animal groups and at multiple spatial scales are rare, hampering the assessment of how biodiversity generally responds to urbanization. We studied aquatic (cladocerans), limno-terrestrial (bdelloid rotifers) and terrestrial (butterflies, ground beetles, ground- and web spiders, macro-moths, orthopterans and snails) invertebrate groups using a hierarchical spatial design, wherein three local-scale (200 m × 200 m) urbanization levels were repeatedly sampled across three landscape-scale (3 km × 3 km) urbanization levels. We tested for local and landscape urbanization effects on abundance and species richness of each group, whereby total richness was partitioned into the average richness of local communities and the richness due to variation among local communities. Abundances of the terrestrial active dispersers declined in response to local urbanization, with reductions up to 85% for butterflies, while passive dispersers did not show any clear trend. Species richness also declined with increasing levels of urbanization, but responses were highly heterogeneous among the different groups with respect to the richness component and the spatial scale at which urbanization impacts richness. Depending on the group, species richness declined due to biotic homogenization and/or local species loss. This resulted in an overall decrease in total richness across groups in urban areas. These results provide strong support to the general negative impact of urbanization on abundance and species richness within habitat patches and highlight the importance of considering multiple spatial scales and taxa to assess the impacts of urbanization on biodiversity.
Collapse
Affiliation(s)
- Elena Piano
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Brussels, Belgium
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Thomas Merckx
- Behavioural Ecology and Conservation Group, Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Lisa F Baardsen
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Brussels, Belgium
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Dries Bonte
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Kristien I Brans
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Marie Cours
- Royal Belgian Institute of Natural Sciences, OD Natural Environment, Brussels, Belgium
| | - Maxime Dahirel
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
- Ecosystems, Biodiversity and Evolution Unit, Université de Rennes 1 (CNRS), Rennes, France
| | - Nicolas Debortoli
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Namur, Belgium
| | | | - Katrien De Wolf
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Brussels, Belgium
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Jessie M T Engelen
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Diego Fontaneto
- CNR-IRSA, National Research Council, Water Research Institute, Verbania-Pallanza, Italy
| | - Andros T Gianuca
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
- Department of Ecology, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Lynn Govaert
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Fabio T T Hanashiro
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Janet Higuti
- Centre of Research in Limnology, Ichthyology and Aquaculture/PEA, State University of Maringá, Maringá, Paraná, Brazil
| | - Luc Lens
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences, OD Natural Environment, Brussels, Belgium
- Laboratory of Limnology, Biology Department, Ghent University, Ghent, Belgium
| | - Hans Matheve
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | - Erik Matthysen
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Eveline Pinseel
- Laboratory of Protistology & Aquatic Ecology, Biology Department, Ghent University, Ghent, Belgium
- Research Department, Meise Botanic Garden, Meise, Belgium
| | - Rose Sablon
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Brussels, Belgium
| | - Isa Schön
- Royal Belgian Institute of Natural Sciences, OD Natural Environment, Brussels, Belgium
- Zoology Research Group, University of Hasselt, Hasselt, Belgium
| | - Robby Stoks
- Evolutionary Stress Ecology and Ecotoxicology, KU Leuven, Leuven, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Namur, Belgium
| | - Hans Van Dyck
- Behavioural Ecology and Conservation Group, Biodiversity Research Centre, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Pieter Vanormelingen
- Laboratory of Protistology & Aquatic Ecology, Biology Department, Ghent University, Ghent, Belgium
| | - Jeroen Van Wichelen
- Laboratory of Protistology & Aquatic Ecology, Biology Department, Ghent University, Ghent, Belgium
- Aquatic Management, Research Institute for Nature and Forest (INBO), Brussels, Belgium
| | - Wim Vyverman
- Laboratory of Protistology & Aquatic Ecology, Biology Department, Ghent University, Ghent, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| |
Collapse
|
11
|
Decaestecker E, Bulteel L. Parasites opt for the best of both worlds. eLife 2019; 8:49615. [PMID: 31368888 PMCID: PMC6675540 DOI: 10.7554/elife.49615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 07/30/2019] [Indexed: 11/27/2022] Open
Abstract
The fungal parasite Podosphaera plantaginis employs both sexual and asexual reproduction to increase its chances of infecting the plant Plantago lanceolata.
Collapse
Affiliation(s)
- Ellen Decaestecker
- Department of Biology, Katholieke Universiteit Leuven Kulak, Kortrijk, Belgium
| | - Lore Bulteel
- Department of Biology, Katholieke Universiteit Leuven Kulak, Kortrijk, Belgium
| |
Collapse
|
12
|
De Meester L, Brans KI, Govaert L, Souffreau C, Mukherjee S, Vanvelk H, Korzeniowski K, Kilsdonk L, Decaestecker E, Stoks R, Urban MC. Analysing eco‐evolutionary dynamics—The challenging complexity of the real world. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13261] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Kristien I. Brans
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Lynn Govaert
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Shinjini Mukherjee
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Héléne Vanvelk
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Konrad Korzeniowski
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Laurens Kilsdonk
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, IRF Life Sciences, KULAK KU Leuven Kortrijk Belgium
| | - Robby Stoks
- Laboratory or Evolutionary Stress Ecology and Ecotoxicology KU Leuven Leuven Belgium
| | - Mark C. Urban
- Department of Ecology and Evolutionary Biology, Center for Biodiversity and Ecological Risk University of Connecticut Storrs Connecticut
| |
Collapse
|
13
|
Reyserhove L, Samaey G, Muylaert K, Coppé V, Van Colen W, Decaestecker E. A historical perspective of nutrient change impact on an infectious disease in Daphnia. Ecology 2018; 98:2784-2798. [PMID: 28845593 DOI: 10.1002/ecy.1994] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/18/2017] [Accepted: 07/10/2017] [Indexed: 01/01/2023]
Abstract
Changes in food quality can play a substantial role in the vulnerability of hosts to infectious diseases. In this study, we focused on the genetic differentiation of the water flea Daphnia magna towards food of different quality (by manipulating C:N:P ratios) and its impact on the interaction with a virulent infectious disease, "White Fat Cell Disease (WFCD)". Via a resurrection ecology approach, we isolated two Daphnia subpopulations from different depths in a sediment core, which were exposed to parasites and a nutrient ratio gradient in a common garden experiment. Our results showed a genetic basis for sensitivity towards food deprivation. Both fecundity and host survival was differently affected when fed with low-quality food. This strongly impacted the way both subpopulations interacted with this parasite. A historical reconstruction of nutrient changes in a sediment core reflected an increase in organic material and phosphorus concentration (more eutrophic conditions) over time in the studied pond. These results enable us to relate patterns of genetic differentiation in sensitivity towards food deprivation to an increasing level of eutrophication of the subpopulations, which ultimately impacts parasite virulence effects. This finding was confirmed via a dynamic energy budgets (DEB), in which energy was partitioned for the host and the parasite. The model was tailored to our study by integrating (1) increased growth and a fecundity shift in the host upon parasitism and (2) differences of food assimilation in the subpopulations showing that a reduced nutrient assimilation resulted in increased parasite virulence. The combination of our experiment with the DEB model shows that it is important to consider genetic diversity when studying the impact of nutritional stress on species interactions, especially in the context of changing environments and emerging infectious diseases.
Collapse
Affiliation(s)
- Lien Reyserhove
- KU Leuven, Interdisciplinary Research Facility Life Sciences, KULAK, Campus Kortrijk, Etienne Sabbelaan 53, Kortrijk, B-8500, Belgium
| | - Giovanni Samaey
- Department of Computer Science, KU Leuven, Celestijnenlaan 200A, Leuven, B-3001, Belgium
| | - Koenraad Muylaert
- KU Leuven, Interdisciplinary Research Facility Life Sciences, KULAK, Campus Kortrijk, Etienne Sabbelaan 53, Kortrijk, B-8500, Belgium
| | - Vincent Coppé
- Department of Computer Science, KU Leuven, Celestijnenlaan 200A, Leuven, B-3001, Belgium
| | - Willem Van Colen
- KU Leuven, Interdisciplinary Research Facility Life Sciences, KULAK, Campus Kortrijk, Etienne Sabbelaan 53, Kortrijk, B-8500, Belgium
| | - Ellen Decaestecker
- KU Leuven, Interdisciplinary Research Facility Life Sciences, KULAK, Campus Kortrijk, Etienne Sabbelaan 53, Kortrijk, B-8500, Belgium
| |
Collapse
|
14
|
Flandroy L, Poutahidis T, Berg G, Clarke G, Dao MC, Decaestecker E, Furman E, Haahtela T, Massart S, Plovier H, Sanz Y, Rook G. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Sci Total Environ 2018; 627:1018-1038. [PMID: 29426121 DOI: 10.1016/j.scitotenv.2018.01.288] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/28/2018] [Accepted: 01/28/2018] [Indexed: 05/03/2023]
Abstract
Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of "One health" that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making.
Collapse
Affiliation(s)
- Lucette Flandroy
- Federal Public Service Health, Food Chain Safety and Environment, Belgium
| | - Theofilos Poutahidis
- Laboratory of Pathology, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Gabriele Berg
- Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maria-Carlota Dao
- ICAN, Institute of Cardiometabolism and Nutrition, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France; INSERM, UMRS U1166 (Eq 6) Nutriomics, Paris 6, France; UPMC, Sorbonne University, Pierre et Marie Curie-Paris 6, France
| | - Ellen Decaestecker
- Aquatic Biology, Department Biology, Science, Engineering & Technology Group, KU Leuven, Campus Kortrijk. E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Eeva Furman
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Finland
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, University of Liège, Passage des deportes, 2, 5030 Gembloux, Belgium
| | - Hubert Plovier
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Graham Rook
- Centre for Clinical Microbiology, Department of Infection, UCL (University College London), London, UK.
| |
Collapse
|
15
|
Callens M, Watanabe H, Kato Y, Miura J, Decaestecker E. Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia. Microbiome 2018; 6:56. [PMID: 29566771 PMCID: PMC5863831 DOI: 10.1186/s40168-018-0444-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/13/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Host-associated microbiota is often acquired by horizontal transmission of microbes present in the environment. It is hypothesized that differences in the environmental pool of colonizers can influence microbiota community assembly on the host and as such affect holobiont composition and host fitness. To investigate this hypothesis, the host-associated microbiota of the invertebrate eco(toxico)logical model Daphnia was experimentally disturbed using different concentrations of the antibiotic oxytetracycline. The community assembly and host-microbiota interactions when Daphnia were colonized by the disturbed microbiota were investigated by inoculating germ-free individuals with the microbiota. RESULTS Antibiotic-induced disturbance of the microbiota had a strong effect on the subsequent colonization of Daphnia by affecting ecological interactions between members of the microbiota. This resulted in differences in community assembly which, in turn, affected Daphnia growth. CONCLUSIONS These results show that the composition of the pool of colonizing microbiota can be an important structuring factor of the microbiota assembly on Daphnia, affecting holobiont composition and host growth. These findings contribute to a better understanding of how the microbial environment can shape the holobiont composition and affect host-microbiota interactions.
Collapse
Affiliation(s)
- Martijn Callens
- Aquatic Biology, Science and Technology, IRF Life Sciences, KU Leuven, Campus Kortrijk, E. Sabbelaan 53, 8500, Kortrijk, Belgium
- Centre d'Ecologie Fonctionelle Evolutive, CNRS Montpellier, UMR 5175, 1919 route de Mende, 34293, Montpellier CEDEX 5, France
| | - Hajime Watanabe
- Bioenvironmental Science, Osaka University, Yamadaoka, Suita, Osaka, 565 0871, Japan
| | - Yasuhiko Kato
- Bioenvironmental Science, Osaka University, Yamadaoka, Suita, Osaka, 565 0871, Japan
| | - Jun Miura
- Bioenvironmental Science, Osaka University, Yamadaoka, Suita, Osaka, 565 0871, Japan
| | - Ellen Decaestecker
- Aquatic Biology, Science and Technology, IRF Life Sciences, KU Leuven, Campus Kortrijk, E. Sabbelaan 53, 8500, Kortrijk, Belgium.
| |
Collapse
|
16
|
Houwenhuyse S, Macke E, Reyserhove L, Bulteel L, Decaestecker E. Back to the future in a petri dish: Origin and impact of resurrected microbes in natural populations. Evol Appl 2018; 11:29-41. [PMID: 29302270 PMCID: PMC5748525 DOI: 10.1111/eva.12538] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/14/2017] [Indexed: 12/17/2022] Open
Abstract
Current natural populations face new interactions because of the re-emergence of ancient microbes and viruses. These risks come from the re-emergence of pathogens kept in laboratories or from pathogens that are retained in the permafrost, which become available upon thawing due to climate change. We here focus on the effects of such re-emergence in natural host populations based on evolutionary theory of virulence and long-term studies, which investigate host-pathogen adaptations. Pathogens tend to be locally and temporally adapted to their co-occurring hosts, but when pathogens from a different environment or different time enter the host community, the degree to which a new host-pathogen interaction is a threat will depend on the specific genotypic associations, the time lag between the host and the pathogen, and the interactions with native or recent host and pathogen species. Some insights can be obtained from long-term studies using a resurrection ecology approach. These long-term studies based on time-shift experiments are essential to obtain insight into the mechanisms underlying host-pathogen coevolution at several ecological and temporal scales. As past pathogens and their corresponding host(s) can differ in infectivity and susceptibility, strong reciprocal selective pressures can be induced by the pathogen. These strong selective pressures often result in an escalating arms race, but do not necessarily result in increased infectivity over time. Human health can also be impacted by these resurrected pathogens as the majority of emerging infectious diseases are zoonoses, which are infectious diseases originating from animal populations naturally transmitted to humans. The sanitary risk associated with pathogen emergence from different environments (spatial or temporal) depends on a combination of socioeconomic, environmental, and ecological factors that affect the virulence or the pathogenic potential of microbes and their ability to infect susceptible host populations.
Collapse
|
17
|
Kim Hue NT, Deruyck B, Decaestecker E, Vandamme D, Muylaert K. Natural chemicals produced by marine microalgae as predator deterrents can be used to control ciliates contamination in microalgal cultures. ALGAL RES 2018. [DOI: 10.1016/j.algal.2017.11.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
18
|
Macke E, Callens M, De Meester L, Decaestecker E. Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria. Nat Commun 2017; 8:1608. [PMID: 29151571 PMCID: PMC5694789 DOI: 10.1038/s41467-017-01714-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 10/11/2017] [Indexed: 12/20/2022] Open
Abstract
The gut microbiota impacts many aspects of its host's biology, and is increasingly considered as a key factor mediating performance of host individuals in continuously changing environments. Here we use gut microbiota transplants to show that both host genotype and gut microbiota mediate tolerance to toxic cyanobacteria in the freshwater crustacean Daphnia magna. Interclonal variation in tolerance to cyanobacteria disappears when Daphnia are made germ-free and inoculated with an identical microbial inoculum. Instead, variation in tolerance among recipient Daphnia mirrors that of the microbiota donors. Metagenetic analyses point to host genotype and external microbial source as important determinants of gut microbiota assembly, and reveal strong differences in gut microbiota composition between tolerant and susceptible genotypes. Together, these results show that both environmentally and host genotype-induced variations in gut microbiota structure mediate Daphnia tolerance to toxic cyanobacteria, pointing to the gut microbiota as a driver of adaptation and acclimatization to cyanobacterial harmful algal blooms in zooplankton.
Collapse
Affiliation(s)
- Emilie Macke
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, B-8500, Kortrijk, Belgium.
| | - Martijn Callens
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, B-8500, Kortrijk, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Charles Deberiotstraat 32, 3000, Leuven, Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, B-8500, Kortrijk, Belgium.
| |
Collapse
|
19
|
Orsini L, Brown JB, Shams Solari O, Li D, He S, Podicheti R, Stoiber MH, Spanier KI, Gilbert D, Jansen M, Rusch DB, Pfrender ME, Colbourne JK, Frilander MJ, Kvist J, Decaestecker E, De Schamphelaere KAC, De Meester L. Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes. Mol Ecol 2017; 27:886-897. [PMID: 28746735 DOI: 10.1111/mec.14261] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/12/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023]
Abstract
Natural habitats are exposed to an increasing number of environmental stressors that cause important ecological consequences. However, the multifarious nature of environmental change, the strength and the relative timing of each stressor largely limit our understanding of biological responses to environmental change. In particular, early response to unpredictable environmental change, critical to survival and fitness in later life stages, is largely uncharacterized. Here, we characterize the early transcriptional response of the keystone species Daphnia magna to twelve environmental perturbations, including biotic and abiotic stressors. We first perform a differential expression analysis aimed at identifying differential regulation of individual genes in response to stress. This preliminary analysis revealed that a few individual genes were responsive to environmental perturbations and they were modulated in a stressor and genotype-specific manner. Given the limited number of differentially regulated genes, we were unable to identify pathways involved in stress response. Hence, to gain a better understanding of the genetic and functional foundation of tolerance to multiple environmental stressors, we leveraged the correlative nature of networks and performed a weighted gene co-expression network analysis. We discovered that approximately one-third of the Daphnia genes, enriched for metabolism, cell signalling and general stress response, drives transcriptional early response to environmental stress and it is shared among genetic backgrounds. This initial response is followed by a genotype- and/or condition-specific transcriptional response with a strong genotype-by-environment interaction. Intriguingly, genotype- and condition-specific transcriptional response is found in genes not conserved beyond crustaceans, suggesting niche-specific adaptation.
Collapse
Affiliation(s)
- Luisa Orsini
- Environmental Genomics Group, School of Biosciences, University of Birmingham Edgbaston, Birmingham, UK
| | - James B Brown
- Environmental Bioinformatics, Centre for Computational Biology, School of Biosciences, University of Birmingham Edgbaston, Birmingham, UK.,Department of Molecular Ecosystems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Statistics Department, University of California, Berkeley, CA, USA.,Preminon LLC, Rodeo, CA, USA
| | | | - Dong Li
- School of Computer Science, University of Birmingham Edgbaston, Birmingham, UK
| | - Shan He
- School of Computer Science, University of Birmingham Edgbaston, Birmingham, UK
| | - Ram Podicheti
- School of Informatics and Computing, Indiana University, Bloomington, IN, USA.,Center for Genomics and Bioinformatics, Indiana University and School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Marcus H Stoiber
- Department of Molecular Ecosystems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katina I Spanier
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Donald Gilbert
- Biology Department, Indiana University, Bloomington, IN, USA
| | - Mieke Jansen
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, School of Informatics and Computing, Indiana University, Bloomington, IN, USA
| | - Michael E Pfrender
- Department of Biological Sciences, Eck Institute for Global Health & Environmental Change Initiative, Galvin Life Science Center, Notre Dame, IN, USA
| | - John K Colbourne
- Environmental Genomics Group, School of Biosciences, University of Birmingham Edgbaston, Birmingham, UK
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jouni Kvist
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ellen Decaestecker
- Aquatic Biology, Interdisciplinary Research Facility Life Sciences KU Leuven Campus Kortrijk, Kortrijk, Belgium
| | - Karel A C De Schamphelaere
- Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab, Ghent University, Ghent, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Leuven, Belgium
| |
Collapse
|
20
|
Reyserhove L, Muylaert K, Vanoverberghe I, Decaestecker E. Synergistic effects of dual parasitism in Daphnia magna under nutrient limitation. BELG J ZOOL 2017. [DOI: 10.26496/bjz.2017.5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Human-induced increases in the bioavailability of carbon (C), nitrogen (N) and phosphorus (P) have the potential to alter the context for host-parasite dynamics in aquatic ecosystems. Given that both eutrophication and infectious diseases are becoming more prominent, it is essential to disentangle the factors that determine virulence expression in keystone grazers. Here, we focus on the impact of nutrient limitation in single versus dual parasite exposure in the water flea Daphnia magna (Crustacea, Branchiopoda). For this, we fed specimens of D. magna with algae differing in C:N:P ratios and exposed them to two virulent parasites, Pasteuria ramosa (bacteria) and the agent causing White Fat Cell (WFCD, unknown classification), both in single and dual parasite exposure treatments. Exposure to the two parasites synergistically reduced host survival, mainly driven by WFCD exposure, especially under severe nutrient limitation. Under these conditions individuals of D. magna began reproducing earlier, which resulted in a higher reproductive output upon dual parasite exposure. We here discuss these results within the framework of host stress responses, nutrient allocation and energy budgets, and conclude that the way food quality interferes with host-parasite interactions varies, depending on the parasite species involved, the nutrient requirements of all actors and the trait investigated.
Collapse
|
21
|
Spanier KI, Jansen M, Decaestecker E, Hulselmans G, Becker D, Colbourne JK, Orsini L, De Meester L, Aerts S. Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia. Genome Biol Evol 2017; 9:1821-1842. [PMID: 28854641 PMCID: PMC5569996 DOI: 10.1093/gbe/evx127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2017] [Indexed: 02/06/2023] Open
Abstract
Ecological genomics aims to understand the functional association between environmental gradients and the genes underlying adaptive traits. Many genes that are identified by genome-wide screening in ecologically relevant species lack functional annotations. Although gene functions can be inferred from sequence homology, such approaches have limited power. Here, we introduce ecological regulatory genomics by presenting an ontology-free gene prioritization method. Specifically, our method combines transcriptome profiling with high-throughput cis-regulatory sequence analysis in the water fleas Daphnia pulex and Daphnia magna. It screens coexpressed genes for overrepresented DNA motifs that serve as transcription factor binding sites, thereby providing insight into conserved transcription factors and gene regulatory networks shaping the expression profile. We first validated our method, called Daphnia-cisTarget, on a D. pulex heat shock data set, which revealed a network driven by the heat shock factor. Next, we performed RNA-Seq in D. magna exposed to the cyanobacterium Microcystis aeruginosa. Daphnia-cisTarget identified coregulated gene networks that associate with the moulting cycle and potentially regulate life history changes in growth rate and age at maturity. These networks are predicted to be regulated by evolutionary conserved transcription factors such as the homologues of Drosophila Shavenbaby and Grainyhead, nuclear receptors, and a GATA family member. In conclusion, our approach allows prioritising candidate genes in Daphnia without bias towards prior knowledge about functional gene annotation and represents an important step towards exploring the molecular mechanisms of ecological responses in organisms with poorly annotated genomes.
Collapse
Affiliation(s)
- Katina I. Spanier
- Department of Biology, Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Belgium
- Department of Human Genetics, Laboratory of Computational Biology, KU Leuven, Belgium
- VIB Center for Brain and Disease Research, KU Leuven, Belgium
| | - Mieke Jansen
- Department of Biology, Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Belgium
| | - Ellen Decaestecker
- Department of Biology, Laboratory of Aquatic Biology, Science and Technology, KU Leuven Campus Kulak, Kortrjik, Belgium
| | - Gert Hulselmans
- Department of Human Genetics, Laboratory of Computational Biology, KU Leuven, Belgium
- VIB Center for Brain and Disease Research, KU Leuven, Belgium
| | - Dörthe Becker
- Environmental Genomics Group, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, United Kingdom
| | - John K. Colbourne
- Environmental Genomics Group, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, United Kingdom
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, United Kingdom
| | - Luc De Meester
- Department of Biology, Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Belgium
| | - Stein Aerts
- Department of Human Genetics, Laboratory of Computational Biology, KU Leuven, Belgium
- VIB Center for Brain and Disease Research, KU Leuven, Belgium
| |
Collapse
|
22
|
Orsini L, Gilbert D, Podicheti R, Jansen M, Brown JB, Solari OS, Spanier KI, Colbourne JK, Rusch DB, Decaestecker E, Asselman J, De Schamphelaere KAC, Ebert D, Haag CR, Kvist J, Laforsch C, Petrusek A, Beckerman AP, Little TJ, Chaturvedi A, Pfrender ME, De Meester L, Frilander MJ. Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Sci Data 2017; 4:170006. [PMID: 28140384 PMCID: PMC5283058 DOI: 10.1038/sdata.2017.6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
23
|
Affiliation(s)
- Emilie Macke
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
| | | | - François Massol
- Univ. Lille; CNRS UMR 8198 Evo-Eco-Paleo SPICI group Lille France
| | - Martijn Callens
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
| | - Ellen Decaestecker
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
| |
Collapse
|
24
|
Asselman J, De Coninck DI, Beert E, Janssen CR, Orsini L, Pfrender ME, Decaestecker E, De Schamphelaere KA. Bisulfite Sequencing with Daphnia Highlights a Role for Epigenetics in Regulating Stress Response to Microcystis through Preferential Differential Methylation of Serine and Threonine Amino Acids. Environ Sci Technol 2017; 51:924-931. [PMID: 27983812 DOI: 10.1021/acs.est.6b03870] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Little is known about the influence that environmental stressors may have on genome-wide methylation patterns, and to what extent epigenetics may be involved in environmental stress response. Yet, studies of methylation patterns under stress could provide crucial insights on stress response and toxicity pathways. Here, we focus on genome-wide methylation patterns in the microcrustacean Daphnia magna, a model organism in ecotoxicology and risk assessment, exposed to the toxic cyanobacterium Microcystis aeruginosa. Bisulfite sequencing of exposed and control animals highlighted differential methylation patterns in Daphnia upon exposure to Microcystis primarily in exonic regions. These patterns are enriched for serine/threonine amino acid codons and genes related to protein synthesis, transport and degradation. Furthermore, we observed that genes with differential methylation corresponded well with genes susceptible to alternative splicing in response to Microcystis stress. Overall, our results suggest a complex mechanistic response in Daphnia characterized by interactions between DNA methylation and gene regulation mechanisms. These results underscore that DNA methylation is modulated by environmental stress and can also be an integral part of the toxicity response in our study species.
Collapse
Affiliation(s)
- Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University , Ghent, B-9000, Belgium
- Department of Biological Sciences, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Dieter Im De Coninck
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University , Ghent, B-9000, Belgium
| | - Eline Beert
- Laboratory of Aquatic Biology, KU Leuven-Kulak , Kortrijk, B-8500, Belgium
| | - Colin R Janssen
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University , Ghent, B-9000, Belgium
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, University of Birmingham , Birmingham, B15 2TT, United Kingdom
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame , Notre Dame, Indiana 46556, United States
- Environmental Change Initiative, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, KU Leuven-Kulak , Kortrijk, B-8500, Belgium
| | - Karel Ac De Schamphelaere
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University , Ghent, B-9000, Belgium
| |
Collapse
|
25
|
Callens M, Macke E, Muylaert K, Bossier P, Lievens B, Waud M, Decaestecker E. Food availability affects the strength of mutualistic host-microbiota interactions in Daphnia magna. ISME J 2015; 10:911-20. [PMID: 26405832 DOI: 10.1038/ismej.2015.166] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 07/14/2015] [Accepted: 08/10/2015] [Indexed: 01/15/2023]
Abstract
The symbiotic gut microbial community is generally known to have a strong impact on the fitness of its host. Nevertheless, it is less clear how the impact of symbiotic interactions on the hosts' fitness varies according to environmental circumstances such as changes in the diet. This study aims to get a better understanding of host-microbiota interactions under different levels of food availability. We conducted experiments with the invertebrate, experimental model organism Daphnia magna and compared growth, survival and reproduction of conventionalized symbiotic Daphnia with germ-free individuals given varying quantities of food. Our experiments revealed that the relative importance of the microbiota for the hosts' fitness varied according to dietary conditions. The presence of the microbiota had strong positive effects on Daphnia when food was sufficient or abundant, but had weaker effects under food limitation. Our results indicate that the microbiota can be a potentially important factor in determining host responses to changes in dietary conditions. Characterization of the host-associated microbiota further showed that Aeromonas sp. was the most prevalent taxon in the digestive tract of Daphnia.
Collapse
Affiliation(s)
- Martijn Callens
- Laboratory of Aquatic Biology, Science & Technology, KULeuven Campus Kulak, Kortrijk, Belgium
| | - Emilie Macke
- Laboratory of Aquatic Biology, Science & Technology, KULeuven Campus Kulak, Kortrijk, Belgium
| | - Koenraad Muylaert
- Laboratory of Aquatic Biology, Science & Technology, KULeuven Campus Kulak, Kortrijk, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Production, UGent, Ghent, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KULeuven Campus De Nayer, Sint-Katelijne-Waver, Belgium
| | - Michael Waud
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KULeuven Campus De Nayer, Sint-Katelijne-Waver, Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Science & Technology, KULeuven Campus Kulak, Kortrijk, Belgium
| |
Collapse
|
26
|
Abstract
Increased productivity due to nutrient enrichment is hypothesized to affect density-dependent processes, such as transmission success of horizontally transmitting parasites. Changes in nutrient availability can also modify the stoichiometry and condition of individual hosts, which may affect their susceptibility for parasites as well as the growth conditions for parasites within the host. Consequently, if not balanced by increased host immuno-competence or life history responses, changes in the magnitude of parasite effects with increasing nutrient availability are expected. If these parasite effects are host-species specific, this may lead to shifts in the host community structure. We here used the Daphnia- parasite model system to study the effect of nutrient enrichment on parasite-mediated competition in experimental mesocosms. In the absence of parasites, D. magna was competitively dominant to D. pulex at both low and high nutrient levels. Introduction of parasites resulted in infections of D. magna, but not of D. pulex and, as such, reversed the competitive hierarchy between these two species. Nutrient addition resulted in an increased prevalence and infection intensity of some of the parasites on D. magna. However, there was no evidence that high nutrient levels enhanced negative effects of parasites on the hosts. Costs associated with parasite infections may have been compensated by better growth conditions for D. magna in the presence of high nutrient levels.
Collapse
|
27
|
Aalto SL, Decaestecker E, Pulkkinen K. A three-way perspective of stoichiometric changes on host-parasite interactions. Trends Parasitol 2015; 31:333-40. [PMID: 25978937 DOI: 10.1016/j.pt.2015.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/09/2015] [Accepted: 04/09/2015] [Indexed: 01/18/2023]
Abstract
Changes in environmental nutrients play a crucial role in driving disease dynamics, but global patterns in nutrient-driven changes in disease are difficult to predict. In this paper we use ecological stoichiometry as a framework to review host-parasite interactions under changing nutrient ratios, focusing on three pathways: (i) altered host resistance and parasite virulence through host stoichiometry (ii) changed encounter or contact rates at population level, and (iii) changed host community structure. We predict that the outcome of nutrient changes on host-parasite interactions depends on which pathways are modified, and suggest that the outcome of infection could depend on the overlap in stoichiometric requirements of the host and the parasite. We hypothesize that environmental nutrient enrichment alters infectivity dynamics leading to fluctuating selection dynamics in host-parasite coevolution.
Collapse
Affiliation(s)
- Sanni L Aalto
- Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, 40014 Jyväskylä, Finland.
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Department of Biology, Katholieke Universiteit Leuven Kulak, Etienne Sabbelaan 53, 8500 Kortrijk, Belgium
| | - Katja Pulkkinen
- Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, 40014 Jyväskylä, Finland
| |
Collapse
|
28
|
Asselman J, De Coninck DIM, Vandegehuchte MB, Jansen M, Decaestecker E, De Meester L, Vanden Bussche J, Vanhaecke L, Janssen CR, De Schamphelaere KAC. Global cytosine methylation in Daphnia magna depends on genotype, environment, and their interaction. Environ Toxicol Chem 2015; 34:1056-1061. [PMID: 25639773 DOI: 10.1002/etc.2887] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/13/2014] [Accepted: 01/06/2015] [Indexed: 06/04/2023]
Abstract
The authors characterized global cytosine methylation levels in 2 different genotypes of the ecotoxicological model organism Daphnia magna after exposure to a wide array of biotic and abiotic environmental stressors. The present study aimed to improve the authors' understanding of the role of cytosine methylation in the organism's response to environmental conditions. The authors observed a significant genotype effect, an environment effect, and a genotype × environment effect. In particular, global cytosine methylation levels were significantly altered after exposure to Triops predation cues, Microcystis, and sodium chloride compared with control conditions. Significant differences between the 2 genotypes were observed when animals were exposed to Triops predation cues, Microcystis, Cryptomonas, and sodium chloride. Despite the low global methylation rate under control conditions (0.49-0.52%), global cytosine methylation levels upon exposure to Triops demonstrated a 5-fold difference between the genotypes (0.21% vs 1.02%). No effects were found in response to arsenic, cadmium, fish, lead, pH of 5.5, pH of 8, temperature, hypoxia, and white fat cell disease. The authors' results point to the potential role of epigenetic effects under changing environmental conditions such as predation (i.e., Triops), diet (i.e., Cryptomonas and Microcystis), and salinity. The results of the present study indicate that, despite global cytosine methylation levels being low, epigenetic effects may be important in environmental studies on Daphnia.
Collapse
Affiliation(s)
- Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab), Ghent University, Ghent, Belgium
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Lange B, Reuter M, Ebert D, Muylaert K, Decaestecker E. Diet quality determines interspecific parasite interactions in host populations. Ecol Evol 2014; 4:3093-102. [PMID: 25247066 PMCID: PMC4161182 DOI: 10.1002/ece3.1167] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 11/08/2022] Open
Abstract
The widespread occurrence of multiple infections and the often vast range of nutritional resources for their hosts allow that interspecific parasite interactions in natural host populations might be determined by host diet quality. Nevertheless, the role of diet quality with respect to multispecies parasite interactions on host population level is not clear. We here tested the effect of host population diet quality on the parasite community in an experimental study using Daphnia populations. We studied the effect of diet quality on Daphnia population demography and the interactions in multispecies parasite infections of this freshwater crustacean host. The results of our experiment show that the fitness of a low-virulent microsporidian parasite decreased in low, but not in high-host-diet quality conditions. Interestingly, infections with the microsporidium protected Daphnia populations against a more virulent bacterial parasite. The observed interspecific parasite interactions are discussed with respect to the role of diet quality-dependent changes in host fecundity. This study reflects that exploitation competition in multispecies parasite infections is environmentally dependent, more in particular it shows that diet quality affects interspecific parasite competition within a single host and that this can be mediated by host population-level effects.
Collapse
Affiliation(s)
- Benjamin Lange
- Laboratory Aquatic Biology, Science & Technology-Kulak, KU LeuvenKortrijk, 8500, Belgium
| | - Max Reuter
- Department of Genetics, Evolution & Environment, University College LondonLondon, WC1E 6BT, UK
| | - Dieter Ebert
- Zoological Institute, University of BaselBasel, CH-4051, Switzerland
| | - Koenraad Muylaert
- Laboratory Aquatic Biology, Science & Technology-Kulak, KU LeuvenKortrijk, 8500, Belgium
| | - Ellen Decaestecker
- Laboratory Aquatic Biology, Science & Technology-Kulak, KU LeuvenKortrijk, 8500, Belgium
| |
Collapse
|
30
|
Decaestecker E, De Gersem H, Michalakis Y, Raeymaekers JA. Damped long-term host-parasite Red Queen coevolutionary dynamics: a reflection of dilution effects? Ecol Lett 2013; 16:1455-62. [DOI: 10.1111/ele.12186] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 08/15/2013] [Accepted: 08/29/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Ellen Decaestecker
- Aquatic Biology; IRF Life Sciences; Science & Technology; KULeuven-Kulak; KULeuven; Kortrijk B-8500 West-Vlaanderen Belgium
| | - Herbert De Gersem
- Wave Propagation and Signal Processing Research Group; Department of Physics and Astronomy; Science & Technology; KULeuven-Kulak; KULeuven; Kortrijk B-8500 Belgium
| | - Yannis Michalakis
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique; Evolution et Contrôle; CNRS IRD; Montpellier 34394 France
| | - Joost A.M. Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics; KULeuven; Leuven B-3000 Belgium
- University of Basel; Zoological Institute; Vesalgasse 1 CH-4051 Basel Switzerland
| |
Collapse
|
31
|
Verreydt D, De Meester L, Decaestecker E, Villena MJ, Van Der Gucht K, Vannormelingen P, Vyverman W, Declerck SA. Dispersal-mediated trophic interactions can generate apparent patterns of dispersal limitation in aquatic metacommunities. Ecol Lett 2012; 15:218-26. [DOI: 10.1111/j.1461-0248.2011.01728.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
32
|
Decaestecker E, Labbé P, Ellegaard K, Allen JE, Little TJ. Candidate innate immune system gene expression in the ecological model Daphnia. Dev Comp Immunol 2011; 35:1068-1077. [PMID: 21550363 PMCID: PMC3170911 DOI: 10.1016/j.dci.2011.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 04/02/2011] [Accepted: 04/02/2011] [Indexed: 05/30/2023]
Abstract
The last ten years have witnessed increasing interest in host-pathogen interactions involving invertebrate hosts. The invertebrate innate immune system is now relatively well characterised, but in a limited range of genetic model organisms and under a limited number of conditions. Immune systems have been little studied under real-world scenarios of environmental variation and parasitism. Thus, we have investigated expression of candidate innate immune system genes in the water flea Daphnia, a model organism for ecological genetics, and whose capacity for clonal reproduction facilitates an exceptionally rigorous control of exposure dose or the study of responses at many time points. A unique characteristic of the particular Daphnia clones and pathogen strain combinations used presently is that they have been shown to be involved in specific host-pathogen coevolutionary interactions in the wild. We choose five genes, which are strong candidates to be involved in Daphnia-pathogen interactions, given that they have been shown to code for immune effectors in related organisms. Differential expression of these genes was quantified by qRT-PCR following exposure to the bacterial pathogen Pasteuria ramosa. Constitutive expression levels differed between host genotypes, and some genes appeared to show correlated expression. However, none of the genes appeared to show a major modification of expression level in response to Pasteuria exposure. By applying knowledge from related genetic model organisms (e.g. Drosophila) to models for the study of evolutionary ecology and coevolution (i.e. Daphnia), the candidate gene approach is temptingly efficient. However, our results show that detection of only weak patterns is likely if one chooses target genes for study based on previously identified genome sequences by comparison to homologues from other related organisms. Future work on the Daphnia-Pasteuria system will need to balance a candidate gene approach with more comprehensive approaches to de novo identify immune system genes specific to the Daphnia-Pasteuria interaction.
Collapse
Affiliation(s)
- Ellen Decaestecker
- Aquatic Biology, Science & Technology, IRF-Life Sciences, K.U.Leuven-Campus Kortrijk, Belgium.
| | | | | | | | | |
Collapse
|
33
|
Pauwels K, De Meester L, Decaestecker E, Stoks R. Phenoloxidase but not lytic activity reflects resistance against Pasteuria ramosa in Daphnia magna. Biol Lett 2010; 7:156-9. [PMID: 20810432 DOI: 10.1098/rsbl.2010.0634] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The field of ecological immunology strongly relies on indicators of immunocompetence. Two major indicators in invertebrates, the activity of phenoloxidase (PO) and lytic activity have recently been questioned in studies showing that, across a natural range of baseline levels, these indicators did not predict resistance against a manipulated challenge with natural parasites. We confirmed this finding by showing that baseline levels of PO and lytic activity in the host Daphnia magna were not related to spore load of the parasite Pasteuria ramosa. Yet, PO levels in infected hosts did predict spore load, indicating PO activity can be useful as an indicator of immunocompetence in this model parasite-host system.
Collapse
Affiliation(s)
- Kevin Pauwels
- Laboratory of Aquatic Ecology and Evolutionary Biology, K.U. Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium.
| | | | | | | |
Collapse
|
34
|
Abstract
This meeting report presents the cutting-edge research that is developing around the waterflea Daphnia, an emerging model system in environmental genomics. Daphnia has been a model species in ecology, toxicology and evolution for many years and is supported by a large community of ecologists, evolutionary biologists and ecotoxicologists. Thanks to new advances in genomics and transciptomics and to the sustained efforts of the Daphnia Genomics Consortium (DGC), Daphnia is also rapidly developing as a model system in environmental genomics. Advances in this emerging field were presented at the DGC 2010, held for the first time in a European University. During the meeting, a plethora of elegant studies were presented on the mechanisms of responses to environmental challenges using recently developed genomic tools. The DGC 2010 is a concrete example of the new trends in ecology and evolution. The times are mature for the application of innovative genomic and transcriptomic tools for studies of environmental genomics in non-model organisms.
Collapse
Affiliation(s)
- Luisa Orsini
- Laboratory of Aquatic Ecology and Evolutionary Biology, , K.U. Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium.
| | | | | | | | | |
Collapse
|
35
|
Jansen M, Stoks R, Decaestecker E, Coors A, Van De Meutter F, De Meester L. Local exposure shapes spatial patterns in infectivity and community structure of Daphnia parasites. J Anim Ecol 2010; 79:1023-33. [PMID: 20584096 DOI: 10.1111/j.1365-2656.2010.01718.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
1. Spatial patterns in parasite community structure are probably driven by the availability of infectious stages. This is because hosts become infected through picking up infectious stages from their environment. Several studies have, however, reported strong genotype by genotype interactions and parasite-mediated selection in hosts. This leads to the prediction of a parasite by host population interaction with respect to infection rates and intensities, which may also shape spatial patterns in parasite community structure. 2. Using the water flea Daphnia magna and its microparasites as a model, we carried out a laboratory experiment to test explicitly to what extent parasite community structure in host populations is determined by the availability of infectious stages in the sediment they are exposed to, and to what extent host population identity and location play a role. 3. We exposed 10 D. magna host populations each to sediment of their own habitat and sediment of the other nine habitats, and monitored the parasite community of the resulting experimental populations. 4. Sediment seems to be a strong determinant of parasite infection rates, while there was no overall effect of host population. Sympatric parasite and host population combinations did in most cases not result in significantly different infection rates than allopatric parasite and host combinations. Our results indicate that spore availability could be the key variable determining parasite community structure in natural Daphnia populations.
Collapse
Affiliation(s)
- Mieke Jansen
- Laboratory of Aquatic Ecology and Evolutionary Biology, K.U.Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium.
| | | | | | | | | | | |
Collapse
|
36
|
|
37
|
Abstract
The description of coevolutionary dynamics requires a characterization of the evolutionary dynamics of both the parasite and its host. However, a thorough description of the underlying genetics of the coevolutionary process is often extremely difficult to carry out. We propose that measures of adaptation (mean population fitness) across time or space may represent a feasible alternative approach for characterizing important features of the coevolutionary process. We discuss recent experimental work in the light of simple mathematical models of coevolution to demonstrate the potential power of this phenotypic experimental approach.
Collapse
Affiliation(s)
- S Gandon
- Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France.
| | | | | | | |
Collapse
|
38
|
Decaestecker E, Gaba S, Raeymaekers JAM, Stoks R, Van Kerckhoven L, Ebert D, De Meester L. Host–parasite ‘Red Queen’ dynamics archived in pond sediment. Nature 2007; 450:870-3. [PMID: 18004303 DOI: 10.1038/nature06291] [Citation(s) in RCA: 413] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 09/21/2007] [Indexed: 11/09/2022]
|
39
|
Pauwels K, Stoks R, Decaestecker E, De Meester L. Evolution of Heat Shock Protein Expression in a Natural Population of Daphnia magna. Am Nat 2007; 170:800-5. [DOI: 10.1086/521956] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Accepted: 06/28/2007] [Indexed: 11/03/2022]
|
40
|
Abstract
It has been suggested that the harm parasites cause to their hosts is an unavoidable consequence of parasite reproduction with costs not only for the host but also for the parasite. Castrating parasites are thought to minimize their costs by reducing host fecundity, which may minimize the chances of killing both host and parasite prematurely. We conducted a series of experiments to understand the evolution of virulence of a castrating bacterium in the planktonic crustacean Daphnia magna. By manipulating food levels during the infection of D. magna with the bacterium Pasteuria ramosa, we showed that both antagonists are resource-limited and that a negative correlation between host and parasite reproduction exists, indicating resource competition among the antagonists. Pasteuria ramosa also induces enhanced growth of its hosts (gigantism), which we found to be negatively correlated with host fecundity but positively correlated with parasite reproduction. Because infected hosts never recovered from infections, we concluded that gigantism is beneficial only for the parasite. Hosts, however, have evolved counteradaptations. We showed that infected hosts have enhanced reproduction before castration. This shift to earlier reproduction increases overall host fecundity and compromises parasite reproduction. Finally, we showed that this resource conflict is subject to genetic variation among host and parasite genotypes within a population and is therefore likely to be an important force in the coevolution of virulence in this system. A verbal model is presented and suggests that the adaptive value of gigantism is to store host resources, which are liberated after parasitic castration for later use by the growing parasite. This hypothesis assumes that infections are long lasting, that is, that they have a high life expectancy.
Collapse
Affiliation(s)
- Dieter Ebert
- Universitat Basel, Zoologisches Institut, Vesalgasse 1, 4051 Basel, Switzerland.
| | | | | | | |
Collapse
|
41
|
Decaestecker E, Declerck S, De Meester L, Ebert D. Ecological implications of parasites in natural Daphnia populations. Oecologia 2005; 144:382-90. [PMID: 15891825 DOI: 10.1007/s00442-005-0083-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Accepted: 02/24/2005] [Indexed: 10/25/2022]
Abstract
In natural host populations, parasitism is considered to be omnipresent and to play an important role in shaping host life history and population dynamics. Here, we study parasitism in natural populations of the zooplankton host Daphnia magna investigating their individual and population level effects during a 2-year field study. Our results revealed a rich and highly prevalent community of parasites, with eight endoparasite species (four microsporidia, one amoeba, two bacteria and one nematode) and six epibionts (belonging to five different taxa: Chlorophyta, Bacillariophyceae, Ciliata, Fungi and Rotifera). Several of the endoparasites were associated with a severe overall fecundity reduction of the hosts, while such effects were not seen for epibionts. In particular, infections by Pasteuria ramosa, White Fat Cell Disease and Flabelliforma magnivora were strongly associated with a reduction in overall D. magna fecundity. Across the sampling period, average population fecundity of D. magna was negatively associated with overall infection intensity and total endoparasite richness. Population density of D. magna was negatively correlated to overall endoparasite prevalence and positively correlated with epibiont richness. Finally, the reduction in host fecundity caused by different parasite species was negatively correlated to both parasite prevalence and the length of the time period during which the parasite persisted in the host population. Consistent with epidemiological models, these results indicate that parasite mediated host damages influence the population dynamics of both hosts and parasites.
Collapse
Affiliation(s)
- Ellen Decaestecker
- Laboratory of Aquatic Ecology, Catholic University of Leuven, Ch. De Bèriotstraat 32, 3000, Leuven, Belgium.
| | | | | | | |
Collapse
|
42
|
Decaestecker K, Decaestecker E, Castellani C, Jaspers M, Cuppens H, De Boeck K. Genotype/phenotype correlation of the G85E mutation in a large cohort of cystic fibrosis patients. Eur Respir J 2004; 23:679-84. [PMID: 15176679 DOI: 10.1183/09031936.04.00014804] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this European study, the phenotype in 68 patients, homozygous or compound heterozygous for the G85E mutation, was investigated. Each index case was compared with two cystic fibrosis (CF) patients from the same clinic, matched for age and sex: one with pancreatic sufficiency (PS) and one with pancreatic insufficiency (PI). When comparing 31 G85E/F508del and F508del/F508del patients, there were no differences in median age at diagnosis, mean sweat chloride value, most recent weight for height, most recent forced expiratory volume in one second % predicted, prevalence of chronic Pseudomonas aeruginosa colonisation and typical CF complications. However, PI was less frequent in the G85E/F508del group. Comparison of 55 G85E patients (with second mutation known and not classified as mild) with PS controls (n=44) showed that the G85E patients had a significantly higher sweat chloride, more often failure to thrive at diagnosis, higher prevalence of PI, worse current weight for height, higher prevalence of chronic P. aeruginosa colonisation and liver cirrhosis. Pulse-chase experiments revealed that G85E cystic fibrosis transmembrane conductance regulator failed to mature on a M470 as well as on a V470 background. Therefore, G85E is a class II mutation. Although there is variability in its clinical presentation, G85E mutation results in a severe phenotype.
Collapse
Affiliation(s)
- K Decaestecker
- Dept of Pediatrics, University of Leuven, Leuven, Belgium
| | | | | | | | | | | |
Collapse
|
43
|
Abstract
Organisms are often confronted with multiple enemy species. Defenses against different parasite species may be traded off against each other. However, if resistance is based on (potentially costly) general defense mechanisms, it may be positively correlated among parasites. In an experimental study, we confronted 19 clones from one Daphnia magna population with two bacterial and three microsporidian parasite species. All parasites were isolated from the same pond as the hosts. Host clones were specific in their susceptibility towards different parasite species, and parasite species were host-clone specific in their infectivity, spore production, and virulence, resulting in highly significant host-parasite interactions. Since the Daphnia's resistance to different parasite species showed no obvious correlation, neither general defense mechanisms nor trade-offs in resistance explain our findings. None of the Daphnia clones were resistant to all parasite species, and the average level of resistance was quite similar among clones. This may reflect a cost of defense, so that the cumulative cost of being resistant to all parasite species might be too high.
Collapse
Affiliation(s)
- Ellen Decaestecker
- Laboratory of Aquatic Ecology, Catholic University of Leuven, Ch. De Bériotstraat 32, 3000 Leuven, Belgium.
| | | | | | | |
Collapse
|
44
|
|
45
|
Abstract
Habitat selection behavior is an important predator-avoidance strategy for many organisms. Its particular expression is often explained as the result of a tradeoff between avoiding antagonists and acquiring resources. However, there is need for a broader perspective on this behavior, as organisms are often simultaneously involved in complex antagonistic relationships with multiple types of enemies. We show experimentally that a tradeoff between predator and parasite avoidance may be important in the evolution of habitat selection behavior in the waterflea, Daphnia magna. In this species, negatively phototactic clones suffer less from visually hunting predators by residing in deeper and darker portions of the water column during the day. However, this behavior increases the risk of parasitic infections when the Daphnia are exposed to pond sediments containing parasite spores. Positively phototactic clones, which are at a higher risk of predation, are less exposed to parasite spores in the sediment and consequently suffer less from parasitic infection. We show that the increased risk of infection remains even if the animals change their phototactic behavior on exposure to chemical cues from fish. This tradeoff highlights a substantial cost of predator-induced changes in habitat selection behavior. Tradeoffs caused by multiple enemies may explain genetic polymorphism for habitat selection behavior in many natural populations.
Collapse
Affiliation(s)
- Ellen Decaestecker
- Laboratory of Aquatic Ecology, Catholic University of Leuven, Charles de Bériotstraat 32, 3000 Leuven, Belgium.
| | | | | |
Collapse
|