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Warter MM, Tetzlaff D, Ring AM, Christopher J, Kissener HL, Funke E, Sparmann S, Mbedi S, Soulsby C, Monaghan MT. Environmental DNA, hydrochemistry and stable water isotopes as integrative tracers of urban ecohydrology. Water Res 2024; 250:121065. [PMID: 38159541 DOI: 10.1016/j.watres.2023.121065] [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] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Urbanization and the persistent environmental changes present a major challenge for urban freshwaters and availability of water for humans and wildlife. In order to increase understanding of urban ecohydrology, we investigated the variability of planktonic bacteria and benthic diatoms - as two key biological indicators - coupled with insights from hydrochemistry and stable water isotopes across four urban streams characterized by different dominant water sources in Berlin, the German capital, over a period of one year (2021-2022). DNA metabarcoding results show that substantial spatio-temporal variability exists across urban streams in terms of microbial diversity and richness, with clear links to abiotic factors and nutrient concentrations. Bacterial communities showed clear distinction between effluent-impacted and non-effluent impacted streams as well as clear seasonal turnover. In-stream benthic diatom assemblages also showed robust seasonal variation as well as high species diversity. Our multiple-tracer approach is relevant for emerging questions regarding the increased use of treated effluent to supplement declining baseflows, the assessment of stream restoration projects and the impact of storm drainage and surface pollution on aquatic ecosystem health. eDNA analysis allows analysis of spatial and temporal patterns not feasibly studied with traditional analyses of macroinvertebrates. This can ultimately be leveraged for future water resource management and restoration planning and monitoring of urban freshwater systems across metropolitan areas.
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Affiliation(s)
| | - Dörthe Tetzlaff
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Department of Geography, Humboldt University of Berlin, Berlin, Germany; Northern Rivers Institute, University of Aberdeen, St. Mary's Building, Kings College, Old Aberdeen, Scotland, United Kingdom
| | - Ann-Marie Ring
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Jan Christopher
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Hanna L Kissener
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Elisabeth Funke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sarah Sparmann
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Susan Mbedi
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Berlin, Germany; Museum für Naturkunde - Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany
| | - Chris Soulsby
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Department of Geography, Humboldt University of Berlin, Berlin, Germany; Chair of Water Resources Management and Modeling of Hydrosystems, Technical University Berlin, Berlin, Germany
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institute of Biology, Freie Universität Berlin, Berlin, Germany
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Thomé PC, Irisarri I, Wolinska J, Monaghan MT, Strassert JFH. Single-cell genomics reveals new rozellid lineages and supports their sister relationship to Microsporidia. Biol Lett 2023; 19:20230398. [PMID: 38087939 PMCID: PMC10716661 DOI: 10.1098/rsbl.2023.0398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The phylum Rozellomycota has been proposed for a group of early-branching holomycotan lineages representing obligate parasites and hyperparasites of zoosporic fungi, oomycotes or phytoplankton. Given their predominantly intracellular lifestyle, rozellids are typically known from environmental ribosomal DNA data, except for the well-studied Rozella species. To date, the phylogenetic relationship between rozellids and microsporidians (Microsporidia) is not fully understood and most reliable hypotheses are based on phylogenomic analyses that incorporate the only publicly available rozellid genome of Rozella allomycis. Here, we provide genomic data of three new rozellid lineages obtained by single-cell sequencing from environmental samples and show with a phylogenomic approach that rozellids form a monophyletic group that is sister to microsporidians, corroborating the previously proposed phylum Rozellomycota. Whereas no mitochondrial genes coding for the respiratory Complex I could be found, we discovered a gene coding for a nucleotide phosphate transporter in one of the three draft genomes. The scattered absence of Complex I genes and scattered presence of nucleotide transporter genes across diverse microsporidian and rozellid lineages suggest that these adaptations to a parasitic lifestyle, which reduce the parasite's capability to synthesize ATP but enables it to steal ATP from its host, evolved independently in microsporidians and rozellids.
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Affiliation(s)
- Pauline C. Thomé
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Iker Irisarri
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature Hamburg, Hamburg, Germany
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Michael T. Monaghan
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Jürgen F. H. Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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3
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Sire L, Schmidt Yáñez P, Bézier A, Courtial B, Mbedi S, Sparmann S, Larrieu L, Rougerie R, Bouget C, Monaghan MT, Herniou EA, Lopez-Vaamonde C. Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps. PeerJ 2023; 11:e16022. [PMID: 37842065 PMCID: PMC10573316 DOI: 10.7717/peerj.16022] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/11/2023] [Indexed: 10/17/2023] Open
Abstract
Background Broad-scale monitoring of arthropods is often carried out with passive traps (e.g., Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates has been found to be faster, efficient and reliable, but the destruction of samples prevents a posteriori validation of species occurrences and relative abundances. Non-destructive metabarcoding of DNA extracted from collection medium has been applied in a limited number of studies, but further tests of efficiency are required with different trap types and collection media to assess the consistency of the method. Methods We quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two combinations of passive traps and collection media: (1) water with monopropylene glycol (H2O-MPG) used in window-flight traps (WFT, 53 in total); (2) ethanol with monopropylene glycol (EtOH-MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba Mill., 1759) stands across a range of climate-induced tree dieback levels and forest management strategies. Results Of the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total, of which none matched any of the 343 beetle species morphologically identified from the same traps. Metabarcoding of 26 EtOH-MPG samples from MTs detected more arthropod MOTUs (233) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders), of which 71 were shared MOTUs, though MOTU richness per trap was similar between treatments. While we acknowledge the failure of metabarcoding from WFT-derived collection medium (H2O-MPG), the treatment of EtOH-based Malaise trapping medium remains promising. We conclude however that DNA metabarcoding from collection medium still requires further methodological developments and cannot replace homogenate metabarcoding as an approach for arthropod monitoring. It can be used nonetheless as a complementary treatment when enhancing the detection of soft-bodied arthropods like spiders and Diptera.
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Affiliation(s)
- Lucas Sire
- Institut de Recherche sur la Biologie de l’Insecte (IRBI), UMR7261 CNRS - Université de Tours, Tours, France
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR7205 Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Paul Schmidt Yáñez
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l’Insecte (IRBI), UMR7261 CNRS - Université de Tours, Tours, France
| | | | - Susan Mbedi
- Museum für Naturkunde –Leibniz Insitute for Evolution and Biodiversity Science, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Sarah Sparmann
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Laurent Larrieu
- Université de Toulouse, INRAE, UMR DYNAFOR, Castanet-Tolosan, France
- CRPF Occitanie, Tarbes, France
| | - Rodolphe Rougerie
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR7205 Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Christophe Bouget
- INRAE ’Forest Ecosystems’ Research Unit Domaine des Barres, Nogent-sur-Vernisson, France
| | - Michael T. Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte (IRBI), UMR7261 CNRS - Université de Tours, Tours, France
| | - Carlos Lopez-Vaamonde
- Institut de Recherche sur la Biologie de l’Insecte (IRBI), UMR7261 CNRS - Université de Tours, Tours, France
- INRAE, UR0633 Zoologie forestière, Orléans, France
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Gamboa M, Serrana J, Takemon Y, Monaghan MT, Watanabe K. Spatial and phylogenetic structure of Alpine stonefly assemblages across seven habitats using DNA-species. Oecologia 2023; 201:513-524. [PMID: 36680607 DOI: 10.1007/s00442-023-05321-0] [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: 09/06/2021] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Stream ecosystems are spatially heterogeneous, with many different habitat patches distributed within a small area. The influence of this heterogeneity on the biodiversity of benthic insect communities is well documented; however, studies of the role of habitat heterogeneity in species coexistence and assembly remain limited. Here, we investigated how habitat heterogeneity influences spatial structure (beta biodiversity) and phylogenetic structure (evolutionary processes) of benthic stonefly (Plecoptera, Insecta) communities. We sampled 20 sites along two Alpine rivers, including seven habitats in four different reaches (headwaters, meandering, bar-braided floodplain, and lowland spring-fed). We identified 21 morphological species and delineated 52 DNA-species based on sequences from mitochondrial cox1 and nuclear ITS markers. Using DNA-species, we first analysed the patterns of variation in richness, diversity, and assemblage composition by quantifing the contribution of each reach and habitat to the overall DNA-species diversity using an additive partition analysis and distance-based redundancy analysis. Using gene-tree phylogenies, we assessed whether environmental filtering could lead to the co-occurrence of DNA-species using a two-step analysis to detect a phylogenetic signal. All four reaches significantly contributed to DNA-species richness, with the meandering reach having the highest contribution. Habitats had an effect on DNA-species diversity, where glide, riffle and, pool influenced the spatial structure of stonefly assemblage possibly due to the high habitat heterogeneity. Among the habitats, the pool showed significant phylogenetic clustering, suggesting high levels of evolutionary adaptation and strong habitat filtering. This assemblage structure may be caused by long-term stability of the habitat and the similar requirements for co-occurring species. Our study shows the importance of different habitats for the spatial and phylogenetic structure of stonefly assemblage and sheds light on the habitat-specific diversity that may help improve conservation practices.
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Affiliation(s)
- Maribet Gamboa
- Department of Ecology, Universidad Católica de La Santísima Concepción, Concepción, Chile.
| | - Joeselle Serrana
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
- Center Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
| | - Yasuhiro Takemon
- Water Resources Research Center, Disaster Prevention Research Institute, Kyoto University, Gokasho, Uji, 6110011, Japan
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
- Institut Für Biologie, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195, Berlin, Germany
| | - Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
- Center Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
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Premke K, Wurzbacher C, Felsmann K, Fabian J, Taube R, Bodmer P, Attermeyer K, Nitzsche KN, Schroer S, Koschorreck M, Hübner E, Mahmoudinejad TH, Kyba CCM, Monaghan MT, Hölker F. Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes. Environ Pollut 2022; 308:119627. [PMID: 35714791 DOI: 10.1016/j.envpol.2022.119627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/17/2021] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Freshwater microbes play a crucial role in the global carbon cycle. Anthropogenic stressors that lead to changes in these microbial communities are likely to have profound consequences for freshwater ecosystems. Using field data from the coordinated sampling of 617 lakes, ponds, rivers, and streams by citizen scientists, we observed linkages between microbial community composition, light and chemical pollution, and greenhouse gas concentration. All sampled water bodies were net emitters of CO2, with higher concentrations in running waters, and increasing concentrations at higher latitudes. Light pollution occurred at 75% of sites, was higher in urban areas and along rivers, and had a measurable effect on the microbial alpha diversity. Genetic elements suggestive of chemical stress and antimicrobial resistances (IntI1, blaOX58) were found in 85% of sites, and were also more prevalent in urban streams and rivers. Light pollution and CO2 were significantly related to microbial community composition, with CO2 inversely related to microbial phototrophy. Results of synchronous nationwide sampling indicate that pollution-driven alterations to the freshwater microbiome lead to changes in CO2 production in natural waters and highlight the vulnerability of running waters to anthropogenic stressors.
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Affiliation(s)
- Katrin Premke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | | | - Katja Felsmann
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Jenny Fabian
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany
| | - Robert Taube
- City University of Applied Science, Bremen, Germany
| | | | - Katrin Attermeyer
- WasserCluster Lunz - Biologische Station, Lunz am See, Austria; Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Kai Nils Nitzsche
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Sibylle Schroer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | | | - Eric Hübner
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | | | - Christopher C M Kyba
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; GFZ German Research Centre for Geosciences, Helmholtz Centre, Potsdam, Germany
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institute für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Franz Hölker
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institute für Biologie, Freie Universität Berlin, Berlin, Germany
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Strassert JFH, Monaghan MT. Phylogenomic insights into the early diversification of fungi. Curr Biol 2022; 32:3628-3635.e3. [PMID: 35830854 DOI: 10.1016/j.cub.2022.06.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 03/23/2022] [Revised: 05/10/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022]
Abstract
Phylogenomic analyses have boosted our understanding of the evolutionary trajectories of all living forms by providing continuous improvements to the tree of life.1-5 Within this tree, fungi represent an ancient eukaryote group,6 having diverged from the animals ∼1.35 billion years ago.7 Estimates of the number of extant species range between 1.5 and 3.8 million.8,9 Recent reclassifications and the discovery of the deep-branching Sanchytriomycota lineage10 have brought the number of proposed phyla to 20,11 21 if the Microsporidia are included.12-14 Uncovering how the diverse and globally distributed fungi are related to each other is fundamental for understanding how their lifestyles, morphologies, and metabolic capacities evolved. To date, many of the proposed relationships among the phyla remain controversial and no phylogenomic study has examined the entire fungal tree using a taxonomically comprehensive dataset and suitable models of evolution. We assembled and curated a 299-protein dataset with a taxon sampling broad enough to encompass all recognized fungal diversity with available data, but selective enough to run computationally intensive analyses using best-fitting models. Using a range of reconstruction methods, we were able to resolve many contested nodes, such as a sister relationship of Chytridiomyceta to all other non-Opisthosporidia fungi (with Chytridiomycota being sister to Monoblepharomycota + Neocallimastigomycota), a branching of Blastocladiomycota + Sanchytriomycota after the Chytridiomyceta but before other non-Opisthosporidia fungi, and a branching of Glomeromycota as sister to the Dikarya. Our up-to-date fungal tree of life will serve as a springboard for future investigations on the early evolution of fungi.
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Affiliation(s)
- Jürgen F H Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.
| | - Michael T Monaghan
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
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Maasri A, Jähnig SC, Adamescu MC, Adrian R, Baigun C, Baird DJ, Batista‐Morales A, Bonada N, Brown LE, Cai Q, Campos‐Silva JV, Clausnitzer V, Contreras‐MacBeath T, Cooke SJ, Datry T, Delacámara G, De Meester L, Dijkstra KB, Do VT, Domisch S, Dudgeon D, Erös T, Freitag H, Freyhof J, Friedrich J, Friedrichs‐Manthey M, Geist J, Gessner MO, Goethals P, Gollock M, Gordon C, Grossart H, Gulemvuga G, Gutiérrez‐Fonseca PE, Haase P, Hering D, Hahn HJ, Hawkins CP, He F, Heino J, Hermoso V, Hogan Z, Hölker F, Jeschke JM, Jiang M, Johnson RK, Kalinkat G, Karimov BK, Kasangaki A, Kimirei IA, Kohlmann B, Kuemmerlen M, Kuiper JJ, Kupilas B, Langhans SD, Lansdown R, Leese F, Magbanua FS, Matsuzaki SS, Monaghan MT, Mumladze L, Muzon J, Mvogo Ndongo PA, Nejstgaard JC, Nikitina O, Ochs C, Odume O, Opperman JJ, Patricio H, Pauls S, Raghavan R, Ramírez A, Rashni B, Ross‐Gillespie V, Samways MJ, Schäfer RB, Schmidt‐Kloiber A, Seehausen O, Shah DN, Sharma S, Soininen J, Sommerwerk N, Stockwell JD, Suhling F, Tachamo Shah RD, Tharme RE, Thorp JH, Tickner D, Tockner K, Tonkin JD, Valle M, Vitule J, Volk M, Wang D, Wolter C, Worischka S. Cover Image. Ecol Lett 2022. [DOI: 10.1111/ele.13793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sire L, Yáñez PS, Wang C, Bézier A, Courtial B, Cours J, Fontaneto D, Larrieu L, Bouget C, Thorn S, Müller J, Yu DW, Monaghan MT, Herniou EA, Lopez-Vaamonde C. Climate-induced forest dieback drives compositional changes in insect communities that are more pronounced for rare species. Commun Biol 2022; 5:57. [PMID: 35042989 PMCID: PMC8766456 DOI: 10.1038/s42003-021-02968-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 12/07/2021] [Indexed: 12/26/2022] Open
Abstract
Species richness, abundance and biomass of insects have recently undergone marked declines in Europe. We metabarcoded 211 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging had an impact on ca. 3000 species of flying insects in silver fir Pyrenean forests. While forest dieback had no measurable impact on species richness, there were significant changes in community composition that were consistent with those observed during natural forest succession. Importantly, most observed changes were driven by rare species. Variation was explained primarily by canopy openness at the local scale, and the tree-related microhabitat diversity and deadwood amount at landscape scales. The levels of salvage logging in our study did not explain compositional changes. We conclude that forest dieback drives changes in species assemblages that mimic natural forest succession, and markedly increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.
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Affiliation(s)
- Lucas Sire
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France.
| | - Paul Schmidt Yáñez
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
| | - Cai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
| | | | - Jérémy Cours
- INRAE 'Forest Ecosystems' Research Unit - Biodiversity team Domaine des Barres, F-45290, Nogent-sur-Vernisson, France
| | - Diego Fontaneto
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Largo Tonolli 50, 28922, Verbania Pallanza, Italy
| | - Laurent Larrieu
- Université de Toulouse, INRAE, UMR DYNAFOR, Castanet-Tolosan, France
- CRPF Occitanie, Tarbes, France
| | - Christophe Bouget
- INRAE 'Forest Ecosystems' Research Unit - Biodiversity team Domaine des Barres, F-45290, Nogent-sur-Vernisson, France
| | - Simon Thorn
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstraße 5, 96181, Rauhenebrach, Germany
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstraße 5, 96181, Rauhenebrach, Germany
- Bavarian Forest National Park, Freyunger Str. 2, 94481, Grafenau, Germany
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, UK
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Königin-Luise-Straße. 1-3, 12489, Berlin, Germany
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
| | - Carlos Lopez-Vaamonde
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
- INRAE, Zoologie Forestière, F-45075, Orléans, France
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Maasri A, Jähnig SC, Adamescu MC, Adrian R, Baigun C, Baird DJ, Batista-Morales A, Bonada N, Brown LE, Cai Q, Campos-Silva JV, Clausnitzer V, Contreras-MacBeath T, Cooke SJ, Datry T, Delacámara G, De Meester L, Dijkstra KDB, Do VT, Domisch S, Dudgeon D, Erös T, Freitag H, Freyhof J, Friedrich J, Friedrichs-Manthey M, Geist J, Gessner MO, Goethals P, Gollock M, Gordon C, Grossart HP, Gulemvuga G, Gutiérrez-Fonseca PE, Haase P, Hering D, Hahn HJ, Hawkins CP, He F, Heino J, Hermoso V, Hogan Z, Hölker F, Jeschke JM, Jiang M, Johnson RK, Kalinkat G, Karimov BK, Kasangaki A, Kimirei IA, Kohlmann B, Kuemmerlen M, Kuiper JJ, Kupilas B, Langhans SD, Lansdown R, Leese F, Magbanua FS, Matsuzaki SIS, Monaghan MT, Mumladze L, Muzon J, Mvogo Ndongo PA, Nejstgaard JC, Nikitina O, Ochs C, Odume ON, Opperman JJ, Patricio H, Pauls SU, Raghavan R, Ramírez A, Rashni B, Ross-Gillespie V, Samways MJ, Schäfer RB, Schmidt-Kloiber A, Seehausen O, Shah DN, Sharma S, Soininen J, Sommerwerk N, Stockwell JD, Suhling F, Tachamo Shah RD, Tharme RE, Thorp JH, Tickner D, Tockner K, Tonkin JD, Valle M, Vitule J, Volk M, Wang D, Wolter C, Worischka S. A global agenda for advancing freshwater biodiversity research. Ecol Lett 2021; 25:255-263. [PMID: 34854211 DOI: 10.1111/ele.13931] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 03/15/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022]
Abstract
Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.
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Affiliation(s)
- Alain Maasri
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,The Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania, USA
| | - Sonja C Jähnig
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mihai C Adamescu
- Research Center in Systems Ecology and Sustainability, University of Bucharest, Bucharest, Romania
| | - Rita Adrian
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Claudio Baigun
- Universidad Nacional de San Martin, San Martin, Argentina
| | - Donald J Baird
- Environment & Climate Change Canada/University of New Brunswick, Fredericton, New Brunswick, Canada
| | | | - Núria Bonada
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Lee E Brown
- School of Geography & water@leeds, University of Leeds, Leeds, UK
| | - Qinghua Cai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Viola Clausnitzer
- Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
| | | | | | | | | | - Luc De Meester
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany.,Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Van Tu Do
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Sami Domisch
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | | | - Tibor Erös
- Balaton Limnological Research Institute, Tihany, Hungary
| | | | - Joerg Freyhof
- Museum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Martin Friedrichs-Manthey
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | | | - Mark O Gessner
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Berlin Institute of Technology, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | | | | | | | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Georges Gulemvuga
- International Commission for Congo-Ubangui-Sangha Basin, Kinshasa, D.R. Congo
| | | | - Peter Haase
- Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany.,University of Duisburg-Essen, Essen, Germany
| | | | - Hans Jürgen Hahn
- University of Koblenz-Landau, Koblenz and Landau, Germany.,Institute for Groundwater Ecology IGÖ GmbH, Landau, Germany
| | | | - Fengzhi He
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Jani Heino
- Finnish Environment Institute, Oulu, Finland
| | - Virgilio Hermoso
- Centre de Ciència i Tecnologia Forestal de Catalunya, Solsona, Spain
| | - Zeb Hogan
- University of Nevada, Reno, Nevada, USA
| | - Franz Hölker
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Jonathan M Jeschke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Meilan Jiang
- Chongqing University of Posts and Telecommunications, Chongqing, China
| | | | - Gregor Kalinkat
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Bakhtiyor K Karimov
- Tashkent Institute of Irrigation and Agricultural Mechanization Engineers, Tashkent, Uzbekistan
| | | | | | | | | | - Jan J Kuiper
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
| | - Benjamin Kupilas
- Norwegian Institute for Water Research, Oslo, Norway.,University of Münster, Münster, Germany
| | - Simone D Langhans
- Basque Centre for Climate Change (BC3), Leioa, Spain.,University of Otago, Dunedin, New Zealand
| | | | | | | | | | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Levan Mumladze
- Institute of Zoology, Ilia State University, Tiblis, Georgia
| | - Javier Muzon
- Universidad Nacional de Avellaneda, Avellaneda, Argentina
| | | | - Jens C Nejstgaard
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | | | - Clifford Ochs
- University of Mississippi, University Park, Mississippi, USA
| | | | | | | | - Steffen U Pauls
- Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany.,Justus-Liebig-University, Gießen, Germany
| | - Rajeev Raghavan
- Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Alonso Ramírez
- North Carolina State University, Raleigh, North Carolina, USA
| | - Bindiya Rashni
- Institute of Applied Science, University of the South Pacific, Suva, Fiji
| | | | | | - Ralf B Schäfer
- University of Koblenz-Landau, Koblenz and Landau, Germany
| | | | - Ole Seehausen
- University of Bern, Bern, Switzerland.,Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland
| | | | | | | | - Nike Sommerwerk
- Museum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Frank Suhling
- Technische Universität Braunschweig, Braunschweig, Germany
| | | | | | | | | | - Klement Tockner
- Senckenberg Society for Nature Research, Frankfurt am Main, Germany.,Goethe University, Frankfurt am Main, Germany
| | - Jonathan D Tonkin
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mireia Valle
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, California, USA.,AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Jean Vitule
- Federal University of Paraná, Curitiba, Brazil
| | - Martin Volk
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Ding Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Christian Wolter
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
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10
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Heeger F, Bourne EC, Wurzbacher C, Funke E, Lipzen A, He G, Ng V, Grigoriev IV, Schlosser D, Monaghan MT. Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica. J Fungi (Basel) 2021; 7:jof7100854. [PMID: 34682274 PMCID: PMC8537685 DOI: 10.3390/jof7100854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 08/31/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
Fungi are ecologically outstanding decomposers of lignocellulose. Fungal lignocellulose degradation is prominent in saprotrophic Ascomycota and Basidiomycota of the subkingdom Dikarya. Despite ascomycetes dominating the Dikarya inventory of aquatic environments, genome and transcriptome data relating to enzymes involved in lignocellulose decay remain limited to terrestrial representatives of these phyla. We sequenced the genome of an exclusively aquatic ascomycete (the aquatic hyphomycete Clavariopsis aquatica), documented the presence of genes for the modification of lignocellulose and its constituents, and compared differential gene expression between C. aquatica cultivated on lignocellulosic and sugar-rich substrates. We identified potential peroxidases, laccases, and cytochrome P450 monooxygenases, several of which were differentially expressed when experimentally grown on different substrates. Additionally, we found indications for the regulation of pathways for cellulose and hemicellulose degradation. Our results suggest that C. aquatica is able to modify lignin to some extent, detoxify aromatic lignin constituents, or both. Such characteristics would be expected to facilitate the use of carbohydrate components of lignocellulose as carbon and energy sources.
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Affiliation(s)
- Felix Heeger
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Department Materials and Environment, Federal Institute for Material Research and Testing, 12203 Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
- Correspondence:
| | - Elizabeth C. Bourne
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, 85748 Garching, Germany;
| | - Elisabeth Funke
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dietmar Schlosser
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany;
| | - Michael T. Monaghan
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, 14195 Berlin, Germany
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11
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Rutschmann S, Chen P, Zhou C, Monaghan MT. Three mitochondrial genomes of early-winged insects (Ephemeroptera: Baetidae and Leptophlebiidae). Mitochondrial DNA B Resour 2021; 6:2969-2971. [PMID: 34553062 PMCID: PMC8451626 DOI: 10.1080/23802359.2021.1974966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/08/2021] [Accepted: 08/21/2021] [Indexed: 11/18/2022] Open
Abstract
Mayflies (Ephemeroptera) are a semi-aquatic insect order with comparatively few genomic data available despite their phylogenetic position at the root of the winged-insects and possession of ancestral traits. Here, we provide three mitochondrial genomes (mtgenomes) from representatives of the two most species-rich families, Baetis rutilocylindratus and Cloeon dipterum (Baetidae), and Habrophlebiodes zijinensis (Leptophlebiidae). All mtgenomes had a complete set of 13 protein-coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. Phylogenetic reconstructions using 21 mayfly mtgenomes and representatives of seven additional orders recovered both Baetidae and Leptophlebiidae as well supported monophyletic clades, with Ephemeroptera as the sister-taxon to all other winged insects (i.e. Odonata and Neoptera).
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Affiliation(s)
- Sereina Rutschmann
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
| | - Ping Chen
- College of Life Sciences, The Key Laboratory of Jiangsu Biodiversity and Biotechnology, Nanjing Normal University, Nanjing, China
| | - Changfa Zhou
- College of Life Sciences, The Key Laboratory of Jiangsu Biodiversity and Biotechnology, Nanjing Normal University, Nanjing, China
| | - Michael T. Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
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12
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Regilme MAF, Sato M, Tamura T, Arai R, Sato MO, Ikeda S, Gamboa M, Monaghan MT, Watanabe K. Comparative population genetic structure of two ixodid tick species (Acari:Ixodidae) (Ixodes ovatus and Haemaphysalis flava) in Niigata prefecture, Japan. Infect Genet Evol 2021; 94:104999. [PMID: 34256167 DOI: 10.1016/j.meegid.2021.104999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/03/2021] [Accepted: 07/07/2021] [Indexed: 11/25/2022]
Abstract
Ixodid ticks (Acari:Ixodidae) are essential vectors of tick-borne diseases in Japan. In this study, we characterized the population genetic structure and inferred genetic divergence in two widespread and abundant ixodid species, Ixodes ovatus and Haemaphysalis flava. Our hypothesis was that genetic divergence would be high in I. ovatus because of the low mobility of their small rodent hosts of immature I. ovatus would limit their gene flow compared to more mobile avian hosts of immature H. flava. We collected 320 adult I. ovatus from 29 locations and 223 adult H. flava from 17 locations across Niigata Prefecture, Japan, and investigated their genetic structure using DNA sequences from fragments of two mitochondrial gene regions, cox1 and the 16S rRNA gene. For I. ovatus, pairwise FST and analysis of molecular variance (AMOVA) analyses of cox1 and 16S sequences indicated significant genetic variation among populations, whereas both markers showed non-significant genetic variation among locations for H. flava. A cox1 gene tree and haplotype network revealed three genetic groups of I. ovatus. One of these groups consisted of haplotypes distributed at lower altitudes (251-471 m.a.s.l.). The cox1 sequences of I. ovatus from Japan clustered separately from I. ovatus sequences reported from China, suggesting the potential for cryptic species in Japan. Our results support our hypothesis and suggest that the host preference of ticks at the immature stage may influence the genetic structure of the ticks. This information may be important for understanding the tick-host interactions in the field to better understand the tick-borne disease transmission and in designing an effective tick control program.
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Affiliation(s)
- Maria Angenica F Regilme
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime 790-8577, Japan; Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Megumi Sato
- Graduate School of Health Sciences, Niigata University, Niigata 951-8518, Japan
| | - Tsutomu Tamura
- Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata 950-2144, Japan
| | - Reiko Arai
- Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata 950-2144, Japan
| | - Marcello Otake Sato
- Department of Tropical Medicine and Parasitology, Dokkyo Medical University, 880 Kitakobayashi, Mibu-machi, Shimotsuga-gun, Tochigi 321-0293, Japan
| | - Sumire Ikeda
- Research Laboratories, Research and Development Headquarters, Earth Corporation, Hyogo 678-0192, Japan
| | - Maribet Gamboa
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime 790-8577, Japan; Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin 12587, Germany; Institut für Biologie, Freie Universität Berlin, Berlin 14195, Germany
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Ehime 790-8577, Japan; Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan.
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13
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Bracamonte SE, Knopf K, Monaghan MT. Encapsulation of Anguillicola crassus reduces the abundance of adult parasite stages in the European eel (Anguilla anguilla). J Fish Dis 2021; 44:771-782. [PMID: 33270932 DOI: 10.1111/jfd.13301] [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] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 06/12/2023]
Abstract
Encapsulation of the parasitic nematode Anguillicola crassus Kuwahara, Niimi & Hagaki is commonly observed in its native host, the Japanese eel (Anguilla japonica Temminck & Schlegel). Encapsulation has also been described in a novel host, the European eel (A. anguilla L.), and there is evidence that encapsulation frequency has increased since the introduction of A. crassus. We examined whether encapsulation of A. crassus provides an advantage to its novel host in Lake Müggelsee, NE Germany. We provide the first evidence that encapsulation was associated with reduced abundance of adult A. crassus. This pattern was consistent in samples taken 3 months apart. There was no influence of infection on the expression of the two metabolic genes studied, but the number of capsules was negatively correlated with the expression of two mhc II genes of the adaptive immune response, suggesting a reduced activation. Interestingly, eels that encapsulated A. crassus had higher abundances of two native parasites compared with non-encapsulating eels. We propose that the response of A. anguilla to infection by A. crassus may interfere with its reaction to other co-occurring parasites.
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Affiliation(s)
- Seraina E Bracamonte
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
- Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
- Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Klaus Knopf
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
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14
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Rodriguez-Ezpeleta N, Morissette O, Bean CW, Manu S, Banerjee P, Lacoursière-Roussel A, Beng KC, Alter SE, Roger F, Holman LE, Stewart KA, Monaghan MT, Mauvisseau Q, Mirimin L, Wangensteen OS, Antognazza CM, Helyar SJ, de Boer H, Monchamp ME, Nijland R, Abbott CL, Doi H, Barnes MA, Leray M, Hablützel PI, Deiner K. Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on "Environmental DNA: What's behind the term?" by Pawlowski et al., (2020). Mol Ecol 2021; 30:4601-4605. [PMID: 34036646 PMCID: PMC8698002 DOI: 10.1111/mec.15942] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/31/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra‐organismal DNA from macro‐organisms. We agree with this view. However, we are concerned that their proposed two‐level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra‐organismal) from which ecological interpretations are derived.
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Affiliation(s)
| | - Olivier Morissette
- Direction de l'expertise sur la Faune Aquatique, Ministère des Forêt de la Faune et des Parcs, Québec, QC, Canada
| | - Colin W Bean
- Scottish Centre for Ecology and the Natural Environment, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Shivakumara Manu
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Pritam Banerjee
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan.,Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Anaïs Lacoursière-Roussel
- Government of Canada, Department of Fisheries and Oceans, St. Andrews Biological Station, St. Andrews, NB, Canada
| | - Kingsly C Beng
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - S Elizabeth Alter
- Department of Biology and Chemistry, California State University Monterey Bay, Seaside, CA, USA
| | - Fabian Roger
- Centre for Environmental and Climate Research (CEC), Lund University, Lund, Sweden
| | - Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - Kathryn A Stewart
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, the Netherlands
| | - Michael T Monaghan
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | | | - Luca Mirimin
- Department of Natural Sciences, School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Caterina M Antognazza
- Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Sarah J Helyar
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Hugo de Boer
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Reindert Nijland
- Marine Animal Ecology Group, Wageningen University, Wageningen, The Netherlands
| | - Cathryn L Abbott
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Matthew A Barnes
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX, USA
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Smithsonian Institution, Panama City, Panama
| | | | - Kristy Deiner
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
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15
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van Rees CB, Waylen KA, Schmidt‐Kloiber A, Thackeray SJ, Kalinkat G, Martens K, Domisch S, Lillebø AI, Hermoso V, Grossart H, Schinegger R, Decleer K, Adriaens T, Denys L, Jarić I, Janse JH, Monaghan MT, De Wever A, Geijzendorffer I, Adamescu MC, Jähnig SC. Safeguarding freshwater life beyond 2020: Recommendations for the new global biodiversity framework from the European experience. Conserv Lett 2020. [DOI: 10.1111/conl.12771] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
| | - Kerry A. Waylen
- Social, Economic and Geographical Sciences Department The James Hutton Institute Aberdeen Scotland UK
| | - Astrid Schmidt‐Kloiber
- Institute of Hydrobiology and Aquatic Ecosystem Management University of Natural Resources and Life Sciences Vienna (BOKU) Vienna Austria
| | | | - Gregor Kalinkat
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences Brussels Belgium
- University of Ghent, Biology Ghent Belgium
| | - Sami Domisch
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
| | - Ana I. Lillebø
- Department of Biology & CESAM University of Aveiro Aveiro Portugal
| | - Virgilio Hermoso
- Centre de Ciència i Tecnologia Forestal de Catalunya (CTFC) Solsona Spain
| | - Hans‐Peter Grossart
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Institute of Biochemistry and Biology University of Potsdam Germany
| | - Rafaela Schinegger
- Institute of Hydrobiology and Aquatic Ecosystem Management University of Natural Resources and Life Sciences Vienna (BOKU) Vienna Austria
| | - Kris Decleer
- Research Institute for Nature and Forest (INBO) Brussels Belgium
| | - Tim Adriaens
- Research Institute for Nature and Forest (INBO) Brussels Belgium
| | - Luc Denys
- Research Institute for Nature and Forest (INBO) Brussels Belgium
| | - Ivan Jarić
- Biology Centre of the Czech Academy of Sciences Institute of Hydrobiology České Budějovice Czech Republic
- Faculty of Science Department of Ecosystem Biology, University of South Bohemia České Budějovice Czech Republic
| | - Jan H. Janse
- PBL Netherlands Environmental Assessment Agency The Hague The Netherlands
- Netherlands Institute of Ecology, NIOO‐KNAW Wageningen The Netherlands
| | - Michael T. Monaghan
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Institut für Biologie Freie Universität Berlin Germany
| | - Aaike De Wever
- Research Institute for Nature and Forest (INBO) Brussels Belgium
| | - Ilse Geijzendorffer
- Tour du Valat Research Institute for the Conservation of Mediterranean Wetlands Arles France
| | - Mihai C. Adamescu
- Research Centre in Systems Ecology and Sustainability University of Bucharest Bucharest Romania
| | - Sonja C. Jähnig
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Geography Department Humboldt‐Universität zu Berlin, Berlin Germany
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16
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Lu Y, Ocaña-Pallarès E, López-Escardó D, Dennis SR, Monaghan MT, Ruiz-Trillo I, Spaak P, Wolinska J. Revisiting the phylogenetic position of Caullerya mesnili (Ichthyosporea), a common Daphnia parasite, based on 22 protein-coding genes. Mol Phylogenet Evol 2020; 151:106891. [PMID: 32562822 DOI: 10.1016/j.ympev.2020.106891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 08/15/2019] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 02/01/2023]
Abstract
Caullerya mesnili is a common and virulent parasite of the water flea, Daphnia. It was classified within the Haplosporidia (Rhizaria) for over a century. However, a recent molecular phylogeny based on the 18S rRNA gene suggested it belonged to the Ichthyosporea, a class of protists closely related to animals within the Opisthokonta clade. The exact phylogenetic position of C. mesnili remained uncertain because it appeared in the 18S rRNA tree with a very long branch and separated from all other taxa, suggesting that its position could be artifactual. A better understanding of its phylogenetic position has been constrained by a lack of molecular markers and the difficulty of obtaining a suitable quantity and quality of DNA from in vitro cultures, as this intracellular parasite cannot be cultured without its host. We isolated and collected spores of C. mesnili and sequenced genomic libraries. Phylogenetic analyses of a newly generated multi-protein data set (22 proteins, 4998 amino acids) and of sequences from the 18S rRNA gene both placed C. mesnili within the Ichthyophonida sub-clade of Ichthyosporea, as sister-taxon to Abeoforma whisleri and Pirum gemmata. Our study highlights the utility of metagenomic approaches for obtaining genomic information from intracellular parasites and for more accurate phylogenetic placement in evolutionary studies.
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Affiliation(s)
- Yameng Lu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
| | - Eduard Ocaña-Pallarès
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - David López-Escardó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain; Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Stuart R Dennis
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany; Institut für Biologie, Freie Universität Berlin (FU), Berlin, Germany
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona 08028, Catalonia, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
| | - Piet Spaak
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Justyna Wolinska
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institut für Biologie, Freie Universität Berlin (FU), Berlin, Germany
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17
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Bracamonte SE, Johnston PR, Monaghan MT, Knopf K. Gene expression response to a nematode parasite in novel and native eel hosts. Ecol Evol 2019; 9:13069-13084. [PMID: 31871630 PMCID: PMC6912882 DOI: 10.1002/ece3.5728] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 01/19/2023] Open
Abstract
Invasive parasites are involved in population declines of new host species worldwide. The high susceptibilities observed in many novel hosts have been attributed to the lack of protective immunity to the parasites which native hosts acquired during their shared evolution. We experimentally infected Japanese eels (Anguilla japonica) and European eels (Anguilla anguilla) with Anguillicola crassus, a nematode parasite that is native to the Japanese eel and invasive in the European eel. We inferred gene expression changes in head kidney tissue from both species, using RNA-seq data to determine the responses at two time points during the early stages of infection (3 and 23 days postinfection). At both time points, the novel host modified the expression of a larger and functionally more diverse set of genes than the native host. Strikingly, the native host regulated immune gene expression only at the earlier time point and to a small extent while the novel host regulated these genes at both time points. A low number of differentially expressed immune genes, especially in the native host, suggest that a systemic immune response was of minor importance during the early stages of infection. Transcript abundance of genes involved in cell respiration was reduced in the novel host which may affect its ability to cope with harsh conditions and energetically demanding activities. The observed gene expression changes in response to a novel parasite that we observed in a fish follow a general pattern observed in amphibians and mammals, and suggest that the disruption of physiological processes, rather than the absence of an immediate immune response, is responsible for the higher susceptibility of the novel host.
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Affiliation(s)
- Seraina E. Bracamonte
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
- Berlin Center for Genomics in Biodiversity ResearchBerlinGermany
- Faculty of Life SciencesHumboldt‐Universität zu BerlinBerlinGermany
| | - Paul R. Johnston
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
- Berlin Center for Genomics in Biodiversity ResearchBerlinGermany
- Institut für BiologieFreie Universität BerlinBerlinGermany
| | - Michael T. Monaghan
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
- Berlin Center for Genomics in Biodiversity ResearchBerlinGermany
- Institut für BiologieFreie Universität BerlinBerlinGermany
| | - Klaus Knopf
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
- Faculty of Life SciencesHumboldt‐Universität zu BerlinBerlinGermany
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18
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Affiliation(s)
- Felix Heeger
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
| | - Christian Wurzbacher
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Chair of Urban Water Systems Engineering Technical University of Munich Garching Germany
| | - Elizabeth C. Bourne
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
| | - Camila J. Mazzoni
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Department of Evolutionary Genetics Leibniz Institute of Zoo‐ and Wildlife Research (IZW) Berlin Germany
| | - Michael T. Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Institut für Biologie Freie Universität Berlin Berlin Germany
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19
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Jähnig SC, Monaghan MT, Hering D. In-depth approach to river restoration. Nature 2019; 572:32. [PMID: 31363199 DOI: 10.1038/d41586-019-02327-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Wegner B, Kronsbein AL, Gillefalk M, van de Weyer K, Köhler J, Funke E, Monaghan MT, Hilt S. Mutual Facilitation Among Invading Nuttall's Waterweed and Quagga Mussels. Front Plant Sci 2019; 10:789. [PMID: 31316530 PMCID: PMC6611401 DOI: 10.3389/fpls.2019.00789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/29/2019] [Indexed: 06/02/2023]
Abstract
Nuttall's waterweed (Elodea nuttallii) is the most abundant invasive aquatic plant species in several European countries. Elodea populations often follow a boom-bust cycle, but the causes and consequences of this dynamics are yet unknown. We hypothesize that both boom and bust periods can be affected by dreissenid mussel invasions. While mutual facilitations between these invaders could explain their rapid parallel expansion, subsequent competition for space might occur. To test this hypothesis, we use data on temporal changes in the water quality and the abundance of E. nuttallii and the quagga mussel Dreissena rostriformis bugensis in a temperate shallow lake. Lake Müggelsee (Germany) was turbid and devoid of submerged macrophytes for 20 years (1970-1989), but re-colonization with macrophytes started in 1990 upon reductions in nutrient loading. We mapped macrophyte abundance from 1999 and mussel abundance from 2011 onwards. E. nuttallii was first detected in 2011, spread rapidly, and was the most abundant macrophyte species by 2017. Native macrophyte species were not replaced, but spread more slowly, resulting in an overall increase in macrophyte coverage to 25% of the lake surface. The increased abundance of E. nuttallii was paralleled by increasing water clarity and decreasing total phosphorus concentrations in the water. These changes were attributed to a rapid invasion by quagga mussels in 2012. In 2017, they covered about one-third of the lake area, with mean abundances of 3,600 mussels m-2, filtering up to twice the lake's volume every day. The increasing light availability in deeper littoral areas supported the rapid spread of waterweed, while in turn waterweed provided surface for mussel colonization. Quantities of dreissenid mussels and E. nuttallii measured at 24 locations were significantly correlated in 2016, and yearly means of E. nuttallii quantities increased with increasing mean dreissenid mussel quantities between 2011 and 2018. In 2018, both E. nuttallii and dreissenid abundances declined. These data imply that invasive waterweed and quagga mussels initially facilitated their establishment, supporting the invasional meltdown hypothesis, while subsequently competition for space may have occurred. Such temporal changes in invasive species interaction might contribute to the boom-bust dynamics that have been observed in Elodea populations.
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Affiliation(s)
- Benjamin Wegner
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Faculty VI: Planning, Building and Environment, Institute for Ecology, Technical University Berlin, Berlin, Germany
| | - Anna Lena Kronsbein
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Mikael Gillefalk
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Faculty VI: Planning, Building and Environment, Institute for Ecology, Technical University Berlin, Berlin, Germany
| | | | - Jan Köhler
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Elisabeth Funke
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Michael T. Monaghan
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Sabine Hilt
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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21
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Bracamonte SE, Johnston PR, Knopf K, Monaghan MT. Experimental infection with Anguillicola crassus alters immune gene expression in both spleen and head kidney of the European eel (Anguilla anguilla). Mar Genomics 2019; 45:28-37. [DOI: 10.1016/j.margen.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 11/25/2022]
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22
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Lu Y, Johnston PR, Dennis SR, Monaghan MT, John U, Spaak P, Wolinska J. Daphnia galeata responds to the exposure to an ichthyosporean gut parasite by down-regulation of immunity and lipid metabolism. BMC Genomics 2018; 19:932. [PMID: 30547741 PMCID: PMC6295042 DOI: 10.1186/s12864-018-5312-7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Regulatory circuits of infection in the emerging experimental model system, water flea Daphnia and their microparasites, remain largely unknown. Here we provide the first molecular insights into the response of Daphnia galeata to its highly virulent and common parasite Caullerya mesnili, an ichthyosporean that infects the gut epithelium. We generated a transcriptomic dataset using RNAseq from parasite-exposed (vs. control) Daphnia, at two time points (4 and 48 h) after parasite exposure. RESULTS We found a down-regulation of metabolism and immunity-related genes, at 48 h (but not 4 h) after parasite exposure. These genes are involved in lipid metabolism and fatty acid biosynthesis, as well as microbe recognition (e.g. c-type lectins) and pathogen attack (e.g. gut chitin). CONCLUSIONS General metabolic suppression implies host energy shift from reproduction to survival, which is in agreement with the known drastic reduction in Daphnia fecundity after Caullerya infection. The down-regulation of gut chitin indicates a possible interaction between the peritrophic matrix and the evading host immune system. Our study provides the first description of host transcriptional responses in this very promising host-parasite experimental system.
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Affiliation(s)
- Yameng Lu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany. .,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany.
| | - Paul R Johnston
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany.,Freie Universität Berlin, Berlin, Germany
| | - Stuart R Dennis
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
| | - Uwe John
- Alfred Wegener Institut Helmholtz Zentrum für Polar und Meeresforschung (AWI), Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Piet Spaak
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Justyna Wolinska
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Freie Universität Berlin, Berlin, Germany
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23
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Heeger F, Bourne EC, Baschien C, Yurkov A, Bunk B, Spröer C, Overmann J, Mazzoni CJ, Monaghan MT. Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments. Mol Ecol Resour 2018; 18:1500-1514. [DOI: 10.1111/1755-0998.12937] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/05/2018] [Accepted: 07/28/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Felix Heeger
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB); Berlin Germany
- Berlin Center for Genomics in Biodiversity Research; Berlin Germany
| | - Elizabeth C. Bourne
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB); Berlin Germany
- Berlin Center for Genomics in Biodiversity Research; Berlin Germany
| | - Christiane Baschien
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures; Braunschweig Germany
| | - Camila J. Mazzoni
- Berlin Center for Genomics in Biodiversity Research; Berlin Germany
- Leibniz Institute of Zoo- and Wildlife Research (IZW); Berlin Germany
| | - Michael T. Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB); Berlin Germany
- Berlin Center for Genomics in Biodiversity Research; Berlin Germany
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24
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Grubisic M, van Grunsven RHA, Manfrin A, Monaghan MT, Hölker F. A transition to white LED increases ecological impacts of nocturnal illumination on aquatic primary producers in a lowland agricultural drainage ditch. Environ Pollut 2018; 240:630-638. [PMID: 29772513 DOI: 10.1016/j.envpol.2018.04.146] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 02/19/2018] [Revised: 04/30/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
The increasing use of artificial light at night (ALAN) has led to exposure of freshwater ecosystems to light pollution worldwide. Simultaneously, the spectral composition of nocturnal illumination is changing, following the current shift in outdoor lighting technologies from traditional light sources to light emitting diodes (LED). LEDs emit broad-spectrum white light, with a significant amount of photosynthetically active radiation, and typically a high content of blue light that regulates circadian rhythms in many organisms. While effects of the shift to LED have been investigated in nocturnal animals, its impact on primary producers is unknown. We performed three field experiments in a lowland agricultural drainage ditch to assess the impacts of a transition from high-pressure sodium (HPS) to white LED illumination (color temperature 4000 K) on primary producers in periphyton. In all experiments, we compared biomass and pigment composition of periphyton grown under a natural light regime to that of periphyton exposed to nocturnal HPS or, consecutively, LED light of intensities commonly found in urban waters (approximately 20 lux). Periphyton was collected in time series (1-13 weeks). We found no effect of HPS light on periphyton biomass; however, following a shift to LED the biomass decreased up to 62%. Neither light source had a substantial effect on pigment composition. The contrasting effects of the two light sources on biomass may be explained by differences in their spectral composition, and in particular the blue content. Our results suggest that spectral composition of the light source plays a role in determining the impacts of ALAN on periphyton and that the ongoing transition to LED may increase the ecological impacts of artificial lighting on aquatic primary producers. Reduced biomass in the base of the food web can impact ecosystem functions such as productivity and food supply for higher trophic levels in nocturnally-lit ecosystems.
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Affiliation(s)
- Maja Grubisic
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, 12587 Berlin, Germany; Institute of Biology, Freie Universität Berlin, Schwendenerstraße 1, 14195 Berlin, Germany.
| | - Roy H A van Grunsven
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, 12587 Berlin, Germany.
| | - Alessandro Manfrin
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, 12587 Berlin, Germany; Institute of Biology, Freie Universität Berlin, Schwendenerstraße 1, 14195 Berlin, Germany; School of Geography, Queen Mary University of London, Mile End Road, E1 4NS London, England.
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, 12587 Berlin, Germany.
| | - Franz Hölker
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, 12587 Berlin, Germany; Institute of Biology, Freie Universität Berlin, Schwendenerstraße 1, 14195 Berlin, Germany.
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Manfrin A, Lehmann D, van Grunsven RHA, Larsen S, Syväranta J, Wharton G, Voigt CC, Monaghan MT, Hölker F. Dietary changes in predators and scavengers in a nocturnally illuminated riparian ecosystem. OIKOS 2018. [DOI: 10.1111/oik.04696] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alessandro Manfrin
- Leibniz Inst. of Freshwater Ecology and Inland Fisheries (IGB); Berlin Germany
- Umwelt-Campus Birkenfeld; Univ. of Applied Sciences Trier; Birkenfeld Germany
| | - David Lehmann
- Leibniz-Inst. for Zoo and Wildlife Research (IZW); Berlin Germany
- Dept of Biological and Environmental Sciences; Univ. of Stirling; Stirling UK
| | | | - Stefano Larsen
- German Center for Integrative Biodiversity Research (iDiv); Leipzig Germany
- Dept of Civil, Environmental and Mechanical Engineering; Univ. of Trento; Trento Italy
| | - Jari Syväranta
- Dept of Environmental and Biological Sciences; Univ. of Eastern Finland; Joensuu Finland
| | | | | | - Michael T. Monaghan
- Leibniz Inst. of Freshwater Ecology and Inland Fisheries (IGB); Berlin Germany
| | - Franz Hölker
- Leibniz Inst. of Freshwater Ecology and Inland Fisheries (IGB); Berlin Germany
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Honnen AC, Monaghan MT. City-Dwellers and Country Folks: Lack of Population Differentiation Along an Urban-Rural Gradient in the Mosquito Culex pipiens (Diptera: Culicidae). J Insect Sci 2017; 17:4560636. [PMID: 29117382 PMCID: PMC5717708 DOI: 10.1093/jisesa/iex086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Mosquitoes (Diptera, Culicidae) occur in natural, urban, and peri-urban areas throughout the globe. Although the characteristics of urban and peri-urban habitats differ from those of natural habitats in many ways (e.g., fragmentation, pollution, noise, and light), few studies have examined the population connectivity of mosquitoes in urban areas. To obtain an overview of the species composition, we sampled mosquitoes from 23 sites in and around the city of Berlin, Germany. Of 23 species, five occurred in urban, 10 in peri-urban, and 20 in rural areas. Culex pipiens Linnaeus (Diptera: Culicidae) was the most common species collected (75% of all individuals) and occurred in all habitats. Hence this species was selected to be analysed at 10 microsatellite markers. There was no significant differentiation (FST = 0.016, P = 0.9) or isolation by distance (P = 0.06) among Cx. pipiens populations along an urban-rural gradient. The only significant differences detected were between Cx. pipiens and a laboratory population of Cx. pipiens f. molestus (pairwise FST = 0.114-0.148, P ≤ 0.001 in all comparisons), suggesting that the markers chosen were suitable for the identification of population differentiation. Our results indicate that Cx. pipiens gene flow is widespread within and among urban, peri-urban, and rural areas and that urban habitat does not necessarily impede or enhance gene flow among these populations.
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Affiliation(s)
- Ann-Christin Honnen
- Swiss Tropical and Public Health Institute (Swiss TPH), Switzerland
- University of Basel, Switzerland
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Germany
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Germany
- Berlin Center for Genomics in Biodiversity Research, Germany
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27
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Wurzbacher C, Attermeyer K, Kettner MT, Flintrop C, Warthmann N, Hilt S, Grossart HP, Monaghan MT. DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom. Environ Microbiol Rep 2017; 9:383-388. [PMID: 28429584 DOI: 10.1111/1758-2229.12540] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 04/02/2017] [Indexed: 06/07/2023]
Abstract
Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. Here we tested whether DNA metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. Significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a 3-month period in spring were found. Patterns followed the same trend as plankton estimates measured using traditional microscopic methods. The bloom of a conditionally rare bacterial taxon belonging to Arcicella was characterized, which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. The data demonstrate the potential of universal DNA metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities.
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Affiliation(s)
- Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, Göteborg, 40530, Sweden
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| | - Katrin Attermeyer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Department of Ecology and Genetics, Limnology, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Marie Therese Kettner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Potsdam University, Institute of Biochemistry and Biology, Maulbeerallee 2, Potsdam, 14469, Germany
| | - Clara Flintrop
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
- Helmholtz Young Investigator Group SEAPUMP, Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, and MARUM, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Norman Warthmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
- Research School of Biology, The Australian National University, Linnaeus Way, Canberra, ACT, 2601, Australia
| | - Sabine Hilt
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Potsdam University, Institute of Biochemistry and Biology, Maulbeerallee 2, Potsdam, 14469, Germany
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
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Wurzbacher C, Attermeyer K, Kettner MT, Flintrop C, Warthmann N, Hilt S, Grossart HP, Monaghan MT. DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom. Environ Microbiol Rep 2017; 9:383-388. [PMID: 28429584 DOI: 10.1101/058628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 04/02/2017] [Indexed: 05/25/2023]
Abstract
Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. Here we tested whether DNA metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. Significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a 3-month period in spring were found. Patterns followed the same trend as plankton estimates measured using traditional microscopic methods. The bloom of a conditionally rare bacterial taxon belonging to Arcicella was characterized, which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. The data demonstrate the potential of universal DNA metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities.
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Affiliation(s)
- Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, Göteborg, 40530, Sweden
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| | - Katrin Attermeyer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Department of Ecology and Genetics, Limnology, Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden
| | - Marie Therese Kettner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Potsdam University, Institute of Biochemistry and Biology, Maulbeerallee 2, Potsdam, 14469, Germany
| | - Clara Flintrop
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
- Helmholtz Young Investigator Group SEAPUMP, Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, and MARUM, University of Bremen, Leobener Strasse, Bremen, 28359, Germany
| | - Norman Warthmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
- Research School of Biology, The Australian National University, Linnaeus Way, Canberra, ACT, 2601, Australia
| | - Sabine Hilt
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775, Germany
- Potsdam University, Institute of Biochemistry and Biology, Maulbeerallee 2, Potsdam, 14469, Germany
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587, Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
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Watanabe K, Monaghan MT. Comparative tests of the species-genetic diversity correlation at neutral and nonneutral loci in four species of stream insect. Evolution 2017; 71:1755-1764. [PMID: 28485820 DOI: 10.1111/evo.13261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 07/28/2015] [Revised: 03/29/2017] [Accepted: 04/16/2017] [Indexed: 11/30/2022]
Abstract
A fundamental question linking population genetics and community ecology is how adaptive processes (e.g., natural selection) and neutral processes (e.g., drift-migration equilibrium) underpin the species-genetic diversity correlation (SGDC). Here, we combine genome scans and outlier loci detection with community analysis to separately test for neutral and nonneutral SGDCs in four species of stream insect. We sampled 60 localities in Japan and examined the relationships among population AFLP band richness (Br), taxon richness of the total community (S) and of the trophic guild (Str ), and 15 habitat parameters that could potentially drive adaptation and influence richness. Neutral Br was positively correlated with S only in the dominant species of these communities, suggesting Br may be constrained when intraspecific competition is pronounced. Nonneutral Br was correlated with Str in a species restricted to high elevations where habitat heterogeneity was highest. Community distance and genetic distance (β-SGDC) was correlated in two of the four species at both neutral and nonneutral loci. Distance-based redundancy analysis found geographic isolation and elevation to drive divergence of both communities and populations. This suggests that both neutral and adaptive divergence occurred through the shared influences of geographic isolation and local adaptation at the two levels of diversity.
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Affiliation(s)
- Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, 14195, Berlin, Germany
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Wurzbacher C, Fuchs A, Attermeyer K, Frindte K, Grossart HP, Hupfer M, Casper P, Monaghan MT. Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment. Microbiome 2017; 5:41. [PMID: 28388930 PMCID: PMC5385010 DOI: 10.1186/s40168-017-0255-9] [Citation(s) in RCA: 21] [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] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 03/15/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. METHODS We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. RESULTS Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. CONCLUSIONS By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.
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Affiliation(s)
- Christian Wurzbacher
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587 Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195 Germany
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 100, Göteborg, Sweden
| | - Andrea Fuchs
- Carl-von-Ossietzky University Oldenburg, Ammerländer Heerstraße 114-118, Oldenburg, 26129 Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
| | - Katrin Attermeyer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18d, Uppsala, 75236 Sweden
| | - Katharina Frindte
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, Nussallee 13, Bonn, 53115 Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
- Institute for Biochemistry and Biology, Potsdam University, Maulbeerallee 2, Potsdam, 14469 Germany
| | - Michael Hupfer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587 Germany
| | - Peter Casper
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, 16775 Germany
| | - Michael T. Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, Berlin, 12587 Germany
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195 Germany
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Rutschmann S, Detering H, Simon S, Funk DH, Gattolliat JL, Hughes SJ, Raposeiro PM, DeSalle R, Sartori M, Monaghan MT. Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome. Mol Phylogenet Evol 2016; 107:27-38. [PMID: 27742475 DOI: 10.1016/j.ympev.2016.10.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 07/14/2016] [Revised: 09/23/2016] [Accepted: 10/10/2016] [Indexed: 12/20/2022]
Abstract
The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.
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Affiliation(s)
- Sereina Rutschmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195 Berlin, Germany; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.
| | - Harald Detering
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195 Berlin, Germany; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Sabrina Simon
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY 10024, USA; Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - David H Funk
- Stroud Water Research Center, Avondale, PA 19311, USA
| | - Jean-Luc Gattolliat
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014 Lausanne, Switzerland; Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
| | - Samantha J Hughes
- Centro de Investigação e de Tecnologias Agro-Ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, Apartado 1013, 5001-801 Vila Real, Portugal
| | - Pedro M Raposeiro
- Research Centre in Biodiversity and Genetic Resources (CIBIO)-Açores and the Biology Department, University of Azores, Rua Mãe de Deus 13A, 9501-855 Ponta Delgada, Portugal
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY 10024, USA
| | - Michel Sartori
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014 Lausanne, Switzerland; Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
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Vuataz L, Rutschmann S, Monaghan MT, Sartori M. Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae). BMC Evol Biol 2016; 16:194. [PMID: 27654122 PMCID: PMC5031269 DOI: 10.1186/s12862-016-0758-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 11/20/2022] Open
Abstract
Background Larvae of the Holarctic mayfly genus Rhithrogena Eaton, 1881 (Ephemeroptera, Heptageniidae) are a diverse and abundant member of stream and river communities and are routinely used as bio-indicators of water quality. Rhithrogena is well diversified in the European Alps, with a number of locally endemic species, and several cryptic species have been recently detected. While several informal species groups are morphologically well defined, a lack of reliable characters for species identification considerably hampers their study. Their relationships, origin, timing of speciation and mechanisms promoting their diversification in the Alps are unknown. Results Here we present a species-level phylogeny of Rhithrogena in Europe using two mitochondrial and three nuclear gene regions. To improve sampling in a genus with many cryptic species, individuals were selected for analysis according to a recent DNA-based taxonomy rather than traditional nomenclature. A coalescent-based species tree and a reconstruction based on a supermatrix approach supported five of the species groups as monophyletic. A molecular clock, mapped on the most resolved phylogeny and calibrated using published mitochondrial evolution rates for insects, suggested an origin of Alpine Rhithrogena in the Oligocene/Miocene boundary. A diversification analysis that included simulation of missing species indicated a constant speciation rate over time, rather than any pronounced periods of rapid speciation. Ancestral state reconstructions provided evidence for downstream diversification in at least two species groups. Conclusions Our species-level analyses of five gene regions provide clearer definitions of species groups within European Rhithrogena. A constant speciation rate over time suggests that the paleoclimatic fluctuations, including the Pleistocene glaciations, did not significantly influence the tempo of diversification of Alpine species. A downstream diversification trend in the hybrida and alpestris species groups supports a previously proposed headwater origin hypothesis for aquatic insects. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0758-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laurent Vuataz
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014, Lausanne, Switzerland. .,Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Sereina Rutschmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, 14195, Berlin, Germany.,Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, 14195, Berlin, Germany
| | - Michel Sartori
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014, Lausanne, Switzerland.,Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
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Rutschmann S, Detering H, Simon S, Fredslund J, Monaghan MT. discomark: nuclear marker discovery from orthologous sequences using draft genome data. Mol Ecol Resour 2016; 17:257-266. [PMID: 27454666 DOI: 10.1111/1755-0998.12576] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 04/12/2016] [Revised: 07/05/2016] [Accepted: 07/11/2016] [Indexed: 11/28/2022]
Abstract
High-throughput sequencing has laid the foundation for fast and cost-effective development of phylogenetic markers. Here we present the program discomark, which streamlines the development of nuclear DNA (nDNA) markers from whole-genome (or whole-transcriptome) sequencing data, combining local alignment, alignment trimming, reference mapping and primer design based on multiple sequence alignments to design primer pairs from input orthologous sequences. To demonstrate the suitability of discomark, we designed markers for two groups of species, one consisting of closely related species and one group of distantly related species. For the closely related members of the species complex of Cloeon dipterum s.l. (Insecta, Ephemeroptera), the program discovered a total of 78 markers. Among these, we selected eight markers for amplification and Sanger sequencing. The exon sequence alignments (2526 base pairs) were used to reconstruct a well-supported phylogeny and to infer clearly structured haplotype networks. For the distantly related species, we designed primers for the insect order Ephemeroptera, using available genomic data from four sequenced species. We developed primer pairs for 23 markers that are designed to amplify across several families. The discomark program will enhance the development of new nDNA markers by providing a streamlined, automated approach to perform genome-scale scans for phylogenetic markers. The program is written in Python, released under a public licence (GNU GPL version 2), and together with a manual and example data set available at: https://github.com/hdetering/discomark.
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Affiliation(s)
- Sereina Rutschmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195, Berlin, Germany.,Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Harald Detering
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195, Berlin, Germany.,Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Sabrina Simon
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA.,Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | | | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195, Berlin, Germany
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Hölker F, Wurzbacher C, Weißenborn C, Monaghan MT, Holzhauer SIJ, Premke K. Microbial diversity and community respiration in freshwater sediments influenced by artificial light at night. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0130. [PMID: 25780242 DOI: 10.1098/rstb.2014.0130] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An increasing proportion of the Earth's surface is illuminated at night. In aquatic ecosystems, artificial light at night (ALAN) may influence microbial communities living in the sediments. These communities are highly diverse and play an important role in the global carbon cycle. We combined field and laboratory experiments using sediments from an agricultural drainage system to examine how ALAN affects communities and alters carbon mineralization. Two identical light infrastructures were installed parallel to a drainage ditch before the start of the experiment. DNA metabarcoding indicated that both sediment communities were similar. After one was lit for five months (July-December 2012) we observed an increase in photoautotroph abundance (diatoms, Cyanobacteria) in ALAN-exposed sediments. In laboratory incubations mimicking summer and winter (six weeks each), communities in sediments that were exposed to ALAN for 1 year (July 2012-June 2013) showed less overall seasonal change compared with ALAN-naive sediments. Nocturnal community respiration was reduced in ALAN-exposed sediments. In long-term exposed summer-sediments, we observed a shift from negative to positive net ecosystem production. Our results indicate ALAN may alter sediment microbial communities over time, with implications for ecosystem-level functions. It may thus have the potential to transform inland waters to nocturnal carbon sinks.
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Affiliation(s)
- Franz Hölker
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, Berlin 12587, Germany
| | - Christian Wurzbacher
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, Berlin 12587, Germany Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Strasse 6-8, Berlin 14195, Germany
| | - Carsten Weißenborn
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, Berlin 12587, Germany
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, Berlin 12587, Germany Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Strasse 6-8, Berlin 14195, Germany
| | - Stephanie I J Holzhauer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, Berlin 12587, Germany
| | - Katrin Premke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301/310, Berlin 12587, Germany Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalderstrasse 84, Müncheberg 15374, Germany
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35
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Honnen AC, Johnston PR, Monaghan MT. Sex-specific gene expression in the mosquito Culex pipiens f. molestus in response to artificial light at night. BMC Genomics 2016; 17:22. [PMID: 26728786 PMCID: PMC4700752 DOI: 10.1186/s12864-015-2336-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 06/24/2015] [Accepted: 12/19/2015] [Indexed: 01/03/2023] Open
Abstract
Background Artificial light at night (ALAN) is a typical feature of urban areas and most organisms living in urban or suburban habitats are exposed to low levels of ALAN. Light is one of the most important environmental cues that organisms use to regulate their activities. Studies have begun to quantify the influence of ALAN on the behavior and ecology of organisms, but research on the effects at the molecular level remains limited. Mosquitoes in the Culex pipiens complex (Diptera, Culicidae) are widespread and abundant in urban areas where they are potential disease vectors. It is thus of particular interest to understand how ALAN may influence biologically and ecologically relevant traits. Results We used RNAseq to evaluate the transcriptome response in a Cx. pipiens f. molestus laboratory population that was exposed to near-natural light conditions (light:dark L16:D8 hours, “control”) and ALAN conditions with 3 h of constant low-level light at night (L16 + Llow3:D5 hours, “low-light”). The resulting transcripts were mapped to the reference genome of the closely related Culex quinquefasciatus. Female expression patterns differed significantly between control and treatment conditions at five genes although none showed an absolute fold change greater than two (FC > 2). In contrast, male expression differed at 230 genes (74 with FC > 2). Of these, 216 genes (72 with FC > 2) showed reduced expression in the low-light treatment, most of which were related to gametogenesis, lipid metabolism, and immunity. Of the 14 genes (two with FC > 2) with increased expression, only five had any functional annotation. There was a pronounced sex-bias in gene expression regardless of treatment, with 11,660 genes (51 % of annotated genes; 8694 with FC > 2; 48 % of annotated genes) differentially expressed between males and females, including 14 genes of the circadian clock. Conclusion Our data suggest a stronger response to artificial light by males of Cx. pipiens f. molestus than by females, and that a wide range of physiological pathways may be affected by ALAN at the molecular level. The fact that differences in gene expression appear to be sex-specific may have a strong influence at the population level. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2336-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ann-Christin Honnen
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.
| | - Paul R Johnston
- Freie Universität Berlin, Königin-Luise-Straße 1-3, 14195, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195, Berlin, Germany
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195, Berlin, Germany
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Danabalan R, Monaghan MT, Ponsonby DJ, Linton YM. Occurrence and host preferences of Anopheles maculipennis group mosquitoes in England and Wales. Med Vet Entomol 2014; 28:169-178. [PMID: 23848304 DOI: 10.1111/mve.12023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 12/10/2012] [Revised: 05/14/2013] [Accepted: 05/24/2013] [Indexed: 06/02/2023]
Abstract
Mosquitoes of the Anopheles maculipennis Meigen (Diptera: Culicidae) group are of public health concern: five of the 11 morphologically indistinct species have been historically considered as vectors of malaria in Europe. Three members of the An. maculipennis group have been reported in the U.K.: Anopheles atroparvus van Thiel; Anopheles messeae Falleroni, and Anopheles daciae Linton, Nicolescu & Harbach. To study the distribution of the three U.K. species, particularly that of An. daciae, we developed a polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP) assay using the nuclear ribosomal internal transcribed spacer 2 (ITS-2) gene. Anopheles daciae was found to be widespread, occurring in four of the five counties surveyed in southern England and on the Welsh island of Anglesey, often in sympatry with the closely related species An. messeae. The host preferences of 237 blood-fed females were determined using either direct sequencing or PCR-based fragment analysis of the mitochondrial cytochrome oxidase b gene with DNA from females' abdomens. All three species were found to be opportunistic, having fed on at least three different hosts. Seventeen individuals contained multiple bloodmeals, including two An. daciae that had fed on humans and birds. Our results show that An. daciae is widespread in England and Wales, occurs in sympatry with other members of the An. maculipennis group, and feeds on humans, which suggests it is a potential vector of disease in the U.K.
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Affiliation(s)
- R Danabalan
- Department of Research, Museum für Naturkunde, Berlin, Germany; Department of Geographical and Life Sciences, Canterbury Christ Church University, Kent, U.K.; Department of Entomology, Natural History Museum, London, U.K
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Watanabe K, Kazama S, Omura T, Monaghan MT. Adaptive genetic divergence along narrow environmental gradients in four stream insects. PLoS One 2014; 9:e93055. [PMID: 24681871 PMCID: PMC3969376 DOI: 10.1371/journal.pone.0093055] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 03/02/2014] [Indexed: 01/30/2023] Open
Abstract
A central question linking ecology with evolutionary biology is how environmental heterogeneity can drive adaptive genetic divergence among populations. We examined adaptive divergence of four stream insects from six adjacent catchments in Japan by combining field measures of habitat and resource components with genome scans of non-neutral Amplified Fragment Length Polymorphism (AFLP) loci. Neutral genetic variation was used to measure gene flow and non-neutral genetic variation was used to test for adaptive divergence. We identified the environmental characteristics contributing to divergence by comparing genetic distances at non-neutral loci between sites with Euclidean distances for each of 15 environmental variables. Comparisons were made using partial Mantel tests to control for geographic distance. In all four species, we found strong evidence for non-neutral divergence along environmental gradients at between 6 and 21 loci per species. The relative contribution of these environmental variables to each species' ecological niche was quantified as the specialization index, S, based on ecological data. In each species, the variable most significantly correlated with genetic distance at non-neutral loci was the same variable along which each species was most narrowly distributed (i.e., highest S). These were gradients of elevation (two species), chlorophyll-a, and ammonia-nitrogen. This adaptive divergence occurred in the face of ongoing gene flow (Fst = 0.01-0.04), indicating that selection was strong enough to overcome homogenization at the landscape scale. Our results suggest that adaptive divergence is pronounced, occurs along different environmental gradients for different species, and may consistently occur along the narrowest components of species' niche.
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Affiliation(s)
- Kozo Watanabe
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, Berlin, Germany
- Present address: Department of Civil and Environmental Engineering, Ehime University, Bunkyo-cho 3, Matsuyama, Japan
| | - So Kazama
- Department of Civil and Environmental Engineering, Tohoku University, Aoba-yama 6-6-06, Sendai, Japan
| | - Tatsuo Omura
- New Industry Creation Hatchery Center (NIChe), Tohoku University, Aoba-yama 6-6-04, Sendai, Japan
| | - Michael T. Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, Berlin, Germany
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Abstract
Inland waters cover less than 1% of Earth's surface but harbor more than 6% of all insect species: Nearly 100,000 species from 12 orders spend one or more life stages in freshwater. Little is known about how this remarkable diversity arose, although allopatric speciation and ecological adaptation are thought to be primary mechanisms. Freshwater habitats are highly susceptible to environmental change and exhibit marked ecological gradients. Standing waters appear to harbor more dispersive species than running waters, but there is little understanding of how this fundamental ecological difference has affected diversification. In contrast to the lack of evolutionary studies, the ecology and habitat preferences of aquatic insects have been intensively studied, in part because of their widespread use as bioindicators. The combination of phylogenetics with the extensive ecological data provides a promising avenue for future research, making aquatic insects highly suitable models for the study of ecological diversification.
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Affiliation(s)
- Klaas-Douwe B. Dijkstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The
Netherlands, and University Museum of Zoology, Cambridge, CB2 3EJ, United Kingdom
| | - Michael T. Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB),
12587 Berlin, Germany;
| | - Steffen U. Pauls
- Biodiversity and Climate Research Centre, Frankfurt, Germany and
Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt,
Germany;
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Scharnweber K, Watanabe K, Syväranta J, Wanke T, Monaghan MT, Mehner T. Effects of predation pressure and resource use on morphological divergence in omnivorous prey fish. BMC Evol Biol 2013; 13:132. [PMID: 23802571 PMCID: PMC3702407 DOI: 10.1186/1471-2148-13-132] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [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: 03/22/2013] [Accepted: 06/19/2013] [Indexed: 11/25/2022] Open
Abstract
Background Body shape is one of the most variable traits of organisms and responds to a broad array of local selective forces. In freshwater fish, divergent body shapes within single species have been repeatedly observed along the littoral-pelagic axes of lakes, where the structural complexity of near shore habitats provides a more diverse set of resources compared to the open-water zones. It remains poorly understood whether similar resource-driven polymorphism occurs among lakes that vary in structural complexity and predation pressure, and whether this variation is heritable. Here, we analyzed body shape in four populations of omnivorous roach (Rutilus rutilus) inhabiting shallow lakes. We tested the relationship between body shape, gradients of resources, predation pressure, and, in a subset of two lakes, diet composition. We used genome scans of 331 polymorphic AFLP markers to test whether there was a heritable component to the observed morphological diversification. Results Body shape differed among lakes and was significantly correlated to differences in predation pressure. Roach from the lake with highest predation pressure were most divergent from the average body shape of all populations, characterized by a more streamlined body and caudally inserted dorsal fins; features that facilitate predator escape. Surprisingly, diet composition was not associated with morphology. AFLP analysis revealed weak genetic differentiation among lakes and no isolation by distance (IBD). Outlier analysis detected three loci under positive selection with differing frequencies in the four populations. General linear models did not support an association of lake-specific genotypes with morphological variation. Conclusion Body shape was divergent among lakes, suggesting that processes previously reported from within single lakes may also be operating at the scale of whole lakes. We found no evidence for body shape being heritable, although sample size was small in these natural populations. Rather than habitat structure and diet, we conclude that predation had a stronger effect on the prevalence of local morphotypes. A variable morphotype facilitating the efficient uptake of a variety of spatially and temporarily scattered resources seems to be favored in these small aquatic systems.
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Affiliation(s)
- Kristin Scharnweber
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.
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Vuataz L, Sartori M, Gattolliat JL, Monaghan MT. Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections. Mol Phylogenet Evol 2012; 66:979-91. [PMID: 23261711 DOI: 10.1016/j.ympev.2012.12.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [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: 02/27/2012] [Revised: 11/26/2012] [Accepted: 12/05/2012] [Indexed: 01/07/2023]
Abstract
The biodiversity and endemism of Madagascar are among the most extraordinary and endangered in the world. This includes the island's freshwater biodiversity, although detailed knowledge of the diversity, endemism, and biogeographic origin of freshwater invertebrates is lacking. The aquatic immature stages of mayflies (Ephemeroptera) are widely used as bio-indicators and form an important component of Malagasy freshwater biodiversity. Many species are thought to be microendemics, restricted to single river basins in forested areas, making them particularly sensitive to habitat reduction and degradation. The Heptageniidae are a globally diverse family of mayflies (>500 species) but remain practically unknown in Madagascar except for two species described in 1996. The standard approach to understanding their diversity, endemism, and origin would require extensive field sampling on several continents and years of taxonomic work followed by phylogenetic analysis. Here we circumvent this using museum collections and freshly collected individuals in a combined approach of DNA taxonomy and phylogeny. The coalescent-based GMYC analysis of DNA barcode data (mitochondrial COI) revealed 14 putative species on Madagascar, 70% of which were microendemics. A phylogenetic analysis that included African and Asian species and data from two mitochondrial and four nuclear loci indicated the Malagasy Heptageniidae are monophyletic and sister to African species. The genus Compsoneuria is shown to be paraphyletic and the genus Notonurus is reinstalled for African and Malagasy species previously placed in Compsoneuria. A molecular clock excluded a Gondwanan vicariance origin and instead favoured a more recent overseas colonization of Madagascar. The observed monophyly and high microendemism highlight their conservation importance and suggest the DNA-based approach can rapidly provide information on the diversity, endemism, and origin of freshwater biodiversity. Our results underline the important role that museum collections can play in molecular studies, especially in critically endangered biodiversity hotspots like Madagascar where entire species or populations may go extinct very quickly.
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Affiliation(s)
- Laurent Vuataz
- Musée cantonal de zoologie, Palais de Rumine, place de la Riponne 6, 1014 Lausanne, Switzerland.
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Bergsten J, Bilton DT, Fujisawa T, Elliott M, Monaghan MT, Balke M, Hendrich L, Geijer J, Herrmann J, Foster GN, Ribera I, Nilsson AN, Barraclough TG, Vogler AP. The effect of geographical scale of sampling on DNA barcoding. Syst Biol 2012; 61:851-69. [PMID: 22398121 PMCID: PMC3417044 DOI: 10.1093/sysbio/sys037] [Citation(s) in RCA: 261] [Impact Index Per Article: 21.8] [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: 06/30/2011] [Revised: 11/28/2011] [Accepted: 03/02/2012] [Indexed: 11/30/2022] Open
Abstract
Eight years after DNA barcoding was formally proposed on a large scale, CO1 sequences are rapidly accumulating from around the world. While studies to date have mostly targeted local or regional species assemblages, the recent launch of the global iBOL project (International Barcode of Life), highlights the need to understand the effects of geographical scale on Barcoding's goals. Sampling has been central in the debate on DNA Barcoding, but the effect of the geographical scale of sampling has not yet been thoroughly and explicitly tested with empirical data. Here, we present a CO1 data set of aquatic predaceous diving beetles of the tribe Agabini, sampled throughout Europe, and use it to investigate how the geographic scale of sampling affects 1) the estimated intraspecific variation of species, 2) the genetic distance to the most closely related heterospecific, 3) the ratio of intraspecific and interspecific variation, 4) the frequency of taxonomically recognized species found to be monophyletic, and 5) query identification performance based on 6 different species assignment methods. Intraspecific variation was significantly correlated with the geographical scale of sampling (R-square = 0.7), and more than half of the species with 10 or more sampled individuals (N = 29) showed higher intraspecific variation than 1% sequence divergence. In contrast, the distance to the closest heterospecific showed a significant decrease with increasing geographical scale of sampling. The average genetic distance dropped from > 7% for samples within 1 km, to < 3.5% for samples up to > 6000 km apart. Over a third of the species were not monophyletic, and the proportion increased through locally, nationally, regionally, and continentally restricted subsets of the data. The success of identifying queries decreased with increasing spatial scale of sampling; liberal methods declined from 100% to around 90%, whereas strict methods dropped to below 50% at continental scales. The proportion of query identifications considered uncertain (more than one species < 1% distance from query) escalated from zero at local, to 50% at continental scale. Finally, by resampling the most widely sampled species we show that even if samples are collected to maximize the geographical coverage, up to 70 individuals are required to sample 95% of intraspecific variation. The results show that the geographical scale of sampling has a critical impact on the global application of DNA barcoding. Scale-effects result from the relative importance of different processes determining the composition of regional species assemblages (dispersal and ecological assembly) and global clades (demography, speciation, and extinction). The incorporation of geographical information, where available, will be required to obtain identification rates at global scales equivalent to those in regional barcoding studies. Our result hence provides an impetus for both smarter barcoding tools and sprouting national barcoding initiatives-smaller geographical scales deliver higher accuracy.
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Affiliation(s)
- Johannes Bergsten
- Department of Entomology, Swedish Museum of Natural History, Stockholm, Sweden.
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Dziallas C, Allgaier M, Monaghan MT, Grossart HP. Act together-implications of symbioses in aquatic ciliates. Front Microbiol 2012; 3:288. [PMID: 22891065 PMCID: PMC3413206 DOI: 10.3389/fmicb.2012.00288] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [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: 05/14/2012] [Accepted: 07/22/2012] [Indexed: 02/01/2023] Open
Abstract
Mutual interactions in the form of symbioses can increase the fitness of organisms and provide them with the capacity to occupy new ecological niches. The formation of obligate symbioses allows for rapid evolution of new life forms including multitrophic consortia. Microbes are important components of many known endosymbioses and their short generation times and strong potential for genetic exchange may be important drivers of speciation. Hosts provide endo- and ectosymbionts with stable, nutrient-rich environments, and protection from grazers. This is of particular importance in aquatic ecosystems, which are often highly variable, harsh, and nutrient-deficient habitats. It is therefore not surprising that symbioses are widespread in both marine and freshwater environments. Symbioses in aquatic ciliates are good model systems for exploring symbiont-host interactions. Many ciliate species are globally distributed and have been intensively studied in the context of plastid evolution. Their relatively large cell size offers an ideal habitat for numerous microorganisms with different functional traits including commensalism and parasitism. Phagocytosis facilitates the formation of symbiotic relationships, particularly since some ingested microorganisms can escape the digestion. For example, photoautotrophic algae and methanogens represent endosymbionts that greatly extend the biogeochemical functions of their hosts. Consequently, symbiotic relationships between protists and prokaryotes are widespread and often result in new ecological functions of the symbiotic communities. This enables ciliates to thrive under a wide range of environmental conditions including ultraoligotrophic or anoxic habitats. We summarize the current understanding of this exciting research topic to identify the many areas in which knowledge is lacking and to stimulate future research by providing an overview on new methodologies and by formulating a number of emerging questions in this field.
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Affiliation(s)
- Claudia Dziallas
- Marine Biological Section, University of CopenhagenHelsingør, Denmark
| | - Martin Allgaier
- Department of Limnology of Stratified Lakes, Leibniz-Institute of Freshwater Ecology and Inland FisheriesStechlin, Germany
- Berlin Center for Genomics in Biodiversity ResearchBerlin, Germany
| | - Michael T. Monaghan
- Department of Limnology of Shallow Lakes and Lowland Rivers, Leibniz-Institute of Freshwater Ecology and Inland FisheriesBerlin, Germany
| | - Hans-Peter Grossart
- Department of Limnology of Stratified Lakes, Leibniz-Institute of Freshwater Ecology and Inland FisheriesStechlin, Germany
- Institute for Biochemistry and Biology, Potsdam UniversityPotsdam, Germany
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Gamboa M, Kimbirauskas RK, Merritt RW, Monaghan MT. A molecular approach to identifying the natural prey of the African creeping water bug Naucoris, a potential reservoir of Mycobacterium ulcerans. J Insect Sci 2012; 12:2. [PMID: 22934669 PMCID: PMC3465933 DOI: 10.1673/031.012.0201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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: 02/16/2011] [Accepted: 08/22/2011] [Indexed: 06/01/2023]
Abstract
The extra-oral digestion of creeping water bugs (Naucoridae: Hemiptera) hinders the study of their diet using the standard method of identifying prey body parts in the gut. Genetic methods are available, but rely on PCR tests or similar diagnostics to confirm suspected prey. Where the potential prey is unknown and a broad search for all possible prey is desirable, methods that can potentially capture any prey item are required. Naucoris sp. is known to harbor Mycobacterium ulcerans (Actinomycetales: Mycobacteriaceae), the causative bacterium of Buruli ulcer. Outbreaks of Buruli ulcer have been associated with disturbed freshwater habitats, but the mode of transmission to humans remains unclear. Here we examine the diet of Naucoris sp., a dominant aquatic predator in water bodies in Ghana where the prevalence of Buruli ulcer is high. We cloned and sequenced 576 PCR products (mtDNA rrnL, cox1) isolated from the gut of 60 Naucoris sp. individuals to determining diet composition as broadly as possible. Using phylogenetic analysis of newly sequenced clones and 6 potential prey taxa collected from the site, sequences isolated from Naucoris sp. guts matched locally collected Coleoptera (Hydrophilidae). Blastn queries to GenBank of other clone sequences produced matches to (Anura) (n = 1), Rotifera (n = 5), and fungi (n = 4) as additional components of the diet. Our results suggest that sp. in this Buruli ulcer-endemic area feeds on a wide range of prey and body sizes, and that the approach could be successfully applied to studies of aquatic food webs where morphological identification of prey is impossible and where little or no a priori knowledge is available.
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Affiliation(s)
- Maribet Gamboa
- Leibniz - Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
| | - Ryan K. Kimbirauskas
- Department of Entomology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Richard W. Merritt
- Department of Entomology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Michael T. Monaghan
- Leibniz - Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
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Vuataz L, Sartori M, Wagner A, Monaghan MT. Toward a DNA taxonomy of Alpine Rhithrogena (Ephemeroptera: Heptageniidae) using a mixed Yule-coalescent analysis of mitochondrial and nuclear DNA. PLoS One 2011; 6:e19728. [PMID: 21611178 PMCID: PMC3096624 DOI: 10.1371/journal.pone.0019728] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Accepted: 04/04/2011] [Indexed: 11/22/2022] Open
Abstract
Aquatic larvae of many Rhithrogena mayflies (Ephemeroptera)
inhabit sensitive Alpine environments. A number of species are on the IUCN Red
List and many recognized species have restricted distributions and are of
conservation interest. Despite their ecological and conservation importance,
ambiguous morphological differences among closely related species suggest that
the current taxonomy may not accurately reflect the evolutionary diversity of
the group. Here we examined the species status of nearly 50% of European
Rhithrogena diversity using a widespread sampling scheme of
Alpine species that included 22 type localities, general mixed Yule-coalescent
(GMYC) model analysis of one standard mtDNA marker and one newly developed nDNA
marker, and morphological identification where possible. Using sequences from
533 individuals from 144 sampling localities, we observed significant clustering
of the mitochondrial (cox1) marker into 31 GMYC species.
Twenty-one of these could be identified based on the presence of topotypes
(expertly identified specimens from the species' type locality) or
unambiguous morphology. These results strongly suggest the presence of both
cryptic diversity and taxonomic oversplitting in Rhithrogena.
Significant clustering was not detected with protein-coding nuclear PEPCK,
although nine GMYC species were congruent with well supported terminal clusters
of nDNA. Lack of greater congruence in the two data sets may be the result of
incomplete sorting of ancestral polymorphism. Bayesian phylogenetic analyses of
both gene regions recovered four of the six recognized
Rhithrogena species groups in our samples as monophyletic.
Future development of more nuclear markers would facilitate multi-locus analysis
of unresolved, closely related species pairs. The DNA taxonomy developed here
lays the groundwork for a future revision of the important but cryptic
Rhithrogena genus in Europe.
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Powell JR, Monaghan MT, Opik M, Rillig MC. Evolutionary criteria outperform operational approaches in producing ecologically relevant fungal species inventories. Mol Ecol 2010; 20:655-66. [PMID: 21199026 DOI: 10.1111/j.1365-294x.2010.04964.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analyses of the structure and function of microbial communities are highly constrained by the diversity of organisms present within most environmental samples. A common approach is to rely almost entirely on DNA sequence data for estimates of microbial diversity, but to date there is no objective method of clustering sequences into groups that is grounded in evolutionary theory of what constitutes a biological lineage. The general mixed Yule-coalescent (GMYC) model uses a likelihood-based approach to distinguish population-level processes within lineages from processes associated with speciation and extinction, thus identifying a distinct point where extant lineages became independent. Using two independent surveys of DNA sequences associated with a group of ubiquitous plant-symbiotic fungi, we compared estimates of species richness derived using the GMYC model to those based on operational taxonomic units (OTUs) defined by fixed levels of sequence similarity. The model predicted lower species richness in these surveys than did traditional methods of sequence similarity. Here, we show for the first time that groups delineated by the GMYC model better explained variation in the distribution of fungi in relation to putative niche-based variables associated with host species identity, edaphic factors, and aspects of how the sampled ecosystems were managed. Our results suggest the coalescent-based GMYC model successfully groups environmental sequences of fungi into clusters that are ecologically more meaningful than more arbitrary approaches for estimating species richness.
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Affiliation(s)
- Jeff R Powell
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, Altensteinstrasse 6, Berlin, Germany.
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Gattolliat JL, Monaghan MT. DNA-based association of adults and larvae in Baetidae (Ephemeroptera) with the description of a new genusAdnoptilumin Madagascar. ACTA ACUST UNITED AC 2010. [DOI: 10.1899/09-119.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Michael T. Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany
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Mehner T, Pohlmann K, Elkin C, Monaghan MT, Nitz B, Freyhof J. Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (Coregonus albula complex, Teleostei, Coregonidae). BMC Evol Biol 2010; 10:85. [PMID: 20350300 PMCID: PMC2853541 DOI: 10.1186/1471-2148-10-85] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [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: 07/01/2009] [Accepted: 03/29/2010] [Indexed: 12/26/2022] Open
Abstract
Background Teleost fishes of the Coregonidae are good model systems for studying postglacial evolution, adaptive radiation and ecological speciation. Of particular interest is whether the repeated occurrence of sympatric species pairs results from in-situ divergence from a single lineage or from multiple invasions of one or more different lineages. Here, we analysed the genetic structure of Baltic ciscoes (Coregonus albula complex), examining 271 individuals from 8 lakes in northern Germany using 1244 polymorphic AFLP loci. Six lakes had only one population of C. albula while the remaining two lakes had C. albula as well as a sympatric species (C. lucinensis or C. fontanae). Results AFLP demonstrated a significant population structure (Bayesian θB = 0.22). Lower differentiation between allopatric (θB = 0.028) than sympatric (0.063-0.083) populations contradicts the hypothesis of a sympatric origin of taxa, and there was little evidence for stocking or ongoing hybridization. Genome scans found only three loci that appeared to be under selection in both sympatric population pairs, suggesting a low probability of similar mechanisms of ecological segregation. However, removal of all non-neutral loci decreased the genetic distance between sympatric pairs, suggesting recent adaptive divergence at a few loci. Sympatric pairs in the two lakes were genetically distinct from the six other C. albula populations, suggesting introgression from another lineage may have influenced these two lakes. This was supported by an analysis of isolation-by-distance, where the drift-gene flow equilibrium observed among allopatric populations was disrupted when the sympatric pairs were included. Conclusions While the population genetic data alone can not unambiguously uncover the mode of speciation, our data indicate that multiple lineages may be responsible for the complex patterns typically observed in Coregonus. Relative differences within and among lakes raises the possibility that multiple lineages may be present in northern Germany, thus understanding the postglacial evolution and speciation in the C. albula complex requires a large-scale phylogenetic analysis of several potential founder lineages.
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Affiliation(s)
- Thomas Mehner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany.
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Lozan AI, Belokobylskij S, Achterberg CVV, Monaghan MT. Diversity and distribution of Braconidae, a family of parasitoid wasps in the central European peatbogs of South Bohemia, Czech Republic. J Insect Sci 2010; 10:16. [PMID: 20578880 PMCID: PMC3014670 DOI: 10.1673/031.010.1601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 12/23/2008] [Indexed: 05/29/2023]
Abstract
An ecological overview of seven years investigation of Braconidae, a family of parasitoid wasps (Hymenoptera: Ichneumonoidea) and a tyrpho-classification of parasitoids in peatbog areas of South Bohemia, Czech Republic are given. A total of 350 species were recorded in investigated sites, but only five tyrphobionts (1.4%) are proposed: Microchelonus basalis, Microchelonus koponeni, Coloneura ate, Coloneura danica and Myiocephalus niger. All of these species have a boreal-alpine distribution that, in Central Europe, is associated only with peatbogs. Tyrphophilous behaviour is seen in at least four (1.1%) species: Microchelonus pedator, Microchelonus subpedator, Microchelonus karadagi and Microchelonus gravenhorstii; however, a number of other braconids prefer peatbogs because they were more frequently encountered within, rather than outside, the bog habitat. The rest of the braconids (342 species, 97.5%) are tyrphoneutrals, many of them being eurytopic components of various habitats throughout their current ranges. Lists of tyrphobiontic braconids and a brief commentary on species composition, distributional picture of actual ranges, and parasitoid association to bog landscape are provided. Being true refugial habitats for populations in an ever-changing world, peatbogs play a significant role in harboring insect communities.
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Affiliation(s)
- Aurel I. Lozan
- Biology Centre, Institute of Entomology, Academy of Sciences of the Czech Republic, Branišovská 31, CZ-370 05 České Budějovice, Czech Republic
| | - Sergey Belokobylskij
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab., I St. Petersburg 199034, Russia; and
Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, Warszawa 00-679, Poland
| | - Cees van Van Achterberg
- Department of Entomology, Nationaal Natuurhistorisch Museum (Naturalis), 2300 RA Leiden, Netherlands
| | - Michael T. Monaghan
- Leibniz-lnstitute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany
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Mehner T, Pohlmann K, Elkin C, Monaghan MT, Freyhof J. Genetic mixing from enhancement stocking in commercially exploited vendace populations. J Appl Ecol 2009. [DOI: 10.1111/j.1365-2664.2009.01733.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Papadopoulou A, Monaghan MT, Barraclough TG, Vogler AP. Sampling Error Does Not Invalidate the Yule-Coalescent Model for Species Delimitation. A Response to Lohse (2009). Syst Biol 2009. [DOI: 10.1093/sysbio/syp038] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anna Papadopoulou
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Michael T. Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Mueggelseedamm 301, 12587 Berlin, Germany
| | - Timothy G. Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Alfried P. Vogler
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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