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Cuesta EB, Coulibaly B, Bukhari T, Eiglmeier K, Kone R, Coulibaly MB, Zongo S, Barry M, Gneme A, Guelbeogo WM, Beavogui AH, Traore SF, Sagnon N, Vernick KD, Riehle MM. Comprehensive Ecological and Geographic Characterization of Eukaryotic and Prokaryotic Microbiomes in African Anopheles. Front Microbiol 2021; 12:635772. [PMID: 34054746 PMCID: PMC8153677 DOI: 10.3389/fmicb.2021.635772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/12/2021] [Indexed: 12/14/2022] Open
Abstract
Exposure of mosquitoes to numerous eukaryotic and prokaryotic microbes in their associated microbiomes has probably helped drive the evolution of the innate immune system. To our knowledge, a metagenomic catalog of the eukaryotic microbiome has not been reported from any insect. Here we employ a novel approach to preferentially deplete host 18S ribosomal RNA gene amplicons to reveal the composition of the eukaryotic microbial communities of Anopheles larvae sampled in Kenya, Burkina Faso and Republic of Guinea (Conakry). We identified 453 eukaryotic operational taxonomic units (OTUs) associated with Anopheles larvae in nature, but an average of 45% of the 18S rRNA sequences clustered into OTUs that lacked a taxonomic assignment in the Silva database. Thus, the Anopheles microbiome contains a striking proportion of novel eukaryotic taxa. Using sequence similarity matching and de novo phylogenetic placement, the fraction of unassigned sequences was reduced to an average of 4%, and many unclassified OTUs were assigned as relatives of known taxa. A novel taxon of the genus Ophryocystis in the phylum Apicomplexa (which also includes Plasmodium) is widespread in Anopheles larvae from East and West Africa. Notably, Ophryocystis is present at fluctuating abundance among larval breeding sites, consistent with the expected pattern of an epidemic pathogen. Species richness of the eukaryotic microbiome was not significantly different across sites from East to West Africa, while species richness of the prokaryotic microbiome was significantly lower in West Africa. Laboratory colonies of Anopheles coluzzii harbor 26 eukaryotic OTUs, of which 38% (n = 10) are shared with wild populations, while 16 OTUs are unique to the laboratory colonies. Genetically distinct An. coluzzii colonies co-housed in the same facility maintain different prokaryotic microbiome profiles, suggesting a persistent host genetic influence on microbiome composition. These results provide a foundation to understand the role of the Anopheles eukaryotic microbiome in vector immunity and pathogen transmission. We hypothesize that prevalent apicomplexans such as Ophryocystis associated with Anopheles could induce interference or competition against Plasmodium within the vector. This and other members of the eukaryotic microbiome may offer candidates for new vector control tools.
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Affiliation(s)
- Eugeni Belda Cuesta
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Boubacar Coulibaly
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Tullu Bukhari
- International Centre of Insect Physiology and Ecology, Department of Human Health. Nairobi,Kenya
| | - Karin Eiglmeier
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Raymond Kone
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Guinea
| | - Mamadou B. Coulibaly
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Soumanaba Zongo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Mamadou Barry
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Guinea
| | - Awa Gneme
- Département de Biologie et Physiologie Animales, Université Joseph Ki-Zerbo, Ouagadougou, Burkina Faso
| | - Wamdaogo M. Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Abdoul H. Beavogui
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Guinea
| | - Sekou F. Traore
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - N’Fale Sagnon
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Kenneth D. Vernick
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Michelle M. Riehle
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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Ros-Rocher N, Pérez-Posada A, Leger MM, Ruiz-Trillo I. The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition. Open Biol 2021; 11:200359. [PMID: 33622103 PMCID: PMC8061703 DOI: 10.1098/rsob.200359] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How animals evolved from a single-celled ancestor, transitioning from a unicellular lifestyle to a coordinated multicellular entity, remains a fascinating question. Key events in this transition involved the emergence of processes related to cell adhesion, cell–cell communication and gene regulation. To understand how these capacities evolved, we need to reconstruct the features of both the last common multicellular ancestor of animals and the last unicellular ancestor of animals. In this review, we summarize recent advances in the characterization of these ancestors, inferred by comparative genomic analyses between the earliest branching animals and those radiating later, and between animals and their closest unicellular relatives. We also provide an updated hypothesis regarding the transition to animal multicellularity, which was likely gradual and involved the use of gene regulatory mechanisms in the emergence of early developmental and morphogenetic plans. Finally, we discuss some new avenues of research that will complement these studies in the coming years.
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Affiliation(s)
- Núria Ros-Rocher
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Alberto Pérez-Posada
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.,Centro Andaluz de Biología del Desarrollo (CSIC-Universidad Pablo de Olavide), Carretera de Utrera Km 1, 41013 Sevilla, Andalusia, Spain
| | - Michelle M Leger
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
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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] [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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Metz S, Lopes dos Santos A, Berman MC, Bigeard E, Licursi M, Not F, Lara E, Unrein F. Diversity of photosynthetic picoeukaryotes in eutrophic shallow lakes as assessed by combining flow cytometry cell-sorting and high throughput sequencing. FEMS Microbiol Ecol 2019; 95:5393366. [DOI: 10.1093/femsec/fiz038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/18/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
- Sebastián Metz
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET. Av. Intendente Marino Km 8.200, Chascomús (7130), Buenos Aires, Argentina
| | - Adriana Lopes dos Santos
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Manuel Castro Berman
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET. Av. Intendente Marino Km 8.200, Chascomús (7130), Buenos Aires, Argentina
| | - Estelle Bigeard
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Magdalena Licursi
- Instituto Nacional de Limnología (INALI), CONICET-UNL. Ciudad Universitaria - Paraje el Pozo s/n (3000), Santa Fé, Argentina
| | - Fabrice Not
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Enrique Lara
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Fernando Unrein
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET. Av. Intendente Marino Km 8.200, Chascomús (7130), Buenos Aires, Argentina
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