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Galià-Camps C, Pegueroles C, Turon X, Carreras C, Pascual M. Genome composition and GC content influence loci distribution in reduced representation genomic studies. BMC Genomics 2024; 25:410. [PMID: 38664648 PMCID: PMC11046876 DOI: 10.1186/s12864-024-10312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge variability of genomic features. However, their variability and the extent to which genomic content determines the distribution of recovered loci in reduced representation sequencing studies is largely unexplored. RESULTS Here, by using 80 genome assemblies, we observed that whereas plants primarily increase their genome size by expanding their intergenic regions, animals expand both intergenic and intronic regions, although the expansion patterns differ between deuterostomes and protostomes. Loci mapping in introns, exons, and intergenic categories obtained by in silico digestion using 2b-enzymes are positively correlated with the percentage of these regions in the corresponding genomes, suggesting that loci distribution mostly mirrors genomic architecture of the selected taxon. However, exonic regions showed a significant enrichment of loci in all groups regardless of the used enzyme. Moreover, when using selective adaptors to obtain a secondarily reduced loci dataset, the percentage and distribution of retained loci also varied. Adaptors with G/C terminals recovered a lower percentage of selected loci, with a further enrichment of exonic regions, while adaptors with A/T terminals retained a higher percentage of loci and slightly selected more intronic regions than expected. CONCLUSIONS Our results highlight how genome composition, genome GC content, RAD enzyme choice and use of base-selective adaptors influence reduced genome representation techniques. This is important to acknowledge in population and conservation genomic studies, as it determines the abundance and distribution of loci.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain.
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, Blanes, 17300, Spain.
| | - Cinta Pegueroles
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, Blanes, 17300, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
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Zarcero J, Antich A, Rius M, Wangensteen OS, Turon X. A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species. iScience 2024; 27:108588. [PMID: 38111684 PMCID: PMC10726295 DOI: 10.1016/j.isci.2023.108588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/04/2023] [Accepted: 11/23/2023] [Indexed: 12/20/2023] Open
Abstract
Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they are often biased by inconsistent sampling methods and incomplete reference databases. Logistic constraints in ports prompt the development of simple, easy-to-deploy samplers. We tested a new device called polyamide mesh for ports organismal monitoring (POMPOM) with a high surface-to-volume ratio. POMPOMS were deployed inside a fishing and recreational port in the Mediterranean alongside conventional settlement plates. We also compiled a curated database with cytochrome oxidase (COI) sequences of Mediterranean NIS. COI metabarcoding of the communities settled in the POMPOMs captured a similar biodiversity than settlement plates, with shared molecular operational units (MOTUs) representing ca. 99% of reads. 38 NIS were detected in the port accounting for ca. 26% of reads. POMPOMs were easy to deploy and handle and provide an efficient method for NIS surveillance.
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Affiliation(s)
- Jesús Zarcero
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
| | - Marc Rius
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park Johannesburg 2006, South Africa
| | - Owen S. Wangensteen
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB), CSIC, 17300 Blanes, Catalonia, Spain
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Cano-Barbacil C, Carrete M, Castro-Díez P, Delibes-Mateos M, Jaques JA, López-Darias M, Nogales M, Pino J, Ros M, Traveset A, Turon X, Vilà M, Altamirano M, Álvarez I, Arias A, Boix D, Cabido C, Cacabelos E, Cobo F, Cruz J, Cuesta JA, Dáder B, Del Estal P, Gallardo B, Gómez Laporta M, González-Moreno P, Hernández JC, Jiménez-Alfaro B, Lázaro Lobo A, Leza M, Montserrat M, Oliva-Paterna FJ, Piñeiro L, Ponce C, Pons P, Rotchés-Ribalta R, Roura-Pascual N, Sánchez M, Trillo A, Viñuela E, García-Berthou E. Identification of potential invasive alien species in Spain through horizon scanning. J Environ Manage 2023; 345:118696. [PMID: 37549639 DOI: 10.1016/j.jenvman.2023.118696] [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: 05/31/2023] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Invasive alien species have widespread impacts on native biodiversity and ecosystem services. Since the number of introductions worldwide is continuously rising, it is essential to prevent the entry, establishment and spread of new alien species through a systematic examination of future potential threats. Applying a three-step horizon scanning consensus method, we evaluated non-established alien species that could potentially arrive, establish and cause major ecological impact in Spain within the next 10 years. Overall, we identified 47 species with a very high risk (e.g. Oreochromis niloticus, Popillia japonica, Hemidactylus frenatus, Crassula helmsii or Halophila stipulacea), 61 with high risk, 93 with moderate risk, and 732 species with low risk. Many of the species categorized as very high or high risk to Spanish biodiversity are either already present in Europe and neighbouring countries or have a long invasive history elsewhere. This study provides an updated list of potential invasive alien species useful for prioritizing efforts and resources against their introduction. Compared to previous horizon scanning exercises in Spain, the current study screens potential invaders from a wider range of terrestrial, freshwater, and marine organisms, and can serve as a basis for more comprehensive risk analyses to improve management and increase the efficiency of the early warning and rapid response framework for invasive alien species. We also stress the usefulness of measuring agreement and consistency as two different properties of the reliability of expert scores, in order to more easily elaborate consensus ranked lists of potential invasive alien species.
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Affiliation(s)
- Carlos Cano-Barbacil
- GRECO, Institute of Aquatic Ecology, University of Girona, 17003, Girona, Spain.
| | - Martina Carrete
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Ctra. de Utrera, km. 1, 41013, Seville, Spain
| | - Pilar Castro-Díez
- Biological Invasions Research Group (BioInv), Departamento de Ciencias de la Vida, Universidad de Alcalá, Pza. San Diego, s/n, 28801, Alcalá de Henares, Madrid, Spain
| | - Miguel Delibes-Mateos
- Instituto de Estudios Sociales Avanzados (IESA-CSIC), Plaza Campo Santo de los Mártires, 7, 14004, Córdoba, Spain
| | - Josep A Jaques
- Departament de Biologia, Bioquímica i Ciències Naturals, Universitat Jaume I, Av. Vicent Sos Baynat, s/n, 12071, Castelló de la Plana, Spain
| | - Marta López-Darias
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206, San Cristóbal de La Laguna, Canarias, Spain
| | - Manuel Nogales
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Avda. Astrofísico Francisco Sánchez, 3, 38206, San Cristóbal de La Laguna, Canarias, Spain
| | - Joan Pino
- CREAF, E08193 Bellaterra, (Cerdanyola del Vallès), Catalonia, Spain; Departament de Biologia Animal, Biologia Vegetal i Ecologia, Edifici C. Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Macarena Ros
- Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Anna Traveset
- Instituto Mediterráneo de Estudios Avanzados (IMEDEA,CSIC-UIB), C/ Miquel Marquès, 21, 07190, Esporles, Mallorca, Illes Balears, Spain
| | - Xavier Turon
- Departamento de Ecología Marina, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Accés a la Cala St. Francesc, 14, 17300, Blanes, Spain
| | - Montserrat Vilà
- Estación Biológica de Doñana (EBD-CSIC), Avda. Américo Vespucio 26, 41092, Sevilla, Spain; Department of Plant Biology and Ecology, University of Sevilla, 41012, Sevilla, Spain
| | - María Altamirano
- Department of Zoology and Physical Anthropology, Faculty of Biology, University of Murcia, CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | - Inés Álvarez
- Real Jardín Botánico (RJB-CSIC), C/ Claudio Moyano 1, 28014, Madrid, Spain
| | - Andrés Arias
- Departamento de Biología de Organismos y Sistemas (Zoología), Universidad de Oviedo, 33071, Oviedo, Spain
| | - Dani Boix
- GRECO, Institute of Aquatic Ecology, University of Girona, 17003, Girona, Spain
| | - Carlos Cabido
- Sociedad de Ciencias Aranzadi, Departamento de Herpetología, Calle Alto de Zorroaga 11, E-20014, San Sebastián, Spain
| | - Eva Cacabelos
- Hydrosphere - Environmental laboratory for the study of aquatic Ecosystems, 36331, Vigo, Spain
| | - Fernando Cobo
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Bioloxía, Universidade de Santiago de Compostela, A Coruña, Spain
| | - Joaquín Cruz
- Departament de Biologia, Bioquímica i Ciències Naturals, Universitat Jaume I, Av. Vicent Sos Baynat, s/n, 12071, Castelló de la Plana, Spain
| | - José A Cuesta
- Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), 11519, Puerto Real, Cádiz, Spain
| | - Beatriz Dáder
- Unit of Crop Protection, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain
| | - Pedro Del Estal
- Unit of Crop Protection, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain
| | - Belinda Gallardo
- Instituto Pirenaico de Ecología (IPE), CSIC, Avda. Montañana 1005, 50192, Zaragoza, Spain
| | | | | | - José Carlos Hernández
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, c/ Astrofísico Francisco Sánchez s/n, 38206, La Laguna, Santa Cruz de Tenerife, Spain
| | - Borja Jiménez-Alfaro
- Biodiversity Research Institute IMIB (Univ. Oviedo-CSIC-Princ. Asturias), Mieres, Spain
| | - Adrián Lázaro Lobo
- Biological Invasions Research Group (BioInv), Departamento de Ciencias de la Vida, Universidad de Alcalá, Pza. San Diego, s/n, 28801, Alcalá de Henares, Madrid, Spain; Biodiversity Research Institute IMIB (Univ. Oviedo-CSIC-Princ. Asturias), Mieres, Spain
| | - Mar Leza
- Departamento de Biología (Zoología), Universitat de les Illes Balears, Crta. Valldemossa, km. 7,5, 07122, Palma, Illes Balears, Spain
| | - Marta Montserrat
- Institute for Mediterranean and Subtropical Horticulture "La Mayora"-UMA-CSIC, Avda Dr Weinberg s/n, 29750, Algarrobo-Costa, Malaga, Spain
| | - Francisco J Oliva-Paterna
- Department of Zoology and Physical Anthropology, Faculty of Biology, University of Murcia, CEIR Campus Mare Nostrum (CMN), Murcia, Spain
| | | | | | - Pere Pons
- Animal Biology Lab & BioLand. Departament de Ciències Ambientals, Universitat de Girona, 17003, Girona, Catalonia, Spain
| | - Roser Rotchés-Ribalta
- CREAF, E08193 Bellaterra, (Cerdanyola del Vallès), Catalonia, Spain; Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, Universitat de Barcelona, 08028, Barcelona, Spain
| | - Núria Roura-Pascual
- Animal Biology Lab & BioLand. Departament de Ciències Ambientals, Universitat de Girona, 17003, Girona, Catalonia, Spain
| | - Marta Sánchez
- Estación Biológica de Doñana (EBD-CSIC), Avda. Américo Vespucio 26, 41092, Sevilla, Spain
| | - Alejandro Trillo
- Estación Biológica de Doñana (EBD-CSIC), Avda. Américo Vespucio 26, 41092, Sevilla, Spain
| | - Elisa Viñuela
- Unit of Crop Protection, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain
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4
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Galià-Camps C, Baños E, Pascual M, Carreras C, Turon X. Multidimensional variability of the microbiome of an invasive ascidian species. iScience 2023; 26:107812. [PMID: 37744040 PMCID: PMC10514470 DOI: 10.1016/j.isci.2023.107812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Animals, including invasive species, are complex entities consisting of a host and its associated symbionts (holobiont). The interaction between the holobiont components is crucial for the host's survival. However, our understanding of how microbiomes of invasive species change across different tissues, localities, and ontogenetic stages, is limited. In the introduced ascidian Styela plicata, we found that its microbiome is highly distinct and specialized among compartments (tunic, gill, and gut). Smaller but significant differences were also found across harbors, suggesting local adaptation, and between juveniles and adults. Furthermore, we found a correlation between the microbiome and environmental trace element concentrations, especially in adults. Functional analyses showed that adult microbiomes possess specific metabolic pathways that may enhance fitness during the introduction process. These findings highlight the importance of integrated approaches in studying the interplay between animals and microbiomes, as a first step toward understanding how it can affect the species' invasive success.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Elena Baños
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Department of Marine Ecology, Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Catalonia, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Avinguda Diagonal 643, 08028 Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre d’Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Catalonia, Spain
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5
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Marlétaz F, Couloux A, Poulain J, Labadie K, Da Silva C, Mangenot S, Noel B, Poustka AJ, Dru P, Pegueroles C, Borra M, Lowe EK, Lhomond G, Besnardeau L, Le Gras S, Ye T, Gavriouchkina D, Russo R, Costa C, Zito F, Anello L, Nicosia A, Ragusa MA, Pascual M, Molina MD, Chessel A, Di Carlo M, Turon X, Copley RR, Exposito JY, Martinez P, Cavalieri V, Ben Tabou de Leon S, Croce J, Oliveri P, Matranga V, Di Bernardo M, Morales J, Cormier P, Geneviève AM, Aury JM, Barbe V, Wincker P, Arnone MI, Gache C, Lepage T. Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes. Cell Genom 2023; 3:100295. [PMID: 37082140 PMCID: PMC10112332 DOI: 10.1016/j.xgen.2023.100295] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 12/24/2022] [Accepted: 03/06/2023] [Indexed: 04/22/2023]
Abstract
Sea urchins are emblematic models in developmental biology and display several characteristics that set them apart from other deuterostomes. To uncover the genomic cues that may underlie these specificities, we generated a chromosome-scale genome assembly for the sea urchin Paracentrotus lividus and an extensive gene expression and epigenetic profiles of its embryonic development. We found that, unlike vertebrates, sea urchins retained ancestral chromosomal linkages but underwent very fast intrachromosomal gene order mixing. We identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes have been recruited in novel structures (water vascular system, Aristotle's lantern, and skeletogenic micromere lineage). Finally, we identified gene-regulatory modules conserved between sea urchins and chordates. Our results suggest that gene-regulatory networks controlling development can be conserved despite extensive gene order rearrangement.
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Affiliation(s)
- Ferdinand Marlétaz
- Center for Life’s Origin & Evolution, Department of Genetics, Evolution, & Environment, University College London, WC1 6BT London, UK
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Sophie Mangenot
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Albert J. Poustka
- Evolution and Development Group, Max-Planck-Institut für Molekulare Genetik, 14195 Berlin, Germany
- Dahlem Center for Genome Research and Medical Systems Biology (Environmental and Phylogenomics Group), 12489 Berlin, Germany
| | - Philippe Dru
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Cinta Pegueroles
- Institute for Research on Biodiversity (IRBio), Department of Genetics, Microbiology, and Statistics, University of Barcelona, 08028 Barcelona, Spain
| | - Marco Borra
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Elijah K. Lowe
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Guy Lhomond
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Lydia Besnardeau
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Stéphanie Le Gras
- Plateforme GenomEast, IGBMC, CNRS UMR7104, INSERM U1258, Université de Strasbourg, 67404 Illirch Cedex, France
| | - Tao Ye
- Plateforme GenomEast, IGBMC, CNRS UMR7104, INSERM U1258, Université de Strasbourg, 67404 Illirch Cedex, France
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, 904-0495 Onna-son, Japan
| | - Roberta Russo
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Caterina Costa
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Francesca Zito
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Letizia Anello
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Aldo Nicosia
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Maria Antonietta Ragusa
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Marta Pascual
- Institute for Research on Biodiversity (IRBio), Department of Genetics, Microbiology, and Statistics, University of Barcelona, 08028 Barcelona, Spain
| | - M. Dolores Molina
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut Biology Valrose, Université Côte d’Azur, 06108 Nice Cedex 2, France
| | - Aline Chessel
- Institut Biology Valrose, Université Côte d’Azur, 06108 Nice Cedex 2, France
| | - Marta Di Carlo
- Institute for Biomedical Research and Innovation (CNR), 90146 Palermo, Italy
| | - Xavier Turon
- Department of Marine Ecology, Centre d’Estudis Avançats de Blanes (CEAB, CSIC), 17300 Blanes, Spain
| | - Richard R. Copley
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Jean-Yves Exposito
- Laboratoire de Biologie Tissulaire et d’Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Institut de Biologie et Chimie des Protéines, Université Lyon 1, 69367 Lyon, France
| | - Pedro Martinez
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), 08028 Barcelona, Spain
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Smadar Ben Tabou de Leon
- Department of Marine Biology, Charney School of Marine Sciences, University of Haifa, 31095 Haifa, Israel
| | - Jenifer Croce
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Paola Oliveri
- Center for Life’s Origin & Evolution, Department of Genetics, Evolution, & Environment, University College London, WC1 6BT London, UK
| | - Valeria Matranga
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l’Innovazione Biomedica (IRIB), 90146 Palermo, Italy
| | - Maria Di Bernardo
- Consiglio Nazionale delle Ricerche, Istituto di Farmacologia Traslazionale, 90146 Palermo, Italy
| | - Julia Morales
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, CNRS, Sorbonne Université, 29680 Roscoff, France
| | - Patrick Cormier
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, CNRS, Sorbonne Université, 29680 Roscoff, France
| | - Anne-Marie Geneviève
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, 66650 Banyuls/Mer, France
| | - Jean Marc Aury
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, 91057 Évry, France
| | - Maria Ina Arnone
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Christian Gache
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Thierry Lepage
- Institut Biology Valrose, Université Côte d’Azur, 06108 Nice Cedex 2, France
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Moreno-Dávila B, Huato-Soberanis L, Gómez-Gutiérrez J, Galván-Tirado C, Sánchez C, Alcoverro T, Balart EF, Turon X. Taxonomic identity of Distapliastylifera (Tunicata, Ascidiacea), a new arrival to the eastern Pacific displaying invasive behavior in the Gulf of California, Mexico. Zookeys 2023; 1157:109-125. [PMID: 37234953 PMCID: PMC10208407 DOI: 10.3897/zookeys.1157.95986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/06/2023] [Indexed: 05/28/2023] Open
Abstract
A colonial ascidian of the genus Distaplia caused a mass mortality of the pen shell Atrinamaura (Sowerby, 1835) during June 2016 in the southwest of the Gulf of California (Mexico), with a significant socio-economic cost. Tentatively identified in previous works as Distapliacf.stylifera, a precise taxonomic determination was still lacking. In the present work, based on a detailed morphological study, it is confirmed that this aggressive species is Distapliastylifera (Kowalevsky, 1874). Originally described from the Red Sea, the species currently has a wide circumtropical distribution (with the exception of the Eastern Pacific to date) and is reported as introduced in parts of its range. The present account thus represents an important range extension of this species. However, when revising the original description and later observations, the reported variability of several characters makes it likely that the binomen is in fact a complex of species, as is common in other ascidians with wide distributions. A complete morphological and genetic study including populations from the entire range of distribution would be necessary to settle the status of D.stylifera. Taxonomic uncertainties hinder a correct interpretation of biogeographical patterns and inference on the origin of the studied population. Nevertheless, the known introduction potential of the species, coupled with an explosive growth in an anthropized environment, and the lack of any previous reports in the Eastern Pacific, strongly suggest that the investigated population represents yet another instance of ascidian introduction. From the point of view of management, its invasive behavior is cause for great concern and warrants mitigation measures.
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Affiliation(s)
- Betzabé Moreno-Dávila
- Programa de Ecología Pesquera, Centro de Investigaciones Biológicas del Noroeste, C.P. 23096, La Paz, BCS, Mexico
| | - Leonardo Huato-Soberanis
- Programa de Ecología Pesquera, Centro de Investigaciones Biológicas del Noroeste, C.P. 23096, La Paz, BCS, Mexico
| | - Jaime Gómez-Gutiérrez
- Departamento de Plancton y Ecología Marina, Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, C.P. 23096, La Paz, BCS, Mexico
| | | | - Carlos Sánchez
- CONACYT, Universidad Autónoma de Baja California Sur, La Paz, BCS, Mexico
| | - Teresa Alcoverro
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, La Paz, BCS, Mexico
| | - Eduardo F. Balart
- Programa de Ecología Pesquera, Centro de Investigaciones Biológicas del Noroeste, C.P. 23096, La Paz, BCS, Mexico
| | - Xavier Turon
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, La Paz, BCS, Mexico
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7
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Antich A, Palacín C, Turon X, Wangensteen OS. DnoisE: distance denoising by entropy. An open-source parallelizable alternative for denoising sequence datasets. PeerJ 2022; 10:e12758. [PMID: 35111399 PMCID: PMC8783565 DOI: 10.7717/peerj.12758] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/16/2021] [Indexed: 01/07/2023] Open
Abstract
DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB- CSIC), Blanes (Girona), Catalonia, Spain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Catalonia, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB- CSIC), Blanes (Girona), Catalonia, Spain
| | - Owen S. Wangensteen
- Norwegian School of Fishery Science, UiT The Arctic University of Norway, Tromsø, Troms og Finnmark, Norway
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Muñoz-Mas R, Carrete M, Castro-Díez P, Delibes-Mateos M, Jaques JA, López-Darias M, Nogales M, Pino J, Traveset A, Turon X, Vilà M, García-Berthou E. Management of invasive alien species in Spain: A bibliometric review. NB 2021. [DOI: 10.3897/neobiota.70.68202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Scientific and grey literature on invasive alien species (IAS) is conditioned by social, economic and political priorities, editorial preferences and species and ecosystem characteristics. This leads to knowledge gaps and mismatches between scientific research interests and management needs. We reviewed the literature on IAS management in Spain found in Scopus, Web of Science, Google Scholar and Dialnet to identify key deficiencies and priority research areas. The collected literature was classified, employing features describing formal aspects and content. We used bibliometric and keyword co-occurrence network analyses to assess the relationship between features and reveal the existence of additional topics. Most of the compiled documents (n = 388) were focused on terrestrial ecosystems and inland waters, whereas marine and urban ecosystems were under-represented. The literature was largely generic and not species-specific, focusing on raising awareness and proposing changes on current regulation as prominent approaches to prevent further introductions. The compiled authors exhibited many clear publishing preferences (e.g. language or document type), but less regarding target taxa. In addition, there was a strong association between species and the different features considered, especially between the methodological approach (e.g. review, field experiment) and the primary emphasis of study (i.e. basic/theoretical, applied or interdisciplinary). This indicates that research on IAS has had a strong species-specific focus. References about terrestrial species focused mainly on vascular plants, whereas references about inland waters were mostly on fishes and the giant reed (Arundo donax), which has been managed with partial success. Animal culling and plant removal were the most frequent eradication and small-scale control treatments, whereas the documents addressing wider spatial scales were largely theoretical. Consequently, the success of described treatments was largely uncertain. Spanish invasion science research has been occasionally innovative, incorporating novel technologies (e.g. species distribution modelling) and engaging society with citizen-science approaches. However, the ratio between basic/theoretical and applied studies indicates that more applied research/management is needed, especially in inland waters and marine ecosystems. We call for increasing effort in the effective dissemination of experience in IAS management to enhance current practical knowledge, including that of schemes undertaken by public agencies.
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Antich A, Palacin C, Wangensteen OS, Turon X. To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics 2021; 22:177. [PMID: 33820526 PMCID: PMC8020537 DOI: 10.1186/s12859-021-04115-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, which have been wrongly presented as alternatives. It has also been suggested that denoised sequence variants should replace clusters as the basic unit of metabarcoding analyses, missing the fact that sequence clusters are a proxy for species-level entities, the basic unit in biodiversity studies. We argue here that methods developed and tested for ribosomal markers have been uncritically applied to highly variable markers such as cytochrome oxidase I (COI) without conceptual or operational (e.g., parameter setting) adjustment. COI has a naturally high intraspecies variability that should be assessed and reported, as it is a source of highly valuable information. We contend that denoising and clustering are not alternatives. Rather, they are complementary and both should be used together in COI metabarcoding pipelines. RESULTS Using a COI dataset from benthic marine communities, we compared two denoising procedures (based on the UNOISE3 and the DADA2 algorithms), set suitable parameters for denoising and clustering, and applied these steps in different orders. Our results indicated that the UNOISE3 algorithm preserved a higher intra-cluster variability. We introduce the program DnoisE to implement the UNOISE3 algorithm taking into account the natural variability (measured as entropy) of each codon position in protein-coding genes. This correction increased the number of sequences retained by 88%. The order of the steps (denoising and clustering) had little influence on the final outcome. CONCLUSIONS We highlight the need for combining denoising and clustering, with adequate choice of stringency parameters, in COI metabarcoding. We present a program that uses the coding properties of this marker to improve the denoising step. We recommend researchers to report their results in terms of both denoised sequences (a proxy for haplotypes) and clusters formed (a proxy for species), and to avoid collapsing the sequences of the latter into a single representative. This will allow studies at the cluster (ideally equating species-level diversity) and at the intra-cluster level, and will ease additivity and comparability between studies.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain
| | - Creu Palacin
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona and Research Institute of Biodiversity (IRBIO), Barcelona, Catalonia, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsö, Norway.
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Catalonia, Spain.
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Taverna A, de Aranzamendi MC, Maggioni T, Alurralde G, Turon X, Tatián M. Morphology, genetics, and historical records support the synonymy of two ascidian species and suggest their spread throughout areas of the Southern Hemisphere. INVERTEBR SYST 2021. [DOI: 10.1071/is20060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Taxonomic uncertainties and the lack of ecological knowledge can hinder the correct identification and the assignment of biogeographic status of marine species. The ascidian Asterocarpa humilis (Heller, 1878), originally described from New Zealand, has a broad distribution in shallow temperate areas of the Southern Hemisphere, having recently colonised areas of the Northern Hemisphere. A closely related species, Cnemidocarpa robinsoni Hartmeyer, 1916, has been reported in the South-Eastern Pacific and the South-Western Atlantic, and several authors considered it a junior synonym of A. humilis. We gathered for the first time morphological and genetic data from specimens from distant areas. We studied the morphology of specimens collected at seven locations of South America. We also re-examined specimens from museum collections and revised the available literature on these species. Genetic data were obtained from specimens from Argentina and compared with available sequences of A. humilis from Chile, New Zealand, England and France. Morphological and genetic analyses showed that all compared specimens were conspecific. Furthermore, specimens from different continents shared haplotypes and exhibited low genetic distance among them. These results, the biological characteristics of this ascidian, and its longstanding presence in different habitats from disjoint areas, allow us to question its native range. We support the idea that A. humilis is a cryptogenic and neocosmopolitan species that has been transported by maritime traffic through the Southern Hemisphere, revealing frequent processes of exchange through this wide area for more than a century, with presumably associated alterations in the marine biota.
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Alexandri M, Blanco-Catalá J, Schneider R, Turon X, Venus J. High L(+)-lactic acid productivity in continuous fermentations using bakery waste and lucerne green juice as renewable substrates. Bioresour Technol 2020; 316:123949. [PMID: 32768995 DOI: 10.1016/j.biortech.2020.123949] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 05/19/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
The biotechnological production of platform chemicals from renewable resources is in the scientific spotlight, as researchers seek to develop environmentally friendly and cost-efficient processes to compete with the petroleum-based ones. Lactic acid (LA) is an established platform chemical, registering an important market share, mainly owing to the increasing demand for polylactic acid. This study investigated the feasibility to produce LA from bakery waste hydrolysates and lucerne green juice (LGJ) as inexpensive substrates, using a Bacillus coagulans strain. A final LA concentration of 62.2 g/L, with a productivity of 2.59 g/(L.h) and a conversion yield of 0.57 g LA/ g bakery waste was achieved in batch fermentation mode. LA productivity reached 11.28 g/(L.h), using a continuous fermentation system coupled with cell retention membranes at a dilution rate of 0.2 h-1. The results indicate that bakery waste hydrolysates and LGJ can be utilized for the production of highly optical pure L(+)-LA.
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Affiliation(s)
- Maria Alexandri
- Department of Bioengineering, Leibniz-Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany
| | - Jorge Blanco-Catalá
- Department of Bioengineering, Leibniz-Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany; Institut Químic de Sarrià (IQS), Universitat Ramon Llull, Barcelona, Spain
| | - Roland Schneider
- Department of Bioengineering, Leibniz-Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany
| | - Xavier Turon
- Institut Químic de Sarrià (IQS), Universitat Ramon Llull, Barcelona, Spain; Lipotec-Lubrizol Active Ingredients, Gavà, Barcelona, Spain
| | - Joachim Venus
- Department of Bioengineering, Leibniz-Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany.
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13
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Antich A, Palacín C, Cebrian E, Golo R, Wangensteen OS, Turon X. Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities? Mol Ecol 2020; 30:3175-3188. [PMID: 32974967 DOI: 10.1111/mec.15641] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/06/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at four distances (0, 0.5, 1.5, and 20 m) from the benthic habitat. Using broad range primers to amplify a ca. 313 bp fragment of the cytochrome oxidase subunit I gene, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs). The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida and Stramenopiles being the most diverse groups in benthic samples, and Hacrobia, Metazoa and Alveolata in the water. Only 265 MOTUs (7.5%) were shared between benthos and water samples and, of these, 180 (5.1%) were identified as benthic taxa that left their DNA in the water. Most of them were found immediately adjacent to the benthos, and their number decreased as we moved apart from the benthic habitat. It was concluded that water eDNA, even in the close vicinity of the benthos, was a poor proxy for the analysis of benthic structure, and that direct sampling methods are required for monitoring these complex communities via metabarcoding.
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Affiliation(s)
- Adrià Antich
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Cruz Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, and Research Institute of Biodiversity (IRBIO), Barcelona, Spain
| | - Emma Cebrian
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Raül Golo
- Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Xavier Turon
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
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Pérez‐Portela R, Riesgo A, Wangensteen OS, Palacín C, Turon X. Enjoying the warming Mediterranean: Transcriptomic responses to temperature changes of a thermophilous keystone species in benthic communities. Mol Ecol 2020; 29:3299-3315. [DOI: 10.1111/mec.15564] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Rocío Pérez‐Portela
- Department of Evolutionary Biology, Ecology and Environmental Sciences University of Barcelona, and Research Institute of Biodiversity (IRBIO) Barcelona Spain
- Center for Advanced Studies of Blanes (CEAB, CSIC) Girona Spain
| | - Ana Riesgo
- Department of Life Sciences The Natural History Museum London UK
| | - Owen S. Wangensteen
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Cruz Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences University of Barcelona, and Research Institute of Biodiversity (IRBIO) Barcelona Spain
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB, CSIC) Girona Spain
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15
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Zhang Z, Capinha C, Karger DN, Turon X, MacIsaac HJ, Zhan A. Impacts of climate change on geographical distributions of invasive ascidians. Mar Environ Res 2020; 159:104993. [PMID: 32662432 DOI: 10.1016/j.marenvres.2020.104993] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 12/16/2019] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
Ocean warming associated with global climate change renders marine ecosystems susceptible to biological invasions. Here, we used species distribution models to project habitat suitability for eight invasive ascidians under present-day and future climate scenarios. Distance to shore and maximum sea surface temperature were identified as the most important variables affecting species distributions. Results showed that eight ascidians might respond differently to future climate change. Alarmingly, currently colonized areas are much smaller than predicted, suggesting ascidians may expand their invasive ranges. Areas such as Americas, Europe and Western Pacific have high risks of receiving new invasions. In contrast, African coasts, excluding the Mediterranean side, are not prone to new invasions, likely due to the high sea surface temperature there. Our results highlight the importance of climate change impacts on future invasions and the need for accurate modelling of invasion risks, which can be used as guides to develop management strategies.
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Affiliation(s)
- Zhixin Zhang
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, Minato, Tokyo, 108-8477, Japan
| | - César Capinha
- Centro de Estudos Geográficos, Instituto de Geografia e Ordenamento do Território - IGOT, Universidade de Lisboa, Rua Branca Edmée Marques, 1600-276, Lisboa, Portugal
| | - Dirk N Karger
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Xavier Turon
- Centre for Advanced Studies of Blanes (CEAB, CSIC), Blanes, Catalonia, Spain
| | - Hugh J MacIsaac
- School of Ecology and Environmental Science, Yunnan University, Kunming, China; Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
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16
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Turon X, Antich A, Palacín C, Præbel K, Wangensteen OS. From metabarcoding to metaphylogeography: separating the wheat from the chaff. Ecol Appl 2020; 30:e02036. [PMID: 31709684 PMCID: PMC7078904 DOI: 10.1002/eap.2036] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 05/13/2019] [Revised: 07/31/2019] [Accepted: 10/03/2019] [Indexed: 05/31/2023]
Abstract
Metabarcoding is by now a well-established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α- and β-diversity estimates, that is, interspecies (or inter-MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra-MOTU) information-mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding data sets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field that we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra-MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co-occurrence patterns of sequences. Using a data set of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two-step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole data set. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between seas component as well. There were intergroup differences in the amount of variability between and within communities in each sea. For two species, the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra- and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.
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Affiliation(s)
- Xavier Turon
- Department of Marine EcologyCentre for Advanced Studies of Blanes (CEAB, CSIC)BlanesCataloniaSpain
| | - Adrià Antich
- Department of Marine EcologyCentre for Advanced Studies of Blanes (CEAB, CSIC)BlanesCataloniaSpain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, and Institute of Biodiversity Research (IRBio)University of BarcelonaBarcelonaCataloniaSpain
| | - Kim Præbel
- Norwegian College of Fishery ScienceUiT the Arctic University of NorwayTromsøNorway
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17
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Carreras C, García‐Cisneros A, Wangensteen OS, Ordóñez V, Palacín C, Pascual M, Turon X. East is East and West is West: Population genomics and hierarchical analyses reveal genetic structure and adaptation footprints in the keystone species
Paracentrotus lividus
(Echinoidea). DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.13016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Carlos Carreras
- Department de Genètica Microbiologia i Estadística and IRBio Universitat de Barcelona Barcelona Spain
| | - Alex García‐Cisneros
- Centre d'Estudis Avançats de Blanes (CEAB, CSIC) Girona Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences and IRBIo University of Barcelona Barcelona Spain
| | - Owen S. Wangensteen
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Víctor Ordóñez
- Department de Genètica Microbiologia i Estadística and IRBio Universitat de Barcelona Barcelona Spain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences and IRBIo University of Barcelona Barcelona Spain
| | - Marta Pascual
- Department de Genètica Microbiologia i Estadística and IRBio Universitat de Barcelona Barcelona Spain
| | - Xavier Turon
- Centre d'Estudis Avançats de Blanes (CEAB, CSIC) Girona Spain
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18
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Casso M, Tagliapietra D, Turon X, Pascual M. High fusibility and chimera prevalence in an invasive colonial ascidian. Sci Rep 2019; 9:15673. [PMID: 31666562 PMCID: PMC6821838 DOI: 10.1038/s41598-019-51950-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 05/13/2019] [Accepted: 10/04/2019] [Indexed: 11/16/2022] Open
Abstract
The formation of chimeric entities through colony fusion has been hypothesized to favour colonisation success and resilience in modular organisms. In particular, it can play an important role in promoting the invasiveness of introduced species. We studied prevalence of chimerism and performed fusion experiments in Mediterranean populations of the worldwide invasive colonial ascidian Didemnum vexillum. We analysed single zooids by whole genome amplification and genotyping-by-sequencing and obtained genotypic information for more than 2,000 loci per individual. In the prevalence study, we analysed nine colonies and identified that 44% of them were chimeric, composed of 2–3 different genotypes. In the fusion experiment 15 intra- and 30 intercolony pairs were assayed but one or both fragments regressed and died in ~45% of the pairs. Among those that survived for the length of the experiment (30 d), 100% isogeneic and 31% allogeneic pairs fused. Fusion was unlinked to global genetic relatedness since the genetic distance between fused or non-fused intercolony pairs did not differ significantly. We could not detect any locus directly involved in allorecognition, but we cannot preclude the existence of a histocompatibility mechanism. We conclude that chimerism occurs frequently in D. vexillum and may be an important factor to enhance genetic diversity and promote its successful expansion.
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Affiliation(s)
- Maria Casso
- Center for Advanced Studies of Blanes (CEAB, CSIC), Catalonia, Spain.,Department of Genetics, Microbiology and Statistics, and IRBio, University of Barcelona, Catalonia, Spain
| | - Davide Tagliapietra
- CNR - National Research Council of Italy, ISMAR - Institute of Marine Sciences, Venice, Italy
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB, CSIC), Catalonia, Spain
| | - Marta Pascual
- Department of Genetics, Microbiology and Statistics, and IRBio, University of Barcelona, Catalonia, Spain.
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Casso M, Turon X, Pascual M. Single zooids, multiple loci: independent colonisations revealed by population genomics of a global invader. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02069-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Davis AR, Becerro M, Turon X. Living on the edge: Early life history phases as determinants of distribution in Pyura praeputialis (Heller, 1878), a rocky shore ecosystem engineer. Mar Environ Res 2018; 142:40-47. [PMID: 30269896 DOI: 10.1016/j.marenvres.2018.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 04/09/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
The distribution of intertidal organisms can depend on processes operating early in their life history. The ascidian Pyura praeputialis, a mid- to low-intertidal habitat-forming ecosystem engineer, was strongly associated with specific types of habitat (biogenic vs. bare rock). We examined field patterns and performed laboratory and field experiments to assess the nature of this association. Recruits were frequently found on the tunics of conspecifics and clumps of turfing coralline algae. Larvae preferred these same habitats in a series of laboratory settlement assays. Laboratory-reared juveniles (20- & 50-days-old) survived poorly on bare rock in the laboratory, while those on rugose surfaces - the tunic of adults and turfing corallines - showed high survivorship. Field-collected juveniles (<2 cm) affixed to these rugose habitats also exhibited high survivorship in the field. We conclude that both pre and post-settlement processes determine spatial pattern in this important habitat-forming taxon. The acute sensitivity of juveniles to desiccating conditions was unexpected in an intertidal organism.
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Affiliation(s)
- Andrew R Davis
- Centre for Sustainable Ecosystem Solutions, School of Biological Sciences, University of Wollongong, NSW, 2522, Australia.
| | - Mikel Becerro
- Centre for Advanced Studies of Blanes (CEAB, CSIC), Blanes, Girona, Spain.
| | - Xavier Turon
- Centre for Advanced Studies of Blanes (CEAB, CSIC), Blanes, Girona, Spain.
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21
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de Caralt S, González J, Turon X, Uriz MJ. -Reproductive strategies of two common sympatric Mediterranean sponges: Dysidea avara (Dictyoceratida) and Phorbas tenacior (Poecilosclerida). PeerJ 2018; 6:e5458. [PMID: 30123723 PMCID: PMC6087620 DOI: 10.7717/peerj.5458] [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: 03/21/2018] [Accepted: 07/26/2018] [Indexed: 11/20/2022] Open
Abstract
Despite their abundance in benthic ecosystems, life cycles and reproductive features of most sponge species remain unknown. We have studied the main reproductive features of two demosponges, Dysidea avara and Phorbas tenacior, belonging to phylogenetically distant groups: Orders Dictyoceratida and Poecilosclerida, respectively. Both sponges are abundant and share habitat in the Mediterranean rocky sublittoral. They brood parenchymella larvae with different morphology and behaviour. Sampling was conducted monthly over a two-year period in a locality where both species coexist. The two species reproduced in spring-summer, and presented species-specific reproductive features despite being subject to the same environmental conditions. D. avara has a shorter reproductive period than P. tenacior, ending before the peak of temperature in summer, while the reproductive period of P. tenacior lasts until beginning of autumn. Brooding larvae were present in June-July in D. avara, and in August-October in P. tenacior. Larval size, reproductive effort and number of larvae produced (measured the month with the maximum production) were significantly higher in D. avara than in P. tenacior. A higher reproductive effort and larval traits point to a more opportunistic life strategy in D. avara than in P. tenacior. A lack of overlap in the timing of larval release, as well as different reproductive traits, may reduce competition and facilitate the coexistence of these two sympatric and abundant sponges.
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Affiliation(s)
- Sonia de Caralt
- Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones Científicas, Blanes, Girona, Spain.,GRMAR, Institut d'Ecologia Aquàtica, Universitat de Girona, Girona, Spain
| | - Janina González
- Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones Científicas, Blanes, Girona, Spain
| | - Xavier Turon
- Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones Científicas, Blanes, Girona, Spain
| | - María J Uriz
- Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones Científicas, Blanes, Girona, Spain
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Wangensteen OS, Palacín C, Guardiola M, Turon X. DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers. PeerJ 2018; 6:e4705. [PMID: 29740514 PMCID: PMC5937484 DOI: 10.7717/peerj.4705] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [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: 11/22/2017] [Accepted: 04/15/2018] [Indexed: 12/21/2022] Open
Abstract
Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase (COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans. The 18S marker lacks species-level resolution and thus cannot be recommended to assess the detailed taxonomic composition of these communities. Our new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities.
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Affiliation(s)
- Owen S Wangensteen
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB, CSIC), Blanes, Spain.,Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, and Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain
| | - Magdalena Guardiola
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB, CSIC), Blanes, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB, CSIC), Blanes, Spain
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Delsuc F, Philippe H, Tsagkogeorga G, Simion P, Tilak MK, Turon X, López-Legentil S, Piette J, Lemaire P, Douzery EJP. A phylogenomic framework and timescale for comparative studies of tunicates. BMC Biol 2018; 16:39. [PMID: 29653534 PMCID: PMC5899321 DOI: 10.1186/s12915-018-0499-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [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: 12/19/2017] [Accepted: 02/20/2018] [Indexed: 01/13/2023] Open
Abstract
Background Tunicates are the closest relatives of vertebrates and are widely used as models to study the evolutionary developmental biology of chordates. Their phylogeny, however, remains poorly understood, and to date, only the 18S rRNA nuclear gene and mitogenomes have been used to delineate the major groups of tunicates. To resolve their evolutionary relationships and provide a first estimate of their divergence times, we used a transcriptomic approach to build a phylogenomic dataset including all major tunicate lineages, consisting of 258 evolutionarily conserved orthologous genes from representative species. Results Phylogenetic analyses using site-heterogeneous CAT mixture models of amino acid sequence evolution resulted in a strongly supported tree topology resolving the relationships among four major tunicate clades: (1) Appendicularia, (2) Thaliacea + Phlebobranchia + Aplousobranchia, (3) Molgulidae, and (4) Styelidae + Pyuridae. Notably, the morphologically derived Thaliacea are confirmed as the sister group of the clade uniting Phlebobranchia + Aplousobranchia within which the precise position of the model ascidian genus Ciona remains uncertain. Relaxed molecular clock analyses accommodating the accelerated evolutionary rate of tunicates reveal ancient diversification (~ 450–350 million years ago) among the major groups and allow one to compare their evolutionary age with respect to the major vertebrate model lineages. Conclusions Our study represents the most comprehensive phylogenomic dataset for the main tunicate lineages. It offers a reference phylogenetic framework and first tentative timescale for tunicates, allowing a direct comparison with vertebrate model species in comparative genomics and evolutionary developmental biology studies. Electronic supplementary material The online version of this article (10.1186/s12915-018-0499-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station d'Ecologie Théorique et Expérimentale, Moulis, France.,Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, Canada
| | - Georgia Tsagkogeorga
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Marie-Ka Tilak
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB, CSIC), Girona, Spain
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Jacques Piette
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Université de Montpellier, Montpellier, France
| | - Patrick Lemaire
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Université de Montpellier, Montpellier, France
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Wangensteen OS, Cebrian E, Palacín C, Turon X. Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding. Mar Pollut Bull 2018; 127:54-66. [PMID: 29475694 DOI: 10.1016/j.marpolbul.2017.11.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 03/13/2017] [Revised: 11/12/2017] [Accepted: 11/15/2017] [Indexed: 06/08/2023]
Abstract
We analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.
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Affiliation(s)
- Owen S Wangensteen
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Emma Cebrian
- Aquatic Ecology Institute, University of Girona, Campus Montilivi, Girona, Spain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Spain.
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Guardiola M, Wangensteen OS, Taberlet P, Coissac E, Uriz MJ, Turon X. Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA. PeerJ 2016; 4:e2807. [PMID: 28028473 PMCID: PMC5180584 DOI: 10.7717/peerj.2807] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [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: 07/05/2016] [Accepted: 11/20/2016] [Indexed: 11/20/2022] Open
Abstract
We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts.
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Affiliation(s)
- Magdalena Guardiola
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes , Spain
| | - Owen S Wangensteen
- Department of Animal Biology and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Spain; Ecosystems & Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique and Université Grenoble-Alpes , Grenoble , France
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique and Université Grenoble-Alpes , Grenoble , France
| | - María Jesús Uriz
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes , Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes , Spain
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Leese F, Altermatt F, Bouchez A, Ekrem T, Hering D, Meissner K, Mergen P, Pawlowski J, Piggott J, Rimet F, Steinke D, Taberlet P, Weigand A, Abarenkov K, Beja P, Bervoets L, Björnsdóttir S, Boets P, Boggero A, Bones A, Borja Á, Bruce K, Bursić V, Carlsson J, Čiampor F, Čiamporová-Zatovičová Z, Coissac E, Costa F, Costache M, Creer S, Csabai Z, Deiner K, DelValls Á, Drakare S, Duarte S, Eleršek T, Fazi S, Fišer C, Flot JF, Fonseca V, Fontaneto D, Grabowski M, Graf W, Guðbrandsson J, Hellström M, Hershkovitz Y, Hollingsworth P, Japoshvili B, Jones J, Kahlert M, Kalamujic Stroil B, Kasapidis P, Kelly M, Kelly-Quinn M, Keskin E, Kõljalg U, Ljubešić Z, Maček I, Mächler E, Mahon A, Marečková M, Mejdandzic M, Mircheva G, Montagna M, Moritz C, Mulk V, Naumoski A, Navodaru I, Padisák J, Pálsson S, Panksep K, Penev L, Petrusek A, Pfannkuchen M, Primmer C, Rinkevich B, Rotter A, Schmidt-Kloiber A, Segurado P, Speksnijder A, Stoev P, Strand M, Šulčius S, Sundberg P, Traugott M, Tsigenopoulos C, Turon X, Valentini A, van der Hoorn B, Várbíró G, Vasquez Hadjilyra M, Viguri J, Vitonytė I, Vogler A, Vrålstad T, Wägele W, Wenne R, Winding A, Woodward G, Zegura B, Zimmermann J. DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. RIO 2016. [DOI: 10.3897/rio.2.e11321] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Pineda MC, Lorente B, López-Legentil S, Palacín C, Turon X. Stochasticity in space, persistence in time: genetic heterogeneity in harbour populations of the introduced ascidian Styela plicata. PeerJ 2016; 4:e2158. [PMID: 27366653 PMCID: PMC4924124 DOI: 10.7717/peerj.2158] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 03/09/2016] [Accepted: 05/31/2016] [Indexed: 11/30/2022] Open
Abstract
Spatio-temporal changes in genetic structure among populations provide crucial information on the dynamics of secondary spread for introduced marine species. However, temporal components have rarely been taken into consideration when studying the population genetics of non-indigenous species. This study analysed the genetic structure of Styela plicata, a solitary ascidian introduced in harbours and marinas of tropical and temperate waters, across spatial and temporal scales. A fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) was sequenced from 395 individuals collected at 9 harbours along the NW Mediterranean coast and adjacent Atlantic waters (> 1,200 km range) at two time points 5 years apart (2009 and 2014). The levels of gene diversity were relatively low for all 9 locations in both years. Analyses of genetic differentiation and distribution of molecular variance revealed strong genetic structure, with significant differences among many populations, but no significant differences among years. A weak and marginally significant correlation between geographic distance and gene differentiation was found. Our results revealed spatial structure and temporal genetic homogeneity in S. plicata, suggesting a limited role of recurrent, vessel-mediated transport of organisms among small to medium-size harbours. Our study area is representative of many highly urbanized coasts with dense harbours. In these environments, the episodic chance arrival of colonisers appears to determine the genetic structure of harbour populations and the genetic composition of these early colonising individuals persists in the respective harbours, at least over moderate time frames (five years) that encompass ca. 20 generations of S. plicata.
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Affiliation(s)
- Mari-Carmen Pineda
- Department of Animal Biology and Biodiversity Research Institute (IRBIO), University of Barcelona, Barcelona, Spain; Sustainable Coastal Ecosystems & Industry in Tropical Australia, Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Beatriz Lorente
- Department of Animal Biology and Biodiversity Research Institute (IRBIO), University of Barcelona , Barcelona , Spain
| | - Susanna López-Legentil
- Department of Biology & Marine Biology and Center for Marine Science, University of North Carolina Wilmington , Wilmington, North Carolina , United States
| | - Creu Palacín
- Department of Animal Biology and Biodiversity Research Institute (IRBIO), University of Barcelona , Barcelona , Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes, Girona , Spain
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Turon X, Cañete JI, Sellanes J, Rocha RM, López-Legentil S. Ascidian fauna (Tunicata, Ascidiacea) of subantarctic and temperate regions of Chile. Zootaxa 2016; 4093:151-80. [PMID: 27394488 DOI: 10.11646/zootaxa.4093.2.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 11/04/2022]
Abstract
We studied the ascidian fauna from two zones located in subantarctic (Punta Arenas, latitude 53º) and temperate Chile (Coquimbo, latitude 29º). The different oceanographic features of the two zones, with influence of the Humboldt Current in the north and the Cape Horn Current System and freshwater inputs in the south, led to markedly different ascidian faunas. A total of 22 species were recorded, with no shared species across the two areas (11 species each). The new species Polyzoa iosune is described, Lissoclinum perforatum is found for the first time in the Pacific Ocean, and Synoicum georgianum and Polyzoa minor are new to the Chilean fauna. The populations of Ciona in the Coquimbo area (formerly attributed to Ciona intestinalis) correspond to the species Ciona robusta. A total of 35 Cytochrome oxidase (COI) sequences of the standard barcode region have been obtained for 17 of the 22 species reported.
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Affiliation(s)
- Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Girona, Spain; unknown
| | - Juan I Cañete
- Facultad de Ciencias, Universidad de Magallanes, Punta Arenas, Chile; unknown
| | - Javier Sellanes
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile; unknown
| | - Rosana M Rocha
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Brazil; unknown
| | - Susanna López-Legentil
- Department of Biology and Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA; unknown
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Ordóñez V, Pascual M, Fernández-Tejedor M, Turon X. When invasion biology meets taxonomy: Clavelina oblonga (Ascidiacea) is an old invader in the Mediterranean Sea. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1062-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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López-Legentil S, Turon X, Erwin PM. Feeding cessation alters host morphology and bacterial communities in the ascidian Pseudodistoma crucigaster. Front Zool 2016; 13:2. [PMID: 26770257 PMCID: PMC4712478 DOI: 10.1186/s12983-016-0134-4] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/07/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Ascidians can associate with abundant and diverse consortia of microbial symbionts, yet these communities remain unexamined for the majority of host ascidians and little is known about host-symbiont interactions. METHODS We coupled electron microscopy and 16S rRNA gene tag pyrosequencing to investigate the bacterial communities associated with the colonial ascidian Pseudodistoma crucigaster, a species endemic to the Mediterranean Sea that has a life cycle with two phases: actively-filtering (active) and non-filtering (resting) forms. RESULTS Resting colonies exhibited a reduced branchial sac (feeding apparatus) and a thickened cuticle. Electron microscope images also suggested higher abundance of colonizing microorganisms on surfaces of resting colonies. Accordingly, bacterial sequences associated with environmental sources (sediment and biofilms, >99 % similarity) were detected exclusively in resting colonies. Bacterial communities of P. crucigaster colonies (active and resting) were dominated by 3 core taxa affiliated (>94 % similarity) with previously described symbiotic Alphaproteobacteria in marine invertebrates. Shifts in rare bacteria were detected when ascidians entered the resting phase, including the appearance of strictly anaerobic lineages and nitrifying bacterial guilds. CONCLUSIONS These findings suggest that physical (thickened cuticle) and metabolic (feeding cessation) changes in host ascidians have cascading effects on associated bacteria, where modified oxygen concentrations and chemical substrates for microbial metabolism may create anaerobic microhabitats and promote colonization by environmental microorganisms.
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Affiliation(s)
- Susanna López-Legentil
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, 28409 Wilmington, USA
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC), Accés Cala S. Francesc 14, 17300 Blanes Girona, Spain
| | - Patrick M Erwin
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, 28409 Wilmington, USA
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Pérez-Portela R, Turon X, Riesgo A. Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchinArbacia lixulausing RNA-seq. Mol Ecol Resour 2015; 16:794-808. [DOI: 10.1111/1755-0998.12500] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 11/19/2015] [Accepted: 11/24/2015] [Indexed: 11/26/2022]
Affiliation(s)
- R. Pérez-Portela
- Center for Advanced Studies of Blanes (CEAB-CSIC); Acceso a la Cala Sant Francesc 14 17300 Girona Spain
- Department of Animal Biology; University of Barcelona; 643 Diagonal Avenue 08028 Barcelona Spain
| | - X. Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC); Acceso a la Cala Sant Francesc 14 17300 Girona Spain
| | - A. Riesgo
- Department of Animal Biology; University of Barcelona; 643 Diagonal Avenue 08028 Barcelona Spain
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Abad S, Turon X. Biotechnological Production of Docosahexaenoic Acid Using Aurantiochytrium limacinum: Carbon Sources Comparison And Growth Characterization. Mar Drugs 2015; 13:7275-84. [PMID: 26690180 PMCID: PMC4699237 DOI: 10.3390/md13127064] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 06/08/2015] [Accepted: 11/30/2015] [Indexed: 11/16/2022] Open
Abstract
Aurantiochytrium limacinum, a marine heterotrophic protist/microalga has shown interesting yields of docosahexaenoic acid (DHA) when cultured with different carbon sources: glucose, pure and crude glycerol. A complete study in a lab-scale fermenter allowed for the characterization and comparison of the growth kinetic parameters corresponding to each carbon source. Artificial Marine Medium (AMM) with glucose, pure and crude glycerol offered similar biomass yields. The net growth rates (0.10–0.12 h−1), biomass (0.7–0.8 g cells/g Substrate) and product (0.14–0.15 g DHA/g cells) yields, as well as DHA productivity were similar using the three carbon sources. Viable potential applications to valorize crude glycerol are envisioned to avoid an environmental problem due to the excess of byproduct.
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Affiliation(s)
- Sergi Abad
- Bioengineering Department, IQS, Ramon Llull University, Via Augusta 390, Barcelona 08017, Spain.
| | - Xavier Turon
- Bioengineering Department, IQS, Ramon Llull University, Via Augusta 390, Barcelona 08017, Spain.
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Guardiola M, Uriz MJ, Taberlet P, Coissac E, Wangensteen OS, Turon X. Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLoS One 2015; 10:e0139633. [PMID: 26436773 PMCID: PMC4593591 DOI: 10.1371/journal.pone.0139633] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [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: 05/31/2015] [Accepted: 09/14/2015] [Indexed: 12/22/2022] Open
Abstract
Marine sediments are home to one of the richest species pools on Earth, but logistics and a dearth of taxonomic work-force hinders the knowledge of their biodiversity. We characterized α- and β-diversity of deep-sea assemblages from submarine canyons in the western Mediterranean using an environmental DNA metabarcoding. We used a new primer set targeting a short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed to obtain extractions enriched in extracellular DNA from replicated sediment corers. With this strategy we captured information from DNA (local or deposited from the water column) that persists adsorbed to inorganic particles and buffered short-term spatial and temporal heterogeneity. We analysed replicated samples from 20 localities including 2 deep-sea canyons, 1 shallower canal, and two open slopes (depth range 100–2,250 m). We identified 1,629 MOTUs, among which the dominant groups were Metazoa (with representatives of 19 phyla), Alveolata, Stramenopiles, and Rhizaria. There was a marked small-scale heterogeneity as shown by differences in replicates within corers and within localities. The spatial variability between canyons was significant, as was the depth component in one of the canyons where it was tested. Likewise, the composition of the first layer (1 cm) of sediment was significantly different from deeper layers. We found that qualitative (presence-absence) and quantitative (relative number of reads) data showed consistent trends of differentiation between samples and geographic areas. The subset of exclusively benthic MOTUs showed similar patterns of β-diversity and community structure as the whole dataset. Separate analyses of the main metazoan phyla (in number of MOTUs) showed some differences in distribution attributable to different lifestyles. Our results highlight the differentiation that can be found even between geographically close assemblages, and sets the ground for future monitoring and conservation efforts on these bottoms of ecological and economic importance.
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Affiliation(s)
- Magdalena Guardiola
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - María Jesús Uriz
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Pierre Taberlet
- Université Grenoble Alpes, Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
- Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
| | - Eric Coissac
- Université Grenoble Alpes, Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
- Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
| | - Owen Simon Wangensteen
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
- Department of Animal Biology, University of Barcelona, Barcelona, Spain
| | - Xavier Turon
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
- * E-mail:
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López-Legentil S, Turon X, Espluga R, Erwin PM. Temporal stability of bacterial symbionts in a temperate ascidian. Front Microbiol 2015; 6:1022. [PMID: 26441944 PMCID: PMC4585324 DOI: 10.3389/fmicb.2015.01022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/08/2015] [Indexed: 12/17/2022] Open
Abstract
In temperate seas, both bacterioplankton communities and invertebrate lifecycles follow a seasonal pattern. To investigate whether the bacterial community associated with the Mediterranean ascidian Didemnum fulgens exhibited similar variations, we monitored its bacterial community structure monthly for over a year using terminal restriction fragment length polymorphism and clone library analyses based on a nearly full length fragment of the 16S rRNA gene. D. fulgens harbored a bacterial consortium typical of ascidians, including numerous members of the phylum Proteobacteria, and a few members of the phyla Cyanobacteria and Acidobacteria. The overall bacterial community in D. fulgens had a distinct signature from the surrounding seawater and was stable over time and across seasonal fluctuations in temperature. Bacterial symbionts were also observed around animal cells in the tunic of adult individuals and in the inner tunic of D. fulgens larvae by transmission electron microscopy. Our results suggest that, as seen for sponges and corals, some species of ascidians host stable and unique bacterial communities that are at least partially inherited by their progeny by vertical transmission.
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Affiliation(s)
- Susanna López-Legentil
- Department of Biology & Marine Biology and Center for Marine Science, University of North Carolina WilmingtonWilmington, NC, USA
| | - Xavier Turon
- Center for Advanced Studies of Blanes – Consejo Superior de Investigaciones CientíficasBlanes, Spain
| | - Roger Espluga
- Department of Animal Biology, University of BarcelonaBarcelona, Spain
| | - Patrick M. Erwin
- Department of Biology & Marine Biology and Center for Marine Science, University of North Carolina WilmingtonWilmington, NC, USA
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Airoldi L, Turon X, Perkol-Finkel S, Rius M. Corridors for aliens but not for natives: effects of marine urban sprawl at a regional scale. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12301] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Laura Airoldi
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali; University of Bologna; Via S. Alberto 163 I-48123 Ravenna Italy
- Hopkins Marine Station; Stanford University; Pacific Grove CA 93950 USA
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC); Accés a la Cala S. Francesc 14 17300 Blanes (Girona) Spain
| | - Shimrit Perkol-Finkel
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali; University of Bologna; Via S. Alberto 163 I-48123 Ravenna Italy
- SeArc - Ecological Marine Consulting; 13 Namirover St. Tel Aviv 69713 Israel
| | - Marc Rius
- Ocean and Earth Science, National Oceanography Centre Southampton; University of Southampton; European Way SO14 3ZH UK
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López-Legentil S, Legentil ML, Erwin PM, Turon X. Harbor networks as introduction gateways: contrasting distribution patterns of native and introduced ascidians. Biol Invasions 2014; 17:1623-1638. [PMID: 26190935 PMCID: PMC4498637 DOI: 10.1007/s10530-014-0821-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [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: 03/26/2014] [Accepted: 12/01/2014] [Indexed: 11/01/2022]
Abstract
Harbors and marinas are well known gateways for species introductions in marine environments but little work has been done to ascertain relationships between species diversity, harbor type, and geographic distance to uncover patterns of secondary spread. Here, we sampled ascidians from 32 harbors along ca. 300 km of the NW Mediterranean coast and investigated patterns of distribution and spread related to harbor type (marina, fishing, commercial) and geographic location using multivariate techniques. In total, 28 ascidians were identified at the species level and another 9 at the genus level based on morphology and genetic barcoding. Eight species were assigned to introduced forms, 15 were given native status and 5 were classified as cryptogenic. Aplidium accarense was reported for the first time in the Mediterranean Sea and was especially abundant in 23 of the harbors. Introduced and cryptogenic species were abundant in most of the surveyed harbors, while native forms were rare and restricted to a few harbors. Significant differences in the distribution of ascidians according to harbor type and latitudinal position were observed. These differences were due to the distribution of introduced species. We obtained a significant correlation between geographic distance and ascidian composition, indicating that closely located harbors shared more ascidian species among them. This study showed that harbors act as dispersal strongholds for introduced species, with native species only appearing sporadically, and that harbor type and geographic location should also be considered when developing management plans to constrain the spread of non-indigenous species in highly urbanized coastlines.
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Affiliation(s)
- Susanna López-Legentil
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409 USA
| | - Miquel L Legentil
- Departament de Biologia Animal, Universitat de Barcelona (UB), Diagonal Avenue 643, 08028 Barcelona, Spain
| | - Patrick M Erwin
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC 28409 USA
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC), Accés Cala S. Francesc 14, 17300 Blanes, Girona, Spain
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Griggio F, Voskoboynik A, Iannelli F, Justy F, Tilak MK, Turon X, Xavier T, Pesole G, Douzery EJP, Mastrototaro F, Gissi C. Ascidian mitogenomics: comparison of evolutionary rates in closely related taxa provides evidence of ongoing speciation events. Genome Biol Evol 2014; 6:591-605. [PMID: 24572017 PMCID: PMC3971592 DOI: 10.1093/gbe/evu041] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [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] [Indexed: 01/22/2023] Open
Abstract
Ascidians are a fascinating group of filter-feeding marine chordates characterized by rapid evolution of both sequences and structure of their nuclear and mitochondrial genomes. Moreover, they include several model organisms used to investigate complex biological processes in chordates. To study the evolutionary dynamics of ascidians at short phylogenetic distances, we sequenced 13 new mitogenomes and analyzed them, together with 15 other available mitogenomes, using a novel approach involving detailed whole-mitogenome comparisons of conspecific and congeneric pairs. The evolutionary rate was quite homogeneous at both intraspecific and congeneric level, and the lowest congeneric rates were found in cryptic (morphologically undistinguishable) and in morphologically very similar species pairs. Moreover, congeneric nonsynonymous rates (dN) were up to two orders of magnitude higher than in intraspecies pairs. Overall, a clear-cut gap sets apart conspecific from congeneric pairs. These evolutionary peculiarities allowed easily identifying an extraordinary intraspecific variability in the model ascidian Botryllus schlosseri, where most pairs show a dN value between that observed at intraspecies and congeneric level, yet consistently lower than that of the Ciona intestinalis cryptic species pair. These data suggest ongoing speciation events producing genetically distinct B. schlosseri entities. Remarkably, these ongoing speciation events were undetectable by the cox1 barcode fragment, demonstrating that, at low phylogenetic distances, the whole mitogenome has a higher resolving power than cox1. Our study shows that whole-mitogenome comparative analyses, performed on a suitable sample of congeneric and intraspecies pairs, may allow detecting not only cryptic species but also ongoing speciation events.
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Affiliation(s)
- Francesca Griggio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
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Rius M, Turon X, Bernardi G, Volckaert FAM, Viard F. Marine invasion genetics: from spatio-temporal patterns to evolutionary outcomes. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0792-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Nishikawa T, Oohara I, Saitoh K, Shigenobu Y, Hasegawa N, Kanamori M, Baba K, Turon X, Bishop JDD. Molecular and morphological discrimination between an invasive ascidian, Ascidiella aspersa, and its congener A. scabra (Urochordata: Ascidiacea). Zoolog Sci 2014; 31:180-5. [PMID: 24601780 DOI: 10.2108/zsj.31.180] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The solitary ascidian Ascidiella aspersa (Müller, 1776) has sometimes been regarded as conspecific with A. scabra (Müller, 1776), although previous detailed morphological comparisons have indicated that the two are distinguishable by internal structures. Resolution of this taxonomic issue is important because A. aspersa has been known as a notoriously invasive ascidian, doing much damage to aquaculture e.g. in Hokkaido, Japan. We collected many specimens from European waters (including the Swedish coast, near the type localities of these two species) and Hokkaido, Japan (as an alien population) and made molecular phylogenetic analyses using the mitochondrial cytochrome c oxidase subunit I (COI) gene, and found that in terms of COI sequences all the analyzed specimens were clustered into two distinct groups, one of which is morphologically referable to A. aspersa and the other to A. scabra. Thus, these two species should be regarded as distinct from each other.
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Affiliation(s)
- Teruaki Nishikawa
- 1 Faculty of Science, Toho University, 2-2-1, Miyama, Funabashi, Chiba 274-8510, Japan
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Abad S, Pérez X, Planas A, Turon X. Rapid monitoring of glycerol in fermentation growth media: Facilitating crude glycerol bioprocess development. Talanta 2014; 121:210-4. [PMID: 24607129 DOI: 10.1016/j.talanta.2013.12.022] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 12/05/2013] [Accepted: 12/11/2013] [Indexed: 10/25/2022]
Abstract
Recently, the need for crude glycerol valorisation from the biodiesel industry has generated many studies for practical and economic applications. Amongst them, fermentations based on glycerol media for the production of high value metabolites are prominent applications. This has generated a need to develop analytical techniques which allow fast and simple glycerol monitoring during fermentation. The methodology should be fast and inexpensive to be adopted in research, as well as in industrial applications. In this study three different methods were analysed and compared: two common methodologies based on liquid chromatography and enzymatic kits, and the new method based on a DotBlot assay coupled with image analysis. The new methodology is faster and cheaper than the other conventional methods, with comparable performance. Good linearity, precision and accuracy were achieved in the lower range (10 or 15 g/L to depletion), the most common range of glycerol concentrations to monitor fermentations in terms of growth kinetics.
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Affiliation(s)
- Sergi Abad
- Bioengineering Department, Institut Químic de Sarrià (IQS), Universitat Ramon Llull. Via Augusta 390, 08017 Barcelona, Spain
| | - Xavier Pérez
- Bioengineering Department, Institut Químic de Sarrià (IQS), Universitat Ramon Llull. Via Augusta 390, 08017 Barcelona, Spain
| | - Antoni Planas
- Bioengineering Department, Institut Químic de Sarrià (IQS), Universitat Ramon Llull. Via Augusta 390, 08017 Barcelona, Spain
| | - Xavier Turon
- Bioengineering Department, Institut Químic de Sarrià (IQS), Universitat Ramon Llull. Via Augusta 390, 08017 Barcelona, Spain.
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Pita L, Erwin PM, Turon X, López-Legentil S. Till death do us part: stable sponge-bacteria associations under thermal and food shortage stresses. PLoS One 2013; 8:e80307. [PMID: 24312210 PMCID: PMC3842930 DOI: 10.1371/journal.pone.0080307] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [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: 08/16/2013] [Accepted: 10/11/2013] [Indexed: 12/03/2022] Open
Abstract
Sporadic mass mortality events of Mediterranean sponges following periods of anomalously high temperatures or longer than usual stratification of the seawater column (i.e. low food availability) suggest that these animals are sensitive to environmental stresses. The Mediterranean sponges Ircinia fasciculata and I. oros harbor distinct, species-specific bacterial communities that are highly stable over time and space but little is known about how anomalous environmental conditions affect the structure of the resident bacterial communities. Here, we monitored the bacterial communities in I. fasciculata (largely affected by mass mortalities) and I. oros (overall unaffected) maintained in aquaria during 3 weeks under 4 treatments that mimicked realistic stress pressures: control conditions (13°C, unfiltered seawater), low food availability (13°C, 0.1 µm-filtered seawater), elevated temperatures (25°C, unfiltered seawater), and a combination of the 2 stressors (25°C, 0.1 µm-filtered seawater). Bacterial community structure was assessed using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA gene sequences and transmission electron microscopy (TEM). As I. fasciculata harbors cyanobacteria, we also measured chlorophyll a (chl a) levels in this species. Multivariate analysis revealed no significant differences in bacterial T-RFLP profiles among treatments for either host sponge species, indicating no effect of high temperatures and food shortage on symbiont community structure. In I. fasciculata, chl a content did not significantly differ among treatments although TEM micrographs revealed some cyanobacteria cells undergoing degradation when exposed to both elevated temperature and food shortage conditions. Arguably, longer-term treatments (months) could have eventually affected bacterial community structure. However, we evidenced no appreciable decay of the symbiotic community in response to medium-term (3 weeks) environmental anomalies purported to cause the recurrent sponge mortality episodes. Thus, changes in symbiont structure are not likely the proximate cause for these reported mortality events.
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Affiliation(s)
- Lucía Pita
- Departament de Biologia Animal and Institute de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Patrick M. Erwin
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, United States of America
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Spain
| | - Susanna López-Legentil
- Departament de Biologia Animal and Institute de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, North Carolina, United States of America
- * E-mail:
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Pita L, Turon X, López-Legentil S, Erwin PM. Host rules: spatial stability of bacterial communities associated with marine sponges (Irciniaspp.) in the Western Mediterranean Sea. FEMS Microbiol Ecol 2013; 86:268-76. [DOI: 10.1111/1574-6941.12159] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/26/2013] [Accepted: 06/04/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Lucía Pita
- Department de Biologia Animal and Institut de Recerca de la Biodiversitat (IRBio); Universitat de Barcelona (UB); Barcelona; Spain
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC); Blanes; Girona; Spain
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Galera J, Turon X, Uriz MJ, Becerro MA. Microstructure variation in sponges sharing growth form: The encrusting demospongesDysidea avaraandCrambe crambe. ACTA ZOOL-STOCKHOLM 2013. [DOI: 10.1046/j.1463-6395.2000.00041.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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De Caralt S, Bry D, Bontemps N, Turon X, Uriz MJ, Banaigs B. Sources of secondary metabolite variation in Dysidea avara (Porifera: Demospongiae): the importance of having good neighbors. Mar Drugs 2013; 11:489-503. [PMID: 23429282 PMCID: PMC3640394 DOI: 10.3390/md11020489] [Citation(s) in RCA: 28] [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: 11/29/2012] [Revised: 01/04/2013] [Accepted: 01/24/2013] [Indexed: 11/22/2022] Open
Abstract
Several studies report temporal, geographical, and intra-individual variation in sponge metabolite yields. However, the internal and/or external factors that regulate the metabolite production remain poorly understood. Dysidea avara is a demosponge that produces sesquiterpenoids (avarol and derivatives) with interesting medical properties, which has prompted addressed studies to obtain enough amounts of these metabolites for research on drug discovery. Within this framework, specimens of Dysidea avara from apopulation of the Northwest Mediterranean were sampled and their secondary metabolites quantified to assess their variability and the possible relationship with external (seasonality, interactions with neighbors) and internal (reproductive stages) factors. The results show a variation of the amount of both avarol and its monoacetate derivative with time, with no clear relationship with seawater temperature. A trade-off with sponge reproduction was not found either. However, our results showed for the first time that sponges are able to increase production or accumulation of secondary metabolites in their peripheral zone depending on the nature of their neighbors. This finding could explain part of the high variability in the amount of secondary metabolites usually found in chemical ecology studies on sponges and opens new biotechnological approaches to enhance the metabolite yield in sponge cultures.
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Affiliation(s)
- Sonia De Caralt
- Center for Advanced Studies of Blanes (CEAB-CSIC), Accés a la Cala St Francesc 14, 17300 Blanes, Girona, Spain; E-Mails: (X.T.); (M.-J.U.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-972-336-101; Fax: +34-972-337-806
| | - Delphine Bry
- Environmental and Biomolecular Chemistry Laboratory, University of Perpignan Via Domita, 52 Paul Alduy Ave., Perpignan Cedex 66860, France; E-Mails: (D.B.); (N.B.); (B.B.)
| | - Nataly Bontemps
- Environmental and Biomolecular Chemistry Laboratory, University of Perpignan Via Domita, 52 Paul Alduy Ave., Perpignan Cedex 66860, France; E-Mails: (D.B.); (N.B.); (B.B.)
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC), Accés a la Cala St Francesc 14, 17300 Blanes, Girona, Spain; E-Mails: (X.T.); (M.-J.U.)
| | - Maria-Jesus Uriz
- Center for Advanced Studies of Blanes (CEAB-CSIC), Accés a la Cala St Francesc 14, 17300 Blanes, Girona, Spain; E-Mails: (X.T.); (M.-J.U.)
| | - Bernard Banaigs
- Environmental and Biomolecular Chemistry Laboratory, University of Perpignan Via Domita, 52 Paul Alduy Ave., Perpignan Cedex 66860, France; E-Mails: (D.B.); (N.B.); (B.B.)
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Erwin PM, Carmen Pineda M, Webster N, Turon X, López-Legentil S. Small core communities and high variability in bacteria associated with the introduced ascidian Styela plicata. Symbiosis 2012. [DOI: 10.1007/s13199-012-0204-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hirose E, Turon X, López-Legentil S, Erwin PM, Hirose M. First records of didemnid ascidians harbouring Prochloron from Caribbean Panama: genetic relationships between Caribbean and Pacific photosymbionts and host ascidians. SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.735716] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Euichi Hirose
- a Faculty of Science , University of the Ryukyus, Senbaru 1 , Nishihara , Okinawa , 903-0213 , Japan
| | - Xavier Turon
- b Center for Advanced Studies of Blanes , Spanish National Research Council (CEAB-CSIC) , Blanes , Girona , Spain
| | - Susanna López-Legentil
- c Department of Animal Biology (Invertebrates) , University of Barcelona, 643 Diagonal Avenue , 08028 , Barcelona , Spain
| | - Patrick M. Erwin
- c Department of Animal Biology (Invertebrates) , University of Barcelona, 643 Diagonal Avenue , 08028 , Barcelona , Spain
| | - Mamiko Hirose
- a Faculty of Science , University of the Ryukyus, Senbaru 1 , Nishihara , Okinawa , 903-0213 , Japan
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Pineda MC, McQuaid CD, Turon X, López-Legentil S, Ordóñez V, Rius M. Tough adults, frail babies: an analysis of stress sensitivity across early life-history stages of widely introduced marine invertebrates. PLoS One 2012; 7:e46672. [PMID: 23077518 PMCID: PMC3470586 DOI: 10.1371/journal.pone.0046672] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [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: 07/06/2012] [Accepted: 09/06/2012] [Indexed: 12/02/2022] Open
Abstract
All ontogenetic stages of a life cycle are exposed to environmental conditions so that population persistence depends on the performance of both adults and offspring. Most studies analysing the influence of abiotic conditions on species performance have focussed on adults, while studies covering early life-history stages remain rare. We investigated the responses of early stages of two widely introduced ascidians, Styela plicata and Microcosmus squamiger, to different abiotic conditions. Stressors mimicked conditions in the habitats where both species can be found in their distributional ranges and responses were related to the selection potential of their populations by analysing their genetic diversity. Four developmental stages (egg fertilisation, larval development, settlement, metamorphosis) were studied after exposure to high temperature (30°C), low salinities (26 and 22‰) and high copper concentrations (25, 50 and 100 µg/L). Although most stressors effectively led to failure of complete development (fertilisation through metamorphosis), fertilisation and larval development were the most sensitive stages. All the studied stressors affected the development of both species, though responses differed with stage and stressor. S. plicata was overall more resistant to copper, and some stages of M. squamiger to low salinities. No relationship was found between parental genetic composition and responses to stressors. We conclude that successful development can be prevented at several life-history stages, and therefore, it is essential to consider multiple stages when assessing species' abilities to tolerate stress. Moreover, we found that early development of these species cannot be completed under conditions prevailing where adults live. These populations must therefore recruit from elsewhere or reproduce during temporal windows of more benign conditions. Alternatively, novel strategies or behaviours that increase overall reproductive success might be responsible for ensuring population survival.
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Affiliation(s)
- M. Carmen Pineda
- Department of Animal Biology (Invertebrates), University of Barcelona, Barcelona, Spain
| | | | - Xavier Turon
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Spain
| | | | - Víctor Ordóñez
- Department of Genetics, University of Barcelona, Barcelona, Spain
| | - Marc Rius
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- * E-mail:
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Erwin PM, López-Legentil S, Turon X. Ultrastructure, molecular phylogenetics, and chlorophyll a content of novel cyanobacterial symbionts in temperate sponges. Microb Ecol 2012; 64:771-783. [PMID: 22526400 DOI: 10.1007/s00248-012-0047-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 03/19/2012] [Indexed: 05/31/2023]
Abstract
Marine sponges often harbor photosynthetic symbionts that may enhance host metabolism and ecological success, yet little is known about the factors that structure the diversity, specificity, and nature of these relationships. Here, we characterized the cyanobacterial symbionts in two congeneric and sympatric host sponges that exhibit distinct habitat preferences correlated with irradiance: Ircinia fasciculata (higher irradiance) and Ircinia variabilis (lower irradiance). Symbiont composition was similar among hosts and dominated by the sponge-specific cyanobacterium Synechococcus spongiarum. Phylogenetic analyses of 16S-23S rRNA internal transcribed spacer (ITS) gene sequences revealed that Mediterranean Ircinia spp. host a specific, novel symbiont clade ("M") within the S. spongiarum species complex. A second, rare cyanobacterium related to the ascidian symbiont Synechocystis trididemni was observed in low abundance in I. fasciculata and likewise corresponded to a new symbiont clade. Symbiont communities in I. fasciculata exhibited nearly twice the chlorophyll a concentrations of I. variabilis. Further, S. spongiarum clade M symbionts in I. fasciculata exhibited dense intracellular aggregations of glycogen granules, a storage product of photosynthetic carbon assimilation rarely observed in I. variabilis symbionts. In both host sponges, S. spongiarum cells were observed interacting with host archeocytes, although the lower photosynthetic activity of Cyanobacteria in I. variabilis suggests less symbiont-derived nutritional benefit. The observed differences in clade M symbionts among sponge hosts suggest that ambient irradiance conditions dictate symbiont photosynthetic activity and consequently may mediate the nature of host-symbiont relationships. In addition, the plasticity exhibited by clade M symbionts may be an adaptive attribute that allows for flexibility in host-symbiont interactions across the seasonal fluctuations in light and temperature characteristic of temperate environments.
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Affiliation(s)
- Patrick M Erwin
- Center for Advanced Studies of Blanes, Accés Cala S. Francesc 14, 17300 Blanes, Girona, Spain.
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Erwin PM, Pita L, López-Legentil S, Turon X. Stability of sponge-associated bacteria over large seasonal shifts in temperature and irradiance. Appl Environ Microbiol 2012; 78:7358-68. [PMID: 22885741 PMCID: PMC3457113 DOI: 10.1128/aem.02035-12] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 08/01/2012] [Indexed: 11/20/2022] Open
Abstract
Complex microbiomes reside in marine sponges and consist of diverse microbial taxa, including functional guilds that may contribute to host metabolism and coastal marine nutrient cycles. Our understanding of these symbiotic systems is based primarily on static accounts of sponge microbiota, while their temporal dynamics across seasonal cycles remain largely unknown. Here, we investigated temporal variation in bacterial symbionts of three sympatric sponges (Ircinia spp.) over 1.5 years in the northwestern (NW) Mediterranean Sea, using replicated terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of bacterial 16S rRNA gene sequences. Bacterial symbionts in Ircinia spp. exhibited host species-specific structure and remarkable stability throughout the monitoring period, despite large fluctuations in temperature and irradiance. In contrast, seawater bacteria exhibited clear seasonal shifts in community structure, indicating that different ecological constraints act on free-living and on symbiotic marine bacteria. Symbiont profiles were dominated by persistent, sponge-specific bacterial taxa, notably affiliated with phylogenetic lineages capable of photosynthesis, nitrite oxidation, and sulfate reduction. Variability in the sponge microbiota was restricted to rare symbionts and occurred most prominently in warmer seasons, coincident with elevated thermal regimes. Seasonal stability of the sponge microbiota supports the hypothesis of host-specific, stable associations between bacteria and sponges. Further, the core symbiont profiles revealed in this study provide an empirical baseline for diagnosing abnormal shifts in symbiont communities. Considering that these sponges have suffered recent, episodic mass mortalities related to thermal stresses, this study contributes to the development of model sponge-microbe symbioses for assessing the link between symbiont fluctuations and host health.
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Affiliation(s)
- Patrick M Erwin
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Girona, Spain.
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