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Sánchez P, Coutinho FH, Sebastián M, Pernice MC, Rodríguez-Martínez R, Salazar G, Cornejo-Castillo FM, Pesant S, López-Alforja X, López-García EM, Agustí S, Gojobori T, Logares R, Sala MM, Vaqué D, Massana R, Duarte CM, Acinas SG, Gasol JM. Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition. Sci Data 2024; 11:154. [PMID: 38302528 PMCID: PMC10834958 DOI: 10.1038/s41597-024-02974-1] [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: 04/06/2023] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
The Ocean microbiome has a crucial role in Earth's biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity and genetic repertoire of marine microbes. Nevertheless, there are still knowledge gaps regarding their diversity patterns throughout depth gradients ranging from the surface to the deep ocean. Here we present a dataset of 76 microbial metagenomes (MProfile) of the picoplankton size fraction (0.2-3.0 µm) collected in 11 vertical profiles covering contrasting ocean regions sampled during the Malaspina Expedition circumnavigation (7 depths, from surface to 4,000 m deep). The MProfile dataset produced 1.66 Tbp of raw DNA sequences from which we derived: 17.4 million genes clustered at 95% sequence similarity (M-GeneDB-VP), 2,672 metagenome-assembled genomes (MAGs) of Archaea and Bacteria (Malaspina-VP-MAGs), and over 100,000 viral genomic sequences. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and sub-tropical ocean, while increasing our general knowledge of the Ocean microbiome.
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Affiliation(s)
- Pablo Sánchez
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
| | - Felipe H Coutinho
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Marta Sebastián
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Massimo C Pernice
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Raquel Rodríguez-Martínez
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Guillem Salazar
- Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | | | - Stéphane Pesant
- EMBL's European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Xabier López-Alforja
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Ester María López-García
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
- Centre National de la Recherche Scientifique (CNRS), UMR5254, IPREM, Pau, France
| | - Susana Agustí
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Ramiro Logares
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Maria Montserrat Sala
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Dolors Vaqué
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Ramon Massana
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Carlos M Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Silvia G Acinas
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
| | - Josep M Gasol
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
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Arbez-Abnal T, García-Martínez E, Ángel-García O, Anzures-Olvera F, Rodríguez-Martínez R, Véliz-Deras F, Chay-Canul A, Legarreta-González M, Vargas-Bello-Pérez E, Robles-Trillo P. Effect of supplementing magnesium oxide or brucite on plasma magnesium, rumen pH, rumen protozoa and plasma glucose levels in dairy goats. Small Rumin Res 2023. [DOI: 10.1016/j.smallrumres.2023.106905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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3
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Rodríguez-Martínez R, Vaqué D, Forn I, Massana R. Dominant marine heterotrophic flagellates are adapted to natural planktonic bacterial abundances. Environ Microbiol 2022; 24:2421-2434. [PMID: 35080092 PMCID: PMC9303649 DOI: 10.1111/1462-2920.15911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 11/28/2022]
Abstract
Grazing controls bacterial abundances and composition in many ecosystems. In marine systems, heterotrophic flagellates (HFs) are important predators. Assemblages of HFs are primarily formed by species still uncultured, therefore many aspects of their trophic behavior are poorly known. Here we assessed the functional response of the whole assemblage and of four taxa grown in an unamended seawater incubation. We used fluorescently labeled bacteria to create a prey gradient of two orders of magnitude in abundance, and estimated ingestion rates. Natural HFs had a half-saturation constant of 6.7x105 prey ml-1 , a value lower than that of cultured flagellates and within the range of marine planktonic bacterial abundances. Minorisa minuta was well adapted to low prey abundances and very efficient in ingesting bacteria. MAST-4 and MAST-7 were also well adapted to the typical marine abundances but less voracious. In contrast, Paraphysomonas imperforata, a typical cultured species, did not achieve ingestion rate saturation even at the highest prey concentration assayed. Our study, beside to set the basis for the fundamental differences between cultured and uncultured bacterial grazers, indicate that the examined predator taxa have different functional responses, suggesting that they occupy distinct ecological niches according to their grazing strategies and prey preferences. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Raquel Rodríguez-Martínez
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Dolors Vaqué
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Irene Forn
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Ramon Massana
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
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4
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Del Campo J, Heger TJ, Rodríguez-Martínez R, Worden AZ, Richards TA, Massana R, Keeling PJ. Corrigendum: Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework. Front Microbiol 2020; 11:576322. [PMID: 33133045 PMCID: PMC7578665 DOI: 10.3389/fmicb.2020.576322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/31/2020] [Indexed: 11/26/2022] Open
Affiliation(s)
- Javier Del Campo
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Thierry J Heger
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Soil Science Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Nyon, Switzerland
| | - Raquel Rodríguez-Martínez
- Department of Biosciences, Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | - Thomas A Richards
- Department of Biosciences, Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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5
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Rodríguez-Martínez R, Leonard G, Milner DS, Sudek S, Conway M, Moore K, Hudson T, Mahé F, Keeling PJ, Santoro AE, Worden AZ, Richards TA. Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink. ISME J 2020; 14:984-998. [PMID: 31919469 PMCID: PMC7082347 DOI: 10.1038/s41396-019-0581-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/04/2019] [Accepted: 12/17/2019] [Indexed: 11/09/2022]
Abstract
Marine sediments are one of the largest carbon reservoir on Earth, yet the microbial communities, especially the eukaryotes, that drive these ecosystems are poorly characterised. Here, we report implementation of a sampling system that enables injection of reagents into sediments at depth, allowing for preservation of RNA in situ. Using the RNA templates recovered, we investigate the 'ribosomally active' eukaryotic diversity present in sediments close to the water/sediment interface. We demonstrate that in situ preservation leads to recovery of a significantly altered community profile. Using SSU rRNA amplicon sequencing, we investigated the community structure in these environments, demonstrating a wide diversity and high relative abundance of stramenopiles and alveolates, specifically: Bacillariophyta (diatoms), labyrinthulomycetes and ciliates. The identification of abundant diatom rRNA molecules is consistent with microscopy-based studies, but demonstrates that these algae can also be exported to the sediment as active cells as opposed to dead forms. We also observe many groups that include, or branch close to, osmotrophic-saprotrophic protists (e.g. labyrinthulomycetes and Pseudofungi), microbes likely to be important for detrital decomposition. The sequence data also included a diversity of abundant amplicon-types that branch close to the Fonticula slime moulds. Taken together, our data identifies additional roles for eukaryotic microbes in the marine carbon cycle; where putative osmotrophic-saprotrophic protists represent a significant active microbial-constituent of the upper sediment layer.
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Affiliation(s)
- Raquel Rodríguez-Martínez
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK. .,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.
| | - Guy Leonard
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK
| | - David S Milner
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Mike Conway
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Karen Moore
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK
| | - Theresa Hudson
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK
| | - Frédéric Mahé
- CIRAD, UMR LSTM, Montpellier, France.,Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Thomas A Richards
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK. .,Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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6
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Wideman JG, Monier A, Rodríguez-Martínez R, Leonard G, Cook E, Poirier C, Maguire F, Milner DS, Irwin NAT, Moore K, Santoro AE, Keeling PJ, Worden AZ, Richards TA. Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists. Nat Microbiol 2019; 5:154-165. [PMID: 31768028 DOI: 10.1038/s41564-019-0605-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 10/08/2019] [Indexed: 11/09/2022]
Abstract
Most eukaryotic microbial diversity is uncultivated, under-studied and lacks nuclear genome data. Mitochondrial genome sampling is more comprehensive, but many phylogenetically important groups remain unsampled. Here, using a single-cell sorting approach combining tubulin-specific labelling with photopigment exclusion, we sorted flagellated heterotrophic unicellular eukaryotes from Pacific Ocean samples. We recovered 206 single amplified genomes, predominantly from underrepresented branches on the tree of life. Seventy single amplified genomes contained unique mitochondrial contigs, including 21 complete or near-complete mitochondrial genomes from formerly under-sampled phylogenetic branches, including telonemids, katablepharids, cercozoans and marine stramenopiles, effectively doubling the number of available samples of heterotrophic flagellate mitochondrial genomes. Collectively, these data identify a dynamic history of mitochondrial genome evolution including intron gain and loss, extensive patterns of genetic code variation and complex patterns of gene loss. Surprisingly, we found that stramenopile mitochondrial content is highly plastic, resembling patterns of variation previously observed only in plants.
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Affiliation(s)
- Jeremy G Wideman
- Living Systems Institute, University of Exeter, Exeter, UK. .,Wissenschaftskolleg zu Berlin, Berlin, Germany. .,Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada. .,Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Adam Monier
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Raquel Rodríguez-Martínez
- Living Systems Institute, University of Exeter, Exeter, UK.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Guy Leonard
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Emily Cook
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Camille Poirier
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean EcoSystems Biology Unit, Division of Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Finlay Maguire
- Living Systems Institute, University of Exeter, Exeter, UK.,Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David S Milner
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Moore
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Patrick J Keeling
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean EcoSystems Biology Unit, Division of Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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7
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Del Campo J, Heger TJ, Rodríguez-Martínez R, Worden AZ, Richards TA, Massana R, Keeling PJ. Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework. Front Microbiol 2019; 10:2373. [PMID: 31708883 PMCID: PMC6819320 DOI: 10.3389/fmicb.2019.02373] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 03/20/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including the causing agents of toxoplasmosis and malaria, and emergent diseases like cryptosporidiosis or babesiosis. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys, and our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of apicomplexan sequences. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections.
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Affiliation(s)
- Javier Del Campo
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Thierry J Heger
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Soil Science Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Nyon, Switzerland
| | - Raquel Rodríguez-Martínez
- Department of Biosciences, Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | - Thomas A Richards
- Department of Biosciences, Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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8
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Wideman JG, Lax G, Leonard G, Milner DS, Rodríguez-Martínez R, Simpson AGB, Richards TA. A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190100. [PMID: 31587636 PMCID: PMC6792441 DOI: 10.1098/rstb.2019.0100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Euglenozoa comprises euglenids, kinetoplastids, and diplonemids, with each group exhibiting different and highly unusual mitochondrial genome organizations. Although they are sister groups, kinetoplastids and diplonemids have very distinct mitochondrial genome architectures, requiring widespread insertion/deletion RNA editing and extensive trans-splicing, respectively, in order to generate functional transcripts. The evolutionary history by which these differing processes arose remains unclear. Using single-cell genomics, followed by small sub unit ribosomal DNA and multigene phylogenies, we identified an isolated marine cell that branches on phylogenetic trees as a sister to known kinetoplastids. Analysis of single-cell amplified genomic material identified multiple mitochondrial genome contigs. These revealed a gene architecture resembling that of diplonemid mitochondria, with small fragments of genes encoded out of order and or on different contigs, indicating that these genes require extensive trans-splicing. Conversely, no requirement for kinetoplastid-like insertion/deletion RNA-editing was detected. Additionally, while we identified some proteins so far only found in kinetoplastids, we could not unequivocally identify mitochondrial RNA editing proteins. These data invite the hypothesis that extensive genome fragmentation and trans-splicing were the ancestral states for the kinetoplastid-diplonemid clade but were lost during the kinetoplastid radiation. This study demonstrates that single-cell approaches can successfully retrieve lineages that represent important new branches on the tree of life, and thus can illuminate major evolutionary and functional transitions in eukaryotes. This article is part of a discussion meeting issue ‘Single cell ecology’.
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Affiliation(s)
- Jeremy G Wideman
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.,Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Gordon Lax
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Guy Leonard
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - David S Milner
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Raquel Rodríguez-Martínez
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Alastair G B Simpson
- Department of Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Thomas A Richards
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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9
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Ruiz-González C, Logares R, Sebastián M, Mestre M, Rodríguez-Martínez R, Galí M, Sala MM, Acinas SG, Duarte CM, Gasol JM. Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean. Mol Ecol 2019; 28:1930-1945. [PMID: 30663830 DOI: 10.1111/mec.15026] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/21/2018] [Accepted: 01/14/2019] [Indexed: 01/21/2023]
Abstract
Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA-defined Operational Taxonomic Units, OTUs) across 108 globally-distributed surface ocean stations. We grouped taxa based on their SpAD shape ("normal-like"- abundant and ubiquitous; "logistic"- globally rare, present in few sites; and "bimodal"- abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan "normal-like" OTUs, yet there was a gradual shift towards assemblages dominated by "logistic" taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer "normal-like" shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members.
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Affiliation(s)
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Marta Sebastián
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Telde, Spain
| | - Mireia Mestre
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Raquel Rodríguez-Martínez
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Martí Galí
- Unité Mixte Internationale Takuvik (Université Laval-CNRS) and Québec-Océan, Département de Biologie, Université Laval, Québec City, Québec, Canada.,Barcelona Supercomputing Centre (BSC), Barcelona, Catalonia, Spain
| | | | - Silvia G Acinas
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Josep M Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Centre for Marine Ecosystem Research, Edith Cowan University, Joondalup, Western Australia, Australia
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10
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Rodríguez-Martínez R, Meza-Herrera CA, Tapia-Robles KI, Alvarado-Espino AS, Luna-Orozco JR, Leyva C, Mellado M, Véliz-Deras FG. Effect of two routes of administration of human chorionic gonadotropin upon oestrus induction and reproductive outcomes in adult acyclic mix-breed goats. Journal of Applied Animal Research 2017. [DOI: 10.1080/09712119.2017.1284075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- R. Rodríguez-Martínez
- Departamento de Ciencias Médico Veterinarias, Universidad Autónoma Agraria Antonio Narro-Unidad Laguna, Torreón, Coahuila, México
| | - C. A. Meza-Herrera
- Programa de Posgrado, Universidad Autónoma Chapingo, Unidad Regional Universitaria de Zonas Áridas, Bermejillo, Durango, México
| | - K. I. Tapia-Robles
- Departamento de Ciencias Médico Veterinarias, Universidad Autónoma Agraria Antonio Narro-Unidad Laguna, Torreón, Coahuila, México
| | - A. S. Alvarado-Espino
- Departamento de Ciencias Médico Veterinarias, Universidad Autónoma Agraria Antonio Narro-Unidad Laguna, Torreón, Coahuila, México
| | - J. R. Luna-Orozco
- Centro de Bachillerato Tecnológico Agropecuario No. 1, Torreón, Coahuila, México
| | - C. Leyva
- Departamento de Ciencias Médico Veterinarias, Universidad Autónoma Agraria Antonio Narro-Unidad Laguna, Torreón, Coahuila, México
| | - M. Mellado
- Departamento de Nutrición Animal, Universidad Autónoma Agraria Antonio Narro, Saltillo, Coahuila, México
| | - F. G. Véliz-Deras
- Departamento de Ciencias Médico Veterinarias, Universidad Autónoma Agraria Antonio Narro-Unidad Laguna, Torreón, Coahuila, México
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Ángel-García O, Meza-Herrera C, Contreras-Villarreal V, Guillen-Muñoz J, Leyva C, Robles-Trillo P, Rivas-Muñoz R, Rodríguez-Martínez R, Mellado M, Véliz F. Effect of different male-to-female ratios and testosterone administration upon the male sexual behavior and the out-of-season reproductive response of anestrous goats. Small Rumin Res 2015. [DOI: 10.1016/j.smallrumres.2015.10.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rodríguez-Martínez R, Rocap G, Logares R, Romac S, Massana R. Low evolutionary diversification in a widespread and abundant uncultured protist (MAST-4). Mol Biol Evol 2011; 29:1393-406. [PMID: 22319144 DOI: 10.1093/molbev/msr303] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent culture-independent studies of marine planktonic protists have unveiled a large diversity at all phylogenetic scales and the existence of novel groups. MAST-4 represents one of these novel uncultured lineages, and it is composed of small (~2 μm) bacterivorous eukaryotes that are widely distributed in marine systems. MAST-4 accounts for a significant fraction of the marine heterotrophic flagellates at the global level, playing key roles in the marine ecological network. In this study, we investigated the diversity of MAST-4, aiming to assess its limits and structure. Using ribosomal DNA (rDNA) sequences obtained in this study (both pyrosequencing reads and clones with large rDNA operon coverage), complemented with GenBank sequences, we show that MAST-4 is composed of only five main clades, which are well supported by small subunit and large subunit phylogenies. The differences in the conserved regions of the internal transcribed spacers 1 and 2 (ITS1 and ITS2) secondary structures strongly suggest that these five clades are different biological species. Based on intraclade divergence, ITS secondary structures and comparisons of ITS1 and ITS2 trees, we did not find evidence of more than one species within clade A, whereas as many as three species might be present within other clades. Overall, the genetic divergence of MAST-4 was surprisingly low for an organism with a global population size estimated to be around 10(24), indicating a very low evolutionary diversification within the group.
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Rodríguez-Martínez R, Labrenz M, del Campo J, Forn I, Jürgens K, Massana R. Distribution of the uncultured protist MAST-4 in the Indian Ocean, Drake Passage and Mediterranean Sea assessed by real-time quantitative PCR. Environ Microbiol 2009; 11:397-408. [PMID: 19196271 DOI: 10.1111/j.1462-2920.2008.01779.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular surveys of marine picoeukaryotes have revealed a large number of sequences unrelated to cultured organisms, such as those forming the marine stramenopile (MAST)-4 clade. Recent FISH (fluorescent in situ hybridization) data have shown that MAST-4 cells are uncultured heterotrophic flagellates of 2-3 microm in size that have a global distribution in non-polar marine waters. However, FISH is time-consuming and hard to apply to the many samples generated during oceanographic cruises, so we developed a real-time quantitative polymerase chain reaction (Q-PCR) protocol to determine rapidly the abundance of this group using environmental DNA. We designed a primer set targeting the 18S rRNA genes (rDNA) of MAST-4 and optimized and calibrated the Q-PCR protocol using a plasmid with the target sequence as insert. The Q-PCR was then applied to quantify MAST-4 rDNA molecules along three marine transects, longitudinal in the Indian Ocean, latitudinal in the Drake Passage and coastal-offshore in the Mediterranean Sea, and to a temporal study in a Mediterranean Sea coastal station. MAST-4 was detected in all samples processed (averaged abundances between 500 and 1000 rDNA molecules ml(-1)) except in mesopelagic and Antarctic samples, where it was virtually absent. In general, it was more abundant in the coast than offshore and in the deep chlorophyll maximum than at surface. A comparison of Q-PCR and FISH signals in well-controlled microbial incubations indicated that MAST-4 cells have around 30 copies of the rDNA operon. This Q-PCR assay quickly yielded quantitative data of uncultured MAST-4 cells and confirmed their wide distribution and putative ecological importance.
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Massana R, Unrein F, Rodríguez-Martínez R, Forn I, Lefort T, Pinhassi J, Not F. Grazing rates and functional diversity of uncultured heterotrophic flagellates. ISME J 2009; 3:588-96. [PMID: 19129862 DOI: 10.1038/ismej.2008.130] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aquatic assemblages of heterotrophic protists are very diverse and formed primarily by organisms that remain uncultured. Thus, a critical issue is assigning a functional role to this unknown biota. Here we measured grazing rates of uncultured protists in natural assemblages (detected by fluorescent in situ hybridization (FISH)), and investigated their prey preference over several bacterial tracers in short-term ingestion experiments. These included fluorescently labeled bacteria (FLB) and two strains of the Roseobacter lineage and the family Flavobacteriaceae, of various cell sizes, which were offered alive and detected by catalyzed reporter deposition-FISH after the ingestion. We obtained grazing rates of the globally distributed and uncultured marine stramenopiles groups 4 and 1 (MAST-4 and MAST-1C) flagellates. Using FLB, the grazing rate of MAST-4 was somewhat lower than whole community rates, consistent with its small size. MAST-4 preferred live bacteria, and clearance rates with these tracers were up to 2 nl per predator per h. On the other hand, grazing rates of MAST-1C differed strongly depending on the tracer prey used, and these differences could not be explained by cell viability. Highest rates were obtained using FLB whereas the flavobacteria strain was hardly ingested. Possible explanations would be that the small flavobacteria cells were outside the effective size range of edible prey, or that MAST-1C selects against this particular strain. Our original dual FISH protocol applied to grazing experiments reveals important functional differences between distinct uncultured protists and offers the possibility to disentangle the complexity of microbial food webs.
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Affiliation(s)
- Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain.
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