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Cornejo-Castillo FM, Inomura K, Zehr JP, Follows MJ. Metabolic trade-offs constrain the cell size ratio in a nitrogen-fixing symbiosis. Cell 2024; 187:1762-1768.e9. [PMID: 38471501 DOI: 10.1016/j.cell.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 10/06/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Biological dinitrogen (N2) fixation is a key metabolic process exclusively performed by prokaryotes, some of which are symbiotic with eukaryotes. Species of the marine haptophyte algae Braarudosphaera bigelowii harbor the N2-fixing endosymbiotic cyanobacteria UCYN-A, which might be evolving organelle-like characteristics. We found that the size ratio between UCYN-A and their hosts is strikingly conserved across sublineages/species, which is consistent with the size relationships of organelles in this symbiosis and other species. Metabolic modeling showed that this size relationship maximizes the coordinated growth rate based on trade-offs between resource acquisition and exchange. Our findings show that the size relationships of N2-fixing endosymbionts and organelles in unicellular eukaryotes are constrained by predictable metabolic underpinnings and that UCYN-A is, in many regards, functioning like a hypothetical N2-fixing organelle (or nitroplast).
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Affiliation(s)
- Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona 08003, Spain; Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA.
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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2
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Turk-Kubo KA, Gradoville MR, Cheung S, Cornejo-Castillo FM, Harding KJ, Morando M, Mills M, Zehr JP. Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters. FEMS Microbiol Rev 2023; 47:fuac046. [PMID: 36416813 PMCID: PMC10719068 DOI: 10.1093/femsre/fuac046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/15/2022] [Accepted: 11/17/2022] [Indexed: 12/17/2023] Open
Abstract
Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
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Affiliation(s)
- Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Mary R Gradoville
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Columbia River Inter-Tribal Fish Commission, Portland, OR, United States
| | - Shunyan Cheung
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Francisco M Cornejo-Castillo
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Pg. Marítim Barceloneta, 37-49 08003 Barcelona, Spain
| | - Katie J Harding
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
- Marine Biology Research Division, Scripps Institute of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Michael Morando
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Matthew Mills
- Department of Earth System Science, Stanford University, 473 Via Ortega, Stanford, CA 94305, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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3
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Bonnet S, Benavides M, Le Moigne FAC, Camps M, Torremocha A, Grosso O, Dimier C, Spungin D, Berman-Frank I, Garczarek L, Cornejo-Castillo FM. Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean. ISME J 2023; 17:47-58. [PMID: 36163270 PMCID: PMC9750961 DOI: 10.1038/s41396-022-01319-3] [Citation(s) in RCA: 2] [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] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022]
Abstract
Diazotrophs are widespread microorganisms that alleviate nitrogen limitation in 60% of our oceans, thereby regulating marine productivity. Yet, the group-specific contribution of diazotrophs to organic matter export has not been quantified, which so far has impeded an accurate assessment of their impact on the biological carbon pump. Here, we examine the fate of five groups of globally-distributed diazotrophs by using an original combination of mesopelagic particle sampling devices across the subtropical South Pacific Ocean. We demonstrate that cyanobacterial and non-cyanobacterial diazotrophs are exported down to 1000 m depth. Surprisingly, group-specific export turnover rates point to a more efficient export of small unicellular cyanobacterial diazotrophs (UCYN) relative to the larger and filamentous Trichodesmium. Phycoerythrin-containing UCYN-B and UCYN-C-like cells were recurrently found embedded in large (>50 µm) organic aggregates or organized into clusters of tens to hundreds of cells linked by an extracellular matrix, presumably facilitating their export. Beyond the South Pacific, our data are supported by analysis of the Tara Oceans metagenomes collected in other ocean basins, extending the scope of our results globally. We show that, when diazotrophs are found in the euphotic zone, they are also systematically present in mesopelagic waters, suggesting their transport to the deep ocean. We thus conclude that diazotrophs are a significant part of the carbon sequestered in the deep ocean and, therefore, they need to be accounted in regional and global estimates of export.
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Affiliation(s)
- Sophie Bonnet
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
| | - Mar Benavides
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France ,grid.5399.60000 0001 2176 4817Turing Center for Living Systems, Aix-Marseille University, 13009 Marseille, France
| | - Frédéric A. C. Le Moigne
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France ,grid.463763.30000 0004 0638 0577LEMAR, Laboratoire des sciences de l’environnement marin, UMR6539, CNRS, UBO, IFREMER, IRD, 29280 Plouzané, Technopôle Brest-Iroise France
| | - Mercedes Camps
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Antoine Torremocha
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Olivier Grosso
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Céline Dimier
- grid.499565.20000 0004 0366 8890Laboratoire d’Océanographie de Villefranche (LOV), Sorbonne Université, CNRS, 06230 Villefranche sur mer, France
| | - Dina Spungin
- grid.18098.380000 0004 1937 0562University of Haifa, The Leon H. Charney School of Marine Sciences, Haifa, 3498838 Israel
| | - Ilana Berman-Frank
- grid.18098.380000 0004 1937 0562University of Haifa, The Leon H. Charney School of Marine Sciences, Haifa, 3498838 Israel
| | - Laurence Garczarek
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Francisco M. Cornejo-Castillo
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France ,grid.418218.60000 0004 1793 765XInstitut de Ciènces del Mar (ICM-CSIC), E08003 Barcelona, Spain
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4
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Salas K, Cabello AM, Turk-Kubo KA, Zehr JP, Cornejo-Castillo FM. Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1. Front Microbiol 2023; 14:1130695. [PMID: 37138636 PMCID: PMC10150950 DOI: 10.3389/fmicb.2023.1130695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/21/2023] [Indexed: 05/05/2023] Open
Abstract
The multiple symbiotic partnerships between closely related species of the haptophyte algae Braarudosphaera bigelowii and the nitrogen-fixing cyanobacteria Candidatus Atelocyanobacterium thalassa (UCYN-A) contribute importantly to the nitrogen and carbon cycles in vast areas of the ocean. The diversity of the eukaryotic 18S rDNA phylogenetic gene marker has helped to identify some of these symbiotic haptophyte species, yet we still lack a genetic marker to assess its diversity at a finer scale. One of such genes is the ammonium transporter (amt) gene, which encodes the protein that might be involved in the uptake of ammonium from UCYN-A in these symbiotic haptophytes. Here, we designed three specific PCR primer sets targeting the amt gene of the haptophyte species (A1-Host) symbiotic with the open ocean UCYN-A1 sublineage, and tested them in samples collected from open ocean and near-shore environments. Regardless of the primer pair used at Station ALOHA, which is where UCYN-A1 is the pre-dominant UCYN-A sublineage, the most abundant amt amplicon sequence variant (ASV) was taxonomically classified as A1-Host. In addition, two out of the three PCR primer sets revealed the existence of closely-related divergent haptophyte amt ASVs (>95% nucleotide identity). These divergent amt ASVs had higher relative abundances than the haptophyte typically associated with UCYN-A1 in the Bering Sea, or co-occurred with the previously identified A1-Host in the Coral Sea, suggesting the presence of new diversity of closely-related A1-Hosts in polar and temperate waters. Therefore, our study reveals an overlooked diversity of haptophytes species with distinct biogeographic distributions partnering with UCYN-A, and provides new primers that will help to gain new knowledge of the UCYN-A/haptophyte symbiosis.
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Affiliation(s)
- Krystal Salas
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Ana M. Cabello
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, Málaga, Spain
| | - Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
- *Correspondence: Jonathan P. Zehr,
| | - Francisco M. Cornejo-Castillo
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA, United States
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
- Francisco M. Cornejo-Castillo,
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5
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Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, González JM, Arrieta JM, Alam IS, Kamau A, Bowler C, Raes J, Pesant S, Bork P, Agustí S, Gojobori T, Vaqué D, Sullivan MB, Pedrós-Alió C, Massana R, Duarte CM, Gasol JM. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun Biol 2021; 4:604. [PMID: 34021239 PMCID: PMC8139981 DOI: 10.1038/s42003-021-02112-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/16/2021] [Indexed: 02/04/2023] Open
Abstract
The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.
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Affiliation(s)
- Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain.
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Pascal Hingamp
- Aix Marseille Univ., Université de Toulon, CNRS, Marseille, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Gipsi Lima-Mendez
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Jesús M Arrieta
- Spanish Institute of Oceanography (IEO), Oceanographic Center of The Canary Islands, Dársena Pesquera, Santa Cruz de Tenerife, Spain
| | - Intikhab S Alam
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Allan Kamau
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, Paris, France
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
- VIB Center for Microbiology, Leuven, Belgium
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Susana Agustí
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Matthew B Sullivan
- Department of Microbiology and Civil Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, 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
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
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6
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Landa M, Turk-Kubo KA, Cornejo-Castillo FM, Henke BA, Zehr JP. Critical Role of Light in the Growth and Activity of the Marine N 2-Fixing UCYN-A Symbiosis. Front Microbiol 2021; 12:666739. [PMID: 34025621 PMCID: PMC8139342 DOI: 10.3389/fmicb.2021.666739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/08/2021] [Indexed: 11/27/2022] Open
Abstract
The unicellular N2-fixing cyanobacteria UCYN-A live in symbiosis with haptophytes in the Braarudosphaera bigelowii lineage. Maintaining N2-fixing symbioses between two unicellular partners requires tight coordination of multiple biological processes including cell growth and division and, in the case of the UCYN-A symbiosis, N2 fixation of the symbiont and photosynthesis of the host. In this system, it is thought that the host photosynthesis supports the high energetic cost of N2 fixation, and both processes occur during the light period. However, information on this coordination is very limited and difficult to obtain because the UCYN-A symbiosis has yet to be available in culture. Natural populations containing the UCYN-A2 symbiosis were manipulated to explore the effects of alterations of regular light and dark periods and inhibition of host photosynthesis on N2 fixation (single cell N2 fixation rates), nifH gene transcription, and UCYN-A2 cell division (fluorescent in situ hybridization and nifH gene abundances). The results showed that the light period is critical for maintenance of regular patterns of gene expression, N2 fixation and symbiont replication and cell division. This study suggests a crucial role for the host as a producer of fixed carbon, rather than light itself, in the regulation and implementation of these cellular processes in UCYN-A.
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Affiliation(s)
- Marine Landa
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Kendra A Turk-Kubo
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | | | - Britt A Henke
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, Santa Cruz, CA, United States
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7
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Cornejo-Castillo FM, Muñoz-Marín MDC, Turk-Kubo KA, Royo-Llonch M, Farnelid H, Acinas SG, Zehr JP. UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N 2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa. Environ Microbiol 2018; 21:111-124. [PMID: 30255541 DOI: 10.1111/1462-2920.14429] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 09/06/2018] [Accepted: 09/22/2018] [Indexed: 12/01/2022]
Abstract
The symbiotic unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is one of the most abundant and widespread nitrogen (N2 )-fixing cyanobacteria in the ocean. Although it remains uncultivated, multiple sublineages have been detected based on partial nitrogenase (nifH) gene sequences, including the four most commonly detected sublineages UCYN-A1, UCYN-A2, UCYN-A3 and UCYN-A4. However, very little is known about UCYN-A3 beyond the nifH sequences from nifH gene diversity surveys. In this study, single cell sorting, DNA sequencing, qPCR and CARD-FISH assays revealed discrepancies involving the identification of sublineages, which led to new information on the diversity of the UCYN-A symbiosis. 16S rRNA and nifH gene sequencing on single sorted cells allowed us to identify the 16S rRNA gene of the uncharacterized UCYN-A3 sublineage. We designed new CARD-FISH probes that allowed us to distinguish and observe UCYN-A2 in a coastal location (SIO Pier; San Diego) and UCYN-A3 in an open ocean location (Station ALOHA; Hawaii). Moreover, we reconstructed about 13% of the UCYN-A3 genome from Tara Oceans metagenomic data. Finally, our findings unveil the UCYN-A3 symbiosis in open ocean waters suggesting that the different UCYN-A sublineages are distributed along different size fractions of the plankton defined by the cell-size ranges of their prymnesiophyte hosts.
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Affiliation(s)
- Francisco M Cornejo-Castillo
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Maria Del Carmen Muñoz-Marín
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Hanna Farnelid
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA.,Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA
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8
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Fridman S, Flores-Uribe J, Larom S, Alalouf O, Liran O, Yacoby I, Salama F, Bailleul B, Rappaport F, Ziv T, Sharon I, Cornejo-Castillo FM, Philosof A, Dupont CL, Sánchez P, Acinas SG, Rohwer FL, Lindell D, Béjà O. A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells. Nat Microbiol 2017; 2:1350-1357. [PMID: 28785078 DOI: 10.1038/s41564-017-0002-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 06/28/2017] [Indexed: 01/27/2023]
Abstract
Cyanobacteria are important contributors to primary production in the open oceans. Over the past decade, various photosynthesis-related genes have been found in viruses that infect cyanobacteria (cyanophages). Although photosystem II (PSII) genes are common in both cultured cyanophages and environmental samples 1-4 , viral photosystem I (vPSI) genes have so far only been detected in environmental samples 5,6 . Here, we have used a targeted strategy to isolate a cyanophage from the tropical Pacific Ocean that carries a PSI gene cassette with seven distinct PSI genes (psaJF, C, A, B, K, E, D) as well as two PSII genes (psbA, D). This cyanophage, P-TIM68, belongs to the T4-like myoviruses, has a prolate capsid, a long contractile tail and infects Prochlorococcus sp. strain MIT9515. Phage photosynthesis genes from both photosystems are expressed during infection, and the resultant proteins are incorporated into membranes of the infected host. Moreover, photosynthetic capacity in the cell is maintained throughout the infection cycle with enhancement of cyclic electron flow around PSI. Analysis of metagenomic data from the Tara Oceans expedition 7 shows that phages carrying PSI gene cassettes are abundant in the tropical Pacific Ocean, composing up to 28% of T4-like cyanomyophages. They are also present in the tropical Indian and Atlantic Oceans. P-TIM68 populations, specifically, compose on average 22% of the PSI-gene-cassette carrying phages. Our results suggest that cyanophages carrying PSI and PSII genes are likely to maintain and even manipulate photosynthesis during infection of their Prochlorococcus hosts in the tropical oceans.
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Affiliation(s)
- Svetlana Fridman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - José Flores-Uribe
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Shirley Larom
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Onit Alalouf
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Oded Liran
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Iftach Yacoby
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Faris Salama
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS and Université Pierre et Marie Curie, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabrice Rappaport
- Institut de Biologie Physico-Chimique, UMR 7141 CNRS and Université Pierre et Marie Curie, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Tamar Ziv
- Smoler Proteomics Center, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona, 11016, Israel.,Tel Hai College, Upper Galilee, 12210, Israel
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, 08003, Barcelona, Spain
| | - Alon Philosof
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, 08003, Barcelona, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, 08003, Barcelona, Spain
| | - Forest L Rohwer
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Debbie Lindell
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
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9
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Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Pesant S, Karsenti E, Wincker P. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci Data 2017; 4:170093. [PMID: 28763055 PMCID: PMC5538240 DOI: 10.1038/sdata.2017.93] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/05/2017] [Indexed: 02/01/2023] Open
Abstract
A unique collection of oceanic samples was gathered by the Tara Oceans
expeditions (2009–2013), targeting plankton organisms ranging from viruses to
metazoans, and providing rich environmental context measurements. Thanks to recent advances in
the field of genomics, extensive sequencing has been performed for a deep genomic analysis of
this huge collection of samples. A strategy based on different approaches, such as
metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for
analysis of size-fractionated plankton communities. Here, we provide detailed procedures
applied for genomic data generation, from nucleic acids extraction to sequence production, and
we describe registries of genomics datasets available at the European Nucleotide Archive (ENA,
www.ebi.ac.uk/ena). The association of these metadata to the experimental
procedures applied for their generation will help the scientific community to access these data
and facilitate their analysis. This paper complements other efforts to provide a full
description of experiments and open science resources generated from the Tara
Oceans project, further extending their value for the study of the world’s planktonic
ecosystems.
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Affiliation(s)
- Adriana Alberti
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Poulain
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Stefan Engelen
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Karine Labadie
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Sarah Romac
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Guillaume Albini
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Jean-Marc Aury
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Caroline Belser
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Alexis Bertrand
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Da Silva
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Carole Dossat
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Frédérick Gavory
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Shahinaz Gas
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Guy
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Maud Haquelle
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - E'krame Jacoby
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Olivier Jaillon
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Arnaud Lemainque
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Eric Pelletier
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Gaëlle Samson
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Mark Wessner
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | | | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Marta Royo-Llonch
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Francisco M Cornejo-Castillo
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Beatriz Fernández-Gómez
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain.,FONDAP Center for Genome Regulation, Moneda 1375, Santiago 8320000, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Libano Macul, Santiago 5524, Chile
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Colomban De Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Elodie Desgranges
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Stefanie Kandels-Lewis
- Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA
| | - Michael E Sieracki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA.,National Science Foundation, Arlington, Virginia 22230, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona 85719, USA
| | | | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, Bremen 28359, Germany.,PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Leobener Str. 8, Bremen 28359, Germany
| | - Eric Karsenti
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France.,Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, 181 Chemin du Lazaret, Villefranche-sur-mer F-06230, France
| | - Patrick Wincker
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
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10
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Royo-Llonch M, Ferrera I, Cornejo-Castillo FM, Sánchez P, Salazar G, Stepanauskas R, González JM, Sieracki ME, Speich S, Stemmann L, Pedrós-Alió C, Acinas SG. Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes. Front Microbiol 2017; 8:1317. [PMID: 28790980 PMCID: PMC5525439 DOI: 10.3389/fmicb.2017.01317] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/29/2017] [Indexed: 12/03/2022] Open
Abstract
Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms.
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Affiliation(s)
- Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | | | - José M González
- Department of Microbiology, University of La LagunaLa Laguna, Spain
| | | | - Sabrina Speich
- École Normale Supérieure, Département de Géosciences, Laboratoire de Météorologie Dynamique, UMR 8539 ENS-CNRS- École PolytechniqueParis, France
| | - Lars Stemmann
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV) UMR7093, Observatoire OcéanologiqueVillefranche-sur-Mer, France
| | - Carlos Pedrós-Alió
- Systems Biology Program, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain.,Departament de Genética i de Microbiologia, Facultat de Biociències, Universitat Autònoma de BarcelonaBellaterra, Spain
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11
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Cabello AM, Cornejo-Castillo FM, Raho N, Blasco D, Vidal M, Audic S, de Vargas C, Latasa M, Acinas SG, Massana R. Global distribution and vertical patterns of a prymnesiophyte-cyanobacteria obligate symbiosis. ISME J 2016; 10:693-706. [PMID: 26405830 PMCID: PMC4817677 DOI: 10.1038/ismej.2015.147] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 07/15/2015] [Accepted: 07/21/2015] [Indexed: 11/09/2022]
Abstract
A marine symbiosis has been recently discovered between prymnesiophyte species and the unicellular diazotrophic cyanobacterium UCYN-A. At least two different UCYN-A phylotypes exist, the clade UCYN-A1 in symbiosis with an uncultured small prymnesiophyte and the clade UCYN-A2 in symbiosis with the larger Braarudosphaera bigelowii. We targeted the prymnesiophyte-UCYN-A1 symbiosis by double CARD-FISH (catalyzed reporter deposition-fluorescence in situ hybridization) and analyzed its abundance in surface samples from the MALASPINA circumnavigation expedition. Our use of a specific probe for the prymnesiophyte partner allowed us to verify that this algal species virtually always carried the UCYN-A symbiont, indicating that the association was also obligate for the host. The prymnesiophyte-UCYN-A1 symbiosis was detected in all ocean basins, displaying a patchy distribution with abundances (up to 500 cells ml(-1)) that could vary orders of magnitude. Additional vertical profiles taken at the NE Atlantic showed that this symbiosis occupied the upper water column and disappeared towards the Deep Chlorophyll Maximum, where the biomass of the prymnesiophyte assemblage peaked. Moreover, sequences of both prymnesiophyte partners were searched within a large 18S rDNA metabarcoding data set from the Tara-Oceans expedition around the world. This sequence-based analysis supported the patchy distribution of the UCYN-A1 host observed by CARD-FISH and highlighted an unexpected homogeneous distribution (at low relative abundance) of B. bigelowii in the open ocean. Our results demonstrate that partners are always in symbiosis in nature and show contrasted ecological patterns of the two related lineages.
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Affiliation(s)
- Ana M Cabello
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | | | - Nicolas Raho
- Department of molecular Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Dolors Blasco
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Montserrat Vidal
- Departament of Ecology, University of Barcelona, Barcelona, Spain
| | - Stéphane Audic
- Station Biologique de Roscoff, Université Pierre et Marie Curie - Paris 6, Roscoff, France
- Laboratoire Adaptation et Diversité en Milieu Marin, CNRS, UMR 7144, Roscoff, France
| | - Colomban de Vargas
- Station Biologique de Roscoff, Université Pierre et Marie Curie - Paris 6, Roscoff, France
- Laboratoire Adaptation et Diversité en Milieu Marin, CNRS, UMR 7144, Roscoff, France
| | - Mikel Latasa
- Centro Oceanográfico de Gijón (IEO), Gijón, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain
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12
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Salazar G, Cornejo-Castillo FM, Borrull E, Díez-Vives C, Lara E, Vaqué D, Arrieta JM, Duarte CM, Gasol JM, Acinas SG. Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol Ecol 2015; 24:5692-706. [DOI: 10.1111/mec.13419] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/29/2015] [Accepted: 10/08/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Guillem Salazar
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
| | - Francisco M. Cornejo-Castillo
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
| | - Encarna Borrull
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
| | - Cristina Díez-Vives
- School of Biotechnology and Biomolecular Sciences; Centre for Marine Bio-Innovation; The University of New South Wales; Sydney NSW 2052 Australia
| | - Elena Lara
- Institute of Marine Sciences (CNR-ISMAR); National Research Council; Castello 2737/F Arsenale-Tesa 104 30122 Venezia Italy
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
| | - Jesús M. Arrieta
- King Abdullah University of Science and Technology (KAUST); Red Sea Research Center (RSRC); Thuwal 23955-6900 Saudi Arabia
| | - Carlos M. Duarte
- King Abdullah University of Science and Technology (KAUST); Red Sea Research Center (RSRC); Thuwal 23955-6900 Saudi Arabia
| | - Josep M. Gasol
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
| | - Silvia G. Acinas
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
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13
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Roitman S, Flores-Uribe J, Philosof A, Knowles B, Rohwer F, Ignacio-Espinoza JC, Sullivan MB, Cornejo-Castillo FM, Sánchez P, Acinas SG, Dupont CL, Béjà O. Closing the gaps on the viral photosystem-I psaDCAB gene organization. Environ Microbiol 2015; 17:5100-8. [PMID: 26310718 PMCID: PMC5019241 DOI: 10.1111/1462-2920.13036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/20/2015] [Indexed: 11/30/2022]
Abstract
Marine photosynthesis is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding for photosystem (PS) I and II reaction centre proteins are found in cyanophages and are believed to increase their fitness. Two viral PSI gene arrangements are known, psaJF→C→A→B→K→E→D and psaD→C→A→B. The shared genes between these gene cassettes and their encoded proteins are distinguished by %G + C and protein sequence respectively. The data on the psaD→C→A→B gene organization were reported from only two partial gene cassettes coming from Global Ocean Sampling stations in the Pacific and Indian oceans. Now we have extended our search to 370 marine stations from six metagenomic projects. Genes corresponding to both PSI gene arrangements were detected in the Pacific, Indian and Atlantic oceans, confined to a strip along the equator (30°N and 30°S). In addition, we found that the predicted structure of the viral PsaA protein from the psaD→C→A→B organization contains a lumenal loop conserved in PsaA proteins from Synechococcus, but is completely absent in viral PsaA proteins from the psaJF→C→A→B→K→E→D gene organization and most Prochlorococcus strains. This may indicate a co-evolutionary scenario where cyanophages containing either of these gene organizations infect cyanobacterial ecotypes biogeographically restricted to the 30°N and 30°S equatorial strip.
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Affiliation(s)
- Sheila Roitman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - José Flores-Uribe
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Alon Philosof
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ben Knowles
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Pablo Sánchez
- Departament of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Silvia G Acinas
- Departament of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J Craig Venter Institute, San Diego, CA, USA
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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14
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Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J. Ocean plankton. Determinants of community structure in the global plankton interactome. Science 2015; 348:1262073. [PMID: 25999517 DOI: 10.1126/science.1262073] [Citation(s) in RCA: 472] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.
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Affiliation(s)
- Gipsi Lima-Mendez
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Karoline Faust
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Nicolas Henry
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Johan Decelle
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Sébastien Colin
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France
| | - Fabrizio Carcillo
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. Interuniversity Institute of Bioinformatics in Brussels (IB), ULB Machine Learning Group, Computer Science Department, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Samuel Chaffron
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | | | - Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Flora Vincent
- VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France
| | - Lucie Bittner
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. Institut de Biologie Paris-Seine, CNRS FR3631, F-75005, Paris, France
| | - Youssef Darzi
- VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jun Wang
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium
| | - Stéphane Audic
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Léo Berline
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels (IB), ULB Machine Learning Group, Computer Science Department, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ana M Cabello
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Laurent Coppola
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Francesco d'Ovidio
- Sorbonne Universités, UPMC, Université Paris 06, CNRS-Institut pour la Recherche et le Développement-Muséum National d'Histoire Naturelle, Laboratoire d'Océanographie et du Climat: Expérimentations et Approches Numériques (LOCEAN) Laboratory, 4 Place Jussieu, 75005, Paris, France
| | - Luc De Meester
- KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Charles Deberiotstraat 32, 3000 Leuven
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Marie-José Garet-Delmas
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Lionel Guidi
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Elena Lara
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Hochschulring 18, 28359 Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Hochschulring 18, 28359 Bremen, Germany
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Marta Sebastian
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Caroline Souffreau
- KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Charles Deberiotstraat 32, 3000 Leuven
| | - Céline Dimier
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France
| | - Marc Picheral
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Sarah Searson
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Gabriel Gorsky
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Fabrice Not
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011 Kyoto, Japan
| | - Sabrina Speich
- Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Océan, Université de Bretagne Occidentale (UBO)-Institut Universaire Européen de la Mer (IUEM), Palce Copernic, 29820 Polouzané, France
| | - Lars Stemmann
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Jean Weissenbach
- Commissariat à l'Énergie Atomique (CEA), Genoscope, 2 rue Gaston Crémieux, 91000 Evry, France. CNRS, UMR 8030, 2 rue Gaston Crémieux, 91000 Evry, France. Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Patrick Wincker
- Commissariat à l'Énergie Atomique (CEA), Genoscope, 2 rue Gaston Crémieux, 91000 Evry, France. CNRS, UMR 8030, 2 rue Gaston Crémieux, 91000 Evry, France. Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Eric Karsenti
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Chris Bowler
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France.
| | - Colomban de Vargas
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
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15
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Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P. Ocean plankton. Structure and function of the global ocean microbiome. Science 2015; 348:1261359. [PMID: 25999513 DOI: 10.1126/science.1261359] [Citation(s) in RCA: 1348] [Impact Index Per Article: 149.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
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Affiliation(s)
- Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Samuel Chaffron
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Karine Labadie
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Bardya Djahanschiri
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel R Mende
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Adriana Alberti
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Corinne Cruaud
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Francesco d'Ovidio
- Sorbonne Universités, UPMC, Université Paris 06, CNRS-IRD-MNHN, LOCEAN Laboratory, 4 Place Jussieu, 75005 Paris France
| | - Stefan Engelen
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Lionel Guidi
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Falk Hildebrand
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Florian Kokoszka
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic 29820 Plouzané, France
| | - Cyrille Lepoivre
- Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France
| | - Gipsi Lima-Mendez
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Julie Poulain
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Hugo Sarmento
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain. Department of Hydrobiology, Federal University of São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, São Paulo, Brazil
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Céline Dimier
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Marc Picheral
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Sarah Searson
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Chris Bowler
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Gabriel Gorsky
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France. Sorbonne Universités Paris 06, OOB UPMC, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France
| | - Pascal Hingamp
- Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-001, Japan
| | - Stephane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Sabrina Speich
- Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic, 29820 Plouzané, France
| | - Lars Stemmann
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | - Jean Weissenbach
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Patrick Wincker
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Eric Karsenti
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany.
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Lara E, Holmfeldt K, Solonenko N, Sà EL, Ignacio-Espinoza JC, Cornejo-Castillo FM, Verberkmoes NC, Vaqué D, Sullivan MB, Acinas SG. Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the northwestern Mediterranean Sea. PLoS One 2015; 10:e0114829. [PMID: 25587991 PMCID: PMC4294664 DOI: 10.1371/journal.pone.0114829] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 11/14/2014] [Indexed: 11/18/2022] Open
Abstract
Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new ‘rare virosphere’ phage–host model system.
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Affiliation(s)
- Elena Lara
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Karin Holmfeldt
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Natalie Solonenko
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Elisabet Laia Sà
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - J. Cesar Ignacio-Espinoza
- University of Arizona, Department of Molecular and Cellular Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Francisco M. Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Nathan C. Verberkmoes
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
| | - Matthew B. Sullivan
- University of Arizona, Department of Ecology and Evolutionary Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
- University of Arizona, Department of Molecular and Cellular Biology, 1007 E. Lowell St., Tucson, AZ, United States of America
| | - Silvia G. Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain
- * E-mail:
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Acinas SG, Ferrera I, Sarmento H, Díez-Vives C, Forn I, Ruiz-González C, Cornejo-Castillo FM, Salazar G, Gasol JM. Validation of a new catalysed reporter deposition-fluorescence in situ hybridization probe for the accurate quantification of marine Bacteroidetes populations. Environ Microbiol 2014; 17:3557-69. [PMID: 24890225 DOI: 10.1111/1462-2920.12517] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 05/18/2014] [Indexed: 11/29/2022]
Abstract
Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used Bacteroidetes CF319a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319a hybridizes with non-Bacteroidetes sequences from the Rhodobacteraceae and Alteromonadaceae families. We test the probes' accuracy in 37 globally distributed marine samples and over two consecutive years at the Blanes Bay Microbial Observatory (NW Mediterranean). We also compared the CARD-FISH data with the Bacteroidetes 16S rRNA gene sequences retrieved from 27 marine metagenomes from the TARA Oceans expedition. We find no significant differences in abundances between both approaches, although CF319a targeted some unspecific sequences and both probes displayed different abundances of specific Bacteroidetes phylotypes. Our results demonstrate that quantitative estimations by using both probes are significantly different in certain oceanographic regions (Mediterranean Sea, Red Sea and Arabian Sea) and that CF968 shows seasonality within marine Bacteroidetes, notably large differences between summer and winter that is overlooked by CF319a. We propose CF968 as an alternative to CF319a for targeting the whole Bacteroidetes phylum since it has better coverage, greater specificity and overall better quantifies marine Bacteroidetes.
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Affiliation(s)
- Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Hugo Sarmento
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.,Department of Hydrobiology, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Cristina Díez-Vives
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Irene Forn
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.,Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Francisco M Cornejo-Castillo
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Guillem Salazar
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
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Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, Sarmento H, Hingamp P, Ogata H, de Vargas C, Lima-Mendez G, Raes J, Poulain J, Jaillon O, Wincker P, Kandels-Lewis S, Karsenti E, Bork P, Acinas SG. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environ Microbiol 2013; 16:2659-71. [PMID: 24102695 DOI: 10.1111/1462-2920.12250] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 08/10/2013] [Indexed: 12/21/2022]
Abstract
Sequencing of 16S rDNA polymerase chain reaction (PCR) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR. Here we show that 16S rDNA fragments derived from Illumina-sequenced environmental metagenomes (mi tags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the Tara Oceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700 Gb). For comparative analyses, a subset of samples was also selected for Roche-454 sequencing using both shotgun (m454 tags; 13 metagenomes, ca. 2.4 Gb) and 16S rDNA amplicon (454 tags; ca. 0.075 Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mi tags may provide more realistic estimates of community richness and evenness than amplicon 454 tags. In addition, mi tags can capture expected beta diversity patterns. Using mi tags is now economically feasible given the dramatic reduction in high-throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic (Bacteria, Archaea and Eukarya) and functional information from the same microbial community.
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Affiliation(s)
- Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Science (ICM), Spanish National Research Council (CSIC), Passeig Marítim de la Barceloneta, 37-49, Barcelona, ES-08003, Spain
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