1
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Alcamán-Arias ME, Cifuentes-Anticevic J, Castillo-Inaipil W, Farías L, Sanhueza C, Fernández-Gómez B, Verdugo J, Abarzua L, Ridley C, Tamayo-Leiva J, Díez B. Dark Diazotrophy during the Late Summer in Surface Waters of Chile Bay, West Antarctic Peninsula. Microorganisms 2022; 10:microorganisms10061140. [PMID: 35744658 PMCID: PMC9227844 DOI: 10.3390/microorganisms10061140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 05/28/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Although crucial for the addition of new nitrogen in marine ecosystems, dinitrogen (N2) fixation remains an understudied process, especially under dark conditions and in polar coastal areas, such as the West Antarctic Peninsula (WAP). New measurements of light and dark N2 fixation rates in parallel with carbon (C) fixation rates, as well as analysis of the genetic marker nifH for diazotrophic organisms, were conducted during the late summer in the coastal waters of Chile Bay, South Shetland Islands, WAP. During six late summers (February 2013 to 2019), Chile Bay was characterized by high NO3− concentrations (~20 µM) and an NH4+ content that remained stable near 0.5 µM. The N:P ratio was approximately 14.1, thus close to that of the Redfield ratio (16:1). The presence of Cluster I and Cluster III nifH gene sequences closely related to Alpha-, Delta- and, to a lesser extent, Gammaproteobacteria, suggests that chemosynthetic and heterotrophic bacteria are primarily responsible for N2 fixation in the bay. Photosynthetic carbon assimilation ranged from 51.18 to 1471 nmol C L−1 d−1, while dark chemosynthesis ranged from 9.24 to 805 nmol C L−1 d−1. N2 fixation rates were higher under dark conditions (up to 45.40 nmol N L−1 d−1) than under light conditions (up to 7.70 nmol N L−1 d−1), possibly contributing more than 37% to new nitrogen-based production (≥2.5 g N m−2 y−1). Of all the environmental factors measured, only PO43- exhibited a significant correlation with C and N2 rates, being negatively correlated (p < 0.05) with dark chemosynthesis and N2 fixation under the light condition, revealing the importance of the N:P ratio for these processes in Chile Bay. This significant contribution of N2 fixation expands the ubiquity and biological potential of these marine chemosynthetic diazotrophs. As such, this process should be considered along with the entire N cycle when further reviewing highly productive Antarctic coastal waters and the diazotrophic potential of the global marine ecosystem.
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Affiliation(s)
- María E. Alcamán-Arias
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Escuela de Medicina, Universidad Espíritu Santo, Guayaquil 0901952, Ecuador
| | - Jerónimo Cifuentes-Anticevic
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Wilson Castillo-Inaipil
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Laura Farías
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
| | - Cynthia Sanhueza
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Beatriz Fernández-Gómez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria (ULPGC), 35001 Las Palmas, Spain
| | - Josefa Verdugo
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany;
| | - Leslie Abarzua
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4030000, Chile; (M.E.A.-A.); (L.F.); (L.A.)
| | - Christina Ridley
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
| | - Javier Tamayo-Leiva
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Center for Genome Regulation (CRG), Universidad de Chile, Blanco Encalada 2085, Santiago 8320000, Chile
| | - Beatriz Díez
- Center for Climate and Resilience Research (CR)2, Universidad de Chile, Blanco Encalada 2002, Santiago 8320000, Chile; (C.R.); (J.T.-L.)
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (J.C.-A.); (W.C.-I.); (C.S.); (B.F.-G.)
- Center for Genome Regulation (CRG), Universidad de Chile, Blanco Encalada 2085, Santiago 8320000, Chile
- Correspondence:
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2
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Melero-Jerez C, Fernández-Gómez B, Lebrón-Galán R, Ortega MC, Sánchez-de Lara I, Ojalvo AC, Clemente D, de Castro F. Myeloid-derived suppressor cells support remyelination in a murine model of multiple sclerosis by promoting oligodendrocyte precursor cell survival, proliferation, and differentiation. Glia 2020; 69:905-924. [PMID: 33217041 PMCID: PMC7894183 DOI: 10.1002/glia.23936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023]
Abstract
The most frequent variant of multiple sclerosis (MS) is the relapsing–remitting form, characterized by symptomatic phases followed by periods of total/partial recovery. Hence, it is possible that these patients can benefit from endogenous agents that control the inflammatory process and favor spontaneous remyelination. In this context, there is increasing interest in the role of myeloid‐derived suppressor cells (MDSCs) during the clinical course of experimental autoimmune encephalomyelitis (EAE). MDSCs speed up infiltrated T‐cell anergy and apoptosis. In different animal models of MS, a milder disease course is related to higher presence/density of MDSCs in the periphery, and smaller demyelinated lesions in the central nervous system (CNS). These observations lead us to wonder whether MDSCs might not only exert an anti‐inflammatory effect but might also have direct influence on oligodendrocyte precursor cells (OPCs) and remyelination. In the present work, we reveal for the first time the relationship between OPCs and MDSCs in EAE, relationship that is guided by the distance from the inflammatory core. We describe the effects of MDSCs on survival, proliferation, as well as potent promoters of OPC differentiation toward mature phenotypes. We show for the first time that osteopontin is remarkably present in the analyzed secretome of MDSCs. The ablation of this cue from MDSCs‐secretome demonstrates that osteopontin is the main MDSC effector on these oligodendroglial cells. These data highlight a crucial pathogenic interaction between innate immunity and the CNS, opening ways to develop MDSC‐ and/or osteopontin‐based therapies to promote effective myelin preservation and repair in MS patients.
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Affiliation(s)
- Carolina Melero-Jerez
- Instituto Cajal-CSIC, Madrid, Spain.,Grupo de Neuroinmuno-Reparación, Hospital Nacional de Parapléjicos-SESCAM, Toledo, Spain
| | | | - Rafael Lebrón-Galán
- Grupo de Neuroinmuno-Reparación, Hospital Nacional de Parapléjicos-SESCAM, Toledo, Spain
| | - Maria Cristina Ortega
- Grupo de Neuroinmuno-Reparación, Hospital Nacional de Parapléjicos-SESCAM, Toledo, Spain
| | - Irene Sánchez-de Lara
- Grupo de Neuroinmuno-Reparación, Hospital Nacional de Parapléjicos-SESCAM, Toledo, Spain
| | - Ana Cristina Ojalvo
- Grupo de Neuroinmuno-Reparación, Hospital Nacional de Parapléjicos-SESCAM, Toledo, Spain
| | - Diego Clemente
- Grupo de Neuroinmuno-Reparación, Hospital Nacional de Parapléjicos-SESCAM, Toledo, Spain
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3
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Llanillo PJ, Aiken CM, Cordero RR, Damiani A, Sepúlveda E, Fernández-Gómez B. Oceanographic Variability induced by Tides, the Intraseasonal Cycle and Warm Subsurface Water intrusions in Maxwell Bay, King George Island (West-Antarctica). Sci Rep 2019; 9:18571. [PMID: 31819101 PMCID: PMC6901452 DOI: 10.1038/s41598-019-54875-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 11/20/2019] [Indexed: 11/09/2022] Open
Abstract
We examine the hydrographic variability induced by tides, winds, and the advance of the austral summer, in Maxwell Bay and tributary fjords, based on two recent oceanographic campaigns. We provide the first description in this area of the intrusion of relatively warm subsurface waters, which have led elsewhere in Antarctica to ice-shelf disintegration and tidewater glacier retreat. During flood tide, meltwater was found to accumulate toward the head of Maxwell Bay, freshening and warming the upper 70 m. Below 70 m, the flood tide enhances the intrusion and mixing of relatively warm modified Upper Circumpolar Deep Water (m-UCDW). Tidal stirring progressively erodes the remnants of Winter Waters found at the bottom of Marian Cove. There is a buoyancy gain through warming and freshening as the summer advances. In Maxwell Bay, the upper 105 m were 0.79 °C warmer and 0.039 PSU fresher in February than in December, changes that cannot be explained by tidal or wind-driven processes. The episodic intrusion of m-UCDW into Maxwell Bay leads to interleaving and eventually to warming, salinification and deoxygenation between 80 and 200 m, with important implications for biological productivity and for the mass balance of tidewater glaciers in the area.
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Affiliation(s)
- P J Llanillo
- Departamento de Física, Facultad de Ciencia, Universidad de Santiago de Chile, Santiago, Chile.
| | - C M Aiken
- Estación Costera de Investigaciones Marinas, Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile.,Departamento de Ingeniería Hidráulica y Ambiental, Facultad de Ingeniería, Pontificia Universidad Católica, Santiago, Chile
| | - R R Cordero
- Departamento de Física, Facultad de Ciencia, Universidad de Santiago de Chile, Santiago, Chile
| | - A Damiani
- Center for Environmental Remote Sensing, Chiba University, Chiba, Japan
| | - E Sepúlveda
- Departamento de Física, Facultad de Ciencia, Universidad de Santiago de Chile, Santiago, Chile
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4
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Rebollo-Hernanz M, Fernández-Gómez B, Herrero M, Aguilera Y, Martín-Cabrejas MA, Uribarri J, del Castillo MD. Inhibition of the Maillard Reaction by Phytochemicals Composing an Aqueous Coffee Silverskin Extract via a Mixed Mechanism of Action. Foods 2019; 8:E438. [PMID: 31557849 PMCID: PMC6835918 DOI: 10.3390/foods8100438] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 12/23/2022] Open
Abstract
This work aimed to evaluate the contribution of isoflavones and melatonin to the aqueous extract obtained from the coffee silverskin (CSE) antiglycative properties, which has not been previously studied. To achieve this goal, two model systems constituted by bovine serum albumin (BSA) and reactive carbonyls (glucose or methylglyoxal) in the presence or absence of pure phytochemicals (chlorogenic acid (CGA), genistein, and melatonin) and CSE were employed. Glucose was used to evaluate the effect on the formation of glycation products formed mainly in the early stage of the reaction, while methylglyoxal was employed for looking at the formation of advanced products of the reaction, also called methylglyoxal-derivative advanced glycation end products (AGE) or glycoxidation products. CGA inhibited the formation of fructosamine, while genistein and melatonin inhibited the formation of advanced glycation end products and protein glycoxidation. It was also observed that phenolic compounds from CSE inhibited protein glycation and glycoxidation by forming BSA-phytochemical complexes. CSE showed a significant antiglycative effect (p < 0.05). Variations in the UV-Vis spectrum and the antioxidant capacity of protein fractions suggested the formation of protein-phytochemical complexes. Fluorescence quenching and in silico analysis supported the formation of antioxidant-protein complexes. For the first time, we illustrate that isoflavones and melatonin may contribute to the antiglycative/antiglycoxidative properties associated with CSE. CGA, isoflavones, and melatonin composing CSE seem to act simultaneously by different mechanisms of action.
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Affiliation(s)
- Miguel Rebollo-Hernanz
- Institute of Food Science Research (CIAL, UAM-CSIC), C/Nicolás Cabrera, 9, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.R.-H.); (B.F.-G.); (M.H.); marí
- Department of Agricultural Chemistry and Food Science, Faculty of Science, C/Francisco Tomás y Valiente, 7, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Beatriz Fernández-Gómez
- Institute of Food Science Research (CIAL, UAM-CSIC), C/Nicolás Cabrera, 9, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.R.-H.); (B.F.-G.); (M.H.); marí
| | - Miguel Herrero
- Institute of Food Science Research (CIAL, UAM-CSIC), C/Nicolás Cabrera, 9, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.R.-H.); (B.F.-G.); (M.H.); marí
| | - Yolanda Aguilera
- Institute of Food Science Research (CIAL, UAM-CSIC), C/Nicolás Cabrera, 9, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.R.-H.); (B.F.-G.); (M.H.); marí
- Department of Agricultural Chemistry and Food Science, Faculty of Science, C/Francisco Tomás y Valiente, 7, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - María A. Martín-Cabrejas
- Institute of Food Science Research (CIAL, UAM-CSIC), C/Nicolás Cabrera, 9, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.R.-H.); (B.F.-G.); (M.H.); marí
- Department of Agricultural Chemistry and Food Science, Faculty of Science, C/Francisco Tomás y Valiente, 7, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Jaime Uribarri
- Department of Medicine, The Icahn School of Medicine at Mount Sinai, 1468 Madison Ave, New York, NY 10029, USA;
| | - María Dolores del Castillo
- Institute of Food Science Research (CIAL, UAM-CSIC), C/Nicolás Cabrera, 9, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.R.-H.); (B.F.-G.); (M.H.); marí
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5
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Fernández-Gómez B, Díez B, Polz MF, Arroyo JI, Alfaro FD, Marchandon G, Sanhueza C, Farías L, Trefault N, Marquet PA, Molina-Montenegro MA, Sylvander P, Snoeijs-Leijonmalm P. Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85-90 °N. ISME J 2019; 13:316-333. [PMID: 30228379 PMCID: PMC6331608 DOI: 10.1038/s41396-018-0268-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/11/2018] [Accepted: 07/24/2018] [Indexed: 01/13/2023]
Abstract
Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4-9.6) and immediate sub-ice seawater (SW; salinity 33.3-34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.
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Affiliation(s)
- Beatriz Fernández-Gómez
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
- INTA-Universidad de Chile, Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile.
- Center for Climate and Resilience Research, Concepción, Chile.
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - José Ignacio Arroyo
- Department of Ecology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Germán Marchandon
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Cynthia Sanhueza
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Laura Farías
- Center for Climate and Resilience Research, Concepción, Chile
- Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Pablo A Marquet
- Department of Ecology, Pontifical University Catholic of Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Marco A Molina-Montenegro
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas, Universidad Católica del Norte, Coquimbo, Chile
| | - Peter Sylvander
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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6
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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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7
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Crespo BG, Pommier T, Fernández-Gómez B, Pedrós-Alió C. Taxonomic composition of the particle-attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA. Microbiologyopen 2013; 2:541-52. [PMID: 23723056 PMCID: PMC3948605 DOI: 10.1002/mbo3.92] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [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: 11/22/2012] [Revised: 03/07/2013] [Accepted: 03/15/2013] [Indexed: 11/08/2022] Open
Abstract
Free-living (FL) and particle-attached (PA) bacterial assemblages in the Northwest Mediterranean Sea were studied using pyrosequencing data of the 16S rRNA. We have described and compared the richness, the distribution of Operational Taxonomic Units (OTUs) within the two fractions, the spatial distribution, and the taxonomic composition of FL and PA bacterial assemblages. The number of OTUs in the present work was two orders of magnitude higher than in previous studies. Only 25% of the total OTUs were common to both fractions, whereas 49% OTUs were exclusive to the PA fraction and 26% to the FL fraction. The OTUs exclusively present in PA or FL assemblages were very low in abundance (6% of total abundance). Detection of the rare OTUs revealed the larger richness of PA bacteria that was hidden in previous studies. Alpha-Proteobacteria dominated the FL bacterial assemblage and gamma-Proteobacteria dominated the PA fraction. Bacteroidetes were important in the PA fraction mainly at the coast. The high number of sequences in this study detected additional phyla from the PA fraction, such as Actinobacteria, Firmicutes, and Verrucomicrobia.
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Affiliation(s)
- Bibiana G Crespo
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
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8
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Zapater C, Chauvigné F, Fernández-Gómez B, Finn RN, Cerdà J. Alternative splicing of the nuclear progestin receptor in a perciform teleost generates novel mechanisms of dominant-negative transcriptional regulation. Gen Comp Endocrinol 2013; 182:24-40. [PMID: 23220040 DOI: 10.1016/j.ygcen.2012.11.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 11/13/2012] [Accepted: 11/21/2012] [Indexed: 01/02/2023]
Abstract
In mammals, downstream function of the nuclear progestin receptor (PGR) can be differentially regulated in each target tissue by altering the expression levels of PGR mRNA variants. Such PGR isoforms have also been identified in birds and reptiles, but not in non-amniote vertebrates. Based upon extensive phylogenetic, syntenic and functional analyses, here we show that higher orders of Teleostei retain a single pgr gene, and that four different pgr transcript variants of the extant gene are expressed in the ovary of an evolutionary advanced perciform teleost, the gilthead seabream (Sparus aurata). Three of the isoforms (pgr_tv2, pgr_tv3 and pgr_tv4) arise from alternative pre-mRNA splicing resulting in different N-terminally truncated receptors, whereas one isoform (pgr_tv1) is a deletion variant. Seabream wild-type Pgr shows the highest transactivational response to native euteleostean progestins, 17α,20β-dihydroxy-4-pregnen-3-one and 17α,20β,21-trihydroxy-4-pregnen-3-one, whereas the Pgr_tv3 and Pgr_tv4 isoforms independently regulate novel nuclear and cytosolic mechanisms of dominant-negative repression of Pgr-mediated transcription. In the seabream ovary, the wild-type Pgr protein is localized in oogonia, in the nuclei of primary (previtellogenic) oocytes, as well as in follicular (granulosa) cells and the oocyte cytoplasm of early and late vitellogenic ovarian follicles. Expression of wild-type pgr, pgr_tv3 and pgr_tv4 was the highest in seabream primary ovaries, while expression of both inhibitory receptor isoforms, but not of pgr, decreased during vitellogenesis. Stimulation of primary ovarian explants in vitro with recombinant piscine follicle-stimulating hormone and estrogen differentially regulated the temporal expression of pgr, pgr_tv3 and pgr_tv4. These findings suggest that, as in mammals, ovarian progestin responsiveness in the seabream, particularly during early oogenesis, may be regulated through alternative splicing of the nuclear pgr mRNA. Thus, the dominant-negative mechanism of PGR transcriptional regulation likely evolved prior to the separation of Actinopterygii (ray-finned fishes) from Sarcopterygii (lobe-finned fishes).
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Affiliation(s)
- Cinta Zapater
- IRTA-Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, 08003 Barcelona, Spain
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9
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Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG, González JM, Pedrós-Alió C. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J 2013; 7:1026-37. [PMID: 23303374 DOI: 10.1038/ismej.2012.169] [Citation(s) in RCA: 400] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. This confirmed the role of this abundant group of marine bacteria as degraders of particulate matter. Marine Bacteroidetes had a significantly larger number of proteases than GHs, while non-marine Bacteroidetes had equal numbers of both. Proteorhodopsin containing Bacteroidetes shared two characteristics: small genome size and a higher number of genes involved in CO2 fixation per Mb. The latter may be important in order to survive when floating freely in the illuminated, but nutrient-poor, ocean surface.
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Affiliation(s)
- Beatriz Fernández-Gómez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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10
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Fernández-Gómez B, Fernàndez-Guerra A, Casamayor EO, González JM, Pedrós-Alió C, Acinas SG. Patterns and architecture of genomic islands in marine bacteria. BMC Genomics 2012; 13:347. [PMID: 22839777 PMCID: PMC3478194 DOI: 10.1186/1471-2164-13-347] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [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: 02/27/2012] [Accepted: 07/10/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic Islands (GIs) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. Despite their importance, GIs in marine bacterial genomes have not been explored systematically to uncover possible trends and to analyze their putative ecological significance. RESULTS We carried out a comprehensive analysis of GIs in 70 selected marine bacterial genomes detected with IslandViewer to explore the distribution, patterns and functional gene content in these genomic regions. We detected 438 GIs containing a total of 8152 genes. GI number per genome was strongly and positively correlated with the total GI size. In 50% of the genomes analyzed the GIs accounted for approximately 3% of the genome length, with a maximum of 12%. Interestingly, we found transposases particularly enriched within Alphaproteobacteria GIs, and site-specific recombinases in Gammaproteobacteria GIs. We described specific Homologous Recombination GIs (HR-GIs) in several genera of marine Bacteroidetes and in Shewanella strains among others. In these HR-GIs, we recurrently found conserved genes such as the β-subunit of DNA-directed RNA polymerase, regulatory sigma factors, the elongation factor Tu and ribosomal protein genes typically associated with the core genome. CONCLUSIONS Our results indicate that horizontal gene transfer mediated by phages, plasmids and other mobile genetic elements, and HR by site-specific recombinases play important roles in the mobility of clusters of genes between taxa and within closely related genomes, modulating the flexible pool of the genome. Our findings suggest that GIs may increase bacterial fitness under environmental changing conditions by acquiring novel foreign genes and/or modifying gene transcription and/or transduction.
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Affiliation(s)
- Beatriz Fernández-Gómez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Pg Marítim de la Barceloneta 37-49, ES-08003 Barcelona, Spain
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11
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Grote J, Bayindirli C, Bergauer K, Carpintero de Moraes P, Chen H, D’Ambrosio L, Edwards B, Fernández-Gómez B, Hamisi M, Logares R, Nguyen D, Rii YM, Saeck E, Schutte C, Widner B, Church MJ, Steward GF, Karl DM, DeLong EF, Eppley JM, Schuster SC, Kyrpides NC, Rappé MS. Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria. Stand Genomic Sci 2011; 5:269-78. [PMID: 22675578 PMCID: PMC3368413 DOI: 10.4056/sigs.1854551] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strain HIMB100 is a planktonic marine bacterium in the class Alphaproteobacteria. This strain is of interest because it is one of the first known isolates from a globally ubiquitous clade of marine bacteria known as SAR116 within the family Rhodospirillaceae. Here we describe preliminary features of the organism, together with the draft genome sequence and annotation. This is the second genome sequence of a member of the SAR116 clade. The 2,458,945 bp genome contains 2,334 protein-coding and 42 RNA genes.
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Affiliation(s)
- Jana Grote
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Hawaii Institute of Marine Biology, SOEST, University of Hawaii, Kaneohe, Hawaii, USA
| | - Cansu Bayindirli
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Plymouth Marine Laboratory, University of East Anglia, Norwich, UK
| | - Kristin Bergauer
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Department of Marine Biology, University of Vienna, Vienna, Austria
| | - Paula Carpintero de Moraes
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Instituto Oceanografico, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Huan Chen
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Environmental Sciences Institute, Florida A&M University, Tallahassee, Florida, USA
| | - Lindsay D’Ambrosio
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Bethanie Edwards
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Beatriz Fernández-Gómez
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Departament de Biologia Marina i Oceanografia, Institut de Cièncias del Mar, CMIMA, CSIC, Barcelona, Spain
| | - Mariam Hamisi
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- School of Natural Sciences and Mathematics, The University of Dodoma, Dodoma, Tanzania
| | - Ramiro Logares
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Departament de Biologia Marina i Oceanografia, Institut de Cièncias del Mar, CMIMA, CSIC, Barcelona, Spain
| | - Dan Nguyen
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Département de Sciences Biologiques, Universitéde Montréal, Montréal, Canada
| | - Yoshimi M. Rii
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Department of Oceanography, SOEST, University of Hawaii, Honolulu, Hawaii, USA
| | - Emily Saeck
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Australian Rivers Institute, Griffith University, Queensland, Australia
| | - Charles Schutte
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
| | - Brittany Widner
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, Virginia, USA
| | - Matthew J. Church
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Department of Oceanography, SOEST, University of Hawaii, Honolulu, Hawaii, USA
| | - Grieg F. Steward
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Department of Oceanography, SOEST, University of Hawaii, Honolulu, Hawaii, USA
| | - David M. Karl
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Department of Oceanography, SOEST, University of Hawaii, Honolulu, Hawaii, USA
| | - Edward F. DeLong
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - John M. Eppley
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stephan C. Schuster
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Nikos C. Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Michael S. Rappé
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA
- Hawaii Institute of Marine Biology, SOEST, University of Hawaii, Kaneohe, Hawaii, USA
- Corresponding author: Michael S. Rappé ()
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