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  • Article

    Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

    (Springer Nature, 2016-09-21) Roux, Simon; Brum, Jennifer R; Dutilh, Bas E.; Sunagawa, Shinichi; Duhaime, Melissa B; Loy, Alexander; Poulos, Bonnie T; Solonenko, Natalie; Lara, Elena; Poulain, Julie; Pesant, Stephane; Kandels-Lewis, Stefanie; Dimier, Celine; Picheral, Marc; Searson, Sarah; Cruaud, Corinne; Alberti, Adriana; Duarte, Carlos M.; Gasol, Josep M M; Vaque, Dolors; Bork, Peer; Acinas, Silvia G; Wincker, Patrick; Sullivan, Matthew B; King Abdullah University of Science and Technology (KAUST); Biological and Environmental Sciences and Engineering (BESE) Division; Marine Science Program; Red Sea Research Center (RSRC); Department of Microbiology, Ohio State University, Columbus, OH, United States; Department of Marine Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands; Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States; Austrian Polar Research Institute, Vienna, Austria; Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, Vienna, Austria; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AR, United States; Institute of Marine Sciences, National Research Council, Venezia, Italy; Department of Marine Biology and Oceanography, Institut de Ciencies Del Mar, CSIC, Barcelona, Spain; MARUM, Bremen University, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany; Department of Research European Molecular Biology Laboratory, Heidelberg, Germany; Institut de Biologie de LfEcole Normale Superieure, Ecole Normale Superieure, Paris Sciences et Lettres Research University, Paris, France; Sorbonne Universite.s, UPMC Universite, Roscoff, France; CNRS, Station Biologique de Roscoff, Roscoff, France; Sorbonne Universites, UPMC Universite, Villefranche-sur-mer, France; CNRS, Laboratoire d'Oceanographie de Villefranche, Observatoire Oceanologique, Villefranche-sur-mer, France; CEA, Institut de Genomique, Evry, France; Mediterranean Institute of Advanced Studies, CSIC, Esporles, Mallorca, Spain; Max-Delbru.ck-Centre for Molecular Medicine, Berlin, Germany; Universite DfEvry, Evry, France; CNRS, Evry, France; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States

    Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface-and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting â global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks. © 2016 Macmillan Publishers Limited, part of Springer Nature.

  • Article

    Large-scale ocean connectivity and planktonic body size

    (Springer Nature, 2018-01-10) Villarino, Ernesto; Watson, James R.; Jönsson, Bror; Gasol, Josep M.; Salazar, Guillem; Acinas, Silvia G.; Estrada, Marta; Massana, Ramón; Logares, Ramiro; Giner, Caterina R.; Pernice, Massimo C.; Olivar, M. Pilar; Citores, Leire; Corell, Jon; Rodríguez-Ezpeleta, Naiara; Acuña, José Luis; Molina-Ramírez, Axayacatl; González-Gordillo, J. Ignacio; Cózar, Andrés; Martí, Elisa; Cuesta, José A.; Agusti, Susana; Fraile-Nuez, Eugenio; Duarte, Carlos M.; Irigoien, Xabier; Chust, Guillem; Biological and Environmental Sciences and Engineering (BESE) Division; Marine Science Program; Red Sea Research Center (RSRC); AZTI, Marine Research Division, Txatxarramendi ugartea z/g, 48395, Sukarrieta, Bizkaia, Spain.; AZTI, Marine Research Division, Txatxarramendi ugartea z/g, 48395, Sukarrieta, Bizkaia, Spain. villarino.ernesto@gmail.com.; College of Earth, Ocean and Atmospheric Sciences, Oregon State University, Corvallis, 97331, USA.; Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, NH, 03824-3525, USA.; Institut de Ciències del Mar, CSIC, 08003, Barcelona, Catalunya, Spain.; Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Calle Catedrático Valentín Andrés Alvarez, sin número, 33006, Oviedo, Spain.; Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Campus de Excelencia Internacional del Mar (CEI-MAR), E-11510, Puerto Real, Cadiz, Spain.; Instituto de Ciencias Marinas de Andalucía, CSIC, Campus de Excelencia Internacional del Mar (CEI-MAR), E-11510, Puerto Real, Cadiz, Spain.; Instituto Español de Oceanografía, Centro Oceanográfico de Canarias, Santa Cruz de Tenerife, 38180, Spain.

    Global patterns of planktonic diversity are mainly determined by the dispersal of propagules with ocean currents. However, the role that abundance and body size play in determining spatial patterns of diversity remains unclear. Here we analyse spatial community structure - β-diversity - for several planktonic and nektonic organisms from prokaryotes to small mesopelagic fishes collected during the Malaspina 2010 Expedition. β-diversity was compared to surface ocean transit times derived from a global circulation model, revealing a significant negative relationship that is stronger than environmental differences. Estimated dispersal scales for different groups show a negative correlation with body size, where less abundant large-bodied communities have significantly shorter dispersal scales and larger species spatial turnover rates than more abundant small-bodied plankton. Our results confirm that the dispersal scale of planktonic and micro-nektonic organisms is determined by local abundance, which scales with body size, ultimately setting global spatial patterns of diversity.

  • Article

    Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine–seawater interface at Erba Deep in the Red Sea

    (Microbiology Society, 2017-10-12) Zhang, Guishan; Haroon, Mohamed; Zhang, Ruifu; Dong, Xiaoyan; Wang, Dandan; Liu, Yunpeng; Xun, Weibing; Dong, Xiuzhu; Stingl, Ulrich; Biological and Environmental Sciences and Engineering (BESE) Division; Marine Science Program; Office of the VP; Red Sea Research Center (RSRC); ​Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; ​State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Florida, UF/IFAS, Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, Davie, FL 33314, USA

    Two moderately halophilic marine bacterial strains of the family Rhodobacteraceae, designated ZGT108T and ZGT118T, were isolated from the brine-seawater interface at Erba Deep in the Red Sea (Saudi Arabia). Cells of both strains were aerobic, rod-shaped, non-motile, and Gram-stain-negative. The sequence similarity of the 16S rRNA genes of strains ZGT108T and ZGT118T was 94.9 %. The highest 16S rRNA gene sequence similarity of strain ZGT108T to its closest relative, Ruegeria conchae JCM 17315T, was 98.9 %, while the 16S rRNA gene of ZGT118T was most closely related to that of Ruegeria intermedia LMG 25539T (97.7 % similarity). The sizes of the draft genomes as presented here are 4 258 055 bp (strain ZGT108T) and 4 012 109 bp (strain ZGT118T), and the G+C contents of the draft genomes are 56.68 mol% (ZGT108T) and 62.94 mol% (ZGT108T). The combined physiological, biochemical, phylogenetic and genotypic data supported placement of both strains in the genus Ruegeria and indicated that the two strains are distinct from each other as well as from all other members in the genus Ruegeria. This was also confirmed by low DNA-DNA hybridization values (<43.6 %) and low ANI values (<91.8 %) between both strains and the most closely related Ruegeria species. Therefore, we propose two novel species in the genus Ruegeria to accommodate these novel isolates: Ruegeriaprofundi sp. nov. (type strain ZGT108T=JCM 19518T=ACCC 19861T) and Ruegeriamarisrubri sp. nov. (type strain ZGT118T=JCM 19519T= ACCC 19862T).

  • Article

    Ponticoccus marisrubri sp. nov., a moderately halophilic marine bacterium of the family Rhodobacteraceae

    (Microbiology Society, 2017-10-06) Zhang, Guishan; Haroon, Mohamed; Zhang, Ruifu; Dong, Xiaoyan; Liu, Di; Xiong, Qin; Xun, Weibing; Dong, Xiuzhu; Stingl, Ulrich; Biological and Environmental Sciences and Engineering (BESE) Division; Marine Science Program; Office of the VP; Red Sea Research Center (RSRC); Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; ​State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; Department of Microbiology and Cell Science, University of Florida, Institute for Food and Agricultural Sciences (IFAS), Fort Lauderdale Research and Education Center, Fort Lauderdale (Davie), FL33314, USA

    Strain SJ5A-1T, a Gram-stain-negative, coccus-shaped, non-motile, aerobic bacterium, was isolated from the brine-seawater interface of the Erba Deep in the Red Sea, Saudi Arabia. The colonies of strain SJ5A-1T have a beige to pale-brown pigmentation, are approximately 0.5-0.7 µm in diameter, and are catalase and oxidase positive. Growth occurred optimally at 30-33 °C, pH 7.0-7.5, and in the presence of 9.0-12.0 % NaCl (w/v). Phylogenetic analysis of the 16S rRNA gene indicates that strain SJ5A-1T is a member of the genus Ponticoccus within the family Rhodobacteraceae. Ponticoccus litoralis DSM 18986T is the most closely related described species based on 16S rRNA gene sequence identity (96.7 %). The DNA-DNA hybridization value between strain SJ5A-1T and P. litoralis DSM 18986T was 36.7 %. The major respiratory quinone of strain SJ5A-1T is Q-10; it predominantly uses the fatty acids C18 : 1 (54.2 %), C18 : 0 (11.2 %), C16 : 0 (8.6 %), 11-methyl C18 : 1ω7c (7.7 %), C19 : 0cyclo ω8c (3.3 %), and C12 : 1 3-OH (3.5 %), and its major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, phosphocholine, an unknown aminolipid, an unknown phospholipid and two unknown lipids. The genome draft of strain SJ5A-1T as presented here is 4 562 830 bp in size and the DNA G+C content is 68.0 mol %. Based on phenotypic, phylogenetic and genotypic data, strain SJ5A-1T represents a novel species in the genus Ponticoccus, for which we propose the name Ponticoccus marisrubri sp. nov. The type strain of P. marisrubri is SJ5A-1T (=JCM 19520T=ACCC19863T).

  • Article

    Genomic Characterization of Two Novel SAR11 Isolates From the Red Sea, Including the First Strain of the SAR11 Ib clade

    (Oxford University Press (OUP), 2017-06-22) Jimenez Infante, Francy M.; Ngugi, David; Vinu, Manikandan; Blom, Jochen; Alam, Intikhab; Bajic, Vladimir B.; Stingl, Ulrich; Red Sea Research Center (RSRC); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Bioscience Program; Marine Science Program; Applied Mathematics and Computational Science Program; Office of the VP; Biological and Environmental Sciences and Engineering (BESE) Division; Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany; University of Florida, UF/IFAS, Department for Microbiology and Cell Science, Fort Lauderdale Research and Education Center, Davie, FL 33314, USA

    The SAR11 clade (Pelagibacterales) is a diverse group that forms a monophyletic clade within the Alphaproteobacteria, and constitutes up to one third of all prokaryotic cells in the photic zone of most oceans. Pelagibacterales are very abundant in the warm and highly saline surface waters of the Red Sea, raising the question of adaptive traits of SAR11 populations in this water body and warmer oceans through the world. In this study, two pure cultures were successfully obtained from surface waters on the Red Sea, one isolate of subgroup Ia and one of the previously uncultured SAR11 Ib lineage. The novel genomes were very similar to each other and to genomes of isolates of SAR11 subgroup Ia (Ia pan-genome), both in terms of gene content and synteny. Among the genes that were not present in the Ia pan-genome, 108 (RS39, Ia) and 151 genes (RS40, Ib) were strain-specific. Detailed analyses showed that only 51 (RS39, Ia) and 55 (RS40, Ib) of these strain-specific genes had not reported before on genome fragments of Pelagibacterales. Further analyses revealed the potential production of phosphonates by some SAR11 members and possible adaptations for oligotrophic life, including pentose sugar utilization and adhesion to marine particulate matter.