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1. Inter-comparison of marine microbiome sampling protocols

Author

Pascoal, Francisco, Tomasino, Maria Paola, Piredda, Roberta, Quero, Grazia Marina, Torgo, Luís, Poulain, Julie, Galand, Pierre E., Fuhrman, Jed A., Mitchell, Alex, Tinta, Tinkara, Turk Dermastia, Timotej, Fernandez-Guerra, Antonio, Vezzi, Alessandro, Logares, Ramiro, Malfatti, Francesca, Endo, Hisashi, Dąbrowska, Anna Maria, De Pascale, Fabio, Sánchez, Pablo, Henry, Nicolas, Fosso, Bruno, Wilson, Bryan, Toshchakov, Stephan, Ferrant, Gregory Kevin, Grigorov, Ivo, Vieira, Fabio Rocha Jimenez, Costa, Rodrigo, Pesant, Stéphane, and Magalhães, Catarina

Published
2023
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4. Inter-comparison of marine microbiome sampling protocols

Author

Agencia Estatal de Investigación (España), European Marine Research Network, Fundação para a Ciência e a Tecnologia (Portugal), Slovenian Research Agency, European Commission, Pascoal, Francisco, Tomasino, Maria Paola, Piredda, Roberta, Quero, Grazia Marina, Torgo, Luís, Poulain, Julie, Galand, Pierre E., Fuhrman, Jed A., Mitchell, Alex, Tinta, Tinkara, Turk Dermastia, Timotej, Fernández-Guerra, Antonio, Vezzi, Alessandro, Logares, Ramiro, Malfatti, Francesca, Endo, Hisashi, Dąbrowska, Anna Maria, De Pascale, Fabio, Sánchez Fernández, Pablo, Henry, Nicolas, Fosso, Bruno, Wilson, Brian, Toshchakov, Stepan V., Ferrant, Gregory Kevin, Grigorov, Ivo, Rocha Jimenez Vieira, Fabio, Costa, Rodrigo, Pesant, Stéphane, Magalhães, Catarina M., Agencia Estatal de Investigación (España), European Marine Research Network, Fundação para a Ciência e a Tecnologia (Portugal), Slovenian Research Agency, European Commission, Pascoal, Francisco, Tomasino, Maria Paola, Piredda, Roberta, Quero, Grazia Marina, Torgo, Luís, Poulain, Julie, Galand, Pierre E., Fuhrman, Jed A., Mitchell, Alex, Tinta, Tinkara, Turk Dermastia, Timotej, Fernández-Guerra, Antonio, Vezzi, Alessandro, Logares, Ramiro, Malfatti, Francesca, Endo, Hisashi, Dąbrowska, Anna Maria, De Pascale, Fabio, Sánchez Fernández, Pablo, Henry, Nicolas, Fosso, Bruno, Wilson, Brian, Toshchakov, Stepan V., Ferrant, Gregory Kevin, Grigorov, Ivo, Rocha Jimenez Vieira, Fabio, Costa, Rodrigo, Pesant, Stéphane, and Magalhães, Catarina M.

Abstract

Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d’Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22–3 µm, 3–20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and “whole water” (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume

Published
2023

5. EMOSE (2017) Inter-Comparison of Marine Plankton Metagenomic Analysis Methods

Author

Pesant, Stephane, Grigorov, Ivo, Malfatti, Francesca, Magalhães, Catarina, Vezzi, Alessandro, Poulain, Julie, Fuhrman, Jed, Mitchell, Alex, Polymenakou, Paraskevi, Fernandez-Guerra, Antonio, Sanchez, Pablo, Vieira, Fabio, Henry, Nicolas, Quero, Grazia, Fosso, Bruno, De Pascale, Fabio, Wilson, Bryan, Kubiszyn, Anna, Dermastia, Timotej, Tinta, Tinkara, Piredda, Roberta, Lauritano, Chiara, Logares, Ramiro, Galand, Pierre, Tomasino, Maria, Desai, Dhwani, FARRANT, Gregory, Endo, Hasashi, Toshchakov, Stepan, Thompson, Luke, Delmont, Tom, Gaonkar, Chetan, Casotti, Raffaella, Garcia-Vazquez, Eva, Sotelo, Carmen, Elbehery, Ali, Martin, Adria, Stankovic, David, Lavergne, Celine, Bour, Monia, Lutz, Holly, Rosales, Stephanie, Messaoudi, Chaimaa, Madduppa, Hawis, Soliman, Taha, Garcia-Maldonado, Jose, Siddiqui, Muhammad, Donnarumma, Vincenzo, Savage, Thomas, and Nyhus, Paul

Abstract

The scientific objective of the first Edition (2017) of EMOSE is to review methods in marine plankton metagenomic analysis, essentially comparing the different filtration, sequencing and analysis pipelines used by recent initiatives, i.e. Tara Oceans, Malaspina and the Ocean Sampling Day. Already published data from these projects will be complemented by a new set of data obtained from a comparative experiment of protocols used in the three initiatives. The bulk of the analyses will be done during a 5‐day hands‐on session in Porto, and a virtual research environment will be used to plan the analysis and to work‐up a review paper.

Published
2022
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8. Large-scale transposon mutagenesis of Photobacterium profundum SS9 reveals new genetic loci important for growth at low temperature and high pressure

Author

Lauro, Federico M., Tran, Khiem, Vezzi, Alessandro, Vitulo, Nicola, Valle, Giorgio, and Bartlett, Douglas H.

Subjects
Gram-negative bacteria -- Physiological aspects, Gram-negative bacteria -- Genetic aspects, Transposons -- Properties, Transposons -- Influence, Mutagenesis -- Research, Quantitative trait loci -- Properties, Quantitative trait loci -- Influence, Bacterial growth -- Genetic aspects, Biological sciences
Abstract

Microorganisms adapted to piezopsychrophilic growth dominate the majority of the biosphere that is at relatively constant low temperatures and high pressures, but the genetic bases for the adaptations are largely unknown. Here we report the use of transposon mutagenesis with the deep-sea bacterium Photobacterium profundum strain SS9 to isolate dozens of mutant strains whose growth is impaired at low temperature and/or whose growth is altered as a function of hydrostatic pressure. In many cases the gene mutation-growth phenotype relationship was verified by complementation analysis. The largest fraction of loci associated with temperature sensitivity were involved in the biosynthesis of the cell envelope, in particular the biosynthesis of extracellular polysaccharide. The largest fraction of loci associated with pressure sensitivity were involved in chromosomal structure and function. Genes for ribosome assembly and function were found to be important for both low-temperature and high-pressure growth. Likewise, both adaptation to temperature and adaptation to pressure were affected by mutations in a number of sensory and regulatory loci, suggesting the importance of signal transduction mechanisms in adaptation to either physical parameter. These analyses were the first global analyses of genes conditionally required for low-temperature or high-pressure growth in a deep-sea microorganism.

Published
2008

9. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla: the French-Italian public consortium for grapevine genome characterization

Author

Jaillon, Olivier, Aury, Jean-Marc, Noel, Benjamin, Policriti, Alberto, Clepet, Christian, Casagrande, Alberto, Choisne, Nathalie, Aubourg, Sebastien, Vitulo, Nicola, Jubin, Claire, Vezzi, Alessandro, Legeai, Fabrice, Hugueney, Philippe, Dasilva, Corinne, Horner, David, Mica, Erica, Jublot, Delphine, Poulain, Julie, Bruyere, Clemence, Billault, Alain, Segurens, Beatrice, Gouyvenoux, Michel, Ugarte, Edgardo, Cattonaro, Federica, Anthouard, Veronique, Vico, Virginie, Del Fabbro, Cristian, Alaux, Michael, Gaspero, Gabriele Di, Dumas, Vincent, Felice, Nicoletta, Paillard, Sophie, Juman, Irena, Moroldo, Marco, Scalabrin, Simone, Canaguier, Aurelie, Clainche, Isabelle Le, Malacrida, Giorgio, Durand, Eleonore, Pesole, Graziano, Laucou, Valerie, Chatelet, Philippe, Merdinoglu, Didier, Delledonne, Massimo, Pezzotti, Mario, Lecharny, Alain, Scarpelli, Claude, Artiguenave, Francois, Pe, M. Enrico, Valle, Giorgio, Morgante, Michele, Caboche, Michel, Adam-Blondon, Anne-Francoise, Weissenbach, Jean, Quetier, Francis, and Wincker, Patrick

Subjects
Grapes -- Genetic aspects, Genomes -- Identification and classification -- Genetic aspects, Angiosperms -- Natural history -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Identification and classification, Genetic aspects, Natural history
Abstract

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics [...]

Published
2007

11. A global gene evolution analysis on Vibrionaceae family using phylogenetic profile

Author

Vitulo Nicola, Vezzi Alessandro, Romualdi Chiara, Campanaro Stefano, and Valle Giorgio

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Vibrionaceae represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens. In this work we propose an improved phylogenetic profile analysis on 14 Vibrionaceae genomes, to study the evolution of this family on the basis of gene content. The phylogenetic profile is based on the observation that genes involved in the same process (e.g. metabolic pathway or structural complex) tend to be concurrently present or absent within different genomes. This allows the prediction of hypothetical functions on the basis of a shared phylogenetic profiles. Moreover this approach is useful to identify putative laterally transferred elements on the basis of their presence on distantly phylogenetically related bacteria. Results Vibrionaceae ORFs were aligned against all the available bacterial proteomes. Phylogenetic profile is defined as an array of distances, based on aminoacid substitution matrixes, from single genes to all their orthologues. Final phylogenetic profiles, derived from non-redundant list of all ORFs, was defined as the median of all the profiles belonging to the cluster. The resulting phylogenetic profiles matrix contains gene clusters on the rows and organisms on the columns. Cluster analysis identified groups of "core genes" with a widespread high similarity across all the organisms and several clusters that contain genes homologous only to a limited set of organisms. On each of these clusters, COG class enrichment has been calculated. The analysis reveals that clusters of core genes have the highest number of enriched classes, while the others are enriched just for few of them like DNA replication, recombination and repair. Conclusion We found that mobile elements have heterogeneous profiles not only across the entire set of organisms, but also within Vibrionaceae; this confirms their great influence on bacteria evolution even inside the same family. Furthermore, several hypothetical proteins highly correlate with mobile elements profiles suggesting a possible horizontal transfer mechanism for the evolution of these genes. Finally, we suggested the putative role of some ORFs having an unknown function on the basis of their phylogenetic profile similarity to well characterized genes.

Published
2007
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12. The tomato genome sequence provides insights into fleshy fruit evolution

Author

Sato, Shusei, Tabata, Satoshi, Hirakawa, Hideki, Asamizu, Erika, Shirasawa, Kenta, Isobe, Sachiko, Kaneko, Takakazu, Nakamura, Yasukazu, Shibata, Daisuke, Aoki, Koh, Egholm, Michael, Knight, James, Bogden, Robert, Li, Changbao, Shuang, Yang, Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Liu, Xin, Ren, Yuanyuan, Wang, Jun, Albiero, Alessandro, Dal Pero, Francesca, Todesco, Sara, Van Eck, Joyce, Buels, Robert M., Bombarely, Aureliano, Gosselin, Joseph R., Huang, Minyun, Leto, Jonathan A., Menda, Naama, Strickler, Susan, Mao, Linyong, Gao, Shan, Tecle, Isaak Y., York, Thomas, Zheng, Yi, Vrebalov, Julia T., Lee, JeMin, Zhong, Silin, Mueller, Lukas A., Stiekema, Willem J., Ribeca, Paolo, Alioto, Tyler, Yang, Wencai, Huang, Sanwen, Du, Yongchen, Zhang, Zhonghua, Gao, Jianchang, Guo, Yanmei, Wang, Xiaoxuan, Li, Ying, He, Jun, Li, Chuanyou, Cheng, Zhukuan, Zuo, Jianru, Ren, Jianfeng, Zhao, Jiuhai, Yan, Liuhua, Jiang, Hongling, Wang, Bao, Li, Hongshuang, Li, Zhenjun, Fu, Fuyou, Chen, Bingtang, Han, Bin, Feng, Qi, Fan, Danlin, Wang, Ying, Ling, Hongqing, Xue, Yongbiao, Ware, Doreen, Richard McCombie, W., Lippman, Zachary B., Chia, Jer-Ming, Jiang, Ke, Pasternak, Shiran, Gelley, Laura, Kramer, Melissa, Anderson, Lorinda K., Chang, Song-Bin, Royer, Suzanne M., Shearer, Lindsay A., Stack, Stephen M., Rose, Jocelyn K. C., Xu, Yimin, Eannetta, Nancy, Matas, Antonio J., McQuinn, Ryan, Tanksley, Steven D., Camara, Francisco, Guigó, Roderic, Rombauts, Stephane, Fawcett, Jeffrey, Van de Peer, Yves, Zamir, Dani, Liang, Chunbo, Spannagl, Manuel, Gundlach, Heidrun, Bruggmann, Remy, Mayer, Klaus, Jia, Zhiqi, Zhang, Junhong, Ye, Zhibiao, Bishop, Gerard J., Butcher, Sarah, Lopez-Cobollo, Rosa, Buchan, Daniel, Filippis, Ioannis, Abbott, James, Dixit, Rekha, Singh, Manju, Singh, Archana, Kumar Pal, Jitendra, Pandit, Awadhesh, Kumar Singh, Pradeep, Kumar Mahato, Ajay, Dogra, Vivek, Gaikwad, Kishor, Raj Sharma, Tilak, Mohapatra, Trilochan, Kumar Singh, Nagendra, Causse, Mathilde, Rothan, Christophe, Schiex, Thomas, Noirot, Céline, Bellec, Arnaud, Klopp, Christophe, Delalande, Corinne, Berges, Hélène, Mariette, Jérôme, Frasse, Pierre, Vautrin, Sonia, Zouine, Mohamed, Latché, Alain, Rousseau, Christine, Regad, Farid, Pech, Jean-Claude, Philippot, Murielle, Bouzayen, Mondher, Pericard, Pierre, Osorio, Sonia, Fernandez del Carmen, Asunción, Monforte, Antonio, Granell, Antonio, Fernandez-Muñoz, Rafael, Conte, Mariana, Lichtenstein, Gabriel, Carrari, Fernando, De Bellis, Gianluca, Fuligni, Fabio, Peano, Clelia, Grandillo, Silvana, Termolino, Pasquale, Pietrella, Marco, Fantini, Elio, Falcone, Giulia, Fiore, Alessia, Giuliano, Giovanni, Lopez, Loredana, Facella, Paolo, Perrotta, Gaetano, Daddiego, Loretta, Bryan, Glenn, Orozco, Modesto, Pastor, Xavier, Torrents, David, van Schriek, Marco G. M., Feron, Richard M.C., van Oeveren, Jan, de Heer, Peter, daPonte, Lorena, Jacobs-Oomen, Saskia, Cariaso, Mike, Prins, Marcel, van Eijk, Michiel J. T., Janssen, Antoine, van Haaren, Mark J. J., Jo, Sung-Hwan, Kim, Jungeun, Kwon, Suk-Yoon, Kim, Sangmi, Koo, Dal-Hoe, Lee, Sanghyeob, Hur, Cheol-Goo, Clouser, Christopher, Rico, Alain, Hallab, Asis, Gebhardt, Christiane, Klee, Kathrin, Jöcker, Anika, Warfsmann, Jens, Göbel, Ulrike, Kawamura, Shingo, Yano, Kentaro, Sherman, Jamie D., Fukuoka, Hiroyuki, Negoro, Satomi, Bhutty, Sarita, Chowdhury, Parul, Chattopadhyay, Debasis, Datema, Erwin, Smit, Sandra, Schijlen, Elio G. W. M., van de Belt, Jose, van Haarst, Jan C., Peters, Sander A., van Staveren, Marjo J., Henkens, Marleen H. C., Mooyman, Paul J. W., Hesselink, Thamara, van Ham, Roeland C. H. J., Jiang, Guoyong, Droege, Marcus, Choi, Doil, Kang, Byung-Cheol, Dong Kim, Byung, Park, Minkyu, Kim, Seungill, Yeom, Seon-In, Lee, Yong-Hwan, Choi, Yang-Do, Li, Guangcun, Gao, Jianwei, Liu, Yongsheng, Huang, Shengxiong, Fernandez-Pedrosa, Victoria, Collado, Carmen, Zuñiga, Sheila, Wang, Guoping, Cade, Rebecca, Dietrich, Robert A., Rogers, Jane, Knapp, Sandra, Fei, Zhangjun, White, Ruth A., Thannhauser, Theodore W., Giovannoni, James J., Angel Botella, Miguel, Gilbert, Louise, Gonzalez, Ramon, Luis Goicoechea, Jose, Yu, Yeisoo, Kudrna, David, Collura, Kristi, Wissotski, Marina, Wing, Rod, Schoof, Heiko, Meyers, Blake C., Bala Gurazada, Aishwarya, Green, Pamela J., Mathur, Saloni, Vyas, Shailendra, Solanke, Amolkumar U., Kumar, Rahul, Gupta, Vikrant, Sharma, Arun K., Khurana, Paramjit, Khurana, Jitendra P., Tyagi, Akhilesh K., Dalmay, Tamas, Mohorianu, Irina, Walts, Brandon, Chamala, Srikar, Brad Barbazuk, W., Li, Jingping, Guo, Hui, Lee, Tae-Ho, Wang, Yupeng, Zhang, Dong, Paterson, Andrew H., Wang, Xiyin, Tang, Haibao, Barone, Amalia, Luisa Chiusano, Maria, Raffaella Ercolano, Maria, D’Agostino, Nunzio, Di Filippo, Miriam, Traini, Alessandra, Sanseverino, Walter, Frusciante, Luigi, Seymour, Graham B., Elharam, Mounir, Fu, Ying, Hua, Axin, Kenton, Steven, Lewis, Jennifer, Lin, Shaoping, Najar, Fares, Lai, Hongshing, Qin, Baifang, Qu, Chunmei, Shi, Ruihua, White, Douglas, White, James, Xing, Yanbo, Yang, Keqin, Yi, Jing, Yao, Ziyun, Zhou, Liping, Roe, Bruce A., Vezzi, Alessandro, D’Angelo, Michela, Zimbello, Rosanna, Schiavon, Riccardo, Caniato, Elisa, Rigobello, Chiara, Campagna, Davide, Vitulo, Nicola, Valle, Giorgio, Nelson, David R., De Paoli, Emanuele, Szinay, Dora, de Jong, Hans H., Bai, Yuling, Visser, Richard G. F., Klein Lankhorst, René M., Beasley, Helen, McLaren, Karen, Nicholson, Christine, Riddle, Claire, and Gianese, Giulio

Published
2012
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17. Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains

Author

Malacrida Giorgio, Cestaro Alessandro, Simonato Francesca, D'Angelo Michela, Lauro Federico M, Vitulo Nicola, Vezzi Alessandro, Campanaro Stefano, Bertoloni Giulio, Valle Giorgio, and Bartlett Douglas H

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure environments. Piezophilic (pressure-loving) organisms are adapted to deep-sea life and grow optimally at pressures higher than 0.1 MPa. To better understand high pressure adaptation from a genomic point of view three different Photobacterium profundum strains were compared. Using the sequenced piezophile P. profundum strain SS9 as a reference, microarray technology was used to identify the genomic regions missing in two other strains: a pressure adapted strain (named DSJ4) and a pressure-sensitive strain (named 3TCK). Finally, the transcriptome of SS9 grown under different pressure (28 MPa; 45 MPa) and temperature (4°C; 16°C) conditions was analyzed taking into consideration the differentially expressed genes belonging to the flexible gene pool. Results These studies indicated the presence of a large flexible gene pool in SS9 characterized by various horizontally acquired elements. This was verified by extensive analysis of GC content, codon usage and genomic signature of the SS9 genome. 171 open reading frames (ORFs) were found to be specifically absent or highly divergent in the piezosensitive strain, but present in the two piezophilic strains. Among these genes, six were found to also be up-regulated by high pressure. Conclusion These data provide information on horizontal gene flow in the deep sea, provide additional details of P. profundum genome expression patterns and suggest genes which could perform critical functions for abyssal survival, including perhaps high pressure growth.

Published
2005
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18. QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Author

Bertoldi, Loris, primary, Forcato, Claudio, additional, Vitulo, Nicola, additional, Birolo, Giovanni, additional, De Pascale, Fabio, additional, Feltrin, Erika, additional, Schiavon, Riccardo, additional, Anglani, Franca, additional, Negrisolo, Susanna, additional, Zanetti, Alessandra, additional, D’Avanzo, Francesca, additional, Tomanin, Rosella, additional, Faulkner, Georgine, additional, Vezzi, Alessandro, additional, and Valle, Giorgio, additional

Published
2017
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21. Genome-wide analysis of alternative splicing in grape

Author

Vitulo, Nicola, Forcato, Claudio, Corteggiani Carpinelli, E., Telatin, A., Campagna, Davide, D'Angelo, Michela, Zimbello, Rosanna, Corso, M., Vannozzi, Alessandro, Vezzi, Alessandro, Bonghi, Claudio, Lucchin, Margherita, and Valle, Giorgio

Published
2014

23. Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon

Author

Rosselli, Riccardo, primary, Romoli, Ottavia, additional, Vitulo, Nicola, additional, Vezzi, Alessandro, additional, Campanaro, Stefano, additional, de Pascale, Fabio, additional, Schiavon, Riccardo, additional, Tiarca, Maurizio, additional, Poletto, Fabio, additional, Concheri, Giuseppe, additional, Valle, Giorgio, additional, and Squartini, Andrea, additional

Published
2016
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25. The ocean sampling day consortium

Author

Kopf, Anna, Bicak, Mesude, Kottmann, Renzo, Schnetzer, Julia, Kostadinov, Ivaylo, Lehmann, Katja, Fernandez-guerra, Antonio, Jeanthon, Christian, Rahav, Eyal, Ullrich, Matthias, Wichels, Antje, Gerdts, Gunnar, Polymenakou, Paraskevi, Kotoulas, Giorgos, Siam, Rania, Abdallah, Rehab Z., Sonnenschein, Eva C., Cariou, Thierry, O'Gara, Fergal, Jackson, Stephen, Orlic, Sandi, Steinke, Michael, Busch, Julia, Duarte, Bernardo, Cacador, Isabel, Canning-clode, Joao, Bobrova, Oleksandra, Marteinsson, Viggo, Reynisson, Eyjolfur, Loureiro, Clara Magalhaes, Luna, Gian Marco, Quero, Grazia Marina, Loescher, Carolin R., Kremp, Anke, Delorenzo, Marie E., Ovreas, Lise, Tolman, Jennifer, Laroche, Julie, Penna, Antonella, Frischer, Marc, Davis, Timothy, Katherine, Barker, Meyer, Christopher P., Ramos, Sandra, Magalhaes, Catarina, Jude-lemeilleur, Florence, Leopoldina Aguirre-macedo, Ma, Wang, Shiao, Poulton, Nicole, Jones, Scott, Collin, Rachel, Fuhrman, Jed A., Conan, Pascal, Alonso, Cecilia, Stambler, Noga, Goodwin, Kelly, Yakimov, Michael M., Baltar, Federico, Bodrossy, Levente, Van De Kamp, Jodie, Frampton, Dion M. F., Ostrowski, Martin, Van Ruth, Paul, Malthouse, Paul, Claus, Simon, Deneudt, Klaas, Mortelmans, Jonas, Pitois, Sophie, Wallom, David, Salter, Ian, Costa, Rodrigo, Schroeder, Declan C., Kandil, Mahrous M., Amaral, Valentina, Biancalana, Florencia, Santana, Rafael, Pedrotti, Maria Luiza, Yoshida, Takashi, Ogata, Hiroyuki, Ingleton, Tim, Munnik, Kate, Rodriguez-ezpeleta, Naiara, Berteaux-lecellier, Veronique, Wecker, Patricia, Cancio, Ibon, Vaulot, Daniel, Bienhold, Christina, Ghazal, Hassan, Chaouni, Bouchra, Essayeh, Soumya, Ettamimi, Sara, Zaid, El Houcine, Boukhatem, Noureddine, Bouali, Abderrahim, Chahboune, Rajaa, Barrijal, Said, Timinouni, Mohammed, El Otmani, Fatima, Bennani, Mohamed, Mea, Marianna, Todorova, Nadezhda, Karamfilov, Ventzislav, Ten Hoopen, Petra, Cochrane, Guy, L'Haridon, Stephane, Bizsel, Kemal Can, Vezzi, Alessandro, Lauro, Federico M., Martin, Patrick, Jensen, Rachelle M., Hinks, Jamie, Gebbels, Susan, Rosselli, Riccardo, De Pascale, Fabio, Schiavon, Riccardo, Dos Santos, Antonina, Villar, Emilie, Pesant, Stephane, Cataletto, Bruno, Malfatti, Francesca, Edirisinghe, Ranjith, Silveira, Jorge A. Herrera, Barbier, Michele, Turk, Valentina, Tinta, Tinkara, Fuller, Wayne J., Salihoglu, Ilkay, Serakinci, Nedime, Ergoren, Mahmut Cerkez, Bresnan, Eileen, Iriberri, Juan, Nyhus, Paul Anders Fronth, Bente, Edvardsen, Karlsen, Hans Erik, Golyshin, Peter N., Gasol, Josep M., Moncheva, Snejana, Dzhembekova, Nina, Johnson, Zackary, Sinigalliano, Christopher David, Gidley, Maribeth Louise, Zingone, Adriana, Danovaro, Roberto, Tsiamis, George, Clark, Melody S., Costa, Ana Cristina, El Bour, Monia, Martins, Ana M., Collins, R. Eric, Ducluzeau, Anne-lise, Martinez, Jonathan, Costello, Mark J., Amaral-zettler, Linda A., Gilbert, Jack A., Davies, Neil, Field, Dawn, Gloeckner, Frank Oliver, Kopf, Anna, Bicak, Mesude, Kottmann, Renzo, Schnetzer, Julia, Kostadinov, Ivaylo, Lehmann, Katja, Fernandez-guerra, Antonio, Jeanthon, Christian, Rahav, Eyal, Ullrich, Matthias, Wichels, Antje, Gerdts, Gunnar, Polymenakou, Paraskevi, Kotoulas, Giorgos, Siam, Rania, Abdallah, Rehab Z., Sonnenschein, Eva C., Cariou, Thierry, O'Gara, Fergal, Jackson, Stephen, Orlic, Sandi, Steinke, Michael, Busch, Julia, Duarte, Bernardo, Cacador, Isabel, Canning-clode, Joao, Bobrova, Oleksandra, Marteinsson, Viggo, Reynisson, Eyjolfur, Loureiro, Clara Magalhaes, Luna, Gian Marco, Quero, Grazia Marina, Loescher, Carolin R., Kremp, Anke, Delorenzo, Marie E., Ovreas, Lise, Tolman, Jennifer, Laroche, Julie, Penna, Antonella, Frischer, Marc, Davis, Timothy, Katherine, Barker, Meyer, Christopher P., Ramos, Sandra, Magalhaes, Catarina, Jude-lemeilleur, Florence, Leopoldina Aguirre-macedo, Ma, Wang, Shiao, Poulton, Nicole, Jones, Scott, Collin, Rachel, Fuhrman, Jed A., Conan, Pascal, Alonso, Cecilia, Stambler, Noga, Goodwin, Kelly, Yakimov, Michael M., Baltar, Federico, Bodrossy, Levente, Van De Kamp, Jodie, Frampton, Dion M. F., Ostrowski, Martin, Van Ruth, Paul, Malthouse, Paul, Claus, Simon, Deneudt, Klaas, Mortelmans, Jonas, Pitois, Sophie, Wallom, David, Salter, Ian, Costa, Rodrigo, Schroeder, Declan C., Kandil, Mahrous M., Amaral, Valentina, Biancalana, Florencia, Santana, Rafael, Pedrotti, Maria Luiza, Yoshida, Takashi, Ogata, Hiroyuki, Ingleton, Tim, Munnik, Kate, Rodriguez-ezpeleta, Naiara, Berteaux-lecellier, Veronique, Wecker, Patricia, Cancio, Ibon, Vaulot, Daniel, Bienhold, Christina, Ghazal, Hassan, Chaouni, Bouchra, Essayeh, Soumya, Ettamimi, Sara, Zaid, El Houcine, Boukhatem, Noureddine, Bouali, Abderrahim, Chahboune, Rajaa, Barrijal, Said, Timinouni, Mohammed, El Otmani, Fatima, Bennani, Mohamed, Mea, Marianna, Todorova, Nadezhda, Karamfilov, Ventzislav, Ten Hoopen, Petra, Cochrane, Guy, L'Haridon, Stephane, Bizsel, Kemal Can, Vezzi, Alessandro, Lauro, Federico M., Martin, Patrick, Jensen, Rachelle M., Hinks, Jamie, Gebbels, Susan, Rosselli, Riccardo, De Pascale, Fabio, Schiavon, Riccardo, Dos Santos, Antonina, Villar, Emilie, Pesant, Stephane, Cataletto, Bruno, Malfatti, Francesca, Edirisinghe, Ranjith, Silveira, Jorge A. Herrera, Barbier, Michele, Turk, Valentina, Tinta, Tinkara, Fuller, Wayne J., Salihoglu, Ilkay, Serakinci, Nedime, Ergoren, Mahmut Cerkez, Bresnan, Eileen, Iriberri, Juan, Nyhus, Paul Anders Fronth, Bente, Edvardsen, Karlsen, Hans Erik, Golyshin, Peter N., Gasol, Josep M., Moncheva, Snejana, Dzhembekova, Nina, Johnson, Zackary, Sinigalliano, Christopher David, Gidley, Maribeth Louise, Zingone, Adriana, Danovaro, Roberto, Tsiamis, George, Clark, Melody S., Costa, Ana Cristina, El Bour, Monia, Martins, Ana M., Collins, R. Eric, Ducluzeau, Anne-lise, Martinez, Jonathan, Costello, Mark J., Amaral-zettler, Linda A., Gilbert, Jack A., Davies, Neil, Field, Dawn, and Gloeckner, Frank Oliver

Abstract

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Published
2015
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28. The ocean sampling day consortium

Author

Kopf, Anna, primary, Bicak, Mesude, additional, Kottmann, Renzo, additional, Schnetzer, Julia, additional, Kostadinov, Ivaylo, additional, Lehmann, Katja, additional, Fernandez-Guerra, Antonio, additional, Jeanthon, Christian, additional, Rahav, Eyal, additional, Ullrich, Matthias, additional, Wichels, Antje, additional, Gerdts, Gunnar, additional, Polymenakou, Paraskevi, additional, Kotoulas, Giorgos, additional, Siam, Rania, additional, Abdallah, Rehab Z, additional, Sonnenschein, Eva C, additional, Cariou, Thierry, additional, O’Gara, Fergal, additional, Jackson, Stephen, additional, Orlic, Sandi, additional, Steinke, Michael, additional, Busch, Julia, additional, Duarte, Bernardo, additional, Caçador, Isabel, additional, Canning-Clode, João, additional, Bobrova, Oleksandra, additional, Marteinsson, Viggo, additional, Reynisson, Eyjolfur, additional, Loureiro, Clara Magalhães, additional, Luna, Gian Marco, additional, Quero, Grazia Marina, additional, Löscher, Carolin R, additional, Kremp, Anke, additional, DeLorenzo, Marie E, additional, Øvreås, Lise, additional, Tolman, Jennifer, additional, LaRoche, Julie, additional, Penna, Antonella, additional, Frischer, Marc, additional, Davis, Timothy, additional, Katherine, Barker, additional, Meyer, Christopher P, additional, Ramos, Sandra, additional, Magalhães, Catarina, additional, Jude-Lemeilleur, Florence, additional, Aguirre-Macedo, Ma Leopoldina, additional, Wang, Shiao, additional, Poulton, Nicole, additional, Jones, Scott, additional, Collin, Rachel, additional, Fuhrman, Jed A, additional, Conan, Pascal, additional, Alonso, Cecilia, additional, Stambler, Noga, additional, Goodwin, Kelly, additional, Yakimov, Michael M, additional, Baltar, Federico, additional, Bodrossy, Levente, additional, Van De Kamp, Jodie, additional, Frampton, Dion MF, additional, Ostrowski, Martin, additional, Van Ruth, Paul, additional, Malthouse, Paul, additional, Claus, Simon, additional, Deneudt, Klaas, additional, Mortelmans, Jonas, additional, Pitois, Sophie, additional, Wallom, David, additional, Salter, Ian, additional, Costa, Rodrigo, additional, Schroeder, Declan C, additional, Kandil, Mahrous M, additional, Amaral, Valentina, additional, Biancalana, Florencia, additional, Santana, Rafael, additional, Pedrotti, Maria Luiza, additional, Yoshida, Takashi, additional, Ogata, Hiroyuki, additional, Ingleton, Tim, additional, Munnik, Kate, additional, Rodriguez-Ezpeleta, Naiara, additional, Berteaux-Lecellier, Veronique, additional, Wecker, Patricia, additional, Cancio, Ibon, additional, Vaulot, Daniel, additional, Bienhold, Christina, additional, Ghazal, Hassan, additional, Chaouni, Bouchra, additional, Essayeh, Soumya, additional, Ettamimi, Sara, additional, Zaid, El Houcine, additional, Boukhatem, Noureddine, additional, Bouali, Abderrahim, additional, Chahboune, Rajaa, additional, Barrijal, Said, additional, Timinouni, Mohammed, additional, El Otmani, Fatima, additional, Bennani, Mohamed, additional, Mea, Marianna, additional, Todorova, Nadezhda, additional, Karamfilov, Ventzislav, additional, ten Hoopen, Petra, additional, Cochrane, Guy, additional, L’Haridon, Stephane, additional, Bizsel, Kemal Can, additional, Vezzi, Alessandro, additional, Lauro, Federico M, additional, Martin, Patrick, additional, Jensen, Rachelle M, additional, Hinks, Jamie, additional, Gebbels, Susan, additional, Rosselli, Riccardo, additional, De Pascale, Fabio, additional, Schiavon, Riccardo, additional, dos Santos, Antonina, additional, Villar, Emilie, additional, Pesant, Stéphane, additional, Cataletto, Bruno, additional, Malfatti, Francesca, additional, Edirisinghe, Ranjith, additional, Silveira, Jorge A Herrera, additional, Barbier, Michele, additional, Turk, Valentina, additional, Tinta, Tinkara, additional, Fuller, Wayne J, additional, Salihoglu, Ilkay, additional, Serakinci, Nedime, additional, Ergoren, Mahmut Cerkez, additional, Bresnan, Eileen, additional, Iriberri, Juan, additional, Nyhus, Paul Anders Fronth, additional, Bente, Edvardsen, additional, Karlsen, Hans Erik, additional, Golyshin, Peter N, additional, Gasol, Josep M, additional, Moncheva, Snejana, additional, Dzhembekova, Nina, additional, Johnson, Zackary, additional, Sinigalliano, Christopher David, additional, Gidley, Maribeth Louise, additional, Zingone, Adriana, additional, Danovaro, Roberto, additional, Tsiamis, George, additional, Clark, Melody S, additional, Costa, Ana Cristina, additional, El Bour, Monia, additional, Martins, Ana M, additional, Collins, R Eric, additional, Ducluzeau, Anne-Lise, additional, Martinez, Jonathan, additional, Costello, Mark J, additional, Amaral-Zettler, Linda A, additional, Gilbert, Jack A, additional, Davies, Neil, additional, Field, Dawn, additional, and Glöckner, Frank Oliver, additional

Published
2015
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29. A Snapshot of the Emerging Tomato Genome Sequence

Author

Mueller, LUKAS A., RENÉ KLEIN LANKHORST, Tanksley, STEVEN D., Giovannoni, JAMES J., Ruth, White, Julia, Vrebalov, Zhangjun, Fei, JOYCE VAN ECK, Robert, Buels, Mills, ADRI A., Naama, Menda, Tecle, ISAAK Y., Aureliano, Bombarely, Stephen, Stack, Royer, SUZANNE M., SONG BIN CHANG, Shearer, LINDSAY A., BYUNG DONG KIM, SUNG HWAN JO, CHEOL GOO HUR, Doil, Choi, CHANG BAO LI, Jiuhai, Zhao, Hongling, Jiang, Geng, Yu, Yuanyuan, Dai, Huajie, Fan, Jinfeng, Chen, Fei, Lu, Jinfeng, Shi, Shouhong, Sun, Jianjun, Chen, Xiaohua, Yang, Chen, Lu, Mingsheng, Chen, Zhukuan, Cheng, Chuanyou, Li, Hongqing, Ling, Yongbiao, Xue, Ying, Wang, Seymour, GRAHAM B., Bishop, GERARD J., Glenn, Bryan, Jane, Rogers, Sarah, Sims, Sarah, Butcher, Daniel, Buchan, James, Abbott, Helen, Beasley, Christine, Nicholson, Clare, Riddle, Sean, Humphray, Karen, Mclaren, Saloni, Mathur, Shailendra, Vyas, Solanke, AMOLKUMAR U., Rahul, Kumar, Vikrant, Gupta, Sharma, ARUN K., Paramjit, Khurana, Khurana, JITENDRA P., Akhilesh, Tyagi, Sarita, Parul, Chowdhury, Smriti, Shridhar, Debasis, Chattopadhyay, Awadhesh, Pandit, Pradeep, Singh, Ajay, Kumar, Rekha, Dixit, Archana, Singh, Sumera, Praveen, Vivek, Dalal, Mahavir, Yadav, IRFAN AHMAD GHAZI, Kishor, Gaikwad, TILAK RAJ SHARMA, Trilochan, Mohapatra, NAGENDRA KUMAR SINGH, Dóra, Szinay, HANS DE JONG, Sander, Peters, MARJO VAN STAVEREN, Erwin, Datema, Fiers, MARK W. E. J., VAN HAM, ROELAND C. H. J., Lindhout, P., Murielle, Philippot, Pierre, Frasse, Farid, Regad, Mohamed, Zouine, Mondher, Bouzayen, Erika, Asamizu, Shusei, Sato, Hiroyuki, Fukuoka, Satoshi, Tabata, Daisuke, Shibata, Botella, MIGUEL A., PEREZ ALONSO, M., FERNANDEZ PEDROSA, V., Sonia, Osorio, Amparo, Mico, Antonio, Granell, Zhonghua, Zhang, Jun, He, Sanwen, Huang, Yongchen, Du, Dongyu, Qu, Longfei, Liu, Dongyuan, Liu, Jun, Wang, Zhibiao, Ye, Wencai, Yang, Guoping, Wang, Vezzi, Alessandro, Sara, Todesco, Valle, Giorgio, Giulia, Falcone, Marco, Pietrella, Giovanni, Giuliano, Silvana, Grandillo, Alessandra, Traini, Nunzio, D'Agostino, MARIA LUISA CHIUSANO, Mara, Ercolano, Amalia, Barone, Luigi, Frusciante, Heiko, Schoof, Anika, Jöcker, Rémy, Bruggmann, Manuel, Spannagl, Mayer, KLAUS X. F., Roderic, Guigó, Francisco, Camara, Stephane, Rombauts, Fawcett, JEFFREY A., YVES VAN DE PEER, Sandra, Knapp, and DANI ZAMIR AND WILLEM STIEKEMA

Published
2009

46. Prokaryotic Response to Phytodetritus-Derived Organic Material in Epi- and Mesopelagic Antarctic Waters

Author

Vincenzo Manna, Francesca Malfatti, Elisa Banchi, Federica Cerino, Fabio De Pascale, Annalisa Franzo, Riccardo Schiavon, Alessandro Vezzi, Paola Del Negro, Mauro Celussi, Manna, Vincenzo, Malfatti, Francesca, Banchi, Elisa, Cerino, Federica, De Pascale, Fabio, Franzo, Annalisa, Schiavon, Riccardo, Vezzi, Alessandro, Del Negro, Paola, and Celussi, Mauro

Subjects
Microbiology (medical), Chlorophyll a, Mesopelagic zone, Heterotroph, lcsh:QR1-502, Microbiology, lcsh:Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Total inorganic carbon, Phytoplankton, carbon cycle, 16S rRNA, extracellular enzymes, free-living, microbial community, particle-attached, particulate organic matter, Southern Ocean, Organic matter, Original Research, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Detritus, 030306 microbiology, Chemistry, fungi, Phytodetritus, extracellular enzyme, Environmental chemistry
Abstract

Particulate organic matter (POM) export represents the underlying principle of the biological carbon pump, driving the carbon flux from the sunlit to the dark ocean. The efficiency of this process is tightly linked to the prokaryotic community, as >70% of POM respiration is carried out by particle-associated prokaryotes. In the Ross Sea, one of the most productive areas of the Southern Ocean, up to 50% of the surface primary production is exported to the mesopelagic ocean as POM. Recent evidence suggests that a significant fraction of the POM in this area is composed of intact phytoplankton cells. During austral summer 2017, we set up bottle enrichment experiments in which we amended free-living surface and deep prokaryotic communities with organic matter pools generated from native microplankton, mimicking the particle export that may derive from mild (1 μg of Chlorophyll a L–1) and intense (10 μg of Chlorophyll a L–1) phytoplankton bloom. Over a course of 4 days, we followed free-living and particle-attached prokaryotes’ abundance, the degradation rates of polysaccharides, proteins and lipids, heterotrophic production as well as inorganic carbon utilization and prokaryotic community structure dynamics. Our results showed that several rare or undetected taxa in the initial community became dominant during the time course of the incubations and that different phytodetritus-derived organic matter sources induced specific changes in microbial communities, selecting for peculiar degradation and utilization processes spectra. Moreover, the features of the supplied detritus (in terms of microplankton taxa composition) determined different colonization dynamics and organic matter processing modes. Our study provides insights into the mechanisms underlying the prokaryotic utilization of phytodetritus, a significant pool of organic matter in the dark ocean.

Published
2020
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