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2. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

Author

Dorrell, Richard G, Kuo, Alan, Füssy, Zoltan, Richardson, Elisabeth H, Salamov, Asaf, Zarevski, Nikola, Freyria, Nastasia J, Ibarbalz, Federico M, Jenkins, Jerry, Karlusich, Juan Jose Pierella, Steindorff, Andrei Stecca, Edgar, Robyn E, Handley, Lori, Lail, Kathleen, Lipzen, Anna, Lombard, Vincent, McFarlane, John, Nef, Charlotte, Vanclová, Anna MG Novák, Peng, Yi, Plott, Chris, Potvin, Marianne, Vieira, Fabio Rocha Jimenez, Barry, Kerrie, de Vargas, Colomban, Henrissat, Bernard, Pelletier, Eric, Schmutz, Jeremy, Wincker, Patrick, Dacks, Joel B, Bowler, Chris, Grigoriev, Igor V, and Lovejoy, Connie

Subjects
Life Below Water, Gene Transfer, Horizontal, Microalgae, Arctic Regions, Oceans and Seas, Ice Cover, Bacteria
Abstract

Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.

Published
2023

3. Ocean-wide comparisons of mesopelagic planktonic community structures

Author

Rigonato, Janaina, Budinich, Marko, Murillo, Alejandro A., Brandão, Manoela C., Pierella Karlusich, Juan J., Soviadan, Yawouvi Dodji, Gregory, Ann C., Endo, Hisashi, Kokoszka, Florian, Vik, Dean, Henry, Nicolas, Frémont, Paul, Labadie, Karine, Zayed, Ahmed A., Dimier, Céline, Picheral, Marc, Searson, Sarah, Poulain, Julie, Kandels, Stefanie, Pesant, Stéphane, Karsenti, Eric, Bork, Peer, Bowler, Chris, de Vargas, Colomban, Eveillard, Damien, Gehlen, Marion, Iudicone, Daniele, Lombard, Fabien, Ogata, Hiroyuki, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Chaffron, Samuel, and Jaillon, Olivier

Published
2023
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4. Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean

Author

Reddy, Maggie M., Goossens, Corentine, Zhou, Yuxiang, Chaib, Slimane, Raviglione, Delphine, Nicolè, Florence, Hume, Benjamin C. C., Forcioli, Didier, Agostini, Sylvain, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, Michel, Furla, Paola, Galand, Pierre E., Gilson, Eric, Lombard, Fabien, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Voolstra, Christian R., Allemand, Denis, Planes, Serge, Thomas, Olivier P., and Banaigs, Bernard

Published
2023
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6. Different environmental response strategies in sympatric corals from Pacific Islands

Author

Porro, Barbara, Zamoum, Thamilla, Forcioli, Didier, Gilson, Eric, Poquet, Adrien, Di Franco, Eugenio, Barnay-Verdier, Stéphanie, Lombard, Fabien, Voolstra, Christian R., Hume, Benjamin C. C., Galand, Pierre E., Moulin, Clémentine, Boissin, Emilie, Bourdin, Guillaume, Iwankow, Guillaume, Poulain, Julie, Romac, Sarah, Agostini, Sylvain, Banaigs, Bernard, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Douville, Eric, Flores, Michel, Pesant, Stéphane, Reynaud, Stéphanie, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Troublé, Romain, Thurber, Rebecca Vega, Wincker, Patrick, Zoccola, Didier, Planes, Serge, Allemand, Denis, Röttinger, Eric, and Furla, Paola

Published
2023
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8. Differences in carbonate chemistry up-regulation of long-lived reef-building corals

Author

Canesi, Marine, Douville, Eric, Montagna, Paolo, Taviani, Marco, Stolarski, Jarosław, Bordier, Louise, Dapoigny, Arnaud, Coulibaly, Gninwoyo Eric Hermann, Simon, Anne-Catherine, Agelou, Mathieu, Fin, Jonathan, Metzl, Nicolas, Iwankow, Guillaume, Allemand, Denis, Planes, Serge, Moulin, Clémentine, Lombard, Fabien, Bourdin, Guillaume, Troublé, Romain, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Flores, Michel, Forcioli, Didier, Furla, Paola, Gilson, Eric, Galand, Pierre E., Pesant, Stéphane, Sunagawa, Shinichi, Thomas, Olivier P., Vega Thurber, Rebecca, Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, and Reynaud, Stéphanie

Published
2023
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13. Sea surface temperature reconstruction in the Pacific Ocean using multi-elemental proxy in Porites and Diploastrea corals: Application to Palau Archipelago

Author

Canesi, Marine, Douville, Eric, Montagna, Paolo, Bordier, Louise, Caquineau, Sandrine, Pons-Branchu, Edwige, Iwankow, Guillaume, Stolarski, Jarosław, Allemand, Denis, Planes, Serge, Moulin, Clémentine, Lombard, Fabien, Bourdin, Guillaume, Troublé, Romain, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bowler, Chris, de Vargas, Colomban, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Gilson, Eric, Galand, Pierre E., Pesant, Stéphane, Sunagawa, Shinichi, Thomas, Olivier P., Thurber, Rebecca Vega, Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, and Reynaud, Stéphanie

Published
2024
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14. Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics

Author

Armbrecht, Linda, Eisenhofer, Raphael, Utge, José, Sibert, Elizabeth C, Rocha, Fabio, Ward, Ryan, Pierella Karlusich, Juan José, Tirichine, Leila, Norris, Richard, Summers, Mindi, and Bowler, Chris

Subjects
Genetics
Abstract

Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.

Published
2021

15. Effects of Empagliflozin on Fluid Overload, Weight, and Blood Pressure in CKD

Author

Mayne, Kaitlin J., Staplin, Natalie, Keane, David F., Wanner, Christoph, Brenner, Susanne, Cejka, Vladimir, Stegbauer, Johannes, Judge, Parminder K., Preiss, David, Emberson, Jonathan, Trinca, Daniele, Dayanandan, Rejive, Lee, Ryonfa, Nolan, John, Omata, Akiko, Green, Jennifer B., Cherney, David Z.I., Hooi, Lai Seong, Pontremoli, Roberto, Tuttle, Katherine R., Lees, Jennifer S., Mark, Patrick B., Davies, Simon J., Hauske, Sibylle J., Steubl, Dominik, Brückmann, Martina, Landray, Martin J., Baigent, Colin, Haynes, Richard, Herrington, William G., Baigent, Colin, Landray, Martin J., Wanner, Christoph, Herrington, William G., Haynes, Richard, Green, Jennifer B., Hauske, Sibylle J., Brueckmann, Martina, Hopley, Mark, von-Eynatten, Maximillian, George, Jyothis, Brenner, Susanne, Cheung, Alfred K., Preiss, David, Liu, Zhi-Hong, Li, Jing, Hooi, Laiseong, Liu, Wen, Kadowaki, Takashi, Nangaku, Masaomi, Levin, Adeera, Cherney, David, Pontremoli, Roberto, Maggioni, Aldo P., Staplin, Natalie, Emberson, Jonathan, Hantel, Stefan, Goto, Shinya, Deo, Rajat, Tuttle, Katherine R., Hill, Michael, Judge, Parminder, Mayne, Kaitlin J., Ng, Sarah Y.A., Rossello, Xavier, Sammons, Emily, Zhu, Doreen, Sandercock, Peter, Bilous, Rudolf, Herzog, Charles, Whelton, Paul, Wittes, Janet, Bennett, Derrick, Achiri, Patricia, Ambrose, Chrissie, Badin, Cristina, Barton, Jill, Brown, Richard, Burke, Andy, Butler, Sebastian, Dayanandan, Rejive, Donaldson, Pia, Dykas, Robert, Fletcher, Lucy, Frederick, Kate, Kingston, Hannah, Gray, Mo, Harding, Emily, Hashimoto, Akiko, Howie, Lyn, Hurley, Susan, Lee, Ryonfa, Luker, Nik, Murphy, Kevin, Nakahara, Mariko, Nolan, John, Nunn, Michelle, Mulligan, Sorcha, Omata, Akiko, Pickworth, Sandra, Qiao, YanRu, Shah, Shraddha, Taylor, Karen, Timadjer, Alison, Willett, Monique, Wincott, Liz, Yan, Qin, Yu, Hui, Bowman, Louise, Chen, Fang, Clarke, Robert, Goonasekera, Michelle, Haynes, Richard, Herrington, William G., Judge, Parminder, Karsan, Waseem, Mafham, Marion, Mayne, Kaitlin J., Ng, Sarah Y. A., Preiss, David, Reith, Christina, Sammons, Emily, Zayed, Mohammed, Zhu, Doreen, Ellison, Ritva, Moys, Rowan, Stevens, Will, Verdel, Kevin, Wallendszus, Karl, Bowler, Chris, Brewer, Anna, Measor, Andy, Cui, Guanguo, Daniels, Charles, Field, Angela, Goodenough, Bob, Lawson, Ashley, Mostefai, Youcef, Radhakrishnan, Dheeptha, Syed, Samee, Xia, Shuang, Adewuyi-Dalton, Ruth, Arnold, Thomas, Beneat, Anne-Marie, Bhatt, Anoushka, Bird, Chloe, Breach, Andrew, Brown, Laura, Caple, Mark, Chavagnon, Tatyana, Chung, Karen, Clark, Sarah, Condurache, Luminita, Eichstadt, Katarzyna, Obrero, Marta Espino, Forest, Scarlett, French, Helen, Goodwin, Nick, Gordon, Andrew, Gordon, Joanne, Guest, Cat, Harding, Tina, Hill, Michael, Hozak, Michal, Lacey, Matthew, MacLean, David, Messinger, Louise, Moffat, Stewart, Radley, Martin, Shenton, Claire, Tipper, Sarah, Tyler, Jon, Weaving, Lesley, Wheeler, James, Williams, Elissa, Williams, Tim, Woodhouse, Hamish, Chamberlain, Angela, Chambers, Jo, Davies, Joanne, Donaldson, Denise, Faria-Shayler, Pati, Fleming-Brown, Denise, Ingell, Jennifer, Knott, Carol, Liew, Anna, Lochhead, Helen, Meek, Juliette, Rodriguez-Bachiller, Isabel, Wilson, Andrea, Zettergren, Patrick, AitSadi, Rach, Barton, Ian, Baxter, Alex, Bu, Yonghong, Danel, Lukasz, Grotjahn, Sonja, Kurien, Rijo, Lay, Michael, Maskill, Archie, Murawska, Aleksandra, Raff, Rachel, Young, Allen, Baigent, Colin, Haynes, Richard, Herrington, William G., Landray, Martin J., Preiss, David, Emberson, Jonathan, Sardell, Rebecca, Staplin, Natalie, Wanner, Christoph, Brenner, Susanne, Cejka, Vladimir, Fajardo-Moser, Marcela, Hartner, Christian, Poehler, Doris, Renner, Janina, Scheidemantel, Franziska, Haynes, Richard, Preiss, David, Herrington, William G., Judge, Parminder, Zhu, Doreen, Ng, Sarah Y. A., Mayne, Kaitlin J., Badin, Cristina, Chambers, Jo, Davies, Joanne, Donaldson, Denise, Gray, Mo, Harding, Emily, Ingell, Jenny, Qiao, Yanru, Shah, Shraddha, Wilson, Andrea, Zettergren, Patrick, Wanner, Christoph, Brenner, Susanne, Cejka, Vladimir, Ghavampour, Sharang, Knoppe, Anja, Schmidt-Gurtler, Hans, Dumann, Hubert, Merscher, Sybille, Patecki, Margret, Schlieper, Georg Rainer, Torp, Anke, Weber, Bianca, Zietz, Maja, Sitter, Thomas, Fuessl, Louise, Krappe, Julia, Loutan, Jerome, Vielhauer, Volker, Andriaccio, Luciano, Maurer, Magdalena, Winkelmann, Bernhard, Dursch, Martin, Seifert, Linda, Tenbusch, Linda, Weinmann-Menke, Julia, Boedecker, Simone, KaluzaSchilling, Wiebke, Kraus, Daniel, Krieger, Carina, Schmude, Margit, Schreiber, Anne, Eckrich, Ewelina, Tschope, Diethelm, Arbi, Abdulwahab, Lee-Barkey, Young, Stratmann, Bernd, Prib, Natalie, Rolfsmeier, Sina, Schneider, Irina, Rump, Lars, Stegbauer, Johannes, Pötz, Christine, Schemmelmann, Mara, Schmidt, Claudia, Haller, Hermann, Kaufeld, Jessica, Menne, Jan, Bahlmann-Kroll, Elisabeth, Bergner, Angela, Haynes, Richard, Herrington, William G., Zhu, Doreen, Gavrila, Madita, Lafferty, Kathryn, Rabara, Ria, Ruse, Sally, Weetman, Maria, Byrne, Cath, Jesky, Mark, Cowley, Alison, McHaffie, Emma, Waterfall, Holly, Taylor, Jo, Bough, Laura, Phillips, Thomas, Goodwin, Barbara Winter-, Frankel, Andrew, Tomlinson, James, Alegata, Marlon, Almasarwah, Rashid, Apostolidi, Anthoula, Vourvou, Maria, Walters, Thomas, Ugni, Shiva, Gunda, Smita, Oluyombo, Rotimi, Brindle, Vicki, Coutts, Ping, Fuller, Tracy, Nadar, Evelyn, Wong, Christopher, Goldsmith, Christopher, Barnes, Sherald, Bennett, Ann, Burston, Claire, Hope, Samantha, Hunt, Nicola, Kurian, Lini, Fish, Richard, Farrugia, Daniela, Lee, Judy, Sadler, Emma, Turner, Hannah, Clarke, Helen, Carnall, Victoria, Benyon, Sarah, Blake, Caroline, Estcourt, Stephanie, Piper, Jane, Morgan, Neal, Hutchinson, Carolyn, McKinley, Teresa, Doulton, Tim, Delaney, Michael, Montasser, Mahmoud, Hansen, Jenny, Loader, David, Moon, Angela, Morris, Frances, Fraser, Donald, Ali, Mohammad Alhadj, Griffin, Sian, Latif, Farah, Witczak, Justyna, Wonnacott, Alexa, Jeffers, Lynda, Webley, Yvette, Bell, Samira, Cosgrove, Leanne, Craik, Rachel, Murray, Shona, Khwaja, Arif, Jackson, Yvonne, Mbuyisa, Angeline, Sellars, Rachel, Lewington, Andrew, Baker, Richard, Dorey, Suzannah, Tobin, Kay, Wheatley, Rosalyn, Patel, Rajan, Mark, Patrick, Rankin, Alastair, Sullivan, Michael, Forsyth, Kirsty, and McDougall, Rowan

Published
2024
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17. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA

Author

Kjær, Kurt H., Winther Pedersen, Mikkel, De Sanctis, Bianca, De Cahsan, Binia, Korneliussen, Thorfinn S., Michelsen, Christian S., Sand, Karina K., Jelavić, Stanislav, Ruter, Anthony H., Schmidt, Astrid M. A., Kjeldsen, Kristian K., Tesakov, Alexey S., Snowball, Ian, Gosse, John C., Alsos, Inger G., Wang, Yucheng, Dockter, Christoph, Rasmussen, Magnus, Jørgensen, Morten E., Skadhauge, Birgitte, Prohaska, Ana, Kristensen, Jeppe Å., Bjerager, Morten, Allentoft, Morten E., Coissac, Eric, Rouillard, Alexandra, Simakova, Alexandra, Fernandez-Guerra, Antonio, Bowler, Chris, Macias-Fauria, Marc, Vinner, Lasse, Welch, John J., Hidy, Alan J., Sikora, Martin, Collins, Matthew J., Durbin, Richard, Larsen, Nicolaj K., and Willerslev, Eske

Published
2022
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18. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities.

Author

Acinas, Silvia G, Sánchez, Pablo, Salazar, Guillem, Cornejo-Castillo, Francisco M, Sebastián, Marta, Logares, Ramiro, Royo-Llonch, Marta, Paoli, Lucas, Sunagawa, Shinichi, Hingamp, Pascal, Ogata, Hiroyuki, Lima-Mendez, Gipsi, Roux, Simon, González, José M, Arrieta, Jesús M, Alam, Intikhab S, Kamau, Allan, Bowler, Chris, Raes, Jeroen, Pesant, Stéphane, Bork, Peer, Agustí, Susana, Gojobori, Takashi, Vaqué, Dolors, Sullivan, Matthew B, Pedrós-Alió, Carlos, Massana, Ramon, Duarte, Carlos M, and Gasol, Josep M

Subjects
Bacteria, DNA, Bacterial, Seawater, Photosynthesis, Metagenome, Carbon Cycle
Abstract

The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

Published
2021

20. Strengthening global-change science by integrating aeDNA with paleoecoinformatics

Author

Alsos, Inger Greve, Bowler, Chris, Coolen, Marco J.L., Cullen, Nicola, Crump, Sarah, Epp, Laura Saskia, Fernandez-Guerra, Antonio, Grimm, Eric, Herzschuh, Ulrike, Mereghetti, Alessandro, Meyer, Rachel Sarah, Nota, Kevin, Pedersen, Mikkel Winther, Pérez, Vilma, Shapiro, Beth, Stoof-Leichsenring, Kathleen R., Wood, Jamie, Williams, John W., Spanbauer, Trisha L., Heintzman, Peter D., Blois, Jessica, Capo, Eric, Goring, Simon J., Monchamp, Marie-Eve, Parducci, Laura, and Von Eggers, Jordan M.

Published
2023
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21. Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid

Author

Dorrell, Richard G, primary, Zhang, Youjun, additional, Liang, Yue, additional, Gueguen, Nolwenn, additional, Nonoyama, Tomomi, additional, Croteau, Dany, additional, Penot, Mathias, additional, Adiba, Sandrine, additional, Bailleul, Benjamin, additional, Gros, Valérie, additional, Pierella Karlusich, Juan José, additional, Zweig, Nathanaël, additional, Fernie, Alisdair R, additional, Jouhet, Juliette, additional, Maréchal, Eric, additional, and Bowler, Chris, additional

Published
2024
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22. Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

Author

Teano, Gianluca, Concia, Lorenzo, Wolff, Léa, Carron, Léopold, Biocanin, Ivona, Adamusová, Kateřina, Fojtová, Miloslava, Bourge, Michael, Kramdi, Amira, Colot, Vincent, Grossniklaus, Ueli, Bowler, Chris, Baroux, Célia, Carbone, Alessandra, Probst, Aline V., Schrumpfová, Petra Procházková, Fajkus, Jiří, Amiard, Simon, Grob, Stefan, Bourbousse, Clara, and Barneche, Fredy

Published
2023
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24. Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

Faktorová, Drahomíra, Nisbet, R Ellen R, Fernández Robledo, José A, Casacuberta, Elena, Sudek, Lisa, Allen, Andrew E, Ares, Manuel, Aresté, Cristina, Balestreri, Cecilia, Barbrook, Adrian C, Beardslee, Patrick, Bender, Sara, Booth, David S, Bouget, François-Yves, Bowler, Chris, Breglia, Susana A, Brownlee, Colin, Burger, Gertraud, Cerutti, Heriberto, Cesaroni, Rachele, Chiurillo, Miguel A, Clemente, Thomas, Coles, Duncan B, Collier, Jackie L, Cooney, Elizabeth C, Coyne, Kathryn, Docampo, Roberto, Dupont, Christopher L, Edgcomb, Virginia, Einarsson, Elin, Elustondo, Pía A, Federici, Fernan, Freire-Beneitez, Veronica, Freyria, Nastasia J, Fukuda, Kodai, García, Paulo A, Girguis, Peter R, Gomaa, Fatma, Gornik, Sebastian G, Guo, Jian, Hampl, Vladimír, Hanawa, Yutaka, Haro-Contreras, Esteban R, Hehenberger, Elisabeth, Highfield, Andrea, Hirakawa, Yoshihisa, Hopes, Amanda, Howe, Christopher J, Hu, Ian, Ibañez, Jorge, Irwin, Nicholas AT, Ishii, Yuu, Janowicz, Natalia Ewa, Jones, Adam C, Kachale, Ambar, Fujimura-Kamada, Konomi, Kaur, Binnypreet, Kaye, Jonathan Z, Kazana, Eleanna, Keeling, Patrick J, King, Nicole, Klobutcher, Lawrence A, Lander, Noelia, Lassadi, Imen, Li, Zhuhong, Lin, Senjie, Lozano, Jean-Claude, Luan, Fulei, Maruyama, Shinichiro, Matute, Tamara, Miceli, Cristina, Minagawa, Jun, Moosburner, Mark, Najle, Sebastián R, Nanjappa, Deepak, Nimmo, Isabel C, Noble, Luke, Novák Vanclová, Anna MG, Nowacki, Mariusz, Nuñez, Isaac, Pain, Arnab, Piersanti, Angela, Pucciarelli, Sandra, Pyrih, Jan, Rest, Joshua S, Rius, Mariana, Robertson, Deborah, Ruaud, Albane, Ruiz-Trillo, Iñaki, Sigg, Monika A, Silver, Pamela A, Slamovits, Claudio H, Jason Smith, G, Sprecher, Brittany N, Stern, Rowena, Swart, Estienne C, Tsaousis, Anastasios D, Tsypin, Lev, Turkewitz, Aaron, and Turnšek, Jernej

Subjects
Genetics, Biotechnology, Life Below Water, Biodiversity, DNA, Ecosystem, Environment, Eukaryota, Green Fluorescent Proteins, Marine Biology, Models, Biological, Species Specificity, Transformation, Genetic, Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

Published
2020

25. Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

Faktorová, Drahomíra, Nisbet, R Ellen R, Fernández Robledo, José A, Casacuberta, Elena, Sudek, Lisa, Allen, Andrew E, Ares, Manuel, Aresté, Cristina, Balestreri, Cecilia, Barbrook, Adrian C, Beardslee, Patrick, Bender, Sara, Booth, David S, Bouget, François-Yves, Bowler, Chris, Breglia, Susana A, Brownlee, Colin, Burger, Gertraud, Cerutti, Heriberto, Cesaroni, Rachele, Chiurillo, Miguel A, Clemente, Thomas, Coles, Duncan B, Collier, Jackie L, Cooney, Elizabeth C, Coyne, Kathryn, Docampo, Roberto, Dupont, Christopher L, Edgcomb, Virginia, Einarsson, Elin, Elustondo, Pía A, Federici, Fernan, Freire-Beneitez, Veronica, Freyria, Nastasia J, Fukuda, Kodai, García, Paulo A, Girguis, Peter R, Gomaa, Fatma, Gornik, Sebastian G, Guo, Jian, Hampl, Vladimír, Hanawa, Yutaka, Haro-Contreras, Esteban R, Hehenberger, Elisabeth, Highfield, Andrea, Hirakawa, Yoshihisa, Hopes, Amanda, Howe, Christopher J, Hu, Ian, Ibañez, Jorge, Irwin, Nicholas AT, Ishii, Yuu, Janowicz, Natalia Ewa, Jones, Adam C, Kachale, Ambar, Fujimura-Kamada, Konomi, Kaur, Binnypreet, Kaye, Jonathan Z, Kazana, Eleanna, Keeling, Patrick J, King, Nicole, Klobutcher, Lawrence A, Lander, Noelia, Lassadi, Imen, Li, Zhuhong, Lin, Senjie, Lozano, Jean-Claude, Luan, Fulei, Maruyama, Shinichiro, Matute, Tamara, Miceli, Cristina, Minagawa, Jun, Moosburner, Mark, Najle, Sebastián R, Nanjappa, Deepak, Nimmo, Isabel C, Noble, Luke, Novák Vanclová, Anna MG, Nowacki, Mariusz, Nuñez, Isaac, Pain, Arnab, Piersanti, Angela, Pucciarelli, Sandra, Pyrih, Jan, Rest, Joshua S, Rius, Mariana, Robertson, Deborah, Ruaud, Albane, Ruiz-Trillo, Iñaki, Sigg, Monika A, Silver, Pamela A, Slamovits, Claudio H, Jason Smith, G, Sprecher, Brittany N, Stern, Rowena, Swart, Estienne C, Tsaousis, Anastasios D, Tsypin, Lev, Turkewitz, Aaron, and Turnšek, Jernej

Subjects
Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

28. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Author

Salazar, Guillem, Paoli, Lucas, Alberti, Adriana, Huerta-Cepas, Jaime, Ruscheweyh, Hans-Joachim, Cuenca, Miguelangel, Field, Christopher M, Coelho, Luis Pedro, Cruaud, Corinne, Engelen, Stefan, Gregory, Ann C, Labadie, Karine, Marec, Claudie, Pelletier, Eric, Royo-Llonch, Marta, Roux, Simon, Sánchez, Pablo, Uehara, Hideya, Zayed, Ahmed A, Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels, Stefanie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Coordinators, Tara Oceans, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stephane, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, and Wincker, Patrick

Subjects
Genetics, Climate Action, Gene Expression Regulation, Geography, Metagenome, Microbiota, Molecular Sequence Annotation, Oceans and Seas, RNA, Messenger, Seawater, Temperature, Transcriptome, Tara Oceans Coordinators, Tara Oceans, biogeochemistry, community turnover, eco-systems biology, gene expression change, global ocean microbiome, metagenome, metatranscriptome, microbial ecology, ocean warming, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.

Published
2019

30. Biosynthetic potential of the global ocean microbiome

Author

Paoli, Lucas, Ruscheweyh, Hans-Joachim, Forneris, Clarissa C., Hubrich, Florian, Kautsar, Satria, Bhushan, Agneya, Lotti, Alessandro, Clayssen, Quentin, Salazar, Guillem, Milanese, Alessio, Carlström, Charlotte I., Papadopoulou, Chrysa, Gehrig, Daniel, Karasikov, Mikhail, Mustafa, Harun, Larralde, Martin, Carroll, Laura M., Sánchez, Pablo, Zayed, Ahmed A., Cronin, Dylan R., Acinas, Silvia G., Bork, Peer, Bowler, Chris, Delmont, Tom O., Gasol, Josep M., Gossert, Alvar D., Kahles, André, Sullivan, Matthew B., Wincker, Patrick, Zeller, Georg, Robinson, Serina L., Piel, Jörn, and Sunagawa, Shinichi

Published
2022
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32. An evolution towards scientific consensus for a sustainable ocean future

Author

Gaill, Françoise, Brodie Rudolph, Tanya, Lebleu, Lara, Allemand, Denis, Blasiak, Robert, Cheung, William W. L., Claudet, Joachim, Gerhardinger, Leopoldo Cavaleri, Le Bris, Nadine, Levin, Lisa, Pörtner, Hans- Otto, Visbeck, Martin, Zivian, Anna, Bahurel, Pierre, Bopp, Laurent, Bowler, Chris, Chlous, Frédérique, Cury, Philippe, Gascuel, Didier, Goyet, Sylvie, Hilmi, Nathalie, Ménard, Frédéric, Micheli, Fiorenza, Mullineaux, Lauren, Parmentier, Rémi, Sicre, Marie-Alexandrine, Speich, Sabrina, Thébaud, Olivier, Thiele, Torsten, Bowler, Martha, Charvis, Philippe, Cuvelier, Raphael, Houllier, François, Palazot, Sarah, Staub, Francis, and Poivre d’Arvor, Olivier

Published
2022
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34. Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Author

Gregory, Ann C, Zayed, Ahmed A, Conceição-Neto, Nádia, Temperton, Ben, Bolduc, Ben, Alberti, Adriana, Ardyna, Mathieu, Arkhipova, Ksenia, Carmichael, Margaux, Cruaud, Corinne, Dimier, Céline, Domínguez-Huerta, Guillermo, Ferland, Joannie, Kandels, Stefanie, Liu, Yunxiao, Marec, Claudie, Pesant, Stéphane, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tremblay, Jean-Éric, Vik, Dean, Coordinators, Tara Oceans, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels-Lewis, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Culley, Alexander I, Dutilh, Bas E, and Roux, Simon

Subjects
Genetics, Infection, Life Below Water, Aquatic Organisms, Biodiversity, DNA Viruses, DNA, Viral, Metagenome, Water Microbiology, Tara Oceans Coordinators, community ecology, diversity gradients, marine biology, metagenomics, population ecology, species, viruses, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.

Published
2019

35. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author

Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J, Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R, Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B, Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Kandels‐Lewis, Stefanie, Searson, Sarah, Dimier, Céline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, Vargas, Colomban, Follows, Michael J, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, d'Alcalà, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, and Jaillon, Olivier

Subjects
Genetics, Life Below Water, Atmospheric Sciences, Geochemistry, Oceanography, Meteorology & Atmospheric Sciences
Abstract

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment.

Published
2019

36. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Author

Sunagawa, Shinichi, Acinas, Silvia G., Bork, Peer, Karsenti, Eric, Bowler, Chris, Sardet, Christian, Stemmann, Lars, de Vargas, Colomban, Wincker, Patrick, Lescot, Magali, Babin, Marcel, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Jaillon, Olivier, Kandels, Stefanie, Iudicone, Daniele, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B., Not, Fabrice, Lee, Karp-Boss, Boss, Emmanuel, Cochrane, Guy, Follows, Michael, Poulton, Nicole, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Frémont, Paul, Vanni, Chiara, Fernandez-Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, and Pelletier, Eric

Published
2022
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37. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

Author

Royo-Llonch, Marta, Sánchez, Pablo, Ruiz-González, Clara, Salazar, Guillem, Pedrós-Alió, Carlos, Sebastián, Marta, Labadie, Karine, Paoli, Lucas, M. Ibarbalz, Federico, Zinger, Lucie, Churcheward, Benjamin, Chaffron, Samuel, Eveillard, Damien, Karsenti, Eric, Sunagawa, Shinichi, Wincker, Patrick, Karp-Boss, Lee, Bowler, Chris, and Acinas, Silvia G.

Published
2021
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40. List of contributors

Author

Al-Kandari, Manal, primary, Allen, Andrew E., additional, Alves-de-Souza, Catharina, additional, Baird, Mark, additional, Berges, John A., additional, Bodrossy, Levente, additional, Bolch, Christopher J.S., additional, Bowler, Chris, additional, Bracher, Astrid, additional, Brewin, Robert J.W., additional, Burford, Michele A., additional, Campbell, Lisa, additional, Ciotti, Aurea M., additional, Clément, Alejandro, additional, Clementson, Lesley A., additional, Correa, Nicole, additional, Countway, Peter D., additional, Coyne, Kathryn J., additional, Craw, Pascal, additional, Dutkiewicz, Stephanie, additional, Gaonkar, Chetan C., additional, Garczarek, Laurence, additional, Gérikas Ribeiro, Catherine, additional, Greenlee, Sydney M., additional, Gutiérrez-Rodríguez, Andres, additional, Harke, Matthew J., additional, Henrichs, Darren W., additional, Hickman, Anna, additional, Highfield, Andrea, additional, Hirata, Takafumi, additional, Hook, Sharon E., additional, Ibarbalz, Federico M., additional, Kolody, Bethany C., additional, Kostadinov, Tihomir S., additional, Krock, Bernd, additional, Lopes dos Santos, Adriana, additional, Marcus, Lara, additional, Mardones, Jorge I., additional, McGregor, Glenn B., additional, Mongin, Mathieu, additional, Mouw, Colleen B., additional, Nagai, Satoshi, additional, Neilan, Brett A., additional, Nodder, Scott D., additional, Ong, Denise, additional, Organelli, Emanuele, additional, Paredes-Mella, Javier, additional, Richardson, Anthony, additional, Schroeder, Declan, additional, Sendall, Barbara C., additional, Shi, Xiao Li, additional, Silva, Sebastian, additional, Skerratt, Jennifer, additional, Smith, Matthew C., additional, Soja-Wozniak, Monika, additional, Stern, Rowena, additional, Steven, Andrew D.L., additional, Taylor, Alison R., additional, Thamatrakoln, Kimberlee, additional, Vaulot, Daniel, additional, Vezzulli, Luigi, additional, Vincent, Flora, additional, Von Dassow, Peter, additional, Wang, Yanfei, additional, Wild-Allen, Karen, additional, Willis, Anusuya, additional, Wood, Susanna A., additional, Woodhouse, Jason N., additional, Yarimizu, Kyoko, additional, and Young, Erica B., additional

Published
2022
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42. Hypometabolism to survive the long polar night and subsequent successful return to light in the diatom Fragilariopsis cylindrus

Author

Joli, Nathalie, primary, Concia, Lorenzo, additional, Mocaer, Karel, additional, Guterman, Julie, additional, Laude, Juliette, additional, Guerin, Sebastien, additional, Sciandra, Theo, additional, Bruyant, Flavienne, additional, Ait‐Mohamed, Ouardia, additional, Beguin, Marine, additional, Forget, Marie‐Helene, additional, Bourbousse, Clara, additional, Lacour, Thomas, additional, Bailleul, Benjamin, additional, Nef, Charlotte, additional, Savoie, Mireille, additional, Tremblay, Jean‐Eric, additional, Campbell, Douglas A., additional, Lavaud, Johann, additional, Schwab, Yannick, additional, Babin, Marcel, additional, and Bowler, Chris, additional

Published
2023
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44. Counting and differentiating aquatic biotic nanoparticles by full-field interferometry: from laboratory tests to Tara Oceans sample analysis

Author

Boccara, Martine, Fedala, Yasmina, Bryan, Catherine Venien, Bailly-Bechet, Marc, Bowler, Chris, and Boccara, Albert Claude

Subjects
Physics - Medical Physics, Physics - Biological Physics
Abstract

There is a huge abundance of viruses and membrane vesicles in seawater. We describe a new full-field, incoherently illuminated, shot-noise limited, common-path interferometric detection method that we couple with the analysis of Brownian motion to detect, quantify, and differentiate biotic nanoparticles. We validated the method with calibrated nanoparticles and homogeneous DNA or RNA.viruses. The smallest virus size that we characterized with a suitable signal-to-noise ratio was around 30 nm in diameter. Analysis of Brownian motions revealed anisotropic trajectories for myoviruses.We further applied the method for vesicles detection and for analysis of coastal and oligotrophic samples from Tara Oceans circumnavigation., Comment: 11 pages 4 figures

Published
2016

45. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Author

Mock, Thomas, Otillar, Robert P, Strauss, Jan, McMullan, Mark, Paajanen, Pirita, Schmutz, Jeremy, Salamov, Asaf, Sanges, Remo, Toseland, Andrew, Ward, Ben J, Allen, Andrew E, Dupont, Christopher L, Frickenhaus, Stephan, Maumus, Florian, Veluchamy, Alaguraj, Wu, Taoyang, Barry, Kerrie W, Falciatore, Angela, Ferrante, Maria I, Fortunato, Antonio E, Glöckner, Gernot, Gruber, Ansgar, Hipkin, Rachel, Janech, Michael G, Kroth, Peter G, Leese, Florian, Lindquist, Erika A, Lyon, Barbara R, Martin, Joel, Mayer, Christoph, Parker, Micaela, Quesneville, Hadi, Raymond, James A, Uhlig, Christiane, Valas, Ruben E, Valentin, Klaus U, Worden, Alexandra Z, Armbrust, E Virginia, Clark, Matthew D, Bowler, Chris, Green, Beverley R, Moulton, Vincent, van Oosterhout, Cock, and Grigoriev, Igor V

Subjects
Diatoms, Carbon Dioxide, Iron, Gene Expression Profiling, Genomics, Ice Cover, Acclimatization, Evolution, Molecular, Phylogeny, Recombination, Genetic, Genetic Drift, Alleles, Genome, Darkness, Freezing, Oceans and Seas, Cold Temperature, Transcriptome, Mutation Rate, Evolution, Molecular, Recombination, Genetic, General Science & Technology
Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.

Published
2017

46. From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance.

Author

Nef, Charlotte, Pierella Karlusich, Juan José, and Bowler, Chris

Subjects
BIOGEOCHEMICAL cycles, ENRICHED foods, FOOD chains, INTERNET research, ECOSYSTEM services
Abstract

Our oceans are populated with a wide diversity of planktonic organisms that form complex dynamic communities at the base of marine trophic networks. Within such communities are phytoplankton, unicellular photosynthetic taxa that provide an estimated half of global primary production and support biogeochemical cycles, along with other essential ecosystem services. One of the major challenges for microbial ecologists has been to try to make sense of this complexity. While phytoplankton distributions can be well explained by abiotic factors such as temperature and nutrient availability, there is increasing evidence that their ecological roles are tightly linked to their metabolic interactions with other plankton members through complex mechanisms (e.g. competition and symbiosis). Therefore, unravelling phytoplankton metabolic interactions is the key for inferring their dependency on, or antagonism with, other taxa and better integrating them into the context of carbon and nutrient fluxes in marine trophic networks. In this review, we attempt to summarize the current knowledge brought by ecophysiology, organismal imaging, in silico predictions and co-occurrence networks using 'omics data, highlighting successful combinations of approaches that may be helpful for future investigations of phytoplankton metabolic interactions within their complex communities. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'. [ABSTRACT FROM AUTHOR]

Published
2024
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50. Plankton networks driving carbon export in the oligotrophic ocean

Author

Guidi, Lionel, Chaffron, Samuel, Bittner, Lucie, Eveillard, Damien, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Brum, Jennifer R, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, and Gorsky, Gabriel

Subjects
Aquatic Organisms, Carbon, Chlorophyll, Dinoflagellida, Ecosystem, Expeditions, Genes, Bacterial, Genes, Viral, Geography, Oceans and Seas, Photosynthesis, Plankton, Seawater, Synechococcus, Tara Oceans coordinators, General Science & Technology
Abstract

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Published
2016

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