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301. Optimizing de novo genome assembly from PCR-amplified metagenomes

Author

Roux, Simon, primary, Trubl, Gareth, additional, Goudeau, Danielle, additional, Nath, Nandita, additional, Couradeau, Estelle, additional, Ahlgren, Nathan A., additional, Zhan, Yuanchao, additional, Marsan, David, additional, Chen, Feng, additional, Fuhrman, Jed A., additional, Northen, Trent R., additional, Sullivan, Matthew B., additional, Rich, Virginia I., additional, Malmstrom, Rex R., additional, and Eloe-Fadrosh, Emiley A., additional

Published
2019
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302. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Author

Bin Jang, Ho, primary, Bolduc, Benjamin, additional, Zablocki, Olivier, additional, Kuhn, Jens H., additional, Roux, Simon, additional, Adriaenssens, Evelien M., additional, Brister, J. Rodney, additional, Kropinski, Andrew M, additional, Krupovic, Mart, additional, Lavigne, Rob, additional, Turner, Dann, additional, and Sullivan, Matthew B., additional

Published
2019
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303. Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Author

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

Published
2019
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305. Discovery of several thousand highly diverse circular DNA viruses

Author

Tisza, Michael J., primary, Pastrana, Diana V., additional, Welch, Nicole L., additional, Stewart, Brittany, additional, Peretti, Alberto, additional, Starrett, Gabriel J., additional, Pang, Yuk-Ying S., additional, Krishnamurthy, Siddharth R., additional, Pesavento, Patricia A., additional, McDermott, David H., additional, Murphy, Philip M., additional, Whited, Jessica L., additional, Miller, Bess, additional, Brenchley, Jason M., additional, Rosshart, Stephan P., additional, Rehermann, Barbara, additional, Doorbar, John, additional, Ta’ala, Blake A., additional, Pletnikova, Olga, additional, Troncoso, Juan, additional, Resnick, Susan M., additional, Bolduc, Ben, additional, Sullivan, Matthew B., additional, Varsani, Arvind, additional, Segall, Anca M., additional, and Buck, Christopher B., additional

Published
2019
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308. Genome‐resolved viral ecology in a marine oxygen minimum zone.

Author

Vik, Dean, Gazitúa, Maria Consuelo, Sun, Christine L., Zayed, Ahmed A., Aldunate, Montserrat, Mulholland, Margaret R., Ulloa, Osvaldo, and Sullivan, Matthew B.

Subjects
VIRAL ecology, OXYGEN content of seawater, MARINE ecology, ANOXIC zones, BIOTIC communities, ANOXIC waters
Abstract

Summary: Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well‐studied, little is known about their viruses. Here, we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of oxygenated to anoxic waters (<0.02 μmol/l O2) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46 127 viral populations (≥5 kb), which augments the known viruses from ETSP by 10‐fold. Viral communities clustered into six groups that correspond to oceanographic features. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. ETSP viruses were largely endemic, with the majority of shared viruses (87%) also present in other OMZ samples. We detected 543 putative viral‐encoded auxiliary metabolic genes (AMGs), of which some have a distribution that reflects physico‐chemical characteristics across depth. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate‐critical environments. [ABSTRACT FROM AUTHOR]

Published
2021
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310. Global Trends in Marine Plankton Diversity across Kingdoms of Life

Author

80795055, Ibarbalz, Federico M., Henry, Nicolas, Brandão, Manoela C., Martini, Séverine, Busseni, Greta, Byrne, Hannah, Coelho, Luis Pedro, Endo, Hisashi, Gasol, Josep M., Gregory, Ann C., Mahé, Frédéric, Rigonato, Janaina, Royo-Llonch, Marta, Salazar, Guillem, Sanz-Sáez, Isabel, Scalco, Eleonora, Soviadan, Dodji, Zayed, Ahmed A., Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels, Stefanie, Picheral, Marc, Dimier, Céline, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stéphane, Babin, Marcel, Boss, Emmanuel, Iudicone, Daniele, Jaillon, Olivier, Acinas, Silvia G., Ogata, Hiroyuki, Pelletier, Eric, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Bopp, Laurent, de Vargas, Colomban, Karp-Boss, Lee, Wincker, Patrick, Lombard, Fabien, Bowler, Chris, Zinger, Lucie, Bork, Peer, Cochrane, Guy, Follows, Mick, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Not, Fabrice, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, 80795055, Ibarbalz, Federico M., Henry, Nicolas, Brandão, Manoela C., Martini, Séverine, Busseni, Greta, Byrne, Hannah, Coelho, Luis Pedro, Endo, Hisashi, Gasol, Josep M., Gregory, Ann C., Mahé, Frédéric, Rigonato, Janaina, Royo-Llonch, Marta, Salazar, Guillem, Sanz-Sáez, Isabel, Scalco, Eleonora, Soviadan, Dodji, Zayed, Ahmed A., Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels, Stefanie, Picheral, Marc, Dimier, Céline, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stéphane, Babin, Marcel, Boss, Emmanuel, Iudicone, Daniele, Jaillon, Olivier, Acinas, Silvia G., Ogata, Hiroyuki, Pelletier, Eric, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Bopp, Laurent, de Vargas, Colomban, Karp-Boss, Lee, Wincker, Patrick, Lombard, Fabien, Bowler, Chris, Zinger, Lucie, Bork, Peer, Cochrane, Guy, Follows, Mick, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Not, Fabrice, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, and Speich, Sabrina

Abstract

The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation.

Published
2019

311. Community-Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems

Author

Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Karlusich, Juan J. Pierella, Vieira, Fabio Rocha Jimenez, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G., Alberti, Adriana, Aury, Jean-marc, Benoiston, Anne-sophie, Bertrand, Arnaud, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Cedric, Busseni, Greta, Carratala, Anna, Claustre, Herve, Coelho, Luis Pedro, Colin, Sbastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Dore, Hugo, Gasparini, Stephane, Kokoszka, Florian, Jamet, Jean-louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima-mendez, Gipsi, Lombard, Fabien, Lukes, Julius, Maillet, Nicolas, Madoui, Mohammed-amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Neou, Mario B., Paz-yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean-baptiste, Roux, Simon, Manta, Daniela Salvagio, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Vesela, Jana, Vincent, Flora, Yau, Sheree, Kandels-lewis, Stefanie, Searson, Sarah, Dimier, Cline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, De 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'Alcala, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, Jaillon, Olivier, Karp-boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Pesant, Stephane, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Velayoudon, Didier, Weissenbach, Jean, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Karlusich, Juan J. Pierella, Vieira, Fabio Rocha Jimenez, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Acinas, Silvia G., Alberti, Adriana, Aury, Jean-marc, Benoiston, Anne-sophie, Bertrand, Arnaud, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Cedric, Busseni, Greta, Carratala, Anna, Claustre, Herve, Coelho, Luis Pedro, Colin, Sbastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Dore, Hugo, Gasparini, Stephane, Kokoszka, Florian, Jamet, Jean-louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima-mendez, Gipsi, Lombard, Fabien, Lukes, Julius, Maillet, Nicolas, Madoui, Mohammed-amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Neou, Mario B., Paz-yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean-baptiste, Roux, Simon, Manta, Daniela Salvagio, Sanges, Remo, Speich, Sabrina, Sprovieri, Mario, Sunagawa, Shinichi, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Vesela, Jana, Vincent, Flora, Yau, Sheree, Kandels-lewis, Stefanie, Searson, Sarah, Dimier, Cline, Picheral, Marc, Bork, Peer, Boss, Emmanuel, De 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'Alcala, Maurizio Ribera, Wincker, Patrick, Bowler, Chris, Iudicone, Daniele, Gorsky, Gabriel, Jaillon, Olivier, Karp-boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Pesant, Stephane, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Velayoudon, Didier, and Weissenbach, Jean

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 ‐omics datasets 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 towards iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole sub‐communities co‐varying 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. Plain Language Summary Marine phytoplankton require iron for their growth and proliferation. According to John Martin's iron hypothesis, fertilizing the ocean with iron could dramatically increase photosynthetic activity, thus representing a biological means to counteract global warming. However, while there is a constantly growing knowledge of how iron is distributed in the ocean and about its role in cellular processes in marine photosynthetic groups such as diatoms and cyanobacteria, less is known about how iron availability shapes plankton communities and how they respond to it. In the present work, we exploite

Published
2019
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312. Minimum Information about an Uncultivated Virus Genome (MIUViG).

Author

Roux, Simon, Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R, Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, Eloe-Fadrosh, Emiley A, Roux, Simon, Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R, Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-Fadrosh, Emiley A

Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

Published
2019

313. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils.

Author

Trubl, Gareth, Trubl, Gareth, Roux, Simon, Solonenko, Natalie, Li, Yueh-Fen, Bolduc, Benjamin, Rodríguez-Ramos, Josué, Eloe-Fadrosh, Emiley A, Rich, Virginia I, Sullivan, Matthew B, Trubl, Gareth, Trubl, Gareth, Roux, Simon, Solonenko, Natalie, Li, Yueh-Fen, Bolduc, Benjamin, Rodríguez-Ramos, Josué, Eloe-Fadrosh, Emiley A, Rich, Virginia I, and Sullivan, Matthew B

Abstract

Soils impact global carbon cycling and their resident microbes are critical to their biogeochemical processing and ecosystem outputs. Based on studies in marine systems, viruses infecting soil microbes likely modulate host activities via mortality, horizontal gene transfer, and metabolic control. However, their roles remain largely unexplored due to technical challenges with separating, isolating, and extracting DNA from viruses in soils. Some of these challenges have been overcome by using whole genome amplification methods and while these have allowed insights into the identities of soil viruses and their genomes, their inherit biases have prevented meaningful ecological interpretations. Here we experimentally optimized steps for generating quantitatively-amplified viral metagenomes to better capture both ssDNA and dsDNA viruses across three distinct soil habitats along a permafrost thaw gradient. First, we assessed differing DNA extraction methods (PowerSoil, Wizard mini columns, and cetyl trimethylammonium bromide) for quantity and quality of viral DNA. This established PowerSoil as best for yield and quality of DNA from our samples, though ∼1/3 of the viral populations captured by each extraction kit were unique, suggesting appreciable differential biases among DNA extraction kits. Second, we evaluated the impact of purifying viral particles after resuspension (by cesium chloride gradients; CsCl) and of viral lysis method (heat vs bead-beating) on the resultant viromes. DNA yields after CsCl particle-purification were largely non-detectable, while unpurified samples yielded 1-2-fold more DNA after lysis by heat than by bead-beating. Virome quality was assessed by the number and size of metagenome-assembled viral contigs, which showed no increase after CsCl-purification, but did from heat lysis relative to bead-beating. We also evaluated sample preparation protocols for ssDNA virus recovery. In both CsCl-purified and non-purified samples, ssDNA viruses were succ

Published
2019

314. Optimizing de novo genome assembly from PCR-amplified metagenomes.

Author

Roux, Simon, Roux, Simon, Trubl, Gareth, Goudeau, Danielle, Nath, Nandita, Couradeau, Estelle, Ahlgren, Nathan A, Zhan, Yuanchao, Marsan, David, Chen, Feng, Fuhrman, Jed A, Northen, Trent R, Sullivan, Matthew B, Rich, Virginia I, Malmstrom, Rex R, Eloe-Fadrosh, Emiley A, Roux, Simon, Roux, Simon, Trubl, Gareth, Goudeau, Danielle, Nath, Nandita, Couradeau, Estelle, Ahlgren, Nathan A, Zhan, Yuanchao, Marsan, David, Chen, Feng, Fuhrman, Jed A, Northen, Trent R, Sullivan, Matthew B, Rich, Virginia I, Malmstrom, Rex R, and Eloe-Fadrosh, Emiley A

Abstract

Background:Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods:Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results:Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes

Published
2019

315. Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies.

Author

Zimmerman, Amy E, Zimmerman, Amy E, Bachy, Charles, Ma, Xiufeng, Roux, Simon, Jang, Ho Bin, Sullivan, Matthew B, Waldbauer, Jacob R, Worden, Alexandra Z, Zimmerman, Amy E, Zimmerman, Amy E, Bachy, Charles, Ma, Xiufeng, Roux, Simon, Jang, Ho Bin, Sullivan, Matthew B, Waldbauer, Jacob R, and Worden, Alexandra Z

Abstract

In marine ecosystems, viruses are major disrupters of the direct flow of carbon and nutrients to higher trophic levels. Although the genetic diversity of several eukaryotic phytoplankton virus groups has been characterized, their infection dynamics are less understood, such that the physiological and ecological implications of their diversity remain unclear. We compared genomes and infection phenotypes of the two most closely related cultured phycodnaviruses infecting the widespread picoprasinophyte Ostreococcus lucimarinus under standard- (1.3 divisions per day) and limited-light (0.41 divisions per day) nutrient replete conditions. OlV7 infection caused early arrest of the host cell cycle, coinciding with a significantly higher proportion of infected cells than OlV1-amended treatments, regardless of host growth rate. OlV7 treatments showed a near-50-fold increase of progeny virions at the higher host growth rate, contrasting with OlV1's 16-fold increase. However, production of OlV7 virions was more sensitive than OlV1 production to reduced host growth rate, suggesting fitness trade-offs between infection efficiency and resilience to host physiology. Moreover, although organic matter released from OlV1- and OlV7-infected hosts had broadly similar chemical composition, some distinct molecular signatures were observed. Collectively, these results suggest that current views on viral relatedness through marker and core gene analyses underplay operational divergence and consequences for host ecology.

Published
2019

316. Numerous cultivated and uncultivated viruses encode ribosomal proteins.

Author

Mizuno, Carolina M, Mizuno, Carolina M, Guyomar, Charlotte, Roux, Simon, Lavigne, Régis, Rodriguez-Valera, Francisco, Sullivan, Matthew B, Gillet, Reynald, Forterre, Patrick, Krupovic, Mart, Mizuno, Carolina M, Mizuno, Carolina M, Guyomar, Charlotte, Roux, Simon, Lavigne, Régis, Rodriguez-Valera, Francisco, Sullivan, Matthew B, Gillet, Reynald, Forterre, Patrick, and Krupovic, Mart

Abstract

Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses. Viruses tend to encode dynamic RPs, easily exchangeable between ribosomes, suggesting these proteins can replace cellular versions in host ribosomes. Functional assays confirm that the two most common virus-encoded RPs, bS21 and bL12, are incorporated into 70S ribosomes when expressed in Escherichia coli. Ecological distribution of virus-encoded RPs suggests some level of ecosystem adaptations as aquatic viruses and viruses of animal-associated bacteria are enriched for different subsets of RPs. Finally, RP genes are under purifying selection and thus likely retained an important function after being horizontally transferred into virus genomes.

Published
2019

317. Scientists' warning to humanity: microorganisms and climate change.

Author

Cavicchioli, Ricardo, Cavicchioli, Ricardo, Ripple, William J, Timmis, Kenneth N, Azam, Farooq, Bakken, Lars R, Baylis, Matthew, Behrenfeld, Michael J, Boetius, Antje, Boyd, Philip W, Classen, Aimée T, Crowther, Thomas W, Danovaro, Roberto, Foreman, Christine M, Huisman, Jef, Hutchins, David A, Jansson, Janet K, Karl, David M, Koskella, Britt, Mark Welch, David B, Martiny, Jennifer BH, Moran, Mary Ann, Orphan, Victoria J, Reay, David S, Remais, Justin V, Rich, Virginia I, Singh, Brajesh K, Stein, Lisa Y, Stewart, Frank J, Sullivan, Matthew B, van Oppen, Madeleine JH, Weaver, Scott C, Webb, Eric A, Webster, Nicole S, Cavicchioli, Ricardo, Cavicchioli, Ricardo, Ripple, William J, Timmis, Kenneth N, Azam, Farooq, Bakken, Lars R, Baylis, Matthew, Behrenfeld, Michael J, Boetius, Antje, Boyd, Philip W, Classen, Aimée T, Crowther, Thomas W, Danovaro, Roberto, Foreman, Christine M, Huisman, Jef, Hutchins, David A, Jansson, Janet K, Karl, David M, Koskella, Britt, Mark Welch, David B, Martiny, Jennifer BH, Moran, Mary Ann, Orphan, Victoria J, Reay, David S, Remais, Justin V, Rich, Virginia I, Singh, Brajesh K, Stein, Lisa Y, Stewart, Frank J, Sullivan, Matthew B, van Oppen, Madeleine JH, Weaver, Scott C, Webb, Eric A, and Webster, Nicole S

Abstract

In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial 'unseen majority'. We must learn not just how microorganisms affect climate change (including production and consumption of greenhouse gases) but also how they will be affected by climate change and other human activities. This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.

Published
2019

318. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks.

Author

Bin Jang, Ho, Bin Jang, Ho, Bolduc, Benjamin, Zablocki, Olivier, Kuhn, Jens H, Roux, Simon, Adriaenssens, Evelien M, Brister, J Rodney, Kropinski, Andrew M, Krupovic, Mart, Lavigne, Rob, Turner, Dann, Sullivan, Matthew B, Bin Jang, Ho, Bin Jang, Ho, Bolduc, Benjamin, Zablocki, Olivier, Kuhn, Jens H, Roux, Simon, Adriaenssens, Evelien M, Brister, J Rodney, Kropinski, Andrew M, Krupovic, Mart, Lavigne, Rob, Turner, Dann, and Sullivan, Matthew B

Abstract

Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.

Published
2019

319. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Roux, Simon, Adriaenssens, Evelien M., Dutilh, Bas E., Koonin, Eugene V., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Lavigne, Rob, Brister, J. Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K., Bordenstein, Seth R., Bork, Peer, Breitbart, Mya, Cochrane, Guy R., Daly, Rebecca A., Desnues, Christelle, Duhaime, Melissa B., Emerson, Joanne B., Enault, François, Fuhrman, Jed A., Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L., Ivanova, Natalia N., Labonté, Jessica M., Lee, Kyung-Bum, Malmstrom, Rex R., Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F., Sullivan, Matthew B., Sunagawa, Shinichi, Suttle, Curtis A., Temperton, Ben, Tringe, Susannah G., Thurber, Rebecca Vega, Webster, Nicole S., Whiteson, Katrine L., Wilhelm, Steven W., Wommack, K. Eric, Woyke, Tanja, Wrighton, Kelly C., Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J., Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C., Eloe-Fadrosh, Emiley A., Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Roux, Simon, Adriaenssens, Evelien M., Dutilh, Bas E., Koonin, Eugene V., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Lavigne, Rob, Brister, J. Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K., Bordenstein, Seth R., Bork, Peer, Breitbart, Mya, Cochrane, Guy R., Daly, Rebecca A., Desnues, Christelle, Duhaime, Melissa B., Emerson, Joanne B., Enault, François, Fuhrman, Jed A., Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L., Ivanova, Natalia N., Labonté, Jessica M., Lee, Kyung-Bum, Malmstrom, Rex R., Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F., Sullivan, Matthew B., Sunagawa, Shinichi, Suttle, Curtis A., Temperton, Ben, Tringe, Susannah G., Thurber, Rebecca Vega, Webster, Nicole S., Whiteson, Katrine L., Wilhelm, Steven W., Wommack, K. Eric, Woyke, Tanja, Wrighton, Kelly C., Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J., Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C., and Eloe-Fadrosh, Emiley A.

Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

Published
2019

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

Author

UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, 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, Jaillon, Olivier, Karp‐Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Pesant, Stéphane, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Velayoudon, Didier, Weissenbach, Jean, UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, 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, Jaillon, Olivier, Karp‐Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Pesant, Stéphane, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Velayoudon, Didier, and Weissenbach, Jean

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. © 2019. American Geophysical Union. All Rights Reserved.

Published
2019

321. Future Ocean Observations to Connect Climate, Fisheries and Marine Ecosystems

Author

Schmidt, Jörn O., Bograd, Steven J., Arrizabalaga, Haritz, Azevedo, José L., Barbeaux, Steven J., Barth, John A., Boyer, Tim, Brodie, Stephanie, Cárdenas, Juan José, Cross, Scott, Druon, Jean-Noël, Fransson, Agneta, Hartog, Jason, Hazen, Elliott L., Hobday, Alistair, Jacox, Michael, Karstensen, Johannes, Kupschus, Sven, Lopez, Jon, Madureira, Lauro A. S.-P., Martinelli Filho, José E., Miloslavich, Patricia, Santos, Catarina P., Scales, Kylie, Speich, Sabrina, Sullivan, Matthew B., Szoboszlai, Amber, Tommasi, Desiree, Wallace, Douglas, Zador, Stephani, Zawislak, Paulo Antônio, Schmidt, Jörn O., Bograd, Steven J., Arrizabalaga, Haritz, Azevedo, José L., Barbeaux, Steven J., Barth, John A., Boyer, Tim, Brodie, Stephanie, Cárdenas, Juan José, Cross, Scott, Druon, Jean-Noël, Fransson, Agneta, Hartog, Jason, Hazen, Elliott L., Hobday, Alistair, Jacox, Michael, Karstensen, Johannes, Kupschus, Sven, Lopez, Jon, Madureira, Lauro A. S.-P., Martinelli Filho, José E., Miloslavich, Patricia, Santos, Catarina P., Scales, Kylie, Speich, Sabrina, Sullivan, Matthew B., Szoboszlai, Amber, Tommasi, Desiree, Wallace, Douglas, Zador, Stephani, and Zawislak, Paulo Antônio

Abstract

Advances in ocean observing technologies and modeling provide the capacity to revolutionize the management of living marine resources. While traditional fisheries management approaches like single-species stock assessments are still common, a global effort is underway to adopt ecosystem-based fisheries management (EBFM) approaches. These approaches consider changes in the physical environment and interactions between ecosystem elements, including human uses, holistically. For example, integrated ecosystem assessments aim to synthesize a suite of observations (physical, biological, socioeconomic) and modeling platforms [ocean circulation models, ecological models, short-term forecasts, management strategy evaluations (MSEs)] to assess the current status and recent and future trends of ecosystem components. This information provides guidance for better management strategies. A common thread in EBFM approaches is the need for high-quality observations of ocean conditions, at scales that resolve critical physical-biological processes and are timely for management needs. Here we explore options for a future observing system that meets the needs of EBFM by (i) identifying observing needs for different user groups, (ii) reviewing relevant datasets and existing technologies, (iii) showcasing regional case studies, and (iv) recommending observational approaches required to implement EBFM. We recommend linking ocean observing within the context of Global Ocean Observing System (GOOS) and other regional ocean observing efforts with fisheries observations, new forecasting methods, and capacity development, in a comprehensive ocean observing framework.

Published
2019
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322. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Author

European Commission, Ministerio de Economía y Competitividad (España), 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 Fernández, Pablo, Uehara, Hideya, Zayed, Ahmed A., Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels‐Lewis, Stefanie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Bowler, Chris, Vargas, Colomban de, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Karp-Boss, Lee, Karsenti, Eric, Ogata, Hiroyuki, Pesant, Stéphane, Speich, Sabrina, Sullivan, Matthew B., Wincker, Patrick, Sunagawa, Shinichi, European Commission, Ministerio de Economía y Competitividad (España), 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 Fernández, Pablo, Uehara, Hideya, Zayed, Ahmed A., Zeller, Georg, Carmichael, Margaux, Dimier, Céline, Ferland, Joannie, Kandels‐Lewis, Stefanie, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Bowler, Chris, Vargas, Colomban de, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Karp-Boss, Lee, Karsenti, Eric, Ogata, Hiroyuki, Pesant, Stéphane, Speich, Sabrina, Sullivan, Matthew B., Wincker, Patrick, and Sunagawa, Shinichi

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

Published
2019

323. Global Trends in Marine Plankton Diversity across Kingdoms of Life

Author

European Commission, Ministerio de Economía y Competitividad (España), Ibarbalz, Federico M., Henry, Nicolas, Brandão, Manoela C., Martini, Séverine, Busseni, Greta, Byrne, Hannah, Coelho, Luis Pedro, Endo, Hisashi, Gasol, Josep M., Gregory, Ann C., Mahé, Frédéric, Rigonato, Janaina, Royo-Llonch, Marta, Salazar, Guillem, Sanz-Sáez, Isabel, Scalco, Eleonora, Soviadan, Yawouvi Dodji, Zayed, Ahmed A., Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels‐Lewis, Stefanie, Picheral, Marc, Dimier, Céline, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stéphane, Babin, Marcel, Boss, Emmanuel, Iudicone, Daniele, Jaillon, Olivier, Acinas, Silvia G., Ogata, Hiroyuki, Pelletier, Eric, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Bopp, Laurent, Vargas, Colomban de, Karp-Boss, Lee, Wincker, Patrick, Lombard, Fabien, Bowler, Chris, Zinger, Lucie, European Commission, Ministerio de Economía y Competitividad (España), Ibarbalz, Federico M., Henry, Nicolas, Brandão, Manoela C., Martini, Séverine, Busseni, Greta, Byrne, Hannah, Coelho, Luis Pedro, Endo, Hisashi, Gasol, Josep M., Gregory, Ann C., Mahé, Frédéric, Rigonato, Janaina, Royo-Llonch, Marta, Salazar, Guillem, Sanz-Sáez, Isabel, Scalco, Eleonora, Soviadan, Yawouvi Dodji, Zayed, Ahmed A., Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels‐Lewis, Stefanie, Picheral, Marc, Dimier, Céline, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stéphane, Babin, Marcel, Boss, Emmanuel, Iudicone, Daniele, Jaillon, Olivier, Acinas, Silvia G., Ogata, Hiroyuki, Pelletier, Eric, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Bopp, Laurent, Vargas, Colomban de, Karp-Boss, Lee, Wincker, Patrick, Lombard, Fabien, Bowler, Chris, and Zinger, Lucie

Abstract

The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation

Published
2019

324. Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Author

Région Bretagne, Veolia Foundation, Fondation Prince Albert II de Monaco, Centre National de la Recherche Scientifique (France), Gregory, Ann C., Zayed, Ahmed A., Conceição-Neto, Nadia, Temperton, Ben, Alberti, Adriana, Ardyna, Mathieu, Arkhipova, Ksenia, Carmichael, Margaux, Cruaud, Corinne, Dimier, Céline, Domínguez-Huerta, Guillermo, Ferland, Joannie, Kandels‐Lewis, Stefanie, Liu, Yunxiao, Marec, Claudie, Pesant, Stéphane, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tremblay, J. E., Vik, Dean, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, Vargas, Colomban de, Follows, Michael J., Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, N.J., Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Wincker, Patrick, Culley, Alexander I., Dutilh, Bas E., Roux, Simon, Sullivan, Matthew B., Région Bretagne, Veolia Foundation, Fondation Prince Albert II de Monaco, Centre National de la Recherche Scientifique (France), Gregory, Ann C., Zayed, Ahmed A., Conceição-Neto, Nadia, Temperton, Ben, Alberti, Adriana, Ardyna, Mathieu, Arkhipova, Ksenia, Carmichael, Margaux, Cruaud, Corinne, Dimier, Céline, Domínguez-Huerta, Guillermo, Ferland, Joannie, Kandels‐Lewis, Stefanie, Liu, Yunxiao, Marec, Claudie, Pesant, Stéphane, Picheral, Marc, Pisarev, Sergey, Poulain, Julie, Tremblay, J. E., Vik, Dean, Acinas, Silvia G., Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, Vargas, Colomban de, Follows, Michael J., Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, N.J., Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Wincker, Patrick, Culley, Alexander I., Dutilh, Bas E., Roux, Simon, and Sullivan, Matthew B.

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

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

Author

Gordon and Betty Moore Foundation, Fondation Prince Albert II de Monaco, National Science Foundation (US), Stazione Zoologica Anton Dohrn, National Fund for Scientific Research (Belgium), Centre National de la Recherche Scientifique (France), Région Bretagne, 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, Sebastien, 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, M. G., Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean-Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, R., Speich, Sabrina, Sprovieri, M., 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 de, Follows, Michael J., Grimsley, Nigel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B., Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, D'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, Ribera d’Alcalà, Maurizio, Wincker, Patrick, Bowler, Chris, Guidi, Lionel, Iudicone, Daniele, Gordon and Betty Moore Foundation, Fondation Prince Albert II de Monaco, National Science Foundation (US), Stazione Zoologica Anton Dohrn, National Fund for Scientific Research (Belgium), Centre National de la Recherche Scientifique (France), Région Bretagne, 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, Sebastien, 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, M. G., Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean-Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, R., Speich, Sabrina, Sprovieri, M., 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 de, Follows, Michael J., Grimsley, Nigel, Hingamp, Pascal, Karsenti, Eric, Sordino, Paolo, Stemmann, Lars, Sullivan, Matthew B., Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, D'Ortenzio, Fabrizio, Testor, Pierre, Not, Fabrice, Ribera d’Alcalà, Maurizio, Wincker, Patrick, Bowler, Chris, Guidi, Lionel, and Iudicone, Daniele

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

326. Life and death in the soil microbiome: how ecological processes influence biogeochemistry

Author

Sokol, Noah W., Slessarev, Eric, Marschmann, Gianna L., Nicolas, Alexa, Blazewicz, Steven J., Brodie, Eoin L., Firestone, Mary K., Foley, Megan M., Hestrin, Rachel, Hungate, Bruce A., Koch, Benjamin J., Stone, Bram W., Sullivan, Matthew B., Zablocki, Olivier, and Pett-Ridge, Jennifer

Abstract

Soil microorganisms shape global element cycles in life and death. Living soil microorganisms are a major engine of terrestrial biogeochemistry, driving the turnover of soil organic matter — Earth’s largest terrestrial carbon pool and the primary source of plant nutrients. Their metabolic functions are influenced by ecological interactions with other soil microbial populations, soil fauna and plants, and the surrounding soil environment. Remnants of dead microbial cells serve as fuel for these biogeochemical engines because their chemical constituents persist as soil organic matter. This non-living microbial biomass accretes over time in soil, forming one of the largest pools of organic matter on the planet. In this Review, we discuss how the biogeochemical cycling of organic matter depends on both living and dead soil microorganisms, their functional traits, and their interactions with the soil matrix and other organisms. With recent omics advances, many of the traits that frame microbial population dynamics and their ecophysiological adaptations can be deciphered directly from assembled genomes or patterns of gene or protein expression. Thus, it is now possible to leverage a trait-based understanding of microbial life and death within improved biogeochemical models and to better predict ecosystem functioning under new climate regimes.

Published
2022
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327. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters.

Author

Gazitúa, M. Consuelo, Vik, Dean R., Roux, Simon, Gregory, Ann C., Bolduc, Benjamin, Widner, Brittany, Mulholland, Margaret R., Hallam, Steven J., Ulloa, Osvaldo, and Sullivan, Matthew B.

Abstract

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models. [ABSTRACT FROM AUTHOR]

Published
2021
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328. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Author

Lombard, Vincent, Carradec, Quentin, Pelletier, Eric, Wessner, Marc, Leconte, Jade, Mangot, Jean-Francois, Poulain, Julie, Labadie, Karine, Logares, Ramiro, Sunagawa, Shinichi, de Berardinis, Véronique, Salanoubat, Marcel, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Acinas, Silvia G., Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Karp-Boss, Lee, Krzic, Uros, Not, Fabrice, Ogata, Hiroyuki, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Velayoudon, Didier, Weissenbach, Jean, Pesant, Stephane, Poulton, Nicole, Stepanauskas, Ramunas, Bork, Peer, Bowler, Chris, Hingamp, Pascal, Sullivan, Matthew B., Iudicone, Daniele, Massana, Ramon, Aury, Jean-Marc, Henrissat, Bernard, Karsenti, Eric, Jaillon, Olivier, Sieracki, Mike, de Vargas, Colomban, Wincker, Patrick, Seeleuthner, Yoann, and Mondy, Samuel

Subjects
fungi, Oceanography, Océanographie
Abstract

Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.

Published
2018

329. To create one (1) new family, Herelleviridae, in the order Caudovirales

Author

Barylski, Jakub, Enault, François, Dutilh, Bas E, Schuller, Margo B P, Edwards, Robert A, Gillis, Annika, Klumpp, Jochen, Knezevic, Petar, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Oksanen, Hanna M, Sullivan, Matthew B, Jang, Ho Bin, Simmonds, Peter, Pakorn Aiewsakun, Wittmann, Johannes, Tolstoy, Igor, J Rodney Brister, Kropinski, Andrew M, and Adriaenssens, Evelien M

Published
2018
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330. Taxonomy proposal: To create one (1) new family, Herelleviridae, in the order Caudovirales

Author

Jakub Barylski, François Enault, Dutilh, Bas E., Schuller, Margo B. P., Edwards, Robert A., Annika Gillis, Jochen Klumpp, Petar Knezevic, Mart Krupovic, Kuhn, Jens H., Rob Lavigne, Hanna Oksanen, Sullivan, Matthew B., Ho Bin Jang, Peter Simmonds, Pakorn Aiewsakun, Johannes Wittmann, Igor Tolstoy, Rodney Brister, J., Kropinski, Andrew M., Adriaenssens, Evelien M., Molecular and Integrative Biosciences Research Programme, Molecular Principles of Viruses, and Faculty of Biological and Environmental Sciences

Subjects
1183 Plant biology, microbiology, virology
Published
2018

331. A global ocean atlas of eukaryotic genes

Author

Carradec, Quentin, Pelletier, Eric, Da Silva, Corinne, Alberti, Adriana, Seeleuthner, Yoann, Blanc-Mathieu, Romain, Lima-Mendez, Gipsi, Rocha, Fabio, Tirichine, Leila, Labadie, Karine, Kirilovsky, Amos, Bertrand, Alexis, Engelen, Stefan, Madoui, Mohammed-Amin, Méheust, Raphaël, Poulain, Julie, Romac, Sarah, Richter, Daniel J., Yoshikawa, Genki, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Jaillon, Olivier, Aury, Jean-Marc, Karsenti, Eric, Sullivan, Matthew B., Sunagawa, Shinichi, Bork, Peer, Not, Fabrice, Hingamp, Pascal, Raes, Jeroen, Guidi, Lionel, Ogata, Hiroyuki, de Vargas, Colomban, Iudicone, Daniele, Bowler, Chris, Wincker, Patrick, Acinas, Silvia G., Boss, Emmanuel, Gorsky, Gabriel, Grimsley, Nigel, Karp-Boss, Lee, Krzic, Uros, Pesant, Stephane, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Speich, Sabrina, Stemmann, Lars, Velayoudon, Didier, Weissenbach, Jean, Follows, Michael J, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, and Follows, Michael J

Subjects
fungi
Abstract

While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.

Published
2017

332. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Author

Alberti, Adriana, Poulain, Julie, Engelen, Stefan, Labadie, Karine, Romac, Sarah, Ferrera, Isabel, Albini, Guillaume, Aury, Jean-marc, Belser, Caroline, Bertrand, Alexis, Cruaud, Corinne, Da Silva, Corinne, Dossat, Carole, Gavory, Frederick, Gas, Shahinaz, Guy, Julie, Haquelle, Maud, Jacoby, E'Krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaelle, Wessner, Mark, Acinas, Silvia G., Royo-llonch, Marta, Cornejo-castillo, Francisco M., Logares, Ramiro, Fernandez-gomez, Beatriz, Bowler, Chris, Cochrane, Guy, Amid, Clara, Ten Hoopen, Petra, De Vargas, Colomban, Grimsley, Nigel, Desgranges, Elodie, Kandels-lewis, Stefanie, Ogata, Hiroyuki, Poulton, Nicole, Sieracki, Michael E., Stepanauskas, Ramunas, Sullivan, Matthew B., Brum, Jennifer R., Duhaime, Melissa B., Poulos, Bonnie T., Hurwitz, Bonnie L., Pesant, Stephane, Karsenti, Eric, Wincker, Patrick, Bork, Peer, Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Hingamp, Pascal, Iudicone, Daniele, Karp-boss, Lee, Not, Fabrice, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Bazire, Pascal, Beluche, Odette, Besnard-gonnet, Marielle, Bordelais, Isabelle, Boutard, Magali, Dubois, Maria, Dumont, Corinne, Ettedgui, Evelyne, Fernandez, Patricia, Garcia, Esperance, Aiach, Nathalie Giordanenco, Guerin, Thomas, Hamon, Chadia, Brun, Elodie, Lebled, Sandrine, Lenoble, Patricia, Louesse, Claudine, Mahieu, Eric, Mairey, Barbara, Martins, Nathalie, Megret, Catherine, Milani, Claire, Muanga, Jacqueline, Orvain, Celine, Payen, Emilie, Perroud, Peggy, Petit, Emmanuelle, Robert, Dominique, Ronsin, Murielle, and Vacherie, Benoit

Subjects
fungi
Abstract

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www. ebi. ac. uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.

Published
2017

333. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Author

Seeleuthner, Yoann, Mondy, Samuel, Lombard, Vincent, Carradec, Quentin, Pelletier, Eric, Wessner, Marc, Leconte, Jade, Mangot, Jean-François, Poulain, Julie, Labadie, Karine, Logares, Ramiro, Sunagawa, Shinichi, de Berardinis, Véronique, Salanoubat, Marcel, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Pesant, Stephane, Poulton, Nicole, Stepanauskas, Ramunas, Bork, Peer, Bowler, Chris, Hingamp, Pascal, Sullivan, Matthew B., Iudicone, Daniele, Massana, Ramon, Aury, Jean-Marc, Henrissat, Bernard, Karsenti, Eric, Jaillon, Olivier, Sieracki, Mike, de Vargas, Colomban, Wincker, Patrick, Acinas, Silvia G., Boss, Emmanuel, Gorsky, Gabriel, Grimsley, Nigel, Karp-Boss, Lee, Krzic, Uros, Not, Fabrice, Ogata, Hiroyuki, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Velayoudon, Didier, Weissenbach, Jean, Follows, Michael J, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, and Follows, Michael J

Subjects
fungi
Abstract

Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.

Published
2017

334. Gene sharing networks to automate genome-based prokaryotic viral taxonomy

Author

Jang, Ho Bin, primary, Bolduc, Benjamin, additional, Zablocki, Olivier, additional, Kuhn, Jens H., additional, Roux, Simon, additional, Adriaenssens, Evelien M., additional, Brister, J. Rodney, additional, Kropinski, Andrew M, additional, Krupovic, Mart, additional, Turner, Dann, additional, and Sullivan, Matthew B., additional

Published
2019
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335. Optimizing de novo genome assembly from PCR-amplified metagenomes

Author

Roux, Simon, primary, Trubl, Gareth, additional, Goudeau, Danielle, additional, Nath, Nandita, additional, Couradeau, Estelle, additional, Ahlgren, Nathan A, additional, Zhan, Yuanchao, additional, Marsan, David, additional, Chen, Feng, additional, Fuhrman, Jed A, additional, Northen, Trent R, additional, Sullivan, Matthew B, additional, Rich, Virginia I, additional, Malmstrom, Rex R, additional, and Eloe-Fadrosh, Emiley A, additional

Published
2018
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336. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Roux, Simon, primary, Adriaenssens, Evelien M, additional, Dutilh, Bas E, additional, Koonin, Eugene V, additional, Kropinski, Andrew M, additional, Krupovic, Mart, additional, Kuhn, Jens H, additional, Lavigne, Rob, additional, Brister, J Rodney, additional, Varsani, Arvind, additional, Amid, Clara, additional, Aziz, Ramy K, additional, Bordenstein, Seth R, additional, Bork, Peer, additional, Breitbart, Mya, additional, Cochrane, Guy R, additional, Daly, Rebecca A, additional, Desnues, Christelle, additional, Duhaime, Melissa B, additional, Emerson, Joanne B, additional, Enault, François, additional, Fuhrman, Jed A, additional, Hingamp, Pascal, additional, Hugenholtz, Philip, additional, Hurwitz, Bonnie L, additional, Ivanova, Natalia N, additional, Labonté, Jessica M, additional, Lee, Kyung-Bum, additional, Malmstrom, Rex R, additional, Martinez-Garcia, Manuel, additional, Mizrachi, Ilene Karsch, additional, Ogata, Hiroyuki, additional, Páez-Espino, David, additional, Petit, Marie-Agnès, additional, Putonti, Catherine, additional, Rattei, Thomas, additional, Reyes, Alejandro, additional, Rodriguez-Valera, Francisco, additional, Rosario, Karyna, additional, Schriml, Lynn, additional, Schulz, Frederik, additional, Steward, Grieg F, additional, Sullivan, Matthew B, additional, Sunagawa, Shinichi, additional, Suttle, Curtis A, additional, Temperton, Ben, additional, Tringe, Susannah G, additional, Thurber, Rebecca Vega, additional, Webster, Nicole S, additional, Whiteson, Katrine L, additional, Wilhelm, Steven W, additional, Wommack, K Eric, additional, Woyke, Tanja, additional, Wrighton, Kelly C, additional, Yilmaz, Pelin, additional, Yoshida, Takashi, additional, Young, Mark J, additional, Yutin, Natalya, additional, Allen, Lisa Zeigler, additional, Kyrpides, Nikos C, additional, and Eloe-Fadrosh, Emiley A, additional

Published
2018
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337. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing

Author

Daly, Rebecca A., primary, Roux, Simon, additional, Borton, Mikayla A., additional, Morgan, David M., additional, Johnston, Michael D., additional, Booker, Anne E., additional, Hoyt, David W., additional, Meulia, Tea, additional, Wolfe, Richard A., additional, Hanson, Andrea J., additional, Mouser, Paula J., additional, Moore, Joseph D., additional, Wunch, Kenneth, additional, Sullivan, Matthew B., additional, Wrighton, Kelly C., additional, and Wilkins, Michael J., additional

Published
2018
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339. Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

Author

Trubl, Gareth, primary, Jang, Ho Bin, additional, Roux, Simon, additional, Emerson, Joanne B., additional, Solonenko, Natalie, additional, Vik, Dean R., additional, Solden, Lindsey, additional, Ellenbogen, Jared, additional, Runyon, Alexander T., additional, Bolduc, Benjamin, additional, Woodcroft, Ben J., additional, Saleska, Scott R., additional, Tyson, Gene W., additional, Wrighton, Kelly C., additional, Sullivan, Matthew B., additional, and Rich, Virginia I., additional

Published
2018
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340. Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

Author

Solden, Lindsey M., primary, Naas, Adrian E., additional, Roux, Simon, additional, Daly, Rebecca A., additional, Collins, William B., additional, Nicora, Carrie D., additional, Purvine, Sam O., additional, Hoyt, David W., additional, Schückel, Julia, additional, Jørgensen, Bodil, additional, Willats, William, additional, Spalinger, Donald E., additional, Firkins, Jeffrey L., additional, Lipton, Mary S., additional, Sullivan, Matthew B., additional, Pope, Phillip B., additional, and Wrighton, Kelly C., additional

Published
2018
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341. Host-linked soil viral ecology along a permafrost thaw gradient

Author

Emerson, Joanne B., primary, Roux, Simon, additional, Brum, Jennifer R., additional, Bolduc, Benjamin, additional, Woodcroft, Ben J., additional, Jang, Ho Bin, additional, Singleton, Caitlin M., additional, Solden, Lindsey M., additional, Naas, Adrian E., additional, Boyd, Joel A., additional, Hodgkins, Suzanne B., additional, Wilson, Rachel M., additional, Trubl, Gareth, additional, Li, Changsheng, additional, Frolking, Steve, additional, Pope, Phillip B., additional, Wrighton, Kelly C., additional, Crill, Patrick M., additional, Chanton, Jeffrey P., additional, Saleska, Scott R., additional, Tyson, Gene W., additional, Rich, Virginia I., additional, and Sullivan, Matthew B., additional

Published
2018
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344. A global ocean atlas of eukaryotic genes

Author

40769056, Carradec, Quentin, Pelletier, Eric, Da Silva, Corinne, Alberti, Adriana, Seeleuthner, Yoann, Blanc-Mathieu, Romain, Lima-Mendez, Gipsi, Rocha, Fabio, Tirichine, Leila, Labadie, Karine, Kirilovsky, Amos, Bertrand, Alexis, Engelen, Stefan, Madoui, Mohammed-Amin, Méheust, Raphaël, Poulain, Julie, Romac, Sarah, Richter, Daniel J., Yoshikawa, Genki, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Jaillon, Olivier, Aury, Jean-Marc, Karsenti, Eric, Sullivan, Matthew B., Sunagawa, Shinichi, Bork, Peer, Not, Fabrice, Hingamp, Pascal, Raes, Jeroen, Guidi, Lionel, Ogata, Hiroyuki, de Vargas, Colomban, Iudicone, Daniele, Bowler, Chris, Wincker, Patrick, 40769056, Carradec, Quentin, Pelletier, Eric, Da Silva, Corinne, Alberti, Adriana, Seeleuthner, Yoann, Blanc-Mathieu, Romain, Lima-Mendez, Gipsi, Rocha, Fabio, Tirichine, Leila, Labadie, Karine, Kirilovsky, Amos, Bertrand, Alexis, Engelen, Stefan, Madoui, Mohammed-Amin, Méheust, Raphaël, Poulain, Julie, Romac, Sarah, Richter, Daniel J., Yoshikawa, Genki, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Jaillon, Olivier, Aury, Jean-Marc, Karsenti, Eric, Sullivan, Matthew B., Sunagawa, Shinichi, Bork, Peer, Not, Fabrice, Hingamp, Pascal, Raes, Jeroen, Guidi, Lionel, Ogata, Hiroyuki, de Vargas, Colomban, Iudicone, Daniele, Bowler, Chris, and Wincker, Patrick

Abstract

While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.

Published
2018

345. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Author

Seeleuthner, Yoann, Mondy, Samuel, Lombard, Vincent, Carradec, Quentin, Pelletier, Eric, Wessner, Marc, Leconte, Jade, Mangot, Jean-François, Poulain, Julie, Labadie, Karine, Logares, Ramiro, Sunagawa, Shinichi, de Berardinis, Véronique, Salanoubat, Marcel, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Pesant, Stephane, Poulton, Nicole, Stepanauskas, Ramunas, Bork, Peer, Bowler, Chris, Hingamp, Pascal, Sullivan, Matthew B., Iudicone, Daniele, Massana, Ramon, Aury, Jean-Marc, Henrissat, Bernard, Karsenti, Eric, Jaillon, Olivier, Sieracki, Mike, de Vargas, Colomban, Wincker, Patrick, Seeleuthner, Yoann, Mondy, Samuel, Lombard, Vincent, Carradec, Quentin, Pelletier, Eric, Wessner, Marc, Leconte, Jade, Mangot, Jean-François, Poulain, Julie, Labadie, Karine, Logares, Ramiro, Sunagawa, Shinichi, de Berardinis, Véronique, Salanoubat, Marcel, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Pesant, Stephane, Poulton, Nicole, Stepanauskas, Ramunas, Bork, Peer, Bowler, Chris, Hingamp, Pascal, Sullivan, Matthew B., Iudicone, Daniele, Massana, Ramon, Aury, Jean-Marc, Henrissat, Bernard, Karsenti, Eric, Jaillon, Olivier, Sieracki, Mike, de Vargas, Colomban, and Wincker, Patrick

Abstract

Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.

Published
2018

346. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-bum, Malmstrom, Rex R, Martinez-garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-espino, David, Petit, Marie-agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, Eloe-fadrosh, Emiley A, Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-bum, Malmstrom, Rex R, Martinez-garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-espino, David, Petit, Marie-agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-fadrosh, Emiley A

Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.

Published
2018

347. A global ocean atlas of eukaryotic genes

Author

Carradec, Quentin, Pelletier, Eric, Da Silva, Corinne, Alberti, Adriana, Seeleuthner, Yoann, Blanc-mathieu, Romain, Lima-mendez, Gipsi, Rocha, Fabio, Tirichine, Leila, Labadie, Karine, Kirilovsky, Amos, Bertrand, Alexis, Engelen, Stefan, Madoui, Mohammed-amin, Meheust, Raphael, Poulain, Julie, Romac, Sarah, Richter, Daniel J., Yoshikawa, Genki, Dimier, Celine, Kandels-lewis, Stefanie, Picheral, Marc, Searson, Sarah, Jaillon, Olivier, Aury, Jean-marc, Karsenti, Eric, Sullivan, Matthew B., Sunagawa, Shinichi, Bork, Peer, Not, Fabrice, Hingamp, Pascal, Raes, Jeroen, Guidi, Lionel, Ogata, Hiroyuki, De Vargas, Colomban, Iudicone, Daniele, Bowler, Chris, Wincker, Patrick, Tara Oceans Coordinators, Carradec, Quentin, Pelletier, Eric, Da Silva, Corinne, Alberti, Adriana, Seeleuthner, Yoann, Blanc-mathieu, Romain, Lima-mendez, Gipsi, Rocha, Fabio, Tirichine, Leila, Labadie, Karine, Kirilovsky, Amos, Bertrand, Alexis, Engelen, Stefan, Madoui, Mohammed-amin, Meheust, Raphael, Poulain, Julie, Romac, Sarah, Richter, Daniel J., Yoshikawa, Genki, Dimier, Celine, Kandels-lewis, Stefanie, Picheral, Marc, Searson, Sarah, Jaillon, Olivier, Aury, Jean-marc, Karsenti, Eric, Sullivan, Matthew B., Sunagawa, Shinichi, Bork, Peer, Not, Fabrice, Hingamp, Pascal, Raes, Jeroen, Guidi, Lionel, Ogata, Hiroyuki, De Vargas, Colomban, Iudicone, Daniele, Bowler, Chris, Wincker, Patrick, and Tara Oceans Coordinators

Abstract

While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.

Published
2018
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348. Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.

Author

Solden, Lindsey M, Solden, Lindsey M, Naas, Adrian E, Roux, Simon, Daly, Rebecca A, Collins, William B, Nicora, Carrie D, Purvine, Sam O, Hoyt, David W, Schückel, Julia, Jørgensen, Bodil, Willats, William, Spalinger, Donald E, Firkins, Jeffrey L, Lipton, Mary S, Sullivan, Matthew B, Pope, Phillip B, Wrighton, Kelly C, Solden, Lindsey M, Solden, Lindsey M, Naas, Adrian E, Roux, Simon, Daly, Rebecca A, Collins, William B, Nicora, Carrie D, Purvine, Sam O, Hoyt, David W, Schückel, Julia, Jørgensen, Bodil, Willats, William, Spalinger, Donald E, Firkins, Jeffrey L, Lipton, Mary S, Sullivan, Matthew B, Pope, Phillip B, and Wrighton, Kelly C

Abstract

Because of their agricultural value, there is a great body of research dedicated to understanding the microorganisms responsible for rumen carbon degradation. However, we lack a holistic view of the microbial food web responsible for carbon processing in this ecosystem. Here, we sampled rumen-fistulated moose, allowing access to rumen microbial communities actively degrading woody plant biomass in real time. We resolved 1,193 viral contigs and 77 unique, near-complete microbial metagenome-assembled genomes, many of which lacked previous metabolic insights. Plant-derived metabolites were measured with NMR and carbohydrate microarrays to quantify the carbon nutrient landscape. Network analyses directly linked measured metabolites to expressed proteins from these unique metagenome-assembled genomes, revealing a genome-resolved three-tiered carbohydrate-fuelled trophic system. This provided a glimpse into microbial specialization into functional guilds defined by specific metabolites. To validate our proteomic inferences, the catalytic activity of a polysaccharide utilization locus from a highly connected metabolic hub genome was confirmed using heterologous gene expression. Viral detected proteins and linkages to microbial hosts demonstrated that phage are active controllers of rumen ecosystem function. Our findings elucidate the microbial and viral members, as well as their metabolic interdependencies, that support in situ carbon degradation in the rumen ecosystem.

Published
2018

349. Host-linked soil viral ecology along a permafrost thaw gradient.

Author

Emerson, Joanne B, Emerson, Joanne B, Roux, Simon, Brum, Jennifer R, Bolduc, Benjamin, Woodcroft, Ben J, Jang, Ho Bin, Singleton, Caitlin M, Solden, Lindsey M, Naas, Adrian E, Boyd, Joel A, Hodgkins, Suzanne B, Wilson, Rachel M, Trubl, Gareth, Li, Changsheng, Frolking, Steve, Pope, Phillip B, Wrighton, Kelly C, Crill, Patrick M, Chanton, Jeffrey P, Saleska, Scott R, Tyson, Gene W, Rich, Virginia I, Sullivan, Matthew B, Emerson, Joanne B, Emerson, Joanne B, Roux, Simon, Brum, Jennifer R, Bolduc, Benjamin, Woodcroft, Ben J, Jang, Ho Bin, Singleton, Caitlin M, Solden, Lindsey M, Naas, Adrian E, Boyd, Joel A, Hodgkins, Suzanne B, Wilson, Rachel M, Trubl, Gareth, Li, Changsheng, Frolking, Steve, Pope, Phillip B, Wrighton, Kelly C, Crill, Patrick M, Chanton, Jeffrey P, Saleska, Scott R, Tyson, Gene W, Rich, Virginia I, and Sullivan, Matthew B

Abstract

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1-7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8-10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.

Published
2018

350. Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.

Author

Trubl, Gareth, Trubl, Gareth, Jang, Ho Bin, Roux, Simon, Emerson, Joanne B, Solonenko, Natalie, Vik, Dean R, Solden, Lindsey, Ellenbogen, Jared, Runyon, Alexander T, Bolduc, Benjamin, Woodcroft, Ben J, Saleska, Scott R, Tyson, Gene W, Wrighton, Kelly C, Sullivan, Matthew B, Rich, Virginia I, Trubl, Gareth, Trubl, Gareth, Jang, Ho Bin, Roux, Simon, Emerson, Joanne B, Solonenko, Natalie, Vik, Dean R, Solden, Lindsey, Ellenbogen, Jared, Runyon, Alexander T, Bolduc, Benjamin, Woodcroft, Ben J, Saleska, Scott R, Tyson, Gene W, Wrighton, Kelly C, Sullivan, Matthew B, and Rich, Virginia I

Abstract

Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteobacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. IMPORTANCE This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in

Published
2018

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