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3. The same strain of Piscine orthoreovirus (PRV-1) is involved with the development of different, but related, diseases in Atlantic and Pacific Salmon in British Columbia

Author

Di Cicco, Emiliano, Ferguson, Hugh W, Kaukinen, Karia H, Schulze, Angela D, Li, Shaorong, Tabata, Amy, Gunther, Oliver P, Mordecai, Gideon, Suttle, Curtis A, and Miller, Kristina M

Subjects
Quantitative Biology - Cell Behavior
Abstract

Piscine orthoreovirus Strain PRV-1 is the causative agent of heart and skeletal muscle inflammation (HSMI) in Atlantic salmon (Salmo salar). Given its high prevalence in net pen salmon, debate has arisen on whether PRV poses a risk to migratory salmon, especially in British Columbia (BC) where commercially important wild Pacific salmon are in decline. Various strains of PRV have been associated with diseases in Pacific salmon, including erythrocytic inclusion body syndrome (EIBS), HSMI-like disease, and jaundice/anemia in Japan, Norway, Chile and Canada. We examine the developmental pathway of HSMI and jaundice/anemia associated with PRV-1 in farmed Atlantic and Chinook (Oncorhynchus tshawytscha) salmon in BC, respectively. In situ hybridization localized PRV-1 within developing lesions in both diseases. The two diseases showed dissimilar pathological pathways, with inflammatory lesions in heart and skeletal muscle in Atlantic salmon, and degenerative-necrotic lesions in kidney and liver in Chinook salmon, plausibly explained by differences in PRV load tolerance in red blood cells. Viral genome sequencing revealed no consistent differences in PRV-1 variants intimately involved in the development of both diseases, suggesting that migratory Chinook salmon may be at more than a minimal risk of disease from exposure to the high levels of PRV occurring on salmon farms., Comment: This is a journal authorized pre-release of an un-copyedited version of an article accepted for publication in FACETS on 23 April 2018 (DOI 10.1139/facets-2018-0008). The final published version is expected to be published online in May/June 2018

Published
2018
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4. 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, and Eloe-Fadrosh, Emiley A

Subjects
Microbiology, Biological Sciences, Genetics, Human Genome, Databases, Genetic, Genome, Viral, Genomics, Virus Cultivation, Viruses
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

5. Virioplankton assemblages from challenger deep, the deepest place in the oceans

Author

Gao, Chen, Liang, Yantao, Jiang, Yong, Paez-Espino, David, Han, Meiaoxue, Gu, Chengxiang, Wang, Meiwen, Yang, Yumei, Liu, Fengjiao, Yang, Qingwei, Gong, Zheng, Zhang, Xinran, Luo, Zhixiang, He, Hui, Guo, Cui, Shao, Hongbing, Zhou, Chun, Shi, Yang, Xin, Yu, Xing, Jinyan, Tang, Xuexi, Qin, Qilong, Zhang, Yu-Zhong, He, Jianfeng, Jiao, Nianzhi, McMinn, Andrew, Tian, Jiwei, Suttle, Curtis A., and Wang, Min

Published
2022
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6. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il-Ryong, Ciuffo, Marina, Clegg, J. Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B. H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas, Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, Martin H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy H., Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Lǐ, Jiànróng, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong-Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, and Zhou, Xueping

Published
2021
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7. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Agwanda, Bernard R., Al Kubrusli, Rim, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Basler, Christopher F., Bavari, Sina, Beer, Martin, Bejerman, Nicolas, Bennett, Andrew J., Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol D., Blasdell, Kim R., Blystad, Dag-Ragnar, Bojko, Jamie, Borth, Wayne B., Bradfute, Steven, Breyta, Rachel, Briese, Thomas, Brown, Paul A., Brown, Judith K., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Büttner, Carmen, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chandran, Kartik, Charrel, Rémi N., Cheng, Qi, Chiaki, Yuya, Chiapello, Marco, Choi, Il-Ryong, Ciuffo, Marina, Clegg, J. Christopher S., Crozier, Ian, Dal Bó, Elena, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Debat, Humberto, Dheilly, Nolwenn M., Di Cicco, Emiliano, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolnik, Olga, Drebot, Michael A., Drexler, J. Felix, Dundon, William G., Duprex, W. Paul, Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Ferguson, Hugh W., Fooks, Anthony R., Forgia, Marco, Formenty, Pierre B. H., Fránová, Jana, Freitas-Astúa, Juliana, Fu, Jingjing, Fürl, Stephanie, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gaskin, Thomas, Gonzalez, Jean-Paul J., Griffiths, Anthony, Goldberg, Tony L., Groschup, Martin H., Günther, Stephan, Hall, Roy A., Hammond, John, Han, Tong, Hepojoki, Jussi, Hewson, Roger, Hong, Jiang, Hong, Ni, Hongo, Seiji, Horie, Masayuki, Hu, John S., Hu, Tao, Hughes, Holly R., Hüttner, Florian, Hyndman, Timothy H., Ilyas, M., Jalkanen, Risto, Jiāng, Dàohóng, Jonson, Gilda B., Junglen, Sandra, Kadono, Fujio, Kaukinen, Karia H., Kawate, Michael, Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Koloniuk, Igor, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kubota, Kenji, Kurath, Gael, Laenen, Lies, Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lefkowitz, Elliot J., Leroy, Eric M., Li, Shaorong, Li, Longhui, Lǐ, Jiànróng, Liu, Huazhen, Lukashevich, Igor S., Maes, Piet, de Souza, William Marciel, Marklewitz, Marco, Marshall, Sergio H., Marzano, Shin-Yi L., Massart, Sebastien, McCauley, John W., Melzer, Michael, Mielke-Ehret, Nicole, Miller, Kristina M., Ming, Tobi J., Mirazimi, Ali, Mordecai, Gideon J., Mühlbach, Hans-Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R. T., Olmedo-Velarde, Alejandro, Palacios, Gustavo, Pallás, Vicente, Pályi, Bernadett, Papa, Anna, Paraskevopoulou, Sofia, Park, Adam C., Parrish, Colin R., Patterson, David A., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Peracchio, Carlotta, Pérez, Daniel R., Postler, Thomas S., Qi, Liying, Radoshitzky, Sheli R., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Luna, Gabriel Robles, Romanowski, Víctor, Rota, Paul, Rubbenstroth, Dennis, Rubino, Luisa, Runstadler, Jonathan A., Sabanadzovic, Sead, Sall, Amadou Alpha, Salvato, Maria S., Sang, Rosemary, Sasaya, Takahide, Schulze, Angela D., Schwemmle, Martin, Shi, Mang, Shí, Xiǎohóng, Shí, Zhènglì, Shimomoto, Yoshifumi, Shirako, Yukio, Siddell, Stuart G., Simmonds, Peter, Sironi, Manuela, Smagghe, Guy, Smither, Sophie, Song, Jin-Won, Spann, Kirsten, Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Sugano, Jari, Suttle, Curtis A., Tabata, Amy, Takada, Ayato, Takeuchi, Shigeharu, Tchouassi, David P., Teffer, Amy, Tesh, Robert B., Thornburg, Natalie J., Tomitaka, Yasuhiro, Tomonaga, Keizō, Tordo, Noël, Torto, Baldwyn, Towner, Jonathan S., Tsuda, Shinya, Tu, Changchun, Turina, Massimo, Tzanetakis, Ioannis E., Uchida, Janice, Usugi, Tomio, Vaira, Anna Maria, Vallino, Marta, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, von Bargen, Susanne, Wada, Jiro, Wahl, Victoria, Walker, Peter J., Wang, Lin-Fa, Wang, Guoping, Wang, Yanxiang, Wang, Yaqin, Waqas, Muhammad, Wèi, Tàiyún, Wen, Shaohua, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wu, Jiangxiang, Xu, Lei, Yanagisawa, Hironobu, Yang, Caixia, Yang, Zuokun, Zerbini, F. Murilo, Zhai, Lifeng, Zhang, Yong-Zhen, Zhang, Song, Zhang, Jinguo, Zhang, Zhe, and Zhou, Xueping

Published
2021
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9. A compendium of multi-omic sequence information from the Saanich Inlet water column.

Author

Hawley, Alyse K, Torres-Beltrán, Mónica, Zaikova, Elena, Walsh, David A, Mueller, Andreas, Scofield, Melanie, Kheirandish, Sam, Payne, Chris, Pakhomova, Larysa, Bhatia, Maya, Shevchuk, Olena, Gies, Esther A, Fairley, Diane, Malfatti, Stephanie A, Norbeck, Angela D, Brewer, Heather M, Pasa-Tolic, Ljiljana, Del Rio, Tijana Glavina, Suttle, Curtis A, Tringe, Susannah, and Hallam, Steven J

Abstract

Marine oxygen minimum zones (OMZs) are widespread regions of the ocean that are currently expanding due to global warming. While inhospitable to most metazoans, OMZs are hotspots for microbial mediated biogeochemical cycling of carbon, nitrogen and sulphur, contributing disproportionately to marine nitrogen loss and climate active trace gas production. Our current understanding of microbial community responses to OMZ expansion is limited by a lack of time-resolved data sets linking multi-omic sequence information (DNA, RNA, protein) to geochemical parameters and process rates. Here, we present six years of time-resolved multi-omic observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique multi-omic framework for studying microbial community responses to ocean deoxygenation along defined geochemical gradients in OMZ waters.

Published
2017

12. Functional Diversity : An Epistemic Roadmap

Author

MALATERRE, CHRISTOPHE, DUSSAULT, ANTOINE C., ROUSSEAU-MERMANS, SOPHIA, BARKER, GILLIAN, BEISNER, BEATRIX E., BOUCHARD, FRÉDÉRIC, DESJARDINS, ERIC, HANDA, I. TANYA, KEMBEL, STEVEN W., LAJOIE, GENEVIÈVE, MARIS, VIRGINIE, MUNSON, ALISON D., ODENBAUGH, JAY, POISOT, TIMOTHÉE, SHAPIRO, B. JESSE, and SUTTLE, CURTIS A.

Published
2019

14. Corrigendum: Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea

Author

Labonté, Jessica M and Suttle, Curtis A

Subjects
Microbiology, Biological Sciences, Genetics, Bayesian model, risk-based surveillance, eradication program, spatial epidemiology, backyard pigs, Gokushovirinae, Microviridae, biogeography, ocean viruses, ssDNA viruses, virus diversity, Environmental Science and Management, Soil Sciences, Medical microbiology
Abstract

[This corrects the article on p. 404 in vol. 4, PMID: 24399999.].

Published
2015

16. Identification of hidden N4-like viruses and their interactions with hosts

Author

Zheng, Kaiyang, primary, Liang, Yantao, additional, Paez-Espino, David, additional, Zou, Xiao, additional, Gao, Chen, additional, Shao, Hongbing, additional, Sung, Yeong Yik, additional, Mok, Wen Jye, additional, Wong, Li Lian, additional, Zhang, Yu-Zhong, additional, Tian, Jiwei, additional, Chen, Feng, additional, Jiao, Nianzhi, additional, Suttle, Curtis A., additional, He, Jianfeng, additional, McMinn, Andrew, additional, and Wang, Min, additional

Published
2023
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21. Author Correction: A compendium of geochemical information from the Saanich Inlet water column

Author

Torres-Beltrán, Mónica, Hawley, Alyse K., Capelle, David, Zaikova, Elena, Walsh, David A., Mueller, Andreas, Scofield, Melanie, Payne, Chris, Pakhomova, Larysa, Kheirandish, Sam, Finke, Jan, Bhatia, Maya, Shevchuk, Olena, Gies, Esther A., Fairley, Diane, Michiels, Céline, Suttle, Curtis A., Whitney, Frank, Crowe, Sean A., Tortell, Philippe D., and Hallam, Steven J.

Published
2019
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23. Patterns of microbial abundance and heterotrophic activity along nitrogen and salinity gradients in coastal wetlands

Author

Ministerio de Economía y Competitividad (España), Ministerio de Ciencia e Innovación (España), Universidad de Granada, Batanero, Gema L. [0000-0001-6657-2392], Green, Andy J. [0000-0002-1268-4951], Amat, Juan A. [0000-0003-1685-1056], Vittecoq, Marion [0000-0002-8930-6051], Suttle, Curtis A. [0000-0002-0372-0033], Reche, Isabel [0000-0003-2908-1724], Batanero, Gema L., Green, Andy J., Amat, Juan A., Vittecoq, Marion, Suttle, Curtis A., Reche, Isabel, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia e Innovación (España), Universidad de Granada, Batanero, Gema L. [0000-0001-6657-2392], Green, Andy J. [0000-0002-1268-4951], Amat, Juan A. [0000-0003-1685-1056], Vittecoq, Marion [0000-0002-8930-6051], Suttle, Curtis A. [0000-0002-0372-0033], Reche, Isabel [0000-0003-2908-1724], Batanero, Gema L., Green, Andy J., Amat, Juan A., Vittecoq, Marion, Suttle, Curtis A., and Reche, Isabel

Abstract

Coastal wetlands are valuable aquatic ecosystems with high biological productivity, which provide services such as a reduction in nitrogen loading into coastal waters and storage of organic carbon acting as carbon dioxide sinks. The predicted rise of sea level or freshwater extractions, particularly in the arid Mediterranean biome, will salinize many coastal wetlands. However, there is considerable uncertainty about how salinization will affect microbial communities and biogeochemical processes. We determined the abundance of total prokaryotes, cyanobacteria, and viruses and quantified the heterotrophic production of prokaryotes sensitive- (predominantly Bacteria) and resistant- (predominantly Archaea) to erythromycin in 112 ponds from nine coastal wetlands. We explored the main drivers of prokaryotic abundance and heterotrophic production using generalized linear models (GLMs). The best GLM, including all the wetlands, indicated that the concentration of total dissolved nitrogen (TDN) positively affected the total abundance of prokaryotes and the heterotrophic erythromycin-resistant (ery-R) production. In contrast, heterotrophic erythromycin-sensitive (ery-S) production was negatively related to TDN. This negative relationship appeared to be mediated by salinity and virus abundance. Heterotrophic ery-S production declined as salinity and virus abundance increased. Consequently, we observed a switch from heterotrophic ery-S production towards ery-R production as salinity and virus abundance increased. Our results imply that microbial activity will change from heterotrophic bacterial-dominated processes to archaeal-dominated processes with anthropogenic nitrogen and salinization increases. However, more studies are required to link the mineralization rates of dissolved nitrogen and organic carbon with specific archaeal taxa to enable more accurate predictions on future scenarios in coastal wetlands.

Published
2022

28. Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming.

Author

Ji, Mengzhi, Suttle, Curtis A1, Ogunseitan, Oladele A, Ji, Mengzhi, Fan, Xiangyu, Cornell, Carolyn R, Zhang, Ya, Yuan, Mengting Maggie, Tian, Zhen, Sun, Kaili, Gao, Rongfeng, Liu, Yang, Zhou, Jizhong, Ji, Mengzhi, Suttle, Curtis A1, Ogunseitan, Oladele A, Ji, Mengzhi, Fan, Xiangyu, Cornell, Carolyn R, Zhang, Ya, Yuan, Mengting Maggie, Tian, Zhen, Sun, Kaili, Gao, Rongfeng, Liu, Yang, and Zhou, Jizhong

Abstract

The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the

Published
2023

38. Divergent RNA viruses infecting sea lice, major ectoparasites of fish.

Author

Chang, Tianyi, Hunt, Brian P. V., Hirai, Junya, and Suttle, Curtis A.

Subjects
FUNGAL viruses, SMALL interfering RNA, RNA viruses, LEPEOPHTHEIRUS salmonis, VIRUS diversity, ECTOPARASITES, PHYTOPATHOGENIC fungi
Abstract

Sea lice, the major ectoparasites of fish, have significant economic impacts on wild and farmed finfish, and have been implicated in the decline of wild salmon populations. As blood-feeding arthropods, sea lice may also be reservoirs for viruses infecting fish. However, except for two groups of negative-strand RNA viruses within the order Mononegavirales, nothing is known about viruses of sea lice. Here, we used transcriptomic data from three key species of sea lice (Lepeophtheirus salmonis, Caligus clemensi, and Caligus rogercresseyi) to identify 32 previously unknown RNA viruses. The viruses encompassed all the existing phyla of RNA viruses, with many placed in deeply branching lineages that likely represent new families and genera. Importantly, the presence of canonical virus-derived small interfering RNAs (viRNAs) indicates that most of these viruses infect sea lice, even though in some cases their closest classified relatives are only known to infect plants or fungi. We also identified both viRNAs and PIWI-interacting RNAs (piRNAs) from sequences of a bunya-like and two qin-like viruses in C. rogercresseyi. Our analyses showed that most of the viruses found in C. rogercresseyi occurred in multiple life stages, spanning from planktonic to parasitic stages. Phylogenetic analysis revealed that many of the viruses infecting sea lice were closely related to those that infect a wide array of eukaryotes with which arthropods associate, including fungi and parasitic tapeworms, implying that over evolutionary time there has been cross-phylum and cross-kingdom switching of viruses between arthropods and other eukaryotes. Overall, this study greatly expands our view of virus diversity in crustaceans, identifies viruses that infect and replicate in sea lice, and provides evidence that over evolutionary time, viruses have switched between arthropods and eukaryotic hosts in other phyla and kingdoms. Author summary: Sea lice are parasitic copepods and the major ectoparasites of fish. They have significant impacts on wild and farmed fish, and have been implicated in the decline of salmon populations; yet, viruses of sea lice are largely unknown. Here, we analyzed transcriptomes and small RNAs from three key species of sea lice and identified 32 previously unknown RNA viruses, many of which were actively replicating. Not only do these data greatly expand the known viral diversity in copepods, phylogenetic analysis provides evidence that over evolutionary time there has been extensive transmission of viruses between arthropods and other eukaryotes. Viruses replicating in sea lice included hypo-like and sobemo-like viruses, which previously were not known to infect arthropods. This study advances our view of the diversity and evolution of RNA viruses associated with sea lice, obtains genetic blueprints of viruses infecting sea lice, and provides approaches that may be further used to identify unknown viral pathogens in other ecologically and economically important crustaceans. [ABSTRACT FROM AUTHOR]

Published
2023
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43. Eye-like ocelloids are built from different endosymbiotically acquired components

Author

Gavelis, Gregory S., Hayakawa, Shiho, White, III, Richard A., Gojobori, Takashi, Suttle, Curtis A., Keeling, Patrick J., and Leander, Brian S.

Subjects
Dinoflagellates -- Physiological aspects, Mitochondria -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Multicellularity is often considered a prerequisite for morphological complexity, as seen in the camera-type eyes found in several groups of animals. A notable exception exists in single-celled eukaryotes called dinoflagellates, some of which have an eye-like 'ocelloid' consisting of subcellular analogues to a cornea, lens, iris, and retina (1). These planktonic cells are uncultivated and rarely encountered in environmental samples, obscuring the function and evolutionary origin of the ocelloid. Here we show, using a combination of electron microscopy, tomography, isolated-organelle genomics, and single-cell genomics, that ocelloids are built from pre-existing organelles, including a cornea-like layer made of mitochondria and a retinal body made of anastomosing plastids. We find that the retinal body forms the central core of a network of peridinin-type plastids, which in dinoflagellates and their relatives originated through an ancient endosymbiosis with a red alga (2). As such, the ocelloid is a chimaeric structure, incorporating organelles with different endosymbiotic histories. The anatomical complexity of single-celled organisms may be limited by the components available for differentiation, but the ocelloid shows that preexisting organelles can be assembled into a structure so complex that it was initially mistaken for a multicellular eye (3). Although mitochondria and plastids are acknowledged chiefly for their metabolic roles, they can also be building blocks for greater structural complexity., Many organisms can orient to light. In some single-celled eukaryotes, such as Chlamydomonas and many dinoflagellates, an 'eyespot' directs photons onto photoreceptors on the flagellum, allowing the cell to respond [...]

Published
2015

48. WTO must ban harmful fisheries subsidies

Author

Sumaila, U. Rashid, primary, Skerritt, Daniel J., additional, Schuhbauer, Anna, additional, Villasante, Sebastian, additional, Cisneros-Montemayor, Andrés M., additional, Sinan, Hussain, additional, Burnside, Duncan, additional, Abdallah, Patrízia Raggi, additional, Abe, Keita, additional, Addo, Kwasi A., additional, Adelsheim, Julia, additional, Adewumi, Ibukun J., additional, Adeyemo, Olanike K., additional, Adger, Neil, additional, Adotey, Joshua, additional, Advani, Sahir, additional, Afrin, Zahidah, additional, Aheto, Denis, additional, Akintola, Shehu L., additional, Akpalu, Wisdom, additional, Alam, Lubna, additional, Alava, Juan José, additional, Allison, Edward H., additional, Amon, Diva J., additional, Anderies, John M., additional, Anderson, Christopher M., additional, Andrews, Evan, additional, Angelini, Ronaldo, additional, Anna, Zuzy, additional, Antweiler, Werner, additional, Arizi, Evans K., additional, Armitage, Derek, additional, Arthur, Robert I., additional, Asare, Noble, additional, Asche, Frank, additional, Asiedu, Berchie, additional, Asuquo, Francis, additional, Badmus, Lanre, additional, Bailey, Megan, additional, Ban, Natalie, additional, Barbier, Edward B., additional, Barley, Shanta, additional, Barnes, Colin, additional, Barrett, Scott, additional, Basurto, Xavier, additional, Belhabib, Dyhia, additional, Bennett, Elena, additional, Bennett, Nathan J., additional, Benzaken, Dominique, additional, Blasiak, Robert, additional, Bohorquez, John J., additional, Bordehore, Cesar, additional, Bornarel, Virginie, additional, Boyd, David R., additional, Breitburg, Denise, additional, Brooks, Cassandra, additional, Brotz, Lucas, additional, Campbell, Donovan, additional, Cannon, Sara, additional, Cao, Ling, additional, Cardenas Campo, Juan C., additional, Carpenter, Steve, additional, Carpenter, Griffin, additional, Carson, Richard T., additional, Carvalho, Adriana R., additional, Castrejón, Mauricio, additional, Caveen, Alex J., additional, Chabi, M. Nicole, additional, Chan, Kai M. A., additional, Chapin, F. Stuart, additional, Charles, Tony, additional, Cheung, William, additional, Christensen, Villy, additional, Chuku, Ernest O., additional, Church, Trevor, additional, Clark, Colin, additional, Clarke, Tayler M., additional, Cojocaru, Andreea L., additional, Copeland, Brian, additional, Crawford, Brian, additional, Crépin, Anne-Sophie, additional, Crowder, Larry B., additional, Cury, Philippe, additional, Cutting, Allison N., additional, Daily, Gretchen C., additional, Da-Rocha, Jose Maria, additional, Das, Abhipsita, additional, de la Puente, Santiago, additional, de Zeeuw, Aart, additional, Deikumah, Savior K. S., additional, Deith, Mairin, additional, Dewitte, Boris, additional, Doubleday, Nancy, additional, Duarte, Carlos M., additional, Dulvy, Nicholas K., additional, Eddy, Tyler, additional, Efford, Meaghan, additional, Ehrlich, Paul R., additional, Elsler, Laura G., additional, Fakoya, Kafayat A., additional, Falaye, A. Eyiwunmi, additional, Fanzo, Jessica, additional, Fitzsimmons, Clare, additional, Flaaten, Ola, additional, Florko, Katie R. N., additional, Aviles, Marta Flotats, additional, Folke, Carl, additional, Forrest, Andrew, additional, Freeman, Peter, additional, Freire, Kátia M. F., additional, Froese, Rainer, additional, Frölicher, Thomas L., additional, Gallagher, Austin, additional, Garcon, Veronique, additional, Gasalla, Maria A., additional, Gephart, Jessica A., additional, Gibbons, Mark, additional, Gillespie, Kyle, additional, Giron-Nava, Alfredo, additional, Gjerde, Kristina, additional, Glaser, Sarah, additional, Golden, Christopher, additional, Gordon, Line, additional, Govan, Hugh, additional, Gryba, Rowenna, additional, Halpern, Benjamin S., additional, Hanich, Quentin, additional, Hara, Mafaniso, additional, Harley, Christopher D. G., additional, Harper, Sarah, additional, Harte, Michael, additional, Helm, Rebecca, additional, Hendrix, Cullen, additional, Hicks, Christina C., additional, Hood, Lincoln, additional, Hoover, Carie, additional, Hopewell, Kristen, additional, Horta e Costa, Bárbara B., additional, Houghton, Jonathan D. R., additional, Iitembu, Johannes. A., additional, Isaacs, Moenieba, additional, Isahaku, Sadique, additional, Ishimura, Gakushi, additional, Islam, Monirul, additional, Issifu, Ibrahim, additional, Jackson, Jeremy, additional, Jacquet, Jennifer, additional, Jensen, Olaf P., additional, Ramon, Jorge Jimenez, additional, Jin, Xue, additional, Jonah, Alberta, additional, Jouffray, Jean-Baptiste, additional, Juniper, S. Kim, additional, Jusoh, Sufian, additional, Kadagi, Isigi, additional, Kaeriyama, Masahide, additional, Kaiser, Michel J., additional, Kaiser, Brooks Alexandra, additional, Kakujaha-Matundu, Omu, additional, Karuaihe, Selma T., additional, Karumba, Mary, additional, Kemmerly, Jennifer D., additional, Khan, Ahmed S., additional, Kimani, Patrick, additional, Kleisner, Kristin, additional, Knowlton, Nancy, additional, Kotowicz, Dawn, additional, Kurien, John, additional, Kwong, Lian E., additional, Lade, Steven, additional, Laffoley, Dan, additional, Lam, Mimi E., additional, Lam, Vicky W. L., additional, Lange, Glenn-Marie, additional, Latif, Mohd T., additional, Le Billon, Philippe, additional, Le Brenne, Valérie, additional, Le Manach, Frédéric, additional, Levin, Simon A., additional, Levin, Lisa, additional, Limburg, Karin E., additional, List, John, additional, Lombard, Amanda T., additional, Lopes, Priscila F. M., additional, Lotze, Heike K., additional, Mallory, Tabitha G., additional, Mangar, Roshni S., additional, Marszalec, Daniel, additional, Mattah, Precious, additional, Mayorga, Juan, additional, McAusland, Carol, additional, McCauley, Douglas J., additional, McLean, Jeffrey, additional, McMullen, Karly, additional, Meere, Frank, additional, Mejaes, Annie, additional, Melnychuk, Michael, additional, Mendo, Jaime, additional, Micheli, Fiorenza, additional, Millage, Katherine, additional, Miller, Dana, additional, Mohamed, Kolliyil Sunil, additional, Mohammed, Essam, additional, Mokhtar, Mazlin, additional, Morgan, Lance, additional, Muawanah, Umi, additional, Munro, Gordon R., additional, Murray, Grant, additional, Mustafa, Saleem, additional, Nayak, Prateep, additional, Newell, Dianne, additional, Nguyen, Tu, additional, Noack, Frederik, additional, Nor, Adibi M., additional, Nunoo, Francis K. E., additional, Obura, David, additional, Okey, Tom, additional, Okyere, Isaac, additional, Onyango, Paul, additional, Oostdijk, Maartje, additional, Orlov, Polina, additional, Österblom, Henrik, additional, Owens, Dwight, additional, Owens, Tessa, additional, Oyinlola, Mohammed, additional, Pacoureau, Nathan, additional, Pakhomov, Evgeny, additional, Abrantes, Juliano Palacios, additional, Pascual, Unai, additional, Paulmier, Aurélien, additional, Pauly, Daniel, additional, Pèlèbè, Rodrigue Orobiyi Edéya, additional, Peñalosa, Daniel, additional, Pennino, Maria G., additional, Peterson, Garry, additional, Pham, Thuy T. T., additional, Pinkerton, Evelyn, additional, Polasky, Stephen, additional, Polunin, Nicholas V. C., additional, Prah, Ekow, additional, Ramírez, Jorge, additional, Relano, Veronica, additional, Reygondeau, Gabriel, additional, Robadue, Don, additional, Roberts, Callum, additional, Rogers, Alex, additional, Roumbedakis, Katina, additional, Sala, Enric, additional, Scheffer, Marten, additional, Segerson, Kathleen, additional, Seijo, Juan Carlos, additional, Seto, Karen C., additional, Shogren, Jason F., additional, Silver, Jennifer J., additional, Singh, Gerald, additional, Soszynski, Ambre, additional, Splichalova, Dacotah-Victoria, additional, Spring, Margaret, additional, Stage, Jesper, additional, Stephenson, Fabrice, additional, Stewart, Bryce D., additional, Sultan, Riad, additional, Suttle, Curtis, additional, Tagliabue, Alessandro, additional, Tall, Amadou, additional, Talloni-Álvarez, Nicolás, additional, Tavoni, Alessandro, additional, Taylor, D. R. Fraser, additional, Teh, Louise S. L., additional, Teh, Lydia C. L., additional, Thiebot, Jean-Baptiste, additional, Thiele, Torsten, additional, Thilsted, Shakuntala H., additional, Thumbadoo, Romola V., additional, Tigchelaar, Michelle, additional, Tol, Richard S. J., additional, Tortell, Philippe, additional, Troell, Max, additional, Uzmanoğlu, M. Selçuk, additional, van Putten, Ingrid, additional, van Santen, Gert, additional, Villaseñor-Derbez, Juan Carlos, additional, Wabnitz, Colette C. C., additional, Walsh, Melissa, additional, Walsh, J. P., additional, Wambiji, Nina, additional, Weber, Elke U., additional, Westley, Frances, additional, Williams, Stella, additional, Wisz, Mary S., additional, Worm, Boris, additional, Xiao, Lan, additional, Yagi, Nobuyuki, additional, Yamazaki, Satoshi, additional, Yang, Hong, additional, and Zeller, Dirk, additional

Published
2021
Full Text
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49. Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas

Author

Gao, Chen, primary, Xia, Jun, additional, Zhou, Xinhao, additional, Liang, Yantao, additional, Jiang, Yong, additional, Wang, Meiwen, additional, Shao, Hongbing, additional, Shi, Xiaochong, additional, Guo, Cui, additional, He, Hui, additional, Wang, Hualong, additional, He, Jianfeng, additional, Hu, Denghui, additional, Wang, Xiaoyu, additional, Zhao, Jinping, additional, Zhang, Yu-Zhong, additional, Sung, Yeong Yik, additional, Mok, Wen Jye, additional, Wong, Li Lian, additional, McMinn, Andrew, additional, Suttle, Curtis A., additional, and Wang, Min, additional

Published
2021
Full Text
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