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101. Gene duplication as a major force driving the genome expansion in some giant viruses

Author

Machado, Talita B., primary, Picorelli, Agnello C. R., additional, de Azevedo, Bruna L., additional, de Aquino, Isabella L. M., additional, Queiroz, Victória F., additional, Rodrigues, Rodrigo A. L., additional, Araújo, João Pessoa, additional, Ullmann, Leila S., additional, dos Santos, Thiago M., additional, Marques, Rafael E., additional, Guimarães, Samuel L., additional, Andrade, Ana Cláudia S. P., additional, Gularte, Juliana S., additional, Demoliner, Meriane, additional, Filippi, Micheli, additional, Pereira, Vyctoria M. A. G., additional, Spilki, Fernando R., additional, Krupovic, Mart, additional, Aylward, Frank O., additional, Del-Bem, Luiz-Eduardo, additional, and Abrahão, Jônatas S., additional

Published
2023
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103. An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity

Author

Athukoralage, Januka S., McMahon, Stephen A., Zhang, Changyi, Grüschow, Sabine, Graham, Shirley, Krupovic, Mart, and Whitaker, Rachel J.

Subjects
Genetic research, Nucleases -- Genetic aspects, Immunity -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The CRISPR system in bacteria and archaea provides adaptive immunity against mobile genetic elements. Type III CRISPR systems detect viral RNA, resulting in the activation of two regions of the Cas10 protein: an HD nuclease domain (which degrades viral DNA).sup.1,2 and a cyclase domain (which synthesizes cyclic oligoadenylates from ATP).sup.3-5. Cyclic oligoadenylates in turn activate defence enzymes with a CRISPR-associated Rossmann fold domain.sup.6, sculpting a powerful antiviral response.sup.7-10 that can drive viruses to extinction.sup.7,8. Cyclic nucleotides are increasingly implicated in host-pathogen interactions.sup.11-13. Here we identify a new family of viral anti-CRISPR (Acr) enzymes that rapidly degrade cyclic tetra-adenylate (cA.sub.4). The viral ring nuclease AcrIII-1 is widely distributed in archaeal and bacterial viruses and in proviruses. The enzyme uses a previously unknown fold to bind cA.sub.4 specifically, and a conserved active site to rapidly cleave this signalling molecule, allowing viruses to neutralize the type III CRISPR defence system. The AcrIII-1 family has a broad host range, as it targets cA.sub.4 signalling molecules rather than specific CRISPR effector proteins. Our findings highlight the crucial role of cyclic nucleotide signalling in the conflict between viruses and their hosts. Bacteria and archaea use cyclic oligoadenylate molecules as part of the CRISPR system for antiviral defence; here, a family of viral enzymes that rapidly degrades cyclic oligoadenylates is identified and biochemically and structurally described., Author(s): Januka S. Athukoralage [sup.1] , Stephen A. McMahon [sup.1] , Changyi Zhang [sup.3] [sup.4] , Sabine Grüschow [sup.1] , Shirley Graham [sup.1] , Mart Krupovic [sup.2] , Rachel J. [...]

Published
2020
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106. Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)

Author

Walker, Peter J., Siddell, Stuart G., Lefkowitz, Elliot J., Mushegian, Arcady R., Dempsey, Donald M., Dutilh, Bas E., Harrach, Balázs, Harrison, Robert L., Hendrickson, R. Curtis, Junglen, Sandra, Knowles, Nick J., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Nibert, Max, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, and Davison, Andrew J.

Published
2019
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109. Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018)

Author

Siddell, Stuart G., Walker, Peter J., Lefkowitz, Elliot J., Mushegian, Arcady R., Adams, Michael J., Dutilh, Bas E., Gorbalenya, Alexander E., Harrach, Balázs, Harrison, Robert L., Junglen, Sandra, Knowles, Nick J., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Nibert, Max, Rubino, Luisa, Sabanadzovic, Sead, Sanfaçon, Hélène, Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, and Davison, Andrew J.

Published
2019
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117. Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

Author

Kuhn, Jens H., primary, Abe, Junya, additional, Adkins, Scott, additional, Alkhovsky, Sergey V., additional, Avšič-Županc, Tatjana, additional, Ayllón, María A., additional, Bahl, Justin, additional, Balkema-Buschmann, Anne, additional, Ballinger, Matthew J., additional, Kumar Baranwal, Virendra, additional, Beer, Martin, additional, Bejerman, Nicolas, additional, Bergeron, Éric, additional, Biedenkopf, Nadine, additional, Blair, Carol D., additional, Blasdell, Kim R., additional, Blouin, Arnaud G., additional, Bradfute, Steven B., additional, Briese, Thomas, additional, Brown, Paul A., additional, Buchholz, Ursula J., additional, Buchmeier, Michael J., additional, Bukreyev, Alexander, additional, Burt, Felicity, additional, Büttner, Carmen, additional, Calisher, Charles H., additional, Cao, Mengji, additional, Casas, Inmaculada, additional, Chandran, Kartik, additional, Charrel, Rémi N., additional, Kumar Chaturvedi, Krishna, additional, Chooi, Kar Mun, additional, Crane, Anya, additional, Dal Bó, Elena, additional, Carlos de la Torre, Juan, additional, de Souza, William M., additional, de Swart, Rik L., additional, Debat, Humberto, additional, Dheilly, Nolwenn M., additional, Di Paola, Nicholas, additional, Di Serio, Francesco, additional, Dietzgen, Ralf G., additional, Digiaro, Michele, additional, Drexler, J. Felix, additional, Duprex, W. Paul, additional, Dürrwald, Ralf, additional, Easton, Andrew J., additional, Elbeaino, Toufic, additional, Ergünay, Koray, additional, Feng, Guozhong, additional, Firth, Andrew E., additional, Fooks, Anthony R., additional, Formenty, Pierre B. H., additional, Freitas-Astúa, Juliana, additional, Gago-Zachert, Selma, additional, Laura García, María, additional, García-Sastre, Adolfo, additional, Garrison, Aura R., additional, Gaskin, Thomas R., additional, Gong, Wenjie, additional, Gonzalez, Jean-Paul J., additional, de Bellocq, JoëlleGoüy, additional, Griffiths, Anthony, additional, Groschup, Martin H., additional, Günther, Ines, additional, Günther, Stephan, additional, Hammond, John, additional, Hasegawa, Yusuke, additional, Hayashi, Kazusa, additional, Hepojoki, Jussi, additional, Higgins, Colleen M., additional, Hongō, Seiji, additional, Horie, Masayuki, additional, Hughes, Holly R., additional, Hume, Adam J., additional, Hyndman, Timothy H., additional, Ikeda, Kenichi, additional, Jiāng, Dàohóng, additional, Jonson, Gilda B., additional, Junglen, Sandra, additional, Klempa, Boris, additional, Klingström, Jonas, additional, Kondō, Hideki, additional, Koonin, Eugene V., additional, Krupovic, Mart, additional, Kubota, Kenji, additional, Kurath, Gael, additional, Laenen, Lies, additional, Lambert, Amy J., additional, Lǐ, Jiànróng, additional, Li, Jun-Min, additional, Liu, Ran, additional, Lukashevich, Igor S., additional, MacDiarmid, Robin M., additional, Maes, Piet, additional, Marklewitz, Marco, additional, Marshall, Sergio H., additional, Marzano, Shin-Yi L., additional, McCauley, John W., additional, Mirazimi, Ali, additional, Mühlberger, Elke, additional, Nabeshima, Tomoyuki, additional, Naidu, Rayapati, additional, Natsuaki, Tomohide, additional, Navarro, Beatriz, additional, Navarro, José A., additional, Neriya, Yutaro, additional, Netesov, Sergey V., additional, Neumann, Gabriele, additional, Nowotny, Norbert, additional, Nunes, Márcio R. T., additional, Ochoa-Corona, Francisco M., additional, Okada, Tomoyuki, additional, Palacios, Gustavo, additional, Pallás, Vicente, additional, Papa, Anna, additional, Paraskevopoulou, Sofia, additional, Parrish, Colin R., additional, Pauvolid-Corrêa, Alex, additional, Pawęska, Janusz T., additional, Pérez, Daniel R., additional, Pfaff, Florian, additional, Plemper, Richard K., additional, Postler, Thomas S., additional, Rabbidge, Lee O., additional, Radoshitzky, Sheli R., additional, Ramos-González, Pedro L., additional, Rehanek, Marius, additional, Resende, Renato O., additional, Reyes, Carina A., additional, Rodrigues, Thaís C. S., additional, Romanowski, Víctor, additional, Rubbenstroth, Dennis, additional, Rubino, Luisa, additional, Runstadler, Jonathan A., additional, Sabanadzovic, Sead, additional, Sadiq, Sabrina, additional, Salvato, Maria S., additional, Sasaya, Takahide, additional, Schwemmle, Martin, additional, Sharpe, Stephen R., additional, Shi, Mang, additional, Shimomoto, Yoshifumi, additional, Kavi Sidharthan, Venkidusamy, additional, Sironi, Manuela, additional, Smither, Sophie, additional, Song, Jin-Won, additional, Spann, Kirsten M., additional, Spengler, Jessica R., additional, Stenglein, Mark D., additional, Takada, Ayato, additional, Takeyama, Sawana, additional, Tatara, Akio, additional, Tesh, Robert B., additional, Thornburg, Natalie J., additional, Tian, Xin, additional, Tischler, Nicole D., additional, Tomitaka, Yasuhiro, additional, Tomonaga, Keizō, additional, Tordo, Noël, additional, Tu, Changchun, additional, Turina, Massimo, additional, Tzanetakis, Ioannis E., additional, Maria Vaira, Anna, additional, van den Hoogen, Bernadette, additional, Vanmechelen, Bert, additional, Vasilakis, Nikos, additional, Verbeek, Martin, additional, von Bargen, Susanne, additional, Wada, Jiro, additional, Wahl, Victoria, additional, Walker, Peter J., additional, Waltzek, Thomas B., additional, Whitfield, Anna E., additional, Wolf, Yuri I., additional, Xia, Han, additional, Xylogianni, Evanthia, additional, Yanagisawa, Hironobu, additional, Yano, Kazutaka, additional, Ye, Gongyin, additional, Yuan, Zhiming, additional, Zerbini, F. Murilo, additional, Zhang, Guilin, additional, Zhang, Song, additional, Zhang, Yong-Zhen, additional, Zhao, Lu, additional, and Økland, Arnfinn Lodden, additional

Published
2023
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127. Interplay of intracellular and trans‐cellular DNA methylation in natural archaeal consortia.

Author

Reva, Oleg N., La Cono, Violetta, Crisafi, Francesca, Smedile, Francesco, Mudaliyar, Manasi, Ghosal, Debnath, Giuliano, Laura, Krupovic, Mart, and Yakimov, Michail M.

Subjects
DNA methylation, GENETIC regulation, TRANSCRIPTOMES, DNA damage, METHYLATION, CATECHOL-O-methyltransferase, DNA methyltransferases
Abstract

DNA methylation serves a variety of functions across all life domains. In this study, we investigated archaeal methylomics within a tripartite xylanolytic halophilic consortium. This consortium includes Haloferax lucertense SVX82, Halorhabdus sp. SVX81, and an ectosymbiotic Candidatus Nanohalococcus occultus SVXNc, a nano‐sized archaeon from the DPANN superphylum. We utilized PacBio SMRT and Illumina cDNA sequencing to analyse samples from consortia of different compositions for methylomics and transcriptomics. Endogenous cTAG methylation, typical of Haloferax, was accompanied in this strain by methylation at four other motifs, including GDGcHC methylation, which is specific to the ectosymbiont. Our analysis of the distribution of methylated and unmethylated motifs suggests that autochthonous cTAG methylation may influence gene regulation. The frequency of GRAGAaG methylation increased in highly expressed genes, while CcTTG and GTCGaGG methylation could be linked to restriction‐modification (RM) activity. Generally, the RM activity might have been reduced during the evolution of this archaeon to balance the protection of cells from intruders, the reduction of DNA damage due to self‐restriction in stressful environments, and the benefits of DNA exchange under extreme conditions. Our methylomics, transcriptomics and complementary electron cryotomography (cryo‐ET) data suggest that the nanohaloarchaeon exports its methyltransferase to methylate the Haloferax genome, unveiling a new aspect of the interaction between the symbiont and its host. [ABSTRACT FROM AUTHOR]

Published
2024
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129. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)

Author

King, Andrew M. Q., Lefkowitz, Elliot J., Mushegian, Arcady R., Adams, Michael J., Dutilh, Bas E., Gorbalenya, Alexander E., Harrach, Balázs, Harrison, Robert L., Junglen, Sandra, Knowles, Nick J., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Nibert, Max L., Rubino, Luisa, Sabanadzovic, Sead, Sanfaçon, Hélène, Siddell, Stuart G., Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, and Davison, Andrew J.

Published
2018
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130. Taxonomy of the order Mononegavirales: update 2018

Author

Amarasinghe, Gaya K., Aréchiga Ceballos, Nidia G., Banyard, Ashley C., Basler, Christopher F., Bavari, Sina, Bennett, Andrew J., Blasdell, Kim R., Briese, Thomas, Bukreyev, Alexander, Caì, Yíngyún, Calisher, Charles H., Campos Lawson, Cristine, Chandran, Kartik, Chapman, Colin A., Chiu, Charles Y., Choi, Kang-Seuk, Collins, Peter L., Dietzgen, Ralf G., Dolja, Valerian V., Dolnik, Olga, Domier, Leslie L., Dürrwald, Ralf, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Echevarría, Juan E., Fooks, Anthony R., Formenty, Pierre B. H., Fouchier, Ron A. M., Freuling, Conrad M., Ghedin, Elodie, Goldberg, Tony L., Hewson, Roger, Horie, Masayuki, Hyndman, Timothy H., Jiāng, Dàohóng, Kityo, Robert, Kobinger, Gary P., Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kurath, Gael, Lamb, Robert A., Lee, Benhur, Leroy, Eric M., Maes, Piet, Maisner, Andrea, Marston, Denise A., Mor, Sunil Kumar, Müller, Thomas, Mühlberger, Elke, Ramírez, Víctor Manuel Neira, Netesov, Sergey V., Ng, Terry Fei Fan, Nowotny, Norbert, Palacios, Gustavo, Patterson, Jean L., Pawęska, Janusz T., Payne, Susan L., Prieto, Karla, Rima, Bertus K., Rota, Paul, Rubbenstroth, Dennis, Schwemmle, Martin, Siddell, Stuart, Smither, Sophie J., Song, Qisheng, Song, Timothy, Stenglein, Mark D., Stone, David M., Takada, Ayato, Tesh, Robert B., Thomazelli, Luciano Matsumiya, Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., Vasilakis, Nikos, Vázquez-Morón, Sonia, Verdugo, Claudio, Volchkov, Viktor E., Wahl, Victoria, Walker, Peter J., Wang, David, Wang, Lin-Fa, Wellehan, James F. X., Wiley, Michael R., Whitfield, Anna E., Wolf, Yuri I., Yè, Gōngyín, Zhāng, Yǒng-Zhèn, and Kuhn, Jens H.

Published
2018
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131. Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018

Author

Maes, Piet, Alkhovsky, Sergey V., Bào, Yīmíng, Beer, Martin, Birkhead, Monica, Briese, Thomas, Buchmeier, Michael J., Calisher, Charles H., Charrel, Rémi N., Choi, Il Ryong, Clegg, Christopher S., de la Torre, Juan Carlos, Delwart, Eric, DeRisi, Joseph L., Di Bello, Patrick L., Di Serio, Francesco, Digiaro, Michele, Dolja, Valerian V., Drosten, Christian, Druciarek, Tobiasz Z., Du, Jiang, Ebihara, Hideki, Elbeaino, Toufic, Gergerich, Rose C., Gillis, Amethyst N., Gonzalez, Jean-Paul J., Haenni, Anne-Lise, Hepojoki, Jussi, Hetzel, Udo, Hồ, Thiện, Hóng, Ní, Jain, Rakesh K., Jansen van Vuren, Petrus, Jin, Qi, Jonson, Miranda Gilda, Junglen, Sandra, Keller, Karen E., Kemp, Alan, Kipar, Anja, Kondov, Nikola O., Koonin, Eugene V., Kormelink, Richard, Korzyukov, Yegor, Krupovic, Mart, Lambert, Amy J., Laney, Alma G., LeBreton, Matthew, Lukashevich, Igor S., Marklewitz, Marco, Markotter, Wanda, Martelli, Giovanni P., Martin, Robert R., Mielke-Ehret, Nicole, Mühlbach, Hans-Peter, Navarro, Beatriz, Ng, Terry Fei Fan, Nunes, Márcio Roberto Teixeira, Palacios, Gustavo, Pawęska, Janusz T., Peters, Clarence J., Plyusnin, Alexander, Radoshitzky, Sheli R., Romanowski, Víctor, Salmenperä, Pertteli, Salvato, Maria S., Sanfaçon, Hélène, Sasaya, Takahide, Schmaljohn, Connie, Schneider, Bradley S., Shirako, Yukio, Siddell, Stuart, Sironen, Tarja A., Stenglein, Mark D., Storm, Nadia, Sudini, Harikishan, Tesh, Robert B., Tzanetakis, Ioannis E., Uppala, Mangala, Vapalahti, Olli, Vasilakis, Nikos, Walker, Peter J., Wáng, Guópíng, Wáng, Lìpíng, Wáng, Yànxiăng, Wèi, Tàiyún, Wiley, Michael R., Wolf, Yuri I., Wolfe, Nathan D., Wú, Zhìqiáng, Xú, Wénxìng, Yang, Li, Yāng, Zuòkūn, Yeh, Shyi-Dong, Zhāng, Yǒng-Zhèn, Zhèng, Yàzhōu, Zhou, Xueping, Zhū, Chénxī, Zirkel, Florian, and Kuhn, Jens H.

Published
2018
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133. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Author

Adriaenssens, Evelien M., Wittmann, Johannes, Kuhn, Jens H., Turner, Dann, Sullivan, Matthew B., Dutilh, Bas E., Jang, Ho Bin, van Zyl, Leonardo J., Klumpp, Jochen, Lobocka, Malgorzata, Moreno Switt, Andrea I., Rumnieks, Janis, Edwards, Robert A., Uchiyama, Jumpei, Alfenas-Zerbini, Poliane, Petty, Nicola K., Kropinski, Andrew M., Barylski, Jakub, Gillis, Annika, Clokie, Martha R. C., Prangishvili, David, Lavigne, Rob, Aziz, Ramy Karam, Duffy, Siobain, Krupovic, Mart, Poranen, Minna M., Knezevic, Petar, Enault, Francois, Tong, Yigang, Oksanen, Hanna M., and Rodney Brister, J.

Published
2018
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137. Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea

Author

La Cono, Violetta, primary, Messina, Enzo, additional, Reva, Oleg, additional, Smedile, Francesco, additional, La Spada, Gina, additional, Crisafi, Francesca, additional, Marturano, Laura, additional, Miguez, Noa, additional, Ferrer, Manuel, additional, Selivanova, Elena A., additional, Golyshina, Olga V., additional, Golyshin, Peter N., additional, Rohde, Manfred, additional, Krupovic, Mart, additional, Merkel, Alexander Y., additional, Sorokin, Dimitry Y., additional, Hallsworth, John E., additional, and Yakimov, Michail M., additional

Published
2023
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138. A 2-million-year-old microbial and viral communities from the Kap København Formation in North Greenland

Author

Fernandez-Guerra, Antonio, primary, Borrel, Guillaume, additional, Delmont, Tom O, additional, Elberling, Bo, additional, Eren, A. Murat, additional, Gribaldo, Simonetta, additional, Jochheim, Annika, additional, Henriksen, Rasmus Amund, additional, Hinrichs, Kai-Uwe, additional, Korneliussen, Thorfinn S., additional, Krupovic, Mart, additional, Larsen, Nicolaj K., additional, Laso-Pérez, Rafael, additional, Pedersen, Mikkel Winther, additional, Pedersen, Vivi K., additional, Sand, Karina K., additional, Sikora, Martin, additional, Steinegger, Martin, additional, Veseli, Iva, additional, Wörmer, Lars, additional, Zhao, Lei, additional, Žure, Marina, additional, Kjær, Kurt, additional, and Willerslev, Eske, additional

Published
2023
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140. Functional diversity of nanohaloarchaea within xylan-degrading consortia

Author

Reva, Oleg, primary, Messina, Enzo, additional, La Cono, Violetta, additional, Crisafi, Francesca, additional, Smedile, Francesco, additional, La Spada, Gina, additional, Marturano, Laura, additional, Selivanova, Elena A., additional, Rohde, Manfred, additional, Krupovic, Mart, additional, and Yakimov, Michail M., additional

Published
2023
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141. Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein

Author

Butkovic, Anamarija, primary, Kraberger, Simona, additional, Smeele, Zoe, additional, Martin, Darren P, additional, Schmidlin, Kara, additional, Fontenele, Rafaela S, additional, Shero, Michelle R, additional, Beltran, Roxanne S, additional, Kirkham, Amy L, additional, Aleamotu’a, Maketalena, additional, Burns, Jennifer M, additional, Koonin, Eugene V, additional, Varsani, Arvind, additional, and Krupovic, Mart, additional

Published
2023
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142. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Author

Siddell, Stuart G., primary, Smith, Donald B., additional, Adriaenssens, Evelien, additional, Alfenas-Zerbini, Poliane, additional, Dutilh, Bas E., additional, Garcia, Maria Laura, additional, Junglen, Sandra, additional, Krupovic, Mart, additional, Kuhn, Jens H., additional, Lambert, Amy J., additional, Lefkowitz, Elliot J., additional, Łobocka, Małgorzata, additional, Mushegian, Arcady R., additional, Oksanen, Hanna M., additional, Robertson, David L., additional, Rubino, Luisa, additional, Sabanadzovic, Sead, additional, Simmonds, Peter, additional, Suzuki, Nobuhiro, additional, Van Doorslaer, Koenraad, additional, Vandamme, Anne-Mieke, additional, Varsani, Arvind, additional, and Zerbini, F. Murilo, additional

Published
2023
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146. Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

Author

Adriaenssens, Evelien, Roux, Simon, Brister, J. Rodney, Karsch-Mizrachi, Ilene, Kuhn, Jens, Varsani, Arvind, Yigang, Tong, Reyes, Alejandro, Lood, Cédric, Lefkowitz, Elliot, Sullivan, Matthew, Edwards, Robert, Simmonds, Peter, Rubino, Luisa, Sabanadzovic, Sead, Krupovic, Mart, Dutilh, Bas, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), National Center for Biotechnology Information (NCBI), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Arizona State University [Tempe] (ASU), University of Cape Town, Beijing University of Chemical Technology, Universidad de los Andes [Bogota] (UNIANDES), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], University of Alabama at Birmingham [ Birmingham] (UAB), Ohio State University [Columbus] (OSU), Flinders University [Adelaide, Australia], University of Oxford, CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Utrecht University [Utrecht], E.M.A. gratefully acknowledges the support of the Biotechnology and Biological Sciences Research Council (BBSRC), and this research was funded by the BBSRC Institute Strategic Program Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356. The work conducted by the US Department of Energy (DOE) Joint Genome Institute (S.R.) was supported by the Office of Science of the DOE under contract no. DE-AC02-05CH11231. Work by J.R.B. and I.K.M. was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), NIH. This work was supported in part through Laulima Government Solutions, LLC, prime contract with the NIAID under contract no. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. M.B.S. was supported by the US National Science Foundation Award #1759874. R.A.E. was supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the NIH under award no. RC2DK116713 and by the Australian Research Council under award no. DP220102915. C.L. was supported by a Postdoctoral Mandate from KU Leuven (PDMt2/21/038) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC 2051 – Project-ID 390713860. E.J.L. was supported by the NIAID, NIH, under award no. U24AI162625. P.S. was supported by a Wellcome Trust Biomedical Resource grant (WT108418AIA). S.S. acknowledges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), US Department of Agriculture (USDA)–Agricultural Research Service project 58-6066-9-033, and the National Institute of Food and Agriculture, USDA, Hatch Project, under accession USDA 1021494. B.E.D. was supported by the European Research Council (ERC) Consolidator Grant 865694: DiversiPHI, the DFG under Germany’s Excellence Strategy – EXC 2051 – Project-ID 390713860, the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt Professorship founded by German Federal Ministry of Education and Research, and the European Union’s Horizon 2020 research and innovation program, under Marie Skłodowska-Curie Actions Innovative Training Networks grant agreement no. 955974 (VIROINF).

Subjects
[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Published
2023
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147. Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea

Author

La Cono, Violetta, Messina, Enzo, Reva, Olga, Smedile, Francesco, La Spada, Gina, Crisafi, Francesca, Marturano, Laura, Miguez, Noa, Ferrer, Manuel, Selivanova, Elena A, Golyshina, Olga V, Golyshin, Peter N, Rohde, Manfred, Krupovic, Mart, Merkel, Alexander Y, Sorokin, Dimitry Y, Hallsworth, John E, and Yakimov, Michail M

Subjects
nanohaloarchaeum, Candidatus Nanohalobium constans, Sustainable Development Goals, Halomicrobium, haloarchaeum, multi-omics, xylan
Abstract

Climate change, desertification, salinisation of soils and the changing hydrology of the Earth are creating or modifying microbial habitats at all scales including the oceans, saline groundwaters and brine lakes. In environments that are saline or hypersaline, the biodegradation of recalcitrant plant and animal polysaccharides can be inhibited by salt-induced microbial stress and/or by limitation of the metabolic capabilities of halophilic microbes. We recently demonstrated that the chitinolytic haloarchaeon Halomicrobium can serve as the host for an ectosymbiont, nanohaloarchaeon ‘Candidatus Nanohalobium constans’. Here, we consider whether nanohaloarchaea can benefit from the haloarchaea-mediated degradation of xylan, a major hemicellulose component of wood. Using samples of natural evaporitic brines and anthropogenic solar salterns, we describe genome-inferred trophic relations in two extremely halophilic xylan-degrading three-member consortia. We succeeded in genome assembly and closure for all members of both xylan-degrading cultures and elucidated the respective food chains within these consortia. We provide evidence that ectosymbiontic nanohaloarchaea is an active ecophysiological component of extremely halophilic xylan-degrading communities (although by proxy) in hypersaline environments. In each consortium, nanohaloarchaea occur as ectosymbionts of Haloferax, which in turn act as scavenger of oligosaccharides produced by xylan-hydrolysing Halorhabdus. We further obtained and characterised the nanohaloarchaea–host associations using microscopy, multi-omics and cultivation approaches. The current study also doubled culturable nanohaloarchaeal symbionts and demonstrated that these enigmatic nano-sized archaea can be readily isolated in binary co-cultures using an appropriate enrichment strategy. We discuss the implications of xylan degradation by halophiles in biotechnology and for the United Nation's Sustainable Development Goals.

Published
2023

148. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Author

Siddell, Stuart G., Smith, Donald B., Adriaenssens, Evelien M., Alfenas-Zerbini, Poliane, Dutilh, Bas E., Garcia, Maria Laura, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Lefkowitz, Elliot J., Lobocka, Malgorzata, Mushegian, Arcady R, Oksanen, Hanna M, Robertson, David L, Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, A. -M., Varsani, Arvind, Zerbini, Francisco Murilo, Molecular and Integrative Biosciences Research Programme, and Molecular Principles of Viruses

Subjects
11832 Microbiology and virology, Virus taxonomy, International Committee of Virus Taxonomy
Published
2023

150. Correction to: Binomial nomenclature for virus species: a consultation

Author

Siddell, Stuart G., Walker, Peter J., Lefkowitz, Elliot J., Mushegian, Arcady R., Dutilh, Bas E., Harrach, Balázs, Harrison, Robert L., Junglen, Sandra, Knowles, Nick J., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Nibert, Max L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Varsani, Arvind, Zerbini, Francisco Murilo, and Davison, Andrew J.

Published
2020
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