Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil
TLDR
It is shown that RNA viruses are diverse, abundant, and active in soil, and may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.Abstract:
Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.read more
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The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut.
Ann C. Gregory,Olivier Zablocki,Ahmed A. Zayed,Allison Howell,Benjamin Bolduc,Matthew B. Sullivan +5 more
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Life and death in the soil microbiome: how ecological processes influence biogeochemistry
Noah W. Sokol,Eric W. Slessarev,G. Marschmann,Alexa M. Nicolas,Steven J. Blazewicz,Eoin L. Brodie,Mary K. Firestone,Megan M. Foley,Rachel Hestrin,Bruce A. Hungate,Benjamin J. Koch,Bram W. G. Stone,Matthew B. Sullivan,Olivier Zablocki,Jennifer Pett-Ridge +14 more
TL;DR: In this paper , the authors 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.
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2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
Jens H. Kuhn,Scott Adkins,Daniela Alioto,S. V. Alkhovsky,Gaya K. Amarasinghe,Simon J. Anthony,Simon J. Anthony,Tatjana Avšič-Županc,María A. Ayllón,Justin Bahl,Anne Balkema-Buschmann,Matthew J. Ballinger,Tomáš Bartonička,Christopher F. Basler,Sina Bavari,Martin Beer,Dennis A. Bente,Eric Bergeron,Brian H. Bird,Carol D. Blair,Kim R. Blasdell,Steven B. Bradfute,Rachel Breyta,Thomas Briese,Paul Brown,Ursula J. Buchholz,Michael J. Buchmeier,Alexander Bukreyev,Felicity J. Burt,Nihal Buzkan,Charles H. Calisher,Mengji Cao,Inmaculada Casas,John Chamberlain,Kartik Chandran,Rémi N. Charrel,Biao Chen,Michela Chiumenti,Il-Ryong Choi,J. Christopher S. Clegg,Ian Crozier,John V. da Graça,Elena Dal Bó,Alberto M. R. Dávila,Juan Carlos de la Torre,Xavier de Lamballerie,Rik L. de Swart,Patrick L. Di Bello,Nicholas Di Paola,Francesco Di Serio,Ralf G. Dietzgen,Michele Digiaro,Valerian V. Dolja,Olga Dolnik,Michael A. Drebot,Jan Felix Drexler,Ralf Dürrwald,Lucie Dufkova,William G. Dundon,W. Paul Duprex,John M. Dye,Andrew J. Easton,Hideki Ebihara,Toufic Elbeaino,Koray Ergünay,Jorlan Fernandes,Anthony R. Fooks,Pierre Formenty,Leonie Forth,Ron A. M. Fouchier,Juliana Freitas-Astúa,Selma Gago-Zachert,Selma Gago-Zachert,George Fú Gāo,María Laura García,Adolfo García-Sastre,Aura R. Garrison,Aiah Gbakima,Tracey Goldstein,Jean-Paul Gonzalez,Anthony Griffiths,Martin H. Groschup,Stephan Günther,Alexandro Guterres,Roy A. Hall,John Hammond,Mohamed Hassan,Jussi Hepojoki,Jussi Hepojoki,Satu Hepojoki,Udo Hetzel,Roger Hewson,Bernd Hoffmann,Seiji Hongo,Dirk Höper,Masayuki Horie,Holly R. Hughes,Timothy H. Hyndman,Amara Jambai,Rodrigo Jardim,Dàohóng Jiāng,Qi Jin,Gilda B. Jonson,Sandra Junglen,Serpil Karadağ,Karen E. Keller,Boris Klempa,Jonas Klingström,Gary P. Kobinger,Hideki Kondō,Eugene V. Koonin,Mart Krupovic,Gael Kurath,Ivan V. Kuzmin,Lies Laenen,Robert A. Lamb,Amy J. Lambert,Stanley L. Langevin,Benhur Lee,Elba Regina Sampaio de Lemos,Eric M. Leroy,Dexin Li,Jiànróng Lǐ,Mifang Liang,Wénwén Liú,Yan Liu,Igor S. Lukashevich,Piet Maes,William Marciel de Souza,Marco Marklewitz,Sergio H. Marshall,Giovanni P. Martelli,Robert R. Martin,Shin-Yi Lee Marzano,Sébastien Massart,John W. McCauley,Nicole Mielke-Ehret,Angelantonio Minafra,Maria Minutolo,Ali Mirazimi,Hans Peter Mühlbach,Elke Mühlberger,Rayapati A. Naidu,Tomohide Natsuaki,Beatriz Navarro,José A. Navarro,Sergey V. Netesov,Gabriele Neumann,Norbert Nowotny,Norbert Nowotny,Márcio Roberto Teixeira Nunes,Are Nylund,Arnfinn Lodden Økland,Renata Carvalho de Oliveira,Gustavo Palacios,Vicente Pallás,Bernadett Pályi,Anna Papa,Colin R. Parrish,Alex Pauvolid-Corrêa,Janusz T. Paweska,Susan Payne,Daniel R. Perez,Florian Pfaff,Sheli R. Radoshitzky,Aziz ul Rahman,Pedro Luis Ramos-González,Renato O. Resende,Carina Andrea Reyes,Bertus K. Rima,Víctor Romanowski,Gabriel Robles Luna,Paul A. Rota,Dennis Rubbenstroth,Jonathan A. Runstadler,Daniel Ruzek,Sead Sabanadzovic,Jiří Salát,Amadou A. Sall,Maria S. Salvato,Kamil Sarpkaya,Takahide Sasaya,Martin Schwemmle,Muhammad Zubair Shabbir,Xiǎohóng Shí,Zhengli Shi,Yukio Shirako,Peter Simmonds,Jana Širmarová,Manuela Sironi,Sophie J. Smither,Teemu Smura,Jin Won Song,Kirsten Spann,Jessica R. Spengler,Mark D. Stenglein,David M. Stone,Petra Straková,Ayato Takada,Robert B. Tesh,Natalie J. Thornburg,Keizō Tomonaga,Noël Tordo,Jonathan S. Towner,Massimo Turina,Ioannis E. Tzanetakis,Rainer G. Ulrich,Anna Maria Vaira,Bernadette G. van den Hoogen,Arvind Varsani,Arvind Varsani,Nikos Vasilakis,Martin Verbeek,Victoria Wahl,Peter J. Walker,Hui Wang,Jianwei Wang,Xifeng Wang,Lin-Fa Wang,Taiyun Wei,Heather L. Wells,Anna E. Whitfield,John V. Williams,Yuri I. Wolf,Zhìqiáng Wú,Xin Yang,Xīnglóu Yáng,Xuejie Yu,Natalya Yutin,F. Murilo Zerbini,Tong Zhang,Yong-Zhen Zhang,Yong-Zhen Zhang,Guohui Zhou,Xueping Zhou +234 more
TL;DR: The updated taxonomy of Negarnaviricota is presented, as now accepted by the ICTV, after the phylum was amended and emended in March 2020.
Journal ArticleDOI
Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
Ahmed A. Zayed,James M. Wainaina,Guillermo Domínguez-Huerta,Eric Pelletier,Jiarong Guo,Mohamed Mohssen,Funing Tian,Akbar Adjie Pratama,Benjamin Bolduc,Olivier Zablocki,Dylan R. Cronin,Lindsey M. Solden,Erwan Delage,Adriana Alberti,Jean-Marc Aury,Quentin Carradec,Corinne Da Silva,Karine Labadie,Julie Poulain,Hans-Joachim Ruscheweyh,Guillem Salazar,Elan A Shatoff,Ralf Bundschuh,Kurt Fredrick,Laura Kubatko,S. Chaffron,Alexander I. Culley,Shinichi Sunagawa,Jens H. Kuhn,Matthew B. Sullivan,Silvia G. Acinas,Marcel Babin,Peer Bork,Emmanuel Boss,Chris Bowler,Guy Cochrane,Colomban de Vargas,Gabriel Gorsky,Lionel Guidi,Nigel Grimsley,Pascal Hingamp,Daniele Iudicone,Olivier Jaillon,Stefanie Kandels,Lee Karp-Boss,Eric Karsenti,Fabrice Not,Hiroyuki Ogata,Nicole J. Poulton,Stephane Pesant,Christian Sardet,Sabrinia Speich,Lars Stemmann,Shinichi Sungawa,Patrick Wincker +54 more
TL;DR: Viruses of two candidate phyla are abundant in the ocean and revise the understanding of early RNA virus evolution, as well as identifying RNA viruses that necessitate substantive revisions of taxonomy and evolutionary understanding.
Journal ArticleDOI
Expansion of known ssRNA phage genomes: From tens to over a thousand
Julie Callanan,Stephen R. Stockdale,Andrey N. Shkoporov,Lorraine A. Draper,R.P. Ross,R.P. Ross,Colin Hill +6 more
TL;DR: A massive expansion in RNA-encoded bacterial viral genomes, which have been overlooked within environments, is reported, including 15,611 nonredundant ssRNA phage sequences, including 1015 near-complete genomes.
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