Diversity and ecological footprint of Global Ocean RNA viruses

Domínguez-Huerta, Guillermo; Zayed, Ahmed A.; Wainaina, James; Guo, Jiarong; Tian, Funing; Pratama, Akbar Adjie; Bolduc, Benjamin; Mohssen, Mohamed; Zablocki, Olivier; Pelletier, Éric; Delage, Erwan; Alberti, Adriana; Aury, Jean‐Marc; Carradec, Quentin; Silva, Corinne Da; Labadie, Karine; Poulain, Julie; Bowler, Chris; Eveillard, Damien; Guidi, Lionel; Karsenti, Eric; Kuhn, Jens H.; Ogata, Hiroyuki; Wincker, Patrick; Culley, Alexander I.; Chaffron, Samuel; Sullivan, Matthew B.

doi:10.1126/science.abn6358

Cited by 66 publications

(59 citation statements)

References 122 publications

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“…Hence, the host prediction of RNA viruses is still at an exploratory stage. Based on abundance co-occurrence suggested by Dominguez-Huerta et al 37 , almost half of the virus-host interactions observed in this study occurred in August of both two years, and all of them were positively correlated (Fig. 5).…”

Section: Discussionsupporting

confidence: 62%

“…Very recently, the importance of the marine RNA virosphere, identi ed by rapid advances in metagenomic and metatranscriptomic analyses, was revealed in a series of key papers 5,6,15−19 . A total of 44,779 RNA viral contigs, identi ed in the ~ 28 terabases (Tb) of Global Ocean RNA sequences, revealed ve new phyla "Taraviricota", "Pomiviricota", "Arctiviricota", "Paraxenoviricota", and "Wamoviricota", and four RNA viral ecological zones 19,20 . However, there remains a lack of research on the spatiotemporal dynamics and community structure changes of RNA viruses and their relationships with hosts, which is critical to the understanding of their activity and ecological roles in the sea.…”

Section: Introductionmentioning

confidence: 99%

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Diverse, abundant and stable coastal RNA viruses identified by spatiotemporal metatranscriptomics

Sun

Zheng

Liang

et al. 2022

Preprint

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The diversity and spatiotemporal dynamics of a coastal RNA virus community, was investigated focusing on the effects of a bloom of the macroalgae U. prolifera through a metatranscriptomic reconstruction of ~ 880Gb of Qingdao Coastal RNA sequences from May 2019 to December 2020. 6,079 RNA viral contigs were identified and these generated 2,351 viral operational taxonomic units within known orders. The analysis found that structural components of the coastal marine RNA virus community are diverse, abundant and stable. The viruses were mainly associated with eukaryotes from Intramacronucleata, Chlorophyta, Bacillariophyta and Dinophyceae, bacteria from Flavobacteriales and Rhodobacterales and MGII and Nitrosopumilales from archaea. The viral auxiliary metabolic genes indicate that coastal RNA viruses manipulate reprogramming of diverse host metabolisms, including carbon cycling, signaling pathways, membrane transport, transcription and translation. Together these results provide critical insights for incorporating RNA viruses into marine ecological and epidemiological models.

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Section: Discussionsupporting

confidence: 62%

Section: Introductionmentioning

confidence: 99%

Diverse, abundant and stable coastal RNA viruses identified by spatiotemporal metatranscriptomics

Sun

Zheng

Liang

et al. 2022

Preprint

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“…The application of high-throughput sequencing technology for virus hunting has greatly promoted the development of virology in recent years that accelerated the discovery of virus diversity, origin and evolution from various materials including animals, plants, fungi and environment ( Adams et al, 2009 ; Roossinck et al., 2015 ; Marzano et al., 2016 ; Shi et al., 2016 ; Chiapello et al., 2020 ; Myers et al., 2020 ; Wang et al., 2021 ; Ruiz-Padilla et al., 2021 ; Kondo et al., 2022 ; Dominguez-Huerta et al., 2022 ). For mycoviruses, many studies have reported that the co-infection of a large number of viruses in single fungal strains is a common phenomenon, which usually appeared in the necrotrophic fungi R. solani and S. sclerotiorum ( Bartholomäus et al., 2016 ; Mu et al., 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Novel and diverse mycoviruses co-infecting a single strain of the phytopathogenic fungus Alternaria dianthicola

Zhong

Li²,

Gao³

et al. 2022

Front. Cell. Infect. Microbiol.

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Alternaria dianthicola is a pathogenic fungus that causes serious leaf or flower blight on some medicinal plants worldwide. In this study, multiple dsRNA bands in the range of 1.2-10 kbp were found in a Alternaria dianthus strain HNSZ-1, and eleven full-length cDNA sequences of these dsRNA were obtained by high-throughput sequencing, RT-PCR detection and conventional Sanger sequencing. Homology search and phylogenetic analyses indicated that the strain HNSZ-1 was infected by at least nine mycoviruses. Among the nine, five viruses were confirmed to represent novel viruses in the families Hypoviridae, Totiviridae, Mymonaviridae and a provisional family Ambiguiviridae. Virus elimination and horizontal transmission indicated that the (-) ssRNA virus, AdNSRV1, might be associated with the slow growth and irregular colony phenotype of the host fungus. As far as we know, this is the first report for virome characterization of A. dianthus, which might provide important insights for screening of mycovirus for biological control and for studying of the interactions between viruses or viruses and their host.

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“…Microbes are the main drivers of the biogeochemical cycles that define ecosystems, but they also are susceptible to virus infection, e.g., it is estimated that ∼20% of the bacteria in the oceans are lysed by viruses per day ( Suttle, 1994 ). These ongoing viral infections shape microbial community structures and are necessary for nutrient cycling ( Dominguez-Huerta et al, 2022 ).…”

Section: Viruses At the Planetary Scale: The Virospherementioning

confidence: 99%

Viruses in astrobiology

Higuera

Lázaro²

2022

Front. Microbiol.

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Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.

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Diversity and ecological footprint of Global Ocean RNA viruses

Cited by 66 publications

References 122 publications

Diverse, abundant and stable coastal RNA viruses identified by spatiotemporal metatranscriptomics

Diverse, abundant and stable coastal RNA viruses identified by spatiotemporal metatranscriptomics

Novel and diverse mycoviruses co-infecting a single strain of the phytopathogenic fungus Alternaria dianthicola

Viruses in astrobiology

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