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Résumé: L'écologie des virus végétaux a commencé à être explorée à la fin du xix e siècle. Depuis lors, des avancées majeures ont mis en évidence de complexes interactions virus-hôte-vecteur dans des environnements variés. Ces progrès ont été accélérés par de nouvelles technologies de détection et de caractérisation des virus, dont la dernière en date est le séquençage à haut débit (HTS). Les technologies HTS permettent, pour la première fois, de caractériser sans information préalable le virome, c'est-à-dire l'ensemble des virus présents dans un échantillon. Ces travaux de phytoviromique basés sur les technologies HTS ont récemment produit d'importants résultats. À titre d'exemples, on peut citer la mise en évidence des influences réciproques entre la dynamique des phytovirus et la structure des communautés hôtes multi-espèces ou des effets de la simplification des écosystèmes causés par les activités humaines sur la biodiversité et l'émergence de nouveaux virus dans les cultures. Cependant, pour être efficaces, les études de phytoviromique doivent surmonter des défis à chaque étape de la procédure, depuis l'échantillonnage des plantes jusqu'aux analyses bio-informatiques. Cette revue résume tout d'abord les progrès historiques majeurs de l'écologie des virus végétaux réalisés en association avec les développements technologiques, puis précise les éléments clés à considérer pour tenter de se projeter à court terme vers des études sans a priori d'écologie des communautés virales. Plant virus ecology began to be explored at the end of the 19th century. Since then, major advances have revealed complex virus–host–vector interactions in a variety of environments. These advances have been accelerated by development of new technologies for virus detection and characterization, the latest of which being high-throughput sequencing (HTS). HTS technologies have proved to be effective for non-targeted characterization of all or nearly all viruses present in a sample without requiring prior information about virus identity, as would be needed for virus-targeted tests. Phytoviromic studies have thus made important advances, including characterization of the complex interactions between phytovirus dynamics and the structure of multi-species host communities, and documentation of the effects of anthropogenic ecosystem simplification on plant virus emergence and diversity. However, such studies must overcome challenges at every stage, from plant sampling to bioinformatics analysis. This review summarizes major advances in plant virus ecology, in association with technological developments, and presents key considerations for use of HTS in the study of the ecology of phytovirus communities. [ABSTRACT FROM AUTHOR]

Résumé: Les bactériophages tiennent une place prépondérante dans le monde vivant. Du point de vue épistémologique, ils participent à la compréhension du vivant via trois aspects fondamentaux : (i) les mécanismes moléculaires les plus intimes du fonctionnement des infections virales et de celui des cellules elles-mêmes (biologie moléculaire) ; (ii) le fonctionnement des écosystèmes (écologie) ; et (iii) la dynamique adaptative des populations virales et bactériennes (évolution). À travers une présentation historique de la découverte des bactériophages et de leurs fascinantes propriétés, cette revue relate la genèse des découvertes fondamentales associées à l'étude des bactériophages et présente une vision synthétique des champs de recherche actuels. Bacteriophages have a prominent place in the living world. They participate to our understanding of the living world through three main aspects : (i) the dissection of the most intimist aspects of viral infection molecular mechanisms (molecular biology), (ii) the description and functioning mechanisms of ecosystems (ecology), and (iii) the adaptive dynamics of integrated viral and host-cell populations (evolution). This review looks back at the genesis of these fundamental findings and draws a picture of the most active fields of current research. [ABSTRACT FROM AUTHOR]

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In this review, available data on the structure (diversity, abundance, biomass) and functional imprints (bacteriolysis, lysogeny, gene transfers, regulation of prokaryotic diversity) of natural viruses in the context of food webs in aquatic microbial ecology, and the related biogeochemical cycles, are summarized. Viruses are the most abundant, and probably the most diverse, biological entities in aquatic ecosystems and in the biosphere (i.e., viriosphere). Aquatic viruses typically exceed 107 particles/mL in mesotrophic conditions, the majority being represented by phages without tails and by tailed-phages such as members of the family Siphoviridae. Both types of phages have a small capsid and a small genome size, which is considered an evolutionary adaptation to planktonic life. Their contribution to microbial mortality is significant. There is strong evidence that phages exert a significant pressure on the community structure and diversity and on the diversification of potential hosts, mainly through two major pathways: biogeochemical catalysis from lysis products and horizontal gene transfers. In turn, phages are sensitive to environmental factors, both in terms of integrity and of infectivity. Some phages contain typical viral genes that code for biological functions of interest, such as photosynthesis. In general, development in viral ecology is a source of new knowledge for the scientific community in the domain of environmental sciences, but also in the context of evolutionary biology of living cellular organisms, the obligatory hosts for viruses. For example, the recent discovery of a giant virus that becomes ill through infection by another virus (i.e., a viriophage) is fuelling debate about whether viruses are alive. Finally, future research directions are identified in the context of general aquatic ecology, including ecological researches on cyanophages and other phytoplanktonic phages as a priority, primarily in freshwater lakes. [ABSTRACT FROM AUTHOR]