Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics

0510169 - BC 2020 RIV GB eng J - Journal Article
Kavagutti, Vinicius Silva - Andrei, Adrian-Stefan - Mehrshad, Maliheh - Salcher, Michaela M. - Ghai, Rohit
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics.
Microbiome. Roč. 7, č. 1 (2019), č. článku 135. ISSN 2049-2618. E-ISSN 2049-2618
R&D Projects: GA ČR(CZ) GA19-23469S; GA ČR(CZ) GA17-04828S; GA MŠMT(CZ) EF16_025/0007417
Grant - others:AV ČR(CZ) MSM200961801; AV ČR(CZ) L200961651
Program: Program na podporu mezinárodní spolupráce začínajících výzkumných pracovníků; Program podpory perspektivních lidských zdrojů
Institutional support: RVO:60077344
Keywords : FRESH-WATER ACTINOBACTERIA * RIBOSOMAL-RNA GENES * COMMUNITY COMPOSITIO
OECD category: Microbiology
Impact factor: 11.607, year: 2019
Method of publishing: Open access
https://microbiomejournal.biomedcentral.com/track/pdf/10.1186/s40168-019-0752-0

The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small miniphages and large megaphages infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13-200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis.
Permanent Link: http://hdl.handle.net/11104/0300830