ArticleMicrobiome2019
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics.
Article in Microbiome, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 127 citations in OpenAlex.
- Phage host range: determinants, dynamics and applications.Nature reviews. Microbiology · 2026Review
- Salinity-driven niche partitioning of aquatic viruses in one of Europe's largest estuaries.Applied and environmental microbiology · 2026Article
- Isolation and genomic analysis of a novel Pseudomonas phage from karst cave in China.Archives of virology · 2026Article
- Boreal and subarctic freshwaters harbour a diversity of jumbophages.ISME communications · 2026Article
- Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order.Microbiome · 2025Article
- Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium.Nature microbiology · 2025Article
- Bringing the uncultivated microbial majority of freshwater ecosystems into culture.Nature communications · 2025Article
- The Global Challenge of Antimicrobial Resistance: Mechanisms, Case Studies, and Mitigation Approaches.Health science reports · 2025Article
- Article
- Genome Sequences of the First Phages InfectingMicroorganisms · 2025Article
- An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov.Microbial ecology · 2025Review
- Cultivation, genomics, and giant viruses of a ubiquitous and heterotrophic freshwater cryptomonad.The ISME journal · 2025Article
- Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.ISME communications · 2025Article
- Unveiling the unknown viral world in groundwater.Nature communications · 2024Article
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- Article
- COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes.Nature microbiology · 2024Article
- Virus-prokaryote infection pairs associated with prokaryotic production in a freshwater lake.mSystems · 2024Article
- Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria.The ISME journal · 2024Article
- Spatiotemporal dynamics of giant viruses within a deep freshwater lake reveal a distinct dark-water community.The ISME journal · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.