ArticleThe ISME journal2021
Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities.
Article in The ISME journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers, 1 of them a synthesis that pooled it.
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Who cites it
96 citing papers in PubMed, 1 synthesis or guideline pooled it, 213 citations in OpenAlex.
- Global research trends in bacteriophage and gut microbiota: a bibliometric and visual analysis from 2012 to 2025.Frontiers in microbiology · 2025Pooled it
- Virome DNA stable isotope probing reveals diverse active soil virus communities across ecosystem contexts.mSystems · 2026Article
- Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.Microbiology spectrum · 2026Article
- theBIGbam: compression and interactive exploration of large-scale sequencing alignments with circular mapping support.Bioinformatics (Oxford, England) · 2026Article
- Preparation method shapes the recovery and ecological interpretation of DNA and RNA soil viral communities.Nature communications · 2026Article
- Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.mSystems · 2026Article
- Article
- Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens.PLoS genetics · 2026Article
- DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.Nature communications · 2026Article
- On the Low Abundance of Antibiotic Resistance Genes in Bacteriophage Genomes and Their Random Acquisition via Specialized Transduction.Genome biology and evolution · 2026Article
- Viral Diversity of Coastal Restinga Soils From Southern Brazil.Environmental microbiology reports · 2026Article
- Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.NPJ biofilms and microbiomes · 2026Article
- DNA Viral Size Fraction Metagenomics for Human Stool Samples.Journal of visualized experiments : JoVE · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- The hidden role of rhizospheric viruses in promoting nitrogen fixation in soils.Nature communications · 2026Article
- Identification and comparative genomic analysis of prophage sequences and CRISPR‒Cas immunity in Methylococcus genomes: insights into industrial methane bioconversion.Biotechnology for biofuels and bioproducts · 2026Article
- Host community activity, but not always composition, explains viral biogeography in bulk and rhizosphere soils over a tomato growing season.The ISME journal · 2026Article
- Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.Nucleic acids research · 2026Article
- Isolation and characterization of TayeBlu, a novel bacteriophage ofMicrobiology spectrum · 2026Article
- Ecology of prokaryotic DNA viruses in a highly impacted coastal lagoon revealed through comparative and temporal metagenomics.ISME communications · 2026Article
36 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Viruses are abundant yet understudied members of soil environments that influence terrestrial biogeochemical cycles. Here, we characterized the dsDNA viral diversity in biochar-amended agricultural soils at the preplanting and harvesting stages of a tomato growing season via paired total metagenomes and viral size fraction metagenomes (viromes). Size fractionation prior to DNA extraction reduced sources of nonviral DNA in viromes, enabling the recovery of a vaster richness of viral populations (vOTUs), greater viral taxonomic diversity, broader range of predicted hosts, and better access to the rare virosphere, relative to total metagenomes, which tended to recover only the most persistent and abundant vOTUs. Of 2961 detected vOTUs, 2684 were recovered exclusively from viromes, while only three were recovered from total metagenomes alone. Both viral and microbial communities differed significantly over time, suggesting a coupled response to rhizosphere recruitment processes and/or nitrogen amendments. Viral communities alone were also structured along an 18 m spatial gradient. Overall, our results highlight the utility of soil viromics and reveal similarities between viral and microbial community dynamics throughout the tomato growing season yet suggest a partial decoupling of the processes driving their spatial distributions, potentially due to differences in dispersal, decay rates, and/or sensitivities to soil heterogeneity.
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