Diversity in the soil virosphere: to infinity and beyond?

Massive expansion of human gut bacteriophage diversity

(2021) Luis F. Camarillo-Guerrero et al.   CELL

Metagenomic tools in microbial ecology research

(2021) Neslihan Taş et al.   CURRENT OPINION IN BIOTECHNOLOGY

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

(2021) Christian Santos-Medellin et al.   ISME Journal

Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR

(2021) Eric G. Sakowski et al.   Nature Microbiology

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

(2021) Olivier Zablocki et al.   PeerJ

Methane-derived carbon flows into host–virus networks at different trophic levels in soil

(2021) Sungeun Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global overview and major challenges of host prediction methods for uncultivated phages

(2021) Clément Coclet et al.   Current Opinion in Virology

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

(2021) Stephen Nayfach et al.   Nature Microbiology

Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils

(2021) Carolyn R. Cornell et al.   mSphere

Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil

(2021) Evan P. Starr et al.   mSphere

DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes

(2021) Jackson W. Sorensen et al.   mSystems

Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers

(2021) Mo-Lian Chen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system

(2021) Xin You et al.   ISME Journal

DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes

(2021) Ruonan Wu et al.   mBio

Current challenges to virus discovery by meta-transcriptomics

(2021) Joanna CA Cobbin et al.   Current Opinion in Virology

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

(2021) Gareth Trubl et al.   Microbiome

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

(2021) Anneliek M. ter Horst et al.   Microbiome

Dormant phages communicate via arbitrium to control exit from lysogeny

(2021) Nitzan Aframian et al.   Nature Microbiology

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

Phage diversity, genomics and phylogeny

(2020) Moïra B. Dion et al.   NATURE REVIEWS MICROBIOLOGY

Lysogenic reproductive strategies of viral communities vary with soil depth and are correlated with bacterial diversity

(2020) Xiaolong Liang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil

(2020) Pauline C. Göller et al.   Microbiome

Expansion of known ssRNA phage genomes: From tens to over a thousand

(2020) J. Callanan et al.   Science Advances

Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils

(2020) Li Bi et al.   ENVIRONMENTAL MICROBIOLOGY

Rewetting of soil: Revisiting the origin of soil CO2 emissions

(2020) Romain L. Barnard et al.   SOIL BIOLOGY & BIOCHEMISTRY

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system

(2020) Will A. Overholt et al.   ENVIRONMENTAL MICROBIOLOGY

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

(2020) Jessica K. Jarett et al.   ISME Journal

Terabase-scale metagenome coassembly with MetaHipMer

(2020) Steven Hofmeyr et al.   Scientific Reports

Temporal Dynamics of Soil Virus and Bacterial Populations in Agricultural and Early Plant Successional Soils

(2020) Krishnakali Roy et al.   Frontiers in Microbiology

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

(2020) Yuri I. Wolf et al.   Nature Microbiology

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

(2020) Ann C. Gregory et al.   Cell Host & Microbe

The physical structure of soil: Determinant and consequence of trophic interactions

(2020) Amandine Erktan et al.   SOIL BIOLOGY & BIOCHEMISTRY

Actinobacteriophages: Genomics, Dynamics, and Applications

(2020) Graham F. Hatfull   Annual Review of Virology

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

(2019) Joanna Warwick-Dugdale et al.   PeerJ

Soil Viruses: A New Hope

(2019) Joanne B. Emerson   mSystems

Systematic review and meta-analysis of decay rates of waterborne mammalian viruses and coliphages in surface waters

(2019) Alexandria B. Boehm et al.   WATER RESEARCH

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps

(2019) Alexander T. Dilthey et al.   Nature Communications

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

(2019) Gareth Trubl et al.   PeerJ

Implication of Viral Infections for Greenhouse Gas Dynamics in Freshwater Wetlands: Challenges and Perspectives

(2019) Giuditta Bonetti et al.   Frontiers in Microbiology

The pan-immune system of bacteria: antiviral defence as a community resource

(2019) Aude Bernheim et al.   NATURE REVIEWS MICROBIOLOGY

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

(2019) Evan P. Starr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust

(2019) Marc W. Van Goethem et al.   mBio

Long-term stability and Red Queen-like strain dynamics in marine viruses

(2019) J. Cesar Ignacio-Espinoza et al.   Nature Microbiology

Deposition rates of viruses and bacteria above the atmospheric boundary layer

(2018) Isabel Reche et al.   ISME Journal

The ‘Neglected’ Soil Virome – Potential Role and Impact

(2018) Akbar Adjie Pratama et al.   TRENDS IN MICROBIOLOGY

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

(2018) Luis M. Rodriguez-R et al.   mSystems

Diversity of active viral infections within the Sphagnum microbiome

(2018) Joshua M.A. Stough et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision

(2018) Justin E. Silpe et al.   CELL

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions

(2018) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

Hidden diversity of soil giant viruses

(2018) Frederik Schulz et al.   Nature Communications

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages

(2018) Samuel Jacquiod et al.   Microbiome

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

Lysogeny in nature: mechanisms, impact and ecology of temperate phages

(2017) Cristina Howard-Varona et al.   ISME Journal

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

(2017) Francisco Martinez-Hernandez et al.   Nature Communications

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory

(2017) Kurt E. Williamson et al.   Annual Review of Virology

Environmental drivers of viral community composition in Antarctic soils identified by viromics

(2017) Evelien M. Adriaenssens et al.   Microbiome

Lytic to temperate switching of viral communities

(2016) B. Knowles et al.   NATURE

Back to the Future of Soil Metagenomics

(2016) Joseph Nesme et al.   Frontiers in Microbiology

Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

(2016) Gareth Trubl et al.   PeerJ

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

(2015) Sarah J Spencer et al.   ISME Journal

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Viromes, Not Gene Markers, for Studying Double-Stranded DNA Virus Communities

(2014) Matthew B. Sullivan   JOURNAL OF VIROLOGY

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

Estimates of viral abundance in soils are strongly influenced by extraction and enumeration methods

(2013) Kurt E. Williamson et al.   BIOLOGY AND FERTILITY OF SOILS

Application of metatranscriptomics to soil environments

(2012) Lilia C. Carvalhais et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Bacteria-Phage Antagonistic Coevolution in Soil

(2011) P. Gomez et al.   SCIENCE

Ecology of viruses in soils: Past, present and future perspectives

(2010) Makoto Kimura et al.   SOIL SCIENCE AND PLANT NUTRITION

Local Adaptation of Bacteriophages to Their Bacterial Hosts in Soil

(2009) M. Vos et al.   SCIENCE

Phages across the biosphere: contrasts of viruses in soil and aquatic environments

(2008) Sharath Srinivasiah et al.   RESEARCH IN MICROBIOLOGY