Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil

(2023) Di Tong et al.   ISME Journal

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

(2022) Ahmed A. Zayed et al.   SCIENCE

Diversity in the soil virosphere: to infinity and beyond?

(2022) Simon Roux et al.   TRENDS IN MICROBIOLOGY

RNA viromes from terrestrial sites across China expand environmental viral diversity

(2022) Yan-Mei Chen et al.   Nature Microbiology

Experimental evidence for the impact of phages on mineralization of soil-derived dissolved organic matter under different temperature regimes

(2022) Shuang Wang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Viruses Ubiquity and Diversity in Atacama Desert Endolithic Communities

(2022) Leora Busse et al.   Viruses-Basel

Response of soil viral communities to land use changes

(2022) Hu Liao et al.   Nature Communications

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

(2022) George Muscatt et al.   Microbiome

How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research

(2022) Laura K. Inglis et al.   Microorganisms

Ecological and functional roles of bacteriophages in contrasting environments: marine, terrestrial and human gut

(2022) Teagan L Brown et al.   CURRENT OPINION IN MICROBIOLOGY

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

(2022) Antonio Pedro Camargo et al.   NUCLEIC ACIDS RESEARCH

RNA Viruses Linked to Eukaryotic Hosts in Thawed Permafrost

(2022) Ruonan Wu et al.   mSystems

Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt

(2021) Arthur A. D. Broadbent et al.   ISME Journal

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

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

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

(2021) Jiarong Guo et al.   Microbiome

BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains

(2021) Adam J. Hockenberry et al.   PeerJ

Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil

(2021) Yunha Hwang et al.   mSystems

DOE JGI Metagenome Workflow

(2021) Alicia Clum et al.   mSystems

The landscape of lysogeny across microbial community density, diversity and energetics

(2021) Cynthia B. Silveira et al.   ENVIRONMENTAL MICROBIOLOGY

Interactions between bacterial and phage communities in natural environments

(2021) Anne Chevallereau et al.   NATURE REVIEWS MICROBIOLOGY

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

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

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

(2021) Ruonan Wu et al.   mBio

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

Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses

(2021) Julie Callanan et al.   Microbial Genomics

Global Organization and Proposed Megataxonomy of the Virus World

(2020) Eugene V. Koonin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

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

Soil Microbes Trade-Off Biogeochemical Cycling for Stress Tolerance Traits in Response to Year-Round Climate Change

(2020) Maria O. Garcia et al.   Frontiers in Microbiology

The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter

(2020) Patrick O. Sorensen et al.   Frontiers in Microbiology

Terabase-scale metagenome coassembly with MetaHipMer

(2020) Steven Hofmeyr et al.   Scientific Reports

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

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

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

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

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

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(2018)   NUCLEIC ACIDS RESEARCH

The East River, Colorado, Watershed: A Mountainous Community Testbed for Improving Predictive Understanding of Multiscale Hydrological–Biogeochemical Dynamics

(2018) Susan S. Hubbard et al.   VADOSE ZONE JOURNAL

RNA Phage Biology in a Metagenomic Era

(2018) Julie Callanan et al.   Viruses-Basel

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Origins and Evolution of the Global RNA Virome

(2018) Yuri I. Wolf et al.   mBio

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

Warming shortens flowering seasons of tundra plant communities

(2018) Janet S. Prevéy et al.   Nature Ecology & Evolution

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins – extended Database

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MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

(2017) Anja Narr et al.   Frontiers in Microbiology

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

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(2016) B. Knowles et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Virus Variation Resource – improved response to emergent viral outbreaks

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Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses

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BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics

(2015) Jennifer R Brum et al.   ISME Journal

Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus–host coevolution

(2015) Eugene V. Koonin et al.   Molecular BioSystems

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

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The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive protein alignment using DIAMOND

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Expanded microbial genome coverage and improved protein family annotation in the COG database

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Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Epifluorescent direct counts of bacteria and viruses from topsoil of various desert dust storm regions

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(2011) E. Jończyk et al.   FOLIA MICROBIOLOGICA

Adaptive seeds tame genomic sequence comparison

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HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

The Unusual Nature of Recent Snowpack Declines in the North American Cordillera

(2011) Gregory T. Pederson et al.   SCIENCE

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

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The Sequence Alignment/Map format and SAMtools

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Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

(2008) A. F. Andersson et al.   SCIENCE