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

Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale

(2021) Sally Hilton et al.   Microbiome

Spatial patterns in phage-Rhizobium coevolutionary interactions across regions of common bean domestication

(2021) Jannick Van Cauwenberghe 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

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

(2021) Ryan Cook et al.   Microbiome

A new family of globally distributed lytic roseophages with unusual deoxythymidine to deoxyuridine substitution

(2021) Branko Rihtman et al.   CURRENT BIOLOGY

Comparative Genomics of Three Novel Jumbo Bacteriophages Infecting Staphylococcus aureus

(2021) Abby M. Korn et al.   JOURNAL OF VIROLOGY

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

(2021) Evan P. Starr et al.   mSphere

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

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

Giant virus diversity and host interactions through global metagenomics

(2020) Frederik Schulz et al.   NATURE

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

YerA41, a Yersinia ruckeri Bacteriophage: Determination of a Non-Sequencable DNA Bacteriophage Genome via RNA-Sequencing

(2020) Katarzyna Leskinen et al.   Viruses-Basel

VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

(2020) Kristopher Kieft et al.   Microbiome

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

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

Soil Viruses: A New Hope

(2019) Joanne B. Emerson   mSystems

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

(2019) Gareth Trubl et al.   PeerJ

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

(2019) Elena Bushmanova et al.   GigaScience

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

Multifaceted Impacts of Bacteriophages in the Plant Microbiome

(2018) Britt Koskella et al.   Annual Review of Phytopathology

Preceding crop and seasonal effects influence fungal, bacterial and nematode diversity in wheat and oilseed rape rhizosphere and soil

(2018) Sally Hilton et al.   APPLIED SOIL ECOLOGY

Energy limitation of cyanophage development: implications for marine carbon cycling

(2018) Richard J. Puxty et al.   ISME Journal

The biomass distribution on Earth

(2018) Yinon M. Bar-On et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ‘Neglected’ Soil Virome – Potential Role and Impact

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

Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice

(2018) Joseph A. Edwards et al.   PLOS BIOLOGY

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Host-linked soil viral ecology along a permafrost thaw gradient

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

Diversity of active viral infections within the Sphagnum microbiome

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

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

(2018) Guangchuang Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone

(2017) Frank O. Aylward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

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

Stable isotope probing of carbon flow in the plant holobiont

(2016) Feth el Zahar Haichar et al.   CURRENT OPINION IN BIOTECHNOLOGY

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Hyperexpansion of RNA Bacteriophage Diversity

(2016) Siddharth R. Krishnamurthy et al.   PLOS BIOLOGY

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes

(2016) Branko Rihtman et al.   PeerJ

Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity

(2015) Barbara Reinhold-Hurek et al.   Annual Review of Phytopathology

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Ecological importance of soil bacterivores for ecosystem functions

(2015) Jean Trap et al.   PLANT AND SOIL

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The elemental composition of virus particles: implications for marine biogeochemical cycles

(2014) Luis F. Jover et al.   NATURE REVIEWS MICROBIOLOGY

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

(2013) Pascal Hingamp et al.   ISME Journal

Impact of Shortened Crop Rotation of Oilseed Rape on Soil and Rhizosphere Microbial Diversity in Relation to Yield Decline

(2013) Sally Hilton et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Marine Viruses Exploit Their Host's Two-Component Regulatory System in Response to Resource Limitation

(2012) Qinglu Zeng et al.   CURRENT BIOLOGY

Meeting the demand for crop production: the challenge of yield decline in crops grown in short rotations

(2011) Amanda J. Bennett et al.   BIOLOGICAL REVIEWS

The influence of external factors on bacteriophages—review

(2011) E. Jończyk et al.   FOLIA MICROBIOLOGICA

The activity level of a microbial community function can be predicted from its metatranscriptome

(2011) Damian E Helbling et al.   ISME Journal

Genome Structure of Caulobacter Phage phiCb5

(2011) A. Kazaks et al.   JOURNAL OF VIROLOGY

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

Bacteria-Phage Antagonistic Coevolution in Soil

(2011) P. Gomez et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Trade-Offs between Competition and Defense Specialists among Unicellular Planktonic Organisms: the "Killing the Winner" Hypothesis Revisited

(2010) C. Winter et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Abundance, composition, diversity and novelty of soil Proteobacteria

(2009) Anne M Spain et al.   ISME Journal

Plant-microbe-soil interactions in the rhizosphere: an evolutionary perspective

(2009) Hans Lambers et al.   PLANT AND SOIL

Local Adaptation of Bacteriophages to Their Bacterial Hosts in Soil

(2009) M. Vos et al.   SCIENCE