Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

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

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

Quantifying aquatic viral community change associated with stormwater runoff in a wet retention pond using metagenomic time series data

(2018) JC Green et al.   AQUATIC MICROBIAL ECOLOGY

The ‘Neglected’ Soil Virome – Potential Role and Impact

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

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

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

Viral and metabolic controls on high rates of microbial sulfur and carbon cycling in wetland ecosystems

(2018) Paula Dalcin Martins et al.   Microbiome

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

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

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

(2018) Lindsey M. Solden et al.   Nature Microbiology

Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing

(2018) Rebecca A. Daly et al.   Nature Microbiology

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

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

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

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Pseudomonas predators: understanding and exploiting phage–host interactions

(2017) Jeroen De Smet et al.   NATURE REVIEWS MICROBIOLOGY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Bacteria–Bacteriophage Coevolution in the Human Gut: Implications for Microbial Diversity and Functionality

(2017) Pauline D. Scanlan   TRENDS IN MICROBIOLOGY

Origins and challenges of viral dark matter

(2017) Siddharth R. Krishnamurthy et al.   VIRUS RESEARCH

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

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

Dietary energy drives the dynamic response of bovine rumen viral communities

(2017) Christopher L. Anderson et al.   Microbiome

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Effectiveness of ecological rescue for altered soil microbial communities and functions

(2016) Kadiya Calderón et al.   ISME Journal

Prophages mediate defense against phage infection through diverse mechanisms

(2016) Joseph Bondy-Denomy et al.   ISME Journal

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Viruses as Winners in the Game of Life

(2016) Ana Georgina Cobián Güemes et al.   Annual Review of Virology

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types

(2015) Brian Reavy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity

(2015) Graham F. Hatfull   JOURNAL OF VIROLOGY

An Optimized Enrichment Technique for the Isolation of Arthrobacter Bacteriophage Species from Soil Sample Isolates

(2015) Trevor Cross et al.   Jove-Journal of Visualized Experiments

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Host diversity drives parasite diversity: meta-analytical insights into patterns and causal mechanisms

(2014) Tsukushi Kamiya et al.   ECOGRAPHY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Acanthamoeba polyphaga mimivirus and other giant viruses: an open field to outstanding discoveries

(2014) Jônatas S Abrahão et al.   Virology Journal

Cell Size Distributions of Soil Bacterial and Archaeal Taxa

(2013) Maria C. Portillo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes

(2013) Emily B. Graham et al.   SOIL BIOLOGY & BIOCHEMISTRY

Coexistence of phage and bacteria on the boundary of self-organized refuges

(2012) S. Heilmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phage–bacteria infection networks

(2012) Joshua S. Weitz et al.   TRENDS IN MICROBIOLOGY

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Bacteria-Phage Antagonistic Coevolution in Soil

(2011) P. Gomez et al.   SCIENCE

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Viruses in soils: morphological diversity and abundance in the rhizosphere

(2009) M.M. Swanson et al.   ANNALS OF APPLIED BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

A safe operating space for humanity

(2009) Johan Rockström et al.   NATURE

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil

(2008) K.-H. Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

NITROGEN LIMITATION OF NET PRIMARY PRODUCTIVITY IN TERRESTRIAL ECOSYSTEMS IS GLOBALLY DISTRIBUTED

(2008) David S. LeBauer et al.   ECOLOGY