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

Multiple mechanisms drive phage infection efficiency in nearly identical hosts

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Host-linked soil viral ecology along a permafrost thaw gradient

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

A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria

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Pseudomonas predators: understanding and exploiting phage–host interactions

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Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

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

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Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

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Phage-host interactions in Streptococcus thermophilus: Genome analysis of phages isolated in Uruguay and ectopic spacer acquisition in CRISPR array

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Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

(2016) Ann C. Gregory et al.   BMC GENOMICS

Prophages mediate defense against phage infection through diverse mechanisms

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

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection

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Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Uncovering Earth’s virome

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Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

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Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

(2016) Rebecca A. Daly et al.   Nature Microbiology

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

(2015) Joshua S Weitz et al.   ISME Journal

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories

(2015) Christine L Sun et al.   ISME Journal

An updated evolutionary classification of CRISPR–Cas systems

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

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Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

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Patterns and ecological drivers of ocean viral communities

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Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

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A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

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Temporal Changes in Microbial Ecology and Geochemistry in Produced Water from Hydraulically Fractured Marcellus Shale Gas Wells

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Correlation between viral production and carbon mineralization under nitrate-reducing conditions in aquifer sediment

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Microbial Community Changes in Hydraulic Fracturing Fluids and Produced Water from Shale Gas Extraction

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Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

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Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia

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Microbial diversity and methanogenic activity of Antrim Shale formation waters from recently fractured wells

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Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

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Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

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Bacterial Communities Associated with Production Facilities of Two Newly Drilled Thermogenic Natural Gas Wells in the Barnett Shale (Texas, USA)

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Fast gapped-read alignment with Bowtie 2

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Abundance and Distribution of Synechococcus spp. and Cyanophages in the Chesapeake Bay

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Complete Genome Sequence of the Haloalkaliphilic, Hydrogen-Producing Bacterium Halanaerobium hydrogeniformans

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Bacteria-Phage Antagonistic Coevolution in Soil

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Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Is the Genetic Landscape of the Deep Subsurface Biosphere Affected by Viruses?

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EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

The phage-host arms race: Shaping the evolution of microbes

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Viruses in the faecal microbiota of monozygotic twins and their mothers

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A simple and efficient method for concentration of ocean viruses by chemical flocculation

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Nasty Viruses, Costly Plasmids, Population Dynamics, and the Conditions for Establishing and Maintaining CRISPR-Mediated Adaptive Immunity in Bacteria

(2010) Bruce R. Levin   PLoS Genetics

Laboratory procedures to generate viral metagenomes

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Major viral impact on the functioning of benthic deep-sea ecosystems

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