Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

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

(2021) Jiarong Guo et al.   Microbiome

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

The Geology and Biogeochemistry of Hydrocarbon Seeps

(2020) Samantha B. Joye   Annual Review of Earth and Planetary Sciences

A complete domain-to-species taxonomy for Bacteria and Archaea

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Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico

(2020) Rui Zhao et al.   Scientific Reports

In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes

(2020) Kento Tominaga et al.   Frontiers in Microbiology

Extreme Viral Partitioning in a Marine-Derived High Arctic Lake

(2020) Myriam Labbé et al.   mSphere

Extraordinary diversity of viruses in deep‐sea sediments as revealed by metagenomics without prior virion separation

(2020) Xiaowei Zheng 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

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

Depth-related variability in viral communities in highly stratified sulfidic mine tailings

(2020) Shao-Ming Gao et al.   Microbiome

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

(2020) Kristopher Kieft et al.   Microbiome

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline

(2020) Paraskevi Mara et al.   ISME Journal

Large freshwater phages with the potential to augment aerobic methane oxidation

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Genome‐resolved viral ecology in a marine oxygen minimum zone

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Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep

(2020) Xiyang Dong et al.   Nature Communications

Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

(2019) Disa Bäckström et al.   mBio

Extremophile deep-sea viral communities from hydrothermal vents: Structural and functional analysis

(2019) Hugo G. Castelán-Sánchez et al.   Marine Genomics

Active and diverse viruses persist in the deep sub-seafloor sediments over thousands of years

(2019) Lanlan Cai et al.   ISME Journal

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

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

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

An Improved Method for Extracting Viruses From Sediment: Detection of Far More Viruses in the Subseafloor Than Previously Reported

(2019) Donald Pan et al.   Frontiers in Microbiology

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

(2019) Xiyang Dong et al.   Nature Communications

Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake

(2019) Yusuke Okazaki et al.   ENVIRONMENTAL MICROBIOLOGY

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs

(2019) Xiaoli Dong et al.   Frontiers in Genetics

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

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Ecology and evolution of seafloor and subseafloor microbial communities

(2018) William D. Orsi   NATURE REVIEWS 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

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

(2018) Cindy J. Castelle et al.   NATURE REVIEWS 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

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

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

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

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

The interaction of climate change and methane hydrates

(2017) Carolyn D. Ruppel et al.   REVIEWS OF GEOPHYSICS

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans

(2017) Felipe H. Coutinho et al.   Nature Communications

Dietary energy drives the dynamic response of bovine rumen viral communities

(2017) Christopher L. Anderson et al.   Microbiome

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

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

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

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 novel sister clade to the enterobacteria microviruses (familyMicroviridae) identified in methane seep sediments

(2015) Samuel Joseph Bryson et al.   ENVIRONMENTAL MICROBIOLOGY

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Global dispersion and local diversification of the methane seep microbiome

(2015) S. Emil Ruff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted diversity generation by intraterrestrial archaea and archaeal viruses

(2015) Blair G. Paul et al.   Nature Communications

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

(2015) Simon Roux et al.   eLife

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Marine cold seeps and their manifestations: geological control, biogeochemical criteria and environmental conditions

(2014) Erwin Suess   INTERNATIONAL JOURNAL OF EARTH SCIENCES

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

A thermogenic hydrocarbon seep in shallow Adriatic Sea (Italy): Gas origin, sediment contamination and benthic foraminifera

(2014) G. Etiope et al.   MARINE AND PETROLEUM GEOLOGY

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

(2013) Connor T. Skennerton et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Limin Fu et al.   BIOINFORMATICS

Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps

(2012) Ulrike Jaekel et al.   ISME Journal

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Prodigal: prokaryotic gene recognition and translation initiation site identification

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Enumeration of viruses and prokaryotes in deep-sea sediments and cold seeps of the Gulf of Mexico

(2010) Christina A. Kellogg   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia

(2009) A. E. Dekas et al.   SCIENCE

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

(2008) Roberto Danovaro et al.   NATURE