Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench

VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families

(2021) Joan Carles Pons et al.   BIOINFORMATICS

ViralRecall—A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in ‘Omic Data

(2021) Frank O. Aylward et al.   Viruses-Basel

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

(2021) Zexin Li et al.   ISME Journal

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

(2021) Jiarong Guo et al.   Microbiome

Diversity and distribution of viruses inhabiting the deepest ocean on Earth

(2021) Huahua Jian et al.   ISME Journal

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

(2021) Kristopher Kieft et al.   Nature Communications

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

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

Double-stranded DNA virioplankton dynamics and reproductive strategies in the oligotrophic open ocean water column

(2020) Elaine Luo et al.   ISME Journal

Phage-specific metabolic reprogramming of virocells

(2020) Cristina Howard-Varona et al.   ISME Journal

Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities

(2020) Katy Hoffmann et al.   ISME Journal

The arms race between bacteria and their phage foes

(2020) Hannah G. Hampton et al.   NATURE

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

Stability and infectivity of allochthonous viruses in deep sea: A long-term high pressure simulation experiment

(2020) Yuan Tian et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

New Insights Into the Virus-to-Prokaryote Ratio (VPR) in Marine Sediments

(2020) Miao Wei et al.   Frontiers in Microbiology

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

(2020) Xiaowei Zheng et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

Spatiotemporal variations of biogenic elements and sources of sedimentary organic matter in the largest oyster mariculture bay (Maowei Sea), Southwest China

(2020) Cheng Xu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

(2020) Kristopher Kieft et al.   Microbiome

Bacteria are important dimethylsulfoniopropionate producers in marine aphotic and high-pressure environments

(2020) Yanfen Zheng et al.   Nature Communications

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

(2020) M. Consuelo Gazitúa et al.   ISME Journal

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

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

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

(2019) Disa Bäckström et al.   mBio

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

(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

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep

(2019) Guojie Cui et al.   PeerJ

Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench

(2019) Jiwen Liu et al.   Microbiome

Diversities and potential biogeochemical impacts of mangrove soil viruses

(2019) Min Jin et al.   Microbiome

In situ meta‐omic insights into the community compositions and ecological roles of hadal microbes in the Mariana Trench

(2019) Zhao‐Ming Gao et al.   ENVIRONMENTAL MICROBIOLOGY

Viral Infections Boost Prokaryotic Biomass Production and Organic C Cycling in Hadal Trench Sediments

(2019) Elisabetta Manea et al.   Frontiers in Microbiology

Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea

(2019) Yantao Liang et al.   Frontiers in Microbiology

Database Resources of the National Genomics Data Center in 2020

(2019) et al.   NUCLEIC ACIDS RESEARCH

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

(2019) Satoshi Hiraoka et al.   ISME Journal

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench

(2018) Takuro Nunoura et al.   MICROBES AND ENVIRONMENTS

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

Seasonal variability of water characteristics in the Challenger Deep observed by four cruises

(2018) Caijing Huang et al.   Scientific Reports

Insight Into the Pico- and Nano-Phytoplankton Communities in the Deepest Biosphere, the Mariana Trench

(2018) Ruoyu Guo et al.   Frontiers in Microbiology

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

(2018) Paula Dalcin Martins et al.   Microbiome

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Provenances, distribution, and accumulation of organic matter in the southern Mariana Trench rim and slope: Implication for carbon cycle and burial in hadal trenches

(2017) Min Luo et al.   MARINE GEOLOGY

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

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

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

(2017) David Paez-Espino et al.   Nature Protocols

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation

(2017) Maria G. Pachiadaki et al.   SCIENCE

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

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

From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments

(2017) Cinzia Corinaldesi et al.   Scientific Reports

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

(2017) Mario López-Pérez et al.   PLoS Genetics

Jumbo Bacteriophages: An Overview

(2017) Yihui Yuan et al.   Frontiers in Microbiology

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

(2017) Jie Ren et al.   Microbiome

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean

(2017) Yosuke Nishimura et al.   mSphere

Viral metabolic reprogramming in marine ecosystems

(2016) Bonnie L Hurwitz et al.   CURRENT OPINION IN MICROBIOLOGY

Microbial Community Composition in the Marine Sediments of Jeju Island: Next-Generation Sequencing Surveys

(2016) Heebok Choi et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Lytic to temperate switching of viral communities

(2016) B. Knowles et al.   NATURE

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Linking Virus Genomes with Host Taxonomy

(2016) Tomoko Mihara et al.   Viruses-Basel

Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific

(2016) Mark Trimmer et al.   Nature Communications

Virus-mediated archaeal hecatomb in the deep seafloor

(2016) R. Danovaro et al.   Science Advances

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Cellulose in algal cell wall : an “in situ” localization

(2015) B Baldan et al.   EUROPEAN JOURNAL OF HISTOCHEMISTRY

Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy

(2015) Jan P Meier-Kolthoff et al.   Standards in Genomic Sciences

Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

(2014) Evelien M. Adriaenssens et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography

(2014) Matthias Wietz et al.   BMC GENOMICS

Factors affecting virus dynamics and microbial host-virus interactions in marine environments

(2014) Kristina D.A. Mojica et al.   FEMS MICROBIOLOGY ECOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Sulfur Oxidation Genes in Diverse Deep-Sea Viruses

(2014) K. Anantharaman et al.   SCIENCE

Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host–virus coevolution

(2014) Mohammad Moniruzzaman et al.   VIROLOGY

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

(2014) Simon Roux et al.   eLife

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

Targeted search for actinomycetes from nearshore and deep-sea marine sediments

(2013) Alejandra Prieto-Davó et al.   FEMS MICROBIOLOGY ECOLOGY

Metagenomic Analysis of Viral Communities in (Hado)Pelagic Sediments

(2013) Mitsuhiro Yoshida et al.   PLoS One

Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

(2012) Roland Hatzenpichler   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink

(2012) Christopher M Jones et al.   ISME Journal

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Marine Viruses: Truth or Dare

(2011) Mya Breitbart   Annual Review of Marine Science

Viral abundance and activity in the deep sub-seafloor biosphere

(2011) M Middelboe et al.   AQUATIC MICROBIAL ECOLOGY

Induction of prophages from deep-subseafloor bacteria

(2011) Tim Engelhardt et al.   Environmental Microbiology Reports

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

(2010) Michael Hügler et al.   Annual Review of Marine Science

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic’s interior

(2010) Thomas Reinthaler et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Viral decay and viral production rates in continental-shelf and deep-sea sediments of the Mediterranean Sea

(2010) Cinzia Corinaldesi et al.   FEMS MICROBIOLOGY ECOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Hadal trenches: the ecology of the deepest places on Earth

(2009) Alan J. Jamieson et al.   TRENDS IN ECOLOGY & EVOLUTION

Prokaryote diversity and viral production in deep-sea sediments and seamounts

(2008) Roberto Danovaro et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Viriobenthos in freshwater and marine sediments: a review

(2008) ROBERTO DANOVARO et al.   FRESHWATER BIOLOGY

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

(2008) Roberto Danovaro et al.   NATURE