Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

(2019) Spencer Diamond et al.   Nature Microbiology

Use and abuse of correlation analyses in microbial ecology

(2019) Alex Carr et al.   ISME Journal

Novel RNA viruses within plant parasitic cyst nematodes

(2018) Casey L. Ruark et al.   PLoS One

Prospecting for viral natural enemies of the fire ant Solenopsis invicta in Argentina

(2018) Steven M. Valles et al.   PLoS One

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

Evidence for contemporary plant mitoviruses

(2018) Max L. Nibert et al.   VIROLOGY

New insight into the RNA aquatic virosphere via viromics

(2018) Alexander Culley   VIRUS RESEARCH

Virome Characterization of a Collection of S. sclerotiorum from Australia

(2018) Fan Mu et al.   Frontiers in Microbiology

Host-linked soil viral ecology along a permafrost thaw gradient

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

Identification of Novel Viruses in Amblyomma americanum , Dermacentor variabilis , and Ixodes scapularis Ticks

(2018) Rafal Tokarz et al.   mSphere

Diversity of active viral infections within the Sphagnum microbiome

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

Microbial community assembly differs across minerals in a rhizosphere microcosm

(2018) Thea Whitman et al.   ENVIRONMENTAL MICROBIOLOGY

ICTV Virus Taxonomy Profile: Fimoviridae

(2018) Toufic Elbeaino et al.   JOURNAL OF GENERAL VIROLOGY

Evolutionary and ecological links between plant and fungal viruses

(2018) Marilyn J. Roossinck   NEW PHYTOLOGIST

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Origins and Evolution of the Global RNA Virome

(2018) Yuri I. Wolf et al.   mBio

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia

(2017) Mang Shi et al.   JOURNAL OF VIROLOGY

The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks

(2017) Saura R. Silva et al.   PLoS One

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics

(2017) Mohammad Moniruzzaman et al.   Nature Communications

Multiple viral infections in Agaricus bisporus - Characterisation of 18 unique RNA viruses and 8 ORFans identified by deep sequencing

(2017) Gregory Deakin et al.   Scientific Reports

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

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

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses

(2017) Lisa Zeigler Allen et al.   mSystems

A novel monopartite dsRNA virus isolated from the entomopathogenic and nematophagous fungus Purpureocillium lilacinum

(2016) Noemi Herrero   ARCHIVES OF VIROLOGY

Taxonomy of the order Mononegavirales: update 2016

(2016) Claudio L. Afonso et al.   ARCHIVES OF VIROLOGY

Design of virus-based nanomaterials for medicine, biotechnology, and energy

(2016) Amy M. Wen et al.   CHEMICAL SOCIETY REVIEWS

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Multiple virus infection in a single strain of Fusarium poae shown by deep sequencing

(2016) Hideki Osaki et al.   VIRUS GENES

Hyperexpansion of RNA Bacteriophage Diversity

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

Interplays between Soil-Borne Plant Viruses and RNA Silencing-Mediated Antiviral Defense in Roots

(2016) Ida Bagus Andika et al.   Frontiers in Microbiology

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

(2016) Cristina N. Butterfield et al.   PeerJ

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

(2015) Itai Sharon et al.   GENOME RESEARCH

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

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

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

Insect vector-mediated transmission of plant viruses

(2015) Anna E. Whitfield et al.   VIROLOGY

Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda

(2015) Shu Wu et al.   PLoS One

Three mitovirus strains infecting a single isolate of Fusarium circinatum are the first putative members of the family Narnaviridae detected in a fungus of the genus Fusarium

(2014) Pablo Martínez-Álvarez et al.   ARCHIVES OF VIROLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

(2014) Kenan Hadziavdic et al.   PLoS One

The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics

(2014) A. I. Culley et al.   mBio

High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities

(2014) Julia A. Gustavsen et al.   Frontiers in Microbiology

A novel single-stranded RNA virus isolated from a phytopathogenic filamentous fungus, Rosellinia necatrix, with similarity to hypo-like viruses

(2014) Rui Zhang et al.   Frontiers in Microbiology

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

(2013) Matthieu Leray et al.   Frontiers in Zoology

Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

(2013) Romain L Barnard et al.   ISME Journal

Classification, genetic variation and pathogenicity of Lymantria dispar nucleopolyhedrovirus isolates from Asia, Europe, and North America

(2013) Robert L. Harrison et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dynamic regulation of mitochondrial transcription as a mechanism of cellular adaptation

(2012) Erik S. Blomain et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Diversity of pili-specific bacteriophages: genome sequence of IncM plasmid-dependent RNA phage M

(2012) Janis Rumnieks et al.   BMC MICROBIOLOGY

Are we missing half of the viruses in the ocean?

(2012) Grieg F Steward et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups

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

Have biopesticides come of age?

(2012) Travis Glare et al.   TRENDS IN BIOTECHNOLOGY

A New WineSaccharomyces cerevisiaeKiller Toxin (Klus), Encoded by a Double-Stranded RNA Virus, with Broad Antifungal Activity Is Evolutionarily Related to a Chromosomal Host Gene

(2011) Nieves Rodríguez-Cousiño et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome Structure of Caulobacter Phage phiCb5

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

DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer

(2011) GREGG P. ROBIDEAU et al.   Molecular Ecology Resources

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Repeating patterns of virioplankton production within an estuarine ecosystem

(2011) D. M. Winget et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Performance of the COX1 gene as a marker for the study of metabolically active Pezizomycotina and Agaricomycetes fungal communities from the analysis of soil RNA

(2010) Coralie Damon et al.   FEMS MICROBIOLOGY ECOLOGY

Genome characterization of a debilitation-associated mitovirus infecting the phytopathogenic fungus Botrytis cinerea

(2010) Mingde Wu et al.   VIROLOGY

Metagenomic analysis of the turkey gut RNA virus community

(2010) J Michael Day et al.   Virology Journal

Viruses of Plant Pathogenic Fungi

(2009) Said A. Ghabrial et al.   Annual Review of Phytopathology

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Carbon sequestration under Miscanthus: a study of 13C distribution in soil aggregates

(2009) MARTA DONDINI et al.   Global Change Biology Bioenergy

Metagenomic Analysis of RNA Viruses in a Fresh Water Lake

(2009) Appolinaire Djikeng et al.   PLoS One

Temporal Changes in the Ectomycorrhizal Community in Two Soil Horizons of a Temperate Oak Forest

(2008) P.-E. Courty et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture

(2008) Olivier Le Gall et al.   ARCHIVES OF VIROLOGY

Selective progressive response of soil microbial community to wild oat roots

(2008) Kristen M DeAngelis et al.   ISME Journal