Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities

(2020) John Beaulaurier et al.   GENOME RESEARCH

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

(2020) Elaine Luo et al.   ISME Journal

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

(2020) Kristopher Kieft et al.   Microbiome

Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

(2020) Hiroto Kaneko et al.   iScience

Numerous cultivated and uncultivated viruses encode ribosomal proteins

(2019) Carolina M. Mizuno et al.   Nature Communications

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean

(2019) Dominique Boeuf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre

(2019) Daniel R. Mende et al.   Frontiers in Microbiology

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems

(2019) Amy E. Zimmerman et al.   NATURE REVIEWS MICROBIOLOGY

DNA metabarcoding reveals organisms contributing to particulate matter flux to abyssal depths in the North East Pacific ocean

(2019) Christina M. Preston et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Expression profiling of host and virus during a coccolithophore bloom provides insights into the role of viral infection in promoting carbon export

(2018) Uri Sheyn et al.   ISME Journal

Sinking particles promote vertical connectivity in the ocean microbiome

(2018) Mireia Mestre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Coccolithovirus facilitation of carbon export in the North Atlantic

(2018) Christien P. Laber et al.   Nature Microbiology

Diverse diazotrophs are present on sinking particles in the North Pacific Subtropical Gyre

(2018) Hanna Farnelid et al.   ISME Journal

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Mechanisms and Pathways of Small-Phytoplankton Export from the Surface Ocean

(2018) Tammi L. Richardson   Annual Review of Marine Science

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

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

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

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

Bacterial Succession on Sinking Particles in the Ocean's Interior

(2017) Erik A. Pelve et al.   Frontiers in Microbiology

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

(2017) Simon Roux et al.   PeerJ

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

(2017) Yosuke Nishimura et al.   mSphere

Temporal and vertical variability in picophytoplankton primary productivity in the North Pacific Subtropical Gyre

(2016) YM Rii et al.   MARINE ECOLOGY PROGRESS SERIES

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

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

Genomes of Abundant and Widespread Viruses from the Deep Ocean

(2016) Carolina Megumi Mizuno et al.   mBio

Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea

(2016) Mario López-Pérez et al.   Frontiers in Microbiology

Temporal and vertical variability in picophytoplankton primary productivity in the North Pacific Subtropical Gyre

(2016) YM Rii et al.   MARINE ECOLOGY PROGRESS SERIES

Effects of sinking velocities and microbial respiration rates on the attenuation of particulate carbon fluxes through the mesopelagic zone

(2015) A. M. P. McDonnell et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Zooplankton fecal pellets, marine snow, phytodetritus and the ocean’s biological pump

(2015) Jefferson T. Turner   PROGRESS IN OCEANOGRAPHY

Particle-Associated Differ from Free-Living Bacteria in Surface Waters of the Baltic Sea

(2015) Angelika Rieck et al.   Frontiers in Microbiology

Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre

(2015) Kristina M. Fontanez et al.   Frontiers in Microbiology

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Man versus microbe: warfare at its worst

(2013)   NATURE REVIEWS MICROBIOLOGY

Crass: identification and reconstruction of CRISPR from unassembled metagenomic data

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

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

Taxonomic composition of the particle-attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA

(2013) Bibiana G. Crespo et al.   MicrobiologyOpen

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Predictable and efficient carbon sequestration in the North Pacific Ocean supported by symbiotic nitrogen fixation

(2012) D. M. Karl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Microbial oceanography of the dark ocean's pelagic realm

(2011) Javier Arístegui et al.   LIMNOLOGY AND OCEANOGRAPHY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

SmashCommunity: a metagenomic annotation and analysis tool: Fig. 1.

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean

(2010) Nianzhi Jiao et al.   NATURE REVIEWS MICROBIOLOGY

Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment

(2010) Emiley A. Eloe et al.   Environmental Microbiology Reports

Ecological Genomics of Marine Picocyanobacteria

(2009) D. J. Scanlan et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

High diversity of cultivable heterotrophic bacteria in association with cyanobacterial water blooms

(2008) Katri A Berg et al.   ISME Journal