Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone

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

(2022) Elaine Luo et al.   ISME Journal

Diverse Genomic Traits Differentiate Sinking-Particle-Associated versus Free-Living Microbes throughout the Oligotrophic Open Ocean Water Column

(2022) Andy O. Leu et al.   mBio

Viral community analysis in a marine oxygen minimum zone indicates increased potential for viral manipulation of microbial physiological state

(2021) Sophie K. Jurgensen et al.   ISME Journal

Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

(2020) Jordan G Okie et al.   eLife

Ocean Biogeochemistry in GFDL's Earth System Model 4.1 and Its Response to Increasing Atmospheric CO 2

(2020) Charles A. Stock et al.   Journal of Advances in Modeling Earth Systems

Genome‐resolved viral ecology in a marine oxygen minimum zone

(2020) Dean Vik et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Community-Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems

(2019) Luigi Caputi et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Nutrient stoichiometry shapes microbial coevolution

(2019) Megan L. Larsen et al.   ECOLOGY LETTERS

Nitrogen sourcing during viral infection of marine cyanobacteria

(2019) Jacob R. Waldbauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Consistent and correctable bias in metagenomic sequencing experiments

(2019) Michael R McLaren et al.   eLife

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems

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

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria

(2018) Sangita Ganesh et al.   ISME Journal

Stoichio-Metagenomics of Ocean Waters: A Molecular Evolution Approach to Trace the Dynamics of Nitrogen Conservation in Natural Communities

(2018) Hannes Dittberner et al.   Frontiers in Microbiology

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

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

Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System

(2018) Jennifer Bachmann et al.   Frontiers in Microbiology

Environmental drivers of a microbial genomic transition zone in the ocean’s interior

(2017) Daniel R. Mende et al.   Nature Microbiology

Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships

(2017) Justin R. Seymour et al.   Nature Microbiology

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2

(2016) Johan Bengtsson-Palme et al.   Ecological Informatics

Evolutionary tradeoffs in cellular composition across diverse bacteria

(2016) Christopher P Kempes et al.   ISME Journal

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Chromophoric and fluorescent dissolved organic matter in and above the oxygen minimum zone off Peru

(2016) A. N. Loginova et al.   JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

(2015) Jennifer B. Glass et al.   Frontiers in Microbiology

Oxygen distribution and aerobic respiration in the north and south eastern tropical Pacific oxygen minimum zones

(2014) Laura Tiano et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

The elemental composition of virus particles: implications for marine biogeochemical cycles

(2014) Luis F. Jover et al.   NATURE REVIEWS MICROBIOLOGY

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile

(2014) Darren J. Parris et al.   Frontiers in Microbiology

Nitrogen cycling driven by organic matter export in the South Pacific oxygen minimum zone

(2013) Tim Kalvelage et al.   Nature Geoscience

Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone

(2013) J. Michael Beman et al.   Nature Communications

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

(2012) Limin Fu et al.   BIOINFORMATICS

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

(2012) Jesse Dabney et al.   BIOTECHNIQUES

Widespread functional anoxia in the oxygen minimum zone of the Eastern South Pacific

(2012) Bo Thamdrup et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Microbial ecology of expanding oxygen minimum zones

(2012) Jody J. Wright et al.   NATURE REVIEWS MICROBIOLOGY

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

(2012) Jens Roat Kultima et al.   PLoS One

Microbial oceanography of anoxic oxygen minimum zones

(2012) O. Ulloa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Marine Microbes See a Sea of Gradients

(2012) R. Stocker   SCIENCE

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

The significance of nitrogen cost minimization in proteomes of marine microorganisms

(2011) Joseph J Grzymski et al.   ISME Journal

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast

(2010) D. E. Canfield et al.   SCIENCE

Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition

(2010) James J. Elser et al.   TRENDS IN ECOLOGY & EVOLUTION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Organic carbon, and not copper, controls denitrification in oxygen minimum zones of the ocean

(2008) Bess B. Ward et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Oxygen minimum zones (OMZs) in the modern ocean

(2008) A. Paulmier et al.   PROGRESS IN OCEANOGRAPHY

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE