Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

Major imprint of surface plankton on deep ocean prokaryotic structure and activity

(2020) Clara Ruiz‐González et al.   MOLECULAR ECOLOGY

Changing perspectives in marine nitrogen fixation

(2020) Jonathan P. Zehr et al.   SCIENCE

Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean

(2020) Frank O. Aylward et al.   mSystems

Multi-faceted particle pumps drive carbon sequestration in the ocean

(2019) Philip W. Boyd et al.   NATURE

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

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival

(2019) Paul R. F. Cordero et al.   ISME Journal

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

(2019) Guillem Salazar et al.   CELL

Ketobacter alkanivorans gen. nov., sp. nov., an n-alkane-degrading bacterium isolated from seawater

(2018) Seol-Hee Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Functional assignment of multiple catabolic pathways for d-apiose

(2018) Michael S. Carter et al.   Nature Chemical Biology

Global niche of marine anaerobic metabolisms expanded by particle microenvironments

(2018) Daniele Bianchi et al.   Nature Geoscience

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

Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes

(2018) Ricardo J. Eloy Alves et al.   Nature Communications

Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO2-Fixing Bathypelagic Prokaryotic Consortia

(2018) Violetta La Cono et al.   Frontiers in Microbiology

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

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

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

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

(2018) Hanna Farnelid et al.   ISME Journal

Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea

(2018) Alexander L Jaffe et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Pfam protein families database in 2019

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

Episodic organic carbon fluxes from surface ocean to abyssal depths during long-term monitoring in NE Pacific

(2018) Kenneth L. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling

(2017) Maliheh Mehrshad et al.   ISME Journal

The role of subduction and gravitational sinking in particle export, carbon sequestration, and the remineralization length scale in the California Current Ecosystem

(2017) Michael R. Stukel et al.   LIMNOLOGY AND OCEANOGRAPHY

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

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

(2017) Kristin Bergauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How microbes survive in the open ocean

(2017) Jonathan P. Zehr et al.   SCIENCE

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

(2017) Maria G. Pachiadaki et al.   SCIENCE

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

(2017) Zachary Landry et al.   mBio

Chasing after Non-cyanobacterial Nitrogen Fixation in Marine Pelagic Environments

(2017) Pia H. Moisander et al.   Frontiers in Microbiology

290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology

(2017) Benjamin J. Tully et al.   PeerJ

Complete Genome of the Starch-Degrading MyxobacteriaSandaracinus amylolyticusDSM 53668T

(2016) Gaurav Sharma et al.   Genome Biology and Evolution

Global genetic capacity for mixotrophy in marine picocyanobacteria

(2016) Alexis P Yelton et al.   ISME Journal

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

Substantial energy input to the mesopelagic ecosystem from the seasonal mixed-layer pump

(2016) Giorgio Dall'Olmo et al.   Nature Geoscience

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081)

(2016) Xiao-jing Chen et al.   Standards in Genomic Sciences

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

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

(2015) Massimo C Pernice et al.   ISME Journal

Global diversity and biogeography of deep-sea pelagic prokaryotes

(2015) Guillem Salazar et al.   ISME Journal

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

(2015) Sangita Ganesh et al.   ISME Journal

Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

(2015) Guillem Salazar et al.   MOLECULAR ECOLOGY

Seasonal copepod lipid pump promotes carbon sequestration in the deep North Atlantic

(2015) Sigrún Huld Jónasdóttir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Eddy-driven subduction exports particulate organic carbon from the spring bloom

(2015) M. M. Omand et al.   SCIENCE

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump

(2015) S. Agusti et al.   Nature Communications

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

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

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

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

(2013) Pascal Hingamp et al.   ISME Journal

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

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

Microbial control of the dark end of the biological pump

(2013) Gerhard J. Herndl et al.   Nature Geoscience

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

(2012) Lisa Zeigler Allen et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria

(2012) K. Anantharaman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role for urea in nitrification by polar marine Archaea

(2012) L. Alonso-Saez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic Evidence for H2 Oxidation and H2 Production by Serpentinite-Hosted Subsurface Microbial Communities

(2012) William J. Brazelton et al.   Frontiers in Microbiology

Nitrogen fixation within the water column associated with two hypoxic basins in the Southern California Bight

(2011) MR Hamersley et al.   AQUATIC MICROBIAL ECOLOGY

Bacterial species may exist, metagenomics reveal

(2011) Alejandro Caro-Quintero et al.   ENVIRONMENTAL MICROBIOLOGY

Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)

(2011) Michail M Yakimov et al.   ISME Journal

Microbial oceanography of the dark ocean's pelagic realm

(2011) Javier Arístegui et al.   LIMNOLOGY AND OCEANOGRAPHY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria

(2011) Hanna Farnelid et al.   PLoS One

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   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

Significance of non-sinking particulate organic carbon and dark CO2fixation to heterotrophic carbon demand in the mesopelagic northeast Atlantic

(2010) Federico Baltar et al.   GEOPHYSICAL RESEARCH LETTERS

Mesoscale eddies: hotspots of prokaryotic activity and differential community structure in the ocean

(2010) Federico Baltar et al.   ISME Journal

High bicarbonate assimilation in the dark by Arctic bacteria

(2010) Laura Alonso-Sáez et al.   ISME Journal

Ballast, sinking velocity, and apparent diffusivity within marine snow and zooplankton fecal pellets: Implications for substrate turnover by attached bacteria

(2010) Helle Ploug et al.   LIMNOLOGY AND OCEANOGRAPHY

CO Dehydrogenase Genes Found in Metagenomic Fosmid Clones from the Deep Mediterranean Sea

(2009) A.-B. Martin-Cuadrado et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Prokaryotic extracellular enzymatic activity in relation to biomass production and respiration in the meso- and bathypelagic waters of the (sub)tropical Atlantic

(2009) Federico Baltar et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity of total and active free-living vs. particle-attached bacteria in the euphotic zone of the NW Mediterranean Sea

(2009) Jean-François Ghiglione et al.   FEMS MICROBIOLOGY LETTERS

Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment

(2009) J. Yuan et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2fixation cycle inChloroflexus aurantiacus

(2009) Jan Zarzycki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution

(2009) Natalya Yutin et al.   Virology Journal