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

Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions

(2021) Chloé M. J. Baumas et al.   ISME Journal

Microbial dynamics of elevated carbon flux in the open ocean’s abyss

(2021) Kirsten E. Poff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2021) Jiarong Guo et al.   Microbiome

Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

(2021) Jake L. Weissman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The landscape of lysogeny across microbial community density, diversity and energetics

(2021) Cynthia B. Silveira et al.   ENVIRONMENTAL MICROBIOLOGY

Relating sinking and suspended microbial communities in the California Current Ecosystem: digestion resistance and the contributions of phytoplankton taxa to export

(2021) Bellineth Valencia et al.   ENVIRONMENTAL MICROBIOLOGY

A sea change in microbial enzymes: Heterogeneous latitudinal and depth‐related gradients in bulk water and particle‐associated enzymatic activities from 30°S to 59°N in the Pacific Ocean

(2021) John Paul Balmonte et al.   LIMNOLOGY AND OCEANOGRAPHY

Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales

(2021) Ashley Isaac et al.   Frontiers in Microbiology

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

(2021) Silvia G. Acinas et al.   Communications Biology

Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

(2021) Marta Royo-Llonch et al.   Nature Microbiology

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

(2020) Elaine Luo et al.   ISME Journal

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

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

Laminarin is a major molecule in the marine carbon cycle

(2020) Stefan Becker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes

(2020) Zihao Zhao et al.   Science Advances

The Biogeochemistry of Marine Polysaccharides: Sources, Inventories, and Bacterial Drivers of the Carbohydrate Cycle

(2020) C. Arnosti et al.   Annual Review of Marine Science

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

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Stephen Nayfach et al.   NATURE BIOTECHNOLOGY

Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria

(2019) Noelle A. Held et al.   mSystems

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

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

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

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

Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus

(2019) Paul M Berube et al.   eLife

Coupling carbon and energy fluxes in the North Pacific Subtropical Gyre

(2019) Eric Grabowski et al.   Nature Communications

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

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

(2019) Takuya Aramaki et al.   BIOINFORMATICS

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

Protein-Injection Machines in Bacteria

(2018) Jorge E. Galán et al.   CELL

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

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

Depth-Resolved Distribution of Particle-Attached and Free-Living Bacterial Communities in the Water Column of the New Britain Trench

(2018) Rulong Liu 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

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber 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

Prokaryotic Niche Partitioning Between Suspended and Sinking Marine Particles

(2018) Manon T Duret et al.   Environmental Microbiology Reports

Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation

(2018) Greta Reintjes et al.   ISME Journal

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

(2017) Benjamin J Tully et al.   ISME Journal

Complex pectin metabolism by gut bacteria reveals novel catalytic functions

(2017) Didier Ndeh et al.   NATURE

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

(2017) Neil D Rawlings et al.   NUCLEIC ACIDS RESEARCH

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

Bacterial Succession on Sinking Particles in the Ocean's Interior

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

Combined Carbohydrates Support Rich Communities of Particle-Associated Marine Bacterioplankton

(2017) Martin Sperling 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

Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera

(2017) Samuel T. Wilson et al.   Nature Microbiology

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

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

Growth Rates of Microbes in the Oceans

(2016) David L. Kirchman   Annual Review of Marine Science

The GH51 α-l-arabinofuranosidase from Paenibacillus sp. THS1 is multifunctional, hydrolyzing main-chain and side-chain glycosidic bonds in heteroxylans

(2016) Hanen Bouraoui et al.   Biotechnology for Biofuels

Identification of protein secretion systems in bacterial genomes

(2016) Sophie S. Abby et al.   Scientific Reports

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

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

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

Global diversity and biogeography of deep-sea pelagic prokaryotes

(2015) Guillem Salazar et al.   ISME Journal

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

(2015) Guillem Salazar et al.   MOLECULAR ECOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

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

(2015) Dongwan D. Kang et al.   PeerJ

Nitrogen and sulfur assimilation in plants and algae

(2014) Mario Giordano et al.   AQUATIC BOTANY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Composition and enzymatic function of particle-associated and free-living bacteria: a coastal/offshore comparison

(2014) Lindsay D'Ambrosio et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

(2014) Sophie S. Abby et al.   PLoS One

Opine Dehydrogenases in Marine Invertebrates

(2013) Matija Harcet et al.   BIOCHEMICAL GENETICS

Lineage specific gene family enrichment at the microscale in marine systems

(2013) Andrew E Allen et al.   CURRENT OPINION IN MICROBIOLOGY

DNA-based molecular fingerprinting of eukaryotic protists and cyanobacteria contributing to sinking particle flux at the Bermuda Atlantic time-series study

(2013) Jessica Amacher et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Temporal changes in particle-associated microbial communities after interception by nonlethal sediment traps

(2013) Gary R. LeCleir et al.   FEMS MICROBIOLOGY ECOLOGY

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

(2013) Sangita Ganesh et al.   ISME Journal

Microbial control of the dark end of the biological pump

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

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem

(2013) Maria W. Smith et al.   Frontiers in Microbiology

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

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

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

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

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

Recalcitrant Dissolved Organic Carbon Fractions

(2011) Dennis A. Hansell   Annual Review of Marine Science

The significance of nitrogen cost minimization in proteomes of marine microorganisms

(2011) Joseph J Grzymski et al.   ISME Journal

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Microbial Extracellular Enzymes and the Marine Carbon Cycle

(2010) Carol Arnosti   Annual Review of Marine Science

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre

(2009) K. T. Konstantinidis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Polysaccharide hydrolysis in aggregates and free enzyme activity in aggregate-free seawater from the north-eastern Gulf of Mexico

(2008) Kai Ziervogel et al.   ENVIRONMENTAL MICROBIOLOGY

A latitudinal diversity gradient in planktonic marine bacteria

(2008) J. A. Fuhrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA