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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Carbon substrate usage by zooplankton-associated bacteria, phytoplankton-associated bacteria, and free-living bacteria under aerobic and anaerobic conditions

(2014) Samantha L. Bickel et al.   MARINE BIOLOGY

Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean

(2014) Sara A. Lincoln et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Associations and dynamics of Vibrionaceae in the environment, from the genus to the population level

(2014) Alison F. Takemura et al.   Frontiers in Microbiology

The Genome of the Alga-Associated Marine Flavobacterium Formosa agariphila KMM 3901TReveals a Broad Potential for Degradation of Algal Polysaccharides

(2013) Alexander J. Mann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Lineage specific gene family enrichment at the microscale in marine systems

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

Detection ofVibrio parahaemolyticus,Vibrio vulnificusandVibrio choleraewith respect to seasonal fluctuations in temperature and plankton abundance

(2013) Jeffrey W. Turner et al.   ENVIRONMENTAL MICROBIOLOGY

Impact of warming on phyto-bacterioplankton coupling and bacterial community composition in experimental mesocosms

(2013) Markus von Scheibner et al.   ENVIRONMENTAL MICROBIOLOGY

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

Bacterial chitinases and chitin-binding proteins as virulence factors

(2013) R. F. Frederiksen et al.   MICROBIOLOGY-SGM

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Bacterial chitin degradation—mechanisms and ecophysiological strategies

(2013) Sara Beier et al.   Frontiers in Microbiology

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

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

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

Molecular characterization of dissolved organic matter (DOM): a critical review

(2012) Antonio Nebbioso et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Characterization of the first alginolytic operons in a marine bacterium: from their emergence in marine Flavobacteriia to their independent transfers to marine Proteobacteria and human gut Bacteroides

(2012) François Thomas et al.   ENVIRONMENTAL MICROBIOLOGY

Free-living and aggregate-associated Planctomycetes in the Black Sea

(2012) Clara A. Fuchsman et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2012) Lisa Zeigler Allen et al.   ISME Journal

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations

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

NMR structure of a lytic polysaccharide monooxygenase provides insight into copper binding, protein dynamics, and substrate interactions

(2012) F. L. Aachmann 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

Marine macroalgae: an untapped resource for producing fuels and chemicals

(2012) Na Wei et al.   TRENDS IN BIOTECHNOLOGY

Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph

(2012) Mario López-Pérez et al.   Scientific Reports

Porticoccus hydrocarbonoclasticus sp. nov., an Aromatic Hydrocarbon-Degrading Bacterium Identified in Laboratory Cultures of Marine Phytoplankton

(2011) Tony Gutierrez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic strategies of free-living and aggregate-associated bacterial communities inferred from biologic and chemical profiles in the Black Sea suboxic zone

(2011) Clara A. Fuchsman et al.   FEMS MICROBIOLOGY ECOLOGY

Adaptive seeds tame genomic sequence comparison

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

Degradation and dissolution of zooplanktonic organic matter and lipids in early diagenesis

(2011) Kazuya Yoshimura et al.   JOURNAL OF OCEANOGRAPHY

Roseobacticides: Small Molecule Modulators of an Algal-Bacterial Symbiosis

(2011) Mohammad R. Seyedsayamdost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Copepod guts as biogeochemical hotspots in the sea: Evidence from microelectrode profiling ofCalanusspp

(2011) Kam W. Tang et al.   LIMNOLOGY AND OCEANOGRAPHY

Putative virulence genes in Moritella viscosa: Activity during in vitro inoculation and in vivo infection

(2011) Hege Smith Tunsjø et al.   MICROBIAL PATHOGENESIS

One Carbon Metabolism in SAR11 Pelagic Marine Bacteria

(2011) Jing Sun 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

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Gamma- and epsilonproteobacterial ectosymbionts of a shallow-water marine worm are related to deep-sea hydrothermal vent ectosymbionts

(2010) Caroline Ruehland et al.   ENVIRONMENTAL MICROBIOLOGY

Metapopulation structure of Vibrionaceae among coastal marine invertebrates

(2010) Sarah P. Preheim et al.   ENVIRONMENTAL MICROBIOLOGY

Diatom-associated bacteria are required for aggregation of Thalassiosira weissflogii

(2010) Astrid Gärdes et al.   ISME Journal

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

(2010) J. McCarren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of macroscopic particles in deep-sea oxygen consumption

(2010) A. B. Bochdansky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Oxidative Enzyme Boosting the Enzymatic Conversion of Recalcitrant Polysaccharides

(2010) Gustav Vaaje-Kolstad et al.   SCIENCE

Indigenous ectosymbiotic bacteria associated with diverse hydrothermal vent invertebrates

(2010) Shana K. Goffredi   Environmental Microbiology Reports

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

Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism

(2010) Astrid Gärdes et al.   Standards in Genomic Sciences

Comparison of free-living, suspended particle, and aggregate-associated Bacterial and Archaeal communities in the Laptev Sea

(2009) CTE Kellogg et al.   AQUATIC MICROBIAL ECOLOGY

Degradation and dissolution properties of photosynthetically-produced phytoplankton lipid materials in early diagenesis

(2009) Kazuya Yoshimura et al.   MARINE CHEMISTRY

Substrate-Specific Clades of Active Marine Methylotrophs Associated with a Phytoplankton Bloom in a Temperate Coastal Environment

(2008) J. D. Neufeld et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The flux of bio- and lithogenic material associated with sinking particles in the mesopelagic “twilight zone” of the northwest and North Central Pacific Ocean

(2008) C.H. Lamborg et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

VERTIGO (VERtical Transport In the Global Ocean): A study of particle sources and flux attenuation in the North Pacific

(2008) K.O. Buesseler et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Pathogenic Vibrio, Aeromonas and Arcobacter spp. associated with copepods in the Straits of Messina (Italy)

(2008) C. Gugliandolo et al.   MARINE POLLUTION BULLETIN

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment

(2008) Torsten Thomas et al.   PLoS One

Particulate organic carbon fluxes to the ocean interior and factors controlling the biological pump: A synthesis of global sediment trap programs since 1983

(2008) Susumu Honjo et al.   PROGRESS IN OCEANOGRAPHY