Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses

A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean

(2023) Federico Baltar et al.   Nature Microbiology

Cyclopropane Fatty Acids Are Important for Salmonella enterica Serovar Typhimurium Virulence

(2021) Joyce E. Karlinsey et al.   INFECTION AND IMMUNITY

Metagenomic insights into zooplankton-associated bacterial communities

(2017) Daniele De Corte et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

(2017) Maria G. Pachiadaki et al.   SCIENCE

Recombinant Escherichia coli with sulfide:quinone oxidoreductase and persulfide dioxygenase rapidly oxidises sulfide to sulfite and thiosulfate via a new pathway

(2016) Yufeng Xin et al.   ENVIRONMENTAL MICROBIOLOGY

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean

(2016) Eva Sintes et al.   Frontiers in Microbiology

Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic

(2016) Federico Baltar et al.   Frontiers in Microbiology

Expanding the World of Marine Bacterial and Archaeal Clades

(2016) Pelin Yilmaz et al.   Frontiers in Microbiology

Dynamics of Metabolic Activities and Gene Expression in the Roseobacter Clade Bacterium Phaeobacter sp. Strain MED193 during Growth with Thiosulfate

(2014) Saraladevi Muthusamy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The complete genome sequence for putative H2- and S-oxidizerCandidatusSulfuricurvum sp., assembledde novofrom an aquifer-derived metagenome

(2014) Kim M. Handley et al.   ENVIRONMENTAL MICROBIOLOGY

Effect of elevated oxygen concentration on bacteria, yeasts, and cells propagated for production of biological compounds

(2014) Antonino Baez et al.   Microbial Cell Factories

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

A Central Role for Carbon-Overflow Pathways in the Modulation of Bacterial Cell Death

(2014) Vinai Chittezham Thomas et al.   PLoS Pathogens

SUP05 Dominates the Gammaproteobacterial Sulfur Oxidizer Assemblages in Pelagic Redoxclines of the Central Baltic and Black Seas

(2013) Sabine Glaubitz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Sulfurimonas gotlandica sp. nov., a chemoautotrophic and psychrotolerant epsilonproteobacterium isolated from a pelagic redoxcline, and an emended description of the genus Sulfurimonas

(2013) M. Labrenz et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Microbial control of the dark end of the biological pump

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

Transcriptome Analyses of Metabolic Enzymes in Thiosulfate- and Hydrogen-GrownHydrogenobacter thermophilusCells

(2012) Yuya SATO et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

ArchaealamoA gene diversity points to distinct biogeography of ammonia-oxidizingCrenarchaeotain the ocean

(2012) Eva Sintes et al.   ENVIRONMENTAL MICROBIOLOGY

Ecology and Physics of Bacterial Chemotaxis in the Ocean

(2012) Roman Stocker et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

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

Identification and removal of ribosomal RNA sequences from metatranscriptomes

(2011) Robert Schmieder et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Control of Proteobacterial Central Carbon Metabolism by the HexR Transcriptional Regulator

(2011) Semen A. Leyn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Microbial oceanography of the dark ocean's pelagic realm

(2011) Javier Arístegui et al.   LIMNOLOGY AND OCEANOGRAPHY

Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones

(2011) J. Grote et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Acetate accumulation through alternative metabolic pathways in ackA − pta − poxB − triple mutant in E. coli B (BL21)

(2010) Je-Nie Phue et al.   BIOTECHNOLOGY LETTERS

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

High bicarbonate assimilation in the dark by Arctic bacteria

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

The l-Cysteine/l-Cystine Shuttle System Provides Reducing Equivalents to the Periplasm in Escherichia coli

(2010) Iwao Ohtsu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dissolved organic matter and bacterial production and respiration in the sea-surface microlayer of the open Atlantic and the western Mediterranean Sea

(2010) Thomas Reinthaler et al.   LIMNOLOGY AND OCEANOGRAPHY

Sodium acetate enhances hydrogen peroxide production inWeissella cibaria

(2009) A. Endo et al.   LETTERS IN APPLIED MICROBIOLOGY

The radiocarbon signature of microorganisms in the mesopelagic ocean

(2009) R. L. Hansman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of transcription by acetate in Escherichia coli: in vivo and in vitro comparisons

(2008) Adam Z. Rosenthal et al.   MOLECULAR MICROBIOLOGY

Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)

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