Metagenomic analysis reveals unusually high incidence of proteorhodopsin genes in the ultraoligotrophic Eastern Mediterranean Sea

Winter diversity and expression of proteorhodopsin genes in a polar ocean

(2015) Dan Nguyen et al.   ISME Journal

Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria

(2015) Laura Gómez-Consarnau et al.   ISME Journal

Oil spill contamination probability in the southeastern Levantine basin

(2015) Ron Goldman et al.   MARINE POLLUTION BULLETIN

Nutrient Limitation in Surface Waters of the Oligotrophic Eastern Mediterranean Sea: an Enrichment Microcosm Experiment

(2015) A. Tsiola et al.   MICROBIAL ECOLOGY

Genomes of Planktonic Acidimicrobiales : Widening Horizons for Marine Actinobacteria by Metagenomics

(2015) Carolina Megumi Mizuno et al.   mBio

Abundance of Broad Bacterial Taxa in the Sargasso Sea Explained by Environmental Conditions but Not Water Mass

(2014) J. Sjostedt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Decoupling Physical from Biological Processes to Assess the Impact of Viruses on a Mesoscale Algal Bloom

(2014) Yoav Lehahn et al.   CURRENT BIOLOGY

Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria

(2014) J. Palovaara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Marked seasonality of aerobic anoxygenic phototrophic bacteria in the coastal NW Mediterranean Sea as revealed by cell abundance, pigment concentration and pyrosequencing ofpufMgene

(2013) Isabel Ferrera et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic Makeup of the Marine Flavobacterium Nonlabens (Donghaeana) dokdonensis and Identification of a Novel Class of Rhodopsins

(2013) Soon-Kyeong Kwon et al.   Genome Biology and Evolution

Bacterial, archaeal and viral-like rhodopsins from the Red Sea

(2013) Alon Philosof et al.   Environmental Microbiology Reports

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Diversity and functional analysis of proteorhodopsin in marine Flavobacteria

(2012) Susumu Yoshizawa et al.   ENVIRONMENTAL MICROBIOLOGY

Global abundance of microbial rhodopsins

(2012) Omri M Finkel et al.   ISME Journal

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Bioenergetics of photoheterotrophic bacteria in the oceans

(2012) David L. Kirchman et al.   Environmental Microbiology Reports

Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

(2011) Johan Bengtsson et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Distribution and Growth of Aerobic Anoxygenic Phototrophs in the Mediterranean Sea

(2011) Eva Hojerová et al.   ENVIRONMENTAL MICROBIOLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Energy Starved Candidatus Pelagibacter Ubique Substitutes Light-Mediated ATP Production for Endogenous Carbon Respiration

(2011) Laura Steindler et al.   PLoS One

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Constitutive Expression of the Proteorhodopsin Gene by a Flavobacterium Strain Representative of the Proteorhodopsin-Producing Microbial Community in the North Sea

(2010) T. Riedel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Summer distribution and diversity of aerobic anoxygenic phototrophic bacteria in the Mediterranean Sea in relation to environmental variables

(2010) Anne-Catherine Lehours et al.   FEMS MICROBIOLOGY ECOLOGY

Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing

(2010) Rohit Ghai et al.   ISME Journal

Fluid dynamical niches of phytoplankton types

(2010) F. d'Ovidio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteorhodopsin Phototrophy Promotes Survival of Marine Bacteria during Starvation

(2010) Laura Gómez-Consarnau et al.   PLOS BIOLOGY

The Light-Driven Proton Pump Proteorhodopsin Enhances Bacterial Survival during Tough Times

(2010) Edward F. DeLong et al.   PLOS BIOLOGY

Dynamics of the SAR11 bacterioplankton lineage in relation to environmental conditions in the oligotrophic North Pacific subtropical gyre

(2009) Alexander Eiler et al.   ENVIRONMENTAL MICROBIOLOGY

Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean

(2009) Martha Schattenhofer et al.   ENVIRONMENTAL MICROBIOLOGY

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Distribution of aerobic anoxygenic phototrophs in temperate freshwater systems

(2008) Michal Man et al.   ENVIRONMENTAL MICROBIOLOGY

Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage

(2008) K. Robert Clarke et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Algal blooming patterns and anomalies in the Mediterranean Sea as derived from the SeaWiFS data set (1998–2003)

(2008) Vittorio Barale et al.   REMOTE SENSING OF ENVIRONMENT