Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi

Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes

(2017) Yusuke Okazaki et al.   ISME Journal

Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations

(2017) Wei Qin et al.   ISME Journal

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria

(2017) Stefan M Neuenschwander et al.   ISME Journal

Spatiotemporal dynamics of bacterial community composition in large shallow eutrophic Lake Taihu: High overlap between free-living and particle-attached assemblages

(2017) Xiangming Tang et al.   LIMNOLOGY AND OCEANOGRAPHY

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

(2017) Zachary Landry et al.   mBio

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

(2017) Pedro J. Cabello-Yeves et al.   Frontiers in Microbiology

Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

(2016) Matthias Hoetzinger et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

(2016) Alexander Eiler et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Vertical partitioning of freshwater bacterioplankton community in a deep mesotrophic lake with a fully oxygenated hypolimnion (Lake Biwa, Japan)

(2016) Yusuke Okazaki et al.   Environmental Microbiology Reports

Comparison and Interpretation of Taxonomical Structure of Bacterial Communities in Two Types of Lakes on Yun-Gui plateau of China

(2016) Maozhen Han et al.   Scientific Reports

Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria

(2016) Vincent J. Denef et al.   Frontiers in Microbiology

Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1Compound Oxidation

(2015) Vincent J. Denef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

(2015) Laura A. Hug et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign

(2015) Michaela M Salcher et al.   ISME Journal

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

(2015) Dongwan D. Kang et al.   PeerJ

Sustainable Growth of Dehalococcoides mccartyi 195 by Corrinoid Salvaging and Remodeling in Defined Lactate-Fermenting Consortia

(2014) Yujie Men et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

(2014) Trevor W Ghylin et al.   ISME Journal

Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production

(2014) Andrew C Doxey et al.   ISME Journal

Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing

(2014) Rohit Ghai et al.   MOLECULAR ECOLOGY

Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

(2014) Y. Zeng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Diversity of the Limnohabitans Genus, an Important Group of Freshwater Bacterioplankton, by Characterization of 35 Isolated Strains

(2013) Vojtěch Kasalický et al.   PLoS One

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Seasonal dominance of CL500-11 bacterioplankton (phylumChloroflexi) in the oxygenated hypolimnion of Lake Biwa, Japan

(2012) Yusuke Okazaki et al.   FEMS MICROBIOLOGY ECOLOGY

In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake

(2012) Michaela M Salcher et al.   ISME Journal

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Harmful filamentous cyanobacteria favoured by reduced water turnover with lake warming

(2012) Thomas Posch et al.   Nature Climate Change

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12)

(2011) Michaela M Salcher et al.   ISME Journal

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war

(2010) Iain C. Sutcliffe   ENVIRONMENTAL MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Multispot live-image autofocusing for high-throughput microscopy of fluorescently stained bacteria

(2009) M. Zeder et al.   CYTOMETRY PART A

Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean

(2009) Martha Schattenhofer et al.   ENVIRONMENTAL MICROBIOLOGY

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

(2009) Dongying Wu et al.   PLoS One

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

New image analysis tool to study biomass and morphotypes of three major bacterioplankton groups in an alpine lake

(2008) T Posch et al.   AQUATIC MICROBIAL ECOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

SAR11 marine bacteria require exogenous reduced sulphur for growth

(2008) H. James Tripp et al.   NATURE