Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

(2018) Michael W. Henson et al.   ISME Journal

Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes

(2018) Christina Bock et al.   Frontiers in Microbiology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats

(2018) Hao Zhang et al.   ENVIRONMENTAL MICROBIOLOGY

Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment

(2018) Katharina Kitzinger et al.   Nature Microbiology

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria

(2017) Stefan M Neuenschwander et al.   ISME Journal

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Erratum for Linz et al., “Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes”

(2017) Alexandra M. Linz et al.   mSphere

The first complete genome sequences of the acI lineage, the most abundant freshwater Actinobacteria, obtained by whole-genome-amplification of dilution-to-extinction cultures

(2017) Ilnam Kang et al.   Scientific Reports

Isolation and cultivation of planktonic freshwater microbes is essential for a comprehensive understanding of their ecology

(2016) MM Salcher et al.   AQUATIC MICROBIAL ECOLOGY

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall 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

Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology

(2016) Jarone Pinhassi et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

(2015) Francy Jimenez-Infante et al.   APPLIED AND ENVIRONMENTAL 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

Methylotrophs in natural habitats: current insights through metagenomics

(2015) Ludmila Chistoserdova   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2015) Michaela M Salcher et al.   ISME Journal

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake

(2015) Jason Nicholas Woodhouse et al.   ISME Journal

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages

(2015) Haiwei Luo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic and proteomic characterization of “CandidatusNitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

(2015) Alyson E. Santoro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu

(2015) Junfeng Li et al.   Scientific Reports

XoxF-Type Methanol Dehydrogenase from the Anaerobic Methanotroph “Candidatus Methylomirabilis oxyfera”

(2014) Ming L. Wu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome

(2014) M. W. Hahn et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

The Expanded Diversity of Methylophilaceae from Lake Washington through Cultivation and Genomic Sequencing of Novel Ecotypes

(2014) David A. C. Beck et al.   PLoS One

Insights into Denitrification in Methylotenera mobilis from Denitrification Pathway and Methanol Metabolism Mutants

(2013) I. Mustakhimov et al.   JOURNAL OF BACTERIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria

(2013) Rohit Ghai et al.   Scientific Reports

Genome Sequence of "Candidatus Aquiluna" sp. Strain IMCC13023, a Marine Member of the Actinobacteria Isolated from an Arctic Fjord

(2012) I. Kang et al.   JOURNAL OF BACTERIOLOGY

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

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

Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria

(2012) Megan J. Huggett et al.   Standards in Genomic Sciences

Methylotrophy in a Lake: from Metagenomics to Single-Organism Physiology

(2011) Ludmila Chistoserdova   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Modularity of methylotrophy, revisited

(2011) Ludmila Chistoserdova   ENVIRONMENTAL MICROBIOLOGY

Synergistic metabolism of a broad range of C1 compounds in the marine methylotrophic bacterium HTCC2181

(2011) Kimberly H. Halsey et al.   ENVIRONMENTAL MICROBIOLOGY

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

Genomes of Three Methylotrophs from a Single Niche Reveal the Genetic and Metabolic Divergence of the Methylophilaceae

(2011) A. Lapidus et al.   JOURNAL OF BACTERIOLOGY

Vertical and longitudinal distribution patterns of different bacterioplankton populations in a canyon-shaped, deep prealpine lake

(2011) Michaela M. Salcher et al.   LIMNOLOGY AND OCEANOGRAPHY

A Guide to the Natural History of Freshwater Lake Bacteria

(2011) R. J. Newton et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

(2011) Laura Steindler et al.   PLoS One

One Carbon Metabolism in SAR11 Pelagic Marine Bacteria

(2011) Jing Sun et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Reconstitution ofGloeobacter violaceusRhodopsin with a Light-Harvesting Carotenoid Antenna

(2009) Eleonora S. Imasheva et al.   BIOCHEMISTRY

Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources

(2009) Stéphane Vuilleumier et al.   PLoS One

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

(2008) Shaobin Hou et al.   Biology Direct

The small genome of an abundant coastal ocean methylotroph

(2008) Stephen J. Giovannoni et al.   ENVIRONMENTAL MICROBIOLOGY

Characterization of a Novel Methanol Dehydrogenase in Representatives of Burkholderiales: Implications for Environmental Detection of Methylotrophy and Evidence for Convergent Evolution

(2008) M. G. Kalyuzhnaya et al.   JOURNAL OF BACTERIOLOGY

High-resolution metagenomics targets specific functional types in complex microbial communities

(2008) Marina G Kalyuzhnaya et al.   NATURE BIOTECHNOLOGY

Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore

(2008) H. Luecke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA