Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”

Adding genomic 'foliage' to the tree of life

(2014) Alan Walker   NATURE REVIEWS MICROBIOLOGY

A brief history of the discovery of hyperthermophilic life

(2013) Karl O. Stetter   BIOCHEMICAL SOCIETY TRANSACTIONS

The Paint Pots, Kootenay National Park, Canada — a natural acid spring analogue for Mars

(2013) Stephen E. Grasby et al.   CANADIAN JOURNAL OF EARTH SCIENCES

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

Dissecting genomic diversity, one cell at a time

(2013) Paul C Blainey et al.   NATURE METHODS

Pyrosequencing Reveals High-Temperature Cellulolytic Microbial Consortia in Great Boiling Spring after In Situ Lignocellulose Enrichment

(2013) Joseph P. Peacock et al.   PLoS One

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

(2013) Weiguo Hou et al.   PLoS One

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

(2013) R. S. Kantor et al.   mBio

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

(2013) Jeremy A. Dodsworth et al.   Nature Communications

Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution

(2013) Anja Spang et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

A Single-Cell Genome for Thiovulum sp.

(2012) Ian P. G. Marshall et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies

(2012) J. Droge et al.   BRIEFINGS IN BIOINFORMATICS

Classification of metagenomic sequences: methods and challenges

(2012) S. S. Mande et al.   BRIEFINGS IN BIOINFORMATICS

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

Characterization ofMelioribacter roseusgen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the classIgnavibacteria, and a proposal of a novel bacterial phylumIgnavibacteriae

(2012) Olga A. Podosokorskaya et al.   ENVIRONMENTAL MICROBIOLOGY

Taxon-specific C/N relative use efficiency for amino acids in an estuarine community

(2012) Xavier Mayali et al.   FEMS MICROBIOLOGY ECOLOGY

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

(2012) J Kirk Harris et al.   ISME Journal

Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

(2012) Jessica K Cole et al.   ISME Journal

Microbiology and geochemistry of smith creek and grass valley hot springs: Emerging evidence for wide distribution of novel thermophilic lineages in the US Great Basin

(2012) Jeremy A. Dodsworth et al.   Journal of Earth Science

Genomic sequencing of uncultured microorganisms from single cells

(2012) Roger S. Lasken   NATURE REVIEWS MICROBIOLOGY

Chemoautotrophy at Deep-Sea Vents: Past, Present, and Future

(2012) Stefan Sievert et al.   OCEANOGRAPHY

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

(2012) Hideto Takami et al.   PLoS One

Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca

(2012) K. Temme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

(2011) Priya Narasingarao et al.   ISME Journal

Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments

(2011) Jennifer F Biddle et al.   ISME Journal

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use

(2011) Xavier Mayali et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Decontamination of MDA Reagents for Single Cell Whole Genome Amplification

(2011) Tanja Woyke et al.   PLoS One

The archaeal ‘TACK’ superphylum and the origin of eukaryotes

(2011) Lionel Guy et al.   TRENDS IN MICROBIOLOGY

New Abundant Microbial Groups in Aquatic Hypersaline Environments

(2011) Rohit Ghai et al.   Scientific Reports

Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species

(2010) D. Nichols et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

(2010) Takuro Nunoura et al.   NUCLEIC ACIDS RESEARCH

Enigmatic, ultrasmall, uncultivated Archaea

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

The many ways of coping with pressure

(2010) Philippe M. Oger et al.   RESEARCH IN MICROBIOLOGY

Prokaryotic Community Structure and Sulfate Reducer Activity in Water from High-Temperature Oil Reservoirs with and without Nitrate Treatment

(2009) A. Gittel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin

(2009) Kyle C. Costa et al.   EXTREMOPHILES

Microbiology and geochemistry of Little Hot Creek, a hot spring environment in the Long Valley Caldera

(2009) T. J. VICK et al.   Geobiology

Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov.

(2009) K. Mori et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge

(2009) Delphine Rivière et al.   ISME Journal

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS

(2008) S. Behrens et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand

(2008) Matthew B. Stott et al.   ENVIRONMENTAL MICROBIOLOGY

A korarchaeal genome reveals insights into the evolution of the Archaea

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