Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils

Rapid isolation of fast-growing methanotrophs from environmental samples using continuous cultivation with gradually increased dilution rates

(2018) Jisun Kim et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genomic and transcriptomic analyses reveal adaptation mechanisms of an Acidithiobacillus ferrivorans strain YL15 to alpine acid mine drainage

(2017) Tangjian Peng et al.   PLoS One

Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog

(2016) Kaitlin C. Esson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum

(2016) Igor Y. Oshkin et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

(2016) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase

(2016) Bram Vekeman et al.   MICROBIAL ECOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions

(2016) Sascha M. B. Krause et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Soil acidification and the importance of liming agricultural soils with particular reference to the United Kingdom

(2016) K. W. T. Goulding   SOIL USE AND MANAGEMENT

Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps

(2016) Tajul Islam et al.   Frontiers in Microbiology

Reconstruction of the Metabolic Potential of Acidophilic Sideroxydans Strains from the Metagenome of an Microaerophilic Enrichment Culture of Acidophilic Iron-Oxidizing Bacteria from a Pilot Plant for the Treatment of Acid Mine Drainage Reveals Metabolic Versatility and Adaptation to Life at Low pH

(2016) Martin Mühling et al.   Frontiers in Microbiology

Pinus sylvestris as a missing source of nitrous oxide and methane in boreal forest

(2016) Katerina Machacova et al.   Scientific Reports

A novel denitrifying methanotroph of the NC10 phylum and its microcolony

(2016) Zhanfei He et al.   Scientific Reports

The CRISPR-Cas immune system: Biology, mechanisms and applications

(2015) Devashish Rath et al.   BIOCHIMIE

Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity

(2015) Poulami Samai et al.   CELL

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

Methane as a Resource: Can the Methanotrophs Add Value?

(2015) P. J. Strong et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

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

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

(2015) Yi Wang et al.   NUCLEIC ACIDS RESEARCH

On the principle of ion selectivity in Na+/H+-coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor

(2015) Vanessa Leone et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Past and future species definitions for Bacteria and Archaea

(2015) Ramon Rosselló-Móra et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

(2015) Claudia Knief   Frontiers in Microbiology

Quantifying Components of Soil Respiration and Their Response to Abiotic Factors in Two Typical Subtropical Forest Stands, Southwest China

(2015) Lei Yu et al.   PLoS One

Genomic and Transcriptomic Analyses of the Facultative Methanotroph Methylocystis sp. Strain SB2 Grown on Methane or Ethanol

(2014) Alexey Vorobev et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metal resistance in acidophilic microorganisms and its significance for biotechnologies

(2014) Mark Dopson et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

(2014) Cristiane C. Thompson et al.   ARCHIVES OF MICROBIOLOGY

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

Distribution of a consortium between unicellular algae and the N2fixing cyanobacterium UCYN-A in the North Atlantic Ocean

(2014) Andreas Krupke et al.   ENVIRONMENTAL MICROBIOLOGY

Distribution and diversity ofVerrucomicrobiamethanotrophs in geothermal and acidic environments

(2014) Christine E. Sharp et al.   ENVIRONMENTAL MICROBIOLOGY

Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response

(2014) Igor Y Oshkin et al.   ISME Journal

Spatial Distribution of Surface Soil Acidity, Electrical Conductivity, Soil Organic Carbon Content and Exchangeable Potassium, Calcium and Magnesium in Some Cropped Acid Soils of India

(2014) Sanjib Kumar Behera et al.   LAND DEGRADATION & DEVELOPMENT

A methanotrophic community in a tropical peatland is unaffected by drainage and forest fires in a tropical peat soil

(2014) Hironori Arai et al.   SOIL SCIENCE AND PLANT NUTRITION

Response of Acidithiobacillus caldus toward suboptimal pH conditions

(2013) Stefanie Mangold et al.   EXTREMOPHILES

The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis

(2013) Ivica Tamas et al.   ISME Journal

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Genome Analysis Coupled with Physiological Studies Reveals a Diverse Nitrogen Metabolism in Methylocystis sp. Strain SC2

(2013) Bomba Dam et al.   PLoS One

Environmental impacts on the diversity of methane-cycling microbes and their resultant function

(2013) Emma L. Aronson et al.   Frontiers in Microbiology

Extreme zinc tolerance in acidophilic microorganisms from the bacterial and archaeal domains

(2012) Stefanie Mangold et al.   EXTREMOPHILES

Methylomonas paludis sp. nov., the first acid-tolerant member of the genus Methylomonas, from an acidic wetland

(2012) O. V. Danilova et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993

(2012) S. E. Belova et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Promiscuous archaeal ATP synthase concurrently coupled to Na+ and H+ translocation

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

Stimulation of Methanotrophic Growth in Cocultures by Cobalamin Excreted by Rhizobia

(2011) Hiroyuki Iguchi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Detection, Isolation, and Characterization of Acidophilic Methanotrophs from Sphagnum Mosses

(2011) Nardy Kip et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Hydrogen-isotopic variability in fatty acids from Yellowstone National Park hot spring microbial communities

(2011) Magdalena R. Osburn et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm

(2011) Daniel S Jones et al.   ISME Journal

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Methane emission from living tree wood

(2011) V. A. Mukhin et al.   RUSSIAN JOURNAL OF PLANT PHYSIOLOGY

Methane emissions from upland forest soils and vegetation

(2011) J. P. Megonigal et al.   TREE PHYSIOLOGY

Cultivating Uncultured Bacteria from Northern Wetlands: Knowledge Gained and Remaining Gaps

(2011) Svetlana N. Dedysh   Frontiers in Microbiology

Bioremediation via Methanotrophy: Overview of Recent Findings and Suggestions for Future Research

(2011) Jeremy D. Semrau   Frontiers in Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Plasmid Encoded AcrAB–TolC Tripartite Multidrug-Efflux System in Acidiphilium symbioticum H8

(2010) Samarendra K. Singh et al.   CURRENT MICROBIOLOGY

Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase

(2010) A. V. Vorobev et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

(2010) Katharina F. Ettwig et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs

(2010) Patricia L. Tavormina et al.   Environmental Microbiology Reports

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Notes on the characterization of prokaryote strains for taxonomic purposes

(2009) B. J. Tindall et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Cytoplasmic Histidine Kinase (HP0244)-Regulated Assembly of Urease with UreI, a Channel for Urea and Its Metabolites, CO2, NH3, and NH4+, Is Necessary for Acid Survival of Helicobacter pylori

(2009) D. R. Scott et al.   JOURNAL OF BACTERIOLOGY

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

Ion binding and selectivity of the rotor ring of the Na+-transporting V-ATPase

(2008) T. Murata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA