High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils

Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches

(2017) C S Lazar et al.   ISME Journal

Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau

(2016) Haiyan Chu et al.   ENVIRONMENTAL MICROBIOLOGY

Spatial scale drives patterns in soil bacterial diversity

(2016) Sarah L. O'Brien et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

(2016) Cassandre Sara Lazar et al.   ENVIRONMENTAL MICROBIOLOGY

High-resolution phylogenetic microbial community profiling

(2016) Esther Singer et al.   ISME Journal

Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen

(2016) Masaru Konishi Nobu et al.   ISME Journal

Archaea catalyze iron-dependent anaerobic oxidation of methane

(2016) Katharina F. Ettwig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes

(2016) Rudiger Ortiz-Alvarez et al.   Environmental Microbiology Reports

Nitrate- and nitrite-dependent anaerobic oxidation of methane

(2016) Cornelia U. Welte et al.   Environmental Microbiology Reports

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils

(2016) Yuanfeng Cai et al.   Nature Communications

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Comparison of community structures of Candidatus Methylomirabilis oxyfera-like bacteria of NC10 phylum in different freshwater habitats

(2016) Li-dong Shen et al.   Scientific Reports

Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu

(2016) Xianfang Fan et al.   Frontiers in Microbiology

Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments

(2016) Y. He et al.   Nature Microbiology

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

(2016) Inka Vanwonterghem et al.   Nature Microbiology

Site History and Edaphic Features Override the Influence of Plant Species on Microbial Communities in Restored Tidal Freshwater Wetlands

(2015) Christine E. Prasse et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria

(2015) Angus Angermeyer et al.   ENVIRONMENTAL MICROBIOLOGY

Environmental controls on intragroup diversity of the uncultured benthicarchaeaof the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA)

(2015) Cassandre Sara Lazar et al.   ENVIRONMENTAL MICROBIOLOGY

Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage

(2015) Mireia Fillol et al.   ISME Journal

Anaerobic oxidation of methane associated with sulfate reduction in a natural freshwater gas source

(2015) Peer HA Timmers et al.   ISME Journal

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands

(2015) Paula Arroyo et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Methane Emissions

(2015) Shaomei He et al.   mBio

High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions

(2015) K. E. A. Segarra et al.   Nature Communications

High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy

(2015) Hyo Jung Lee et al.   Frontiers in Microbiology

A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea

(2015) Arslan Arshad et al.   Frontiers in Microbiology

Air-Adapted Methanosarcina acetivorans Shows High Methane Production and Develops Resistance against Oxygen Stress

(2015) Ricardo Jasso-Chávez et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem

(2014) Hyo Jung Lee et al.   FEMS MICROBIOLOGY ECOLOGY

Southern Appalachian Peatlands Support High Archaeal Diversity

(2014) A. N. Hawkins et al.   MICROBIAL ECOLOGY

Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands

(2014) B.-l. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Iron oxides stimulate sulfate-driven anaerobic methane oxidation in seeps

(2014) Orit Sivan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake

(2014) Joerg S. Deutzmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional microbial diversity explains groundwater chemistry in a pristine aquifer

(2013) Theodore M Flynn et al.   BMC MICROBIOLOGY

Microbial minorities modulate methane consumption through niche partitioning

(2013) Paul LE Bodelier et al.   ISME Journal

Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses

(2013) Jun Meng et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

(2013) Mohamed F. Haroon et al.   NATURE

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

Three decades of global methane sources and sinks

(2013) Stefanie Kirschke et al.   Nature Geoscience

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments

(2013) Christopher S. Miller et al.   PLoS One

Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences

(2013) Swee Hoe Ong et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Bacteria distribution and dynamics in constructed wetlands based on modelling results

(2013) Roger Samsó et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Methane-Cycling Microbial Communities and Methane Emission in Natural and Restored Peatlands

(2012) Heli Juottonen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags

(2012) Yu Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales

(2012) Scott D. Bridgham et al.   GLOBAL CHANGE BIOLOGY

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

(2012) Kyoko Kubo et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Stratification of Archaea in the Deep Sediments of a Freshwater Meromictic Lake: Vertical Shift from Methanogenic to Uncultured Archaeal Lineages

(2012) Guillaume Borrel et al.   PLoS One

Methanogenic Pathway and Archaeal Communities in Three Different Anoxic Soils Amended with Rice Straw and Maize Straw

(2012) Ralf Conrad et al.   Frontiers in Microbiology

Spatial Patterns of Iron- and Methane-Oxidizing Bacterial Communities in an Irregularly Flooded, Riparian Wetland

(2012) Juanjuan Wang et al.   Frontiers in Microbiology

Seasonal Changes in Methanogenesis and Methanogenic Community in Three Peatlands, New York State

(2012) Christine L. Sun et al.   Frontiers in Microbiology

Peatland Microbial Communities and Decomposition Processes in the James Bay Lowlands, Canada

(2012) Michael D. Preston et al.   Frontiers in Microbiology

Stratified active archaeal communities in the sediments of Jiulong River estuary, China

(2012) Qianqian Li et al.   Frontiers in Microbiology

DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

(2011) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

(2011) William A. Walters et al.   BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Changes in methanogenic substrate utilization and communities with depth in a salt-marsh, creek sediment in southern England

(2011) R. John Parkes et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal

(2011) Vitaly V. Kadnikov et al.   FEMS MICROBIOLOGY ECOLOGY

Evidence for anaerobic oxidation of methane in sediments of  a freshwater system (Lago di Cadagno)

(2011) Carsten J. Schubert et al.   FEMS MICROBIOLOGY ECOLOGY

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

(2011) Jeffrey J Werner et al.   ISME Journal

Geochemical evidence for iron-mediated anaerobic oxidation of methane

(2011) Orit Sivan et al.   LIMNOLOGY AND OCEANOGRAPHY

Drought-induced carbon loss in peatlands

(2011) Nathalie Fenner et al.   Nature Geoscience

Activation of Methanogenesis in Arid Biological Soil Crusts Despite the Presence of Oxygen

(2011) Roey Angel et al.   PLoS One

Drivers of bacterial  -diversity depend on spatial scale

(2011) J. B. H. Martiny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Production and consumption of methane in freshwater lake ecosystems

(2011) Guillaume Borrel et al.   RESEARCH IN MICROBIOLOGY

Freshwater Methane Emissions Offset the Continental Carbon Sink

(2011) D. Bastviken et al.   SCIENCE

Aerobic and anaerobic methane oxidation in terrestrial mud volcanoes in the Northern Apennines

(2011) C. Wrede et al.   SEDIMENTARY GEOLOGY

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

(2011) Christopher S Miller et al.   GENOME BIOLOGY

Vertical Distribution of Ammonia-Oxidizing Crenarchaeota and Methanogens in the Epipelagic Waters of Lake Kivu (Rwanda-Democratic Republic of the Congo)

(2010) M. Lliros et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Methanogen activity in relation to water table level in two boreal fens

(2010) Mirkka Kotiaho et al.   BIOLOGY AND FERTILITY OF SOILS

Examining the global distribution of dominant archaeal populations in soil

(2010) Scott T Bates et al.   ISME Journal

Novel primers for 16S rRNA-based archaeal community analyses in environmental samples

(2010) Stephan Gantner et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

Methane Emissions From Created Riverine Wetlands

(2010) Amanda M. Nahlik et al.   WETLANDS

The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu

(2009) Wenjin Ye et al.   FEMS MICROBIOLOGY ECOLOGY

Characterization of the Archaeal Community in a Minerotrophic Fen and Terminal Restriction Fragment Length Polymorphism-Directed Isolation of a Novel Hydrogenotrophic Methanogen

(2008) H. Cadillo-Quiroz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A comparison of soil carbon pools and profiles in wetlands in Costa Rica and Ohio

(2008) Blanca Bernal et al.   ECOLOGICAL ENGINEERING

Methanogen community in Zoige wetland of Tibetan plateau and phenotypic characterization of a dominant uncultured methanogen cluster ZC-I

(2008) Guishan Zhang et al.   ENVIRONMENTAL MICROBIOLOGY

Changes in microbial community structure in the wake of Hurricanes Katrina and Rita

(2008) Linda A. Amaral-Zettler et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Molecular Studies on the Microbial Diversity Associated with Mining-Impacted Coeur d’Alene River Sediments

(2008) Gurdeep Rastogi et al.   MICROBIAL ECOLOGY