Influence of DNA Extraction Method, 16S rRNA Targeted Hypervariable Regions, and Sample Origin on Microbial Diversity Detected by 454 Pyrosequencing in Marine Chemosynthetic Ecosystems

Hot-Alkaline DNA Extraction Method for Deep-Subseafloor Archaeal Communities

(2014) Yuki Morono et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

(2013) Karen G. Lloyd et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial communities and syntrophic associations involved in anaerobic oxidation of methane process of the Sonora Margin cold seeps, Guaymas Basin

(2013) Adrien Vigneron et al.   ENVIRONMENTAL MICROBIOLOGY

Commercial DNA extraction kits impact observed microbial community composition in permafrost samples

(2013) Tatiana A. Vishnivetskaya et al.   FEMS MICROBIOLOGY ECOLOGY

Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California)

(2013) Adrien Vigneron et al.   ISME Journal

Advances in monitoring environmental microbes

(2012) Terry C Hazen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Distribution andin situabundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments

(2012) Sara Kleindienst et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2012) Kyoko Kubo 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

High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction Procedure, Primer Length and Annealing Temperature

(2012) Martin J. Sergeant et al.   PLoS One

Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

(2012) S. L. Jorgensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Autotrophy as a predominant mode of carbon fixation in anaerobic methane-oxidizing microbial communities

(2012) M. Y. Kellermann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

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

(2011) Jennifer F Biddle et al.   ISME Journal

DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols

(2011) Karine Alain et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Diversity and Spatial Distribution of Prokaryotic Communities Along A Sediment Vertical Profile of A Deep-Sea Mud Volcano

(2011) Maria G. Pachiadaki et al.   MICROBIAL ECOLOGY

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

(2010) A. Y. Pei et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bar-Coded Pyrosequencing of 16S rRNA Gene Amplicons Reveals Changes in Ileal Porcine Bacterial Communities Due to High Dietary Zinc Intake

(2010) W. Vahjen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pyrosequencing analysis for characterization of soil bacterial populations as affected by an integrated livestock-cotton production system

(2010) V. Acosta-Martínez et al.   APPLIED SOIL ECOLOGY

A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies

(2010) Maxime Galan et al.   BMC GENOMICS

Impact of natural oil and higher hydrocarbons on microbial diversity, distribution, and activity in Gulf of Mexico cold-seep sediments

(2010) Beth N. Orcutt et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade

(2010) Lars Schreiber et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea

(2010) Hongyue Dang et al.   FEMS MICROBIOLOGY ECOLOGY

Prokaryotic community structure and diversity in the sediments of an active submarine mud volcano (Kazan mud volcano, East Mediterranean Sea)

(2010) Maria G. Pachiadaki et al.   FEMS MICROBIOLOGY ECOLOGY

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

(2010) On On Lee et al.   ISME Journal

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

(2010) Minseok Kim et al.   JOURNAL OF MICROBIOLOGICAL METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep

(2010) Karen G. Lloyd et al.   PLoS One

Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum

(2009) K. F. Ettwig et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Variations in Archaeal and Bacterial Diversity Associated with the Sulfate-Methane Transition Zone in Continental Margin Sediments (Santa Barbara Basin, California)

(2009) B. K. Harrison et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity and distribution of methane-oxidizing microbial communities associated with different faunal assemblages in a giant pockmark of the Gabon continental margin

(2009) M.A. Cambon-Bonavita et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Quantitative PCR methods for RNA and DNA in marine sediments: maximizing yield while overcoming inhibition

(2009) Karen G. Lloyd et al.   FEMS MICROBIOLOGY ECOLOGY

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine

(2009) Marcus J. Claesson et al.   PLoS One