Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Effect of DNA Extraction Method on the Apparent Microbial Diversity of Soil

(2010) O. Inceoglu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Deriving enzymatic and taxonomic signatures of metagenomes from short read data

(2010) Uri Weingart et al.   BMC BIOINFORMATICS

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu et al.   BMC BIOINFORMATICS

Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules

(2010) Jacob J Banik et al.   CURRENT OPINION IN MICROBIOLOGY

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

A ‘rare biosphere’ microorganism contributes to sulfate reduction in a peatland

(2010) Michael Pester et al.   ISME Journal

Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale

(2010) D Bru et al.   ISME Journal

In Situ Dynamics and Spatial Heterogeneity of Soil Bacterial Communities Under Different Crop Residue Management

(2010) Noémie Pascault et al.   MICROBIAL ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys

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

Investigating the mechanisms for the opposing pH relationships of fungal and bacterial growth in soil

(2010) Johannes Rousk et al.   SOIL BIOLOGY & BIOCHEMISTRY

Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil

(2009) L. M. Feinstein et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Estimating DNA coverage and abundance in metagenomes using a gamma approximation

(2009) Sean D. Hooper et al.   BIOINFORMATICS

The effect of sequencing errors on metagenomic gene prediction

(2009) Katharina J Hoff   BMC GENOMICS

An improved electroelution method for separation of DNA from humic substances in marine sediment DNA extracts

(2009) Jens Kallmeyer et al.   FEMS MICROBIOLOGY ECOLOGY

Exploration of hitherto-uncultured bacteria from the rhizosphere

(2009) Ulisses Nunes da Rocha et al.   FEMS MICROBIOLOGY ECOLOGY

An in situ method for cultivating microorganisms using a double encapsulation technique

(2009) Eitan Ben-Dov et al.   FEMS MICROBIOLOGY ECOLOGY

Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil

(2009) Karin Hjort et al.   FEMS MICROBIOLOGY ECOLOGY

Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing

(2009) Ben Temperton et al.   ISME Journal

Bias in assessments of marine SAR11 biodiversity in environmental fosmid and BAC libraries?

(2009) Roi Feingersch et al.   ISME Journal

An improved method to extract RNA from soil with efficient removal of humic acids

(2009) Y. Wang et al.   JOURNAL OF APPLIED MICROBIOLOGY

Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation

(2009) M. Kumar et al.   JOURNAL OF APPLIED MICROBIOLOGY

Molecular tools in rhizosphere microbiology—from single-cell to whole-community analysis

(2009) Jan Sørensen et al.   PLANT AND SOIL

Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies

(2009) Kate L. Baker et al.   SOIL BIOLOGY & BIOCHEMISTRY

Re-establishment of suppressiveness to soil- and air-borne diseases by re-inoculation of soil microbial communities

(2009) Barbara Thuerig et al.   SOIL BIOLOGY & BIOCHEMISTRY

Exploiting plant–microbe partnerships to improve biomass production and remediation

(2009) Nele Weyens et al.   TRENDS IN BIOTECHNOLOGY

Recovery, Purification, and Cloning of High-Molecular-Weight DNA from Soil Microorganisms

(2008) M. R. Liles et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

(2008) M. S. Elshahed et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics

(2008) M. Sagova-Mareckova et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Strategies for accessing soil metagenome for desired applications

(2008) J. Rajendhran et al.   BIOTECHNOLOGY ADVANCES

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

The development and impact of 454 sequencing

(2008) Jonathan M Rothberg et al.   NATURE BIOTECHNOLOGY

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Seasonal changes in the soil microbial community in a grassland plant diversity gradient four years after establishment

(2008) Maike Habekost et al.   SOIL BIOLOGY & BIOCHEMISTRY

Importance of DNA quality in comparative soil microbial community structure analyses

(2008) Dwipendra Thakuria et al.   SOIL BIOLOGY & BIOCHEMISTRY

The influence of soil properties on the structure of bacterial and fungal communities across land-use types

(2008) Christian L. Lauber et al.   SOIL BIOLOGY & BIOCHEMISTRY

The metagenomics of disease-suppressive soils – experiences from the METACONTROL project

(2008) Jan Dirk van Elsas et al.   TRENDS IN BIOTECHNOLOGY

Short read fragment assembly of bacterial genomes

(2007) M. J. Chaisson et al.   GENOME RESEARCH