(Q33918934)

30 July 2017

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title

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

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30 July 2017

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3

Jan Dirk van Elsas

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Pascal Simonet

series ordinal

4

object named as

Pascal Simonet

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30 July 2017

Nathalie Lombard

1

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30 July 2017

Emmanuel Prestat

series ordinal

2

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30 July 2017

language of work or name

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28 June 2011

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FEMS Microbiology Ecology

30 July 2017

number of pages

19

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based on heuristic

inferred from page(s)

published in

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30 July 2017

volume

78

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30 July 2017

issue

1

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30 July 2017

page(s)

31-49

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Basic local alignment search tool

30 July 2017

cites work

1 reference

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

21 January 2018

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

21 January 2018

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Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage

21 January 2018

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Isolation of high molecular weight DNA from soil for cloning into BAC vectors.

21 January 2018

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High molecular weight DNA recovery from soils prerequisite for biotechnological metagenomic library construction

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

A new enzymatic method for the detachment of particle associated soil bacteria.

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

QIIME allows analysis of high-throughput community sequencing data

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Isolation of lightning-competent soil bacteria

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Short read fragment assembly of bacterial genomes

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Bacterial adhesion to silica sand as related to Gibbs energy variations.

21 January 2018

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

21 January 2018

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Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Estimating prokaryotic diversity and its limits

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

The soil metagenome--a rich resource for the discovery of novel natural products

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

21 January 2018

The metagenomics of soil

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Exploration of hitherto-uncultured bacteria from the rhizosphere

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Contribution of the hydrophobic effect to microbial infection

21 January 2018

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Search and clustering orders of magnitude faster than BLAST

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Novelty and uniqueness patterns of rare members of the soil biosphere

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Microbial reductive dechlorination of aroclor 1260 in Baltimore harbor sediment microcosms is catalyzed by three phylotypes within the phylum Chloroflexi

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Assessment of bias associated with incomplete extraction of microbial DNA from soil.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

The diversity and biogeography of soil bacterial communities

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

The Relation Between the Number of Species and the Number of Individuals in a Random Sample of an Animal Population

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Soil washing improves the recovery of total community DNA from polluted and high organic content sediments

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

‘Super bugs’ for bioremediation

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Efficient recovery of environmental DNA for expression cloning by indirect extraction methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Quantifying the accessibility of the metagenome by random expression cloning techniques.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Computational improvements reveal great bacterial diversity and high metal toxicity in soil

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Spatial scales of soil bacterial diversity--the size of a clone

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Effect of carbon and nitrogen input on the bacterial community structure of Neocaledonian nickel mine spoils

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

The effect of sequencing errors on metagenomic gene prediction

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Estimating DNA coverage and abundance in metagenomes using a gamma approximation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

A quantitative analysis of DNA extraction and purification from compost

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Effect of DNA extraction method on the apparent microbial diversity of soil

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Adsorption of Pseudomonas putida on clay minerals and iron oxide.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

The effect of sample size in studies of soil microbial community structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

DNA isolation from soil samples for cloning in different hosts.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from compost for microbial community analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Recovery, purification, and cloning of high-molecular-weight DNA from soil microorganisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Applications of free living plant growth-promoting rhizobacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

An experimental metagenome data management and analysis system

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

The diversity and function of soil microbial communities exposed to different disturbances.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Spatial stratification of soil bacterial populations in aggregates of diverse soils

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Analysis of soil whole- and inner-microaggregate bacterial communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Structure and function of alpine and arctic soil microbial communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Spatial analysis of archaeal community structure in grassland soil

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Identifying biologically relevant differences between metagenomic communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

In situ dynamics and spatial heterogeneity of soil bacterial communities under different crop residue management.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Antibiotic production by bacterial biocontrol agents.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Strategies for accessing soil metagenome for desired applications.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Quantitative and qualitative microscale distribution of bacteria in soil

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Uncultured soil bacteria are a reservoir of new antibiotic resistance genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Plasmid DNA in a groundwater aquifer microcosm--adsorption, DNAase resistance and natural genetic transformation of Bacillus subtilis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Impact of protozoan grazing on bacterial community structure in soil microcosms

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Influence of texture on habitable pore space and bacterial-protozoan populations in soil

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Innovative methods for soil DNA purification tested in soils with widely differing characteristics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Synergistic interactions in the microbial world

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Toward a census of bacteria in soil

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Microbial surface thermodynamics and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Prokaryotic diversity--magnitude, dynamics, and controlling factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Assembling millions of short DNA sequences using SSAKE.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Deriving enzymatic and taxonomic signatures of metagenomes from short read data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Exploiting plant-microbe partnerships to improve biomass production and remediation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Interactions and self-organization in the soil-microbe complex.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

Cultivating the uncultured

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

A greedy algorithm for aligning DNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6941.2011.01140.X

10.1111/J.1574-6941.2011.01140.X

21 January 2018

Identifiers

DOI

1 reference

30 July 2017

1 reference