Hidden heterogeneity and co‐occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates

Biogeography of soil microbial habitats across France

(2020) Battle Karimi et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales

(2019) Regina L. Wilpiszeski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Taxon-specific fungal preference for distinct soil particle size fractions

(2019) Michael Hemkemeyer et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Towards an integrative understanding of soil biodiversity

(2019) Madhav P. Thakur et al.   BIOLOGICAL REVIEWS

The influence of aggregate size fraction and horizon position on microbial community composition

(2018) Aaron Fox et al.   APPLIED SOIL ECOLOGY

Greatest soil microbial diversity found in micro-habitats

(2018) Elizabeth M. Bach et al.   SOIL BIOLOGY & BIOCHEMISTRY

Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses

(2018) Michael Hemkemeyer et al.   Frontiers in Microbiology

Biogeography of soil bacteria and archaea across France

(2018) Battle Karimi et al.   Science Advances

Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities

(2018) Eric R. Hester et al.   mSystems

Chemical nature of soil organic carbon under different long-term fertilization regimes is coupled with changes in the bacterial community composition in a Calcaric Fluvisol

(2018) Dandan Li et al.   BIOLOGY AND FERTILITY OF SOILS

Soil aggregates as massively concurrent evolutionary incubators

(2017) Matthias C Rillig et al.   ISME Journal

The microbial habitat in soil: Scale, heterogeneity and functional consequences

(2017) Naoise Nunan   JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community

(2016) Yong Wang et al.   ACTA OCEANOLOGICA SINICA

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

Microbial interactions and community assembly at microscales

(2016) Otto X Cordero et al.   CURRENT OPINION IN MICROBIOLOGY

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil

(2016) Samiran Banerjee et al.   SOIL BIOLOGY & BIOCHEMISTRY

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

zCompositions — R package for multivariate imputation of left-censored data under a compositional approach

(2015) Javier Palarea-Albaladejo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

The structure of microbial community in aggregates of a typical chernozem aggregates under contrasting variants of its agricultural use

(2015) E. A. Ivanova et al.   EURASIAN SOIL SCIENCE

The spatial distribution of exoenzyme activities across the soil micro-landscape, as measured in micro- and macro-aggregates, and ecosystem processes

(2015) Haryun Kim et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil particle size fractions harbour distinct microbial communities and differ in potential for microbial mineralisation of organic pollutants

(2015) Michael Hemkemeyer et al.   SOIL BIOLOGY & BIOCHEMISTRY

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Spatial Ecology of Bacteria at the Microscale in Soil

(2014) Xavier Raynaud et al.   PLoS One

Limitations and recommendations for successful DNA extraction from forensic soil samples: A review

(2014) Jennifer M. Young et al.   SCIENCE & JUSTICE

Intra-aggregate Pore Structure Influences Phylogenetic Composition of Bacterial Community in Macroaggregates

(2014) Alexandra N. Kravchenko et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Microscale evidence for a high decrease of soil bacterial density and diversity by cropping

(2013) Florentin Constancias et al.   Agronomy for Sustainable Development

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Systematic evaluation of bias in microbial community profiles induced by whole genome amplification

(2013) Susana O. L. Direito et al.   ENVIRONMENTAL MICROBIOLOGY

Linking microbial community structure to β-glucosidic function in soil aggregates

(2013) Vanessa L Bailey et al.   ISME Journal

Micrometer-scale physical structure and microbial composition of soil macroaggregates

(2013) Vanessa L. Bailey et al.   SOIL BIOLOGY & BIOCHEMISTRY

Acidobacterial community responses to agricultural management of soybean in Amazon forest soils

(2012) Acácio A. Navarrete et al.   FEMS MICROBIOLOGY ECOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Long-term fertilization effects on crop yields, soil fertility and sustainability in the Static Fertilization Experiment Bad Lauchstädt under climatic conditions 2001–2010

(2012) Ines Merbach et al.   Archives of Agronomy and Soil Science

The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

(2011) Michael Pester et al.   CURRENT OPINION IN MICROBIOLOGY

The bacterial biogeography of British soils

(2011) Robert I. Griffiths et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2011) Nathalie Lombard et al.   FEMS MICROBIOLOGY ECOLOGY

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

(2011) Gaddy T. Bergmann et al.   SOIL BIOLOGY & BIOCHEMISTRY

Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition

(2011) Marko Davinic et al.   SOIL BIOLOGY & BIOCHEMISTRY

Effects of fertilization and soil management on crop yields and carbon stabilization in soils. A review

(2010) B. Ludwig et al.   Agronomy for Sustainable Development

Microbial Biogeography: From Taxonomy to Traits

(2008) J. L. Green et al.   SCIENCE