Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

Research priorities for harnessing plant microbiomes in sustainable agriculture

(2017) Posy E. Busby et al.   PLOS BIOLOGY

Deciphering composition and function of the root microbiome of a legume plant

(2017) Kyle Hartman et al.   Microbiome

Cover crops support ecological intensification of arable cropping systems

(2017) Raphaël A. Wittwer et al.   Scientific Reports

Responses of soil fungi to 5-year conservation tillage treatments in the drylands of northern China

(2016) Ziting Wang et al.   APPLIED SOIL ECOLOGY

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

(2016) Bin Ma et al.   ISME Journal

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

An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability

(2016) S. Franz Bender et al.   TRENDS IN ECOLOGY & EVOLUTION

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

(2016) Matthew T. Agler et al.   PLOS BIOLOGY

Networking in the Plant Microbiome

(2016) Marcel G. A. van der Heijden et al.   PLOS BIOLOGY

Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies

(2016) Davide Francioli et al.   Frontiers in Microbiology

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

(2015) Davide Bulgarelli et al.   Cell Host & Microbe

The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application

(2015) Yun Kit Yeoh et al.   ENVIRONMENTAL MICROBIOLOGY

The Plant Microbiome at Work

(2015) Klaus Schlaeppi et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse et al.   NEW PHYTOLOGIST

Structure, variation, and assembly of the root-associated microbiomes of rice

(2015) Joseph Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Soil Microbiome Influences Grapevine-Associated Microbiota

(2015) Iratxe Zarraonaindia et al.   mBio

Distinct soil microbial diversity under long-term organic and conventional farming

(2014) Martin Hartmann et al.   ISME Journal

Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

(2014) Gregory Bonito et al.   MOLECULAR ECOLOGY

Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach

(2014) Guillaume Lentendu et al.   MOLECULAR ECOLOGY

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

(2014) T.B.K. Reddy et al.   NUCLEIC ACIDS RESEARCH

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

(2014) Zhen Zhen et al.   PLoS One

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Newly Cultured Bacteria with Broad Diversity Isolated from Eight-Week Continuous Culture Enrichments of Cow Feces on Complex Polysaccharides

(2013) Cherie J. Ziemer   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Rhizosphere microbiome assemblage is affected by plant development

(2013) Jacqueline M Chaparro et al.   ISME Journal

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

(2013) Natacha Bodenhausen 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

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Changes in Bacterial Community Structure of Agricultural Land Due to Long-Term Organic and Chemical Amendments

(2012) Vasvi Chaudhry et al.   MICROBIAL ECOLOGY

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Ecological intensification: harnessing ecosystem services for food security

(2012) Riccardo Bommarco et al.   TRENDS IN ECOLOGY & EVOLUTION

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations

(2011) Orin C. Shanks et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Environmental Impact of Different Agricultural Management Practices: Conventional vs. Organic Agriculture

(2011) Tiziano Gomiero et al.   CRITICAL REVIEWS IN PLANT SCIENCES

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

(2011) Albert Barberán et al.   ISME Journal

Effects of organic amendment and tillage on soil microorganisms and microfauna

(2010) Amy M. Treonis et al.   APPLIED SOIL ECOLOGY

Soil biota community structure and abundance under agricultural intensification and extensification

(2010) Maria B. Postma-Blaauw et al.   ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

Improving indicator species analysis by combining groups of sites

(2010) Miquel De Cáceres et al.   OIKOS

Pyrosequencing Assessment of Soil Microbial Communities in Organic and Conventional Potato Farms

(2010) Akifumi Sugiyama et al.   PLANT DISEASE

Food Security: The Challenge of Feeding 9 Billion People

(2010) H. C. J. Godfray et al.   SCIENCE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Fungal community structure in soils of conventional and organic farming systems

(2009) S. Schneider et al.   Fungal Ecology

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

The role of conservation agriculture in sustainable agriculture

(2007) P. R Hobbs et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Differences in the composition and diversity of bacterial communities from agricultural and forest soils

(2007) Rima Upchurch et al.   SOIL BIOLOGY & BIOCHEMISTRY