Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality

Shared and host-specific microbiome diversity and functioning of grapevine and accompanying weed plants

(2017) Abdul Samad et al.   ENVIRONMENTAL MICROBIOLOGY

The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine

(2017) Chiara Pagliarani et al.   PLANT PHYSIOLOGY

Using null models to infer microbial co-occurrence networks

(2017) Nora Connor et al.   PLoS One

Plant cultivars imprint the rhizosphere bacterial community composition and association networks

(2017) Yuji Jiang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Disentangling Interactions in the Microbiome: A Network Perspective

(2017) Mehdi Layeghifard et al.   TRENDS IN MICROBIOLOGY

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass

(2016) Erin E. Nuccio et al.   ECOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Root-associated bacteria promote grapevine growth: from the laboratory to the field

(2016) Eleonora Rolli et al.   PLANT AND SOIL

Modifications of ‘Summer Black’ grape berry quality as affected by the different rootstocks

(2016) Zhong-Xin Jin et al.   SCIENTIA HORTICULTURAE

Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes

(2016) Emily J. Warschefsky et al.   TRENDS IN PLANT SCIENCE

Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition

(2016) Matthew Shenton et al.   Rice

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

(2016) Nicholas A. Bokulich et al.   mBio

Microbes Drive Evolution of Animals and Plants: the Hologenome Concept

(2016) Eugene Rosenberg et al.   mBio

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

(2016) Maggie R. Wagner et al.   Nature Communications

Networking in the Plant Microbiome

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

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

(2016) Murali Gopal et al.   Frontiers in Microbiology

Roostocks/Scion/Nitrogen Interactions Affect Secondary Metabolism in the Grape Berry

(2016) Aude Habran et al.   Frontiers in Plant Science

Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

(2016) Kristin Kaiser et al.   Scientific Reports

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Beneficial Bacteria Isolated from Grapevine Inner Tissues Shape Arabidopsis thaliana Roots

(2015) Enrico Baldan et al.   PLoS One

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features

(2015) Kayla N. Burns et al.   SOIL BIOLOGY & BIOCHEMISTRY

Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features

(2015) Zaira Martín-Moldes et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Oasis desert farming selects environment-specific date palm root endophytic communities and cultivable bacteria that promote resistance to drought

(2015) Hanene Cherif et al.   Environmental Microbiology Reports

The Soil Microbiome Influences Grapevine-Associated Microbiota

(2015) Iratxe Zarraonaindia et al.   mBio

Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir

(2015) Sarah Knight et al.   Scientific Reports

Comparison of soil microbial communities inhabiting vineyards and native sclerophyllous forests in central Chile

(2015) Luis E. Castañeda et al.   Ecology and Evolution

Associations with rhizosphere bacteria can confer an adaptive advantage to plants

(2015) Cara H. Haney et al.   Nature Plants

Water limitation and rootstock genotype interact to alter grape berry metabolism through transcriptome reprogramming

(2015) Mariam Berdeja et al.   Horticulture Research

Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina

(2014) A. D. Vega-Avila et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process

(2014) Daniela Bulgari et al.   BMC MICROBIOLOGY

Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait

(2014) Eleonora Rolli et al.   ENVIRONMENTAL MICROBIOLOGY

An abundant ‘Candidatus Phytoplasma solani’ tuf b strain is associated with grapevine, stinging nettle and Hyalesthes obsoletus

(2014) A. Aryan et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

(2014) Pier Luigi Buttigieg et al.   FEMS MICROBIOLOGY ECOLOGY

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria

(2014) Javad Hamedi et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Unravelling the Diversity of Grapevine Microbiome

(2014) Cátia Pinto et al.   PLoS One

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

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

Host immune responses accelerate pathogen evolution

(2013) Pankaj Trivedi et al.   ISME Journal

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Characterization of Epiphytic Bacterial Communities from Grapes, Leaves, Bark and Soil of Grapevine Plants Grown, and Their Relations

(2013) Guilherme Martins et al.   PLoS One

Microbial terroir for wine grapes

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

PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

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

Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments

(2013) Ramona Marasco et al.   Biomed Research International

Grapevine rootstock effects on scion sap phenolic levels, resistance to Xylella fastidiosa infection, and progression of Pierce's disease

(2013) Christopher M. Wallis et al.   Frontiers in Plant Science

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming

(2012) Ramona Marasco et al.   PLoS One

Mapping genetic loci for tolerance to lime-induced iron deficiency chlorosis in grapevine rootstocks (Vitis sp.)

(2012) Pierre-François Bert et al.   THEORETICAL AND APPLIED GENETICS

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

The generation and maintenance of diversity in microbial communities

(2011) Noah Fierer et al.   AMERICAN JOURNAL OF BOTANY

Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere

(2011) Pankaj Trivedi et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

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

(2011) Albert Barberán et al.   ISME Journal

Mineral–microbe interactions: Biotechnological potential of bioweathering

(2011) Francesca Mapelli et al.   JOURNAL OF BIOTECHNOLOGY

Endophytes of Grapevine Flowers, Berries, and Seeds: Identification of Cultivable Bacteria, Comparison with Other Plant Parts, and Visualization of Niches of Colonization

(2011) Stéphane Compant et al.   MICROBIAL ECOLOGY

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Soil beneficial bacteria and their role in plant growth promotion: a review

(2010) Rifat Hayat et al.   ANNALS OF MICROBIOLOGY

Huanglongbing, a Systemic Disease, Restructures the Bacterial Community Associated with Citrus Roots

(2010) P. Trivedi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Dormancy contributes to the maintenance of microbial diversity

(2010) S. E. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Do not log-transform count data

(2010) Robert B. O’Hara et al.   Methods in Ecology and Evolution

Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

(2009) Stéphane Compant et al.   SOIL BIOLOGY & BIOCHEMISTRY

Selective progressive response of soil microbial community to wild oat roots

(2008) Kristen M DeAngelis et al.   ISME Journal

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE

Properties of bacterial endophytes and their proposed role in plant growth

(2008) Pablo R. Hardoim et al.   TRENDS IN MICROBIOLOGY