Genome Sequences of a Plant Beneficial Synthetic Bacterial Community Reveal Genetic Features for Successful Plant Colonization

Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia

(2018) Ruben Garrido-Oter et al.   Cell Host & Microbe

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome

(2018) Jaderson Silveira Leite Armanhi et al.   Frontiers in Plant Science

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Root microbiota drive direct integration of phosphate stress and immunity

(2017) Gabriel Castrillo et al.   NATURE

Simplified and representative bacterial community of maize roots

(2017) Ben Niu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Steering Soil Microbiomes to Suppress Aboveground Insect Pests

(2017) Ana Pineda et al.   TRENDS IN PLANT SCIENCE

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

(2017) Hongwei Liu et al.   Frontiers in Microbiology

Synthesis of Rhizobial Exopolysaccharides and Their Importance for Symbiosis with Legume Plants

(2017) Małgorzata Marczak et al.   Genes

Icarus: visualizer for de novo assembly evaluation

(2016) Alla Mikheenko et al.   BIOINFORMATICS

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

(2016) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System

(2016) Collin M. Timm et al.   Frontiers in Plant Science

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

(2016) Hsin-Hung Lin et al.   Scientific Reports

Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome

(2016) Rafael Soares Correa de Souza et al.   Scientific Reports

Multiplex amplicon sequencing for microbe identification in community-based culture collections

(2016) Jaderson Silveira Leite Armanhi et al.   Scientific Reports

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

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

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse et al.   NEW PHYTOLOGIST

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

(2015) Devin Coleman-Derr et al.   NEW PHYTOLOGIST

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa

(2015) S. L. Lebeis et al.   SCIENCE

The Soil Microbiome Influences Grapevine-Associated Microbiota

(2015) Iratxe Zarraonaindia et al.   mBio

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

(2015) Marcel Huntemann et al.   Standards in Genomic Sciences

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

(2014) J. Dröge et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance

(2014) Devin Coleman-Derr et al.   Frontiers in Microbiology

Structure and Functions of the Bacterial Microbiota of Plants

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

ACC deaminase and IAA producing growth promoting bacteria from the rhizosphere soil of tropical rice plants

(2013) Himadri Bhusan Bal et al.   JOURNAL OF BASIC MICROBIOLOGY

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Culturing a plant microbiome community at the cross-Rhodes

(2012) Sarah L. Lebeis et al.   NEW PHYTOLOGIST

Involvement of auxin pathways in modulating root architecture during beneficial plant-microorganism interactions

(2012) POORNIMA SUKUMAR et al.   PLANT CELL AND ENVIRONMENT

Functional genomics analysis of plant growth-promoting rhizobacterial traits involved in rhizosphere competence

(2011) Matthieu Barret et al.   BIOLOGY AND FERTILITY OF SOILS

Root Nodulation: A Paradigm for How Plant-Microbe Symbiosis Influences Host Developmental Pathways

(2011) Guilhem J. Desbrosses et al.   Cell Host & Microbe

Exopolysaccharide Production Is Required for Biofilm Formation and Plant Colonization by the Nitrogen-Fixing EndophyteGluconacetobacter diazotrophicus

(2011) Carlos H. S. G. Meneses et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Evidence from field nitrogen balance and 15N natural abundance data for the contribution of biological N2 fixation to Brazilian sugarcane varieties

(2011) Segundo Urquiaga et al.   PLANT AND SOIL

Microbial phytases in phosphorus acquisition and plant growth promotion

(2011) Bijender Singh et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Bacillus species enhance growth parameters of chickpea (Cicer arietinum L.) in chromium stressed soils

(2010) Parvaze Ahmad Wani et al.   FOOD AND CHEMICAL TOXICOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Auxin and Plant-Microbe Interactions

(2010) S. Spaepen et al.   Cold Spring Harbor Perspectives in Biology

Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis

(2010) Paola Bonfante et al.   Nature Communications

Phosphate-Solubilizing and Plant-Growth-Promoting Pseudomonas aeruginosa PS1 Improves Greengram Performance in Quizalafop-p-ethyl and Clodinafop Amended Soil

(2009) Munees Ahemad et al.   ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY

Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids

(2009) J. Prell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes

(2009) Konstantinos Mavromatis et al.   Standards in Genomic Sciences

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