Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

(2016) Sagar M. Utturkar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation

(2016) Yu Xia et al.   Biotechnology for Biofuels

Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome

(2016) Bram Beckers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Poplar trees reconfigure the transcriptome and metabolome in response to drought in a genotype- and time-of-day-dependent manner

(2015) Erin T Hamanishi et al.   BMC GENOMICS

Altered fecal microbiota composition in patients with major depressive disorder

(2015) Haiyin Jiang et al.   BRAIN BEHAVIOR AND IMMUNITY

Microbiota and Host Nutrition across Plant and Animal Kingdoms

(2015) Stéphane Hacquard et al.   Cell Host & Microbe

Metabolomic profiling in tomato reveals diel compositional changes in fruit affected by source–sink relationships

(2015) Camille Bénard et al.   JOURNAL OF EXPERIMENTAL BOTANY

Pinus sylvestrisswitches respiration substrates under shading but not during drought

(2015) Sarah Fischer et al.   NEW PHYTOLOGIST

Involvement of plant stress hormones in Burkholderia phytofirmans-induced shoot and root growth promotion

(2015) Leonid V. Kurepin et al.   PLANT GROWTH REGULATION

Metabolite profiles of maize leaves in drought, heat and combined stress field trials reveal the relationship between metabolism and grain yield

(2015) Toshihiro Obata et al.   PLANT PHYSIOLOGY

Mycorrhiza and PGPB modulate maize biomass, nutrient uptake and metabolic pathways in maize grown in mining-impacted soil

(2015) Faten Dhawi et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) S. L. Lebeis et al.   SCIENCE

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Transcriptome Profiling of the Endophyte Burkholderia phytofirmans PsJN Indicates Sensing of the Plant Environment and Drought Stress

(2015) Raheleh Sheibani-Tezerji et al.   mBio

Transcriptional Responses to Sucrose Mimic the Plant-Associated Life Style of the Plant Growth Promoting Endophyte Enterobacter sp. 638

(2015) Safiyh Taghavi et al.   PLoS One

L-Tryptophan-dependent biosynthesis of indole-3-acetic acid (IAA) improves plant growth and colonization of maize by Burkholderia phytofirmans PsJN

(2014) Muhammad Naveed et al.   ANNALS OF MICROBIOLOGY

Poplar nutrition under drought as affected by ectomycorrhizal colonization

(2014) Lara Danielsen et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

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

(2014) Gregory Bonito et al.   MOLECULAR ECOLOGY

Light intensity affects the growth and flavonol biosynthesis of Ginkgo (Ginkgo biloba L.)

(2014) You Xu et al.   NEW FORESTS

Shading decreases plant carbon preferential allocation towards the most beneficial mycorrhizal mutualist

(2014) Chaoyuan Zheng et al.   NEW PHYTOLOGIST

Analysis of the Drought Stress-Responsive Transcriptome of Black Cottonwood (Populus trichocarpa) Using Deep RNA Sequencing

(2014) Sha Tang et al.   PLANT MOLECULAR BIOLOGY REPORTER

Metabolomic Analysis Using Ultra-Performance Liquid Chromatography-Quadrupole-Time of Flight Mass Spectrometry (UPLC-Q-TOF MS) Uncovers the Effects of Light Intensity and Temperature under Shading Treatments on the Metabolites in Tea

(2014) Qunfeng Zhang et al.   PLoS One

Emergent Biosynthetic Capacity in Simple Microbial Communities

(2014) Hsuan-Chao Chiu et al.   PLoS Computational Biology

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

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

Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus

(2014) Jessy L. Labbé et al.   Frontiers in Plant Science

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Structure and Functions of the Bacterial Microbiota of Plants

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

The effects of exogenous putrescine on sex-specific responses of Populus cathayana to copper stress

(2013) Lianghua Chen et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

(2013) Romain L Barnard et al.   ISME Journal

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Resource Availability and Competition Shape the Evolution of Survival and Growth Ability in a Bacterial Community

(2013) Minna Pekkonen et al.   PLoS One

Linking Plant Nutritional Status to Plant-Microbe Interactions

(2013) Lilia C. Carvalhais et al.   PLoS One

A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees

(2013) Migun Shakya et al.   PLoS One

Investigating the drought-stress response of hybrid poplar genotypes by metabolite profiling

(2013) G. L. H. Barchet et al.   TREE PHYSIOLOGY

Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog

(2012) Timothy J Tschaplinski et al.   Biotechnology for Biofuels

Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations

(2012) Yongchao Li et al.   Biotechnology for Biofuels

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

(2012) Kevin R. Foster et al.   CURRENT BIOLOGY

Phenotypic plasticity of sun and shade ecotypes of Stellaria longipes in response to light quality signaling: Cytokinins

(2012) Leonid V. Kurepin et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Physiological and molecular responses to drought in Petunia: the importance of stress severity

(2012) Jongyun Kim et al.   JOURNAL OF EXPERIMENTAL BOTANY

Phenotypic and developmental plasticity of xylem in hybrid poplar saplings subjected to experimental drought, nitrogen fertilization, and shading

(2012) Lenka Plavcová et al.   JOURNAL OF EXPERIMENTAL BOTANY

Pseudomonas fluorescensInduces Strain-Dependent and Strain-Independent Host Plant Responses in Defense Networks, Primary Metabolism, Photosynthesis, and Fitness

(2012) David J. Weston et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

Rapid responses of soil microorganisms improve plant fitness in novel environments

(2012) J. A. Lau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types

(2011) Neil R. Gottel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Influence of arbuscular mycorrhizae on biomass and root morphology of selected strawberry cultivars under salt stress

(2011) Li Fan et al.   Botany

Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico

(2011) Kalin Vetsigian et al.   PLOS BIOLOGY

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Metagenomic analysis of stressed coral holobionts

(2009) Rebecca Vega Thurber et al.   ENVIRONMENTAL MICROBIOLOGY

A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize

(2009) BJÖRN USADEL et al.   PLANT CELL AND ENVIRONMENT

Priming in Systemic Plant Immunity

(2009) Ho Won Jung et al.   SCIENCE

Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates

(2008) Daniel J. Kvitek et al.   PLoS Genetics