A New Approach to Modify Plant Microbiomes and Traits by Introducing Beneficial Bacteria at Flowering into Progeny Seeds

Burkholderia phytofirmans Inoculation-Induced Changes on the Shoot Cell Anatomy and Iron Accumulation Reveal Novel Components of Arabidopsis-Endophyte Interaction that Can Benefit Downstream Biomass Deconstruction

(2016) Shuai Zhao et al.   Frontiers in Plant Science

A Complex Molecular Interplay of Auxin and Ethylene Signaling Pathways Is Involved in Arabidopsis Growth Promotion by Burkholderia phytofirmans PsJN

(2016) María J. Poupin et al.   Frontiers in Plant Science

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Burkholderia phytofirmans strain PsJN advanced development and altered leaf level physiology of switchgrass

(2015) Bingxue Wang et al.   BIOMASS & BIOENERGY

Terroir is a key driver of seed-associated microbial assemblages

(2015) Stephanie Klaedtke et al.   ENVIRONMENTAL MICROBIOLOGY

Global gene expression profiling of two switchgrass cultivars following inoculation withBurkholderia phytofirmansstrain PsJN

(2015) Alejandra Lara-Chavez et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

(2015) Pablo R. Hardoim et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

(2015) Johan Bengtsson-Palme et al.   Molecular Ecology Resources

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Raheleh Sheibani-Tezerji et al.   mBio

Microbial communities on flower surfaces act as signatures of pollinator visitation

(2015) Masayuki Ushio et al.   Scientific Reports

Burkholderia phytofirmans PsJN induces long-term metabolic and transcriptional changes involved in Arabidopsis thaliana salt tolerance

(2015) Ignacio Pinedo et al.   Frontiers in Plant Science

Emergence Shapes the Structure of the Seed Microbiota

(2014) Matthieu Barret et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The microbial ecology of flowers: an emerging frontier in phyllosphere research

(2014) Kristin Aleklett et al.   Botany

Root microbiome relates to plant host evolution in maize and other Poaceae

(2014) Marie-Lara Bouffaud et al.   ENVIRONMENTAL MICROBIOLOGY

Interkingdom Transfer of the Acne-Causing Agent, Propionibacterium acnes, from Human to Grapevine

(2014) Andrea Campisano et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial seed endophytes: genera, vertical transmission and interaction with plants

(2014) Sascha Truyens et al.   Environmental Microbiology Reports

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

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

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

(2014) Pierre-Marc Delaux et al.   PLoS Genetics

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

Increased drought stress resilience of maize through endophytic colonization by Burkholderia phytofirmans PsJN and Enterobacter sp. FD17

(2013) Muhammad Naveed et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Going back to the roots: the microbial ecology of the rhizosphere

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Effects of the Plant Growth-Promoting Bacterium Burkholderia phytofirmans PsJN throughout the Life Cycle of Arabidopsis thaliana

(2013) María Josefina Poupin et al.   PLoS One

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Dynamics of Seed-Borne Rice Endophytes on Early Plant Growth Stages

(2012) Pablo R. Hardoim et al.   PLoS One

Methylobacterium-Induced Endophyte Community Changes Correspond with Protection of Plants against Pathogen Attack

(2012) Pavlo Ardanov et al.   PLoS One

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

(2011) Daniel McDonald et al.   ISME Journal

Conservation and Diversity of Seed Associated Endophytes in Zea across Boundaries of Evolution, Ethnography and Ecology

(2011) David Johnston-Monje et al.   PLoS One

Effect of bacterial inoculation, plant genotype and developmental stage on root-associated and endophytic bacterial communities in potato (Solanum tuberosum)

(2010) Fernando Dini Andreote et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models forIn SilicoEvaluation of Oligonucleotide Probes for FluorescenceIn SituHybridization

(2010) L. Safak Yilmaz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Endophytic bacteria in cacti seeds can improve the development of cactus seedlings

(2009) M. Esther Puente et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY