The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response

A specialized metabolic network selectively modulates Arabidopsis root microbiota

(2019) Ancheng C. Huang et al.   SCIENCE

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

(2018) Ling Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assembly and ecological function of the root microbiome across angiosperm plant species

(2018) Connor R. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health

(2018) Ioannis A. Stringlis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design of synthetic bacterial communities for predictable plant phenotypes

(2018) Sur Herrera Paredes et al.   PLOS BIOLOGY

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

(2018) Paloma Durán et al.   CELL

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Root microbiota drive direct integration of phosphate stress and immunity

(2017) Gabriel Castrillo et al.   NATURE

Genomic features of bacterial adaptation to plants

(2017) Asaf Levy et al.   NATURE GENETICS

Root type and soil phosphate determine the taxonomic landscape of colonizing fungi and the transcriptome of field-grown maize roots

(2017) Peng Yu et al.   NEW PHYTOLOGIST

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes

(2017) Christian Santos-Medellín et al.   mBio

Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree

(2016) Omri M. Finkel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent

(2016) Kei Hiruma et al.   CELL

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

(2016) Stéphane Hacquard et al.   Nature Communications

Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity

(2016) Zhilin Yuan et al.   Scientific Reports

Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon

(2015) Marcela Hernández et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2015) Yun Kit Yeoh et al.   ENVIRONMENTAL MICROBIOLOGY

The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome

(2015) Tanya Z. Berardini et al.   GENESIS

Microbial and biochemical basis of a Fusarium wilt-suppressive soil

(2015) Jae-Yul Cha et al.   ISME Journal

Non-targeted profiling of semi-polar metabolites in Arabidopsis root exudates uncovers a role for coumarin secretion and lignification during the local response to phosphate limitation

(2015) Jörg Ziegler et al.   JOURNAL OF EXPERIMENTAL BOTANY

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Soils naturally suppressive to banana Fusarium wilt disease harbor unique bacterial communities

(2015) Zongzhuan Shen et al.   PLANT AND SOIL

Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping

(2015) Rakesh Santhanam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

(2015) Jonathan W. Leff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Associations with rhizosphere bacteria can confer an adaptive advantage to plants

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MT-Toolbox: improved amplicon sequencing using molecule tags

(2014) Scott M Yourstone et al.   BMC BIOINFORMATICS

Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment

(2014) Kateryna Zhalnina et al.   MICROBIAL ECOLOGY

Identification of primary and secondary metabolites with phosphorus status-dependent abundance inArabidopsis, and of the transcription factor PHR1 as a major regulator of metabolic changes during phosphorus limitation

(2014) BIKRAM-DATT PANT et al.   PLANT CELL AND ENVIRONMENT

Drought Tolerance Conferred to Sugarcane by Association with Gluconacetobacter diazotrophicus: A Transcriptomic View of Hormone Pathways

(2014) Lívia Vargas et al.   PLoS One

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Incorporation of plant carbon and microbial nitrogen into the rhizosphere food web of beech and ash

(2013) Verena Eissfeller et al.   SOIL BIOLOGY & BIOCHEMISTRY

Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes

(2012) Kelly S. Ramirez et al.   GLOBAL CHANGE BIOLOGY

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Bacterial anoxygenic photosynthesis on plant leaf surfaces

(2012) Nof Atamna-Ismaeel et al.   Environmental Microbiology Reports

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

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

The bacterial biogeography of British soils

(2011) Robert I. Griffiths et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial rhodopsins on leaf surfaces of terrestrial plants

(2011) Nof Atamna-Ismaeel et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

(2011) Noah Fierer et al.   ISME Journal

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

(2011) Claudia Knief et al.   ISME Journal

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis

(2010) Regla Bustos et al.   PLoS Genetics

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Biogeography of soil archaea and bacteria along a steep precipitation gradient

(2009) Roey Angel et al.   ISME Journal

The leaf ionome as a multivariable system to detect a plant's physiological status

(2008) I. R. Baxter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA