Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia

The Impact of Genetic Changes during Crop Domestication

(2018) Petr Smýkal et al.   Agronomy-Basel

The wild side of plant microbiomes

(2018) Juan E. Pérez-Jaramillo et al.   Microbiome

Acidicapsa ferrireducens sp. nov., Acidicapsa acidiphila sp. nov., and Granulicella acidiphila sp. nov.: novel acidobacteria isolated from metal-rich acidic waters

(2017) Carmen Falagán et al.   EXTREMOPHILES

CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks

(2017) Min Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits

(2017) Juan E Pérez-Jaramillo et al.   ISME Journal

The impact of the omics era on the knowledge and use of Lysobacter species to control phytopathogenic micro-organisms

(2017) G. Puopolo et al.   JOURNAL OF APPLIED MICROBIOLOGY

Let the Core Microbiota Be Functional

(2017) Philippe Lemanceau et al.   TRENDS IN PLANT SCIENCE

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

(2017) Yun Kit Yeoh et al.   Nature Communications

Biogeographical Patterns of Legume-Nodulating Burkholderia spp.: from African Fynbos to Continental Scales

(2016) Benny Lemaire et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Root-associated bacterial diversities of Oryza rufipogon and Oryza sativa and their influencing environmental factors

(2016) Lei Tian et al.   ARCHIVES OF MICROBIOLOGY

Improving the fertility of tropical acid soils: Liming versus biochar application? A long term comparison in the highlands of Madagascar

(2016) Louis-Marie Raboin et al.   FIELD CROPS RESEARCH

Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus

(2016) Jonathan W. Leff et al.   NEW PHYTOLOGIST

Crop Domestication and Its Impact on Naturally Selected Trophic Interactions

(2015) Yolanda H. Chen et al.   Annual Review of Entomology

Comparative genomics and metabolic profiling of the genus Lysobacter

(2015) Irene de Bruijn et al.   BMC GENOMICS

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

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

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

(2015) Yun Kit Yeoh et al.   ENVIRONMENTAL MICROBIOLOGY

Long-term nitrogen addition causes the evolution of less-cooperative mutualists

(2015) Dylan J. Weese et al.   EVOLUTION

Impact of plant domestication on rhizosphere microbiome assembly and functions

(2015) Juan E. Pérez-Jaramillo et al.   PLANT MOLECULAR BIOLOGY

Diversity and Activity of Lysobacter Species from Disease Suppressive Soils

(2015) Ruth Gómez Expósito et al.   Frontiers in Microbiology

Land Use History Shifts In Situ Fungal and Bacterial Successions following Wheat Straw Input into the Soil

(2015) Vincent Tardy et al.   PLoS One

Genomic Potential for Polysaccharide Deconstruction in Bacteria

(2014) Renaud Berlemont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Bacterial networks and co-occurrence relationships in the lettuce root microbiota

(2014) Massimiliano Cardinale et al.   ENVIRONMENTAL MICROBIOLOGY

Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes

(2014) Shahal Abbo et al.   TRENDS IN PLANT SCIENCE

Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima—ancestor of all beet crops—and modern sugar beets

(2014) Christin Zachow et al.   Frontiers in Microbiology

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Genus-wide acid tolerance accounts for the biogeographical distribution of soilBurkholderiapopulations

(2013) Nejc Stopnisek et al.   ENVIRONMENTAL MICROBIOLOGY

Genetics and Consequences of Crop Domestication

(2013) Sherry A. Flint-Garcia   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Diversity and heritability of the maize rhizosphere microbiome under field conditions

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

Chloroplast Microsatellite Diversity in Phaseolus vulgaris

(2013) F. Desiderio et al.   Frontiers in Plant Science

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

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

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

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities

(2012) J. L. M. Rodrigues et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data

(2012) E. Bitocchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Soil characteristics more strongly influence soil bacterial communities than land-use type

(2011) Eiko E. Kuramae et al.   FEMS MICROBIOLOGY ECOLOGY

Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood

(2011) I. S. Kulichevskaya et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2011) Albert Barberán et al.   ISME Journal

Indigenous Populations of Three Closely Related Lysobacter spp. in Agricultural Soils Using Real-Time PCR

(2011) Joeke Postma et al.   MICROBIAL ECOLOGY

Environmental and Gut Bacteroidetes: The Food Connection

(2011) François Thomas et al.   Frontiers in Microbiology

Burkholderia phymatum Strains Capable of Nodulating Phaseolus vulgaris Are Present in Moroccan Soils

(2010) C. Talbi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils

(2009) N. L. Ward et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

(2009) Ryan T Jones et al.   ISME Journal

StenotrophomonasandLysobacter: ubiquitous plant-associatedgamma-proteobacteria of developing significance in applied microbiology

(2009) A.C. Hayward et al.   JOURNAL OF APPLIED MICROBIOLOGY

The nature of selection during plant domestication

(2009) Michael D. Purugganan et al.   NATURE

Burkholderiaspp. are the most competitive symbionts ofMimosa, particularly under N-limited conditions

(2008) Geoffrey N. Elliott et al.   ENVIRONMENTAL MICROBIOLOGY