A preliminary examination of bacterial, archaeal, and fungal communities inhabiting different rhizocompartments of tomato plants under real-world environments

Tomato root microbiota and Phytophthora parasitica-associated disease

(2017) Marie Larousse et al.   Microbiome

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

(2017) Bram Beckers et al.   Microbiome

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere

(2016) Yan Yan et al.   ISME Journal

Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea

(2016) Jeong Myeong Kim et al.   JOURNAL OF MICROBIOLOGY

Daily magnesium fluxes regulate cellular timekeeping and energy balance

(2016) Kevin A. Feeney et al.   NATURE

Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers

(2016) Sarah M. Allard et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Impact of a Bacterial Volatile 2,3-Butanediol on Bacillus subtilis Rhizosphere Robustness

(2016) Hwe-Su Yi et al.   Frontiers in Microbiology

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity

(2016) Citlali Fonseca-García et al.   Frontiers in Microbiology

Divergent habitat filtering of root and soil fungal communities in temperate beech forests

(2016) Kezia Goldmann et al.   Scientific Reports

Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens

(2016) Longfei Jiang 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

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

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

Structure, variation, and assembly of the root-associated microbiomes of rice

(2015) Joseph Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deterministic processes vary during community assembly for ecologically dissimilar taxa

(2015) Jeff R. Powell et al.   Nature Communications

Metagenomic insights into communities, functions of endophytes and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots

(2015) Bao-Yu Tian et al.   Scientific Reports

Relations of microbiome characteristics to edaphic properties of tropical soils from Trinidad

(2015) Vidya de Gannes et al.   Frontiers in Microbiology

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes

(2015) Kathryn M. Docherty et al.   PLoS One

The communities of tomato (Solanum lycopersicumL.) leaf endophytic bacteria, analyzed by 16S-ribosomal RNA gene pyrosequencing

(2014) Fernando M. Romero et al.   FEMS MICROBIOLOGY LETTERS

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

Effect of long-term different fertilization on bacterial community structures and diversity in citrus orchard soil of volcanic ash

(2014) Jae Ho Joa et al.   JOURNAL OF MICROBIOLOGY

A Model to Explain Plant Growth Promotion Traits: A Multivariate Analysis of 2,211 Bacterial Isolates

(2014) Pedro Beschoren da Costa et al.   PLoS One

High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China

(2014) Junjie Liu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Structure and Functions of the Bacterial Microbiota of Plants

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

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)

(2013) Andrea R Ottesen et al.   BMC MICROBIOLOGY

Rhizosphere microbiome assemblage is affected by plant development

(2013) Jacqueline M Chaparro et al.   ISME Journal

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

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

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

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

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

Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

(2013) K. Schlaeppi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Multiple impacts of the plant growth-promoting rhizobacterium Variovorax paradoxus 5C-2 on nutrient and ABA relations of Pisum sativum

(2012) F. Jiang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

The rhizosphere microbiome and plant health

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

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

Beyond the Venn diagram: the hunt for a core microbiome

(2011) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

The bacterial biogeography of British soils

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

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

A ‘rare biosphere’ microorganism contributes to sulfate reduction in a peatland

(2010) Michael Pester et al.   ISME Journal

Insidious effects of sequencing errors on perceived diversity in molecular surveys

(2010) Ian A. Dickie   NEW PHYTOLOGIST

Auxin and Plant-Microbe Interactions

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

Plants, Mycorrhizal Fungi, and Bacteria: A Network of Interactions

(2009) Paola Bonfante et al.   Annual Review of Microbiology

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

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Chrysosporium pseudomerdarium produces gibberellins and promotes plant growth

(2009) Muhammad Hamayun et al.   JOURNAL OF MICROBIOLOGY

The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors

(2009) M. Buée et al.   PLANT AND SOIL

Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

(2009) Stéphane Compant et al.   SOIL BIOLOGY & BIOCHEMISTRY

Ammonia-oxidizing archaea: important players in paddy rhizosphere soil?

(2008) Xue-Ping Chen et al.   ENVIRONMENTAL MICROBIOLOGY

Synergistic interactions between the ACC deaminase-producing bacterium Pseudomonas putida UW4 and the AM fungus Gigaspora rosea positively affect cucumber plant growth

(2008) Elisa Gamalero et al.   FEMS MICROBIOLOGY ECOLOGY

Properties of bacterial endophytes and their proposed role in plant growth

(2008) Pablo R. Hardoim et al.   TRENDS IN MICROBIOLOGY

Rhizosphere bacteria help plants tolerate abiotic stress

(2008) Jungwook Yang et al.   TRENDS IN PLANT SCIENCE

Trichoderma–plant–pathogen interactions

(2007) Francesco Vinale et al.   SOIL BIOLOGY & BIOCHEMISTRY