The Structure of Rhizosphere Fungal Communities of Wild and Domesticated Rice: Changes in Diversity and Co-occurrence Patterns

Self-Crossing Leads to Weak Co-Variation of the Bacterial and Fungal Communities in the Rice Rhizosphere

(2021) Jingjing Chang et al.   Microorganisms

Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison

(2020) Andrzej Tkacz et al.   mBio

Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

(2020) Hyun Kim et al.   Microbiome

The proportion of soil-borne pathogens increases with warming at the global scale

(2020) Manuel Delgado-Baquerizo et al.   Nature Climate Change

The DROOPING LEAF (DR) gene encoding GDSL esterase is involved in silica deposition in rice (Oryza sativa L.)

(2020) Yoye Yu et al.   PLoS One

Combined Metabarcoding and Co-occurrence Network Analysis to Profile the Bacterial, Fungal and Fusarium Communities and Their Interactions in Maize Stalks

(2019) José Francisco Cobo-Díaz et al.   Frontiers in Microbiology

Proteomics Analysis of E. angustifolia Seedlings Inoculated with Arbuscular Mycorrhizal Fungi under Salt Stress

(2019) Tingting Jia et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: insights from rice and soybean

(2019) Shaohua Shi et al.   ARCHIVES OF MICROBIOLOGY

Comparative study of the mycorrhizal root transcriptomes of wild and cultivated rice in response to the pathogen Magnaporthe oryzae

(2019) Lei Tian et al.   Rice

Cultivated rice rhizomicrobiome is more sensitive to environmental shifts than that of wild rice in natural environments

(2019) Shangqi Xu et al.   APPLIED SOIL ECOLOGY

Fungal community composition in sodic soils subjected to long-term rice cultivation

(2019) Jiaxu Zhang et al.   Archives of Agronomy and Soil Science

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

(2019) Juan E. Pérez-Jaramillo et al.   Microbiome

The influence of host genotype and salt stress on the seed endophytic community of salt-sensitive and salt-tolerant rice cultivars

(2018) Denver I. Walitang et al.   BMC PLANT BIOLOGY

Co-evolutionary associations between root-associated microbiomes and root transcriptomes in wild and cultivated rice varieties

(2018) Lei Tian et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

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

Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

(2018) Joelle Sasse et al.   TRENDS IN PLANT SCIENCE

Rhizosphere microbiota assemblage associated with wild and cultivated soybeans grown in three types of soil suspensions

(2018) Chunling Chang et al.   Archives of Agronomy and Soil Science

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

ASIAN CULTIVATED RICE DOMESTICATION SUPPRESSES THE EXPRESSION OF ABIOTIC STRESS- AND REACTIVE OXYGEN SPECIES SCAVENGING-RELATED GENES IN ROOTS

(2018) FAHAD NASIR et al.   PAKISTAN JOURNAL OF BOTANY

Impact of domestication on the evolution of rhizomicrobiome of rice in response to the presence of Magnaporthe oryzae

(2018) Shaohua Shi et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

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

Nutrient Exchange and Regulation in Arbuscular Mycorrhizal Symbiosis

(2017) Wanxiao Wang et al.   Molecular Plant

Fatty acids in arbuscular mycorrhizal fungi are synthesized by the host plant

(2017) Leonie H. Luginbuehl et al.   SCIENCE

Plant cultivars imprint the rhizosphere bacterial community composition and association networks

(2017) Yuji Jiang et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

(2016) Lei Tian et al.   ARCHIVES OF MICROBIOLOGY

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

Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition

(2016) Matthew Shenton et al.   Rice

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

(2016) Matthew T. Agler et al.   PLOS BIOLOGY

Flood and drought tolerance in rice: opposite but may coexist

(2016) A. N. M. Rubaiyath Bin Rahman et al.   Food and Energy Security

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

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

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

(2015) Andrzej Tkacz et al.   ISME Journal

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

Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars

(2015) Márton Szoboszlay et al.   SOIL BIOLOGY & BIOCHEMISTRY

The Hologenome Concept: Helpful or Hollow?

(2015) Nancy A. Moran et al.   PLOS BIOLOGY

Water strategy of mycorrhizal rice at low temperature through the regulation of PIP aquaporins with the involvement of trehalose

(2014) Zhilei Liu et al.   APPLIED SOIL ECOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Root traits and cellular level tolerance hold the key in maintaining higher spikelet fertility of rice under water limited conditions

(2014) Bheemanahalli R. Raju et al.   FUNCTIONAL PLANT BIOLOGY

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

(2014) Muhua Wang et al.   NATURE GENETICS

Relative contributions of plant traits and soil microbial properties to mountain grassland ecosystem services

(2013) Karl Grigulis et al.   JOURNAL OF ECOLOGY

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Differences in the arbuscular mycorrhizal fungi-improved rice resistance to low temperature at two N levels: Aspects of N and C metabolism on the plant side

(2013) Zhi-Lei Liu et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen

(2012) Derrick E. Fouts et al.   PLoS One

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Can arbuscular mycorrhizal fungi improve grain yield, As uptake and tolerance of rice grown under aerobic conditions?

(2011) H. Li et al.   ENVIRONMENTAL POLLUTION

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS