Disease-induced changes in plant microbiome assembly and functional adaptation

Environmental stress destabilizes microbial networks

(2021) Damian J. Hernandez et al.   ISME Journal

Rhizosphere community selection reveals bacteria associated with reduced root disease

(2021) Chuntao Yin et al.   Microbiome

Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics

(2020) Cheng Gao et al.   Nature Communications

Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

(2020) Antonio J. Fernández-González et al.   Microbiome

Harnessing rhizosphere microbiomes for drought-resilient crop production

(2020) Franciska T. de Vries et al.   SCIENCE

Microbiome-Mediated Stress Resistance in Plants

(2020) Hongwei Liu et al.   TRENDS IN PLANT SCIENCE

Competition for iron drives phytopathogen control by natural rhizosphere microbiomes

(2020) Shaohua Gu et al.   Nature Microbiology

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt

(2020) Jun Yuan et al.   ISME Journal

Plant–microbiome interactions: from community assembly to plant health

(2020) Pankaj Trivedi et al.   NATURE REVIEWS MICROBIOLOGY

Abundance of kinless hubs within soil microbial networks are associated with high functional potential in agricultural ecosystems

(2020) Yu Shi et al.   ENVIRONMENT INTERNATIONAL

Rare taxa maintain the stability of crop mycobiomes and ecosystem functions

(2020) Chao Xiong et al.   ENVIRONMENTAL MICROBIOLOGY

Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease

(2020) Sang-Moo Lee et al.   ISME Journal

Host selection shapes crop microbiome assembly and network complexity

(2020) Chao Xiong et al.   NEW PHYTOLOGIST

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

(2020) Shingo Miyauchi et al.   Nature Communications

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

(2020) Chengyuan Tao et al.   Microbiome

Evidence for the plant recruitment of beneficial microbes to suppress soil‐borne pathogens

(2020) Hongwei Liu et al.   NEW PHYTOLOGIST

Organism body size structures the soil microbial and nematode community assembly at a continental and global scale

(2020) Lu Luan et al.   Nature Communications

Host-microbiota interactions: from holobiont theory to analysis

(2019) Jean-Christophe Simon et al.   Microbiome

Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases

(2019) Heather Armstrong et al.   Microbiome

An Ecological Loop: Host Microbiomes across Multitrophic Interactions

(2019) Hongwei Liu et al.   TRENDS IN ECOLOGY & EVOLUTION

Initial soil microbiome composition and functioning predetermine future plant health

(2019) Zhong Wei et al.   Science Advances

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

(2019) Víctor J. Carrión et al.   SCIENCE

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

(2019) Keara L. Grady et al.   Nature Communications

Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

(2019) Cameron Wagg et al.   Nature Communications

The Soil-Borne Legacy

(2018) Peter A.H.M. Bakker et al.   CELL

Calling from distance: attraction of soil bacteria by plant root volatiles

(2018) Kristin Schulz-Bohm et al.   ISME Journal

Disease-induced assemblage of a plant-beneficial bacterial consortium

(2018) Roeland L. Berendsen et al.   ISME Journal

Phyllosphere microbiology: at the interface between microbial individuals and the plant host

(2018) Mitja N. P. Remus-Emsermann et al.   NEW PHYTOLOGIST

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

Microbial interactions within the plant holobiont

(2018) M. Amine Hassani et al.   Microbiome

Network hubs in root-associated fungal metacommunities

(2018) Hirokazu Toju et al.   Microbiome

The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome

(2018) M. A. Cregger et al.   Microbiome

Soil bacterial networks are less stable under drought than fungal networks

(2018) Franciska T. de Vries et al.   Nature Communications

Root exudates drive the soil-borne legacy of aboveground pathogen infection

(2018) Jun Yuan et al.   Microbiome

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

(2018) Paloma Durán et al.   CELL

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Current status of Fusarium oxysporum formae speciales and races

(2018) Véronique Edel-Hermann et al.   PHYTOPATHOLOGY

Influence of resistance breeding in common bean on rhizosphere microbiome composition and function

(2017) Lucas William Mendes et al.   ISME Journal

Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere

(2017) Franciska T. de Vries et al.   JOURNAL OF ECOLOGY

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity

(2017) Sigrid Dassen et al.   MOLECULAR ECOLOGY

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships

(2017) Isabelle Laforest-Lapointe et al.   NATURE

Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria

(2017) Francis M. Martin et al.   SCIENCE

Bio-fertilizer application induces soil suppressiveness against Fusarium wilt disease by reshaping the soil microbiome

(2017) Wu Xiong et al.   SOIL BIOLOGY & BIOCHEMISTRY

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

Escherichia colibiofilm: development and therapeutic strategies

(2016) G. Sharma et al.   JOURNAL OF APPLIED MICROBIOLOGY

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Etiological and epidemiological concerns about Pepper root and lower stem rot caused by Fusarium oxysporum f. sp. radicis-capsici f. sp. nova

(2016) Tomás Lomas-Cano et al.   PHYTOPARASITICA

The sapro-rhizosphere: Carbon flow from saprotrophic fungi into fungus-feeding bacteria

(2016) Max-Bernhard Ballhausen et al.   SOIL BIOLOGY & BIOCHEMISTRY

Engineering the Rhizosphere

(2016) Yves Dessaux et al.   TRENDS IN PLANT SCIENCE

Modularity and stability in ecological communities

(2016) Jacopo Grilli et al.   Nature Communications

Microbial diversity drives multifunctionality in terrestrial ecosystems

(2016) Manuel Delgado-Baquerizo et al.   Nature Communications

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

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

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure

(2016) Isabelle Laforest-Lapointe et al.   Microbiome

phoDAlkaline Phosphatase Gene Diversity in Soil

(2015) Sabine A. Ragot et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbiota and Host Nutrition across Plant and Animal Kingdoms

(2015) Stéphane Hacquard et al.   Cell Host & Microbe

In vivo toxicity studies of fusarium mycotoxins in the last decade: A review

(2015) L. Escrivá et al.   FOOD AND CHEMICAL TOXICOLOGY

Fungal invasion of the rhizosphere microbiome

(2015) Emilie Chapelle et al.   ISME Journal

A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment

(2015) Marcel GA van der Heijden et al.   ISME Journal

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse 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

Phytophthoraeffector targets a novel component of small RNA pathway in plants to promote infection

(2015) Yongli Qiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Pseudomonaschemotaxis

(2014) Inmaculada Sampedro et al.   FEMS MICROBIOLOGY REVIEWS

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Comparison of phloem and xylem hydraulic architecture inPicea abiesstems

(2014) Tuula Jyske et al.   NEW PHYTOLOGIST

Soil biodiversity and soil community composition determine ecosystem multifunctionality

(2014) C. Wagg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

(2014) S. W. Kembel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and Functions of the Bacterial Microbiota of Plants

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

The UDP-glucuronosyltransferases: Their role in drug metabolism and detoxification

(2013) Andrew Rowland et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

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

Ecological determinism increases with organism size

(2012) Vinicius F. Farjalla et al.   ECOLOGY

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

A general and simple method for obtainingR2from generalized linear mixed-effects models

(2012) Shinichi Nakagawa et al.   Methods in Ecology and Evolution

High plant diversity is needed to maintain ecosystem services

(2011) Forest Isbell et al.   NATURE

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Shifts in metabolic scaling, production, and efficiency across major evolutionary transitions of life

(2010) J. P. DeLong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Pathogen profile update:Fusarium oxysporum

(2009) CAROLINE B. MICHIELSE et al.   MOLECULAR PLANT PATHOLOGY

Evolutionary ecology of pungency in wild chilies

(2008) J. J. Tewksbury et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA