Genomic features of bacterial adaptation to plants

Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens

(2016) Panagiotis F. Sarris et al.   BMC BIOLOGY

Polarized Defense Against Fungal Pathogens Is Mediated by the Jacalin-Related Lectin Domain of Modular Poaceae -Specific Proteins

(2016) Denise Weidenbach et al.   Molecular Plant

Bacterial pathogenesis of plants: future challenges from a microbial perspective

(2016) Sebastian Pfeilmeier et al.   MOLECULAR PLANT PATHOLOGY

Swimming and twitching motility are essential for attachment and virulence of Pantoea ananatis in onion seedlings

(2016) Tania Weller-Stuart et al.   MOLECULAR PLANT PATHOLOGY

Elucidation of gibberellin biosynthesis in bacteria reveals convergent evolution

(2016) Ryan S Nett et al.   Nature Chemical Biology

Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread

(2016) Thomas Kroj et al.   NEW PHYTOLOGIST

Chemotaxis signaling systems in model beneficial plant–bacteria associations

(2016) Birgit E. Scharf et al.   PLANT MOLECULAR BIOLOGY

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone

(2016) Stilianos Louca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Genome-Wide RNA Sequencing Analysis of Quorum Sensing-Controlled Regulons in the Plant-Associated Burkholderia glumae PG1 Strain

(2015) Rong Gao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Receptor Pair with an Integrated Decoy Converts Pathogen Disabling of Transcription Factors to Immunity

(2015) Clémentine Le Roux et al.   CELL

A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors

(2015) Panagiotis F. Sarris et al.   CELL

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

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

Microbiota and Host Nutrition across Plant and Animal Kingdoms

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

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

(2015) Pablo R. Hardoim et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Plant-Influenced Gene Expression in the Rice Endophyte Burkholderia kururiensis M130

(2015) Bruna G. Coutinho et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

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

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

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: 2015 update

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

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

IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites

(2015) Michalis Hadjithomas et al.   mBio

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

(2015) Marcel Huntemann et al.   Standards in Genomic Sciences

Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42 – a review

(2015) Soumitra Paul Chowdhury et al.   Frontiers in Microbiology

Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov.

(2014) A. Sen et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The type VI protein secretion system contributes to biofilm formation and seed-to-seedling transmission ofAcidovorax citrullion melon

(2014) Yanli Tian et al.   MOLECULAR PLANT PATHOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Niche and host-associated functional signatures of the root surface microbiome

(2014) Maya Ofek-Lalzar et al.   Nature Communications

A novel conserved mechanism for plant NLR protein pairs: the “integrated decoy” hypothesis

(2014) Stella Cesari et al.   Frontiers in Plant Science

Structure and Functions of the Bacterial Microbiota of Plants

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

Tit-for-Tat: Type VI Secretion System Counterattack during Bacterial Cell-Cell Interactions

(2013) Marek Basler et al.   CELL

A View to a Kill: The Bacterial Type VI Secretion System

(2013) Brian T. Ho et al.   Cell Host & Microbe

AmphoraNet: The webserver implementation of the AMPHORA2 metagenomic workflow suite

(2013) Csaba Kerepesi et al.   GENE

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

(2013) Thomas R Turner et al.   ISME Journal

Functional Conservation of the Capacity for ent-Kaurene Biosynthesis and an Associated Operon in Certain Rhizobia

(2013) D. M. Hershey et al.   JOURNAL OF BACTERIOLOGY

A Phylum-Level Bacterial Phylogenetic Marker Database

(2013) Zhang Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

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

Unexpected Diversity during Community Succession in the Apple Flower Microbiome

(2013) A. Shade et al.   mBio

Activation of Ran GTPase by a Legionella Effector Promotes Microtubule Polymerization, Pathogen Vacuole Motility and Infection

(2013) Eva Rothmeier et al.   PLoS Pathogens

Global abundance of microbial rhodopsins

(2012) Omri M Finkel et al.   ISME Journal

Pseudomonas fluorescensInduces Strain-Dependent and Strain-Independent Host Plant Responses in Defense Networks, Primary Metabolism, Photosynthesis, and Fitness

(2012) David J. Weston et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

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

Lectin-Mediated Resistance Impairs Plant Virus Infection at the Cellular Level

(2012) Y. Yamaji et al.   PLANT CELL

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

Key physiological properties contributing to rhizosphere adaptation and plant growth promotion abilities of Azospirillum brasilense

(2011) Sharon Fibach-Paldi et al.   FEMS MICROBIOLOGY LETTERS

A jacalin-related lectin-like gene in wheat is a component of the plant defence system

(2011) Yang Xiang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network

(2011) M. S. Mukhtar et al.   SCIENCE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Average genome size: a potential source of bias in comparative metagenomics

(2010) Bánk Beszteri et al.   ISME Journal

NADPH-dependent Reductases Involved in the Detoxification of Reactive Carbonyls in Plants

(2010) Yasuo Yamauchi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Vibrio cholerae type VI secretion system displays antimicrobial properties

(2010) D. L. MacIntyre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved Fungal LysM Effector Ecp6 Prevents Chitin-Triggered Immunity in Plants

(2010) R. de Jonge et al.   SCIENCE

Diazotrophic endophytes of native black cottonwood and willow

(2010) Sharon L. Doty et al.   SYMBIOSIS

Overexpression of a wheat jasmonate-regulated lectin increases pathogen resistance

(2009) Qing-Hu Ma et al.   BIOCHIMIE

Type III Protein Secretion in Plant Pathogenic Bacteria

(2009) D. Buttner et al.   PLANT PHYSIOLOGY

Phylogenetic Logistic Regression for Binary Dependent Variables

(2009) Anthony R. Ives et al.   SYSTEMATIC BIOLOGY

Genome-Scale Identification of Legionella pneumophila Effectors Using a Machine Learning Approach

(2009) David Burstein et al.   PLoS Pathogens

Molecular Mimicry by an F-Box Effector of Legionella pneumophila Hijacks a Conserved Polyubiquitination Machinery within Macrophages and Protozoa

(2009) Christopher T. Price et al.   PLoS Pathogens

60Ma of legume nodulation. What's new? What's changing?

(2008) J. I. Sprent   JOURNAL OF EXPERIMENTAL BOTANY

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY