Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

(2019) Johanna Nelkner et al.   Genes

Secondary metabolites of fluorescent pseudomonads in biocontrol of phytopathogens for sustainable agriculture

(2018) Jitendra Mishra et al.   APPLIED SOIL ECOLOGY

Assembly, structure, function and regulation of type III secretion systems

(2017) Wanyin Deng et al.   NATURE REVIEWS MICROBIOLOGY

Comprehensive classification of the PIN domain-like superfamily

(2017) Dorota Matelska et al.   NUCLEIC ACIDS RESEARCH

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

(2017) Claire Bertelli et al.   NUCLEIC ACIDS RESEARCH

Isolation and characterization of Bacillus altitudinis JSCX-1 as a new potential biocontrol agent against Phytophthora sojae in soybean [Glycine max (L.) Merr.]

(2017) Xiaoxue Lu et al.   PLANT AND SOIL

Complete genome sequence of Pseudomonas brassicacearum strain L13-6-12, a biological control agent from the rhizosphere of potato

(2017) Christin Zachow et al.   Standards in Genomic Sciences

Microbial Phosphorus Solubilization and Its Potential for Use in Sustainable Agriculture

(2017) Elizabeth T. Alori et al.   Frontiers in Microbiology

In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas

(2017) Phuong N. Tran et al.   Frontiers in Microbiology

Bacterial GCN5-Related N-Acetyltransferases: From Resistance to Regulation

(2016) Lorenza Favrot et al.   BIOCHEMISTRY

Gram-positive bacterial cell envelopes: The impact on the activity of antimicrobial peptides

(2016) Nermina Malanovic et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

ReadXplorer 2—detailed read mapping analysis and visualization from one single source

(2016) Rolf Hilker et al.   BIOINFORMATICS

Quantification of antifungal lipopeptide gene expression levels in Bacillus subtilis B1 during antagonism against sapstain fungus on rubberwood

(2016) K.L. Sajitha et al.   BIOLOGICAL CONTROL

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

(2016) Michele Perazzolli et al.   BMC GENOMICS

Overlapping riboflavin supply pathways in bacteria

(2016) Víctor Antonio García-Angulo   CRITICAL REVIEWS IN MICROBIOLOGY

EDGAR 2.0: an enhanced software platform for comparative gene content analyses

(2016) Jochen Blom et al.   NUCLEIC ACIDS RESEARCH

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees

(2016) Zilong He et al.   NUCLEIC ACIDS RESEARCH

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Signaling in the Rhizosphere

(2016) Vittorio Venturi et al.   TRENDS IN PLANT SCIENCE

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

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

Integrative and Conjugative Elements (ICEs): What They Do and How They Work

(2015) Christopher M. Johnson et al.   Annual Review of Genetics

Biocontrol of the Potato Blackleg and Soft Rot Diseases Caused by Dickeya dianthicola

(2015) Yannick Raoul des Essarts et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Breaking a pathogen's iron will: Inhibiting siderophore production as an antimicrobial strategy

(2015) Audrey L. Lamb   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Characterization of the antifungal and plant growth-promoting effects of diffusible and volatile organic compounds produced by Pseudomonas fluorescens strains

(2015) Rocío Hernández-León et al.   BIOLOGICAL CONTROL

Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species

(2015) Morgane Rossi-Tamisier et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

(2015) Magali Lescot et al.   ISME Journal

Genetic and biochemical characterization of arginine biosynthesis in Sinorhizobium meliloti 1021

(2015) Victor M. Hernández et al.   MICROBIOLOGY-SGM

Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing

(2015) Areski Flissi et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Nonribosomal Peptides, Key Biocontrol Components for Pseudomonas fluorescens In5, Isolated from a Greenlandic Suppressive Soil

(2015) Charlotte F. Michelsen et al.   mBio

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

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

Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds

(2015) Menno Van Der Voort et al.   Frontiers in Microbiology

Rhizosphere ecology of lumichrome and riboflavin, two bacterial signal molecules eliciting developmental changes in plants

(2015) Felix D. Dakora et al.   Frontiers in Plant Science

Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species

(2015) Ana Gutiérrez-Preciado et al.   PLoS One

Induced Systemic Resistance by Beneficial Microbes

(2014) Corné M.J. Pieterse et al.   Annual Review of Phytopathology

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

Distinct soil microbial diversity under long-term organic and conventional farming

(2014) Martin Hartmann et al.   ISME Journal

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

(2014) Chengwei Luo et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Transcriptional responses of the bacterial antagonistSerratia plymuthicato the fungal phytopathogenRhizoctonia solani

(2014) Saraswoti Neupane et al.   Environmental Microbiology Reports

A new NAD(H)-dependent meso-2,3-butanediol dehydrogenase from an industrially potential strain Serratia marcescens H30

(2013) Liaoyuan Zhang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides

(2013) Auke J. van Heel et al.   NUCLEIC ACIDS RESEARCH

The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

(2013) Jin Duan et al.   PLoS One

Effects of Bacillus amyloliquefaciens FZB42 on Lettuce Growth and Health under Pathogen Pressure and Its Impact on the Rhizosphere Bacterial Community

(2013) Soumitra Paul Chowdhury et al.   PLoS One

Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria

(2013) Bryan Troxell et al.   Frontiers in Cellular and Infection Microbiology

Corynebacterium glutamicumpromoters: a practical approach

(2013) Miroslav Pátek et al.   Microbial Biotechnology

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

(2012) Brian J Haas et al.   BMC GENOMICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Isolation and characterization of Pseudomonas brassicacearum J12 as an antagonist against Ralstonia solanacearum and identification of its antimicrobial components

(2012) Tiantian Zhou et al.   MICROBIOLOGICAL RESEARCH

Production of DAPG and HCN byPseudomonassp. LBUM300 Contributes to the Biological Control of Bacterial Canker of Tomato

(2012) Carine Lanteigne et al.   PHYTOPATHOLOGY

HAD hydrolase function unveiled by substrate screening: enzymatic characterization of Arabidopsis thaliana subclass I phosphosugar phosphatase AtSgpp

(2012) José A. Caparrós-Martín et al.   PLANTA

Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions

(2012) Joyce E. Loper et al.   PLoS Genetics

Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review

(2011) Rogier F. Doornbos et al.   Agronomy for Sustainable Development

Plant growth promoting rhizobacteria as alternative to chemical crop protectors from pathogens (review)

(2011) I. V. Maksimov et al.   APPLIED BIOCHEMISTRY AND MICROBIOLOGY

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Complete Genome Sequence of a Beneficial Plant Root-Associated Bacterium, Pseudomonas brassicacearum

(2011) P. Ortet et al.   JOURNAL OF BACTERIOLOGY

The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

(2010) S. Sri Krishna et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Recent advances in siderophore biosynthesis

(2009) Sarah M Barry et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Mqo, a Tricarboxylic Acid Cycle Enzyme, Is Required for Virulence of Pseudomonas syringae pv. tomato Strain DC3000 on Arabidopsis thaliana

(2009) E. M. Mellgren et al.   JOURNAL OF BACTERIOLOGY

Pseudomonas fluorescensand closely-related fluorescent pseudomonads as biocontrol agents of soil-borne phytopathogens

(2009) O. Couillerot et al.   LETTERS IN APPLIED MICROBIOLOGY

A Toxin–Antitoxin System Promotes the Maintenance of an Integrative Conjugative Element

(2009) Rachel A. F. Wozniak et al.   PLoS Genetics

The pyrroloquinoline quinone biosynthesis pathway revisited: A structural approach

(2008) Sandra Puehringer et al.   BMC BIOCHEMISTRY

Effect of bacterial antagonists on lettuce: active biocontrol of Rhizoctonia solani and negligible, short-term effects on nontarget microorganisms

(2008) Katja Scherwinski et al.   FEMS MICROBIOLOGY ECOLOGY

Inactivation ofpqqgenes ofEnterobacter intermedium60-2G reduces antifungal activity and induction of systemic resistance

(2008) Song Hee Han et al.   FEMS MICROBIOLOGY LETTERS

The plant pathogenic fungus Gaeumannomyces graminis var. tritici improves bacterial growth and triggers early gene regulations in the biocontrol strain Pseudomonas fluorescens Pf29Arp

(2008) M. Barret et al.   NEW PHYTOLOGIST

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Functional analysis of aromatic biosynthetic pathways inPseudomonas putidaKT2440

(2008) M. Antonia Molina-Henares et al.   Microbial Biotechnology

Type III secretion in plant growth-promoting Pseudomonas fluorescens SBW25

(2003) Gail M. Preston et al.   MOLECULAR MICROBIOLOGY