title: Deciphering the rhizosphere microbiome for disease-suppressive bacteria.
abstract: Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms. For most disease-suppressive soils, the microbes and mechanisms involved in pathogen control are unknown. By coupling PhyloChip-based metagenomics of the rhizosphere microbiome with culture-dependent functional analyses, we identified key bacterial taxa and genes involved in suppression of a fungal root pathogen. More than 33,000 bacterial and archaeal species were detected, with Proteobacteria, Firmicutes, and Actinobacteria consistently associated with disease suppression. Members of the γ-Proteobacteria were shown to have disease-suppressive activity governed by nonribosomal peptide synthetases. Our data indicate that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections.
authors.affiliation: Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen 6700 EE, Netherlands.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Mendes
authors.forename: Marco
authors.initials: M
authors.lastname: Kruijt
authors.forename: Irene
authors.initials: I
authors.lastname: de Bruijn
authors.forename: Ester
authors.initials: E
authors.lastname: Dekkers
authors.forename: Menno
authors.initials: M
authors.lastname: van der Voort
authors.forename: Johannes H M
authors.initials: JH
authors.lastname: Schneider
authors.forename: Yvette M
authors.initials: YM
authors.lastname: Piceno
authors.forename: Todd Z
authors.initials: TZ
authors.lastname: DeSantis
authors.forename: Gary L
authors.initials: GL
authors.lastname: Andersen
authors.forename: Peter A H M
authors.initials: PA
authors.lastname: Bakker
authors.forename: Jos M
authors.initials: JM
authors.lastname: Raaijmakers
mesh_terms: D039903:Actinobacteria / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D000898:Antibiosis; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D027461:Beta vulgaris / Q000382:microbiology; D054892:Metagenome; D059013:Microbial Consortia; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010453:Peptide Synthases / Q000235:genetics / Q000378:metabolism; D010935:Plant Diseases / Q000382:microbiology / Q000517:prevention & control*; D018517:Plant Roots / Q000382:microbiology; D020560:Proteobacteria / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D011548:Pseudomonadaceae / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D012232:Rhizoctonia / Q000502:physiology*; D058441:Rhizosphere; D012988:Soil Microbiology
chemical_list: D010453:Peptide Synthases; C104385:non-ribosomal peptide synthase