title: Deciphering the Pathobiome: Intra- and Interkingdom Interactions Involving the Pathogen Erysiphe alphitoides.
abstract: Plant-inhabiting microorganisms interact directly with each other, forming complex microbial interaction networks. These interactions can either prevent or facilitate the establishment of new microbial species, such as a pathogen infecting the plant. Here, our aim was to identify the most likely interactions between Erysiphe alphitoides, the causal agent of oak powdery mildew, and other foliar microorganisms of pedunculate oak (Quercus robur L.). We combined metabarcoding techniques and a Bayesian method of network inference to decipher these interactions. Our results indicate that infection with E. alphitoides is accompanied by significant changes in the composition of the foliar fungal and bacterial communities. They also highlight 13 fungal operational taxonomic units (OTUs) and 13 bacterial OTUs likely to interact directly with E. alphitoides. Half of these OTUs, including the fungal endophytes Mycosphaerella punctiformis and Monochaetia kansensis, could be antagonists of E. alphitoides according to the inferred microbial network. Further studies will be required to validate these potential interactions experimentally. Overall, we showed that a combination of metabarcoding and network inference, by highlighting potential antagonists of pathogen species, could potentially improve the biological control of plant diseases.
authors.affiliation: BIOGECO, INRA, University of Bordeaux, F-33615, Bordeaux, Pessac, France.
authors.forename: Boris
authors.initials: B
authors.lastname: Jakuschkin
authors.affiliation: BIOGECO, INRA, University of Bordeaux, F-33615, Bordeaux, Pessac, France.
authors.forename: Virgil
authors.initials: V
authors.lastname: Fievet
authors.affiliation: AgroParisTech, UMR 518 MIA, F-75005, Paris, France.|INRA, UMR 518 MIA, F-75005, Paris, France.
authors.forename: Loïc
authors.initials: L
authors.lastname: Schwaller
authors.affiliation: BIOGECO, INRA, University of Bordeaux, F-33615, Bordeaux, Pessac, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Fort
authors.affiliation: BIOGECO, INRA, University of Bordeaux, F-33615, Bordeaux, Pessac, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Robin
authors.affiliation: BIOGECO, INRA, University of Bordeaux, F-33615, Bordeaux, Pessac, France. corinne.vacher@pierroton.inra.fr.
authors.forename: Corinne
authors.initials: C
authors.lastname: Vacher
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000472:pathogenicity; D001483:Base Sequence; D004271:DNA, Fungal / Q000235:genetics; D060467:Disease Resistance / Q000502:physiology; D056265:Microbial Interactions / Q000502:physiology*; D064307:Microbiota / Q000502:physiology; D010935:Plant Diseases / Q000382:microbiology*; D018515:Plant Leaves / Q000382:microbiology*; D029963:Quercus / Q000382:microbiology*; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal
keywords: Biocontrol; Disease resistance; Microbial network; Network inference; Pathobiome; Plant microbiota; Plant-pathogen interaction; Powdery mildew