Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10× metagenomics

Vittorio Tracanna, Adam Ossowicki, Marloes L.C. Petrus, Sam Overduin, Barbara R. Terlouw, George Lund, Serina L. Robinson, Sven Warris, Elio G.W.M. Schijlen, Gilles P. Van Wezel, Jos M. Raaijmakers, Paolina Garbeva*, Marnix H. Medema*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

26 Citations (Scopus)

Abstract

Disease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10x metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotype.

Original languageEnglish
Article numbere01116-20
JournalmSystems
Volume6
Issue number3
DOIs
Publication statusPublished - 8 Jun 2021

Keywords

  • 10x metagenomics
  • Biosynthetic gene cluster
  • Disease suppression
  • Dom2BGC
  • Functional amplicon
  • Fusarium
  • Nonribosomal peptide synthetase
  • Pathogenic fungi
  • Rhizosphere
  • Siderophores
  • Software
  • Suppressive soils
  • Wheat

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