Host or pathogen primed bacterial consortia alters microbial community structures in Arabidopsis roots and suppresses Fusarium oxysporum

Abstract

Background: The plant-associated microbiota confers beneficial traits to the plant host that promote growth and prevents disease. It is, however, not fully understood how the host, and pathogens, modulate the assembly of the associated microbiota. In this work, we investigated the effects of inoculation with bacterial consortia (BCs) that had been primed with either the host plant Arabidopsis thaliana alone or by a combination of the host and the pathogen Fusarium oxysporum f. sp. mathioli (FOM), on the root-associated microbiota and FOM. We used 16S rRNA and ITS amplicon sequencing for profiling root bacterial and fungal communities, respectively. qPCR was employed for the assessment of FOM quantities in the shoots of Arabidopsis. Results: Our results showed distinct effects of host or pathogen primed BCs on microbial community structures and networks. The host-primed BCs inhibited FOM proliferation in shoots, distinctively affected rhizo-microbial community structures and further enhanced the connectivity of the microbial networks. Beneficial bacterial genera including Flavobacterium, Azospirillum, Massilia and Pedobacter were significant biomarkers in the samples inoculated with host-primed BCs and could potentially be involved in FOM antagonism. Likewise, FOM-primed BCs reduced FOM in the shoots of Arabidopsis and altered microbial networks. Bacterial taxa Bacteriodetes, Flavobacterium and Chthoniabacteraceae and the fungal, Exophiala and Phaeosphaeriaceae were the most enriched biomarker taxa in the samples treated with FOM-primed BCs. Moreover, the host genotype effect was significant in overall microbial community network structuring and could contribute to resistance to FOM pathogens. Conclusions: Altogether, these findings deepen our understanding of both host- and pathogen-priming on plant-associated microbiomes, thus, revealing pivotal engineering routes in exploring microbiomes to manage plant diseases.