Background: Plants actively shape their associated microbial communities by synthesizing bio-active substances. Plant secondary metabolites are known for their signaling and plant defense functions, yet little is known about their overall effect on the plant microbiome. In this work, we studied the effects of benzoxazinoids (BXs), a group of secondary metabolites present in maize, on the host-associated microbial structure. Using BX knockout mutants and their W22 parental lines, we employed 16S and ITS2 rRNA gene amplicon analysis to characterize the maize microbiome at early growth stages. Results: Rhizo-box experiment showed that BXs affected microbial communities not only in roots and shoots, but also in the rhizosphere. Fungal richness in roots was more affected by BXs than root bacterial richness. Maize genotype (BX mutants and their parental lines) as well as plant age explained both fungal and bacterial community structure. Genotypic effect on microbial communities was stronger in roots than in rhizosphere. Diverse, but specific, microbial taxa were affected by BX in both roots and shoots, for instance, many plant pathogens were negatively correlated to BX content. In addition, a co-occurrence analysis of the root microbiome revealed that BXs affected specific groups of the microbiome. Conclusions: This study provides insights into the role of BXs for microbial community assembly in the rhizosphere and in roots and shoots. Coupling the quantification of BX metabolites with bacterial and fungal communities, we were able to suggest a gatekeeper role of BX by showing its correlation with specific microbial taxa and thus providing insights into effects on specific fungal and bacterial taxa in maize roots and shoots. Root microbial cooccurrence networks revealed that BXs affect specific microbial clusters.

Although the effects of plant secondary metabolites on plant defense have been studied for decades, the exact roles of secondary metabolites in shaping plant-associated microbial and nematode communities remain elusive. We evaluated the effects of benzoxazinoids (BXs), a group of secondary metabolites present in several cereals, on root-associated nematodes. We employed 18S rRNA metabarcoding to compare maize root-associated nematode communities in a bx1 knock-out maize line impaired in BX synthesis and in its parental wild type (WT). Both genotype and plant age affected nematode community composition in the roots, and the effects of BXs on nematode communities were higher in the roots compared to the rhizosphere. Differential abundance analysis and quantitative PCR showed that the root lesion nematode Pratylenchus neglectus was enriched in the bx1 mutant line, while another root lesion nematode Pratylenchus crenatus was reduced. Correlation analysis showed that BX contents in maize roots mostly correlated negatively with the relative abundance of nematode reads. However, positive correlations between BXs and nematode taxa, including several plant parasitic nematodes, were also identified. Our detailed nematode community analysis suggested differential and selective effects of BXs on soil nematodes depending on both the nematode species and BX compound.

Plant associated microbiomes are known to confer fitness advantages to the host. Understanding how plant factors including biochemical traits influence host associated microbiome assembly could facilitate the development of microbiome-mediated solutions for sustainable plant production. Here, we examined microbial community structures of a set of well-characterized Arabidopsis thaliana mutants disrupted in metabolic pathways for the production of glucosinolates, flavonoids, or a number of defense signalling molecules. A. thaliana lines were grown in a natural soil and maintained under greenhouse conditions for 4 weeks before collection of roots for bacterial and fungal community profiling. We found distinct relative abundances and diversities of bacterial and fungal communities assembled in the individual A. thaliana mutants compared to their parental lines. Bacterial and fungal genera were mostly enriched than depleted in secondary metabolite and defense signaling mutants, except for flavonoid mutations on fungi communities. Bacterial genera Azospirillum and Flavobacterium were significantly enriched in most of the glucosinolate, flavonoid and signalling mutants while the fungal taxa Sporobolomyces and Emericellopsis were enriched in several glucosinolates and signalling mutants. Whilst the present study revealed marked differences in microbiomes of Arabidopsis mutants and their parental lines, it is suggestive that unknown enzymatic and pleiotropic activities of the mutated genes could contribute to the identified host-associated microbiomes. Notwithstanding, this study revealed interesting gene-microbiota links, and thus represents valuable resource data for selecting candidate A. thaliana mutants for analyzing the links between host genetics and the associated microbiome.

Rice diterpenoid phytoalexins (DPs) are secondary metabolites with a well known role in resistance to foliar pathogens. As DPs are also known to be produced and exuded by rice roots, we hypothesised that they might play an important role in plant-nematode interactions, and particularly in defence against phytoparasitic nematodes.We used transcriptome analysis on rice roots to analyse the effect of infection by the rootknot nematode Meloidogyne graminicola or treatment with resistance-inducing chemical stimuli on DP biosynthesis genes, and assessed the susceptibility of mutant rice lines impaired in DP biosynthesis to M. graminicola. Moreover, we grew these mutants and their wild-type in field soil and used metabarcoding to assess the effect of impairment in DP biosynthesis on rhizosphere and root nematode communities.We show that M. graminicola suppresses DP biosynthesis genes early in its invasion process and, conversely, that resistance-inducing stimuli transiently induce the biosynthesis of DPs. Moreover, we show that loss of DPs increases susceptibility to M. graminicola. Metabarcoding on wild-type and DP-deficient plants grown in field soil reveals that DPs significantly alter the composition of rhizosphere and root nematode communities.Diterpenoid phytoalexins are important players in basal and inducible defence against nematode pathogens of rice and help shape rice-associated nematode communities.

Plant health and fitness are determined by plant-microbe interactions which are guided by host-synthesized metabolites. To understand the orchestration of this interaction, we analyzed the distinct interomic dynamics in resistant and susceptible Arabidopsis ecotypes across different time points after infection with Fusarium oxysporum (FOM).