The Interaction between Rice Genotype and Magnaporthe oryzae Regulates the Assembly of Rice Root-Associated Microbiota

Abstract

Background Utilizating the plant microbiome to enhance pathogen resistance in crop production is an emerging alternative to the use of chemical pesticides. However, the diversity and structure of the microbiota, and the assembly mechanisms of root-associated microbial communities of plants are still poorly understood. Results We invstigated the microbiota of the root endosphere and rhizosphere soils of the rice cultivar Nipponbare (NPB) and its Piz-t-transgenic line (NPB-Piz-t) when infected with the filamentous fungus Magnaporthe oryzae (M. oryzae) isolate KJ201, using 16S rRNA and internal transcribed spacer 1 (ITS1) amplicon sequencing. The rhizosphere soils showed higher bacterial and fungal richness and diversity than the endosphere except for fungal richness in the rhizosphere soils of the mock treatment. Bacteria richness and diversity increased in the endospheric communities of NPB and Piz-t under inoculation with KJ201 (referred to as ‘NPB-KJ201’ and ‘Piz-t-KJ201’, respectively) compared with the corresponding mock treatments, with the NPB-KJ201 showing the highest diversity in the four bacterial endocompartments. In contrast, fungal richness and diversity decreased in the endospheric communities of NPB-KJ201 and Piz-t-KJ201, relative to the corresponding mock treatments, with NPB-KJ201 and Piz-t-KJ201 having the lowest richness and diversity, respectively, across the four fungal endocompartments. Principal component analysis (PCA) indicated that the microbiota of Piz-t-KJ201 of root endophytes were mostly remarkablely distinct from that of NPB-KJ201. Co-occurrence network analysis revealed that the phyla Proteobacteria and Ascomycota were the key contributors to the bacterial and fungal communities, respectively. Furthermore, a comparative metabolic analysis showed that the contents of tryptophan metabolism and indole alkaloid biosynthesis were significantly lower in the Piz-t-KJ201 plants. Conclusions In this study, we compared the diversity, composition, and assembly of microbial communities associated with the rhizosphere soils and endosphere of Piz-t-KJ201 and NPB-KJ201. On the basis of the different compositions, diversities, and assemblies of the microbial communities among different compartments, we propose that the host genotype and inoculation pattern of M. oryzae played dominant roles in determining the microbial community assemblage. Further metabolomics analysis revealed that some metabolites may influence changes in bacterial communities. This study improves our understanding of the complex interactions between rice and M. oryzae, which could be useful in developing new strategies to improve rice resistance through the manipulation of soil microorganisms.

The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer’s fields in western Burkina Faso

“…2017 for rice blast). On the other hand, disease was shown to affect root-associated microbiomes, with for example the effect of Magnaporthe grisea inoculation on microbial endosphere diversity (Tian et al . 2021).…”

The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso

“…In rice, various studies evidenced an inhibition of disease development by root-associated micro-organisms (see Yasmin et al 2016 for bacterial diseases;and Spence et al 2014;Law et al 2017 for rice blast). On the other hand, disease was shown to affect root-associated microbiomes, with for example the effect of Magnaporthe grisea inoculation on microbial endosphere diversity (Tian et al 2021). A promising avenue of research is consequently to investigate the relationship between root-associated microbiota and rice diseases in the particular ricegrowing systems of Burkina Faso.…”

Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system

“…In addition, several species of archaea, oomycetes, and other microbial species play crucial roles in mediating diverse ecosystem activities and other ecological functions that balance soil health and productivity ( Wang et al, 2017 , 2021b ), and bacterial and fungal species have been observed to play leading roles under certain conditions. Generally, bacterial communities during differential soil conditions under the paddy system are mainly dominated by Proteobacteria , Chloroflexi , Actinobacteria , and Acidobacteria , whereas the dominant fungal communities include Ascomycota , Basidiomycota , and Glomeromycota ( Yuan et al, 2019 ; Tian et al, 2021 ).…”