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Summary  Cassava is one of the most important staple food crops in tropical regions. To date, an understanding of the relationship between microbial communities and disease resistance in cassava has remained elusive. In order to explore the relationship among microbiome and phenotypes for further targeted design of microbial community, 16S rRNA and ITS of microbiome of ten cassava varieties were analysed, and a distinctive microbial community in the rhizosphere showed significant interdependence with disease resistance. Shotgun metagenome sequencing was performed to elucidate the structure of microbiomes of cassava rhizosphere. Comprehensive microbiome studies were performed to assess the correlation between the rhizosphere microbiome and disease resistance. Subsequently, the metagenome of rhizosphere microbiome was annotated to obtain taxonomic information at species level and identify metabolic pathways that were significantly associated with cassava disease resistance. Notably, cassava disease resistance was significantly associated with  Lactococcus  sp., which specifically produces nisin. To definitively explain the role of nisin and underlying mechanism, analysis of nisin biosynthesis‐associated genes together with  in vitro  and  in vivo  experiments highlighted the effect of nisin on inhibiting the growth of  Xanthomonas axonopodis  pv.  manihotis  ( Xam ) and activating immune response in cassava. The new insights between cassava rhizosphere microbiome especially  Lactococcus  sp. and disease resistance provide valuable information into further control of cassava disease.

plant biotechnology journal

Microbiome‐wide association studies reveal correlations between the structure and metabolism of the rhizosphere microbiome and disease resistance in cassava