Root type and soil phosphate determine the taxonomic landscape of colonizing fungi and the transcriptome of field‐grown maize roots

Summary Different root types of plants are colonized by a myriad of soil microorganisms, including fungi, which influence plant health and performance. The distinct functional and metabolic characteristics of these root types may influence root type‐inhabiting fungal communities. We performed internal transcribed spacer ( ITS ) DNA profiling to determine the composition of fungal communities in field‐grown axial and lateral roots of maize ( Zea mays ) and in response to two different soil phosphate (P) regimes. In parallel, these root types were subjected to transcriptome profiling by RNA sequencing ( RNA ‐Seq). We demonstrated that fungal communities were influenced by soil P levels in a manner specific to root types. Moreover, maize transcriptome sequencing revealed root type‐specific shifts in cell wall metabolism and defense gene expression in response to high P. Furthermore, lateral roots specifically accumulated defense‐related transcripts at high P levels. This observation was correlated with a shift in fungal community composition, including a reduction in colonization by arbuscular mycorrhizal fungi, as observed in ITS sequence data and microscopic evaluation of root colonization. Our findings suggest soil nutrient‐dependent changes in functional niches within root systems and provide new insights into the interaction of individual root types with soil microbiota.