Many plants have natural partnerships with microbes that can boost their nitrogen (N) and/or phosphorus (P) acquisition. To assess whether wheat may have undiscovered associations of these types, we tested if N/P-starved
Triticum aestivum
show microbiome profiles that are simultaneously different from those of N/P-amended plants and those of their own bulk soils. The bacterial and fungal communities of root, rhizosphere, and bulk soil samples from the Historical Dryland Plots (Lethbridge, Canada), which hold
T
.
aestivum
that is grown both under N/P fertilization and in conditions of extreme N/P-starvation, were taxonomically described and compared (bacterial 16S rRNA genes and fungal Internal Transcribed Spacers—ITS). As the list may include novel N- and/or P-providing wheat partners, we then identified all the operational taxonomic units (OTUs) that were proportionally enriched in one or more of the nutrient starvation- and plant-specific communities. These analyses revealed: a) distinct N-starvation root and rhizosphere bacterial communities that were proportionally enriched, among others, in OTUs belonging to families
Enterobacteriaceae
,
Chitinophagaceae
,
Comamonadaceae
,
Caulobacteraceae
,
Cytophagaceae
,
Streptomycetaceae
, b) distinct N-starvation root fungal communities that were proportionally enriched in OTUs belonging to taxa
Lulworthia
,
Sordariomycetes
,
Apodus
,
Conocybe
,
Ascomycota
,
Crocicreas
, c) a distinct P-starvation rhizosphere bacterial community that was proportionally enriched in an OTU belonging to genus
Agrobacterium
, and d) a distinct P-starvation root fungal community that was proportionally enriched in OTUs belonging to genera
Parastagonospora
and
Phaeosphaeriopsis
. Our study might have exposed wheat-microbe connections that can form the basis of novel complementary yield-boosting tools.