| Summary: | Waste-based fertilizers provide an alternative to fertilizers made from non-renewable phosphate rock. Fungal communities colonizing the grain of spring wheat fertilized with preparation from sewage sludge ash and dried animal blood (Rec) and the same fertilizer activated by <i>Bacillus megaterium</i> (Bio) were evaluated against those resulting from superphosphate (SP) and no phosphorus (control, C0) treatments. The Illumina MiSeq sequencing system helped to group fungal communities into three clades. Clade 1 (communities from C0, Bio 60 and 80, Rec 80 and SP 40 kg P<sub>2</sub>O<sub>5</sub> ha<sup>−1</sup> treatments) was characterized by a high prevalence of <i>Alternaria infectoria</i>, <i>Monographella nivalis</i> and <i>Gibberella tricincta</i> pathogens. Clade 2 (Bio 40 kg, Rec 40 and 60 kg, and SP 60 kg P<sub>2</sub>O<sub>5</sub> ha<sup>−1</sup>) was characterized by the lowest amount of the identified pathogens. Commercial SP applied at 80 kg P<sub>2</sub>O<sub>5</sub> ha<sup>−1</sup> (clade 3) induced the most pronounced changes in the fungal taxa colonizing wheat grain relative to non-fertilized plants. The above was attributed mainly to the lower amount of <i>A. infectoria</i> and higher counts of species of the family <i>Nectriaceae</i>, mostly epiphytic pathogens <i>Fusarium culmorum</i> and <i>Fusarium poae</i>.
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