**Magdalena Jastrz ˛ebska 1,\*, Urszula Wachowska <sup>2</sup> and Marta K. Kostrzewska <sup>1</sup>**


Received: 23 April 2020; Accepted: 17 June 2020; Published: 19 June 2020

**Abstract:** 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 *Bacillus megaterium* (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 P2O5 ha−<sup>1</sup> treatments) was characterized by a high prevalence of *Alternaria infectoria*, *Monographella nivalis* and *Gibberella tricincta* pathogens. Clade 2 (Bio 40 kg, Rec 40 and 60 kg, and SP 60 kg P2O5 ha−1) was characterized by the lowest amount of the identified pathogens. Commercial SP applied at 80 kg P2O5 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 *A. infectoria* and higher counts of species of the family *Nectriaceae*, mostly epiphytic pathogens *Fusarium culmorum* and *Fusarium poae*.

**Keywords:** *Alternaria*; *Fusarium*; Illumina MiSeq; secondary raw materials
