The role of long-term mineral and organic fertilisation treatment in changing pathogen and symbiont community composition in soil. The effect of fertilisation on fungal communities

Application of organic fertilisers prevents soil degradation, improves soil fertility and may suppress certain plant pathogens in soil, but it is still unclear how pathogen community composition responds to long-term fertilisation treatment. Therefore, the objective of the study was to examine the effect of nitrogen fertilisation (WOM), nitrogen fertilisation with manure amendment (FYM) and alternative organic fertilisation (AOF) on fungal and oomycete pathogen and mycorrhizal symbiont diversity and community structure in both soil and roots. Each fertiliser treatment was applied at five different rates. Soil samples were collected three times during the growing season, while the root samples were collected during the flowering stage. The community composition was analysed using PacBio SMRT sequencing with three forward primers ITS1ngs, ITS1Fngs and ITS1Oo, in combination with a reverse primer ITS4ngs. Results revealed no influence of studied variables on soil and root pathogen richness. Contrary to our hypothesis, pathogen relative abundance in both soil and roots was significantly higher in plots with the AOF treatment. Furthermore, richness and relative abundance of arbuscular mycorrhizal (AM) fungi decreased significantly in the AOF treatment. Permutational analysis of variance (PERMANOVA) demonstrated the effect of fertilisation treatment on pathogen community composition in both soil and roots. Our findings indicate that organic fertilisers may not always benefit soil microbial community composition. Therefore, further studies are needed to provide understanding of how fertilisation affects different functional fungal and oomycetes groups in both soil and roots.