Short-term soil amendment by sewage sludge anaerobic digestate in a tomato monoculture suppresses Fusarium vascular wilt disease by changing the taxonomic characteristics of soil microbiota

Digestate incorporation into topsoil determines soil fertility improvement by changing composition and structure of soil microbiota. However, how microbiota responds to short-term soil amendment by sewage sludge anaerobic digestate (SSD) for suppressing Fusarium vascular wilt disease is unknown. This study compares the effects of three SSD-based treatments to suppress Fusarium oxysporum f. sp. lycopersici (Fol) in a long-term cherry tomato monoculture under field condition in a 3-year trial. Three sampling sites with two application times (two bulk soils at 3–12 weeks after amendment and one tomato rhizosphere soil at 12 weeks post-amendment) were chosen. Three digestate typologies (liquid, centrifuged, and dried) having physicochemical features and heavy metals content below the legal limits were tested at 50 l, 3.5 kg and 2.5 kg m−2y−1 dose, respectively. Fusarium wilt disease was measured for three consecutive years by severity index and Fol abundance in tomato vascular tissue was assessed by ITS rDNA gene sequencing. Fol abundance and taxonomic structure of Fusarium community in the rhizosphere were determined at specie level at the end of the trial by ITS rDNA and EF1α rDNA genes sequencing, respectively. The taxonomic structure (α-, β-diversity) of soil bacterial community (SBC) was characterized from phylum up to genus level at the end of the trial in all the sites by 16S rRNA gene sequencing. The results showed that dry SSD reduced disease severity in field up to 18 % and Fol abundance in tomato up to 0.9 ITS copies g−1 tissue. Fol abundance was decreased in the rhizosphere up to 0.0027 ng μl−1 DNA, while the Fusarium community shifted between treated-soils and un-amended. The SBC composition (α-diversity) changed in the rhizosphere by applying dry digestate, while the SBC structure (β-diversity) shifted either among treatments or sites. Bacterial members related to Fol suppression (Bacillus, Chitinophaga, Flavihumibacter, Flavobacterium, Pseudomonas and Terrimonas) increased in the rhizosphere (P < 0.01, P < 0.001) more than in the bulk soils by applying both dewatered-SSDs. Thus, digestate soil amendment carried out for three consecutive years has affected tomato Fusarium wilt severity by changing the taxonomic characteristics of fusaria and bacteria communities of the amended soil.