Rhizospheric changes of fungal and bacterial communities in relation to soil health of multi-generation apple orchards

• Microbial changes linked to plant health were analyzed in apple tree rhizosphere.
• Microbial communities of native and re-colonized soils were compared.
• Both bacterial and fungal communities resulted modified in re-colonized soils.
• Pseudomonas and Novosphingobium were mainly involved in bacterial changes.
• Changes in composition within Fusarium were linked to plant health.

The study focused on changes of rhizosphere microbial communities in apple trees in long-term replanted orchards of Central Europe, aiming at developing cropping practices to mitigate replant problems. It started from the evidence of a previous study which showed that a slight modification of root-colonizing fungal communities was responsible for a great increase of plant growth in soil samples which had previously been subjected to a gamma-irradiation cycle (25 kGy for 8 h), as compared to that observed in the corresponding untreated native soils.The study was performed on rhizospheric soil from nine multi-generation apple orchards after a plant growth assay with M9 rootstock plantlets. PCR-DGGE analysis of soil DNA was performed to evaluate fungal and bacterial communities in fallow and replanted soils, as well as corresponding gamma-irradiated samples. Findings showed that rhizospheric fungal and bacterial communities within apple orchards did not differ according to their position within the orchard; while, they showed a shift in the gamma-irradiated soils. Pseudomonas fluorescens, Pseudomonas tolasii, Pseudomonas spp. and Novosphingobium spp. were the bacteria which were mainly attributed to this change. A shifting in composition of Fusarium communities toward Fusarium oxysporum and Fusarium equiseti resulted the most linked to the changes at rhizosphere level after re-colonization; to the contrary, Fusarium venenatum and Fusarium avenaceum, Truncatella sp. and Gibellolopsis sp., only occurred in native soils. Findings of this study suggest that disturbance events such as a gamma-irradiation can modify microbial communities in long-term apple orchards thus allowing a soil re-colonization suitable to increase soil suppressiveness.