Fumigation with dazomet modifies soil microbiota in apple orchards affected by replant disease

Apple replant disease (ARD) is a disorder that affects apple trees when they are replanted in soil where the same species was previously grown. ARD has been known for a long time, but the precise cause is not yet identified. Although ARD is most probably due to a combination of abiotic and biotic factors, the fact that soil fumigation commonly prevents the symptoms, at least temporarily, supports the hypothesis that microorganisms play an important role in it. In order to find possible relations between taxa composition of soil microbial communities and plant growth in ARD-affected orchards, we compared fumigated (dazomet 99%) and untreated soils by using next-generation sequencing (NGS) technologies. Soil sampling was carried out when the difference between fumigated and untreated plots became significant in terms of shoot growth and fruit yield and specifically at the end of the second growing season. Total soil DNA was extracted and two target regions (ITS for fungi and 16S rDNA for bacteria), were pyrosequenced with Roche’s 454 Platform. Both bacterial and fungal communities differed significantly in fumigated and untreated soils of our study. Bacillus sp. (r = 0.64), Streptomyces sp. (r = 0.64), Pseudomonas sp. (r = 0.59), and Chaetomium sp. (r = 0.85) were some of the taxa positively correlated with asymptomatic apple trees. Although a cause-effect relation with ARD cannot be proven, our results confirm that, fumigation with dazomet reduces ARD symptoms, and also modifies soil microbial communities at length, in particular by increasing the presence of some beneficial microorganisms known for their action against plant pathogens.