Fumigation with Dazomet modifies soil bacterial and fungal communities in soil of apple orchards affected by Specific Replant Disease

Specific Apple Replant Disease (SARD) is a disorder that affects apple trees when they are re-planted in soil where the same species was previously grown. Although it is long-time known problem, the specific causes are still poorly understood. Because soil fumigation commonly relieves, at least temporarily, the symptoms, one of the main hypotheses is that microorganisms play an important role, although SARD is most probably the outcome of a more complex interplay between abiotic and biotic factors. Until last decade, unravelling the complex dynamics of soil microbial communities was almost impossible, because only a small fraction of microorganisms is cultivable in vitro. The recent advances in culture-independent technologies opened new opportunities to improve our knowledge on the role of microorganisms in SARD. The aim of this study was to uncover the complex dynamics of microbial communities in SARD affected soils in apple orchards especially focusing on the differences in taxa abundances between fumigated (F) and non-fumigated soils (NF) by using NGS technologies. Soil samples were collected in both fumigated (Basamid; a.i. Dazomet 99%) and non-fumigated sites in SARD affected apple orchards from an area in the Trentino-Alto Adige region (Italy) having the same climate and soil characteristics. Because we were interested in the long term changes, sampling was carried out 18 months after fumigation, at the end of the second growing season. Total DNA was extracted and the fungal ITS and bacterial 16S regions were pyrosequenced with the Roche’s 454 Platform. Both bacterial and fungal communities significantly differed between fumigated and control soils (PERMANOVA P=0.036 and P=0.042, respectively). Bacillus sp., Pseudomonas sp., Streptomyces sp. and Cheatomium sp. are the taxa identified by LEfSe as the most discriminative microbial biomarkers of fumigated soils (abundances: 1.5%±0.4% in NF vs. 2.7%±0.4% in F; 0.5%±0.2% in NF vs. 1.6%±0.4% in F; 0.3%±0.1% in NF vs. 0.8%±0.1%; 0,2%±0.1% in NF vs. 3.1%±1.9%, respectively), where apple trees thrived compared to the ones in untreated soils (non-fumigated). Our results suggest that, although a cause-effect relation with SARD cannot be proven, fumigation with Dazomet reduces SARD symptoms and modifies soil microbial communities, enhancing the presence of some beneficial microorganisms, known for their action against plant pathogens.