Structure and variation of root-associated microbiomes of potato grown in alfisol

© 2019, Springer Nature B.V. Root-associated fungi and bacteria play a pivotal role in the plant–soil ecosystem by influencing both plant growth and immunity. The aim of this study was to unravel the biodiversity of the bacterial and fungal rhizosphere (RS) and rhizoplane (RP) microbiota of Zhukovskij rannij potato (Solanum tuberosum L.) cultivar growing in the Alfisol of Tatarstan, Russia. To assess the structure and diversity of microbial communities, we employed the 16S rRNA and internal transcribed spacer gene library technique. Overall, sequence analysis showed the presence of 3982 bacterial and 188 fungal operational taxonomic units (OTUs) in the RP, and 6018 bacterial and 320 fungal OTUs for in the RS. Comparison between microbial community structures in the RS and RP showed significant differences between these compartments. Biodiversity was higher in the RS than in the RP. Although members of Proteobacteria (RS—59.1 ± 4.9%; RP—54.5 ± 9.2%), Bacteroidetes (RS—23.19 ± 10.2%; RP—34.52 ± 10.4%) and Actinobacteria (RS—11.55 ± 4.9%; RP—7.7 ± 5.1%) were the three most dominant phyla, accounting for 94–98% of all bacterial taxa in both compartments, notable variations were observed in the primary dominance of classes and genera in RS and RP samples. In addition, our results demonstrated that the potato rhizoplane was significantly enriched with the genera Flavobacterium, Pseudomonas, Acinetobacter and other potentially beneficial bacteria. The fungal community was predominantly inhabited by members of the Ascomycota phylum (RS—81.4 ± 8.1%; RP—81.7 ± 5.7%), among which the genera Fusarium (RS—10.34 ± 3.41%; RP—9.96 ± 4.79%), Monographella (RS—7.66 ± 4.43%; RP—9.91 ± 5.87%), Verticillium (RS—4.6 ± 1.43%; RP—8.27 ± 3.63%) and Chaetomium (RS—4.95 ± 2.07%; RP—8.33 ± 4.93%) were particularly abundant. Interestingly, potato rhizoplane was significantly enriched with potentially useful fungal genera, such as Mortierella and Metacordiceps. A comparative analysis revealed that the abundance of Fusarium (a cosmopolitan plant pathogen) varied significantly depending on rotation variants, indicating a possible control of phytopathogenic fungi via management-induced shifts through crop rotational methods. Analysis of the core microbiome of bacterial and fungal community structure showed that the formation of bacterial microbiota in the rhizosphere and rhizoplane is dependent on the host plant