Rhizosphere Bacteriobiome of the Husk Tomato Grown in the Open Field in West Siberia

• Published in: Agriculture 2019-12, Vol.65 (4), p.147-154
• Main Authors: Naumova, Natalia B., Savenkov, Oleg A., Alikina, Tatiana Y., Kabilov, Marsel R.
• Format: Article
• Language: English
• Subjects: 16s rdna sequencing; Abundance; Bacteria; bacterial diversity; Biodiversity; Fertilization; Gene sequencing; Microbial activity; Microbiomes; Microorganisms; Mineral fertilizers; Nitrogen fixation; Nitrogen-fixing bacteria; physalis philadelphica; Physalis pubescens; Plant communities; Plant growth; Plant roots; Relative abundance; Rhizosphere; rhizosphere soil; rRNA 16S; Tomatoes
• ISSN: 1338-4376; 0551-3677; 1338-4376
• DOI: 10.2478/agri-2019-0015

The composition and structure of rhizosphere bacteriobiome of the husk tomato ( Physalis philadelphica Lam.) plants grown on Phaeozem in the open field in West Siberia, Russia (55°15’ NL, 83°31’ EL) were studied using Illumina MiSeq sequencing of the V3-V4 hypervariable region of 16S rRNA genes. In total 5898 OTUs (Operational Taxonomic Units) were found in the study, representing 20 phyla and 53 identified and 15 non-identified (below the phylum level) classes. The most OTU-rich phyla were Proteobacteria , Acidobacteria and Actinobacteria , their relative abundance in the total number of sequence reads being 26, 22 and 19%, respectively. Bacteroidetes , Gemmatimonadetes and Verrucomicrobia phyla each accounted for 2 ‒ 4%. The rest 14 of the identified phyla were quite negligible, contributing less than 0.5% each. At the OTUs level, the structure was very even and equitable, as only 7 OTUs had relative abundance ranging from 0.5 to 1.1%. The main dominant OTU represented Bradyrhizobiaceae family, implying the importance of nitrogen-fixing bacteria for plant growth and development without any mineral fertilisation. The dominance biodiversity index was very low (0.001), while Shannon index was rather high (7.5). We believe the presented husk tomato rhizosphere bacteriobiome, as the first study using new generation sequencing platform for this species, will help get a better picture of Solanaceae microbiomes in different environments, thus contributing to a more comprehensive understanding of shaping microbial communities by plant roots.