Mikrobiol. Z. 2022; 84(1):3-16.
doi: https://doi.org/10.15407/microbiolj84.01.003

The Features of Taxonomic Structure Formation of Soil Microbial Biome in Beta vulgaris Rhizosphere

Yu.P. Borko1, M.V. Patyka2, M.V. Boiko2, A.M. Honchar2, V.M. Sinchenko3

1Institute of Agriculture, NAAS of Ukraine
2-B Machinobudivnykiv Str., Chabany, 08162, Ukraine

2National University of Life and Environmental Sciences of Ukraine
15 Heroyiv Oborony Str., Kyiv, 03041, Ukraine

3Institute of Bioenergy Cultures and Sugar Beets, NAAS of Ukraine
25 Clinical Str., Kyiv, 03141, Ukraine

The necessity to increase the production of quality agricultural products in order to minimize using of agrochemicals while maintaining high profitability of production are required a comprehensive study of the determining factor of soil fertility – its biological component. Research of the microbiocenoses formation in the plants rhizosphere at all ontogenesis stages will allow to uncover the mechanisms of microbial-plant interaction and develop effective ways to increase crop productivity with high functional activity and homeostasis of the soil microbiome. The goal is to study the structure of the microbial complex and biodiversity of Beta vulgaris rhizosphere during ontogenesis by classical microbiological and molecular-biological methods. Methods. The number of microorganisms was determined by the method of inoculation soil microbial suspension on agar nutrient media, the structure of the qualitative composition of microorganisms was identified by morphologically-cultural properties, the morphology of isolated isolates – by microscopy of fixed preparations. The diversity of soil microbial complexes was evaluated by the Shannon, Simpson, and Berger-Parker ecological indices. The taxonomic structure of prokaryotes was determined by pyrosequencing. Results. The differentiation of the soil microbiota number was observed during the Beta vulgaris ontogenesis due to the intensity production of root exudates by the plant. The number of bacteria and micromycetes are increased 1.8–2.3 times, however, in the phase of leaves closing in-row spacing, the number of fungal microbiota decreased by 46.4%. Microbial complexes were differed in the number of detected morphotypes (27–50) and in the structure of the distribution of dominant forms (the total number of dominant forms of bacteria was decreased during the growing season, micromycetes – was increased). Analysis of the prokaryotes metagenome by pyrosequencing made it possible to identify 214 operational taxonomic units, 10.1% of which are forms that are not cultivated on nutrient media, 23.3% are unclassified. Among the identified taxonomic units, 96.2% were identified at the order level, 85.7% – at the family level, 76.7% – at the genus level. Among the identified taxonomic units were 15 phyla bacteria and 1 – archaea, among which 96 taxonomic units, families – 167, genera – 214 we found at the level of microbial orders. The dominant forms among the identified phyla were Proteobacteria (65.7%) and Actinobacteria (20.5%); orders – Burkholderiales (38.7%) and Pseudomonadales (20.1%); families – Alcaligenacea (37.9%), Pseudomonadaceae (20.1 %); Gaiellaceae (5.7%), Nitrososphaeraceae (4.2%); genera – Achromobacter (31.5%) and Pseudomonas (19.9%). The soil microbial complex was characterized by high biodiversity according to the indicators According to the indicators of ecological indices, determined on the basis of the results of classical microbiological and molecular biological research methods, it is established that the microbial complex of the soil was characterized by high biodiversity. Although the Shannon (ISh=5.36) and Simpson (IS=0.87) indexes, based on the pyrosequencing method results, were significantly higher than similar indicators identified by classical microbiological methods. Conclusions. During the ontogenesis of Beta Vulgaris, including due to the intensity of plant production of root exudates, the number of bacteria and micromycetes in the rhizosphere of plants increased. It was accompanied by a redistribution of structural composition and an increase of the microorganisms’ diversity (ISh=5.36). It found that among the identified 214 taxonomic units, 10.1% – forms that are not cultivated on nutrient media, 23.3% – are unclassified. Our studies showed that the structure of the microbial complex of the plants’ rhizosphere reflects the characteristics of the soil and can be used as an indicator of ecological status. The obtained results (conducted for the first time in the Forest-Steppe of Ukraine) deepen the knowledge about the true scale of natural genetic diversity of microbial complexes and are a valuable asset for substantiating practical proposals for effective adaptive interactions in the plant-microorganism system to preserve the homeostasis agroecosystems.

Keywords: metagenome, taxonomic structure, pyrosequencing, morphotypes, rhizosphere, sugar beet, ontogenesis, biodiversity indices.

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