X-ray computed tomography of the structure of roots and dynamics of soil biota in the early growth stages of barley (Hordeum vulgare L.)

The architecture of the seed bed, a certain alternation of compacted and loose sections of the arable horizon, largely determines the development of the root system of plants. The morphology and growth of the root system of the germinating seed in the created seed bed is also determined by the composition of the surrounding soil biota. Dynamic studies of the development of the root system and composition of the surrounding soil biota is an essential methodological and practical problem in soil cultivation, agrophysics, and soil biology. This task is especially important in the first few days when the root system is laid and the plant rhizosphere is formed. Modern tomography makes it possible to carry out such studies that do not violate the soil-root biological system, in particular, in model mesoscale experimental physical models. The aim of this research was to use x-ray computed tomography to study the structure of the roots of barley seedlings in the early stages of development, while simultaneously studying changes in the number and dominant groups of microorganisms in the basal biota. Barley seeds (variety Mikhailovsky) in a model physical experiment with a two-layer soil bed density (soil density range from 0.7 to 1.2 g / cm³) Albic Glossic Retisols (Lomic, Cutanic), WRB, 2014 were laid for germination at the layer boundary in a special cylindrical box with a volume of about 3 cm³ at optimal humidity. The position of the seed in the soil of the seedbed model is shown in the tomographic image (See Fig. 1). During the period from planting to 7 days, the dynamics of the root system was studied using a Bruker X-ray microtomography “SkyScan 1172G” (Bruker, Belgium) while studying the composition of soil biota, which was reconstructed by microbial markers (fatty acids and their derivatives). Markers were determined by molecular gas chromatography - mass spectrometry. Computer tomography allowed to record the volume distribution of roots at different periods of germination in the aggregated and compacted layers of agro-sod-podzolic soil. In this case, the roots successfully mastered the entire soil space, regardless of the plowing architecture of soil density created at the initial stage of germination. The total number of bacteria also increased by the 5th day with the constant dominance of 3 phyla: Actinobacteria, Proteobacteria and Firmicutes in the biota; the other two, Bacteroidetes and Cyanobacteria, were represented in relatively small numbers. In the phylum Actinobacteria, aerobic hydrolytics of complex carbohydrates Rhodococcus equi were presented in the largest amount on the 5th day, in the Firmicutes phylum it is anaerobic hydrolytic Ruminococcus sp. and the anaerobic nitrogen fixator Clostridium pasteurianum, in the phylum Proteobacteria-the aerobic nitrifier Nitrobacter sp. with a subsequent decrease in the number on the 7th day. The increase in these species indicates the initial destruction of the cellulose shell of the grain and the processes of fixation and conversion of nitrogen in the microbiota of the germinating seed, necessary for the formation of the C/N ratio. During the germination of the seed, pores are formed that are filled with water, gas, or organic matter. The structure of the microbial community changes in response to the ongoing processes, while the accumulation of metabolic products of aerobic and anaerobic species of microorganisms occurs. The quantitative study of the complex of microorganisms by the molecular method allows us to display the reaction of the microbiome to structural changes in the soil, since certain conditions stimulate an increase in the share of species with appropriate ecological functions in the community. The combination with the computer visualization obtained as a result of the application of the X-ray tomography method makes it possible to more clearly characterize the processes occurring in the rhizosphere. The paper contains 3 Figures, 1 Table and 27 References. The Authors declare no conflict of interest.