A. K. Tkhakakhova

• Senior Researcher at V.V. Dokuchaev Soil Science Institute

The regular application of mineral and organic fertilizers is one of the essential components of the agricultural intensification. The applied fertilizers lead to artificial enrichment of the soil environment with readily available substrates and biophilic elements, which can have a significant impact on the soil and rhizosphere microbiome. The aim...

The loss of soil organic matter (SOM) due to agricultural land use has a negative impact on soil properties and is one of the major contributors to the increase in atmospheric CO2 concentrations. An appropriate way for simultaneous restoration of POM stocks and deposition of sequestered carbon is the straw application to the soil. The aim of the st...

The review summarizes the most relevant microbiological characteristics that can serve as indicators of soil ecological functions: bioresource, phytosanitary, as well as the functions of carbon transformation and plant nutrition. The indices of diversity and taxonomic structure of microbial communities as well as abundance of certain groups of micr...

Loss of tropical forests leads both to the loss of aboveground biodiversity and to the changes in belowground biological activity. Planted secondary forests return canopy cover, but the reversibility of belowground changes may depend on soil properties, forest age and tree species composition. We studied microbial communities in an array of soils i...

Biological control of pathogenic Fusarium species through the promotion of detrital food webs is a promising option for agricultural production and could be of high value in organic farming. To obtain quantitative information on the impact of detrital subsidy on the development of Fusarium infection in winter wheat seedlings, we established a 60-da...

The physicochemical parameters, plant community, and the structure of prokaryotic complexes of differently-aged young soils formed in the Kursk magnetic anomaly region (KMA, Russia) are analyzed. The objects were technozems of 1-year (with and without vegetative cover), as well as 25- and 50-year-old embryonic soils. Prokaryotic communities of tech...

Using the method of inoculation on elective nutrient media, the abundance and activity of taxonomic (bacteria, actinomycetes, micromycetes) and functional (nitrogen fixers, ammonifiers, denitrifiers of amylolytic, cellulolytic) groups of microorganisms in agrochernozems of the Stavropol region under the influence of various tillage systems – direct...

The effect of the addition of detrital subsidy on the winter wheat ecosystem was evaluated. Already during the first growing season after the addition, detrital subsidy led to an increase in yield by 17% and twofold population growth of soil saprophagous macrofauna. A significant correlation (r = 0.39) between abundance of Collembola species P. not...

Numbers of bacterial, archaeal, and fungal ribosomal gene copies and the taxonomic structure of prokaryotic communities in virgin tropical soils under weakly impacted monsoon forests at the Kat Tien National Park (Southern Vietnam) were determined, and their relation with the major physicochemical parameters of the studied soils were investigated....

A chronosequence approach, i.e., a comparison of spatially distinct plots with different stages of succession, is commonly used for studying microbial community dynamics during paedogenesis. The successional traits of prokaryotic communities following sand fixation processes have previously been characterized for arid and semi-arid regions, but the...

Minimal data set Figs 2 and 3. (XLSX)

Correlations between total organic carbon (TOC), nitrogen (TON) percentage and phyla abundances. Significant correlations (p<0.05) are marked red. (XLSX)

Results of ANOSIM. R values and p values calculated for Weighted UniFrac, Unweighted UniFrac and Bray-Curtis metrics. (XLSX)

Results of t-test for independent samples (pairwise comparisons) of gene abundances. Significant difference (p<0.05) is marked red. (XLSX)

Minimal data set Fig 5. (XLSX)

Using high-throughput sequencing, we performed a full-profile analysis of the taxonomic structure and diversity of prokaryotic communities of zonal soil series: sod-podzolic, dark gray, typical chernozem, brown soil, meadow-chestnut soil and solonets. Phyla Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Pla...

The microbiomes of the soils buried under earthwork structures of different age (burial mounds and defensive earth walls) and of surface soils were investigated. Microbial DNA was analyzed by quantitative PCR and sequencing of the 16S rRNA gene amplicons. Both microbial abundance and diversity in buried soils were found to be lower. The taxonomic s...

A chronosequence approach, i.e., a comparison of spatially distinct plots with different stages of succession, is commonly used for studying microbial community dynamics during paedogenesis. The successional traits of prokaryotic communities following sand fixation processes have previously been characterized for arid and semi-arid regions, but the...

The analysis of ribosomal genes has been applied to study microbiomes of two soils of the solonetzic soil complex in the northern Caspian region. These soils—solonetz and quasigleyic chestnut soil—drastically differ in their salinity characteristics. The specificity of the vertical distribution of prokaryotes by the genetic soil horizons from the s...

The impact of soil cultivation methods (tillage with soil overturning at a depth of 20-22 and 14-16 cm, beardless plowing and surface treatment respectively at a depth of 14-16 and 6-8 cm, and also zero or minimal tillage)) on biological activity of various ecology-trophic groups of microorganisms on agronochernozems of the Kamennaya Steppe (Vorone...

Land use affects physical, chemical and biological properties and processes in soil. Long-term field experiments were employed to reveal changes of soil characteristics induced by land use. Using high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR, comparative analyses were conducted on prokaryotic community structure in differen...

The assessment of the microbial biomass structure in the soil samples from A and C horizons, stored at the temperature of +5 and -70ºС was conducted by a luminescence method. For the samples from the humus layer a significant decrease of biomass during the cryostorage was revealed. However, in the sample from the mineral layer at the same storage c...

The changes in microbiological parameters of aggregates (1–2 mm) in typical chernozems under different land uses as dependent on the intensity and character of anthropogenic loads were studied with the help of the real-time polymerase chain reaction (PCR). The samples from the following long-term field experiments were examined: permanent black fal...

The taxonomic structure of the microbiota in two associated soils—solonetz on a microhigh and meadow-chestnut soil in a microlow—was studied in the semidesert of the Caspian Lowland. A highthroughput sequencing of the 16S rRNA gene was used for the soil samples from genetic horizons. A considerable reduction in the bacterial diversity was found in...

Molecular biology techniques provided the data on the composition of the metagenome of the prokaryotic community of chernozem soils with different anthropogenic loads by means of sequencing the 16S rRNA gene. The family markers that characterize the arable soil, fertilizers, and fallow soil were identified. The presence of a core (conservative) and...

Under study were the soils developed in flat watersheds with suffusion depressions and subjected to excessive seasonal flooding in Kamennaya Steppe, Talov district and Voronezh region of Russia. Among them are migrational-mycellary chernozem (Haplic Chernozem (Clavic, Pachic) on convex microrelief elements, the clay-illuvial eluvial weakly gleyic c...

The seasonal variability (spring–summer–autumn) of the taxonomic structure of prokaryotic microbiomes in chernozems of Kamennaya Steppe was studied using sequencing of the 16S rRNA gene. The samples were collected from the topsoil (0–20 cm) horizons of a long-term fallow and croplands differing in the rates of application of mineral fertilizers (NP...

The taxonomic structure of microbiomes in aggregates of different sizes from typical chernozems was investigated using sequencing of the 16S rRNA gene. The aggregate fractions of <0.25, 2–5, and >7 mm obtained by sieving of the soil samples at natural moisture were used for analysis. The highest prokaryote biomass (bacteria, archaea) was determined...

Molecular-biological methods permitted to study the structure of the microbial community in the profile of dark-gray soil (Luvic Retic Greyzemic Phaeozem) in Kashira district of the Moscow region. Microorganisms playing an important role in transformation of the soil organic matter are mainly concentrated in the topsoil and the major microbiologica...

For the first time, the composition of microbiomes in the biological crust (AKL) horizons of extremely arid desert soils (Aridic Calcisols) developed from saline and nonsaline alluvial deposits in the Ili Depression (eastern Kazakhstan) was analyzed. To describe the diversity of microorganisms in the soil samples, a novel method of pyrosequencing (...

The diversity indices used in ecology for assessing the metagenomes of soil prokaryotic communities at different phylogenetic levels were compared. The following indices were considered: the number of detected taxa and the Shannon, Menhinick, Margalef, Simpson, Chao1, and ACE indices. The diversity analysis of the prokaryotic communities in the upp...

Under study was the microbiome structure in virgin light-colored hydromorphized solonetz soil by using molecular-genetic and cultural methods. It was shown that the diversity of the microbial community is constantly decreasing down the soil profile being sharply declined in the solonetz horizon. Against the background of decreasing the biodiversity...

The problem of reproduction of soil fertility of chernozems are solved with integrated action, the ecological condition of the soil can be assessed by the activity of physiological groups of microorganisms. Microorganisms are the most important in the transformation of compounds of biogenic elements and therefore it is very interesting to study th...

Extremely arid soils of stony deserts (hamadas) along the southern periphery of the Ili Depression are considered to be analogous to extremely arid soils of Mongolia, also named as "ultra-arid primitive gray-brown soils." In general, the morphology of extremely arid soils of hamadas in the Ili Depression is similar to that of the soils of stony des...