Agricultural practices significantly impact soil properties and ecological functions, highlighting the importance of comprehensive soil health assessments. Traditionally, these assessments have focused on physical and chemical indicators, often neglecting microbiological properties. This review explores the potential of microbiological indicators in evaluating the effects of agricultural practices on soil ecological functions, emphasizing their significance and addressing challenges associated with their application. A key advantage of microbiological indicators is their high sensitivity and rapid response to environmental changes. These indicators can be grouped into three categories: microbial biomass and abundance, microbial taxonomic composition and diversity, and microbial activity. Among these, microbial biomass carbon, basal respiration, and decomposition rates are considered the most reliable and interpretable indicators. Microbial taxonomic composition and diversity remain limited in their diagnostic and predictive capabilities due to challenges in interpretation. Integrating microbiological indicators offers a more holistic understanding of the interactions between agricultural practices and soil health, enhancing our ability to monitor, manage, and preserve soil ecosystems. To facilitate their adoption in agricultural production and land management, further efforts are needed to improve the interpretability of these indicators and to establish standardized criteria for soil health assessment.

Chicken manure and composts derived from it are valuable organic fertilizers that have a positive impact on soil fertility and significantly enhance crop yields. However, the application of fresh manure can lead to excessive concentrations of nitrogen and other nutrients in the soil, as well as contamination of the soil with microorganisms that are pathogenic to humans and animals. Therefore, it is recommended to compost chicken manure prior to its use in agriculture. This review examines the composition and properties of chicken manure, the techniques involved in its composting, and its influence on the physical, chemical, and biological properties of the soil. The utilization of composted manure results in increased levels of organic carbon (on average by 1–1.5%), nitrogen (by 0.1–0.2%), and other biophilic elements. Moreover, it improves various physical properties of the soil, such as porosity, aeration, and density. Levels of pH increase (by 0.2–0.4), as well as electrical conductivity (by 2–2.5 times), and the quantity of water-resistant aggregates (by 5–10%). The application of these fertilizers also promotes biological activity, microbial diversity, microbial biomass carbon (by 25–75%), and soil enzymatic activity (phosphatase and catalase increase by 5–7 times, and urease by 3–5 times). When chicken manure is incorporated into the soil, a significant (2–4 times) increase in the population of bacteria from the phyla Firmicutes, Bacteroidetes, and Actinobacteria is observed. The necessity of investigating the effects of compost derived from chicken manure on the chemical composition and storage of soil organic matter, pore space, and the ecotrophic structure of the soil microbiome is also discussed.

Molecular genetic techniques (FISH, RT-PCR, and metagenomic analysis) were used to investigate the comparative functional biodiversity in the prokaryotic complex in grassland and forests’ sod-podzol under polycyclic aromatic hydrocarbon influence. The polluted samples showed a decrease in the biomass of the prokaryotic community representatives and a change in the metabolically active dominants–representatives of the Bacteria and Archaea domains compared to the control samples. The suppression of the metabolic activity of prokaryote cells under the influence of PAHs in sod-podzolic soil under meadow vegetation was more pronounced compared to soils under forest vegetation. The representatives of prokaryotes that are sensitive and resistant to the studied PAHs were identified. The representatives of the phylogenetic groups from the bacterial complex resistant to PAH pollution were Proteobacteria (Alphaproteobacteria), Bacteroidetes, Firmicutes, Chloroflexi, and Thaumarhaeota in the archaeal complex. Representatives of the phylum Acidobacteria and Actinobacteria (Streptosporangiales) are noted among those sensitive to PAH contamination. The presence and expression of the functional alkane monooxygenase (alkB) gene were established in all the experimental variants studied. In the plant variants, the number of copies of alkB genes increased by an order of magnitude and the biomass of metabolically active prokaryotic representatives with the functional alkB gene doubled compared to the unpolluted territories. The copy number index of the alkB gene can be used as one of the parameters when characterizing an ecosystem for the presence of PAH pollutants.

The collapse of collective farming in Russia after 1990 led to the abandonment of 23% of the agricultural area. Microbial biomass is a transit pool between fresh and soil organic matter; therefore, structural changes in soil microbial community determine the carbon cycle processes caused by self-restoration of arable lands after abandonment. Here, we assessed the influence of monthly changes in moisture and temperature on the bacterial community structure and abundance in Retisols under long-term abandoned cropland. Two periods with pronounced differences in bacterial properties were revealed: the growing period from March to September and the dormant period from October to February. The growing period was characterized by higher bacterial abundance and diversity compared to the dormant period. The relative abundances of the bacterial community dominants (Alpha-, Gamma- and Deltaproteobacteria, subgroup 6 of phylum Acidobacteria) did not change significantly over the year, either in total or active communities. The relative abundances of Bacteroidetes and Verrucomicrobia increased in the growing period, whereas Actinobacteria and Chloroflexi were more abundant in the dormant period. The microbial gene abundances positively correlated with soil and air temperature, but not with soil moisture. Thus, the seasonal dynamics of soil microbial communities are closely related to soil temperature and should be considered when assessing carbon cycles in abandoned lands.

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 SOM stocks and deposition of sequestered carbon is the straw application into the soil. The aim of the study was to evaluate the effect of straw application on the quantitative indicators of different groups of microorganisms in a soddy-podzolic soil (Umbric Retisol) in a long-term field experiment. Straw application increased microbial biomass carbon (Cmic) by 1.25–2 times, with the greatest increase in microbial biomass in trials without mineral fertilizer. Basal respiration and metabolic quotient (qCO₂) increased in the sequence: control < NPK < NPK + straw < straw. Application of straw increased the gene copy number of fungi and bacteria up to 2 times and archaea up to 1.5 times. Application of mineral fertilizers without straw reduced qCO₂, fungi biomass, and archaeal gene copy number by 1.5–3.0 times. The fungi/bacteria ratio varied from 4 to 15 as determined by the fluorescent microscopy and from 0.17 to 0.33 as determined by quantitative PCR. The lowest values of fungi/bacteria ratios were found in soils with the application of mineral fertilizers, and the highest ones, in soils with the straw application. Thus, the regular application of fresh organic matter of straw is an important technological procedure to increase the soil microbiological activity and mitigate the negative impact of mineral fertilizers on soil microbiota.

To investigate the combined impacts of temperature and plant residues on the mineralization capacity of soil organic matter, in addition to the impact on the taxonomic composition and activity of the soil microbiome, a 364-day experiment involving gray forest soil (Greyzemic Phaeozem Albic) was conducted under controlled laboratory conditions. Three substrate treatments were applied, control (C), amendment with aspen leaves (L), and amendment with aspen branches (B), combined with three temperature regimes (2, 12, and 22 °C). The results showed that long-term experimental warming reduced microbial alpha diversity (number of species and richness), increased microbial respiration and decomposition rates, and altered community composition. Over the year, the percentage of mineralization of added carbon was higher for leaves (29.9%–57.8%) than for branches (20.1%–47.6%). The efficiency of organic matter decomposition increased by 1.5- to 2-fold between 2 and 12 °C. Across all treatments, Proteobacteria were found to be the dominant phylum. According to α-diversity analysis, leaves served as the most preferred substrate for enhancing species representation. β-diversity analysis results indicated that temperature was the most significant factor shaping the microbial community’s structure. Our research findings provide new insights into soil organic matter formation and highlight the need for further research on microbial functional genes.