The increasing rate of natural resource use leads to an increase in the anthropogenic load on the soil. As the result of industrial, metallurgical and mining activities, excessive amounts of heavy metals (HMs) enter the soil. In addition, they can be introduced with waste and drainage water from various enterprises. Accumulating in the soil, HMs can negatively affect the soil bacterial community, which is one of the main factors of its “health”. Molecular genetic methods based on shotgun sequencing or metabarcoding of standard DNA sequences (for example, the 16S rRNA gene for bacteria) are the modern ways to assess the bacterial diversity of soils. This review presents the results of modern studies on the effect of HMs on the soil bacterial communities, using metagenomic methods. Based on the analysis of publications over the past two decades, a generally negative effect of pollutants on the taxonomic composition and diversity of bacterial communities has been shown. The influence of factors modulating the toxicity of metals and metalloids was noted: the amount and composition of salts, soil pH, ecosystem type, rhizosphere presence and other soil properties. In this paper, promising directions of research are outlined.

Bacterial communities play an important role in maintaining stable functioning of soil ecosystems, participating in decomposition of plant residues, accumulation of organic matter, formation of soil aggregates and in the cycle of nutrients. For agroecosystems, maintaining the diversity of microbiocenosis is especially critical because they are essentially less stable and are dependent on external control. The agricultural practices used today (plowing, application of synthetic fertilizers) can negatively affect the richness and diversity of the soil bacterial communities. The solution to this problem may be the application of alternative farming methods to preserve the structural and functional richness of soil (reduced tillage, conservation tillage, no tillage, organic farming). Data on composition and diversity of soil microbiocenosis are important for further forecasting the impact of agriculture and development of effective methods on preserving and increasing soil fertility. This review presents the results of recent studies on the impact of agriculture on the soil bacterial communities. Attention is mainly paid to the effects of applying inorganic and organic fertilizers on the structure and diversity of soil microbiocenosis; the influence of the farming system (different methods of soil cultivation, organic and traditional systems); the influence of cover crops and crop rotation on the microbial community of agricultural soils.

Antibiotics are widely used in animal husbandry at present. Due to their excessive and incorrect use, they have led to the rapid spread of antibiotic resistance genes (ARGs), as well as antibiotic-resistant bacteria (ARB) in microbial communities of the environment. The review examines works on the use of antibiotics in animal husbandry, the transmission of ARGs and ARB from animals to humans, their spread in the environment with wastewater from livestock enterprises and water and air flows. The role of manure as a reservoir of ARGs and the effect of the processing and storage of manure on the abundance and diversity of ARB and ARGs have been also analyzed. We have also touched on issues related to the presence of ARGs and ARB in animal and plant products and their introduction into the human microbiome with food.

In this study, we compared the expression of CYP153, sodA, sodC, and recA genes and ROS generation in hydrocarbon‐degrading Rhodococcus erythropolis in the presence of cyclohexane, naphthalene, and diesel fuel. The expression of cytochrome P450, sodA (encoding Fe/Mn superoxide dismutase), recA, and superoxide anion radical generation rate increased after the addition of all studied hydrocarbons. The peak of CYP153, sodA, and recA gene expression was registered in the presence of naphthalene. The same substrate upregulated the Cu/Zn superoxide dismutase gene, sodC. Cyclohexane generated the highest level of superoxide anion radical production. Hydrogen peroxide accumulated in the medium enriched with diesel fuel. Taken together, hydrocarbon biotransformation leads to oxidative stress and upregulation of antioxidant enzymes and CYP153 genes, and increases DNA reparation levels in R. erythropolis cells.