Experiments were carried out in soil microcosms with the treatment of pesticide formulations—imidacloprid, benomyl, and metribuzin in single and tenfold application rates. For additional stimulation of microorganisms, a starch–mineral mixture was added to some variants. For all samples, high-throughput sequencing on the Illumina MiSeq platform of the V4 (16S rRNA) and ITS1 (18S rRNA) fragments was carried out. As a result, it was possible to establish the characteristic changes in the structure of the soil fungal and bacterial communities under pesticides application. The application of pesticides was accompanied by dramatic shifts in alfa-diversity of the fungal community. The phylum Basidiomycota was likely to be involved in the degradation of pesticides. The changes in the relative abundance of the genera Terrabacter, Kitasatospora, Streptomyces, Sphingomonas, Apiotrichum, Solicoccozyma, Gamsia, and Humicola can be proposed as an indicator of pesticide contamination. It is suggested to use these markers for large-scale assessment of the effect of pesticides on soil microbial communities instead of classical integral methods, including within the framework of state registration of pesticides. It is also recommended to research the effect of pesticides on the soil microbiome during artificially initiated successions using the additional source of carbon.

Excessive use of antibiotics in the healthcare sector and livestock farming has amplified antimicrobial resistance (AMR) as a major environmental threat in recent years. Abiotic stresses, including soil salinity and water pollutants, can affect AMR in soils, which in turn reduces the yield and quality of agricultural products. The objective of this study was to investigate the effects of antibiotic resistance and abiotic stresses on antimicrobial resistance in agricultural soils. A systematic review of the peer-reviewed published literature showed that soil contaminants derived from organic and chemical fertilizers, heavy metals, hydrocarbons, and untreated sewage sludge can significantly develop AMR through increasing the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in agricultural soils. Among effective technologies developed to minimize AMR’s negative effects, salinity and heat were found to be more influential in lowering ARGs and subsequently AMR. Several strategies to mitigate AMR in agricultural soils and future directions for research on AMR have been discussed, including integrated control of antibiotic usage and primary sources of ARGs. Knowledge of the factors affecting AMR has the potential to develop effective policies and technologies to minimize its adverse impacts.

Earthworms play a vital role in the terrestrial ecosystem functioning and maintenance of soil fertility. However, many pesticides, for example, imidacloprid, benomyl, and metribuzin that are world-widely used in agriculture, may be potentially dangerous to earthworms. At the same time, standard tests for pesticides acute and chronic toxicity do not reflect all aspects of their negative impact and might not be enough sensitive for effective assessment. In this paper, we studied the effects of non-lethal concentrations of imidacloprid, benomyl, and metribuzin on the gut bacterial community of Lumbricus terrestris using high-throughput sequencing approach. We found that pesticides reduced the total bacterial diversity in the earthworm’s gut even at the recommended application rate. Under the applied pesticides, the structure of the gut prokaryotic community underwent changes in the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Planctomyces, Verrucomicrobia, and Cyanobacteria, as well as the genera Haliangium, Gaiella, Paenisporosarcina, Oryzihumus, Candidatus Udaeobacter, and Aquisphaera. Moreover, the pesticides affected the abundance of Verminephrobacter—the earthworms’ nephridia specific symbionts. In general, the negative impact of pesticides on bacterial biodiversity was significant even under pesticides content, which was much lower than their acute and chronic toxicity values for the earthworms. These results highlighted the fact that the earthworm’s gut microbial community is highly sensitive to soil contamination with pesticides. Therefore, such examination should be considered in the pesticide risk assessment protocols.

The impact of three types of pesticides (herbicide metribuzin, insecticide imidacloprid, and fungicide benomyl) on the structure of microbial complexes and indicators of biological activity of agrosoddy-podzolic soil (Moscow oblast) has been assessed using the method of next-generation sequencing (NGS). The pesticides have been applied both separately and together at one- and tenfold rates. It has been found that pesticides have a greater impact on the fungal community in comparison with the prokaryotic community; in the latter, only changes in the abundances of the phyla of Actinobacteria and Proteobacteria have been observed. The study of fungal communities with the use of molecular-genetic analysis has revealed two dominant divisions of fungi in all soil samples: Ascomycota (72.6 ± 8.0%) and Basidiomycota (26.0 ± 7.7%). Moreover, in the samples treated with tenfold rate of pesticides (both in mixture and separately), the abundances of representatives of the Basidiomycota division have increased. Pesticide application has a short-term stimulating effect on the carbon content of microbial biomass. It has been shown that insecticide imidacloprid stimulates nitrogen fixation, whereas other types of pesticides do not affect this factor.

Pesticide preparations based on benomyl, metribuzin and imidacloprid were used on a potato plot for three years. Every year soil samples were taken at 0, 7, 14, 28, 56 and 84 days after treatment. For all samples, the pesticide residues in the soil were measured. A study of the soil’s bacterial and fungal community structures was preformed using next-generation sequencing. It was found that the rate of decomposition of the pesticides increased every year, while the pesticides affected only certain phylogenetic groups of microorganisms. The most significant effect was the decrease in the proportion of Ascomycota. Additionally, in the field, as well as previously in the laboratory, pesticides have had an impact on the relative abundance of the genera Haliangium, Solicoccozyma and Humicola. It can be assumed that the repeated application of pesticides does not have a significant effect on the microbial communities of soils, provided that they are applied according to the application rate.

Agriculture is the main contributor to nitrous oxide (N₂O) emission, but the emission intensity can be controlled by various factors, in particular, the activity of earthworms, one of the most common groups of soil invertebrates. We conducted an incubation experiment to evaluate N₂O emission in earthworm soil samples compared to non-earthworm ones with applications of high (200 kg ha⁻¹) and low (50 kg ha⁻¹) mineral N fertilizer doses. We assessed the cumulative N₂O emission, the dynamics of the soil dissolved organic carbon, and the soil microbial carbon and nitrogen content, as well as the number of nirK and nirS gene copies in bulk soil samples and in isolates from the earthworms’ gut. Our study showed a significant role of the earthworm activity in changing the intensity of N₂O emission after the application of mineral N fertilizers. The main factor leading to an increase in nitrous oxide emission in the presence of earthworms is the stimulation of free-living soil denitrifiers by the organic matter of the earthworms’ excretions, as well as the thorough mixing of plant residues and soil. Contrary to our expectations, earthworms did not increase the representation of nitrite reductase genes in soil, although the earthworm’s gut can be considered as a refugium for denitrifiers. Our results indicate a possible risk of increased N₂O emission from arable temperate soils with an increase in earthworm populations as the climate warms, even if application rates of mineral fertilizers are reduced.