The effect of long-term application of nitrogen-rich fertilizers on soil resistome: A study of conventional and organic cropping systems

Highlights

● Soil resistomes of conventional and organic systems were similar in terms of ARG biodiversity.

● Soil resistomes of conventional and organic systems were different regarding individual ARGs.

● Uncultivated bacteria and archaea can contribute significantly to soil resistome.

Abstract

Metagenomic studies of various soil environments have previously revealed the widespread distribution of antibiotic resistance genes (ARGs) around the globe. In this study, we applied shotgun metagenomics to investigate differences in microbial communities and resistomes in Chernozem soils that have been under long-term organic and conventional cropping practices. The organic cropping system was seeded with Triticum spelta without any fertilizer. The conventional cropping system was seeded with Tríticum durum Desf and used mineral fertilizer (NPK), that resulted in an increased amount of total and available carbon and nitrogen in soils. Across all samples, we identified a total of 21 ARG classes, among which the dominant were vancomycin, tetracycline and multidrug. Profiling of soil microbial communities revealed differences between the studied fields in the relative abundances of 14 and 53 genera in topsoil and subsoil, respectively. Correlation analysis showed significant correlations (positive and negative) among 18 genera and 6 ARGs, as well as between these ARGs and some chemical properties of soils. The analysis of metagenome-assembled genomes revealed that Nitrospirota, Thermoproteota, Actinobacteriota and Binatota phyla of archaea and bacteria serve as hosts for glycopeptide and fluoroquinolone/tetracycline ARGs. Collectively, the data obtained enrich knowledge about the consequences of human agricultural activities in terms of soil microbiome modification and highlight the role of nitrogen cycling taxa, including uncultivated genera, in the formation of soil resistome.

Graphical abstract

Keywords

soil microbiome / inorganic fertilizer / nitrogen cycle / uncultured bacteria / chemolithotrophs / Binatia

References

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Funding

This study was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies for 2019-2027 (agreement Nº075-15-2021-1345, unique identifier RF— -193021X0012).

Conflicts of interest

The authors declare no conflict of interest.

Author contributions

Conceptualization, A.S.V.; methodology, A.S.V., E.O.B., A.V.V.; formal analysis, A.S.V., E.O.B., A.V.V.; investigation, D.S.G., D.V.P., S.V.K., A.V.I.; resources, A.S.V.; data curation, A.S.V., A.V.V.; writing—original draft preparation, A.S.V.; writing—review and editing, N.L.; funding acquisition, A.S.V. All authors have read and agreed to the published version of the manuscript.

Acknowledgments

We acknowledged Dr. Natalya Tomashevich (Federal Scientific Center for Biological Plant Protection, Krasnodar, Russia) for her assistance in selecting study sites. This work was partially performed using resources of the Research Resource Center & Natural Resource Management and Physico-Chemical Research (University of Tyumen).

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