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Chemical attributes, bacterial community, and antibiotic resistance genes are affected by intensive use of soil in agro-ecosystems of the Atlantic Forest, Southeastern Brazil

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Abstract

Soil is one of the largest reservoirs of microbial diversity in nature. Although soil management is vital for agricultural purposes, intensive practices can have a significant impact on fertility, microbial community, and resistome. Thus, the aim of this study was to evaluate the effects of an intensive soil management system on the chemical attributes, composition and structure of prevalent bacterial communities, and presence and abundance of antimicrobial resistance genes (ARGs). The chemical characterization, bacterial diversity and relative abundance of ARGs were evaluated in soils from areas of intensive vegetable cultivation and forests. Results indicate that levels of nutrients and heavy metals were higher in soil samples from cultivated areas. Similarly, greater enrichment and diversity of bacterial genera was detected in agricultural areas. Of the 18 target ARGs evaluated, seven were detected in studied soils. The oprD gene exhibited the highest abundance among the studied genes and was the only one that showed a significantly different prevalence between areas. The oprD gene was identified only from soil of the cultivated areas. The blaSFO, erm(36), oprD and van genes, in addition to the pH, showed greater correlation with in soil of cultivated areas, which in turn exhibited higher contents of nutrients. Thus, in addition to changes in chemical attributes and in the microbial community of the soil, intensive agricultural cultivation systems cause a modification of its resistome, reinforcing the importance of the study of antimicrobial resistance in a One Health approach.

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Acknowledgements

This project was partially supported by AFRI food safety Grant No. 2021-68015-33495 from the USDA National Institute of Food and Agriculture.

Funding

This work was supported by the Carlos Chagas Filho Foundation for the Support of Research in the State of Rio de Janeiro (FAPERJ) (project E-26/202.740/2018); the Brazilian National Council for Scientific and Technological Development (CNPq) (research fellowships provided to Irene da Silva Coelho - project 309002/2018-4); and the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – CAPES (finance code 001) for the scholarship provided to Paula Fernanda Alves Ferreira.

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Authors and Affiliations

  1. Departament of Soil, Institute of Agronomy, Federal Rural University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-970, Brazil

    Paula Fernanda Alves Ferreira, Daniele Rodrigues Barbosa & Nelson Moura Brasil do Amaral Sobrinho

  2. Mokichi Okada Research Center, Korin Agriculture and Environment, Ipeúna, São Paulo, Brazil

    Fernando Igne Rocha

  3. Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA

    Adina Howe

  4. Embrapa Agrobiology, Brazilian Agricultural Research Corporation, Seropédica, Rio de Janeiro, 23891-000, Brazil

    Ederson da Conceição Jesus

  5. Department of Veterinary Microbiology and Immunology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-970, Brazil

    Irene da Silva Coelho

Authors
  1. Paula Fernanda Alves Ferreira
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  2. Fernando Igne Rocha
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  3. Adina Howe
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  4. Daniele Rodrigues Barbosa
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  5. Ederson da Conceição Jesus
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  6. Nelson Moura Brasil do Amaral Sobrinho
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  7. Irene da Silva Coelho
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Contributions

All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by Fernando Igne Rocha, Adina Howe, Daniele Rodrigues Barbosa, Ederson da Conceição Jesus and Nelson Moura Brasil do Amaral Sobrinho. The first draft of the manuscript was written by Paula Fernanda Alves Ferreira e Irene da Silva Coelho and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Irene da Silva Coelho.

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Ferreira, P.F.A., Rocha, F.I., Howe, A. et al. Chemical attributes, bacterial community, and antibiotic resistance genes are affected by intensive use of soil in agro-ecosystems of the Atlantic Forest, Southeastern Brazil. Environ Geochem Health 46, 123 (2024). https://doi.org/10.1007/s10653-024-01894-8

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