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. 2025 May 27:16:1508157.
doi: 10.3389/fmicb.2025.1508157. eCollection 2025.

Characterization of antibiotic resistance genes in soils from agroecosystems of the Brazilian Amazon

Taynara Cristina Santos Tavares #  1 , Lívia Freitas da Silva Pinto #  1 , Oscar Victor Cardenas-Alegria  2 , Carlos William Dias Dantas  2 , Sandro Patroca da Silva  3 , Ana Cecília Ribeiro Cruz  3 , Aníbal Coutinho do Rêgo  4 , Hervé Louis Ghislain Rogez  1 , Rommel Thiago Juca Ramos  2 , Cristian Faturi  5 , Adriana Ribeiro Carneiro Nunes  1
Affiliations

Characterization of antibiotic resistance genes in soils from agroecosystems of the Brazilian Amazon

Taynara Cristina Santos Tavares et al. Front Microbiol. .

Abstract

The conversion of forests to pastureland in the Amazon has increased over the years, resulting in significant impacts on ecosystem diversity, particularly on the soil microbiota. These changes affect the physical and biological properties of the soil, influencing the resistome and contributing to the selection and spread of antibiotic resistance genes (ARGs) in the soil environment. This study aimed to analyze the soil resistome under different managements in an Amazonian agrosystem. Soil samples were collected from the organic layer in forest and pasture areas within the municipality of São Miguel do Guamá, which included pastures managed with fertilization and those without the use of fertilizers. The samples underwent processing to extract genetic material and were sequenced using the Illumina platform. The sequences obtained were analyzed using bioinformatics tools to identify bacterial taxonomy and diversity. In addition, genetic annotation was performed using specialized databases to characterize functional genes, mobile elements, and resistance genes. The results showed changes in bacterial composition in pasture soils, where species such as Staphylococcus aureus, Staphylococcus cohnii, and Bacillus coagulans were more prevalent. In forest soils, differences in the composition of functional genes were detected, while soils without fertilizers exhibited a higher abundance of transposable elements. In addition, antibiotic resistance genes, such as macrolides, tetracyclines, aminoglycosides, among others, were more abundant in pasture soils.

Keywords: antibiotic resistance genes; bacterial diversity; mobile genetic elements; native forest; pasture soils.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Distribution of abundance of the taxonomic classification at the phylum level of the bacteria domain in the different locations under study.
Figure 2
Figure 2
Bacterial composition at the taxonomic level of (A) family and (B) species in different locations.
Figure 3
Figure 3
Composition of functional genes classified in the SEED Subsystems database, (A) classification at level 1, genes in the classification at level (B). DNA metabolism and (C) stress response.
Figure 4
Figure 4
Box plot of mobile genetic elements and their components distributed in different locations (*p < 0.05).
Figure 5
Figure 5
(A) Distribution of resistance/multiresistance in the resistome in soils with and without pasture. (B) Euler diagram of the presence of resistance genes. (C) Fisher's alpha-diversity analysis of antimicrobial resistance genes in different locations.
Figure 6
Figure 6
Abundance of antibiotic-resistant drug classes from different locations.
Figure 7
Figure 7
Correlations between bacterial genes by network analysis. (A) In soil NF, each gene presents up to five interactions. (B) In soil PT1, each node presents up to six interactions. (C) In soil PT2, up to nine interactions are observed between genes.
See this image and copyright information in PMC

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