Amazon deforestation boosts the presence of bacteria with antibiotic resistance genes in soil
Dr. Lucas William Mendes
Center for Nuclear Energy in Agriculture, University of Sao Paulo, Brazil
Figure 1. (A) Soybean crop field in the deforested area of the Amazon where soil samples were collected. (B) DNA extraction from soil samples for metagenomic sequencing.
The Amazon rainforest is the largest reservoir of macro and micro biodiversity on Earth. However, in the last years, it has been disappearing due to deforestation for agriculture and cattle pastures. Many researchers sought to understand the effects of deforestation on the climate, animal and plants species, as well as on the microbiome. The microbiome is the collection of all microorganisms in a given environment, including bacteria, archaea, fungi, viruses, and protists. The soil microbiome plays important ecosystem services, such as organic matter decomposition, nutrient cycling, and fertilization, among others. In previous studies, we showed that the conversion of native forest to areas of agriculture and pasture affects the structure, composition, and diversity of the microbial communities, with negative impacts on ecosystem functions. Thus, to give a step forward to disentangle the effects of deforestation on the soil microbial communities, we focused our analysis on the soil resistome. The resistome is the group of all antibiotic resistance genes (ARGs) present in communities of both pathogenic and non-pathogenic bacteria. These genes occur naturally and are important for bacteria to thrive in a very competitive environment. Considering that the increase of ARGs is a threat to global health and food security, we evaluated how the land-use change in the Amazon region impacts the soil resistome. For this, we collect soil samples from areas of native forest, agriculture, and pastures and assessed the genes through metagenome sequencing (Figure 1).
In general, we found that several antibiotic resistance mechanisms and genes are common to both native forests and altered areas. However, deforestation and subsequent conversion to other land-use systems increased the diversity and the abundance of these genes. This enrichment is correlated with the increased microbial diversity in response to deforestation, together with changes in soil chemical properties, such as pH and aluminum. The process of Amazon occupation consists of, first, overthrowing the most valuable trees to exploit the wood through slash-and-burn, to then give space to agricultural crops or grass for cattle. In addition to the ash of the vegetation that lived there, the soil receives limestone to reduce acidity and other agricultural inputs. This plenty of nutrients generates a proliferation of bacteria and fierce competition for resources. We suggest that replacing native vegetation by pasture or plantations increases the competition between microorganisms, favoring those that have resistant genes. Thus, considering that Amazon land use aims to produce food, there is a possibility of transfer these genes to humans. However, we stressed that further investigation is still needed to understand if these ARGs can be transferred via food chain (e.g. agricultural soils) to humans, jeopardizing antibiotic treatments effectiveness and compromising public health.
Publication: Lemos LN, Pedrinho A, Vasconcelos ATR, Tsai SM, Mendes LW (2021) Amazon deforestation enriches antibiotic resistance genes. Soil Biology and Biochemistry 153:108110. https://doi.org/10.1016/j.soilbio.2020.108110