In Brazil, a study conducted by researchers affiliated with the University of São Paulo (USP) and collaborators showed that deforestation in the Amazon causes an increase in the diversity of antibiotic-resistant bacteria.
An article on the study, published in Soil Biology and Biochemistry, compares the microorganisms that live in the land of indigenous forest with those found in pasture and croplands. The researchers found a much larger number of genes considered markers of antibiotic resistance in deforested than forested areas.
The analysis was part of a project linked to the FAPESP Research Program on Biodiversity Characterization, Conservation, Restoration and Sustainable Use (BIOTA-FAPESP) and headed by Tsai Siu Mui, a professor at CENA-USP.
Antibiotic resistance is a global public health crisis, according to the World Health Organization (WHO), which says drug-resistant diseases cause some 700,000 deaths annually worldwide.
In the study, the researchers in CENA-USP, collaborating with colleagues in the Luiz de Queiroz College of Agriculture (ESALQ-USP) and scientists at the National Laboratory for Scientific Computing at Petrópolis, Rio de Janeiro State, analyzed some 800 million DNA sequences extracted from 48 soil samples collected in Pará State and northern Mato Grosso State, both of which are part of the Amazon biome.
Using bioinformatics tools, the researchers conducted the DNA sequences in the samples against a genetic database and found 145 antibiotic-resistant genes that activate 21 distinct molecular mechanisms. Although antibiotic-resistant bacteria are present in forest soil, these microorganisms and their resistance mechanisms are considerably more abundant in the soil of pasture, deforested areas, and croplands.
“The practice of job in the Amazon consists of first logging the most valuable trees and then burning and clearing all of the rest to make way for crops or forage grass for cows,” Mendes said. “Besides ash from the burnt vegetation, the soil is limed to decrease the acidity and other agrochemicals are applied.
Previous studies by the CENA-USP group revealed that despite the decrease in forest soil microorganism diversity, the abundance of bacteria benefited plants by nutrient cycling and fortified photosynthesis, and also had favorable impacts on the atmosphere, including carbon fixation and consumption of methane, the second most important greenhouse gas after carbon dioxide.
In the latest study, the researchers were struck by the huge quantity of bacteria that were resistant to two specific classes of antibiotics, tetracyclines and beta-lactamases.
Medications with these active ingredients are widely used to treat cattle diseases and can reach the soil via feces and urine because absorption of antibiotics in cattle is reduced. Moreover, the use of livestock manure as fertilizer can contribute to the spread of drug-resistant bacteria, according to the researchers.
Scientists cannot be confident that bacteria immune to antibiotics are capable of migrating from the soil of the Amazon to food produced there, such as grain, sugarcane, and beef. “Some research assumes the transfer can happen, but to date, no studies have shown it,” Mendes said. “It needs to be watched carefully because if those drug-resistant bacteria reach humans, they will lead to a serious public health problem.”
Nor are there any immediate solutions to prevent bacteria from multiplying in cultivated soil. Management techniques which take into account other functions of germs besides boosting crop yield, such as nutrient cycling and reducing species that produce methane, as an example, can help mitigate the issue.
This can be accomplished by transplanting natural soil to a cultivated area or using inoculants, microorganism-based products which perform important functions in the soil and also reduce the demand for fertilizer and agrochemicals. Indeed, the market for microbiome-based agricultural products is expected to be worth more than 10 billion US dollars by 2025.
In the Amazon, solutions and opportunities may be quite near a pasture or plantation, in the soil of the native forest.
Lemos, L. N., et al. (2021) Amazon deforestation enriches antibiotic resistance genes. Soil Biology and Biochemistry. doi.org/10.1016/j.soilbio.2020.108110.