Combining various plant species promotes the availability of more types of compounds in the soil. That increases the variety of microbial communities, so there is more competition for resources and high-risk bacteria are less able to multiply.
Combining vegetable crops reduces populations of soil antibiotic-resistant bacteria
The World Bank has predicted that antibiotic-resistant bacteria — strains that can survive exposure to drugs designed to kill them — could be responsible for more than 10 million human deaths a year by 2050. Agricultural soil is a major breeding ground for these microorganisms, due to the use of manure packed with such microbes and antibiotic residues. Against that backdrop, a groundbreaking study published in the journal Advanced Science has revealed that combining different crop species can curb the proliferation of antibiotic-resistant bacteria and stimulate the growth of more beneficial bacteria. More specifically, the study’s results indicate that, depending on the soil type, greater plant diversity reduces the abundance of antibiotic resistance genes and mobile genetic elements (DNA sequences that jump from one microorganism to another and facilitate the transfer of resistance genes) by between around 20% and 50%. Data suggests that this effect is attributable to exudates, the compounds that roots release into the soil, such as sugars, hormones, vitamins, organic acids and amino acids, which are sources of food for microbes. Root exudate composition varies from plant to plant, and different types of bacteria prefer different compounds. The study has shown that greater exudate diversity leads to a greater abundance of harmless bacteria.
“Combining various plant species promotes the availability of more types of compounds in the soil,” remarks CREAF-based CSIC researcher Josep Peñuelas, one of the study’s co-authors. “That increases the variety of microbial communities, so there is more competition for resources and high-risk bacteria are less able to multiply,” he continues.
Another finding is that soils with more organic matter benefit most from high plant diversity. This could be because greater use of manure to fertilize such soils results in them containing larger quantities of resistant bacteria. As Peñuelas explains: “Farm animals are given antibiotics to treat diseases. If antibiotics are administered excessively, bacteria can develop resistance to them. Resistant bacteria end up in excrement used to make fertilizer and can contaminate it.”
Combining vegetables
Combining vegetables
The study’s authors conducted a seven-month-long experiment in which they simulated agricultural soil in 90 pots. Animal-based fertilizer, used to enrich land, was added to each pot. Working with six crops (lettuce, tomato, garlic, alfalfa, celery and pepper), the researchers planted a single species in half the pots, simulating monoculture, and combinations of three or four species in the other half. Additionally, they used three types of soil: black soil, rich in organic matter, where they observed a 51.2% reduction in antibiotic resistance genes; and fluvo-aquic and red soils, with less organic matter, where a reduction of approximately 20% was observed.
To quantify antibiotic resistance genes and mobile genetic elements, the researchers used advanced genetic techniques like qPCR, as well as metagenomic, microbiological and microbial network analyses. “Those techniques help us identify bacterial species, determine which of them carry resistant genes, and calculate how abundant resistant DNA sequences are,” states Peñuelas. Among the bacteria that promote soil health and reduce the spread of resistant genes, the researchers highlight the phylum of nitrogen-fixing actinobacteria, which were more abundant in the pots with greater crop diversity. In contrast, proteobacteria and firmicutes, which are more capable of carrying and transferring antibiotic resistance genes through mobile elements, were found in greater abundance in the pots used to simulate monoculture.
From soil to stomachs
From soil to stomachs
Antibiotic-resistant bacteria present in agricultural soils can be transmitted to humans in various ways. For example, they can adhere to the surface of leaves, fruits and vegetables, resulting in us ingesting them if contaminated foods are not washed or cooked properly. Once in our digestive system, they can contribute to the transmission of antibiotic resistance genes to the microbiota; “this can make antibiotics used to treat bacterial infections less effective or prevent them from working properly,” warns Peñuelas.
To prevent that risk, the researchers say, it is vital that the agricultural sector take measures, and the study demonstrates that promoting polyculture or crop rotation can be an effective solution. They also emphasize how important it is to avoid using unprocessed manure, refrain from irrigating with waste water (which can also contain antibiotic residues and microorganisms) and, in general, reduce the unnecessary use of antibiotics in animals.
The study was led by Nanjing Normal University in China, and also involved CREAF and CSIC (both in Spain), as well as the Jiangsu Engineering Research Center for Soil Utilization and Sustainable Agriculture and the Jiangsu Center for Collaborative Innovation in Geographical Information (both in China). “The results of the study are very promising,” concludes Peñuelas. “The next step will be to scale up our research and include more types of crops.”
Referenced article: S. Li, X. Zhou, L. Liu, Z. Su, J. Zhao, J. Zhang, Z. Cai, J. Peñuelas, X. Huang, Plant Diversity Reduces the Risk of Antibiotic Resistance Genes in Agroecosystems. Adv. Sci. 2025, 2410990. https://doi.org/10.1002/advs.202410990
