Study reveals fungi as overlooked players in agricultural antibiotic resistance

Antibiotic resistance is a growing global health concern, but its spread may depend on an unexpected group of organisms: fungi. A new study published in Agricultural Ecology and Environment reveals that fungi play a previously overlooked role in helping antibiotic resistance genes survive and spread during livestock manure composting.

“Fungi are more than just decomposers in composting systems. Our findings suggest that they also help create microbial connections that allow antibiotic resistance genes to persist and potentially spread,” said Jing Yuan, corresponding author of the study at China Agricultural University.

Fungi enter the AMR picture

Livestock manure is widely recycled into organic fertilizer. However, it can contain antibiotic residues, heavy metals, and bacteria carrying antibiotic resistance genes. If these genes survive composting, they may enter agricultural soils and contribute to the wider environmental spread of resistance. While previous studies have focused mainly on bacteria, the role of fungi in this process has received far less attention.

To investigate this hidden relationship, researchers conducted a 30-day composting experiment using pig manure. They applied different concentrations of cycloheximide, a chemical that inhibits fungal activity, to examine how changes in fungal populations affected bacteria and resistance genes.

The results revealed a striking pattern. Reducing fungal activity increased the removal of antibiotic resistance genes from 34.32% to 51.50%. The removal of mobile genetic elements, which can help resistance genes move between bacteria, also improved substantially, rising from 38.61% to 68.02%.

Importantly, the treatment also enhanced the removal of high-risk antibiotic resistance genes and reduced the accumulation of genes associated with heavy metal resistance.

But how can fungi influence antibiotic resistance in bacteria?

The researchers found that fungi help maintain complex microbial networks. Their thread-like structures, known as hyphae, can provide pathways for bacterial movement, while fungal secretions may influence bacterial growth and interactions.

When fungal activity was suppressed, these microbial connections weakened. The abundance of certain bacterial groups, including Lactobacillus and Anaerococcus, also declined. These bacteria were identified as potential carriers of multiple resistance genes.

The findings suggest that fungi may indirectly support antibiotic resistance by promoting the survival and interactions of bacteria that carry resistance genes. Disrupting these relationships could reduce both the persistence of resistance genes and their potential transfer between microorganisms.

Rethinking composting strategies

The study offers a new perspective on managing antibiotic resistance in agricultural waste. Rather than focusing exclusively on bacteria, future composting strategies could also consider the relationships between fungi and bacterial communities.

However, the researchers emphasize that further investigation is needed. The experiments were conducted in a controlled, small-scale composting system, and the precise mechanisms linking fungi to resistance gene transfer remain unresolved. The findings do not establish that applying fungicides to agricultural compost is a safe or practical treatment.

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By identifying fungi as an important biological factor in antibiotic resistance dynamics, this research opens new directions for improving manure treatment and reducing the environmental risks associated with livestock waste recycling. Ultimately, understanding how microorganisms cooperate may be just as important as understanding how individual microorganisms behave.