The same manure, different resistance risks
Livestock manure can add valuable nutrients to agricultural soil, but it can also introduce antibiotic residues, resistant bacteria and resistance genes. Yaqiong Song’s PhD research examines what happens after the manure is applied.
‘The same manure does not have the same effect in every soil. In some soils, resistance genes disappear relatively quickly, while in others they remain for longer and thus have more time and opportunities to spread,’ Yaqiong Song says.
The work combined greenhouse, plant and field studies.
A broad problem, a specific question
Yaqiong Song joined SDC’s Water and Environment programme in 2017 and later continued into a double-degree PhD at the University of Chinese Academy of Sciences and the University of Copenhagen, supervised by Professor Yongguan Zhu and Associate Professor Kristian Koefoed Brandt.
Her choice of field was strongly influenced by Professor Yongguan Zhu, an Academician of the Chinese Academy of Sciences.
‘It was Professor Yongguan Zhu’s deep commitment to antimicrobial resistance that first opened the door for me, and working alongside Associate Professor Kristian Koefoed Brandt provided me with an invaluable international outlook, teaching me how to think and collaborate on a global scale. While I initially stepped into this field under their guidance, I soon found myself captivated by the sheer scale of the challenge AMR poses to global health. I realized that this wasn't just a scientific puzzle; it was a global crisis that concerns the very future of humanity. That was the moment of clarity for me: this was the 'broad problem' I wanted to dedicate more time to research. My goal became to find that one 'specific question', a focused niche where I can truly make a difference and use it to confront this era-defining challenge,’ Yaqiong Song says.
Six soils, different outcomes
Under the same greenhouse conditions, Yaqiong Song and her colleagues applied the same amount of composted pig manure to six different soil types: red soil from Guangdong, yellow-brown soil from Zhejiang, yellow soil from Hunan, black soil from Jilin, brown earth from Beijing and sierozem from Ningxia. Elevated levels of resistance genes persisted for up to two months in red soil, yellow soil and sierozem, while the increase was shorter-lived in the other three soils.
‘Risk assessment should consider the receiving soil as well as the manure. In higher-risk soils, fertiliser use and field management may need particular attention. My study does not identify one solution, but it shows that the same approach may not be suitable everywhere,’ Yaqiong Song says.
The differences were closely linked to the soils’ bacterial communities and mobile genetic elements, which can carry resistance genes between bacteria.
Following resistance towards the plant
Yaqiong Song used cherry radish because it is often eaten raw and has an edible root in direct contact with the fertilised soil. Yaqiong Song and her colleagues collected material washed from the roots and leaf surfaces, along with surface-sterilised tissue from inside the roots and leaves. They analysed the samples for resistance genes and bacterial communities.
Resistance genes were most abundant around the roots and on leaf surfaces, while lower levels were found inside the plant. Red soil and yellow soil again showed particularly clear enrichment.
‘I was surprised that the leaf compartments were comparable to the area around the roots. I had expected the roots to present the greater risk because they are in direct contact with the fertilised soil. This serves as a reminder that we should remain just as cautious regarding leafy greens that are often eaten raw, such as lettuce, Yaqiong Song says.
The plant itself does not become resistant. The concern is that bacteria carrying resistance genes can persist around it and, in some cases, be detected inside plant tissue, creating a possible route towards human exposure through food.
Taking the research into real fields
The final study tested whether the greenhouse patterns could also be found in agricultural fields. Yaqiong Song investigated three farms in Guangdong with red soil and a history of using composted pig or cattle manure.
Fertilised fields contained higher levels of antibiotic residues and resistance genes than unfertilised soils. In flowering cabbage from one farm, Yaqiong Song and her colleagues also found a DNA marker linked to Klebsiella pneumoniae, a bacterium that can cause serious human infections and includes strains resistant to multiple antibiotics. The marker was found around and inside the roots and on and inside the leaves.
This suggests that the bacterium or its genetic material may have entered the plant. However, the method did not establish whether living bacteria had travelled from the manure into the crop, carried resistance genes or presented an immediate health risk.
From evidence to action
The findings could help policymakers and farmers assess manure use under different local soil conditions. Turning the evidence into action is difficult because the research identifies a potential risk without proving that exposure through a particular crop will directly cause illness.
‘This is one of the most difficult parts of our field. Farmers naturally focus on yield and income, while policymakers often ask us to show that eating a plant carrying these genes will directly cause disease. While we may not be able to map a direct, linear path from a single leaf to a specific case of disease, the cumulative risk is undeniable. If we persist in overlooking these risks, we risk allowing antimicrobial resistance to escalate into an uncontrollable crisis,’ Yaqiong Song says.
Supervisor Kristian Kofoed Brandt, Fellow PhD Mia Staal Jensen, Yaqiong Song
A long journey – and the next chapter
Yaqiong Song began her PhD in 2020 and spent the following years conducting experiments, analysing complex data and moving between China and Denmark. Min Qiao provided close day-to-day guidance, Professor Yongguan Zhu encouraged broad questions, and Associate Professor Kristian Koefoed Brandt focused on scientific analysis and writing.
‘It has been a long and challenging journey, and there was a great deal I had to learn along the way. Working in China and Denmark introduced me to different ways of approaching research. Denmark also taught me that you need time to rest so that you can return to the work in a better state,’ Yaqiong Song says.
After defending the Chinese part of her double degree in late 2025 and completing her University of Copenhagen PhD, Yaqiong Song has started a postdoctoral position at the University of Copenhagen. She can now continue exploring which bacteria carry resistance genes and how easily the genes can move.
‘Finishing was a big relief. It felt as if a heavy burden had been lifted from my shoulders. I now have the knowledge, the skills and a better understanding of both cultures. I feel that I am in a better state than ever and excited about the new journey,’ Yaqiong Song says.
Supervisor Kristian Kofoed Brandt, Fellow PhD Mia Staal Jensen, Yaqiong Song