Aging of urine fertilizer prevents transfer of antibiotic resistance

The use of human urine as fertilizer is an important step towards sustainable agriculture because the starting reagent is free, plentiful and useless in most other contexts. It has been used as such for centuries, but with the current focus on environmental sustainability, the possibility of creating a nutrient cycle is under scrutiny. In other words, sourcing fertilizer from urine can be a green way to supply plants with the nutrients they need.

Again, by decreasing the amount of urine in the wastewater, the consequent need to treat the water to remove the nutrient substances in urine is reduced, which brings down the energy consumption at wastewater plants Moreover, it can help to set up local sources of farm fertilizer.

As study author Krista Wigginton says, “There are two main reasons we think urine fertilizer is the way of the future. Our current agricultural system is not sustainable, and the way we address nutrients in our wastewater can be much more efficient.”

Urine fertilizer. Image Credit: TippaPatt / Shutterstock
Urine fertilizer. Image Credit: TippaPatt / Shutterstock

The reason for the study

The current study comes from the University of Michigan which is leading a large group of researchers studying all about fertilizers derived from urine – their synthesis, their social acceptability, and the kind of systems required to reap benefit from this resource. One focus of this research is how to make this urine safe for use by removing bacteria, viruses and pharmaceuticals from it.

The study came about in an attempt to answer the question of whether antibiotic resistance can be transferred through bacterial genes in urine that is applied as fertilizer, by measuring the rate of breakdown of these fragments of DNA.

These genes are discrete circular bits of DNA called plasmids, that are separate from the main genome, and which carry traits that produce resistance to antibiotics. These plasmids are important because they can be freely transferred from one bacterium to another, thus allowing antibiotic resistance traits to be communicated from species to species.

The study and its findings

One such approach was examined in the current study. The researchers collected urine from over 100 individuals and kept it in sealed containers to undergo aging for 12 to 16 months. The activity of the enzyme urease breaks down urea in fresh urine, leading to raised ammonia levels over this period. The resulting decrease in acidity leads to the death of the vast majority of bacteria present in donor urine. Yet, there are bacteria remaining even after months that can both be cultured and are metabolically active.

However, many of the bacteria that cause urinary tract infections are found to carry genes for antibiotic resistance. The killed bacteria release DNA into the urine during further storage. The scientists therefore incubated two antibiotic resistance plasmids conferring resistance to ampicillin and tetracycline and assessed their capacity to transform a model organism called Acinetobacter baylyi, which is both commonly found in soil and can rapidly take up plasmids to undergo transformation. Thus, the outcome would show the ability of the plasmids in aged urine to transform this bacterium.

The scientists concluded that this practice inactivates almost 99% of plasmids present in the urine. The mechanism postulated by the researchers is the microbial or biochemical breakdown of the plasmids at a rapid pace, to convert the circular DNA into a linear fragment, hindering its transformation efficiency severely.

Implications and future directions

Wigginton sums up, “If bacteria in the collected urine are resistant to antibiotics and the bacteria die, as they do when they are stored in urine, the released DNA won't pose a risk of transferring resistance to bacteria in the environment when the fertilizer is applied.”

However, the scientists point out that other bacterial models and other plasmids need to be tested to see how they react to urine aging and to confirm these findings. The enzymes or bacteria that cause the actual degradation of the plasmids are still to be identified. However, they conclude that there is no risk of transferring antibiotic resistance genes to other bacteria when aged urine is used as fertilizer.

The researchers are now looking at ways to process urine to produce this type of safe and sustainable fertilizer which could promote the growth of crops grown for food as well as of flowering plants. Their field experiments in this area are showing promising results, they say.

Journal reference:

Fate of Extracellular DNA in the Production of Fertilizers from Source-Separated Urine, Heather E. GoetschNancy G. LoveKrista R. Wigginton, doi: 10.1021/acs.est.9b04263 Environ. Sci. Technol. 2020,

Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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