Closing the loop: Assessing the viability and environmental risks of human excreta-derived fertilizers in sustainable food systems

There is a need to increase food security and sustainability in food systems to ensure food production for generations to come. Currently, most food production is done through conventional agriculture which relies on synthetic fertilizers. While synthetic fertilizers help to sustain food production, their use is not always sustainable and the reliance on them can lead to contamination of soil and water. Moreover, their production is energy-intensive and is dependent on non-renewable resources. A sustainable alternative to synthetic fertilizers is the use of human excreta. Human excreta is usually considered a waste product and is often dumped in the environment without treatment, causing unsafe sanitation and contamination of drinking water. The reframing of human excreta as a resource, rather than a waste product, would be a considerable win for both sustainable agriculture and safe sanitation. Human excreta holds particular potential as a fertilizer, as human excreta-derived fertilizer (HEDF), because it is rich in macro- and micronutrients essential for plant growth. However, there are still many unknowns about HEDFs, such as whether they are a viable alternative to conventional fertilizers. Moreover, there are concerns that HEDFs transfer contaminants like antibiotics to the environment and that they contribute to antibiotic resistance development. In this dissertation, we investigated the ecological and agronomic viability of HEDFs in agricultural systems by assessing their impact on soil and plant health with a specific focus on residual antibiotics and the development of antibiotic resistance. To assess this, we conducted a literature review (chapter 2) and two research studies (chapter 3 and 4). The goal of chapter 2 was to gain an overview of the current state of research on HEDFs in agriculture. Here, we explored the suitability of these fertilizers compared to synthetic fertilizers, explored HEDF production procedures, investigated how HEDFs impact different facets of environmental health (e.g. crops, water and soil) and finally, considered societal benefits and public acceptance of HEDFs. We concluded that HEDFs are nutrient-rich, high potential fertilizers that can have a positive impact on the environment, but the response is soil and crop type dependent and hinges on proper treatment, clear regulations and public outreach. The goal of chapter 3 was to conduct a mechanistic study to understand the impact of increasing antibiotic concentrations on plant productivity, the soil microbial community and the development of antibiotic resistance. We found that antibiotic concentrations significantly impact prokaryotic diversity, with particular consequences for plant-growth promoting bacteria. The latter can have particular consequences for plant health and soil nutrient cycling. We only detected one of five II antibiotic resistance genes, which was only impacted in high antibiotic concentrations. Moreover, crops were differently affected by antibiotics, where radish biomass and nitrogen uptake were significantly lower because of antibiotic exposure, spinach remained largely unaffected. The goal of chapter 4 was to conduct a case study with different HEDFs on contrasting tropical soils to understand the impact on plant growth, antibiotic concentrations and the development of antibiotic resistance. We found that crop biomass was highly dependent on HEDF type and soil type, likely driven by divergent soil properties. Some crop HEDF combinations yielded positive results, while others remained unaffected. Positively, HEDFs only contained minimal antibiotics but this antibiotic resistance development was still a significant risk. Antibiotic resistance development was driven mainly by soil type and HEDF-driven soil acidification rather than HEDF type. Particularly, the soils inherently contained resistance to last-resort antibiotics, which might form a clinical risk if transferred from crop to humans. This indicates that risk assessments of HEDFs is complex and highly context dependent. In conclusion, there are clear benefits to the use of HEDFs particular when there is low availability of other fertilizers. However, the agronomic viability of HEDFs is complex and requires adaptation based on crop, fertilizer and soil type. Moreover, the risks of these fertilizers are not straightforward. For the selected HEDFs, the low antibiotic concentrations are unlikely to have direct negative environmental effects and will likely not affect the microbial community. However, changes in soil properties brought on by HEDF application may increase antibiotic resistance development which can still form a significant risk. Moreover, the selected soils in our study inherently contained resistance to last-resort antibiotics, forming a potential clinical risk. Therefore, the usage of HEDFs warrants context-dependent application where monitoring of antibiotic residues and antibiotic resistance development is crucial.

Grantor dc:publisher

ETH Zurich

Year dc:date

2025

Author dc:creator

• van den Broek, Sarah W.E.B.; id_orcid0000-0003-0980-338X

Contributors dc:contributor

• Doetterl, Sebastian; id_orcid0000-0003-0980-338X
• Garland , Gina
• Hartmann, Martin; id_orcid0000-0003-0980-338X
• Nybom, Inna; id_orcid0000-0003-0980-338X
• Raaijmakers, J. M.

• human excreta-derived fertilizer; antibiotic resistance; antibiotics; microbial ecology; soil microbiology
• Agriculture

Statement dc:rights

• info:eu-repo/semantics/openAccess
• Creative Commons Attribution 4.0 International

Licence

• http://creativecommons.org/licenses/by/4.0/

Language dc:language

en

Identifier

https://doi.org/10.3929/ethz-c-000796452

OAI identifier oai:identifier

oai:www.research-collection.ethz.ch:20.500.11850/796452