Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting

Hanpeng Liao, Ville-Petri Friman, Stefan Geisen, Qian Zhao, Peng Cui, Xiaomei Lu, Zhi Chen, Zhen Yu, Shungui Zhou

Research output: Contribution to journalArticlepeer-review


About 1.3 billion tons of food waste (FW) is annually produced at a global scale. A major fraction of FW is deposited into landfills thereby contributing to environmental pollution and emission of greenhouse gasses. While increasing amounts of FW are recycled more sustainably into fertilizers in industrial-scale composting, very little is known about the antibiotic resistance genes (ARGs) present in FW and how their abundance is affected by composting. To study this, we quantified the diversity and abundance of ARGs, mobile genetic elements (MGEs) and bacterial communities in the beginning, during and at the end of the FW composting. All targeted 27 ARGs and 5 MGEs were detected in every sample suggesting that composted FW remains a reservoir of ARGs and MGEs. While the composting drastically changed the abundance, composition and diversity of bacterial communities, an increase in total ARG and MGE abundances was observed. Changes in ARGs were linked with shifts in the composition of bacterial communities as revealed by a Procrustes analysis (P < 0.01). Crucially, even though the high composting temperatures reduced the abundance and diversity of initially ARG-associated bacterial taxa, ARG abundances were maintained in other associated bacterial taxa. This was likely driven by horizontal gene transfer and physicochemical composting properties as revealed by a clear positive correlation between ARGs, MGEs, pH, NO 3 and moisture. Together our findings suggest that traditional composting is not efficient at removing ARGs and MGEs from FW. More effective composting strategies are thus needed to minimize ARG release from composted FW into agricultural environments.

Original languageEnglish
Pages (from-to)841-850
Number of pages10
JournalScience of the Total Environment
Early online date26 Dec 2018
Publication statusPublished - 10 Apr 2019

Bibliographical note

This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy.


  • Antibiotic resistance genes
  • Bacterial community composition
  • Composting physicochemical parameters
  • Mobile genetic elements
  • Municipal solid waste

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