Skip to main content
Research article - Peer-reviewed, 2022

Uncovering antimicrobial resistance in three agricultural biogas plants using plant-based substrates

Sun, He; Schnuerer, Anna; Mueller, Bettina; Moessnang, Bettina; Lebuhn, Michael; Makarewicz, Oliwia


Antimicrobial resistance (AMR) is becoming an increasing global concern and the anaerobic digestion (AD) process represents a potential transmission route when digestates are used as fertilizing agents. AMR contaminants, e.g. antibiotic-resistant bacteria (ARB) and plasmid-mediated antibiotic resistance genes (ARGs) have been found in different substrates and AD systems, but not yet been investigated in plant-based substrates. AMR transfer from soils to vegetable microbiomes has been observed, and thus crop material potentially represents a so far neglected AMR load in agricultural AD processes, contributing to AMR spread. In order to test this hypothesis, this study examined the AMR situation throughout the process of three biogas plants using plant-based substrates only, or a mixture of plant-based and manure substrates. The evaluation included a combination of culture-independent and -dependent methods, i.e., identification of ARGs, plasmids, and pathogenic bacteria by DNA arrays, and phylogenetic classification of bacterial isolates and their phenotypic resistance pattern. To our knowledge, this is the first study on AMR in plant based substrates and the corresponding biogas plant. The results showed that the bacterial community isolated from the investigated substrates and the AD processing facilities were mainly Gram-positive Bacillus spp. Apart from Pantoea agglomerans, no other Gram-negative species were found, either by bacteria culturing or by DNA typing array. In contrast, the presence of ARGs and plasmids clearly indicated the existence of Gram-negative pathogenic bacteria, in both substrate and AD process. Compared with substrates, digestates had lower levels of ARGs, plasmids, and culturable ARB. Thus, digestate could pose a lower risk of spreading AMR than substrates per se. In conclusion, plant-based substrates are associated with AMR, including culturable Gram-positive ARB and Gram-negative pathogenic bacteria associated ARGs and plasmids. Thus, the AMR load from plant-based substrates should be taken into consideration in agricultural biogas processing.


Antimicrobial resistance; Agricultural biogas plant; Substrate; Digestate; Antibiotic-resistant bacteria; Antibiotic resistance genes

Published in

Science of the Total Environment
2022, volume: 829, article number: 154556
Publisher: ELSEVIER

Authors' information

Swedish University of Agricultural Sciences, Department of Molecular Sciences
Swedish University of Agricultural Sciences, Department of Molecular Sciences
Swedish University of Agricultural Sciences, Department of Molecular Sciences
Mößnang, Bettina
Bavarian State Research Center for Agriculture
Lebuhn, Michael
Bavarian State Research Center for Agriculture
Makarewicz, Oliwia
Friedrich Schiller University of Jena

Sustainable Development Goals

SDG3 Good health and well-being

UKÄ Subject classification

Environmental Sciences related to Agriculture and Land-use

Publication Identifiers


URI (permanent link to this page)